diff --git a/.flake8 b/.flake8 new file mode 100644 index 00000000..a4e7dcbc --- /dev/null +++ b/.flake8 @@ -0,0 +1,3 @@ +[flake8] +max-line-length = 120 +ignore = E203 diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml new file mode 100644 index 00000000..a1b225e3 --- /dev/null +++ b/.github/workflows/ci-tests.yml @@ -0,0 +1,44 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Unit tests + +on: + pull_request: + branches: + - main + push: + # Run on main because caches are inherited from parent branches + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.7"] + + # Set default shell to allow conda activate env to be passed from one step to the next + defaults: + run: + shell: bash -l {0} + + steps: + - uses: actions/checkout@v2 + - name: Setup Miniconda with Python ${{ matrix.python-version }} + uses: conda-incubator/setup-miniconda@v2.1.1 + with: + python-version: ${{ matrix.python-version }} + environment-file: environment.yml + clean-patched-environment-file: false + - name: Check Conda configuration + run: | + conda info -a + python --version + - name: Install repo using pip + run: | + python -m pip install . + - name: Test with pytest + run: | + # Limit to just the most problematic test during debugging + pytest --durations=0 diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 00000000..eccbced1 --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,41 @@ +--- +# Adapted from https://github.com/alan-turing-institute/Python-quality-tools +name: pre-commit action +on: + pull_request: + branches: + - main + push: + # Run on main because caches are inherited from parent branches +env: + # This should be the default but we'll be explicit + PRE_COMMIT_HOME: ~/.caches/pre-commit +jobs: + pre-commit_job: + runs-on: ubuntu-latest + steps: + - name: Checkout Code + uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v3 + with: + python-version: "3.7" + - name: Install Pre-Commit + shell: bash + run: | + python -m pip install pre-commit + - name: Cache Pre-Commit Hooks + id: cache + uses: actions/cache@v3 + with: + path: ${{ env.PRE_COMMIT_HOME }} + key: ${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }} + - name: Install Pre-Commit Hooks + shell: bash + if: steps.cache.outputs.cache-hit != 'true' + run: | + pre-commit install-hooks + - name: Run Pre-Commit Hooks + shell: bash + run: | + pre-commit run --all-files diff --git a/.gitignore b/.gitignore index 0e68f4fc..e5493394 100644 --- a/.gitignore +++ b/.gitignore @@ -113,4 +113,10 @@ pyveg/azure_config.py #docs things docs/build docs/source/_static -docs/source/_templates \ No newline at end of file +docs/source/_templates + +# Test data +pyveg/testdata/test_ne_england/ + +# Virtual Environments +env/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..75afc996 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,38 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks + +# Ignore RVeg and Notebooks for now +exclude: (^rveg|^notebooks|^binder) +default_language_version: + # force all unspecified python hooks to run python3 + python: python3.7 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.2.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: check-xml + - id: check-added-large-files +- repo: https://github.com/psf/black + rev: 22.3.0 + hooks: + - id: black + exclude: (^pyveg/configs|^pyveg/zenodo_config_template.py|^pyveg/azure_config_template.py) +- repo: https://github.com/pre-commit/mirrors-autopep8 + rev: 'v1.6.0' # Use the sha / tag you want to point at + hooks: + - id: autopep8 +- repo: https://github.com/pycqa/isort + rev: 5.10.1 + hooks: + - id: isort + args: ["--profile", "black", "--filter-files"] + +# Ignore type checking for now, as this would require non-trival change to the code +# in order to pass `mypy` tests +# - repo: https://github.com/pre-commit/mirrors-mypy +# rev: 'v0.960' # Use the sha / tag you want to point at +# hooks: +# - id: mypy diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 063a6f88..dc54f7f4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -11,13 +11,17 @@ Don't let trying to be perfect get in the way of being good - exciting ideas are ## Table of contents -- [Where to start: issues](#where-to-start-issues) -- [Making a change with a pull request](#making-a-change-with-a-pull-request) - - [1. Comment on an existing issue or open a new issue referencing your addition](#1-comment-on-an-existing-issue-or-open-a-new-issue-referencing-your-addition) - - [2. Create a new branch (if you have *write* access to the repository) or fork the repository to your profile (if you don't currently have _write_ access)](#2-create-a-new-branch-or-fork-the-repository-to-your-profile) - - [3. Make the changes you've discussed](#3-make-the-changes-youve-discussed) - - [4. Submit a pull request](#4-submit-a-pull-request) -- [Style guide](#style-guide) +- [Contributing to monitoring-ecosystem-resilience (the repo!)](#contributing-to-monitoring-ecosystem-resilience-the-repo) + - [Table of contents](#table-of-contents) + - [Where to start: issues](#where-to-start-issues) + - [Making a change with a pull request](#making-a-change-with-a-pull-request) + - [1. Comment on an existing issue or open a new issue referencing your addition](#1-comment-on-an-existing-issue-or-open-a-new-issue-referencing-your-addition) + - [2. Create a new branch to your profile](#2-create-a-new-branch-or-forkgithub-fork-the-monitoring-ecosystem-resilience-repositorymonitoring-ecosystem-resilience-repo-to-your-profile) + - [2a) Create a branch](#2a-create-a-branch) + - [2b. Fork the repository](#2b-fork-the-repository) + - [3. Make the changes you've discussed](#3-make-the-changes-youve-discussed) + - [4. Submit a pull request](#4-submit-a-pull-request) + - [Style Guide](#style-guide) ## Where to start: issues @@ -138,8 +142,7 @@ Simply make your edits on their files and open a pull request to their branch! What happens if the continuous integration (CI) fails (for example, if the pull request notifies you that "Some checks were not successful")? The CI could fail for a number of reasons. -At the bottom of the pull request, where it says whether your build passed or failed, you can click “Details” next to the test, which takes you to the Travis page. -You can view the log or rerun the checks if you have write access to the repo by clicking the “Restart build” button in the top right (you must be logged in to Travis CI with your GitHub account see the “Restart build” button). +At the bottom of the pull request, where it says whether your build passed or failed, you can click “Details” next to the test, which takes you to the [GitHub Actions](https://github.com/urbangrammarai/gee_pipeline/actions) page. From there you can view the log or rerun the checks (if you have write-access to the repo). GitHub has a [nice introduction][github-flow] to the pull request workflow, but please get in touch if you have any questions. diff --git a/LICENSE.md b/LICENSE.md index 14634151..26f17d95 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -4,4 +4,4 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/MANIFEST.in b/MANIFEST.in index 58e95011..fba783bf 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1 +1 @@ -include pyveg/testdata/* \ No newline at end of file +include pyveg/testdata/* diff --git a/binder/requirements.txt b/binder/requirements.txt index 830307b4..ba6ee436 100644 --- a/binder/requirements.txt +++ b/binder/requirements.txt @@ -12,4 +12,4 @@ earthengine-api==0.1.210 geetools pillow imageio -opencv-python \ No newline at end of file +opencv-python diff --git a/docs/source/conf.py b/docs/source/conf.py index bcda161a..8f6a0be2 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -12,56 +12,57 @@ # import os import sys -sys.path.insert(0, os.path.abspath('../../pyveg')) + +sys.path.insert(0, os.path.abspath("../../pyveg")) # -- Project information ----------------------------------------------------- -project = 'pyveg' -copyright = '2020, Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton.' -author = 'Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton.' +project = "pyveg" +copyright = "2020, Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton." +author = "Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton." # The full version, including alpha/beta/rc tags -release = '1.0.0' +release = "1.0.0" # -- General configuration --------------------------------------------------- -master_doc = 'index' +master_doc = "index" # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.autosummary', - 'sphinx.ext.doctest', - 'sphinx.ext.intersphinx', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.napoleon', - 'sphinx.ext.viewcode', - 'recommonmark' + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.doctest", + "sphinx.ext.intersphinx", + "sphinx.ext.todo", + "sphinx.ext.coverage", + "sphinx.ext.mathjax", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", + "recommonmark", ] napoleon_use_ivar = True # for Sphinx-1.3 -source_suffix = ['.rst', '.md'] +source_suffix = [".rst", ".md"] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = 'y' +language = "y" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # -- Options for HTML output ------------------------------------------------- @@ -69,9 +70,9 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_rtd_theme' +html_theme = "sphinx_rtd_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] diff --git a/environment.yml b/environment.yml new file mode 100644 index 00000000..78be7211 --- /dev/null +++ b/environment.yml @@ -0,0 +1,9 @@ +name: gee_pipeline +channels: + - defaults + - conda-forge +dependencies: + - python=3.7 + - earthengine-api + - rasterio + - coverage diff --git a/pyveg/README.md b/pyveg/README.md index 1849c3ba..01df2e5d 100644 --- a/pyveg/README.md +++ b/pyveg/README.md @@ -1,6 +1,6 @@ # The `pyveg` Package -## Introduction +## Introduction The `pyveg` package is developed to study the evolution of vegetation patterns in semi-arid environments using data downloaded from Google Earth Engine. @@ -9,20 +9,20 @@ The code in this repository is intended to perform two main tasks: **1. Download and process GEE data**: * Download satellite data from Google Earth Engine (images and weather data). - * Downloaded images are divided into 50x50 pixel sub-images, network centrality metrics are used to describe the pattern vegetation are then calculated on the sub-image level. Both colour (RGB) and Normalised Difference Vegetation Index (NDVI) images are downloaded and stored on the sub-image level. + * Downloaded images are divided into 50x50 pixel sub-images, network centrality metrics are used to describe the pattern vegetation are then calculated on the sub-image level. Both colour (RGB) and Normalised Difference Vegetation Index (NDVI) images are downloaded and stored on the sub-image level. * For weather collections the precipitation and temperature "images" are averaged into a single value at each point in the time series. -* The download job is fully specified by a configuration file that can be generated by specifying the details of the data to be downloaded via prompts (satellite to use, coordinates, time period, number of time points, etc.). +* The download job is fully specified by a configuration file that can be generated by specifying the details of the data to be downloaded via prompts (satellite to use, coordinates, time period, number of time points, etc.). **2. Time series analysis on downloaded data**: * Time series analysis of the following metrics: raw NDVI mean pixel intensity across the image, vegetation network centrality metric, and precipitation. - * The time series are processed (outliers removed and resampled to avoid gaps). All time series of each sub-image are aggregated into one summary time series that is used for analysis. + * The time series are processed (outliers removed and resampled to avoid gaps). All time series of each sub-image are aggregated into one summary time series that is used for analysis. * The summary time series is de-seasonalised and smoothed. * Residuals between the raw and de-seasonalised and smoothed time series are calculated and used for an early warning resilience analysis. * Time series plots are produced, along with auto- and cross-correlation plots. Early warning signals are also computed using the [ewstools package](https://github.com/ThomasMBury/ewstools), including Lag-1 autocorrelation and standard deviation moving window plots. A sensitivity and significance analysis is also performed in order to determine whether any trends are statistically significant. * Time series summary statistics and resilience metrics are saved into files. -* A PDF report is created showcasing the main figures resulting from the analyses. +* A PDF report is created showcasing the main figures resulting from the analyses. **Other functionalities**: @@ -31,11 +31,11 @@ The code in this repository is intended to perform two main tasks: * Analysis of a collection of summary data that has been created with the `pyveg` pipeline (downloading + time series analysis). * Simulate the generation and evolution of patterned vegetation * A stand-alone network centrality estimation for a 50x50 pixel image. -* A functionality to upload results to the Zenodo open source repository +* A functionality to upload results to the Zenodo open source repository ### `pyveg` flow -The diagram below represents the high level flow of the main functionalities of the `pyveg` package. For each main component there is a CLI console scripts defined, that is shown in the diagram. +The diagram below represents the high level flow of the main functionalities of the `pyveg` package. For each main component there is a CLI console scripts defined, that is shown in the diagram. ![The`pyveg` program flow.](paper/pveg_flow.png) @@ -64,9 +64,9 @@ Install the package using `pip`. ``` pip install . ``` -If you are using Windows and encounter issues during this stage, a solution may be found here: https://github.com/NREL/OpenOA/issues/37. If you plan on making changes to the source code, you can instead run `pip install -e .`. +If you are using Windows and encounter issues during this stage, a solution may be found here: https://github.com/NREL/OpenOA/issues/37. If you plan on making changes to the source code, you can instead run `pip install -e .`. -Before using the Google Earth Engine API, you need to sign up with a Google account. You can read more in [here](https://developers.google.com/earth-engine/guides/python_install), how to open an account and authenticate using [gcloud](https://cloud.google.com/sdk/docs/install). +Before using the Google Earth Engine API, you need to sign up with a Google account. You can read more in [here](https://developers.google.com/earth-engine/guides/python_install), how to open an account and authenticate using [gcloud](https://cloud.google.com/sdk/docs/install). To authenticate for the first time open python and run ``` ee.Initialize() @@ -92,9 +92,9 @@ The download job is fully specified by a configuration file, which you point to Note that we use the GEE convention for coordinates, i.e. `(longitude,latitude)`. -#### Generating a download configuration file +#### Generating a download configuration file -To create a configuration file for use in the pyveg pipeline described above, use the command +To create a configuration file for use in the pyveg pipeline described above, use the command ``` pyveg_generate_config ``` @@ -143,7 +143,7 @@ This generates a file named `config_Sentinel2_11.58N_27.94E_Sudan_2016-01-01_202 pyveg_run_pipeline --config_file pyveg/configs/config_Sentinel2_11.58N_27.94E_Sudan_2016-01-01_2020-06-30_1m_local.py ``` -Individual options can be specified by the user via prompt. The options for this can be found by typing ```pyveg_generate_config --help```. +Individual options can be specified by the user via prompt. The options for this can be found by typing ```pyveg_generate_config --help```. ### More Details on Downloading @@ -169,7 +169,7 @@ If you have access to Microsoft Azure cloud computing facilities, downloading an ### Downloading data using the API -Although `pyveg` has been mostly designed to be used with the CLI as shown above, we can also use `pyveg` functions through the API. A tutorial of how to download data this way is included in the ``notebooks/tutorial_download_and_process_gee_images.ipynb`` notebook tutorial. +Although `pyveg` has been mostly designed to be used with the CLI as shown above, we can also use `pyveg` functions through the API. A tutorial of how to download data this way is included in the ``notebooks/tutorial_download_and_process_gee_images.ipynb`` notebook tutorial. ## Analysing the Downloaded Data with `pyveg` @@ -183,7 +183,7 @@ The analysis code preprocesses the data and produces a number of plots. These wi Note that in order to have a meaningful analysis, the dowloaded time series should have at least 4 points (and more thant 12 for an early warning analysis) and not being the result of a "test" config file, in this case the analysis fails. - + The commands also allows for other options to be added to the execution of the script (e.g. run analysis from a downloaded data in Azure blob storage, define a different output directly, don't include a time series analysis, etc), which can be displayed by typing: ``` @@ -215,12 +215,12 @@ In the `analysis/` subdirectory, `pyveg` creates the following plots: ### Running the analysis using the API -Although `pyveg` has been mostly designed to be used with the CLI as shown above, we can also use `pyveg` functions through the API. A tutorial of how to run the data analysis in this way is included in the ```notebooks/tutorial_analyse_gee_data.ipynb``` notebook tutorial. +Although `pyveg` has been mostly designed to be used with the CLI as shown above, we can also use `pyveg` functions through the API. A tutorial of how to run the data analysis in this way is included in the ```notebooks/tutorial_analyse_gee_data.ipynb``` notebook tutorial. ## Other functionalities of `pyveg` -### Analysis summary statistics data +### Analysis summary statistics data The ```analyse_pyveg_summary_data.py``` functionality processes collections of data produced by the main `pyveg` pipeline described in the section above (download + time series analysis for different locations and time periods) and creates a number of plots of the summary statistics of these time series. @@ -251,7 +251,7 @@ to see the options. The most useful option is the `--rainfall` parameter which #### Running the pattern simulation using the API -Although `pyveg` has been mostly designed to be used with the CLI as shown above, we can also use `pyveg` functions through the API. A tutorial of how to run the simulation of the pattern generation in this way is included in [here](notebooks/tutorial_simulate_patterned_vegetation.ipynb). +Although `pyveg` has been mostly designed to be used with the CLI as shown above, we can also use `pyveg` functions through the API. A tutorial of how to run the simulation of the pattern generation in this way is included in [here](notebooks/tutorial_simulate_patterned_vegetation.ipynb). ### Network centrality @@ -284,7 +284,7 @@ pyveg_calc_EC --input_txt ../binary_image.txt --do_EC See [here](UsingZenodo.md) for more details. -# Contributing +# Contributing We welcome contributions from anyone who is interested in the project. There are lots of ways to contribute, not just writing code. See our [Contributor Guidelines](CONTRIBUTING.md) to learn more about how you can contribute and how we work together as a community. diff --git a/pyveg/UsingAzure.md b/pyveg/UsingAzure.md index 965730ee..271f90b6 100644 --- a/pyveg/UsingAzure.md +++ b/pyveg/UsingAzure.md @@ -100,4 +100,4 @@ The execution of a single Task on a batch node (which is an Ubuntu-16.04 VM) is The function `processor_modules.run_batch` will submit all the tasks and then return straightaway, rather than waiting for the tasks to finish. This means that other Modules or Sequences (e.g. WeatherSequence) that do not depend on the results of this Module can still be executed. However, usually the final Sequence in a Pipeline will be a "combiner" Sequence, that has a `depends_on` attribute. -If a Sequence listed in `depends_on` has one-or-more Modules with "run_mode" set to "batch", the logic in the `run` method of the `Sequence` class in `pyveg/src/pyveg_pipeline.py` will loop through all the Modules in that Sequence, and call `check_if_finished()` on all of them. This in turn will query the Batch Job to see the status of all the Tasks. \ No newline at end of file +If a Sequence listed in `depends_on` has one-or-more Modules with "run_mode" set to "batch", the logic in the `run` method of the `Sequence` class in `pyveg/src/pyveg_pipeline.py` will loop through all the Modules in that Sequence, and call `check_if_finished()` on all of them. This in turn will query the Batch Job to see the status of all the Tasks. diff --git a/pyveg/azure_config_template.py b/pyveg/azure_config_template.py index 91df6be8..d37f6c3c 100644 --- a/pyveg/azure_config_template.py +++ b/pyveg/azure_config_template.py @@ -1,17 +1,17 @@ -## copy this file to azure_config.py and fill in the fields below with values -## that you should be able to obtain from the Azure portal https://portal.azure.com -## when you have an Azure batch account, and linked Azure storage account. +# copy this file to azure_config.py and fill in the fields below with values +# that you should be able to obtain from the Azure portal https://portal.azure.com +# when you have an Azure batch account, and linked Azure storage account. config = { - "batch_account_name": , - "batch_account_key": , - "batch_account_url": , - "storage_account_name": , - "storage_account_key": - "batch_pool_id": , - "pool_low_priority_node_count": , - "pool_dedicated_node_count": , - "pool_vm_size": , + "batch_account_name": < INSERT_BATCH_ACCOUNT_NAME_HERE > , + "batch_account_key": < INSERT_BATCH_ACCOUNT_KEY_HERE > , + "batch_account_url": < INSERT_BATCH_ACCOUNT_URL_HERE > , + "storage_account_name": < INSERT_STORAGE_ACCOUNT_NAME_HERE > , + "storage_account_key": < INSERT_STORAGE_ACCOUNT_ACCESS_KEY_HERE > + "batch_pool_id": < UNIQUE_NAME_FOR_POOL > , + "pool_low_priority_node_count": < N_LOW_PRIORITY_NODES > , + "pool_dedicated_node_count": < N_DEDICATED_NODES > , + "pool_vm_size": < VM_SIZE, e.g. 'STANDARD_A1_v2' > , "stdout_file_name": 'stdout.txt' } diff --git a/pyveg/configs/collections.py b/pyveg/configs/collections.py index 33a27fc0..eb9410fd 100644 --- a/pyveg/configs/collections.py +++ b/pyveg/configs/collections.py @@ -11,7 +11,7 @@ "cloudy_pix_flag": "CLOUDY_PIXEL_PERCENTAGE", "min_date": "2016-01-01", "max_date": "2022-01-01", # Get to current year. -# "max_date": time.strftime("%Y-%m-%d"), + # "max_date": time.strftime("%Y-%m-%d"), "time_per_point": "1m", }, "Landsat8": { diff --git a/pyveg/configs/config_all.py b/pyveg/configs/config_all.py index 1ebb5c78..1347c78c 100644 --- a/pyveg/configs/config_all.py +++ b/pyveg/configs/config_all.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" diff --git a/pyveg/configs/config_birmingham_example.py b/pyveg/configs/config_birmingham_example.py index 8b4401d0..b8da8817 100644 --- a/pyveg/configs/config_birmingham_example.py +++ b/pyveg/configs/config_birmingham_example.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "birmingham" @@ -39,6 +39,6 @@ special_config = { "Sentinel2": {"time_per_point": "3m", "region_size": 0.10, -} # this is a whole Sequence - # and another Module + } # this is a whole Sequence + # and another Module } diff --git a/pyveg/configs/config_coords-17_Sentinel2.py b/pyveg/configs/config_coords-17_Sentinel2.py index 25e31b8a..e9ce95f0 100644 --- a/pyveg/configs/config_coords-17_Sentinel2.py +++ b/pyveg/configs/config_coords-17_Sentinel2.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" @@ -36,4 +36,5 @@ } # The following demonstrates how parameters can be set for individual Modules: -special_config = {"NetworkCentralityCalculator": {"n_sub_images": -1, "n_threads": 8}} +special_config = {"NetworkCentralityCalculator": { + "n_sub_images": -1, "n_threads": 8}} diff --git a/pyveg/configs/config_coords-17_Sentinel2_batch.py b/pyveg/configs/config_coords-17_Sentinel2_batch.py index e56eddc7..0b9d4cf2 100644 --- a/pyveg/configs/config_coords-17_Sentinel2_batch.py +++ b/pyveg/configs/config_coords-17_Sentinel2_batch.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" diff --git a/pyveg/configs/config_coords-18_Sentinel2_batch.py b/pyveg/configs/config_coords-18_Sentinel2_batch.py index c3c12f0c..83df1915 100644 --- a/pyveg/configs/config_coords-18_Sentinel2_batch.py +++ b/pyveg/configs/config_coords-18_Sentinel2_batch.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" diff --git a/pyveg/configs/config_leicester_example.py b/pyveg/configs/config_leicester_example.py index eccbcd93..3c6133db 100644 --- a/pyveg/configs/config_leicester_example.py +++ b/pyveg/configs/config_leicester_example.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "leicester" @@ -38,6 +38,6 @@ special_config = { "Sentinel2": {"time_per_point": "3m", "region_size": 0.10, -} # this is a whole Sequence - # and another Module + } # this is a whole Sequence + # and another Module } diff --git a/pyveg/configs/config_liverpool_example.py b/pyveg/configs/config_liverpool_example.py index 7d7702aa..b07a24ad 100644 --- a/pyveg/configs/config_liverpool_example.py +++ b/pyveg/configs/config_liverpool_example.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "liverpool" @@ -37,6 +37,6 @@ # The following demonstrates how parameters can be set for individual Modules or Sequences: special_config = { "Sentinel2": {"time_per_point": "3m", "region_size": 0.10 -} # this is a whole Sequence - # and another Module + } # this is a whole Sequence + # and another Module } diff --git a/pyveg/configs/config_london_example.py b/pyveg/configs/config_london_example.py index dd5c8405..21907c14 100644 --- a/pyveg/configs/config_london_example.py +++ b/pyveg/configs/config_london_example.py @@ -1,7 +1,7 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store -#Name of job +# Name of job name = "london" # Define location to save all outputs diff --git a/pyveg/configs/config_template.py b/pyveg/configs/config_template.py index 4cde6279..64b0b975 100644 --- a/pyveg/configs/config_template.py +++ b/pyveg/configs/config_template.py @@ -1,8 +1,8 @@ -############## config file for running pyveg_run_pipeline +# config file for running pyveg_run_pipeline ## -## This file was generated from the command -## pyveg_generate_config -## on CURRENT_TIME +# This file was generated from the command +# pyveg_generate_config +# on CURRENT_TIME from pyveg.configs.collections import data_collections diff --git a/pyveg/configs/test_Sentinel2_azure.py b/pyveg/configs/test_Sentinel2_azure.py index 466eb76a..80a1171c 100644 --- a/pyveg/configs/test_Sentinel2_azure.py +++ b/pyveg/configs/test_Sentinel2_azure.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" diff --git a/pyveg/configs/test_Sentinel2_batch.py b/pyveg/configs/test_Sentinel2_batch.py index 1cfe2025..9a8f2dcf 100644 --- a/pyveg/configs/test_Sentinel2_batch.py +++ b/pyveg/configs/test_Sentinel2_batch.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" diff --git a/pyveg/configs/test_Sentinel2_local.py b/pyveg/configs/test_Sentinel2_local.py index 852330b5..7c1131c1 100644 --- a/pyveg/configs/test_Sentinel2_local.py +++ b/pyveg/configs/test_Sentinel2_local.py @@ -1,5 +1,5 @@ -from pyveg.coordinates import coordinate_store from pyveg.configs.collections import data_collections +from pyveg.coordinates import coordinate_store name = "pyvegtest" @@ -38,8 +38,9 @@ # The following demonstrates how parameters can be set for individual Modules or Sequences: special_config = { - "Sentinel2": {"time_per_point": "1m"}, # this is a whole Sequence - "VegetationImageProcessor": {"run_type": "local"}, # this is a Module + # this is a whole Sequence + "Sentinel2": {"time_per_point": "1m"}, + "VegetationImageProcessor": {"run_type": "local"}, # this is a Module "NetworkCentralityCalculator": { # also a Module "n_sub_images": 10, "n_threads": 4, diff --git a/pyveg/configs/testconfig_Sentinel2_55.00N_-1.60E_UnitedKingdom_0.08_unknown_2016-01-01_2020-06-30_1m_local.py b/pyveg/configs/testconfig_Sentinel2_55.00N_-1.60E_UnitedKingdom_0.08_unknown_2016-01-01_2020-06-30_1m_local.py new file mode 100644 index 00000000..aa012dce --- /dev/null +++ b/pyveg/configs/testconfig_Sentinel2_55.00N_-1.60E_UnitedKingdom_0.08_unknown_2016-01-01_2020-06-30_1m_local.py @@ -0,0 +1,65 @@ +# config file for running pyveg_run_pipeline +## +# This file was generated from the command +# pyveg_generate_config +# on 22-07-15 13:35:17 + +from pyveg.configs.collections import data_collections + +# this name doesn't do anything - it's just an id given to the Pipeline instance +name = "pyveg" + +# Define location to save all outputs. Note that every time the pipeline job +# is rerun, a datestamp will be appended to the output_location. +output_location = "./pyveg/testdata/test_ne_england/Sentinel2-55.00N-1.60W-UnitedKingdom" +output_location_type = "local" + +# parse selection. Note (long, lat) GEE convention. +coordinates = (-1.60, 55.00) + +# optional coords_id setting + + +# pattern_type description +pattern_type = "unknown" + +date_range = ["2016-01-01", "2020-06-30"] + +# From the dictionary entries in data_collections.py, which shall we use +# (these will become "Sequences") +collections_to_use = ["Sentinel2", "ERA5"] + +# Dictionary defining what Modules should run in each Sequence. + +modules_to_use = { + "ERA5": ["WeatherDownloader", "WeatherImageToJSON"], + "Sentinel2": [ + "VegetationDownloader", + "VegetationImageProcessor", + "NetworkCentralityCalculator", + "NDVICalculator", + ], + "combine": ["VegAndWeatherJsonCombiner"], +} + +# The following demonstrates how parameters can be set for individual Modules: +special_config = { + "Sentinel2": { + "time_per_point": "1m" + }, + "ERA5": { + "time_per_point": "1m", + "date_range": ["2016-01-01", "2020-06-30"] + }, + "VegetationDownloader": {"region_size": 0.08}, + "VegetationImageProcessor": {"run_mode": "local"}, + "NetworkCentralityCalculator": { + "n_threads": 4, + "run_mode": "local", + "n_sub_images": 10 + }, + "NDVICalculator": { + "run_mode": "local", + "n_sub_images": 10 + } +} diff --git a/pyveg/configs/testconfig_Sentinel2_55.00N_-1.60E_ne_england_test_0.08_unknown_2016-01-01_2020-06-30_1m_local.py b/pyveg/configs/testconfig_Sentinel2_55.00N_-1.60E_ne_england_test_0.08_unknown_2016-01-01_2020-06-30_1m_local.py new file mode 100644 index 00000000..d5c9c3af --- /dev/null +++ b/pyveg/configs/testconfig_Sentinel2_55.00N_-1.60E_ne_england_test_0.08_unknown_2016-01-01_2020-06-30_1m_local.py @@ -0,0 +1,57 @@ +# config file for running pyveg_run_pipeline +## +# This file was generated from the command +# pyveg_generate_config +# on 22-07-15 15:01:54 + +from pyveg.configs.collections import data_collections + +# this name doesn't do anything - it's just an id given to the Pipeline instance +name = "pyveg" + +# Define location to save all outputs. Note that every time the pipeline job +# is rerun, a datestamp will be appended to the output_location. +output_location = "./Sentinel2-55.00N-1.60W-ne_england_test" +output_location_type = "local" + +# parse selection. Note (long, lat) GEE convention. +coordinates = (-1.60, 55.00) + +# optional coords_id setting + + +# pattern_type description +pattern_type = "unknown" + +date_range = ["2016-01-01", "2020-06-30"] + +# From the dictionary entries in data_collections.py, which shall we use +# (these will become "Sequences") +collections_to_use = ["Sentinel2", "ERA5"] + +# Dictionary defining what Modules should run in each Sequence. + +modules_to_use = { + "ERA5": ["WeatherDownloader", "WeatherImageToJSON"], + "Sentinel2": [ + "VegetationDownloader", + "VegetationImageProcessor", + "NetworkCentralityCalculator", + "NDVICalculator", + ], + "combine": ["VegAndWeatherJsonCombiner"], +} + +# The following demonstrates how parameters can be set for individual Modules: +special_config = { + "Sentinel2": {"time_per_point": "1m"}, + "ERA5": {"time_per_point": "1m", "date_range": ["2016-01-01", "2020-06-30"]}, + "VegetationDownloader": {"region_size": 0.08}, + "VegetationImageProcessor": {"run_mode": "local"}, + "NetworkCentralityCalculator": { + "n_threads": 4, + "run_mode": "local", + "n_sub_images": 10, + }, + "NDVICalculator": {"run_mode": "local", "n_sub_images": 10}, +} diff --git a/pyveg/coordinates.py b/pyveg/coordinates.py index f5d11746..00dd2711 100644 --- a/pyveg/coordinates.py +++ b/pyveg/coordinates.py @@ -34,7 +34,7 @@ "type": "spots", "latitude": 11.58, "longitude": 27.94, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["01"] = { "continent": "Africa", @@ -42,7 +42,7 @@ "type": "labyrinths", "latitude": 11.12, "longitude": 28.37, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["02"] = { "continent": "Africa", @@ -50,7 +50,7 @@ "type": "gaps", "latitude": 10.96, "longitude": 28.20, - "region_size": 0.08 + "region_size": 0.08, } # niger @@ -60,7 +60,7 @@ "type": "labyrinths", "latitude": 13.12, "longitude": 2.59, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["04"] = { "continent": "Africa", @@ -68,7 +68,7 @@ "type": "labyrinths", "latitude": 13.17, "longitude": 1.58, - "region_size": 0.08 + "region_size": 0.08, } # senegal @@ -78,7 +78,7 @@ "type": "labyrinths", "latitude": 15.20, "longitude": -15.20, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["06"] = { "continent": "Africa", @@ -86,7 +86,7 @@ "type": "labyrinths", "latitude": 15.09, "longitude": -15.04, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["07"] = { "continent": "Africa", @@ -94,7 +94,7 @@ "type": "gaps", "latitude": 15.80, "longitude": -14.36, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["08"] = { "continent": "Africa", @@ -102,7 +102,7 @@ "type": "gaps", "latitude": 15.11, "longitude": -14.53, - "region_size": 0.08 + "region_size": 0.08, } # zambia @@ -112,7 +112,7 @@ "type": "gaps", "latitude": -15.34, "longitude": 22.22, - "region_size": 0.08 + "region_size": 0.08, } # kenya @@ -122,7 +122,7 @@ "type": "spots", "latitude": 0.43, "longitude": 40.30, - "region_size": 0.08 + "region_size": 0.08, } # somalia @@ -132,7 +132,7 @@ "type": "labyrinths", "latitude": 8.09, "longitude": 47.44, - "region_size": 0.08 + "region_size": 0.08, } # australia @@ -142,7 +142,7 @@ "type": "gaps", "latitude": -15.71, "longitude": 133.10, - "region_size": 0.08 + "region_size": 0.08, } # usa @@ -152,7 +152,7 @@ "type": "labyrinths", "latitude": 26.82, "longitude": -112.86, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["14"] = { "continent": "America", @@ -160,7 +160,7 @@ "type": "labyrinths", "latitude": 31.05, "longitude": -103.09, - "region_size": 0.08 + "region_size": 0.08, } # -------------------------------------------------------------------------------- @@ -172,7 +172,7 @@ "type": "labyrinths", "latitude": 14.91, "longitude": -0.66, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["16"] = { "continent": "Africa", @@ -180,7 +180,7 @@ "type": "spots-labyrinths", "latitude": 15.03, "longitude": -0.87, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["17"] = { "continent": "Africa", @@ -188,7 +188,7 @@ "type": "declining", "latitude": 15.23, "longitude": -0.97, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["18"] = { "continent": "Africa", @@ -196,7 +196,7 @@ "type": "spots-labyrinths", "latitude": 15.34, "longitude": -1.15, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["19"] = { "continent": "Africa", @@ -204,7 +204,7 @@ "type": "declining", "latitude": 15.14, "longitude": -1.16, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["20"] = { "continent": "Africa", @@ -212,7 +212,7 @@ "type": "spots-labyrinths", "latitude": 14.85, "longitude": -1.43, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["21"] = { "continent": "Africa", @@ -220,7 +220,7 @@ "type": "spots-labyrinths", "latitude": 14.92, "longitude": -0.99, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["22"] = { "continent": "Africa", @@ -228,7 +228,7 @@ "type": "labyrinths", "latitude": 15.14, "longitude": -1.56, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["23"] = { "continent": "Africa", @@ -236,7 +236,7 @@ "type": "spots-labyrinths", "latitude": 15.02, "longitude": -1.35, - "region_size": 0.08 + "region_size": 0.08, } # degraded locations in West Niger @@ -246,7 +246,7 @@ "type": "degraded", "latitude": 16.26, "longitude": -1.83, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["25"] = { "continent": "Africa", @@ -254,7 +254,7 @@ "type": "spots-labyrinths", "latitude": 16.19, "longitude": -1.83, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["26"] = { "continent": "Africa", @@ -262,7 +262,7 @@ "type": "spots-labyrinths", "latitude": 16.17, "longitude": -2.03, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["27"] = { "continent": "Africa", @@ -270,7 +270,7 @@ "type": "spots-labyrinths", "latitude": 16.48, "longitude": -1.87, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["28"] = { "continent": "Africa", @@ -278,7 +278,7 @@ "type": "spots-labyrinths", "latitude": 15.95, "longitude": -1.52, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["29"] = { "continent": "Africa", @@ -286,7 +286,7 @@ "type": "spots-labyrinths", "latitude": 15.86, "longitude": -2.05, - "region_size": 0.08 + "region_size": 0.08, } # healthy locations in West Niger @@ -296,7 +296,7 @@ "type": "labyrinths", "latitude": 14.8, "longitude": -3.38, - "region_size": 0.08 + "region_size": 0.08, } coordinate_store.loc["31"] = { "continent": "Africa", @@ -304,7 +304,7 @@ "type": "labyrinths", "latitude": 14.94, "longitude": -3.56, - "region_size": 0.08 + "region_size": 0.08, } # location with recent drought in Namibia (Issue #283) @@ -314,7 +314,7 @@ "type": "declining", "latitude": -18.05, "longitude": 12.76, - "region_size": 0.08 + "region_size": 0.08, } # Baja @@ -324,332 +324,329 @@ "type": "labyrinths", "latitude": 26.77, "longitude": -112.92, - "region_size": 0.08 + "region_size": 0.08, } # Australia -coordinate_store.loc['34'] = { - 'continent' : 'Australia', - 'country': 'Australia', - 'type': 'labyrinths', - 'latitude': -23.35, - 'longitude': 133.36, # featured in June tech talk results - "region_size": 0.08 +coordinate_store.loc["34"] = { + "continent": "Australia", + "country": "Australia", + "type": "labyrinths", + "latitude": -23.35, + "longitude": 133.36, # featured in June tech talk results + "region_size": 0.08, } -coordinate_store.loc['35'] = { - 'continent' : 'Australia', - 'country': 'Australia', - 'type': 'labyrinths', - 'latitude': -22.98, - 'longitude': 119.89, - "region_size": 0.08 +coordinate_store.loc["35"] = { + "continent": "Australia", + "country": "Australia", + "type": "labyrinths", + "latitude": -22.98, + "longitude": 119.89, + "region_size": 0.08, } -## Sites added by Josh: - -#Australia -coordinate_store.loc['36'] = { - 'continent' : 'Australia', - 'country': 'Australia', - 'type': 'labyrinths', - 'latitude': -25, - 'longitude': 119.99, - "region_size": 0.08 +# Sites added by Josh: +# Australia +coordinate_store.loc["36"] = { + "continent": "Australia", + "country": "Australia", + "type": "labyrinths", + "latitude": -25, + "longitude": 119.99, + "region_size": 0.08, } -#Somalia -coordinate_store.loc['37'] = { - 'continent' : 'Africa', - 'country': 'Somalia', - 'type': 'labyrinths', - 'latitude': 9.34, - 'longitude': 48.64, - 'region_size': 0.08 +# Somalia +coordinate_store.loc["37"] = { + "continent": "Africa", + "country": "Somalia", + "type": "labyrinths", + "latitude": 9.34, + "longitude": 48.64, + "region_size": 0.08, } -coordinate_store.loc['38'] = { - 'continent' : 'Africa', - 'country': 'Somalia', - 'type': 'bands', - 'latitude': 9.63, - 'longitude': 47.93, - "region_size": 0.08 +coordinate_store.loc["38"] = { + "continent": "Africa", + "country": "Somalia", + "type": "bands", + "latitude": 9.63, + "longitude": 47.93, + "region_size": 0.08, } -coordinate_store.loc['39'] = { - 'continent' : 'Africa', - 'country': 'Somalia', - 'type': 'labyrinths', - 'latitude': 9.98, - 'longitude': 48.44, - "region_size": 0.08 +coordinate_store.loc["39"] = { + "continent": "Africa", + "country": "Somalia", + "type": "labyrinths", + "latitude": 9.98, + "longitude": 48.44, + "region_size": 0.08, } -coordinate_store.loc['40'] = { - - 'continent' : 'Africa', - 'country': 'Somalia', - 'type': 'labyrinths', - 'latitude': 4.64, - 'longitude': 43.26, - "region_size": 0.08 +coordinate_store.loc["40"] = { + "continent": "Africa", + "country": "Somalia", + "type": "labyrinths", + "latitude": 4.64, + "longitude": 43.26, + "region_size": 0.08, } -#Ethiopia -coordinate_store.loc['41'] = { - 'continent' : 'Africa', - 'country': 'Ethiopia', - 'type': 'gaps', - 'latitude': 4.69, - 'longitude': 43.21, - "region_size": 0.08 +# Ethiopia +coordinate_store.loc["41"] = { + "continent": "Africa", + "country": "Ethiopia", + "type": "gaps", + "latitude": 4.69, + "longitude": 43.21, + "region_size": 0.08, } -coordinate_store.loc['42'] = { - 'continent' : 'Africa', - 'country': 'Ethiopia', - 'type': 'labyrinths', - 'latitude': 7.43, - 'longitude': 42.9, - "region_size": 0.08 +coordinate_store.loc["42"] = { + "continent": "Africa", + "country": "Ethiopia", + "type": "labyrinths", + "latitude": 7.43, + "longitude": 42.9, + "region_size": 0.08, } -#Kenya -coordinate_store.loc['43'] = { - 'continent' : 'Africa', - 'country': 'Kenya', - 'type': 'gaps', - 'latitude': 0.96, - 'longitude': 40.37, - "region_size": 0.08 +# Kenya +coordinate_store.loc["43"] = { + "continent": "Africa", + "country": "Kenya", + "type": "gaps", + "latitude": 0.96, + "longitude": 40.37, + "region_size": 0.08, } -#Mali -coordinate_store.loc['44'] = { - 'continent' : 'Africa', - 'country': 'Mali', - 'type': 'labyrinths', - 'latitude': 14.80, - 'longitude': -3.38, - "region_size": 0.08 +# Mali +coordinate_store.loc["44"] = { + "continent": "Africa", + "country": "Mali", + "type": "labyrinths", + "latitude": 14.80, + "longitude": -3.38, + "region_size": 0.08, } -#Mexico -coordinate_store.loc['45'] = { - 'continent' : 'America', - 'country': 'Mexico', - 'type': 'labyrinths', - 'latitude': 27.19, - 'longitude': -103.92, - "region_size": 0.08 +# Mexico +coordinate_store.loc["45"] = { + "continent": "America", + "country": "Mexico", + "type": "labyrinths", + "latitude": 27.19, + "longitude": -103.92, + "region_size": 0.08, } -#Chad +# Chad coordinate_store.loc["46"] = { - 'continent' : 'Africa', - 'country': 'Chad', - 'type': 'gaps', - 'latitude': 12, - 'longitude': 19.99, - 'region_size': 0.08 -} - -coordinate_store.loc['47'] = { - 'continent' : 'Africa', - 'country': 'Chad', - 'type': 'gaps', - 'latitude': 12.05, - 'longitude': 20.08, - 'region_size': 0.08 -} - -#Mali -coordinate_store.loc['48'] = { - 'continent' : 'Africa', - 'country': 'Mali', - 'type': 'labyrinths', - 'latitude': 15.48, - 'longitude': -5.83, - 'region_size': 0.08 -} - -#Mauritania -coordinate_store.loc['49'] = { - 'continent' : 'Africa', - 'country': 'Mauritania', - 'type': 'labyrinths', - 'latitude': 15.57, - 'longitude': -5.92, - "region_size": 0.08 -} - - -coordinate_store.loc['50'] = { - - 'continent' : 'Africa', - 'country': 'Mauritania', - 'type': 'gaps', - 'latitude': 15.58, - 'longitude': -13.00, - "region_size": 0.08 -} - -#Nigeria - -coordinate_store.loc['51'] = { - 'continent' : 'Africa', - 'country': 'Nigeria', - 'type': 'gaps', - 'latitude': 12.58, - 'longitude': 3.75, - 'region_size': 0.08 -} - -#Niger -coordinate_store.loc['52'] = { - 'continent' : 'Africa', - 'country': 'Niger', - 'type': 'gaps', - 'latitude': 12.7, - 'longitude': 2.63, - "region_size": 0.08 -} - -coordinate_store.loc['53'] = { - 'continent' : 'Africa', - 'country': 'Niger', - 'type': 'gaps', - 'latitude': 12.54, - 'longitude': 2.26, - 'region_size': 0.08 -} - -coordinate_store.loc['54'] = { - 'continent' : 'Africa', - 'country': 'Niger', - 'type': 'labyrinths', - 'latitude': 13.12, - 'longitude': 2.17, - "region_size": 0.08 -} - -coordinate_store.loc['55'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'gaps', - 'latitude': 11.07, - 'longitude': 27.93, - "region_size": 0.08 -} - -coordinate_store.loc['56'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'gaps', - 'latitude': 11.28, - 'longitude': 27.96, - "region_size": 0.08 -} - -coordinate_store.loc['57'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.27, - 'longitude': 27.55, - "region_size": 0.08 -} - -coordinate_store.loc['58'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.47, - 'longitude': 27.97, - "region_size": 0.08 -} - -coordinate_store.loc['59'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.51, - 'longitude': 27.87, - "region_size": 0.08 -} - -coordinate_store.loc['60'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.22, - 'longitude': 27.73, - "region_size": 0.08 -} - -coordinate_store.loc['61'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.62, - 'longitude': 27.86, - "region_size": 0.08 -} - - -coordinate_store.loc['62'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.32, - 'longitude': 27.88, - "region_size": 0.08 -} - -coordinate_store.loc['63'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.37, - 'longitude': 27.68, - "region_size": 0.08 + "continent": "Africa", + "country": "Chad", + "type": "gaps", + "latitude": 12, + "longitude": 19.99, + "region_size": 0.08, +} + +coordinate_store.loc["47"] = { + "continent": "Africa", + "country": "Chad", + "type": "gaps", + "latitude": 12.05, + "longitude": 20.08, + "region_size": 0.08, +} + +# Mali +coordinate_store.loc["48"] = { + "continent": "Africa", + "country": "Mali", + "type": "labyrinths", + "latitude": 15.48, + "longitude": -5.83, + "region_size": 0.08, +} + +# Mauritania +coordinate_store.loc["49"] = { + "continent": "Africa", + "country": "Mauritania", + "type": "labyrinths", + "latitude": 15.57, + "longitude": -5.92, + "region_size": 0.08, +} + + +coordinate_store.loc["50"] = { + "continent": "Africa", + "country": "Mauritania", + "type": "gaps", + "latitude": 15.58, + "longitude": -13.00, + "region_size": 0.08, } - - -coordinate_store.loc['64'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.60, - 'longitude': 27.73, - "region_size": 0.08 -} - -coordinate_store.loc['65'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.46, - 'longitude': 27.68, - "region_size": 0.08 + +# Nigeria + +coordinate_store.loc["51"] = { + "continent": "Africa", + "country": "Nigeria", + "type": "gaps", + "latitude": 12.58, + "longitude": 3.75, + "region_size": 0.08, } - -coordinate_store.loc['66'] = { - 'continent' : 'Africa', - 'country': 'Sudan', - 'type': 'spots', - 'latitude': 11.71, - 'longitude': 27.91, - "region_size": 0.08 + +# Niger +coordinate_store.loc["52"] = { + "continent": "Africa", + "country": "Niger", + "type": "gaps", + "latitude": 12.7, + "longitude": 2.63, + "region_size": 0.08, +} + +coordinate_store.loc["53"] = { + "continent": "Africa", + "country": "Niger", + "type": "gaps", + "latitude": 12.54, + "longitude": 2.26, + "region_size": 0.08, +} + +coordinate_store.loc["54"] = { + "continent": "Africa", + "country": "Niger", + "type": "labyrinths", + "latitude": 13.12, + "longitude": 2.17, + "region_size": 0.08, +} + +coordinate_store.loc["55"] = { + "continent": "Africa", + "country": "Sudan", + "type": "gaps", + "latitude": 11.07, + "longitude": 27.93, + "region_size": 0.08, +} + +coordinate_store.loc["56"] = { + "continent": "Africa", + "country": "Sudan", + "type": "gaps", + "latitude": 11.28, + "longitude": 27.96, + "region_size": 0.08, +} + +coordinate_store.loc["57"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.27, + "longitude": 27.55, + "region_size": 0.08, +} + +coordinate_store.loc["58"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.47, + "longitude": 27.97, + "region_size": 0.08, +} + +coordinate_store.loc["59"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.51, + "longitude": 27.87, + "region_size": 0.08, +} + +coordinate_store.loc["60"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.22, + "longitude": 27.73, + "region_size": 0.08, +} + +coordinate_store.loc["61"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.62, + "longitude": 27.86, + "region_size": 0.08, +} + + +coordinate_store.loc["62"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.32, + "longitude": 27.88, + "region_size": 0.08, +} + +coordinate_store.loc["63"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.37, + "longitude": 27.68, + "region_size": 0.08, +} + + +coordinate_store.loc["64"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.60, + "longitude": 27.73, + "region_size": 0.08, +} + +coordinate_store.loc["65"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.46, + "longitude": 27.68, + "region_size": 0.08, +} + +coordinate_store.loc["66"] = { + "continent": "Africa", + "country": "Sudan", + "type": "spots", + "latitude": 11.71, + "longitude": 27.91, + "region_size": 0.08, } # hardcode a check to make sure we don't overwrite any rows -assert( len(coordinate_store) == 67 ) +assert len(coordinate_store) == 67 diff --git a/pyveg/gee_editor/analyse_gee_editor_output.py b/pyveg/gee_editor/analyse_gee_editor_output.py index 80ec3a06..ef5403f5 100644 --- a/pyveg/gee_editor/analyse_gee_editor_output.py +++ b/pyveg/gee_editor/analyse_gee_editor_output.py @@ -3,23 +3,23 @@ """ Using the `time_series.js` file in this repository, and the GEE editor (https://code.earthengine.google.com/), You can download a precipitation -and NDVI time series for a given location quickly. This script let's you +and NDVI time series for a given location quickly. This script let's you run the `pyveg` analysis on the downloaded result. """ -import os import argparse import datetime +import os import pandas as pd -from pyveg.src.analysis_preprocessing import resample_dataframe, detrend_df from pyveg.scripts.analyse_gee_data import ( - run_time_series_analysis, run_early_warnings_resilience_analysis, + run_time_series_analysis, ) +from pyveg.src.analysis_preprocessing import detrend_df, resample_dataframe def convert_gee_date(gee_date_series): @@ -60,7 +60,7 @@ def convert_gee_outputs(input_dir): Returns ---------- str : - Path to single csv file that can be read by the pyveg analysis + Path to single csv file that can be read by the pyveg analysis code. """ diff --git a/pyveg/gee_editor/map_declines.js b/pyveg/gee_editor/map_declines.js index 271bee7e..e0973060 100644 --- a/pyveg/gee_editor/map_declines.js +++ b/pyveg/gee_editor/map_declines.js @@ -18,7 +18,7 @@ var precip_bandname = "total_precipitation"; var precip_before = ee.ImageCollection(precip_collection) .select(precip_bandname) .filter(ee.Filter.date(date_1, date_2)).mean(); - + var precip_now = ee.ImageCollection(precip_collection) .select(precip_bandname) .filter(ee.Filter.date(date_3, date_4)).mean(); @@ -27,7 +27,7 @@ var precip_now = ee.ImageCollection(precip_collection) var precipitation_change = precip_now .subtract(precip_before) .divide(precip_before); - + // mask regions that are initially too dry or too wet var precip_mask = precip_before.gt(0.0001).and(precip_before.lt(0.05)); precipitation_change = precipitation_change.multiply(precip_mask); @@ -45,8 +45,8 @@ var veg_bandname = "EVI"; // or "NDVI" // calculate mean vegetation index var veg_before = ee.ImageCollection(veg_collection) .select(veg_bandname) - .filter(ee.Filter.date(date_1, date_2)); - + .filter(ee.Filter.date(date_1, date_2)); + var veg_now = ee.ImageCollection(veg_collection) .select(veg_bandname) .filter(ee.Filter.date(date_3, date_4)); @@ -92,9 +92,9 @@ var vis_grayscale = { min: -1.0, max: 1.0, palette: [ - '#000000', '#111111', '#222222', '#333333', - '#444444', '#555555', '#666666', '#777777', - '#888888', '#999999', '#AAAAAA', '#BBBBBB', + '#000000', '#111111', '#222222', '#333333', + '#444444', '#555555', '#666666', '#777777', + '#888888', '#999999', '#AAAAAA', '#BBBBBB', '#CCCCCC', '#DDDDDD', '#EEEEEE', '#FFFFFF' ].reverse() }; @@ -130,7 +130,7 @@ Map.addLayer( Map.addLayer( sum_changes, vis_grayscale_sum, 'Sum Change'); - + Map.addLayer( prod_changes, vis_grayscale_prod, 'Prod Change'); diff --git a/pyveg/gee_editor/time_series.js b/pyveg/gee_editor/time_series.js index fa193679..43e7292f 100644 --- a/pyveg/gee_editor/time_series.js +++ b/pyveg/gee_editor/time_series.js @@ -17,7 +17,7 @@ var precip_collection = "ECMWF/ERA5/MONTHLY"; var precip_bandname = "total_precipitation"; // specify NDVI data source -//var veg_collection = "LANDSAT/LE07/C01/T1_8DAY_EVI"; +//var veg_collection = "LANDSAT/LE07/C01/T1_8DAY_EVI"; //var veg_collection = "LANDSAT/LE07/C01/T1_8DAY_NDVI" //var veg_collection = "LANDSAT/LT05/C01/T1_32DAY_NDVI" var veg_collection = "MODIS/006/MOD13Q1"; // MODIS seems to be cleaner @@ -27,12 +27,12 @@ var veg_bandname = "NDVI"; // or "EVI" var precipitation = ee.ImageCollection(precip_collection) .select(precip_bandname) .filter(ee.Filter.date(date_1, date_2)); - + // veg time series var veg = ee.ImageCollection(veg_collection) .select(veg_bandname) .filter(ee.Filter.date(date_1, date_2)); - + /* // L7 scan line masking as per https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544617/ var veg = veg.map(function(img) { @@ -51,4 +51,3 @@ print('Precipitation') print(ui.Chart.image.series(precipitation, geom, ee.Reducer.mean(), region_size)); print('Vegetation') print(ui.Chart.image.series(veg, geom, ee.Reducer.median(), region_size)); - \ No newline at end of file diff --git a/pyveg/paper/paper.md b/pyveg/paper/paper.md index 03c00cd5..9e2c6618 100644 --- a/pyveg/paper/paper.md +++ b/pyveg/paper/paper.md @@ -87,7 +87,7 @@ supported). `pyveg` will then form a series of date ranges, and query GEE for the relevant data in each date range. Colour (RGB) and Normalised Difference vegetation -Index (NDVI) images are downloaded from vegetation collections. Supported +Index (NDVI) images are downloaded from vegetation collections. Supported vegetation collections include Landsat [@landsat] and Sentinel-2 [@sentinel2] GEE collections. Cloud masking logic is included to improve data quality using the `geetools` package [@geetools]. diff --git a/pyveg/scripts/analyse_gee_data.py b/pyveg/scripts/analyse_gee_data.py index cb1ccad2..4ab0db57 100644 --- a/pyveg/scripts/analyse_gee_data.py +++ b/pyveg/scripts/analyse_gee_data.py @@ -7,49 +7,47 @@ """ -import os import argparse import json +import os import re -import pandas as pd import ewstools +import pandas as pd +from pyveg.scripts.create_analysis_report import create_markdown_pdf_report +from pyveg.scripts.upload_to_zenodo import upload_summary_stats from pyveg.src.analysis_preprocessing import ( - read_results_summary, preprocess_data, - save_ts_summary_stats + read_results_summary, + save_ts_summary_stats, ) - from pyveg.src.data_analysis_utils import ( - create_lat_long_metric_figures, - convert_to_geopandas, coarse_dataframe, - moving_window_analysis, - early_warnings_sensitivity_analysis, + convert_to_geopandas, + create_lat_long_metric_figures, early_warnings_null_hypothesis, + early_warnings_sensitivity_analysis, + moving_window_analysis, ) - from pyveg.src.plotting import ( - plot_stl_decomposition, - plot_feature_vector, - plot_time_series, - plot_ndvi_time_series, + kendall_tau_histograms, plot_autocorrelation_function, + plot_correlation_mwa, plot_cross_correlations, - plot_moving_window_analysis, plot_ews_resiliance, + plot_feature_vector, + plot_moving_window_analysis, + plot_ndvi_time_series, plot_sensitivity_heatmap, - plot_correlation_mwa, - kendall_tau_histograms, + plot_stl_decomposition, + plot_time_series, ) -from pyveg.scripts.create_analysis_report import create_markdown_pdf_report -from pyveg.scripts.upload_to_zenodo import upload_summary_stats - # if time-series is fewer than 12 points, can't do Early Warning Signals analysis MIN_TS_SIZE_FOR_EWS = 12 + def run_time_series_analysis(filename, output_dir, detrended=False): """ Make plots for the time series data. This function can @@ -97,7 +95,9 @@ def run_time_series_analysis(filename, output_dir, detrended=False): # plot the result of running STL decomposition if not detrended: - plot_stl_decomposition(ts_df, MIN_TS_SIZE_FOR_EWS, os.path.join(output_dir, "detrended/STL")) + plot_stl_decomposition( + ts_df, MIN_TS_SIZE_FOR_EWS, os.path.join(output_dir, "detrended/STL") + ) # ------------------------------------------------ @@ -167,12 +167,14 @@ def run_early_warnings_resilience_analysis(filename, output_dir): # run resilience analysis on vegetation data - ews_dic_veg = ewstools.core.ews_compute(ts_df[column_name].dropna(), - roll_window=0.5, - smooth='Gaussian', - lag_times=[1, 2], - ews=ews, - band_width=6) + ews_dic_veg = ewstools.core.ews_compute( + ts_df[column_name].dropna(), + roll_window=0.5, + smooth="Gaussian", + lag_times=[1, 2], + ews=ews, + band_width=6, + ) # make plots series_name = column_name.replace("_", " ") @@ -192,12 +194,14 @@ def run_early_warnings_resilience_analysis(filename, output_dir): # significance tests - significance = early_warnings_null_hypothesis(ts_df[column_name].dropna(), - roll_window=0.5, - smooth='Gaussian', - lag_times=[1, 2], - indicators=ews, - band_width=6) + significance = early_warnings_null_hypothesis( + ts_df[column_name].dropna(), + roll_window=0.5, + smooth="Gaussian", + lag_times=[1, 2], + indicators=ews, + band_width=6, + ) kendall_tau_histograms(series_name, significance, mwa_subdir) @@ -211,14 +215,16 @@ def run_early_warnings_resilience_analysis(filename, output_dir): ) -def analyse_gee_data(input_location, - input_location_type="local", - input_json_file=None, - output_dir=None, - do_time_series=True, - do_spatial=False, - upload_to_zenodo=False, - upload_to_zenodo_test=False): +def analyse_gee_data( + input_location, + input_location_type="local", + input_json_file=None, + output_dir=None, + do_time_series=True, + do_spatial=False, + upload_to_zenodo=False, + upload_to_zenodo_test=False, +): """ Run analysis on dowloaded gee data @@ -249,8 +255,9 @@ def analyse_gee_data(input_location, if input_json_file: input_json = json.load(open(input_json_file)) else: - input_json = read_results_summary(input_location, - input_location_type=input_location_type) + input_json = read_results_summary( + input_location, input_location_type=input_location_type + ) # preprocess input data ts_dirname, dfs = preprocess_data( input_json, output_dir, n_smooth=4, resample=False, period="MS" @@ -272,21 +279,22 @@ def analyse_gee_data(input_location, # time-series analysis and plotting # check first if data is a time series - ts_df = pd.read_csv(os.path.join(ts_dirname,ts_filenames[0])) + ts_df = pd.read_csv(os.path.join(ts_dirname, ts_filenames[0])) size_ts = ts_df.shape[0] if size_ts <= 2: - print ('WARNING: Less than 3 times points, not possible to do a time series analysis') + print( + "WARNING: Less than 3 times points, not possible to do a time series analysis" + ) do_time_series = False # ----------------------------------- - # for each time series if do_time_series: # put output plots in the results dir input_dir_ts = os.path.join(output_dir, "processed_data") - save_ts_summary_stats(input_dir_ts, output_analysis_dir,input_json['metadata']) + save_ts_summary_stats(input_dir_ts, output_analysis_dir, input_json["metadata"]) for filename in ts_filenames: @@ -301,7 +309,9 @@ def analyse_gee_data(input_location, # resilience analysis only done in large enough time series if size_ts > MIN_TS_SIZE_FOR_EWS: - ews_subdir = os.path.join(output_analysis_dir, "resiliance/deseasonalised") + ews_subdir = os.path.join( + output_analysis_dir, "resiliance/deseasonalised" + ) run_early_warnings_resilience_analysis(ts_file, ews_subdir) else: @@ -310,7 +320,9 @@ def analyse_gee_data(input_location, # resilience analysis only done in large enough time series if size_ts > MIN_TS_SIZE_FOR_EWS: - ews_subdir = os.path.join(output_analysis_dir, "resiliance/seasonal") + ews_subdir = os.path.join( + output_analysis_dir, "resiliance/seasonal" + ) run_early_warnings_resilience_analysis(ts_file, ews_subdir) print("." * 50, "\n") @@ -336,55 +348,64 @@ def analyse_gee_data(input_location, ) # ------------------------------------------------ - print('\nCreating report.\n') + print("\nCreating report.\n") for collection_name, df in dfs.items(): - if collection_name == 'COPERNICUS/S2' or 'LANDSAT' in collection_name: + if collection_name == "COPERNICUS/S2" or "LANDSAT" in collection_name: try: - metadata = input_json["metadata"] if "metadata" in input_json.keys() else None + metadata = ( + input_json["metadata"] if "metadata" in input_json.keys() else None + ) - if input_location_type=='local': + if input_location_type == "local": from pathlib import Path parent_path = Path(input_location).parent rgb_location = parent_path else: rgb_location = input_location - create_markdown_pdf_report(output_dir, - "local", - rgb_location, - input_location_type, - do_time_series, - output_dir, - collection_name, - metadata) + create_markdown_pdf_report( + output_dir, + "local", + rgb_location, + input_location_type, + do_time_series, + output_dir, + collection_name, + metadata, + ) except Exception as e: - print ("Warning: A problem was found, the report was not created. There might be missing figures needed " - "for the report or a problem with the pandoc installation. {}".format(e)) + print( + "Warning: A problem was found, the report was not created. There might be missing figures needed " + "for the report or a problem with the pandoc installation. {}".format( + e + ) + ) # ------------------------------------------------ # ------------------------------------------------ # upload the summary csv file to Zenodo if upload_to_zenodo or upload_to_zenodo_test: - print('\nUploading results to Zenodo.\n') + print("\nUploading results to Zenodo.\n") analysis_dir = os.path.join(output_dir, "analysis") - filenames = [f for f in os.listdir(analysis_dir) if f.endswith(".csv") - and f != "time_series_summary_stats.csv"] + filenames = [ + f + for f in os.listdir(analysis_dir) + if f.endswith(".csv") and f != "time_series_summary_stats.csv" + ] if filenames: filepath = os.path.join(analysis_dir, filenames[0]) - - - uploaded = upload_summary_stats(filepath, - upload_to_zenodo_test) + uploaded = upload_summary_stats(filepath, upload_to_zenodo_test) if uploaded: print("Uploaded {} to Zenodo.".format(filenames[0])) else: - print("Couldn't find time series summary stats csv file. Not uploading to Zenodo.") - + print( + "Couldn't find time series summary stats csv file. Not uploading to Zenodo." + ) # ------------------------------------------------ @@ -431,11 +452,17 @@ def main(): ) # off by default as this takes a non-negligable amount of time parser.add_argument( - "--upload_to_zenodo", help="store the summary_stats.csv file on Zenodo", action="store_true", default=False + "--upload_to_zenodo", + help="store the summary_stats.csv file on Zenodo", + action="store_true", + default=False, ) # off by deafult parser.add_argument( - "--upload_to_zenodo_test", help="store the summary_stats.csv file on Zenodo sandbox", action="store_true", default=False + "--upload_to_zenodo_test", + help="store the summary_stats.csv file on Zenodo sandbox", + action="store_true", + default=False, ) # off by deafult print("-" * 35) @@ -447,25 +474,34 @@ def main(): # check we have the bare minimum of args set that we need output_dir = args.output_dir if args.output_dir else args.input_dir if not output_dir: - raise RuntimeError("Need to specify --output_dir argument if reading from Azure blob storage or Zenodo") + raise RuntimeError( + "Need to specify --output_dir argument if reading from Azure blob storage or Zenodo" + ) # read the input json, using either input_dir or input_container arguments if args.input_json and (args.input_dir or args.input_container): - raise RuntimeError(""" + raise RuntimeError( + """ Please use only one of --input_dir or --input_json (for local input), or --onput_container (for Azure), or --zenodo_coords_id (for production Zenodo deposition) or --zenodo_test_coords_id (for Zenodo sandbox) - """) + """ + ) elif args.input_dir and args.input_container: - raise RuntimeError(""" + raise RuntimeError( + """ Please use only one of --input_dir or --input_json (for local input), or --onput_container (for Azure), or --zenodo_coords_id (for production Zenodo deposition) or --zenodo_test_coords_id (for Zenodo sandbox) - """) - elif (args.input_dir or args.input_json or args.input_container) and \ - (args.input_zenodo_coords or args.input_zenodo_test_coords): - raise RuntimeError(""" + """ + ) + elif (args.input_dir or args.input_json or args.input_container) and ( + args.input_zenodo_coords or args.input_zenodo_test_coords + ): + raise RuntimeError( + """ Please use only one of --input_dir or --input_json (for local input), or --onput_container (for Azure), or --zenodo_coords_id (for production Zenodo deposition) or --zenodo_test_coords_id (for Zenodo sandbox) - """) + """ + ) if args.input_container: input_location = args.input_container input_location_type = "azure" @@ -488,14 +524,16 @@ def main(): upload_to_zenodo = args.upload_to_zenodo upload_to_zenodo_test = args.upload_to_zenodo_test # run analysis code - analyse_gee_data(input_location, - input_location_type, - input_json, - output_dir, - do_time_series, - do_spatial, - upload_to_zenodo, - upload_to_zenodo_test) + analyse_gee_data( + input_location, + input_location_type, + input_json, + output_dir, + do_time_series, + do_spatial, + upload_to_zenodo, + upload_to_zenodo_test, + ) if __name__ == "__main__": diff --git a/pyveg/scripts/analyse_pyveg_summary_data.py b/pyveg/scripts/analyse_pyveg_summary_data.py index 999dcc32..a292577d 100644 --- a/pyveg/scripts/analyse_pyveg_summary_data.py +++ b/pyveg/scripts/analyse_pyveg_summary_data.py @@ -5,26 +5,27 @@ """ -import os import argparse import json +import os import re import tempfile + +import matplotlib.pyplot as plt import numpy as np import pandas as pd import seaborn as sns -import matplotlib.pyplot as plt from scipy.stats import pearsonr + sns.set_style("whitegrid") try: - from pyveg.src.zenodo_utils import download_file, list_files, get_deposition_id + from pyveg.src.zenodo_utils import download_file, get_deposition_id, list_files except: print("Unable to import zenodo_utils") def barplot_plots(df, output_dir): - """ Create barplots of summary data. @@ -37,21 +38,26 @@ def barplot_plots(df, output_dir): """ plt.figure() - ax30 = sns.barplot(x='name',y='S2_offset50_mean_max',hue='total_precipitation_mean',data=df) + ax30 = sns.barplot( + x="name", y="S2_offset50_mean_max", hue="total_precipitation_mean", data=df + ) ax30.set_xlabel("Mean precipitation over time series") ax30.set_ylabel("Max Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_precipitation_bar.png')) + plt.savefig(os.path.join(output_dir, "offset50_precipitation_bar.png")) plt.figure() - ax31 = sns.barplot(x='name',y='S2_offset50_mean_max',hue='S2_offset50_mean_Lag-1 AC (0.99 rolling window)',data=df) + ax31 = sns.barplot( + x="name", + y="S2_offset50_mean_max", + hue="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", + data=df, + ) ax31.set_xlabel("Offset50 Lag-1 AC (0.99 rolling window)") ax31.set_ylabel("Max Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_lag1ACvalue_bar.png')) - + plt.savefig(os.path.join(output_dir, "offset50_lag1ACvalue_bar.png")) def scatter_plots(df, output_dir): - """ Create scatter plots and correlation plots of summary data. @@ -64,172 +70,373 @@ def scatter_plots(df, output_dir): """ plt.figure() - ax = sns.scatterplot(y="S2_offset50_mean_mean", x="total_precipitation_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax = sns.scatterplot( + y="S2_offset50_mean_mean", + x="total_precipitation_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax.set_xlabel("Mean precipitation over time series") ax.set_ylabel("Mean Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_vs_precipitation.png')) + plt.savefig(os.path.join(output_dir, "offset50_vs_precipitation.png")) plt.figure() - ax1 = sns.scatterplot(x="longitude", y="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax1 = sns.scatterplot( + x="longitude", + y="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax1.set_ylabel("Mean Offset50 over time series") ax1.set_xlabel("Longitude") - plt.savefig(os.path.join(output_dir,'offset50_vs_Longitude.png')) + plt.savefig(os.path.join(output_dir, "offset50_vs_Longitude.png")) plt.figure() - ax2 = sns.scatterplot(x="latitude", y="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax2 = sns.scatterplot( + x="latitude", + y="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax2.set_ylabel("Mean Offset50 over time series") ax2.set_xlabel("Latitude") - plt.savefig(os.path.join(output_dir,'offset50_vs_Latitude.png')) + plt.savefig(os.path.join(output_dir, "offset50_vs_Latitude.png")) plt.figure() - ax3 = sns.scatterplot(x="longitude", y="latitude", size="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax3 = sns.scatterplot( + x="longitude", + y="latitude", + size="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax3.set_ylabel("Latitude") ax3.set_xlabel("Longitude") - plt.savefig(os.path.join(output_dir,'lat_long_offset50.png')) + plt.savefig(os.path.join(output_dir, "lat_long_offset50.png")) plt.figure() - ax4 = sns.scatterplot(y="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", x="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax4 = sns.scatterplot( + y="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", + x="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax4.set_ylabel("Offset50 Lag-1 AC (0.99 rolling window)") ax4.set_xlabel("Mean Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_offset50AR1.png')) + plt.savefig(os.path.join(output_dir, "offset50_offset50AR1.png")) plt.figure() - ax5 = sns.scatterplot(y="S2_offset50_mean_Variance (0.99 rolling window)", x="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax5 = sns.scatterplot( + y="S2_offset50_mean_Variance (0.99 rolling window)", + x="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax5.set_ylabel("Offset50 Variance (0.99 rolling window)") ax5.set_xlabel("Mean Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_offset50Variance.png')) + plt.savefig(os.path.join(output_dir, "offset50_offset50Variance.png")) plt.figure() - ax6 = sns.scatterplot(y="S2_offset50_mean_Kendall tau Lag-1 AC (0.5 rolling window)", x="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax6 = sns.scatterplot( + y="S2_offset50_mean_Kendall tau Lag-1 AC (0.5 rolling window)", + x="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax6.set_ylabel("Offset50 Kendal tau Lag-1 AC (0.5 rolling window)") ax6.set_xlabel("Mean Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_offset50KendaltauAR1.png')) + plt.savefig(os.path.join(output_dir, "offset50_offset50KendaltauAR1.png")) plt.figure() - ax7 = sns.scatterplot(y="S2_offset50_mean_Kendall tau Variance (0.5 rolling window)", x="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax7 = sns.scatterplot( + y="S2_offset50_mean_Kendall tau Variance (0.5 rolling window)", + x="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax7.set_ylabel("Offset50 Kendal tau Variance (0.5 rolling window)") ax7.set_xlabel("Mean Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50_offset50KendaltauVariance.png')) + plt.savefig(os.path.join(output_dir, "offset50_offset50KendaltauVariance.png")) plt.figure() - ax8 = sns.scatterplot(y="S2_offset50_mean_max", x="total_precipitation_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax8 = sns.scatterplot( + y="S2_offset50_mean_max", + x="total_precipitation_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax8.set_xlabel("Mean precipitation over time series") ax8.set_ylabel("Max Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50max_vs_precipitation.png')) + plt.savefig(os.path.join(output_dir, "offset50max_vs_precipitation.png")) plt.figure() - ax9 = sns.scatterplot(y="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", x="S2_offset50_mean_max", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax9 = sns.scatterplot( + y="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", + x="S2_offset50_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax9.set_ylabel("Offset50 Lag-1 AC (0.99 rolling window)") ax9.set_xlabel("Max Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50max_offset50AR1.png')) + plt.savefig(os.path.join(output_dir, "offset50max_offset50AR1.png")) plt.figure() - ax10 = sns.scatterplot(y="S2_offset50_mean_Variance (0.99 rolling window)", x="S2_offset50_mean_max", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax10 = sns.scatterplot( + y="S2_offset50_mean_Variance (0.99 rolling window)", + x="S2_offset50_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax10.set_ylabel("Offset50 Variance (0.99 rolling window)") ax10.set_xlabel("Max Offset50 over time series") - plt.savefig(os.path.join(output_dir,'offset50max_offset50Variance.png')) + plt.savefig(os.path.join(output_dir, "offset50max_offset50Variance.png")) plt.figure() - ax11 = sns.scatterplot(y="total_precipitation_mean", x="S2_offset50_mean_Variance (0.99 rolling window)", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax11 = sns.scatterplot( + y="total_precipitation_mean", + x="S2_offset50_mean_Variance (0.99 rolling window)", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax11.set_ylabel("Mean precipitation over time series") ax11.set_xlabel("Offset50 Variance (0.99 rolling window)") - plt.savefig(os.path.join(output_dir,'precipitation_vs_offset50Variance.png')) + plt.savefig(os.path.join(output_dir, "precipitation_vs_offset50Variance.png")) plt.figure() - ax12 = sns.scatterplot(y="total_precipitation_mean", x="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax12 = sns.scatterplot( + y="total_precipitation_mean", + x="S2_offset50_mean_Lag-1 AC (0.99 rolling window)", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax12.set_ylabel("Mean precipitation over time series") ax12.set_xlabel("Offset50 Lag-1 AC (0.99 rolling window)") - plt.savefig(os.path.join(output_dir,'precipitation_vs_offset50AR1.png')) + plt.savefig(os.path.join(output_dir, "precipitation_vs_offset50AR1.png")) plt.figure() - ax13 = sns.scatterplot(y="S2_offset50_mean_max", x="S2_ndvi_mean_max", data=df, hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax13 = sns.scatterplot( + y="S2_offset50_mean_max", + x="S2_ndvi_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax13.set_ylabel("Max offset50 over time series") ax13.set_xlabel("Max NDVI over time series") - plt.savefig(os.path.join(output_dir, 'offset50max_vs_NDVImax.png')) + plt.savefig(os.path.join(output_dir, "offset50max_vs_NDVImax.png")) plt.figure() - ax14 = sns.scatterplot(y="S2_offset50_mean_mean", x="S2_ndvi_mean_mean", data=df, hue="S2_offset50_mean_pattern_type",palette="Accent_r",edgecolor="k",linewidth=1) + ax14 = sns.scatterplot( + y="S2_offset50_mean_mean", + x="S2_ndvi_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax14.set_ylabel("Mean offset50 over time series") ax14.set_xlabel("Mean NDVI over time series") - plt.savefig(os.path.join(output_dir, 'offset50max_vs_NDVImean.png')) + plt.savefig(os.path.join(output_dir, "offset50max_vs_NDVImean.png")) plt.figure() - ax15 = sns.scatterplot(y="S2_offset50_mean_Lag-1 AC (0.99 rolling window) Seasonal", x="S2_offset50_mean_max", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax15 = sns.scatterplot( + y="S2_offset50_mean_Lag-1 AC (0.99 rolling window) Seasonal", + x="S2_offset50_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax15.set_ylabel("Offset50 Lag-1 AC (0.99 rolling window) Seasonal") ax15.set_xlabel("Mean NDVI over time series") - plt.savefig(os.path.join(output_dir, 'offset50max_vs_offset50AR1_0.99_Seasonal.png')) + plt.savefig( + os.path.join(output_dir, "offset50max_vs_offset50AR1_0.99_Seasonal.png") + ) plt.figure() - ax16 = sns.scatterplot(y="S2_offset50_mean_Variance (0.99 rolling window) Seasonal", x="S2_offset50_mean_max", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax16 = sns.scatterplot( + y="S2_offset50_mean_Variance (0.99 rolling window) Seasonal", + x="S2_offset50_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax16.set_ylabel("Offset50 Variance (0.99 rolling window) Seasonal") ax16.set_xlabel("Max offset50") - plt.savefig(os.path.join(output_dir, 'offset50max_vs_offset50Variance_0.99_Seasonal.png')) + plt.savefig( + os.path.join(output_dir, "offset50max_vs_offset50Variance_0.99_Seasonal.png") + ) plt.figure() - ax17 = sns.scatterplot(y="S2_offset50_mean_Lag-1 AC (0.99 rolling window) Seasonal", x="total_precipitation_mean", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax17 = sns.scatterplot( + y="S2_offset50_mean_Lag-1 AC (0.99 rolling window) Seasonal", + x="total_precipitation_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax17.set_ylabel("Offset50 Lag-1 AC (0.99 rolling window) Seasonal") ax17.set_xlabel("Mean precipitation") - plt.savefig(os.path.join(output_dir, 'precipitationmean_vs_offset50AR1_0.99_Seasonal.png')) + plt.savefig( + os.path.join(output_dir, "precipitationmean_vs_offset50AR1_0.99_Seasonal.png") + ) plt.figure() - ax18 = sns.scatterplot(y="S2_offset50_mean_Variance (0.99 rolling window) Seasonal", x="total_precipitation_mean", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax18 = sns.scatterplot( + y="S2_offset50_mean_Variance (0.99 rolling window) Seasonal", + x="total_precipitation_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax18.set_ylabel("Offset50 Variance (0.99 rolling window) Seasonal") ax18.set_xlabel("Mean precipitation") - plt.savefig(os.path.join(output_dir, 'precipitationmean_vs_offset50Variance_0.99_Seasonal.png')) - + plt.savefig( + os.path.join( + output_dir, "precipitationmean_vs_offset50Variance_0.99_Seasonal.png" + ) + ) plt.figure() - ax19 = sns.scatterplot(y="offset50_cb_return_rate", x="S2_offset50_mean_max", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax19 = sns.scatterplot( + y="offset50_cb_return_rate", + x="S2_offset50_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax19.set_ylabel("Offset50 return rate") ax19.set_xlabel("Max offset50") - plt.savefig(os.path.join(output_dir, 'offset50max_vs_offset50returnrate.png')) + plt.savefig(os.path.join(output_dir, "offset50max_vs_offset50returnrate.png")) plt.figure() - ax20 = sns.scatterplot(y="offset50_cb_return_rate", x="total_precipitation_mean", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax20 = sns.scatterplot( + y="offset50_cb_return_rate", + x="total_precipitation_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax20.set_ylabel("Offset50 return rate") ax20.set_xlabel("Mean precipitation over time series") - plt.savefig(os.path.join(output_dir, 'meanprecipitation_vs_offset50returnrate.png')) + plt.savefig(os.path.join(output_dir, "meanprecipitation_vs_offset50returnrate.png")) plt.figure() - ax21 = sns.scatterplot(y="ndvi_cb_return_rate", x="S2_ndvi_mean_max", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax21 = sns.scatterplot( + y="ndvi_cb_return_rate", + x="S2_ndvi_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax21.set_ylabel("NDVI crystall ball return rate") ax21.set_xlabel("Max NDVI in time series") - plt.savefig(os.path.join(output_dir, 'NDVImax_vs_NDVIreturnrate.png')) + plt.savefig(os.path.join(output_dir, "NDVImax_vs_NDVIreturnrate.png")) plt.figure() - ax22 = sns.scatterplot(y="ndvi_cb_return_rate", x="total_precipitation_mean", data=df, - hue="S2_offset50_mean_pattern_type", palette="Accent_r", edgecolor="k", linewidth=1) + ax22 = sns.scatterplot( + y="ndvi_cb_return_rate", + x="total_precipitation_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + edgecolor="k", + linewidth=1, + ) ax22.set_ylabel("NDVI crystall ball return rate") ax22.set_xlabel("Mean precipitation over time series") - plt.savefig(os.path.join(output_dir, 'meanprecipitation_vs_NDVIreturnrate.png')) + plt.savefig(os.path.join(output_dir, "meanprecipitation_vs_NDVIreturnrate.png")) + def correlation_plots(df, output_dir): + """ + Create correlation plots of summary data. + Parameters + ----------- + df : dataframe + Dataframe of summary data. + output_dir : str + Path to the directory to save plots to. """ - Create correlation plots of summary data. - - Parameters - ----------- - df : dataframe - Dataframe of summary data. - output_dir : str - Path to the directory to save plots to. - """ - - #Calculate Correlations and p-values - selected_df = df[["total_precipitation_mean","S2_offset50_mean_mean","S2_offset50_mean_max", - "S2_offset50_mean_Lag-1 AC (0.99 rolling window)","S2_offset50_mean_Variance (0.99 rolling window)", - "latitude","longitude"]] - df_labels = ["Precipitation mean", "Ofset50 mean", "Offset50 max", "Offset50 AR1 (0.99 r.w)", - "Offset50 variance (0.99 r.w)", "latitude","longitude"] - selected_corr=selected_df.corr(method="pearson") + + # Calculate Correlations and p-values + selected_df = df[ + [ + "total_precipitation_mean", + "S2_offset50_mean_mean", + "S2_offset50_mean_max", + "S2_offset50_mean_Lag-1 AC (0.99 rolling window)", + "S2_offset50_mean_Variance (0.99 rolling window)", + "latitude", + "longitude", + ] + ] + df_labels = [ + "Precipitation mean", + "Ofset50 mean", + "Offset50 max", + "Offset50 AR1 (0.99 r.w)", + "Offset50 variance (0.99 r.w)", + "latitude", + "longitude", + ] + selected_corr = selected_df.corr(method="pearson") # Set up the matplotlib figure f, ax = plt.subplots(figsize=(11, 9)) @@ -237,11 +444,11 @@ def correlation_plots(df, output_dir): # Generate a custom diverging colormap cmap = sns.diverging_palette(230, 20, as_cmap=True) - #Calculate p-value matrix + # Calculate p-value matrix def calculate_pvalues(df): df = df.dropna()._get_numeric_data() dfcols = pd.DataFrame(columns=df.columns) - pvalues = dfcols.transpose().join(dfcols, how='outer') + pvalues = dfcols.transpose().join(dfcols, how="outer") for r in df.columns: for c in df.columns: pvalues[r][c] = round(pearsonr(df[r], df[c])[1], 4) @@ -257,49 +464,98 @@ def calculate_pvalues(df): p_mask_01 = np.invert(p_matrix < 0.1) # Draw the heatmap with the mask and correct aspect ratio - sns.heatmap(selected_corr, cmap=cmap, vmax=1, vmin=-1, center=0, xticklabels=df_labels, yticklabels=df_labels, - square=True, annot=True, linewidths=.5, cbar=False, cbar_kws={"shrink": .5}) - plt.savefig(os.path.join(output_dir,'pearsons_correlation_plot.png')) - - sns.heatmap(selected_corr, cmap=cmap, vmax=1, vmin=-1, center=0,xticklabels=df_labels, yticklabels=df_labels, - square=True, annot=True, linewidths=.5, cbar=False, cbar_kws={"shrink": .5},mask=p_mask) - plt.savefig(os.path.join(output_dir, 'significant_0.05_pearsons_correlation.png')) - - sns.heatmap(selected_corr, cmap=cmap, vmax=1, vmin=-1, center=0,xticklabels=df_labels, yticklabels=df_labels, - square=True, annot=True, linewidths=.5, cbar=False, cbar_kws={"shrink": .5},mask=p_mask_01) - plt.savefig(os.path.join(output_dir, 'significant_0.1_pearsons_correlation.png')) + sns.heatmap( + selected_corr, + cmap=cmap, + vmax=1, + vmin=-1, + center=0, + xticklabels=df_labels, + yticklabels=df_labels, + square=True, + annot=True, + linewidths=0.5, + cbar=False, + cbar_kws={"shrink": 0.5}, + ) + plt.savefig(os.path.join(output_dir, "pearsons_correlation_plot.png")) + + sns.heatmap( + selected_corr, + cmap=cmap, + vmax=1, + vmin=-1, + center=0, + xticklabels=df_labels, + yticklabels=df_labels, + square=True, + annot=True, + linewidths=0.5, + cbar=False, + cbar_kws={"shrink": 0.5}, + mask=p_mask, + ) + plt.savefig(os.path.join(output_dir, "significant_0.05_pearsons_correlation.png")) + + sns.heatmap( + selected_corr, + cmap=cmap, + vmax=1, + vmin=-1, + center=0, + xticklabels=df_labels, + yticklabels=df_labels, + square=True, + annot=True, + linewidths=0.5, + cbar=False, + cbar_kws={"shrink": 0.5}, + mask=p_mask_01, + ) + plt.savefig(os.path.join(output_dir, "significant_0.1_pearsons_correlation.png")) - selected_corr.to_csv(os.path.join(output_dir,"Pearson_correlation.csv")) - p_matrix.to_csv(os.path.join(output_dir,"Pearson_p_value.csv")) + selected_corr.to_csv(os.path.join(output_dir, "Pearson_correlation.csv")) + p_matrix.to_csv(os.path.join(output_dir, "Pearson_p_value.csv")) def boxplot_plots(df, output_dir): """ - Create boxplots of summary data. + Create boxplots of summary data. - Parameters - ----------- - df : dataframe - Dataframe of summary data. - output_dir : str - Path to the directory to save plots to. - """ + Parameters + ----------- + df : dataframe + Dataframe of summary data. + output_dir : str + Path to the directory to save plots to. + """ plt.figure() - ax23 = sns.boxplot(x="S2_offset50_mean_pattern_type", y="S2_offset50_mean_max", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r") + ax23 = sns.boxplot( + x="S2_offset50_mean_pattern_type", + y="S2_offset50_mean_max", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + ) ax23.set_ylabel("Max Offset50 Values") ax23.set_xlabel("Pattern Type") - plt.savefig(os.path.join(output_dir, 'Max_offset50_boxplot.png')) + plt.savefig(os.path.join(output_dir, "Max_offset50_boxplot.png")) plt.figure() - ax24 = sns.boxplot(x="S2_offset50_mean_pattern_type", y="S2_offset50_mean_mean", data=df,hue="S2_offset50_mean_pattern_type",palette="Accent_r") + ax24 = sns.boxplot( + x="S2_offset50_mean_pattern_type", + y="S2_offset50_mean_mean", + data=df, + hue="S2_offset50_mean_pattern_type", + palette="Accent_r", + ) ax24.set_ylabel("Mean Offset50 Values") ax24.set_xlabel("Pattern Type") - plt.savefig(os.path.join(output_dir, 'Mean_offset50_boxplot.png')) + plt.savefig(os.path.join(output_dir, "Mean_offset50_boxplot.png")) def process_input_data(input_location): - """Read all input summary statistics and transform data into a more analysis-friendly format @@ -315,16 +571,21 @@ def process_input_data(input_location): df: DataFrame containing all the time-series data concatenated together. """ df_list = [] - if input_location == 'zenodo' or input_location == 'zenodo_test': - is_test = input_location == 'zenodo_test' + if input_location == "zenodo" or input_location == "zenodo_test": + is_test = input_location == "zenodo_test" deposition_id = get_deposition_id(is_test) with tempfile.TemporaryDirectory() as tmpdir: - ts_filenames = [download_file(f, deposition_id, tmpdir, is_test) \ - for f in list_files(deposition_id, "csv", is_test)] + ts_filenames = [ + download_file(f, deposition_id, tmpdir, is_test) + for f in list_files(deposition_id, "csv", is_test) + ] df_list = [pd.read_csv(filename) for filename in ts_filenames] else: ts_filenames = [f for f in os.listdir(input_location) if "_summary_stats" in f] - df_list = [pd.read_csv(os.path.join(input_location, filename)) for filename in ts_filenames] + df_list = [ + pd.read_csv(os.path.join(input_location, filename)) + for filename in ts_filenames + ] df = pd.concat(df_list) @@ -333,21 +594,19 @@ def process_input_data(input_location): dict_list = {} - for ts in np.unique(group['ts_id']): + for ts in np.unique(group["ts_id"]): for col in group: - dict_list[ts + "_" + col] = group[group['ts_id'] == ts][col].values[0] - dict_list['name'] = name - dict_list['latitude'] = group['latitude'].values[0] - dict_list['longitude'] = group['longitude'].values[0] + dict_list[ts + "_" + col] = group[group["ts_id"] == ts][col].values[0] + dict_list["name"] = name + dict_list["latitude"] = group["latitude"].values[0] + dict_list["longitude"] = group["longitude"].values[0] ts_dict_list.append(dict_list) return pd.DataFrame(ts_dict_list) - def analyse_pyveg_summary_data(input_location, output_dir): - """ Run analysis on summary statistics data @@ -363,18 +622,20 @@ def analyse_pyveg_summary_data(input_location, output_dir): df = process_input_data(input_location) - #add new variable to the dataframe - df["offset50_cb_return_rate"] = (df["S2_offset50_mean_CB_fit_alpha"] ** 2).divide(2.0) + # add new variable to the dataframe + df["offset50_cb_return_rate"] = (df["S2_offset50_mean_CB_fit_alpha"] ** 2).divide( + 2.0 + ) df["ndvi_cb_return_rate"] = (df["S2_ndvi_mean_CB_fit_alpha"] ** 2).divide(2.0) summary_plots = os.path.join(output_dir, "summary_plots") if not os.path.exists(summary_plots): os.makedirs(summary_plots, exist_ok=True) - scatter_plots(df,summary_plots) - barplot_plots(df,summary_plots) - correlation_plots(df,summary_plots) - boxplot_plots(df,summary_plots) + scatter_plots(df, summary_plots) + barplot_plots(df, summary_plots) + correlation_plots(df, summary_plots) + boxplot_plots(df, summary_plots) def main(): @@ -389,11 +650,9 @@ def main(): help="results directory from `download_gee_data` script, containing `summary_stats.csv`, OR 'zenodo' or 'zenodo_test' to download the files from the production or sandbox Zenodo depositions.", ) parser.add_argument( - "--output_dir", - help="location where analysis plots will be put.",default="." + "--output_dir", help="location where analysis plots will be put.", default="." ) - print("-" * 35) print("Running analyse_pyveg_summary_data.py") print("-" * 35) @@ -401,10 +660,8 @@ def main(): # parse args args = parser.parse_args() - # run analysis code - analyse_pyveg_summary_data(args.input_location, - args.output_dir) + analyse_pyveg_summary_data(args.input_location, args.output_dir) if __name__ == "__main__": diff --git a/pyveg/scripts/calc_euler_characteristic.py b/pyveg/scripts/calc_euler_characteristic.py index b199d81a..291374b4 100644 --- a/pyveg/scripts/calc_euler_characteristic.py +++ b/pyveg/scripts/calc_euler_characteristic.py @@ -7,15 +7,15 @@ src/subgraph_centrality.py """ -import os import argparse +import os from pyveg.src.subgraph_centrality import ( - subgraph_centrality, feature_vector_metrics, generate_sc_images, - text_file_to_array, image_file_to_array, + subgraph_centrality, + text_file_to_array, ) diff --git a/pyveg/scripts/create_analysis_report.py b/pyveg/scripts/create_analysis_report.py index 6a5e44de..ea126e26 100644 --- a/pyveg/scripts/create_analysis_report.py +++ b/pyveg/scripts/create_analysis_report.py @@ -1,11 +1,12 @@ -from mdutils.mdutils import MdUtils -import os import argparse import glob -from pathlib import Path -import pypandoc import json +import os import tempfile +from pathlib import Path + +import pypandoc +from mdutils.mdutils import MdUtils from pyveg.src.azure_utils import download_rgb, download_summary_json @@ -24,182 +25,285 @@ def get_collection_and_suffix(collection_name): suffix: str, contraction of collection name, used in the filenames of plots """ - if collection_name == 'COPERNICUS/S2': - collection = 'Sentinel2' - satellite_suffix = 'S2' + if collection_name == "COPERNICUS/S2": + collection = "Sentinel2" + satellite_suffix = "S2" - elif collection_name == 'LANDSAT8': - collection = 'Landsat8' - satellite_suffix = 'L8' + elif collection_name == "LANDSAT8": + collection = "Landsat8" + satellite_suffix = "L8" - elif collection_name == 'LANDSAT7': - collection = 'Landsat7' - satellite_suffix = 'L7' + elif collection_name == "LANDSAT7": + collection = "Landsat7" + satellite_suffix = "L7" - elif collection_name == 'LANDSAT5': - collection = 'Landsat5' - satellite_suffix = 'L5' + elif collection_name == "LANDSAT5": + collection = "Landsat5" + satellite_suffix = "L5" - elif collection_name == 'LANDSAT4': - collection = 'Landsat4' - satellite_suffix = 'L4' + elif collection_name == "LANDSAT4": + collection = "Landsat4" + satellite_suffix = "L4" else: raise RuntimeError("Unknown collection_name {}".format(collection_name)) return collection, satellite_suffix -def add_time_series_plots(mdFile, analysis_plots_location, analysis_plots_location_type, satellite_suffix): +def add_time_series_plots( + mdFile, analysis_plots_location, analysis_plots_location_type, satellite_suffix +): if analysis_plots_location_type != "local": print("Only local disk location for analysis plots is currently supported") return mdFile, 0 fig_count = 0 # Time series figures - mdFile.new_header(level=1, title='Time series') - ts_path = os.path.join(analysis_plots_location,'analysis','time-series') + mdFile.new_header(level=1, title="Time series") + ts_path = os.path.join(analysis_plots_location, "analysis", "time-series") fig_count += 1 - mdFile.new_line(mdFile.new_inline_image(text='Time series Offset50', path=os.path.join(ts_path,satellite_suffix+'-time-series_smooth.png'))) - #mdFile.new_paragraph('Figure '+str(count)+': '+'Time series Offset50') + mdFile.new_line( + mdFile.new_inline_image( + text="Time series Offset50", + path=os.path.join(ts_path, satellite_suffix + "-time-series_smooth.png"), + ) + ) + # mdFile.new_paragraph('Figure '+str(count)+': '+'Time series Offset50') fig_count += 1 - mdFile.new_line(mdFile.new_inline_image(text='Time series NDVI', path=os.path.join(ts_path,satellite_suffix+'-ndvi-time-series.png'))) - #mdFile.new_paragraph('Figure '+str(count)+': '+'Time series NDVI') - mdFile.new_line('') + mdFile.new_line( + mdFile.new_inline_image( + text="Time series NDVI", + path=os.path.join(ts_path, satellite_suffix + "-ndvi-time-series.png"), + ) + ) + # mdFile.new_paragraph('Figure '+str(count)+': '+'Time series NDVI') + mdFile.new_line("") # STL figures - mdFile.new_header(level=1, title='STL decomposition') - stl_path = os.path.join(analysis_plots_location, 'analysis', 'detrended','STL') + mdFile.new_header(level=1, title="STL decomposition") + stl_path = os.path.join(analysis_plots_location, "analysis", "detrended", "STL") fig_count += 1 - mdFile.new_line(mdFile.new_inline_image(text='STL Offset50', path=os.path.join(stl_path, satellite_suffix+'_offset50_mean_STL_decomposition.png'))) - #mdFile.new_paragraph('Figure '+str(count)+': '+'STL Offset50') + mdFile.new_line( + mdFile.new_inline_image( + text="STL Offset50", + path=os.path.join( + stl_path, satellite_suffix + "_offset50_mean_STL_decomposition.png" + ), + ) + ) + # mdFile.new_paragraph('Figure '+str(count)+': '+'STL Offset50') fig_count += 1 - mdFile.new_line(mdFile.new_inline_image(text='STL NDVI', path=os.path.join(stl_path, satellite_suffix+'_ndvi_mean_STL_decomposition.png'))) - #mdFile.new_paragraph('Figure '+str(count)+': '+'STL NDVI') - mdFile.new_line('') - - if os.path.exists(os.path.join(analysis_plots_location, 'analysis', 'resiliance','deseasonalised','ewstools')): + mdFile.new_line( + mdFile.new_inline_image( + text="STL NDVI", + path=os.path.join( + stl_path, satellite_suffix + "_ndvi_mean_STL_decomposition.png" + ), + ) + ) + # mdFile.new_paragraph('Figure '+str(count)+': '+'STL NDVI') + mdFile.new_line("") + + if os.path.exists( + os.path.join( + analysis_plots_location, + "analysis", + "resiliance", + "deseasonalised", + "ewstools", + ) + ): # Early warning figures - mdFile.new_header(level=1, title='Early warnings analysis') - ews_path = os.path.join(analysis_plots_location, 'analysis', 'resiliance','deseasonalised','ewstools') + mdFile.new_header(level=1, title="Early warnings analysis") + ews_path = os.path.join( + analysis_plots_location, + "analysis", + "resiliance", + "deseasonalised", + "ewstools", + ) fig_count += 1 - mdFile.new_line(mdFile.new_inline_image(text='EWS Offset50', path=os.path.join(ews_path, satellite_suffix+'-offset50-mean-ews.png'))) - #mdFile.new_paragraph('Figure '+str(count)+': '+'EWS Offset50') + mdFile.new_line( + mdFile.new_inline_image( + text="EWS Offset50", + path=os.path.join( + ews_path, satellite_suffix + "-offset50-mean-ews.png" + ), + ) + ) + # mdFile.new_paragraph('Figure '+str(count)+': '+'EWS Offset50') mdFile.new_line() fig_count += 1 mdFile.new_line( - mdFile.new_inline_image(text='EWS NDVI', path=os.path.join(ews_path, satellite_suffix+'-ndvi-mean-ews.png'))) - mdFile.new_line('') - - mdFile.new_header(level=1, title='Average annual time series CB fit') + mdFile.new_inline_image( + text="EWS NDVI", + path=os.path.join(ews_path, satellite_suffix + "-ndvi-mean-ews.png"), + ) + ) + mdFile.new_line("") + + mdFile.new_header(level=1, title="Average annual time series CB fit") fig_count += 1 mdFile.new_line( - mdFile.new_inline_image(text='Offset50 CB fit', path=os.path.join(analysis_plots_location,'analysis', 'fit_ts_CB_S2_offset50_mean.png'))) - mdFile.new_line('') + mdFile.new_inline_image( + text="Offset50 CB fit", + path=os.path.join( + analysis_plots_location, "analysis", "fit_ts_CB_S2_offset50_mean.png" + ), + ) + ) + mdFile.new_line("") fig_count += 1 mdFile.new_line( - mdFile.new_inline_image(text='NDVI CB fit', - path=os.path.join(analysis_plots_location, 'analysis','fit_ts_CB_S2_ndvi_mean.png'))) - mdFile.new_line('') + mdFile.new_inline_image( + text="NDVI CB fit", + path=os.path.join( + analysis_plots_location, "analysis", "fit_ts_CB_S2_ndvi_mean.png" + ), + ) + ) + mdFile.new_line("") fig_count += 1 mdFile.new_line( - mdFile.new_inline_image(text='total precipitation CB fit', - path=os.path.join(analysis_plots_location, 'analysis','fit_ts_CB_total_precipitation.png'))) - mdFile.new_line('') + mdFile.new_inline_image( + text="total precipitation CB fit", + path=os.path.join( + analysis_plots_location, "analysis", "fit_ts_CB_total_precipitation.png" + ), + ) + ) + mdFile.new_line("") return mdFile, fig_count def add_rgb_images(mdFile, rgb_location, rgb_location_type, fig_count): - mdFile.new_header(level=1, title='RGB images through time') # style is set 'atx' format by default. + # style is set 'atx' format by default. + mdFile.new_header(level=1, title="RGB images through time") rgb_filenames = [] if rgb_location_type == "local": for root, dirs, files in os.walk(rgb_location): for filename in files: - if filename.endswith("RGB.png") and os.path.basename(filename).startswith('sub')==False: + if ( + filename.endswith("RGB.png") + and os.path.basename(filename).startswith("sub") == False + ): rgb_filenames.append(os.path.join(rgb_location, root, filename)) elif rgb_location_type == "azure": tmpdir = tempfile.mkdtemp() download_rgb(rgb_location, tmpdir) rgb_filenames = [os.path.join(tmpdir, fname) for fname in os.listdir(tmpdir)] else: - print(""" + print( + """ Trying to add RGB images to report - unknown value for rgb_location_type - {}. Currently accepted values are ['local','azure'] - """.format(rgb_location_type)) + """.format( + rgb_location_type + ) + ) return mdFile rgb_filenames.sort() for i, rgb_figure in enumerate(rgb_filenames): rgb_figure_name = os.path.basename(rgb_figure) mdFile.new_line(mdFile.new_inline_image(text=rgb_figure, path=rgb_figure)) - mdFile.new_line('Figure '+str(fig_count)+': '+rgb_figure_name) - mdFile.new_line('') + mdFile.new_line("Figure " + str(fig_count) + ": " + rgb_figure_name) + mdFile.new_line("") fig_count += 1 return mdFile -def create_markdown_pdf_report(analysis_plots_location, - analysis_plots_location_type, - rgb_location, - rgb_location_type, - do_timeseries, - output_dir=None, - collection_name=None, - metadata=None): +def create_markdown_pdf_report( + analysis_plots_location, + analysis_plots_location_type, + rgb_location, + rgb_location_type, + do_timeseries, + output_dir=None, + collection_name=None, + metadata=None, +): if not metadata: - if os.path.exists(os.path.join(analysis_plots_location, "results_summary.json")): + if os.path.exists( + os.path.join(analysis_plots_location, "results_summary.json") + ): try: - metadata = json.load(open(os.path.join(analysis_plots_location, "results_summary.json")))["metadata"] + metadata = json.load( + open(os.path.join(analysis_plots_location, "results_summary.json")) + )["metadata"] except: - print("Couldn't retrieve metadata from {}".format(analysis_plots_location, "results_summary.json")) + print( + "Couldn't retrieve metadata from {}".format( + analysis_plots_location, "results_summary.json" + ) + ) elif rgb_location_type == "azure": tmpdir = tempfile.mkdtemp() download_summary_json(rgb_location, tmpdir) try: - metadata = json.load(open(os.path.join(tmpdir, "results_summary.json")))["metadata"] + metadata = json.load( + open(os.path.join(tmpdir, "results_summary.json")) + )["metadata"] except: - print("Couldn't retrieve metadata from {}".format(tmpdir, "results_summary.json")) + print( + "Couldn't retrieve metadata from {}".format( + tmpdir, "results_summary.json" + ) + ) if metadata and not collection_name: - collection_name = metadata['collection'] + collection_name = metadata["collection"] if not collection_name: - raise RuntimeError("please provide either a metadata dictionary or a collection name (e.g. 'COPERNICUS/S2')") + raise RuntimeError( + "please provide either a metadata dictionary or a collection name (e.g. 'COPERNICUS/S2')" + ) collection, satellite_suffix = get_collection_and_suffix(collection_name) if metadata: - coordinates = (metadata['longitude'], metadata['latitude']) + coordinates = (metadata["longitude"], metadata["latitude"]) if not coordinates: - raise RuntimeError("Unable to find coordinates from path. Please provide a metadata dict.") + raise RuntimeError( + "Unable to find coordinates from path. Please provide a metadata dict." + ) if not output_dir: # put the output report in the same directory as the analysis plots output_dir = analysis_plots_location os.makedirs(output_dir, exist_ok=True) - output_path = os.path.join(output_dir,'analysis_report_{}_{}_{}'.format(coordinates[0],coordinates[1],collection)) + output_path = os.path.join( + output_dir, + "analysis_report_{}_{}_{}".format(coordinates[0], coordinates[1], collection), + ) # create the markdown file - mdFile = MdUtils(file_name=output_path, - title='Results for {} and coordinates {} (longitude) and {} (latitude)'\ - .format(collection, - coordinates[0], - coordinates[1])) + mdFile = MdUtils( + file_name=output_path, + title="Results for {} and coordinates {} (longitude) and {} (latitude)".format( + collection, coordinates[0], coordinates[1] + ), + ) fig_count = 0 if do_timeseries: - mdFile, fig_count = add_time_series_plots(mdFile, - analysis_plots_location, - analysis_plots_location_type, - satellite_suffix) + mdFile, fig_count = add_time_series_plots( + mdFile, + analysis_plots_location, + analysis_plots_location_type, + satellite_suffix, + ) # add RGB images mdFile = add_rgb_images(mdFile, rgb_location, rgb_location_type, fig_count) # Create a table of contents and save file - mdFile.new_table_of_contents(table_title='Contents', depth=2) + mdFile.new_table_of_contents(table_title="Contents", depth=2) mdFile.create_md_file() - print ('Converting to pdf.') - output = pypandoc.convert_file(output_path+'.md', 'pdf', outputfile=output_path+".pdf") + print("Converting to pdf.") + output = pypandoc.convert_file( + output_path + ".md", "pdf", outputfile=output_path + ".pdf" + ) assert output == "" @@ -207,18 +311,45 @@ def main(): """ CLI interface for gee data analysis. """ - parser = argparse.ArgumentParser(description="Collect all figures from analysis and get them into report") - parser.add_argument("--input_analysis_plots_location", help="results directory from `download_gee_data` script, containing `results_summary.json` and `analysis` directory") - parser.add_argument("--input_analysis_plots_location_type", help="currently supports 'local' or 'azure'",default="local") - parser.add_argument("--input_rgb_location", help="location of the RGB plots - either an Azure container or a local directory") - parser.add_argument("--input_rgb_location_type", help="currently supports 'local' or 'azure'", default="local") - parser.add_argument("--output_dir", help="(optional) directory to store output report. If not specified, will use input_analysis_plots_location") - parser.add_argument("--do_timeseries", action="store_true", help="include time-series plots in the report") - parser.add_argument("--collection", help="Satellite to be used in the report ",default='COPERNICUS/S2') - - print('-' * 35) - print('Running create_analysis_report.py') - print('-' * 35) + parser = argparse.ArgumentParser( + description="Collect all figures from analysis and get them into report" + ) + parser.add_argument( + "--input_analysis_plots_location", + help="results directory from `download_gee_data` script, containing `results_summary.json` and `analysis` directory", + ) + parser.add_argument( + "--input_analysis_plots_location_type", + help="currently supports 'local' or 'azure'", + default="local", + ) + parser.add_argument( + "--input_rgb_location", + help="location of the RGB plots - either an Azure container or a local directory", + ) + parser.add_argument( + "--input_rgb_location_type", + help="currently supports 'local' or 'azure'", + default="local", + ) + parser.add_argument( + "--output_dir", + help="(optional) directory to store output report. If not specified, will use input_analysis_plots_location", + ) + parser.add_argument( + "--do_timeseries", + action="store_true", + help="include time-series plots in the report", + ) + parser.add_argument( + "--collection", + help="Satellite to be used in the report ", + default="COPERNICUS/S2", + ) + + print("-" * 35) + print("Running create_analysis_report.py") + print("-" * 35) # parse args args = parser.parse_args() @@ -231,13 +362,15 @@ def main(): collection = args.collection # run markdown code - create_markdown_pdf_report(input_analysis_plots_location, - input_analysis_plots_location_type, - input_rgb_location, - input_rgb_location_type, - do_timeseries, - output_dir, - collection) + create_markdown_pdf_report( + input_analysis_plots_location, + input_analysis_plots_location_type, + input_rgb_location, + input_rgb_location_type, + do_timeseries, + output_dir, + collection, + ) if __name__ == "__main__": diff --git a/pyveg/scripts/crop_and_convert_images.py b/pyveg/scripts/crop_and_convert_images.py index 09ecdf54..9692a899 100644 --- a/pyveg/scripts/crop_and_convert_images.py +++ b/pyveg/scripts/crop_and_convert_images.py @@ -44,7 +44,7 @@ def main(): type=int, ) args = parser.parse_args() - ## now call the crop_and_convert function + # now call the crop_and_convert function crop_and_convert_all( args.input_dir, args.output_dir, args.threshold, args.num_pix_x, args.num_pix_y ) diff --git a/pyveg/scripts/download_from_azure.py b/pyveg/scripts/download_from_azure.py index d51d22a0..7950b901 100644 --- a/pyveg/scripts/download_from_azure.py +++ b/pyveg/scripts/download_from_azure.py @@ -16,15 +16,15 @@ """ -import os -import tempfile import argparse +import os import subprocess +import tempfile from azure.storage.blob import BlockBlobService -from pyveg.src.azure_utils import download_summary_json, download_rgb from pyveg.azure_config import config +from pyveg.src.azure_utils import download_rgb, download_summary_json def create_zip_archive(temp_dir, output_zipname, json_dir=None, rgb_dir=None): @@ -36,9 +36,9 @@ def create_zip_archive(temp_dir, output_zipname, json_dir=None, rgb_dir=None): """ if json_dir: - subprocess.run(["cp","-r",json_dir, temp_dir]) + subprocess.run(["cp", "-r", json_dir, temp_dir]) if rgb_dir: - subprocess.run(["cp","-r",rgb_dir, temp_dir]) + subprocess.run(["cp", "-r", rgb_dir, temp_dir]) subprocess.run(["zip", "-r", os.path.basename(output_zipname), "."], cwd=temp_dir) subprocess.run( ["cp", os.path.join(temp_dir, os.path.basename(output_zipname)), output_zipname] @@ -52,18 +52,12 @@ def main(): parser.add_argument( "--container", help="name of blob storage container", required=True ) + parser.add_argument("--output_dir", help="name of output_directory", required=True) parser.add_argument( - "--output_dir", help="name of output_directory", required=True - ) - parser.add_argument( - "--summary_json", help="download results_summary.json?", action='store_true' - ) - parser.add_argument( - "--rgb", help="download RGB images?", action='store_true' - ) - parser.add_argument( - "--output_zipfile", help="name of zipfile to write to" + "--summary_json", help="download results_summary.json?", action="store_true" ) + parser.add_argument("--rgb", help="download RGB images?", action="store_true") + parser.add_argument("--output_zipfile", help="name of zipfile to write to") args = parser.parse_args() if args.output_dir: diff --git a/pyveg/scripts/generate_config_file.py b/pyveg/scripts/generate_config_file.py index e3e2c0d8..8566b1fc 100644 --- a/pyveg/scripts/generate_config_file.py +++ b/pyveg/scripts/generate_config_file.py @@ -30,108 +30,109 @@ """ +import argparse import os import re -import argparse import time from pyveg.configs import collections from pyveg.coordinates import coordinate_store from pyveg.src.coordinate_utils import lookup_country + def get_template_text(): template_filepath = os.path.join( - os.path.dirname(__file__), - "..", - "configs", - "config_template.py" + os.path.dirname(__file__), "..", "configs", "config_template.py" ) if not os.path.exists(template_filepath): raise RuntimeError("Unable to find template {}".format(template_filepath)) return open(template_filepath).read() -def make_output_location(coords_id, - collection_name, - latitude, - longitude, - country): +def make_output_location(coords_id, collection_name, latitude, longitude, country): # quite restricted on characters allowed in Azure container names - # use NSEW rather than negative numbers in coordinates if latitude.startswith("-"): - latitude = latitude[1:]+"S" + latitude = latitude[1:] + "S" else: - latitude = latitude+"N" + latitude = latitude + "N" if longitude.startswith("-"): - longitude = longitude[1:]+"W" + longitude = longitude[1:] + "W" else: - longitude = longitude+"E" + longitude = longitude + "E" if coords_id: - output_location = f"{coords_id}-{collection_name}-{latitude}-{longitude}-{country}" + output_location = ( + f"{coords_id}-{collection_name}-{latitude}-{longitude}-{country}" + ) else: output_location = f"{collection_name}-{latitude}-{longitude}-{country}" return output_location -def make_filename(configs_dir, - test_mode, - longitude, - latitude, - country, - pattern_type, - start_date, - end_date, - time_per_point, - region_size, - collection_name, - run_mode, - coords_id): +def make_filename( + configs_dir, + test_mode, + longitude, + latitude, + country, + pattern_type, + start_date, + end_date, + time_per_point, + region_size, + collection_name, + run_mode, + coords_id, +): """ Construct a filename from the specified parameters. """ filename_start = "testconfig" if test_mode else "config" if coords_id: - filename_start += "_"+coords_id + filename_start += "_" + coords_id filepath = os.path.join( configs_dir, - f"{filename_start}_{collection_name}_{latitude}N_{longitude}E_{country}_{region_size}_{pattern_type}_{start_date}_{end_date}_{time_per_point}_{run_mode}.py" - ) + f"{filename_start}_{collection_name}_{latitude}N_{longitude}E_{country}_{region_size}_{pattern_type}_{start_date}_{end_date}_{time_per_point}_{run_mode}.py", + ) return filepath -def write_file(configs_dir, - output_location, - longitude, - latitude, - country, - pattern_type, - start_date, - end_date, - time_per_point, - region_size, - collection_name, - run_mode, - n_threads, - test_mode=False, - coords_id=None - ): +def write_file( + configs_dir, + output_location, + longitude, + latitude, + country, + pattern_type, + start_date, + end_date, + time_per_point, + region_size, + collection_name, + run_mode, + n_threads, + test_mode=False, + coords_id=None, +): """ Take the arguments, construct a filename, and write contents """ - filename = make_filename(configs_dir, - test_mode, - longitude, - latitude, - country, - pattern_type, - start_date, - end_date, - time_per_point, - region_size, - collection_name, - run_mode, - coords_id) + filename = make_filename( + configs_dir, + test_mode, + longitude, + latitude, + country, + pattern_type, + start_date, + end_date, + time_per_point, + region_size, + collection_name, + run_mode, + coords_id, + ) if time_per_point.endswith("d") or time_per_point.endswith("w"): weather_collection_name = "ERA5_daily" @@ -142,7 +143,9 @@ def write_file(configs_dir, weather_start_date = start_date else: # also include historical weather data - weather_start_date = collections.data_collections[weather_collection_name]["min_date"] + weather_start_date = collections.data_collections[weather_collection_name][ + "min_date" + ] text = get_template_text() current_time = time.strftime("%y-%m-%d %H:%M:%S") @@ -151,7 +154,7 @@ def write_file(configs_dir, text = text.replace("COLLECTION_NAME", collection_name) text = text.replace("WEATHER_COLL_NAME", weather_collection_name) text = text.replace("OUTPUT_LOCATION_TYPE", output_location_type) - text = text.replace("OUTPUT_LOCATION",output_location) + text = text.replace("OUTPUT_LOCATION", output_location) text = text.replace("LATITUDE", latitude) text = text.replace("LONGITUDE", longitude) text = text.replace("PATTERN_TYPE", pattern_type) @@ -162,7 +165,7 @@ def write_file(configs_dir, text = text.replace("REGION_SIZE", region_size) text = text.replace("RUN_MODE", run_mode) text = text.replace("NUM_THREADS", str(n_threads)) - n_subimages = '10' if test_mode else '-1' + n_subimages = "10" if test_mode else "-1" text = text.replace("NUM_SUBIMAGES", n_subimages) if coords_id: text = text.replace("COORDS_ID_STRING", 'coords_id = "{}"'.format(coords_id)) @@ -170,20 +173,27 @@ def write_file(configs_dir, text = text.replace("COORDS_ID_STRING", "") with open(filename, "w") as configfile: configfile.write(text) - print("================================\nWrote file \n {}\nWe recommend that you add and commit this to your version control repository.\n================================".format(filename)) + print( + "================================\nWrote file \n {}\nWe recommend that you add and commit this to your version control repository.\n================================".format( + filename + ) + ) return filename def main(): # get lists of options for the user to choose from. - collection_names = [k for k in collections.data_collections.keys() \ - if collections.data_collections[k]["data_type"] == "vegetation"] - run_modes = ["local","batch"] + collection_names = [ + k + for k in collections.data_collections.keys() + if collections.data_collections[k]["data_type"] == "vegetation" + ] + run_modes = ["local", "batch"] date_regex = re.compile("[\d]{4}-[01][\d]-[0123][\d]") time_per_point_regex = re.compile("[\d]+[dwmy]") - lat_range = [-90.,90.] - long_range = [-180., 180.] - n_threads_range = range(1,17) + lat_range = [-90.0, 90.0] + long_range = [-180.0, 180.0] + n_threads_range = range(1, 17) default_n_threads = 4 # create argument parser in case user wants to use command line args @@ -198,48 +208,46 @@ def main(): parser.add_argument( "--configs_dir", help="path to directory containing config files" ) - parser.add_argument( - "--collection_name", help="collection name (e.g. 'Sentinel2')" - ) + parser.add_argument("--collection_name", help="collection name (e.g. 'Sentinel2')") parser.add_argument( "--output_dir", help="Directory for local output data", type=str ) parser.add_argument( - "--test_mode", help="Run in test mode, over fewer months and with fewer sub-images", action='store_true' - ) - parser.add_argument( - "--latitude", help="latitude in degrees N", type=float - ) - parser.add_argument( - "--longitude", help="longitude in degrees E", type=float - ) - parser.add_argument( - "--country", help="Country of location", type=str - ) - parser.add_argument( - "--start_date", help="start date, format YYYY-MM-DD", type=str - ) - parser.add_argument( - "--end_date", help="end date, format YYYY-MM-DD", type=str + "--test_mode", + help="Run in test mode, over fewer months and with fewer sub-images", + action="store_true", ) + parser.add_argument("--latitude", help="latitude in degrees N", type=float) + parser.add_argument("--longitude", help="longitude in degrees E", type=float) + parser.add_argument("--country", help="Country of location", type=str) + parser.add_argument("--start_date", help="start date, format YYYY-MM-DD", type=str) + parser.add_argument("--end_date", help="end date, format YYYY-MM-DD", type=str) parser.add_argument( "--time_per_point", help="frequency of image, e.g. '1m', '1w'", type=str ) parser.add_argument( - "--region_size", help="Size of region to download, in degrees lat/long", type=float + "--region_size", + help="Size of region to download, in degrees lat/long", + type=float, ) parser.add_argument( - "--pattern_type", help="Type of patterned vegetation, e.g. 'spots', 'labyrinths'", type=str + "--pattern_type", + help="Type of patterned vegetation, e.g. 'spots', 'labyrinths'", + type=str, ) parser.add_argument( - "--run_mode", help=""" + "--run_mode", + help=""" 'local' for running on local machine, 'azure' for running some time-consuming parts (i.e. vegetation image processing) on Azure batch - """, type=str + """, + type=str, ) parser.add_argument( - "--n_threads", help=""" + "--n_threads", + help=""" How many threads (cores) to parallelize some processing functions over - """, type=int + """, + type=int, ) args = parser.parse_args() @@ -256,26 +264,36 @@ def main(): # configs_dir configs_dir = args.configs_dir if args.configs_dir else "" while not os.path.exists(configs_dir): - if os.path.exists(os.path.join("pyveg","configs")): - default_configs_dir = os.path.join("pyveg","configs") + if os.path.exists(os.path.join("pyveg", "configs")): + default_configs_dir = os.path.join("pyveg", "configs") elif os.path.exists("configs"): default_configs_dir = "configs" else: default_configs_dir = "." - configs_dir = input("Enter path to directory containing config files, or press Return for default path ('{}') : ".format(default_configs_dir)) + configs_dir = input( + "Enter path to directory containing config files, or press Return for default path ('{}') : ".format( + default_configs_dir + ) + ) if len(configs_dir) == 0: configs_dir = default_configs_dir # test mode test_mode = args.test_mode if args.test_mode else False if not test_mode: - do_test = input("Would you like to make a test config file, with fewer months, and only a subset of sub-images? Press 'y' if so, or press Return for a normal config. : ") + do_test = input( + "Would you like to make a test config file, with fewer months, and only a subset of sub-images? Press 'y' if so, or press Return for a normal config. : " + ) test_mode = do_test.startswith("y") or do_test.startswith("Y") # collection name collection_name = args.collection_name if args.collection_name else None while not collection_name in collection_names: - collection_name = input("Please enter a valid collection name from this list: {} : ".format(collection_names)) + collection_name = input( + "Please enter a valid collection name from this list: {} : ".format( + collection_names + ) + ) # (optional) ID from coordinates.py coords_id = args.coords_id if args.coords_id else None @@ -292,28 +310,50 @@ def main(): country = row["country"] region_size = row["region_size"] pattern_type = row["type"] - except(KeyError): + except (KeyError): print("Unknown id {} - please enter coordinates manually".format(coords_id)) # latitude and longitude if not latitude: - latitude = args.latitude if args.latitude else -999. - - while not (isinstance(latitude, float) and latitude > lat_range[0] and latitude < lat_range[1]): - latitude = float(input("please enter Latitude (degrees N) in the range {} : ".format(lat_range))) + latitude = args.latitude if args.latitude else -999.0 + + while not ( + isinstance(latitude, float) + and latitude > lat_range[0] + and latitude < lat_range[1] + ): + latitude = float( + input( + "please enter Latitude (degrees N) in the range {} : ".format( + lat_range + ) + ) + ) if not longitude: - longitude = args.longitude if args.longitude else -999. - while not (isinstance(longitude, float) and longitude > long_range[0] and longitude < long_range[1]): - longitude = float(input("please enter Longitude (degrees E) in the range {} : ".format(long_range))) + longitude = args.longitude if args.longitude else -999.0 + while not ( + isinstance(longitude, float) + and longitude > long_range[0] + and longitude < long_range[1] + ): + longitude = float( + input( + "please enter Longitude (degrees E) in the range {} : ".format( + long_range + ) + ) + ) # country country = args.country if args.country else "" if not country: - country = input("Enter name of country, or press return to use OpenCage country lookup based on coordinates : ") + country = input( + "Enter name of country, or press return to use OpenCage country lookup based on coordinates : " + ) if len(country) == 0: country = lookup_country(latitude, longitude) # remove spaces - country = re.sub("[\s]+","",country) + country = re.sub("[\s]+", "", country) # start date start_date = args.start_date if args.start_date else "" @@ -322,7 +362,11 @@ def main(): else: default_start_date = collections.data_collections[collection_name]["min_date"] while not date_regex.search(start_date): - start_date = input("Enter start date in format YYYY-MM-DD, or press Return for default ({}) : ".format(default_start_date)) + start_date = input( + "Enter start date in format YYYY-MM-DD, or press Return for default ({}) : ".format( + default_start_date + ) + ) if len(start_date) == 0: start_date = default_start_date @@ -333,15 +377,25 @@ def main(): else: default_end_date = collections.data_collections[collection_name]["max_date"] while not date_regex.search(end_date): - end_date = input("Enter end date in format YYYY-MM-DD, or press Return for default ({}) : ".format(default_end_date)) + end_date = input( + "Enter end date in format YYYY-MM-DD, or press Return for default ({}) : ".format( + default_end_date + ) + ) if len(end_date) == 0: end_date = default_end_date # time per point time_per_point = args.time_per_point if args.time_per_point else "" - default_time_per_point = collections.data_collections[collection_name]["time_per_point"] + default_time_per_point = collections.data_collections[collection_name][ + "time_per_point" + ] while not time_per_point_regex.search(time_per_point): - time_per_point = input("Enter time per point in format e.g. '1m' for 1 month, '1w' for 1 week, or press Return for default ({}) : ".format(default_time_per_point)) + time_per_point = input( + "Enter time per point in format e.g. '1m' for 1 month, '1w' for 1 week, or press Return for default ({}) : ".format( + default_time_per_point + ) + ) if len(time_per_point) == 0: time_per_point = default_time_per_point @@ -349,8 +403,14 @@ def main(): if not region_size: region_size = args.region_size if args.region_size else -1.0 default_region_size = 0.08 - while not (isinstance(region_size, float) and region_size > 0. and region_size <= 0.08): - region_size = input("Enter region size in degrees latitude/longitude, or press Return for max/default ({}) : ".format(default_region_size)) + while not ( + isinstance(region_size, float) and region_size > 0.0 and region_size <= 0.08 + ): + region_size = input( + "Enter region size in degrees latitude/longitude, or press Return for max/default ({}) : ".format( + default_region_size + ) + ) if len(region_size) == 0: region_size = default_region_size else: @@ -363,43 +423,54 @@ def main(): pattern_type = args.pattern_type if args.pattern_type else "" default_pattern_type = "unknown" while len(pattern_type) < 1: - pattern_type = input("Enter type of patterned vegetation (e.g. 'spots', 'labyrinths', or press Return for default ('{}') : ".format(default_pattern_type)) + pattern_type = input( + "Enter type of patterned vegetation (e.g. 'spots', 'labyrinths', or press Return for default ('{}') : ".format( + default_pattern_type + ) + ) if len(pattern_type) == 0: pattern_type = default_pattern_type - pattern_type = pattern_type.replace(" ","-").lower() + pattern_type = pattern_type.replace(" ", "-").lower() # run mode run_mode = args.run_mode if args.run_mode else "" default_run_mode = "local" while not run_mode in run_modes: - run_mode = input("Would you like time-consuming functions to be run on the cloud? Choose from the following: {}, or press Return for default option '{}': ".format(run_modes, default_run_mode)) + run_mode = input( + "Would you like time-consuming functions to be run on the cloud? Choose from the following: {}, or press Return for default option '{}': ".format( + run_modes, default_run_mode + ) + ) if len(run_mode) == 0: run_mode = default_run_mode # output directory output_dir = args.output_dir if args.output_dir else "" if run_mode == "local" and not output_dir: - output_dir = input("Enter location for output, or press Return for default ('.') : ") + output_dir = input( + "Enter location for output, or press Return for default ('.') : " + ) if len(output_dir) == 0: - output_dir = "." + output_dir = "." lat_string = "{:.2f}".format(latitude) long_string = "{:.2f}".format(longitude) - output_location = make_output_location(coords_id, - collection_name, - lat_string, - long_string, - country) + output_location = make_output_location( + coords_id, collection_name, lat_string, long_string, country + ) if run_mode == "local": output_location = os.path.join(output_dir, output_location) - # num threads n_threads = args.n_threads if args.n_threads else 0 while not (isinstance(n_threads, int) and n_threads in n_threads_range): if run_mode == "local": - n_threads = input("How many threads would you like time-consuming processing functions to use? (Many computers will have 4 or 8 threads available). Press return for default value {} : ".format(default_n_threads)) + n_threads = input( + "How many threads would you like time-consuming processing functions to use? (Many computers will have 4 or 8 threads available). Press return for default value {} : ".format( + default_n_threads + ) + ) if len(n_threads) == 0: n_threads = default_n_threads else: @@ -410,7 +481,8 @@ def main(): else: n_threads = 1 - print(""" + print( + """ output_location {} collection: {} latitude: {} @@ -423,29 +495,49 @@ def main(): region_size: {} run_mode: {} n_threads: {} - """.format(output_location, collection_name, lat_string, long_string, country, pattern_type, start_date, end_date, time_per_point, region_size, run_mode, n_threads)) - - config_filename = write_file(configs_dir, - output_location, - long_string, - lat_string, - country, - pattern_type, - start_date, - end_date, - time_per_point, - region_size, - collection_name, - run_mode, - n_threads, - test_mode, - coords_id) - print(""" + """.format( + output_location, + collection_name, + lat_string, + long_string, + country, + pattern_type, + start_date, + end_date, + time_per_point, + region_size, + run_mode, + n_threads, + ) + ) + + config_filename = write_file( + configs_dir, + output_location, + long_string, + lat_string, + country, + pattern_type, + start_date, + end_date, + time_per_point, + region_size, + collection_name, + run_mode, + n_threads, + test_mode, + coords_id, + ) + print( + """ To run pyveg using this configuration, do: pyveg_run_pipeline --config_file {} -""".format(config_filename)) +""".format( + config_filename + ) + ) if __name__ == "__main__": diff --git a/pyveg/scripts/generate_pattern.py b/pyveg/scripts/generate_pattern.py index aa472a29..9b5eea3b 100644 --- a/pyveg/scripts/generate_pattern.py +++ b/pyveg/scripts/generate_pattern.py @@ -5,6 +5,7 @@ """ import argparse + from pyveg.src.pattern_generation import PatternGenerator diff --git a/pyveg/scripts/plot_feature_vectors.py b/pyveg/scripts/plot_feature_vectors.py index 2e17a6be..9d25dcdf 100644 --- a/pyveg/scripts/plot_feature_vectors.py +++ b/pyveg/scripts/plot_feature_vectors.py @@ -13,8 +13,7 @@ import matplotlib.pyplot as plt from generate_patterns import generate_pattern - -from subgraph_centrality import subgraph_centrality, generate_sc_images +from subgraph_centrality import generate_sc_images, subgraph_centrality LABELS = ["bo", "ro", "go", "b^", "r^", "g^"] diff --git a/pyveg/scripts/run_pyveg_module.py b/pyveg/scripts/run_pyveg_module.py index b6fc03de..467e66ac 100644 --- a/pyveg/scripts/run_pyveg_module.py +++ b/pyveg/scripts/run_pyveg_module.py @@ -1,15 +1,14 @@ """ Build and run a pyveg pipeline based on a configuration json file. """ - -import os -import sys -import time -import json import argparse +import datetime import inspect +import json +import os import re -import datetime +import sys +import time import ee @@ -21,15 +20,14 @@ except (ee.ee_exception.EEException): print("Earth Engine not initialized - will not be able to download from GEE") pass +from pyveg.src.combiner_modules import VegAndWeatherJsonCombiner from pyveg.src.processor_modules import ( - VegetationImageProcessor, - NetworkCentralityCalculator, NDVICalculator, + NetworkCentralityCalculator, + VegetationImageProcessor, WeatherImageToJSON, ) -from pyveg.src.combiner_modules import VegAndWeatherJsonCombiner - def build_module(config_file): """ diff --git a/pyveg/scripts/run_pyveg_pipeline.py b/pyveg/scripts/run_pyveg_pipeline.py index 9a2322b3..b8a51ed8 100644 --- a/pyveg/scripts/run_pyveg_pipeline.py +++ b/pyveg/scripts/run_pyveg_pipeline.py @@ -2,16 +2,16 @@ Build and run a pyveg pipeline based on a configuration json file. """ -import os -import sys -import time -import json import argparse +import datetime import importlib.util import inspect -from shutil import copyfile +import json +import os import re -import datetime +import sys +import time +from shutil import copyfile import ee @@ -23,15 +23,14 @@ except (ee.ee_exception.EEException): print("Earth Engine not initialized - will not be able to download from GEE") pass +from pyveg.src.combiner_modules import VegAndWeatherJsonCombiner from pyveg.src.processor_modules import ( - VegetationImageProcessor, - NetworkCentralityCalculator, NDVICalculator, + NetworkCentralityCalculator, + VegetationImageProcessor, WeatherImageToJSON, ) -from pyveg.src.combiner_modules import VegAndWeatherJsonCombiner - def build_pipeline(config_file, from_cache=False): """ diff --git a/pyveg/scripts/upload_to_zenodo.py b/pyveg/scripts/upload_to_zenodo.py index 80623c99..bf68c561 100644 --- a/pyveg/scripts/upload_to_zenodo.py +++ b/pyveg/scripts/upload_to_zenodo.py @@ -9,19 +9,19 @@ for testing. Use the '--test_api' argument to use this. """ -import os import argparse -import tempfile import json +import os +import tempfile -from pyveg.src.file_utils import get_tag, construct_filename_from_metadata from pyveg.src.analysis_preprocessing import read_results_summary +from pyveg.src.file_utils import construct_filename_from_metadata, get_tag from pyveg.src.zenodo_utils import ( + create_deposition, get_deposition_id, prepare_results_zipfile, upload_file, - create_deposition, - upload_standard_metadata + upload_standard_metadata, ) @@ -42,24 +42,30 @@ def create_new_deposition(use_sandbox=False): deposition_json = create_deposition(use_sandbox) deposition_id = deposition_json["id"] metadata_response = upload_standard_metadata(deposition_id, use_sandbox) - print("Created new deposition with deposition_id={}. We recommend that you now copy this deposition_id into the {} section of pyveg/zenodo_config.py".format(deposition_id, section_str)) + print( + "Created new deposition with deposition_id={}. We recommend that you now copy this deposition_id into the {} section of pyveg/zenodo_config.py".format( + deposition_id, section_str + ) + ) return deposition_id -def upload_results_summary(json_location, - json_location_type, - use_test_api): +def upload_results_summary(json_location, json_location_type, use_test_api): """ Upload the results summary json from running pyveg pipeline to download and process data from GEE. """ deposition_id = get_deposition_id("json", test=use_test_api) # read in the json - results_summary = read_results_summary(json_location, input_location_type=json_location_type) + results_summary = read_results_summary( + json_location, input_location_type=json_location_type + ) if (not results_summary) or (not "metadata" in results_summary.keys()): print("Unable to find metadata in json file in {}".format(json_location)) return False - filename = construct_filename_from_metadata(results_summary["metadata"],"results_summary.json") + filename = construct_filename_from_metadata( + results_summary["metadata"], "results_summary.json" + ) tmpdir = tempfile.mkdtemp() filepath = os.path.join(tmpdir, filename) with open(filepath, "w") as outfile: @@ -81,22 +87,41 @@ def upload_summary_stats(csv_filepath, use_test_api): def main(): parser = argparse.ArgumentParser(description="upload to zenodo") - parser.add_argument("--create_deposition", help="create a new deposition", action="store_true") - parser.add_argument("--input_location",help="directory or container with file of interest",required=True) - parser.add_argument("--input_location_type",help="'local' or 'azure'", default="local") + parser.add_argument( + "--create_deposition", help="create a new deposition", action="store_true" + ) + parser.add_argument( + "--input_location", + help="directory or container with file of interest", + required=True, + ) + parser.add_argument( + "--input_location_type", help="'local' or 'azure'", default="local" + ) parser.add_argument("--test_api", help="use the test API", action="store_true") - parser.add_argument("--summary_csv", help="upload the summary stats csv rather than the results_summary.json", action="store_true") + parser.add_argument( + "--summary_csv", + help="upload the summary stats csv rather than the results_summary.json", + action="store_true", + ) args = parser.parse_args() if args.create_deposition: repo_string = "sandbox" if args.test_api else "production" - confirm = input(""" + confirm = input( + """ Are you sure you want to create a new deposition on the {} repository? We normally do this just once per project. Please confirm (y/n) -""".format(repo_string)) +""".format( + repo_string + ) + ) if confirm in ["y", "Y", "yes", "Yes"]: deposition_id = create_new_deposition(args.test_api) - print("Created new deposition in {} repository with deposition_id={}."\ - .format(repo_string, deposition_id)) + print( + "Created new deposition in {} repository with deposition_id={}.".format( + repo_string, deposition_id + ) + ) return else: print("Confirmation not received - exiting with no action") @@ -106,13 +131,14 @@ def main(): if args.summary_csv: result = upload_summary_stats(args.input_location, test_api) else: - result = upload_results_summary(args.input_location, - args.input_location_type, - test_api) + result = upload_results_summary( + args.input_location, args.input_location_type, test_api + ) if result: print("Uploaded OK") else: print("Problem uploading") + if __name__ == "__main__": main() diff --git a/pyveg/src/analysis_preprocessing.py b/pyveg/src/analysis_preprocessing.py index 052cc5a5..90600416 100644 --- a/pyveg/src/analysis_preprocessing.py +++ b/pyveg/src/analysis_preprocessing.py @@ -9,16 +9,13 @@ import math import os +import ewstools import numpy as np import pandas as pd -import ewstools - from statsmodels.nonparametric.smoothers_lowess import lowess -from pyveg.src.data_analysis_utils import write_to_json, cball_parfit, cball - +from pyveg.src.data_analysis_utils import cball, cball_parfit, write_to_json from pyveg.src.date_utils import get_time_diff - from pyveg.src.file_utils import construct_filename_from_metadata try: @@ -32,9 +29,9 @@ print("Unable to import azure_utils") -def read_results_summary(input_location, - input_filename="results_summary.json", - input_location_type="local"): +def read_results_summary( + input_location, input_filename="results_summary.json", input_location_type="local" +): """ Read the results_summary.json, either from local storage, Azure blob storage, or zenodo. @@ -58,7 +55,9 @@ def read_results_summary(input_location, return json_data elif input_location_type == "zenodo" or input_location_type == "zenodo_test": use_sandbox = input_location_type == "zenodo_test" - json_location = download_results_by_coord_id(input_location, "json", test=use_sandbox) + json_location = download_results_by_coord_id( + input_location, "json", test=use_sandbox + ) if os.path.exists(json_location): json_data = json.load(open(json_location)) return json_data @@ -71,17 +70,23 @@ def read_results_summary(input_location, for subdir in subdirs: print("looking at subdir {}".format(subdir)) if "combine" in subdir: - files = azure_utils.list_directory(input_location+"/"+subdir, - input_location) + files = azure_utils.list_directory( + input_location + "/" + subdir, input_location + ) if input_filename in files: - return azure_utils.read_json(input_location+"/"+subdir+"/"+input_filename, - input_location) + return azure_utils.read_json( + input_location + "/" + subdir + "/" + input_filename, + input_location, + ) else: - raise RuntimeError("No {} found in {}".format(input_filename, subdir)) + raise RuntimeError( + "No {} found in {}".format(input_filename, subdir) + ) return {} else: - raise RuntimeError("input_location_type needs to be either 'local','azure', 'zenodo' or 'zenodo_test'") - + raise RuntimeError( + "input_location_type needs to be either 'local','azure', 'zenodo' or 'zenodo_test'" + ) def read_json_to_dataframes(data): @@ -122,10 +127,14 @@ def read_json_to_dataframes(data): for space_point in time_point: # Scale NDVI values - in the image they will be between 0 and 255 to give a greyscale # (8-bit) image, but the actual NDVI values are between -1 and 1 - if 'ndvi' in space_point.keys(): - space_point['ndvi'] = space_point['ndvi'] * (2.0/255.0) - 1 - if 'ndvi_veg' in space_point.keys(): - space_point['ndvi_veg'] = space_point['ndvi_veg'] * (2.0/255.0) - 1 + if "ndvi" in space_point.keys(): + space_point["ndvi"] = ( + space_point["ndvi"] * (2.0 / 255.0) - 1 + ) + if "ndvi_veg" in space_point.keys(): + space_point["ndvi_veg"] = ( + space_point["ndvi_veg"] * (2.0 / 255.0) - 1 + ) rows_list.append(space_point) # otherwise, just add the row @@ -216,16 +225,20 @@ def make_time_series(dfs): # if there is a big (>10yr) gap between the start of veg and weather time-series, # we want to make a separate historic time-series. - veg_col_name = [col for col in ts_df.columns if col.startswith(veg_satellite_prefix)][0] + veg_col_name = [ + col for col in ts_df.columns if col.startswith(veg_satellite_prefix) + ][0] earliest_date = ts_df.iloc[0]["date"] earliest_veg_date = ts_df[ts_df[veg_col_name].notna()].iloc[0]["date"] - if get_time_diff(earliest_veg_date,earliest_date) > 10: - ts_df_historic = ts_df[ts_df["date"] < earliest_veg_date][["date","mean_2m_air_temperature","total_precipitation"]] + if get_time_diff(earliest_veg_date, earliest_date) > 10: + ts_df_historic = ts_df[ts_df["date"] < earliest_veg_date][ + ["date", "mean_2m_air_temperature", "total_precipitation"] + ] ts_df = ts_df[ts_df["date"] >= earliest_veg_date] ts_list.append(ts_df) ts_list.append(ts_df_historic) - else : + else: ts_list.append(ts_df) return ts_list @@ -838,15 +851,15 @@ def detrend_data(dfs, period="MS"): def preprocess_data( - input_json, - output_basedir, - drop_outliers=True, - fill_missing=True, - resample=True, - smoothing=True, - detrend=True, - n_smooth=4, - period="MS", + input_json, + output_basedir, + drop_outliers=True, + fill_missing=True, + resample=True, + smoothing=True, + detrend=True, + n_smooth=4, + period="MS", ): """ This function reads and process data downloaded by GEE. Processing @@ -885,7 +898,6 @@ def preprocess_data( # put output plots in the results dir output_dir = os.path.join(output_basedir, "processed_data") - # make output subdir if not os.path.exists(output_dir): os.makedirs(output_dir, exist_ok=True) @@ -924,9 +936,9 @@ def preprocess_data( # average over sub-images ts_list = make_time_series(dfs) ts_df = ts_list[0] - if len(ts_list) > 1 : + if len(ts_list) > 1: ts_historic = ts_list[1] - else : + else: ts_historic = pd.DataFrame() # resample the averaged time series using linear interpolation @@ -943,14 +955,14 @@ def preprocess_data( ts_filename = os.path.join(output_dir, "time_series.csv") print(f'- Saving time series to "{ts_filename}".') ts_df.to_csv(ts_filename, index=False) - if not ts_historic.empty : + if not ts_historic.empty: ts_filename = os.path.join(output_dir, "time_series_historic.csv") print(f'- Saving time series to "{ts_filename}".') ts_historic.to_csv(ts_filename, index=False) # additionally save resampled & detrended time series # this detrending option (one year seasonality substraction) only works in monthly data that has at least 2 years of data - if detrend and ts_df.shape[0]>24 and period=='MS': + if detrend and ts_df.shape[0] > 24 and period == "MS": print("- Detrending time series...") # remove seasonality from sub-image time series @@ -971,145 +983,166 @@ def preprocess_data( def save_ts_summary_stats(ts_dirname, output_dir, metadata): - """ - Given a time series DataFrames (constructed with `make_time_series`), - give summary statistics of all the avalaible time series. + """ + Given a time series DataFrames (constructed with `make_time_series`), + give summary statistics of all the avalaible time series. - Parameters - ---------- - ts_dirname : str - Directory where the time series are saved. + Parameters + ---------- + ts_dirname : str + Directory where the time series are saved. + + output_dir : str + Directory to save the plots in. - output_dir : str - Directory to save the plots in. + metadata: dict + Dictionary with metadata from location - metadata: dict - Dictionary with metadata from location + """ - """ + # read processed data - # read processed data + # get filenames of preprocessed data time series + ts_filenames = [f for f in os.listdir(ts_dirname) if "time_series" in f] - # get filenames of preprocessed data time series - ts_filenames = [f for f in os.listdir(ts_dirname) if "time_series" in f] + # we should get one seasonal time series and a detrended one + ts_df_detrended = pd.DataFrame() + ts_df_historic = pd.DataFrame() + for filename in ts_filenames: + if "detrended" in filename: + ts_df_detrended = pd.read_csv(os.path.join(ts_dirname, filename)) + elif "historic" in filename: + ts_df_historic = pd.read_csv(os.path.join(ts_dirname, filename)) + else: + ts_df = pd.read_csv(os.path.join(ts_dirname, filename)) + + def get_ts_summary_stats(series): + """Function that gets the summary stats of the time series and returns a dictionary""" + stats_dict = {} + + stats_dict["min"] = series.min() + stats_dict["max"] = series.max() + stats_dict["mean"] = series.mean() + stats_dict["median"] = series.median() + stats_dict["std"] = series.std() + + return stats_dict + + # calculate summary statistics for each relevant time series + ts_dict_list = [] + # only look at relevant time series (offset50, ndvi and precipitation) + if not ts_df_historic.empty: + column_dict = get_ts_summary_stats(ts_df_historic["total_precipitation"]) + column_dict["ts_id"] = "total_precipitation_historic" + for key in metadata: + column_dict[key] = metadata[key] + ts_dict_list.append(column_dict) + + column_names = [ + c + for c in ts_df.columns + if "offset50_mean" in c or "ndvi_mean" in c or "total_precipitation" in c + ] - # we should get one seasonal time series and a detrended one - ts_df_detrended = pd.DataFrame() - ts_df_historic = pd.DataFrame() - for filename in ts_filenames: - if "detrended" in filename: - ts_df_detrended = pd.read_csv(os.path.join(ts_dirname,filename)) - elif "historic" in filename: - ts_df_historic = pd.read_csv(os.path.join(ts_dirname,filename)) - else: - ts_df = pd.read_csv(os.path.join(ts_dirname,filename)) - - - def get_ts_summary_stats(series): - ''' Function that gets the summary stats of the time series and returns a dictionary''' - stats_dict = {} - - stats_dict['min'] = series.min() - stats_dict['max'] = series.max() - stats_dict['mean'] = series.mean() - stats_dict['median'] = series.median() - stats_dict['std'] = series.std() - - return stats_dict - - # calculate summary statistics for each relevant time series - ts_dict_list = [] - # only look at relevant time series (offset50, ndvi and precipitation) - if not ts_df_historic.empty : - column_dict = get_ts_summary_stats(ts_df_historic["total_precipitation"]) - column_dict["ts_id"] = "total_precipitation_historic" - for key in metadata: - column_dict[key] = metadata[key] - ts_dict_list.append(column_dict) - - - column_names = [c for c in ts_df.columns if 'offset50_mean' in c or - 'ndvi_mean' in c or - 'total_precipitation' in c] - - - for column in column_names: - - print(f'Calculating summary stats for "{column}"...') - - column_dict = get_ts_summary_stats(ts_df[column]) - column_dict['ts_id'] = column - - # make sure is a dated time series for resampling later in the CB calculation - ts_df[column].index = pd.DatetimeIndex(ts_df['date']) - cb_params, sucess, residuals = cball_parfit([1.5, 150.0, 8.0, 2.0],ts_df[column],column, output_dir) - column_dict['CB_fit_success'] = sucess - column_dict['CB_fit_residuals'] = residuals - column_dict['CB_fit_alpha'] = cb_params[0] - column_dict['CB_fit_N'] = cb_params[1] - column_dict['CB_fit_xbar'] = cb_params[2] - column_dict['CB_fit_sigma'] = cb_params[3] - - for key in metadata: - column_dict[key] = metadata[key] - - # We want the AR1 and Standard deviation of the detreded timeseries for the summary stats - if ts_df_detrended.empty==False: - ews_dic_veg = ewstools.core.ews_compute(ts_df_detrended[column].dropna(), - roll_window=0.999 , - smooth='Gaussian', - lag_times=[1], - ews= ["var", "ac"], - band_width=6) - - EWSmetrics_df = ews_dic_veg['EWS metrics'] - column_dict["Lag-1 AC (0.99 rolling window)"] = EWSmetrics_df["Lag-1 AC"].iloc[-1] - column_dict["Variance (0.99 rolling window)"] = EWSmetrics_df["Variance"].iloc[-1] - - ews_dic_veg_50 = ewstools.core.ews_compute(ts_df_detrended[column].dropna(), - roll_window=0.5, - smooth='Gaussian', - lag_times=[1], - ews=["var", "ac"], - band_width=6) - - Kendall_tau_50 = ews_dic_veg_50['Kendall tau'] - column_dict["Kendall tau Lag-1 AC (0.5 rolling window)"] = Kendall_tau_50["Lag-1 AC"].iloc[-1] - column_dict["Kendall tau Variance (0.5 rolling window)"] = Kendall_tau_50["Variance"].iloc[-1] - - # We also want the AR1 and Standard deviation of the raw seasonal timeseries for the summary stats - if ts_df.empty == False: - - # make sure in this case that the index is numeric and not datetime - - ts = ts_df[column].dropna() - ts.index = pd.to_numeric(ts.index) - ews_dic_veg_seasonal = ewstools.core.ews_compute(ts, - roll_window=0.999, - smooth='None', - lag_times=[1], - ews=["var", "ac"]) - - EWSmetrics_df_seasonal = ews_dic_veg_seasonal['EWS metrics'] - column_dict["Lag-1 AC (0.99 rolling window) Seasonal"] = EWSmetrics_df_seasonal["Lag-1 AC"].iloc[-1] - column_dict["Variance (0.99 rolling window) Seasonal"] = EWSmetrics_df_seasonal["Variance"].iloc[-1] - - ews_dic_veg_50_seasonal = ewstools.core.ews_compute(ts, - roll_window=0.5, - smooth='None', - lag_times=[1], - ews=["var", "ac"]) - - Kendall_tau_50_seasonal = ews_dic_veg_50_seasonal['Kendall tau'] - column_dict["Kendall tau Lag-1 AC (0.5 rolling window) Seasonal"] = Kendall_tau_50_seasonal["Lag-1 AC"].iloc[-1] - column_dict["Kendall tau Variance (0.5 rolling window) Seasonal"] = Kendall_tau_50_seasonal["Variance"].iloc[-1] - - ts_dict_list.append(column_dict) - - ss_name = construct_filename_from_metadata(metadata, "summary_stats.csv") - # turn the list of dictionary to dataframe and save it - ts_df_summary = pd.DataFrame(ts_dict_list) - - #save both name specific and generic (might be useful inside the analysis later) - ts_df_summary.to_csv(os.path.join(output_dir, "time_series_summary_stats.csv")) - ts_df_summary.to_csv(os.path.join(output_dir, ss_name)) + for column in column_names: + + print(f'Calculating summary stats for "{column}"...') + + column_dict = get_ts_summary_stats(ts_df[column]) + column_dict["ts_id"] = column + + # make sure is a dated time series for resampling later in the CB calculation + ts_df[column].index = pd.DatetimeIndex(ts_df["date"]) + cb_params, sucess, residuals = cball_parfit( + [1.5, 150.0, 8.0, 2.0], ts_df[column], column, output_dir + ) + column_dict["CB_fit_success"] = sucess + column_dict["CB_fit_residuals"] = residuals + column_dict["CB_fit_alpha"] = cb_params[0] + column_dict["CB_fit_N"] = cb_params[1] + column_dict["CB_fit_xbar"] = cb_params[2] + column_dict["CB_fit_sigma"] = cb_params[3] + + for key in metadata: + column_dict[key] = metadata[key] + + # We want the AR1 and Standard deviation of the detreded timeseries for the summary stats + if ts_df_detrended.empty == False: + ews_dic_veg = ewstools.core.ews_compute( + ts_df_detrended[column].dropna(), + roll_window=0.999, + smooth="Gaussian", + lag_times=[1], + ews=["var", "ac"], + band_width=6, + ) + + EWSmetrics_df = ews_dic_veg["EWS metrics"] + column_dict["Lag-1 AC (0.99 rolling window)"] = EWSmetrics_df[ + "Lag-1 AC" + ].iloc[-1] + column_dict["Variance (0.99 rolling window)"] = EWSmetrics_df[ + "Variance" + ].iloc[-1] + + ews_dic_veg_50 = ewstools.core.ews_compute( + ts_df_detrended[column].dropna(), + roll_window=0.5, + smooth="Gaussian", + lag_times=[1], + ews=["var", "ac"], + band_width=6, + ) + + Kendall_tau_50 = ews_dic_veg_50["Kendall tau"] + column_dict["Kendall tau Lag-1 AC (0.5 rolling window)"] = Kendall_tau_50[ + "Lag-1 AC" + ].iloc[-1] + column_dict["Kendall tau Variance (0.5 rolling window)"] = Kendall_tau_50[ + "Variance" + ].iloc[-1] + + # We also want the AR1 and Standard deviation of the raw seasonal timeseries for the summary stats + if ts_df.empty == False: + + # make sure in this case that the index is numeric and not datetime + + ts = ts_df[column].dropna() + ts.index = pd.to_numeric(ts.index) + ews_dic_veg_seasonal = ewstools.core.ews_compute( + ts, + roll_window=0.999, + smooth="None", + lag_times=[1], + ews=["var", "ac"], + ) + + EWSmetrics_df_seasonal = ews_dic_veg_seasonal["EWS metrics"] + column_dict[ + "Lag-1 AC (0.99 rolling window) Seasonal" + ] = EWSmetrics_df_seasonal["Lag-1 AC"].iloc[-1] + column_dict[ + "Variance (0.99 rolling window) Seasonal" + ] = EWSmetrics_df_seasonal["Variance"].iloc[-1] + + ews_dic_veg_50_seasonal = ewstools.core.ews_compute( + ts, roll_window=0.5, smooth="None", lag_times=[1], ews=["var", "ac"] + ) + + Kendall_tau_50_seasonal = ews_dic_veg_50_seasonal["Kendall tau"] + column_dict[ + "Kendall tau Lag-1 AC (0.5 rolling window) Seasonal" + ] = Kendall_tau_50_seasonal["Lag-1 AC"].iloc[-1] + column_dict[ + "Kendall tau Variance (0.5 rolling window) Seasonal" + ] = Kendall_tau_50_seasonal["Variance"].iloc[-1] + + ts_dict_list.append(column_dict) + + ss_name = construct_filename_from_metadata(metadata, "summary_stats.csv") + # turn the list of dictionary to dataframe and save it + ts_df_summary = pd.DataFrame(ts_dict_list) + + # save both name specific and generic (might be useful inside the analysis later) + ts_df_summary.to_csv(os.path.join(output_dir, "time_series_summary_stats.csv")) + ts_df_summary.to_csv(os.path.join(output_dir, ss_name)) diff --git a/pyveg/src/azure_utils.py b/pyveg/src/azure_utils.py index b627391e..5a4ba2be 100644 --- a/pyveg/src/azure_utils.py +++ b/pyveg/src/azure_utils.py @@ -1,30 +1,26 @@ -import os import io import json - -import arrow +import os import re import tempfile + +import arrow +from azure.common import AzureMissingResourceHttpError +from azure.storage.blob import BlockBlobService, ContainerPermissions, PublicAccess from PIL import Image from pyveg.src.file_utils import split_filepath -AZURE_CONFIG_FOUND=False +AZURE_CONFIG_FOUND = False # load the azure configuration if we have the azure_config.py file try: from pyveg.azure_config import config - AZURE_CONFIG_FOUND=True + + AZURE_CONFIG_FOUND = True except: pass -from azure.storage.blob import ( - BlockBlobService, - PublicAccess, - ContainerPermissions -) -from azure.common import AzureMissingResourceHttpError - def sanitize_container_name(orig_name): """ @@ -43,7 +39,7 @@ def sanitize_container_name(orig_name): sanitized_name += character.lower() previous_character = character if "\\" in sanitized_name: - sanitized_name = sanitized_name.replace("\\","/") + sanitized_name = sanitized_name.replace("\\", "/") return sanitized_name diff --git a/pyveg/src/batch_utils.py b/pyveg/src/batch_utils.py index b3f9ba58..2ea698ac 100644 --- a/pyveg/src/batch_utils.py +++ b/pyveg/src/batch_utils.py @@ -2,20 +2,19 @@ Functions for submitting batch jobs. Currently only support Azure Batch. Largely taken from https://github.com/Azure-Samples/batch-python-quickstart """ +import datetime +import json import os import sys -import json import tempfile -import datetime import time -import azure.storage.blob as azureblob -import azure.batch.batch_service_client as batch import azure.batch.batch_auth as batch_auth +import azure.batch.batch_service_client as batch import azure.batch.models as batchmodels +import azure.storage.blob as azureblob from azure.storage.blob import BlockBlobService - try: from pyveg.azure_config import config except: @@ -262,14 +261,16 @@ def check_task_failed_dependencies(task, job_id, batch_service_client=None): return False for dependency in dependencies: dep_task = batch_service_client.task.get(job_id, dependency) - if dep_task.state == batchmodels.TaskState.completed and \ - dep_task.execution_info.exit_code != 0: + if ( + dep_task.state == batchmodels.TaskState.completed + and dep_task.execution_info.exit_code != 0 + ): # return True if any of the dependencies failed return True # use this a recursive function - dep_dep_failed = check_task_failed_dependencies(dep_task, - job_id, - batch_service_client) + dep_dep_failed = check_task_failed_dependencies( + dep_task, job_id, batch_service_client + ) if dep_dep_failed: return True @@ -298,8 +299,12 @@ def check_tasks_status(job_id, task_name_prefix="", batch_service_client=None): tasks = [task for task in tasks if task.id.startswith(task_name_prefix)] running_tasks = [ - task for task in tasks if (task.state == batchmodels.TaskState.running \ - or task.state == batchmodels.TaskState.preparing) + task + for task in tasks + if ( + task.state == batchmodels.TaskState.running + or task.state == batchmodels.TaskState.preparing + ) ] num_running = len(running_tasks) @@ -326,7 +331,7 @@ def check_tasks_status(job_id, task_name_prefix="", batch_service_client=None): "num_failed": len(task_success) - num_success, "num_running": num_running, "num_waiting": num_waiting, - "num_cannot_run": num_cannot_run + "num_cannot_run": num_cannot_run, } diff --git a/pyveg/src/combiner_modules.py b/pyveg/src/combiner_modules.py index e7710191..766f229e 100644 --- a/pyveg/src/combiner_modules.py +++ b/pyveg/src/combiner_modules.py @@ -2,11 +2,11 @@ Modules that can consolidate inputs from different sources and produce combined output file (typically JSON). """ -import os import json +import os -from pyveg.src.file_utils import save_json, get_tag from pyveg.src.date_utils import get_date_strings_for_time_period +from pyveg.src.file_utils import get_tag, save_json from pyveg.src.pyveg_pipeline import BaseModule, logger @@ -35,7 +35,6 @@ def __init__(self, name=None): ("output_filename", [str]), ] - def set_default_parameters(self): """ See if we can set our input directories from the output directories @@ -94,7 +93,7 @@ def combine_json_lists(self, json_lists): return None elif len(json_lists) == 1: return json_lists[0] - ## any way to do this without a huge nested loop? + # any way to do this without a huge nested loop? # loop over all the lists apart from the first, which we will add to for jlist in json_lists[1:]: @@ -169,7 +168,9 @@ def get_veg_time_series(self): ) # list the JSON subdirectories and find any .json files in them dir_contents = self.list_directory( - self.join_path(self.input_veg_location, date_string, "JSON", subdir), + self.join_path( + self.input_veg_location, date_string, "JSON", subdir + ), self.input_veg_location_type, ) json_files = [ @@ -224,9 +225,11 @@ def check_output_dict(self, output_dict): weather_dates = output_dict[self.weather_collection]["time-series-data"].keys() for date in veg_dates: - if output_dict[self.veg_collection]["time-series-data"][date] \ - and date in weather_dates \ - and output_dict[self.weather_collection]["time-series-data"][date]: + if ( + output_dict[self.veg_collection]["time-series-data"][date] + and date in weather_dates + and output_dict[self.weather_collection]["time-series-data"][date] + ): self.run_status["succeeded"] += 1 return @@ -279,9 +282,9 @@ def run(self): self.output_location_type, ) - logger.info("{}: Wrote output to {}".format( - self.name, - self.join_path(self.output_location, self.output_filename) - ) + logger.info( + "{}: Wrote output to {}".format( + self.name, self.join_path(self.output_location, self.output_filename) + ) ) self.is_finished = True diff --git a/pyveg/src/coordinate_utils.py b/pyveg/src/coordinate_utils.py index 96562c1a..72d612a6 100644 --- a/pyveg/src/coordinate_utils.py +++ b/pyveg/src/coordinate_utils.py @@ -4,6 +4,7 @@ """ import re + import requests @@ -46,7 +47,7 @@ def coords_dict_to_coords_string(coords): rounding to 2 decimal places. """ longitude, latitude = None, None - for k,v in coords.items(): + for k, v in coords.items(): if "at" in k: latitude = v if "ong" in k: @@ -107,13 +108,15 @@ def get_sub_image_coords(coords, region_size, x_parts, y_parts): return sub_image_coords - - def lookup_country(latitude, longitude): """ Use the OpenCage API to do reverse geocoding """ - r = requests.get("https://api.opencagedata.com/geocode/v1/json?q={}+{}&key=1a43cea9caa6420a8faf6e3b4bf13abb".format(latitude, longitude)) + r = requests.get( + "https://api.opencagedata.com/geocode/v1/json?q={}+{}&key=1a43cea9caa6420a8faf6e3b4bf13abb".format( + latitude, longitude + ) + ) if r.status_code != 200: print("Error accessing OpenCage API: {}".format(r.content)) return "Unknown" diff --git a/pyveg/src/data_analysis_utils.py b/pyveg/src/data_analysis_utils.py index 3d529208..75e034f4 100644 --- a/pyveg/src/data_analysis_utils.py +++ b/pyveg/src/data_analysis_utils.py @@ -3,27 +3,24 @@ and functions analyse and plot the data. """ +import datetime import json import math import os -import datetime - -import numpy as np -import pandas as pd -from shapely.geometry import Point +import ewstools import geopandas as gpd - -import matplotlib.pyplot as plt import matplotlib.cm as cm - +import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +import scipy +import scipy.optimize as sco from scipy.fftpack import fft -from scipy.stats import sem, t, norm +from scipy.stats import norm, sem, t +from shapely.geometry import Point from statsmodels.tsa.seasonal import STL -import ewstools -import scipy -import scipy.optimize as sco def convert_to_geopandas(df): """ @@ -192,8 +189,8 @@ def coarse_dataframe(geodf, side_square): for j in range(side_square): if ( - n + n_grids * i + j < n_grids * n_grids - and data_df["category"].iloc[n + n_grids * i + j] == -1 + n + n_grids * i + j < n_grids * n_grids + and data_df["category"].iloc[n + n_grids * i + j] == -1 ): indexes.append(n + n_grids * i + j) @@ -316,7 +313,7 @@ def fft_series(time_series): fourier = fft(ts) # x-axis values xvals = np.linspace(0.0, 1.0 / (20 * T), N // 20) - yvals = 2.0 / N * np.abs(fourier[0: N // 20]) + yvals = 2.0 / N * np.abs(fourier[0 : N // 20]) return xvals, yvals @@ -372,7 +369,6 @@ def get_AR1_parameter_estimate(ys): # more sophisticated models to consider: # from statsmodels.tsa.statespace.sarimax import SARIMAX # from statsmodels.tsa.arima_model import ARMA - # create and fit the AR(1) model if pd.infer_freq(ys.index) is not None: # explicitly add frequency to index to prevent warnings @@ -380,7 +376,8 @@ def get_AR1_parameter_estimate(ys): model = AutoReg(ys, lags=1, missing="drop").fit() # currently warning else: # remove index - model = AutoReg(ys.values, lags=1, missing="drop").fit() # currently warning + # currently warning + model = AutoReg(ys.values, lags=1, missing="drop").fit() # get the single parameter value parameter = model.params[1] @@ -509,13 +506,13 @@ def get_max_lagged_cor(dirname, veg_prefix): if veg_prefix + "_offset50_mean_lagged_correlation" in lagged_cor.keys(): max_corr_unsmoothed = lagged_cor[ veg_prefix + "_offset50_mean_lagged_correlation" - ] + ] else: max_corr_unsmoothed = (np.NaN, np.NaN) if veg_prefix + "_offset50_smooth_mean_lagged_correlation" in lagged_cor.keys(): max_corr_smooth = lagged_cor[ veg_prefix + "_offset50_smooth_mean_lagged_correlation" - ] + ] else: max_corr_smooth = (np.NaN, np.NaN) @@ -573,7 +570,7 @@ def ar1_moving_average_time_series(series, length=1): for i in range(len(series) - length): # print(series[i:(length + i)]) - param, se = get_AR1_parameter_estimate(series[i: (length + i)]) + param, se = get_AR1_parameter_estimate(series[i : (length + i)]) ar1.append(param) ar1_se.append(se) index.append(series.index[length + i]) @@ -683,9 +680,9 @@ def get_correlation_lag_ts(series_A, series_B, window_size=0.5): # for each step along the moving window for i in range(len(series_A) - length): # get the slices of the timeseries - frame_A = series_A[i: (length + i)] - frame_A_lagged = series_A_lagged[i: (length + i)] - frame_B = series_B[i: (length + i)] + frame_A = series_A[i : (length + i)] + frame_A_lagged = series_A_lagged[i : (length + i)] + frame_B = series_B[i : (length + i)] # compute the lagged correlation using the lag # which maximises the global correlation @@ -702,7 +699,7 @@ def get_correlation_lag_ts(series_A, series_B, window_size=0.5): s = "ndvi" if "ndvi" in series_A else "offest50" correlations_mva_series_name = ( - series_A.name.split("_")[0] + "_" + s + "_precip_corr" + series_A.name.split("_")[0] + "_" + s + "_precip_corr" ) mag_max_cors_mw_series_name = series_A.name.split("_")[0] + "_" + s + "_precip_lag" @@ -740,9 +737,9 @@ def moving_window_analysis(df, output_dir, window_size=0.5): # run moving window analysis veg and precip columns if ( - ("offset50" in column or "ndvi" in column) - and "mean" in column - or "total_precipitation" in column + ("offset50" in column or "ndvi" in column) + and "mean" in column + or "total_precipitation" in column ): # reindex time series using data time_series = df.set_index("date")[column] @@ -755,9 +752,9 @@ def moving_window_analysis(df, output_dir, window_size=0.5): if "total_precipitation" in column: for column_veg in df.columns: if ( - ("offset50" in column_veg or "ndvi" in column_veg) - and "mean" in column_veg - and "smooth" not in column_veg + ("offset50" in column_veg or "ndvi" in column_veg) + and "mean" in column_veg + and "smooth" not in column_veg ): mwa_df = mwa_df.merge( get_correlation_lag_ts( @@ -799,15 +796,15 @@ def get_datetime_xs(df): def early_warnings_sensitivity_analysis( - series, - indicators=["var", "ac"], - winsizerange=[0.10, 0.8], - incrwinsize=0.10, - smooth="Gaussian", - bandwidthrange=[0.05, 1.0], - spanrange=[0.05, 1.1], - incrbandwidth=0.2, - incrspanrange=0.1, + series, + indicators=["var", "ac"], + winsizerange=[0.10, 0.8], + incrwinsize=0.10, + smooth="Gaussian", + bandwidthrange=[0.05, 1.0], + spanrange=[0.05, 1.1], + incrbandwidth=0.2, + incrspanrange=0.1, ): """ Function to estimate the sensitivity of the early warnings analysis to @@ -852,7 +849,7 @@ def early_warnings_sensitivity_analysis( if smooth == "Gaussian": for bw in np.arange( - bandwidthrange[0], bandwidthrange[1] + 0.01, incrbandwidth + bandwidthrange[0], bandwidthrange[1] + 0.01, incrbandwidth ): bw = round(bw, 3) ews_dic_veg = ewstools.core.ews_compute( @@ -911,14 +908,14 @@ def early_warnings_sensitivity_analysis( def early_warnings_null_hypothesis( - series, - indicators=["var", "ac"], - roll_window=0.4, - smooth="Lowess", - span=0.1, - band_width=0.2, - lag_times=[1], - n_simulations=1000, + series, + indicators=["var", "ac"], + roll_window=0.4, + smooth="Lowess", + span=0.1, + band_width=0.2, + lag_times=[1], + n_simulations=1000, ): """ Function to estimate the significance of the early warnings analysis @@ -1055,15 +1052,15 @@ def compute_indicators(series): # List of EWS that can be used for Kendall tau computation ktau_metrics = [ - "Variance", - "Standard deviation", - "Skewness", - "Kurtosis", - "Coefficient of variation", - "Smax", - "Smax/Var", - "Smax/Mean", - ] + ["Lag-" + str(i) + " AC" for i in lag_times] + "Variance", + "Standard deviation", + "Skewness", + "Kurtosis", + "Coefficient of variation", + "Smax", + "Smax/Var", + "Smax/Mean", + ] + ["Lag-" + str(i) + " AC" for i in lag_times] # Find intersection with this list and EWS computed ews_list = df_ews.columns.values.tolist() ktau_metrics = list(set(ews_list) & set(ktau_metrics)) @@ -1125,15 +1122,19 @@ def mean_annual_ts(x, resolution=12): if len(missing_inds) > 0: for i in range(len(missing_inds)): print(i) - x[missing_inds[i]] = np.mean([x[missing_inds[i] - 1], x[missing_inds[i] + 1]]) + x[missing_inds[i]] = np.mean( + [x[missing_inds[i] - 1], x[missing_inds[i] + 1]] + ) mean_cycle = np.repeat(np.nan, resolution, axis=0) for i in range(resolution): - mean_cycle[i] = np.nanmean(x[np.linspace(start=i, stop=len(x) - 1, num=resolution, dtype=int)]) + mean_cycle[i] = np.nanmean( + x[np.linspace(start=i, stop=len(x) - 1, num=resolution, dtype=int)] + ) return mean_cycle -def decay_rate(x, resolution=12, method='basic'): +def decay_rate(x, resolution=12, method="basic"): """ Calculates the decay rate between the max and min values of a time series. Parameters @@ -1156,9 +1157,9 @@ def decay_rate(x, resolution=12, method='basic'): annual_cycle = mean_annual_ts(x, resolution) - if method == 'basic': + if method == "basic": ts = annual_cycle - elif method == 'adjusted': + elif method == "adjusted": ts = annual_cycle - np.min(annual_cycle) + 1 else: ts = np.nan # causes fail if method is not specified properly @@ -1174,7 +1175,7 @@ def decay_rate(x, resolution=12, method='basic'): return dr -def exp_model_fit(x, resolution=12, method='basic'): +def exp_model_fit(x, resolution=12, method="basic"): """ Fits an exponential model from the maximum to the minimum of the mean annual time series. A raw time series is expected as an input. @@ -1197,9 +1198,9 @@ def exp_model_fit(x, resolution=12, method='basic'): """ annual_cycle = mean_annual_ts(x, resolution) - if method == 'basic': + if method == "basic": ts = annual_cycle - elif method == 'adjusted': + elif method == "adjusted": ts = annual_cycle - np.min(annual_cycle) + 1 else: ts = np.nan # causes fail if method is not specified properly @@ -1215,7 +1216,11 @@ def exp_model_fit(x, resolution=12, method='basic'): else: exp_ts = ts[max_ind:min_ind] - exp_mod = np.polyfit(np.log(exp_ts), np.linspace(start=0, stop=len(exp_ts) - 1, num=len(exp_ts), dtype=int), 1) + exp_mod = np.polyfit( + np.log(exp_ts), + np.linspace(start=0, stop=len(exp_ts) - 1, num=len(exp_ts), dtype=int), + 1, + ) return exp_mod @@ -1235,7 +1240,7 @@ def reverse_normalise_ts(x): """ min_ind = np.where(x == np.min(x))[0][0] - arrangex = np.append(x[(min_ind + 1):len(x)], x[0:(min_ind + 1)]) + arrangex = np.append(x[(min_ind + 1) : len(x)], x[0 : (min_ind + 1)]) revx = arrangex[::-1] normx = (revx - np.min(revx)) / sum(revx - np.min(revx)) return normx @@ -1284,10 +1289,16 @@ def D(alpha): fx = np.repeat(np.nan, len(x), axis=0) for i in range(len(x)): - if (((x[i] - xbar) / sigma) > -alpha): - fx[i] = N(sigma, C(alpha, n), D(alpha)) * np.exp((-(x[i] - xbar) ** 2) / (2 * sigma ** 2)) - if (((x[i] - xbar) / sigma) <= -alpha): - fx[i] = N(sigma, C(alpha, n), D(alpha)) * A(alpha, n) * (B(alpha, n) - (x[i] - xbar) / sigma) ** (-n) + if ((x[i] - xbar) / sigma) > -alpha: + fx[i] = N(sigma, C(alpha, n), D(alpha)) * np.exp( + (-((x[i] - xbar) ** 2)) / (2 * sigma**2) + ) + if ((x[i] - xbar) / sigma) <= -alpha: + fx[i] = ( + N(sigma, C(alpha, n), D(alpha)) + * A(alpha, n) + * (B(alpha, n) - (x[i] - xbar) / sigma) ** (-n) + ) return fx @@ -1311,7 +1322,9 @@ def err_func(params, ts): Residuals/differences between Crytal Ball pdf and supplied time series """ - model_output = cball(range(1, len(ts) + 1), params[0], params[1], params[2], params[3]) + model_output = cball( + range(1, len(ts) + 1), params[0], params[1], params[2], params[3] + ) residuals = [] for i in range(0, len(ts)): @@ -1321,7 +1334,7 @@ def err_func(params, ts): return residuals -def cball_parfit(p0, timeseries, plot_name = 'CB_fit.png', output_dir = ''): +def cball_parfit(p0, timeseries, plot_name="CB_fit.png", output_dir=""): """ Uses least squares regression to optimise the parameters in cball to fit the timeseries supplied. The supplied time series should be the original series @@ -1348,14 +1361,13 @@ def cball_parfit(p0, timeseries, plot_name = 'CB_fit.png', output_dir = ''): The residuals from the best CB fit """ try: - mean_ts= timeseries.groupby(timeseries.index.month).mean() + mean_ts = timeseries.groupby(timeseries.index.month).mean() - if min(mean_ts)<0 and max(mean_ts)<0: + if min(mean_ts) < 0 and max(mean_ts) < 0: mean_ts = mean_ts - min(mean_ts) - p0 = [1.5,150,8.5,1.1] + p0 = [1.5, 150, 8.5, 1.1] except: - raise RuntimeError('Input time series for CB fit must have a datetime index') - + raise RuntimeError("Input time series for CB fit must have a datetime index") ts = reverse_normalise_ts(mean_ts) @@ -1363,9 +1375,13 @@ def cball_parfit(p0, timeseries, plot_name = 'CB_fit.png', output_dir = ''): for i in range(5): params, success = sco.leastsq(err_func, p0, args=ts) residuals = sum(err_func(params, ts)) - plt.plot(ts, 'k.', label='data') - plt.plot(cball(range(1, len(ts) + 1), params[0], params[1], params[2], params[3]), 'r', - label='Crystal ball fit', linewidth=1) + plt.plot(ts, "k.", label="data") + plt.plot( + cball(range(1, len(ts) + 1), params[0], params[1], params[2], params[3]), + "r", + label="Crystal ball fit", + linewidth=1, + ) if residuals < residuals_min: residuals_min = residuals p0 = params @@ -1373,20 +1389,42 @@ def cball_parfit(p0, timeseries, plot_name = 'CB_fit.png', output_dir = ''): final_sucess = success fig, ax = plt.subplots() - plt.plot(ts, 'k.', label='data') - plt.plot(cball(range(1, len(ts) + 1), final_params[0], final_params[1], final_params[2], final_params[3]), 'r', label='Crystal ball fit', linewidth=1) - plt.legend(loc='upper right') + plt.plot(ts, "k.", label="data") + plt.plot( + cball( + range(1, len(ts) + 1), + final_params[0], + final_params[1], + final_params[2], + final_params[3], + ), + "r", + label="Crystal ball fit", + linewidth=1, + ) + plt.legend(loc="upper right") ax.set_xticks(np.arange(len(ts))) - labels = ['Dec', 'Nov','Oct','Sep','Aug','Jul','Jun','May','Apr','Mar','Feb','Jan'] + labels = [ + "Dec", + "Nov", + "Oct", + "Sep", + "Aug", + "Jul", + "Jun", + "May", + "Apr", + "Mar", + "Feb", + "Jan", + ] ax.set_xticklabels(labels) # Rotate the tick labels and set their alignment. - plt.setp(ax.get_xticklabels(), rotation=45, ha="right", - rotation_mode="anchor") + plt.setp(ax.get_xticklabels(), rotation=45, ha="right", rotation_mode="anchor") - plt.xlabel('Month (reversed)') - plt.ylabel('PDF') - plt.title('Crystal ball fit for ' + plot_name) - plt.savefig(os.path.join(output_dir, "fit_ts_CB_"+plot_name+".png")) + plt.xlabel("Month (reversed)") + plt.ylabel("PDF") + plt.title("Crystal ball fit for " + plot_name) + plt.savefig(os.path.join(output_dir, "fit_ts_CB_" + plot_name + ".png")) return final_params, final_sucess, residuals_min - diff --git a/pyveg/src/date_utils.py b/pyveg/src/date_utils.py index f9a2c5a4..83c65e29 100644 --- a/pyveg/src/date_utils.py +++ b/pyveg/src/date_utils.py @@ -6,10 +6,11 @@ """ -import dateparser +import re from datetime import datetime, timedelta + +import dateparser from dateutil.relativedelta import relativedelta -import re def get_num_n_day_slices(start_date, end_date, days_per_chunk): @@ -51,7 +52,7 @@ def slice_time_period_into_n(start_date, end_date, n): for i in range(n): chunk_start = start + timedelta(days=(i * days_per_chunk)) chunk_end = start + timedelta(days=((i + 1) * days_per_chunk)) - ## unless we are in the last chunk, which should finish at end_date + # unless we are in the last chunk, which should finish at end_date if i == n - 1: chunk_end = end output_list.append( @@ -225,4 +226,4 @@ def get_time_diff(date1, date2, units="years"): return diff.days else: print("unknown units for time_diff: {}".format(units)) - return None \ No newline at end of file + return None diff --git a/pyveg/src/download_modules.py b/pyveg/src/download_modules.py index b5d77102..ee4e27c7 100644 --- a/pyveg/src/download_modules.py +++ b/pyveg/src/download_modules.py @@ -2,34 +2,33 @@ Classes for modules that download from GEE """ +import logging import os -import requests -from datetime import datetime, timedelta -import dateparser -import tempfile import subprocess +import tempfile +from datetime import datetime, timedelta -from geetools import cloud_mask import cv2 as cv - +import dateparser import ee +import requests +from geetools import cloud_mask -ee.Initialize() - +from pyveg.src.coordinate_utils import get_region_string from pyveg.src.date_utils import ( find_mid_period, get_num_n_day_slices, - slice_time_period_into_n, slice_time_period, + slice_time_period_into_n, ) from pyveg.src.file_utils import download_and_unzip -from pyveg.src.coordinate_utils import get_region_string -from pyveg.src.gee_interface import apply_mask_cloud, add_NDVI - +from pyveg.src.gee_interface import add_NDVI, apply_mask_cloud from pyveg.src.pyveg_pipeline import BaseModule, logger +ee.Initialize() + # silence google API WARNING -import logging + logging.getLogger("googleapiclient.discovery_cache").setLevel(logging.ERROR) @@ -54,8 +53,7 @@ def __init__(self, name): ("output_location_type", [str]), ("replace_existing_files", [bool]), ("ndvi", [bool]), - ("count", [bool]) - + ("count", [bool]), ] return @@ -157,7 +155,6 @@ def prep_data(self, date_range): ) return url_list - def download_data(self, download_urls, download_location): """ Download zip file(s) from GEE to configured output location. @@ -196,7 +193,9 @@ def run(self): for date_range in date_ranges: mid_date = find_mid_period(date_range[0], date_range[1]) location = self.join_path(self.output_location, mid_date, "RAW") - logger.debug("{} Will check for existing files in {}".format(self.name, location)) + logger.debug( + "{} Will check for existing files in {}".format(self.name, location) + ) if not self.replace_existing_files and self.check_for_existing_files( location, self.num_files_per_point ): @@ -208,11 +207,19 @@ def run(self): downloaded_ok = self.download_data(urls, location) if downloaded_ok: self.run_status["succeeded"] += 1 - logger.info("{}: download succeeded for date range {}".format(self.name, date_range)) + logger.info( + "{}: download succeeded for date range {}".format( + self.name, date_range + ) + ) download_locations.append(location) else: self.run_status["failed"] += 1 - logger.error("{}: download did not succeed for date range {}".format(self.name, date_range)) + logger.error( + "{}: download did not succeed for date range {}".format( + self.name, date_range + ) + ) self.is_finished = True return self.run_status @@ -289,7 +296,7 @@ def prep_images(self, dataset): # add count image as a band image = image.addBands(image_count) - bands_to_select = bands_to_select + ['COUNT'] + bands_to_select = bands_to_select + ["COUNT"] # select relevant bands image = image.select(bands_to_select) diff --git a/pyveg/src/file_utils.py b/pyveg/src/file_utils.py index 7f7ac412..60f3e9bf 100644 --- a/pyveg/src/file_utils.py +++ b/pyveg/src/file_utils.py @@ -1,12 +1,12 @@ -import os import datetime -import dateparser import json -import requests +import os import re import subprocess +from zipfile import BadZipFile, ZipFile -from zipfile import ZipFile, BadZipFile +import dateparser +import requests from .date_utils import find_mid_period @@ -54,7 +54,7 @@ def get_filepath_after_directory(path, dirname, include_dirname=False): dirname_found = False for part in path_parts: if part == dirname: - dirname_found=True + dirname_found = True if include_dirname: output_parts.append(part) else: @@ -83,14 +83,15 @@ def download_and_unzip(url, output_tmpdir): # GET the URL r = requests.get(url) if not r.status_code == 200: - raise RuntimeError(" HTTP Error {} getting download link {}".format(r.status_code, - url)) + raise RuntimeError( + " HTTP Error {} getting download link {}".format(r.status_code, url) + ) os.makedirs(output_tmpdir, exist_ok=True) output_zipfile = os.path.join(output_tmpdir, "gee.zip") with open(output_zipfile, "wb") as outfile: outfile.write(r.content) - ## catch zipfile-related exceptions here, and if they arise, - ## write the name of the zipfile and the url to a logfile + # catch zipfile-related exceptions here, and if they arise, + # write the name of the zipfile and the url to a logfile try: with ZipFile(output_zipfile, "r") as zip_obj: zip_obj.extractall(path=output_tmpdir) @@ -205,7 +206,7 @@ def get_tag(): """ Get the git tag currently checked out. """ - p=subprocess.Popen(["git","describe","--tags"],stdout=subprocess.PIPE) + p = subprocess.Popen(["git", "describe", "--tags"], stdout=subprocess.PIPE) tag = p.communicate()[0].decode("utf-8").strip() return tag @@ -220,12 +221,16 @@ def construct_filename_from_metadata(metadata, suffix): filename = metadata["coords_id"] else: filename = "coords" - filename += "_{}N_{}E_{}_freq-{}".format(metadata["latitude"], metadata["longitude"], - metadata["collection"], metadata["time_per_point"]) + filename += "_{}N_{}E_{}_freq-{}".format( + metadata["latitude"], + metadata["longitude"], + metadata["collection"], + metadata["time_per_point"], + ) if "region_size" in metadata.keys(): filename += "region-{}".format(region_size) if "tag" in metadata.keys(): filename += "_{}".format(metadata["tag"]) filename += "_{}".format(suffix) - filename = filename.replace("/","") + filename = filename.replace("/", "") return filename diff --git a/pyveg/src/gee_interface.py b/pyveg/src/gee_interface.py index e8905b8b..e58c5797 100644 --- a/pyveg/src/gee_interface.py +++ b/pyveg/src/gee_interface.py @@ -5,14 +5,15 @@ import os import shutil from datetime import datetime -from geetools import cloud_mask -import cv2 as cv +import cv2 as cv import ee +from geetools import cloud_mask + +from .file_utils import download_and_unzip ee.Initialize() -from .file_utils import download_and_unzip if os.name == "posix": TMPDIR = "/tmp/" @@ -90,6 +91,7 @@ def add_NDVI(image, red_band, near_infrared_band): print("Something went wrong in the NDVI variable construction") return image + def ee_prep_data( collection_dict, coords, date_range, region_size=0.1, scale=10, mask_cloud=True ): diff --git a/pyveg/src/image_utils.py b/pyveg/src/image_utils.py index 20c9ee6f..1a5637c2 100644 --- a/pyveg/src/image_utils.py +++ b/pyveg/src/image_utils.py @@ -6,25 +6,23 @@ ``` """ +import json import os import sys -import json - -import pandas as pd -import numpy as np import cv2 as cv -from PIL import Image import imageio - import matplotlib - -matplotlib.use("PS") import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +from PIL import Image from .coordinate_utils import get_sub_image_coords from .file_utils import save_image +matplotlib.use("PS") + def image_from_array(input_array, output_size=None, sel_val=200): """ @@ -114,7 +112,7 @@ def get_pix_val(ix, iy, col): int( band_dict[col]["pix_vals"][ix, iy] * 255 - / (overall_max + 1) # band_dict[col]["max_val"] + / (overall_max + 1) # band_dict[col]["max_val"] ), ) @@ -169,6 +167,7 @@ def get_pix_val(ix, iy): ) return new_img + def create_count_heatmap(input_filename): """ Given only a single band, get a heatmap based on the raw values @@ -186,10 +185,13 @@ def create_count_heatmap(input_filename): pix = cv.imread(input_filename, cv.IMREAD_ANYDEPTH) image_plt = plt.matshow(pix) - scaled_img = (image_plt.get_array() - image_plt.get_clim()[0]) / (image_plt.get_clim()[1] - image_plt.get_clim()[0]) + scaled_img = (image_plt.get_array() - image_plt.get_clim()[0]) / ( + image_plt.get_clim()[1] - image_plt.get_clim()[0] + ) new_image = Image.fromarray(np.uint8(image_plt.get_cmap()(scaled_img) * 255)) return new_image + def convert_to_rgb(band_dict): """ If we are given three or more bands, interpret the first as red, @@ -332,7 +334,6 @@ def crop_and_convert_to_bw( def create_gif_from_images(directory_path, output_name, string_in_filename=""): - """ Loop through a directory and convert all images in it into a gif chronologically diff --git a/pyveg/src/pattern_generation.py b/pyveg/src/pattern_generation.py index 1d6d7f73..ce3afcf6 100644 --- a/pyveg/src/pattern_generation.py +++ b/pyveg/src/pattern_generation.py @@ -1,11 +1,11 @@ """ Translation of Matlab code to model patterned vegetation in semi-arid landscapes. """ +import json import os import random -import json -import numpy as np +import numpy as np from matplotlib import pyplot as plt @@ -128,12 +128,15 @@ def configure(self): self.surface_water_frac = self.config[ "alpha" ] # proportion of surface water available for infiltration (d-1) - self.bare_soil_infiltration = self.config["W0"] # Bare soil infiltration (-) - self.grazing_loss = self.config["beta"] # Plant loss rate due to grazing (d-1) + # Bare soil infiltration (-) + self.bare_soil_infiltration = self.config["W0"] + # Plant loss rate due to grazing (d-1) + self.grazing_loss = self.config["beta"] self.soil_water_loss = self.config[ "rw" ] # Soil water loss rate due to seepage and evaporation (d-1) - self.plant_uptake = self.config["c"] # Plant uptake constant (g.mm-1.m-2) + # Plant uptake constant (g.mm-1.m-2) + self.plant_uptake = self.config["c"] self.plant_growth = self.config[ "gmax" ] # Plant growth constant (mm.g-1.m-2.d-1) diff --git a/pyveg/src/plotting.py b/pyveg/src/plotting.py index 59ff6306..6469b071 100644 --- a/pyveg/src/plotting.py +++ b/pyveg/src/plotting.py @@ -2,26 +2,25 @@ Plotting code. """ -import os -import json import datetime +import json +import os +import matplotlib.dates as mdates +import matplotlib.pyplot as plt import numpy as np import pandas as pd - -import matplotlib.pyplot as plt -import matplotlib.dates as mdates import seaborn as sns from pandas.plotting import register_matplotlib_converters from pyveg.src.data_analysis_utils import ( get_AR1_parameter_estimate, - get_kendell_tau, - write_to_json, - stl_decomposition, - get_max_lagged_cor, get_corrs_by_lag, get_datetime_xs, + get_kendell_tau, + get_max_lagged_cor, + stl_decomposition, + write_to_json, ) # globally set image quality @@ -42,51 +41,66 @@ def plot_time_series(df, output_dir, plot_smoothed=True): Directory to save the plots in. """ - def make_plot(df, - veg_prefix, - output_dir, - veg_prefix_b=None, - smoothing_option='smooth'): + def make_plot( + df, veg_prefix, output_dir, veg_prefix_b=None, smoothing_option="smooth" + ): # handle the case where vegetation and precipitation have mismatched NaNs - veg_df = df.dropna(subset=[veg_prefix+'_offset50_mean']) + veg_df = df.dropna(subset=[veg_prefix + "_offset50_mean"]) # get vegetation x values to datetime objects veg_xs = get_datetime_xs(veg_df) # get vegetation y values - veg_means = veg_df[veg_prefix + '_offset50_mean'] - veg_std = veg_df[veg_prefix + '_offset50_std'] + veg_means = veg_df[veg_prefix + "_offset50_mean"] + veg_std = veg_df[veg_prefix + "_offset50_std"] # create a figure fig, ax = plt.subplots(figsize=(15, 4.5)) - plt.xlabel('Time', fontsize=14) + plt.xlabel("Time", fontsize=14) # set up veg y axis - color = 'tab:green' - ax.set_ylabel(f'{veg_prefix} Offset50', color=color, fontsize=14) - ax.tick_params(axis='y', labelcolor=color) - ax.set_ylim([veg_means.min() - 1*veg_std.max(), veg_means.max() + 3*veg_std.max()]) - + color = "tab:green" + ax.set_ylabel(f"{veg_prefix} Offset50", color=color, fontsize=14) + ax.tick_params(axis="y", labelcolor=color) + ax.set_ylim( + [veg_means.min() - 1 * veg_std.max(), veg_means.max() + 3 * veg_std.max()] + ) # plot smoothed vegetation means and std - ax.plot(veg_xs, veg_means, marker='o', markersize=7, - markeredgecolor=(0.9172, 0.9627, 0.9172), markeredgewidth=2, - label='Offset50', linewidth=2, color='green') + ax.plot( + veg_xs, + veg_means, + marker="o", + markersize=7, + markeredgecolor=(0.9172, 0.9627, 0.9172), + markeredgewidth=2, + label="Offset50", + linewidth=2, + color="green", + ) - ax.fill_between(veg_xs, veg_means - veg_std, veg_means + veg_std, - facecolor='green', alpha=0.1, label='Std Dev') + ax.fill_between( + veg_xs, + veg_means - veg_std, + veg_means + veg_std, + facecolor="green", + alpha=0.1, + label="Std Dev", + ) # # get smoothed mean, std - veg_means_smooth = veg_df[veg_prefix+'_offset50_'+smoothing_option+'_mean'] + veg_means_smooth = veg_df[ + veg_prefix + "_offset50_" + smoothing_option + "_mean" + ] # plot vegetation legend - plt.legend(loc='upper left') + plt.legend(loc="upper left") # plot precipitation if availible - if 'total_precipitation' in df.columns: + if "total_precipitation" in df.columns: # handle the case where vegetation and precipitation have mismatched NaNs - precip_df = df.dropna(subset=['total_precipitation']) + precip_df = df.dropna(subset=["total_precipitation"]) precip_ys = precip_df.total_precipitation # get precipitation x values to datetime objects @@ -94,84 +108,134 @@ def make_plot(df, # duplicate axis for preciptation ax2 = ax.twinx() - color = 'tab:blue' - ax2.set_ylabel(f'Precipitation [mm]', color=color, fontsize=14) - ax2.tick_params(axis='y', labelcolor=color) - ax2.set_ylim([min(precip_ys)-1*np.array(precip_ys).std(), max(precip_ys)+2*np.array(precip_ys).std()]) + color = "tab:blue" + ax2.set_ylabel(f"Precipitation [mm]", color=color, fontsize=14) + ax2.tick_params(axis="y", labelcolor=color) + ax2.set_ylim( + [ + min(precip_ys) - 1 * np.array(precip_ys).std(), + max(precip_ys) + 2 * np.array(precip_ys).std(), + ] + ) # plot precipitation ax2.plot(precip_xs, precip_ys, linewidth=2, color=color, alpha=0.75) # add veg-precip correlation try: - max_corr_smooth, max_corr = get_max_lagged_cor(os.path.dirname(output_dir), veg_prefix) - textstr = f'$r_{{t-{max_corr[1]}}}={max_corr[0]:.2f}$' + max_corr_smooth, max_corr = get_max_lagged_cor( + os.path.dirname(output_dir), veg_prefix + ) + textstr = f"$r_{{t-{max_corr[1]}}}={max_corr[0]:.2f}$" # old correlation just calculates the 0-lag correlation - #raw_corr = veg_means.corr(precip_ys) - #smoothed_corr = veg_means_smooth.corr(precip_ys) - #textstr = f'$r={smoothed_corr:.2f}$ (${raw_corr:.2f}$ unsmoothed)' - ax2.text(0.13, 0.95, textstr, transform=ax2.transAxes, fontsize=14, verticalalignment='top') - except(FileNotFoundError): - print("Warning - lagged correlations file not found - call plot_autocorrelation_function() first to print correlations on plot") + # raw_corr = veg_means.corr(precip_ys) + # smoothed_corr = veg_means_smooth.corr(precip_ys) + # textstr = f'$r={smoothed_corr:.2f}$ (${raw_corr:.2f}$ unsmoothed)' + ax2.text( + 0.13, + 0.95, + textstr, + transform=ax2.transAxes, + fontsize=14, + verticalalignment="top", + ) + except (FileNotFoundError): + print( + "Warning - lagged correlations file not found - call plot_autocorrelation_function() first to print correlations on plot" + ) # plot second vegetation time series if availible if veg_prefix_b: # handle the case where vegetation and precipitation have mismatched NaNs - veg_df_b = df.dropna(subset=[veg_prefix_b+'_offset50_mean']) + veg_df_b = df.dropna(subset=[veg_prefix_b + "_offset50_mean"]) # get vegetation x values to datetime objects veg_xs_b = get_datetime_xs(veg_df_b) # get vegetation y values - veg_means_b = veg_df_b[veg_prefix_b+'_offset50_mean'] - veg_means_smooth_b = veg_df_b[veg_prefix_b+'_offset50_smooth_mean'] - veg_stds_smooth_b = veg_df_b[veg_prefix_b+'_offset50_smooth_std'] + veg_means_b = veg_df_b[veg_prefix_b + "_offset50_mean"] + veg_means_smooth_b = veg_df_b[veg_prefix_b + "_offset50_smooth_mean"] + veg_stds_smooth_b = veg_df_b[veg_prefix_b + "_offset50_smooth_std"] # plot secondary time series ax3 = ax.twinx() ax3.spines["left"].set_position(("axes", -0.08)) ax3.spines["left"].set_visible(True) - color = 'tab:purple' - ax3.set_ylabel(veg_prefix_b + ' Offset50', color=color, fontsize=14) - ax3.tick_params(axis='y', labelcolor=color) + color = "tab:purple" + ax3.set_ylabel(veg_prefix_b + " Offset50", color=color, fontsize=14) + ax3.tick_params(axis="y", labelcolor=color) ax3.yaxis.tick_left() - ax3.yaxis.set_label_position('left') - ax3.set_ylim([veg_means.min() - 1*veg_std.max(), veg_means.max() + 3*veg_std.max()]) + ax3.yaxis.set_label_position("left") + ax3.set_ylim( + [ + veg_means.min() - 1 * veg_std.max(), + veg_means.max() + 3 * veg_std.max(), + ] + ) # plot unsmoothed vegetation means - ax.plot(veg_xs_b, veg_means_b, label='Unsmoothed', linewidth=1, color='indigo', linestyle='dashed', alpha=0.2) + ax.plot( + veg_xs_b, + veg_means_b, + label="Unsmoothed", + linewidth=1, + color="indigo", + linestyle="dashed", + alpha=0.2, + ) # plot smoothed vegetation means and std - ax3.plot(veg_xs_b, veg_means_smooth_b, marker='o', markersize=7, - markeredgecolor=(0.8172, 0.7627, 0.9172), markeredgewidth=2, - label='Smoothed', linewidth=2, color=color) + ax3.plot( + veg_xs_b, + veg_means_smooth_b, + marker="o", + markersize=7, + markeredgecolor=(0.8172, 0.7627, 0.9172), + markeredgewidth=2, + label="Smoothed", + linewidth=2, + color=color, + ) - ax3.fill_between(veg_xs_b, veg_means_smooth_b - veg_stds_smooth_b, veg_means_smooth_b + veg_stds_smooth_b, - facecolor='tab:purple', alpha=0.1, label='Std Dev') + ax3.fill_between( + veg_xs_b, + veg_means_smooth_b - veg_stds_smooth_b, + veg_means_smooth_b + veg_stds_smooth_b, + facecolor="tab:purple", + alpha=0.1, + label="Std Dev", + ) # add veg-veg correlation vegveg_corr = veg_means.corr(veg_means_b) vegveg_corr_smooth = veg_means_smooth.corr(veg_means_smooth_b) - textstr = f'$r_{{vv}} = {vegveg_corr:.2f}$' - ax2.text(0.55, 0.85, textstr, transform=ax2.transAxes, fontsize=14, verticalalignment='top') + textstr = f"$r_{{vv}} = {vegveg_corr:.2f}$" + ax2.text( + 0.55, + 0.85, + textstr, + transform=ax2.transAxes, + fontsize=14, + verticalalignment="top", + ) # update prefix for filename use - veg_prefix = veg_prefix + '+' + veg_prefix_b + veg_prefix = veg_prefix + "+" + veg_prefix_b # add autoregression info veg_means.index = veg_df.date # layout - sns.set_style('white') + sns.set_style("white") fig.tight_layout() - filename_suffix = '_' + smoothing_option + filename_suffix = "_" + smoothing_option # save the plot - output_filename = veg_prefix + '-time-series' + filename_suffix + '.png' + output_filename = veg_prefix + "-time-series" + filename_suffix + ".png" plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) - #plt.close(fig) + # plt.close(fig) # make output dir if necessary if not os.path.exists(output_dir): @@ -179,18 +243,20 @@ def make_plot(df, # make plots for selected columns for column in df.columns: - if 'offset50_mean' in column: - veg_prefix = column.split('_')[0] - print(f'Plotting {veg_prefix} time series.') + if "offset50_mean" in column: + veg_prefix = column.split("_")[0] + print(f"Plotting {veg_prefix} time series.") make_plot(df, veg_prefix, output_dir) if plot_smoothed: - make_plot(df, veg_prefix, output_dir, smoothing_option='smooth_res') + make_plot(df, veg_prefix, output_dir, smoothing_option="smooth_res") # if we have two vegetation time series availible, plot them both - if np.sum(df.columns.str.contains('offset50_mean')) == 2: - veg_columns = df.columns[np.where(df.columns.str.contains('offset50_mean'))].values - veg_prefixes = [c.split('_')[0] for c in veg_columns] - assert( len(veg_prefixes) == 2 ) + if np.sum(df.columns.str.contains("offset50_mean")) == 2: + veg_columns = df.columns[ + np.where(df.columns.str.contains("offset50_mean")) + ].values + veg_prefixes = [c.split("_")[0] for c in veg_columns] + assert len(veg_prefixes) == 2 make_plot(df, veg_prefixes[0], output_dir, veg_prefix_b=veg_prefixes[1]) @@ -204,37 +270,56 @@ def make_plot(df, veg_prefix, col_name, utput_dir): # get vegetation y values veg_means = veg_df[col_name] - #veg_means = veg_df[veg_prefix + '_ndvi_veg_mean'] - if any([col_name.replace('mean', 'std') == c for c in df.columns]): - veg_std = veg_df[col_name.replace('mean', 'std')] + # veg_means = veg_df[veg_prefix + '_ndvi_veg_mean'] + if any([col_name.replace("mean", "std") == c for c in df.columns]): + veg_std = veg_df[col_name.replace("mean", "std")] # create a figure fig, ax = plt.subplots(figsize=(15, 4.5)) - plt.xlabel('Time', fontsize=14) + plt.xlabel("Time", fontsize=14) # set up veg y axis - color = 'tab:green' - ax.set_ylabel(f'{veg_prefix} NDVI', color=color, fontsize=14) - ax.tick_params(axis='y', labelcolor=color) - - if any([col_name.replace('mean', 'std') == c for c in df.columns]): - ax.set_ylim([veg_means.min() - 1*veg_std.max(), veg_means.max() + 3*veg_std.max()]) + color = "tab:green" + ax.set_ylabel(f"{veg_prefix} NDVI", color=color, fontsize=14) + ax.tick_params(axis="y", labelcolor=color) + + if any([col_name.replace("mean", "std") == c for c in df.columns]): + ax.set_ylim( + [ + veg_means.min() - 1 * veg_std.max(), + veg_means.max() + 3 * veg_std.max(), + ] + ) # plot ndvi - #ax.plot(veg_xs, ndvi_means, label='Unsmoothed', linewidth=1, color='dimgray', linestyle='dotted') - - ax.plot(veg_xs, veg_means, marker='o', markersize=7, - markeredgecolor=(0.9172, 0.9627, 0.9172), markeredgewidth=2, - label='Smoothed', linewidth=2, color='green') + # ax.plot(veg_xs, ndvi_means, label='Unsmoothed', linewidth=1, color='dimgray', linestyle='dotted') + + ax.plot( + veg_xs, + veg_means, + marker="o", + markersize=7, + markeredgecolor=(0.9172, 0.9627, 0.9172), + markeredgewidth=2, + label="Smoothed", + linewidth=2, + color="green", + ) - if any([col_name.replace('mean', 'std') == c for c in df.columns]): - ax.fill_between(veg_xs, veg_means - veg_std, veg_means + veg_std, - facecolor='green', alpha=0.1, label='Std Dev') + if any([col_name.replace("mean", "std") == c for c in df.columns]): + ax.fill_between( + veg_xs, + veg_means - veg_std, + veg_means + veg_std, + facecolor="green", + alpha=0.1, + label="Std Dev", + ) # plot precipitation if availible - if 'total_precipitation' in df.columns: + if "total_precipitation" in df.columns: # handle the case where vegetation and precipitation have mismatched NaNs - precip_df = df.dropna(subset=['total_precipitation']) + precip_df = df.dropna(subset=["total_precipitation"]) precip_ys = precip_df.total_precipitation # get precipitation x values to datetime objects @@ -242,27 +327,39 @@ def make_plot(df, veg_prefix, col_name, utput_dir): # duplicate axis for preciptation ax2 = ax.twinx() - color = 'tab:blue' - ax2.set_ylabel(f'Precipitation [mm]', color=color, fontsize=14) - ax2.tick_params(axis='y', labelcolor=color) - ax2.set_ylim([min(precip_ys)-1*np.array(precip_ys).std(), max(precip_ys)+2*np.array(precip_ys).std()]) + color = "tab:blue" + ax2.set_ylabel(f"Precipitation [mm]", color=color, fontsize=14) + ax2.tick_params(axis="y", labelcolor=color) + ax2.set_ylim( + [ + min(precip_ys) - 1 * np.array(precip_ys).std(), + max(precip_ys) + 2 * np.array(precip_ys).std(), + ] + ) # plot precipitation ax2.plot(precip_xs, precip_ys, linewidth=2, color=color, alpha=0.75) # add correlation information - correlations = get_corrs_by_lag(df[col_name], df['total_precipitation']) + correlations = get_corrs_by_lag(df[col_name], df["total_precipitation"]) max_corr = np.max(np.array(correlations)) max_corr_lag = np.array(np.argmax(correlations)) - textstr = f'$r_{{t-{max_corr_lag}}}={max_corr:.2f}$ ' - ax2.text(0.13, 0.95, textstr, transform=ax2.transAxes, fontsize=14, verticalalignment='top') + textstr = f"$r_{{t-{max_corr_lag}}}={max_corr:.2f}$ " + ax2.text( + 0.13, + 0.95, + textstr, + transform=ax2.transAxes, + fontsize=14, + verticalalignment="top", + ) # layout - sns.set_style('white') + sns.set_style("white") fig.tight_layout() # save the plot - output_filename = veg_prefix + '-ndvi-time-series.png' + output_filename = veg_prefix + "-ndvi-time-series.png" plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) plt.close(fig) @@ -272,13 +369,13 @@ def make_plot(df, veg_prefix, col_name, utput_dir): # make plots for selected columns for column in df.columns: - if 'ndvi' in column and 'mean' in column: - veg_prefix = column.split('_')[0] - print(f'Plotting {veg_prefix} NDVI time series.') + if "ndvi" in column and "mean" in column: + veg_prefix = column.split("_")[0] + print(f"Plotting {veg_prefix} NDVI time series.") make_plot(df, veg_prefix, column, output_dir) -def plot_autocorrelation_function(df, output_dir, filename_suffix=''): +def plot_autocorrelation_function(df, output_dir, filename_suffix=""): """ Given a time series DataFrames (constructed with `make_time_series`), plot the autocorrelation function relevant columns. @@ -292,35 +389,43 @@ def plot_autocorrelation_function(df, output_dir, filename_suffix=''): Directory to save the plots in. """ - def make_plots(series, output_dir, filename_suffix=''): + def make_plots(series, output_dir, filename_suffix=""): # make the full autocorrelation function plot - fig, _ = plt.subplots(figsize=(8,5)) + fig, _ = plt.subplots(figsize=(8, 5)) pd.plotting.autocorrelation_plot(series, label=series.name) plt.legend() # save the plot - output_filename = series.name + '-autocorrelation-function' + filename_suffix + '.png' + output_filename = ( + series.name + "-autocorrelation-function" + filename_suffix + ".png" + ) plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) plt.close(fig) # use statsmodels for partial autocorrelation from statsmodels.graphics.tsaplots import plot_pacf - fig, ax = plt.subplots(figsize=(8,5)) + + fig, ax = plt.subplots(figsize=(8, 5)) plot_pacf(series, label=series.name, ax=ax, zero=False) plt.ylim([-1.0, 1.0]) - plt.xlabel('Lag') - plt.ylabel('Partial Autocorrelation') + plt.xlabel("Lag") + plt.ylabel("Partial Autocorrelation") # save the plot - output_filename = series.name + '-partial-autocorrelation-function' + filename_suffix + '.png' + output_filename = ( + series.name + "-partial-autocorrelation-function" + filename_suffix + ".png" + ) plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) - #plt.close(fig) - + # plt.close(fig) # make plots for selected columns for column in df.columns: - if ('offset50' in column or 'ndvi' in column) and 'mean' in column or 'total_precipitation' in column: + if ( + ("offset50" in column or "ndvi" in column) + and "mean" in column + or "total_precipitation" in column + ): print(f'Plotting autocorrelation functions for "{column}"...') make_plots(df[column].dropna(), output_dir, filename_suffix=filename_suffix) @@ -340,8 +445,8 @@ def plot_cross_correlations(df, output_dir): """ # check precipitation time series present - if 'total_precipitation' not in df.columns: - print('Missing precipitation time series, skipping cross correlation plots.') + if "total_precipitation" not in df.columns: + print("Missing precipitation time series, skipping cross correlation plots.") return def make_plot(veg_ys, precip_ys, output_dir): @@ -352,12 +457,11 @@ def make_plot(veg_ys, precip_ys, output_dir): # make a new df to ensure NaN veg values are explicit df_ = pd.DataFrame() - df_['precip'] = precip_ys - df_['offset50'] = veg_ys + df_["precip"] = precip_ys + df_["offset50"] = veg_ys # create fig - fig, axs = plt.subplots(3, 3, sharex='col', sharey='row', - figsize=(8, 8)) + fig, axs = plt.subplots(3, 3, sharex="col", sharey="row", figsize=(8, 8)) # loop through offsets for lag in range(0, lags): @@ -366,39 +470,41 @@ def make_plot(veg_ys, precip_ys, output_dir): ax = axs.flat[lag] # format this subplot - ax.set_title(f'$t-{lag}$') + ax.set_title(f"$t-{lag}$") ax.grid(False) # plot data - lagged_data = df_['offset50'].shift(-lag) + lagged_data = df_["offset50"].shift(-lag) corr = precip_ys.corr(lagged_data) - correlations.append(round(corr,4)) - sns.regplot(precip_ys, lagged_data, label=f'$r={corr:.2f}$', ax=ax) + correlations.append(round(corr, 4)) + sns.regplot(precip_ys, lagged_data, label=f"$r={corr:.2f}$", ax=ax) - # format axis label + # format axis label if lag < 6: - ax.set_xlabel('') + ax.set_xlabel("") if lag % 3 != 0: - ax.set_ylabel('') + ax.set_ylabel("") ax.legend() plt.tight_layout() # save the plot - output_filename = veg_ys.name + '-scatterplot-matrix.png' + output_filename = veg_ys.name + "-scatterplot-matrix.png" plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) - #plt.close(fig) + # plt.close(fig) # write out correlations as a function of lag - correlations_dict = {veg_ys.name + '_lagged_correlation': correlations} - write_to_json(os.path.join(output_dir, 'lagged_correlations.json'), correlations_dict) + correlations_dict = {veg_ys.name + "_lagged_correlation": correlations} + write_to_json( + os.path.join(output_dir, "lagged_correlations.json"), correlations_dict + ) # make plots for selected columns for column in df.columns: - if 'offset50' in column and 'mean' in column: + if "offset50" in column and "mean" in column: print(f'Plotting cross correlation matrix for "{column}"...') - make_plot(df[column], df['total_precipitation'], output_dir) + make_plot(df[column], df["total_precipitation"], output_dir) def plot_feature_vector(output_dir): @@ -413,15 +519,15 @@ def plot_feature_vector(output_dir): """ # assume feature vectors have been saved in the above location - fv_dir = os.path.join(os.path.dirname(output_dir), 'processed_data') + fv_dir = os.path.join(os.path.dirname(output_dir), "processed_data") if not os.path.exists(fv_dir): - print('No feature vectors found, skipping plot!') + print("No feature vectors found, skipping plot!") return # get feature vectors for different collections - fvs = [f for f in os.listdir(fv_dir) if '_feature_vectors.csv' in f] + fvs = [f for f in os.listdir(fv_dir) if "_feature_vectors.csv" in f] if len(fvs) == 0: - print('No feature vectors found, skipping plot!') + print("No feature vectors found, skipping plot!") return # for each collection @@ -431,32 +537,41 @@ def plot_feature_vector(output_dir): df = pd.read_csv(os.path.join(fv_dir, fv_filename)).dropna() # percentile columns - cols = [c for c in df.columns if 'percentile' in c] + cols = [c for c in df.columns if "percentile" in c] # compute feature vector averaged over all sub-images feature_vector = df[cols].mean() feature_vector_std = df[cols].std() # generate x-values - xs = np.linspace(0,100,len(feature_vector)) + xs = np.linspace(0, 100, len(feature_vector)) # make the plot - fig, _ = plt.subplots(figsize=(6,5)) - - plt.errorbar(xs, feature_vector, marker='o', markersize=5, linestyle='', - yerr=feature_vector_std, color='black', capsize=2, elinewidth=1) + fig, _ = plt.subplots(figsize=(6, 5)) + + plt.errorbar( + xs, + feature_vector, + marker="o", + markersize=5, + linestyle="", + yerr=feature_vector_std, + color="black", + capsize=2, + elinewidth=1, + ) - plt.xlabel('Pixel Rank (%)', fontsize=14) - plt.ylabel('$X(V-E)$', fontsize=14) + plt.xlabel("Pixel Rank (%)", fontsize=14) + plt.ylabel("$X(V-E)$", fontsize=14) plt.tight_layout() # create new subdir for feature vectors - fv_subdir = os.path.join(output_dir, 'feature-vectors') + fv_subdir = os.path.join(output_dir, "feature-vectors") if not os.path.exists(fv_subdir): os.makedirs(fv_subdir, exist_ok=True) # save the plot - output_filename = fv_filename.split('_')[0] + '-feature-vector-summary.png' + output_filename = fv_filename.split("_")[0] + "-feature-vector-summary.png" print(f'Plotting feature vector "{os.path.abspath(output_filename)}"...') plt.savefig(os.path.join(fv_subdir, output_filename), dpi=DPI) plt.close(fig) @@ -467,13 +582,15 @@ def plot_feature_vector(output_dir): dates = [] # loop through time points - for date, group in df.groupby('date'): + for date, group in df.groupby("date"): # calculate feature vector and offset50 feature_vector = group.mean()[cols] feature_vecs.append(feature_vector) feature_vecs_stds.append(group.std()[cols]) - offset50s.append((feature_vector[-1] - feature_vector[len(feature_vector)//2])) + offset50s.append( + (feature_vector[-1] - feature_vector[len(feature_vector) // 2]) + ) dates.append(date) # get max and min @@ -488,41 +605,61 @@ def plot_feature_vector(output_dir): min_date = dates[imin] # plot the min/max veg feature vectors - fig, _ = plt.subplots(figsize=(6,5)) + fig, _ = plt.subplots(figsize=(6, 5)) - # add to plot - plt.errorbar(xs, max_fv, marker='o', markersize=5, linestyle='', label=f'max veg: {max_date}', - yerr=max_fv_std, color='tab:green', capsize=2, elinewidth=1) - plt.errorbar(xs, min_fv, marker='o', markersize=5, linestyle='', label=f'min veg: {min_date}', - yerr=min_fv_std, color='tab:red', capsize=2, elinewidth=1) + # add to plot + plt.errorbar( + xs, + max_fv, + marker="o", + markersize=5, + linestyle="", + label=f"max veg: {max_date}", + yerr=max_fv_std, + color="tab:green", + capsize=2, + elinewidth=1, + ) + plt.errorbar( + xs, + min_fv, + marker="o", + markersize=5, + linestyle="", + label=f"min veg: {min_date}", + yerr=min_fv_std, + color="tab:red", + capsize=2, + elinewidth=1, + ) # format plot - plt.xlabel('Pixel Rank (%)', fontsize=14) - plt.ylabel('$X(V-E)$', fontsize=14) + plt.xlabel("Pixel Rank (%)", fontsize=14) + plt.ylabel("$X(V-E)$", fontsize=14) plt.legend() plt.tight_layout() # save the plot - output_filename = fv_filename.split('_')[0] + '-feature-vector-minmax.png' + output_filename = fv_filename.split("_")[0] + "-feature-vector-minmax.png" print(f'Plotting minmax feature vector "{os.path.abspath(output_filename)}"...') plt.savefig(os.path.join(fv_subdir, output_filename), dpi=DPI) - #plt.close(fig) + # plt.close(fig) def plot_stl_decomposition(df, period, output_dir): """ - Run the STL decomposition and plot the results network centrality and - precipitation DataFrames in `df`. - - Parameters - ---------- - df : DataFrame - The time-series results. - period : float - Periodicity to model. - output_dir : str - Directory to save the plot in. - """ + Run the STL decomposition and plot the results network centrality and + precipitation DataFrames in `df`. + + Parameters + ---------- + df : DataFrame + The time-series results. + period : float + Periodicity to model. + output_dir : str + Directory to save the plot in. + """ def make_plot(df, column, output_dir): """ @@ -545,10 +682,10 @@ def make_plot(df, column, output_dir): xs = get_datetime_xs(df) # formatting - default_figsize = plt.rcParams['figure.figsize'] - default_fontsize = plt.rcParams['font.size'] - plt.rc('figure', figsize=(20, 8)) - plt.rc('font', size=15) + default_figsize = plt.rcParams["figure.figsize"] + default_fontsize = plt.rcParams["font.size"] + plt.rc("figure", figsize=(20, 8)) + plt.rc("font", size=15) fig = res.plot() ax_list = fig.axes @@ -556,16 +693,16 @@ def make_plot(df, column, output_dir): ax.tick_params(labelbottom=False) # set xlabel with datetime object - #ax_list[-1].set_xticklabels(xs, rotation=0, va="center") + # ax_list[-1].set_xticklabels(xs, rotation=0, va="center") # save plot - filename = os.path.join(output_dir, column+'_STL_decomposition.png') + filename = os.path.join(output_dir, column + "_STL_decomposition.png") plt.savefig(filename, dpi=DPI) - #plt.close(fig) + # plt.close(fig) # undo rc changes - plt.rc('figure', figsize=default_figsize) - plt.rc('font', size=default_fontsize) + plt.rc("figure", figsize=default_figsize) + plt.rc("font", size=default_fontsize) # make output dir if necessary if not os.path.exists(output_dir): @@ -573,7 +710,11 @@ def make_plot(df, column, output_dir): # make plots for selected columns for column in df.columns: - if ('offset50' in column or 'ndvi' in column) and 'mean' in column or 'total_precipitation' in column: + if ( + ("offset50" in column or "ndvi" in column) + and "mean" in column + or "total_precipitation" in column + ): print(f'Plotting STL decomposition for "{column}"...') @@ -581,7 +722,7 @@ def make_plot(df, column, output_dir): make_plot(df.dropna(), column, output_dir) -def plot_moving_window_analysis(df, output_dir, filename_suffix=''): +def plot_moving_window_analysis(df, output_dir, filename_suffix=""): """ Given a moving window time series DataFrame, plot the time series of AR1 and Variance. @@ -611,10 +752,12 @@ def make_plot(df, column, output_dir, smoothing_option): """ # get short string prefix on column name - collection_prefix = column.split('_')[0] if 'offset50' in column else 'precipitation' + collection_prefix = ( + column.split("_")[0] if "offset50" in column else "precipitation" + ) # hand mismatched NaNs - ar1_df = df.dropna(subset=[column.replace('var', 'ar1')]) + ar1_df = df.dropna(subset=[column.replace("var", "ar1")]) var_df = df.dropna(subset=[column]) # extract x values and convert to datetime objects @@ -623,61 +766,104 @@ def make_plot(df, column, output_dir, smoothing_option): # extract individual time series variance = var_df[column] - ar1 = ar1_df[column.replace('var', 'ar1')] - ar1_se = ar1_df[column.replace('var', 'ar1_se')] + ar1 = ar1_df[column.replace("var", "ar1")] + ar1_se = ar1_df[column.replace("var", "ar1_se")] if any([smoothing_option in c for c in df.columns]): - variance_smooth = var_df[column.replace('offset50_mean', 'offset50_' + smoothing_option + '_mean')] - ar1_smooth = ar1_df[column.replace('var', 'ar1').replace('offset50_mean', 'offset50_' + smoothing_option + '_mean')] - ar1_se_smooth = ar1_df[column.replace('var', 'ar1_se').replace('offset50_mean', 'offset50_' + smoothing_option + '_mean')] + variance_smooth = var_df[ + column.replace( + "offset50_mean", "offset50_" + smoothing_option + "_mean" + ) + ] + ar1_smooth = ar1_df[ + column.replace("var", "ar1").replace( + "offset50_mean", "offset50_" + smoothing_option + "_mean" + ) + ] + ar1_se_smooth = ar1_df[ + column.replace("var", "ar1_se").replace( + "offset50_mean", "offset50_" + smoothing_option + "_mean" + ) + ] # create a figure fig, ax = plt.subplots(figsize=(15, 5)) - plt.xlabel('Time', fontsize=12) + plt.xlabel("Time", fontsize=12) # set up veg y axis - color = 'tab:blue' - ax.set_ylabel(f'{collection_prefix} AR1', color=color, fontsize=12) - ax.tick_params(axis='y', labelcolor=color) + color = "tab:blue" + ax.set_ylabel(f"{collection_prefix} AR1", color=color, fontsize=12) + ax.tick_params(axis="y", labelcolor=color) # plot unsmoothed vegetation ar1 and std - ax.plot(ar1_xs, ar1, label='AR1', linewidth=2, color='tab:blue') - ax.fill_between(ar1_xs, ar1 - ar1_se, ar1 + ar1_se, - facecolor='blue', alpha=0.1, label='AR1 SE') + ax.plot(ar1_xs, ar1, label="AR1", linewidth=2, color="tab:blue") + ax.fill_between( + ar1_xs, + ar1 - ar1_se, + ar1 + ar1_se, + facecolor="blue", + alpha=0.1, + label="AR1 SE", + ) if any([smoothing_option in c for c in df.columns]): # plot smoothed vegetation ar1 and std - ax.plot(ar1_xs, ar1_smooth, label='AR1 Smoothed', linewidth=2, color='tab:blue', linestyle='dotted') - ax.fill_between(ar1_xs, ar1_smooth - ar1_se_smooth, ar1_smooth + ar1_se_smooth, - facecolor='none', alpha=0.15, label='AR1 SE Smoothed', hatch='X', edgecolor='tab:blue') + ax.plot( + ar1_xs, + ar1_smooth, + label="AR1 Smoothed", + linewidth=2, + color="tab:blue", + linestyle="dotted", + ) + ax.fill_between( + ar1_xs, + ar1_smooth - ar1_se_smooth, + ar1_smooth + ar1_se_smooth, + facecolor="none", + alpha=0.15, + label="AR1 SE Smoothed", + hatch="X", + edgecolor="tab:blue", + ) # set y lim - try: # in case there are no ar1 values, the array will be empty - ax.set_ylim([min(ar1-ar1_se)-0.8*max(ar1+ar1_se), 1.8*max(ar1+ar1_se)]) + try: #  in case there are no ar1 values, the array will be empty + ax.set_ylim( + [min(ar1 - ar1_se) - 0.8 * max(ar1 + ar1_se), 1.8 * max(ar1 + ar1_se)] + ) except: return # plot legend - plt.legend(loc='upper left') + plt.legend(loc="upper left") # duplicate x-axis for variance ax2 = ax.twinx() - color = 'tab:red' - ax2.set_ylabel(f'{collection_prefix} Variance', color=color, fontsize=12) - ax2.tick_params(axis='y', labelcolor=color) + color = "tab:red" + ax2.set_ylabel(f"{collection_prefix} Variance", color=color, fontsize=12) + ax2.tick_params(axis="y", labelcolor=color) # plot variance - ax2.plot(var_xs, variance, linewidth=2, color=color, alpha=0.75, label='Variance') + ax2.plot( + var_xs, variance, linewidth=2, color=color, alpha=0.75, label="Variance" + ) if any([smoothing_option in c for c in df.columns]): - ax2.plot(var_xs, variance_smooth, linewidth=2, color=color, alpha=0.75, - linestyle='dotted', label='Variance Smoothed') + ax2.plot( + var_xs, + variance_smooth, + linewidth=2, + color=color, + alpha=0.75, + linestyle="dotted", + label="Variance Smoothed", + ) # set y lim - ax2.set_ylim([0, 2*max(variance)]) - + ax2.set_ylim([0, 2 * max(variance)]) # add legend - plt.legend(loc='lower left') + plt.legend(loc="lower left") # add Kendall tau @@ -689,35 +875,49 @@ def make_plot(df, column, output_dir, smoothing_option): tau_var_smooth, p_var_smooth = get_kendell_tau(variance_smooth) # add to plot - textstr = '' + textstr = "" if any([smoothing_option in c for c in df.columns]): - textstr += f'AR1 Kendall $\\tau,~p$-$\\mathrm{{value}}={tau_smooth:.2f}$, ${p_smooth:.2f}$' - textstr += f' (${tau:.2f}$, ${p:.2f}$ unsmoothed)' - ax2.text(0.43, 0.95, textstr, transform=ax2.transAxes, fontsize=14, verticalalignment='top') + textstr += f"AR1 Kendall $\\tau,~p$-$\\mathrm{{value}}={tau_smooth:.2f}$, ${p_smooth:.2f}$" + textstr += f" (${tau:.2f}$, ${p:.2f}$ unsmoothed)" + ax2.text( + 0.43, + 0.95, + textstr, + transform=ax2.transAxes, + fontsize=14, + verticalalignment="top", + ) - textstr = '' + textstr = "" if any([smoothing_option in c for c in df.columns]): - textstr += f'Variance Kendall $\\tau,~p$-$\\mathrm{{value}}={tau_var_smooth:.2f}$, ${p_var_smooth:.2f}$' - textstr += f' (${tau_var:.2f}$, ${p_var:.2f}$ unsmoothed)' - ax2.text(0.43, 0.85, textstr, transform=ax2.transAxes, fontsize=14, verticalalignment='top') + textstr += f"Variance Kendall $\\tau,~p$-$\\mathrm{{value}}={tau_var_smooth:.2f}$, ${p_var_smooth:.2f}$" + textstr += f" (${tau_var:.2f}$, ${p_var:.2f}$ unsmoothed)" + ax2.text( + 0.43, + 0.85, + textstr, + transform=ax2.transAxes, + fontsize=14, + verticalalignment="top", + ) # layout fig.tight_layout() # save the plot - output_filename = collection_prefix + '-AR1-var-' + smoothing_option + '.png' - print(f'Plotting {collection_prefix} moving window time series...') + output_filename = collection_prefix + "-AR1-var-" + smoothing_option + ".png" + print(f"Plotting {collection_prefix} moving window time series...") plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) plt.close(fig) - for column in df.columns: - if (('offset50_mean' in column or 'total_precipitation' in column) and - 'var' in column): - make_plot(df, column, output_dir, 'smooth_res') + if ( + "offset50_mean" in column or "total_precipitation" in column + ) and "var" in column: + make_plot(df, column, output_dir, "smooth_res") -def plot_correlation_mwa(df, output_dir, filename_suffix=''): +def plot_correlation_mwa(df, output_dir, filename_suffix=""): """ Given a moving window time series DataFrame, plot the time series of veg-precip correlation. @@ -742,23 +942,30 @@ def make_plot(df, column_name, output_dir, filename_suffix): plt.plot(xs, df[column_name]) # label axes - plt.xlabel('Time', fontsize=12) + plt.xlabel("Time", fontsize=12) plt.ylabel(column_name, fontsize=12) # calculate Kendall taus and annotate plot tau, p = get_kendell_tau(df[column_name].dropna()) - textstr = f'Kendall $\\tau,~p = {tau:.3f}$, ${p:.4f}$' - ax.text(0.1, 0.95, textstr, transform=ax.transAxes, fontsize=14, verticalalignment='top') + textstr = f"Kendall $\\tau,~p = {tau:.3f}$, ${p:.4f}$" + ax.text( + 0.1, + 0.95, + textstr, + transform=ax.transAxes, + fontsize=14, + verticalalignment="top", + ) # save the plot - output_filename = f'{column_name}' + filename_suffix + '.png' - collection_prefix = column_name.split('_')[0] - print(f'Plotting {collection_prefix} correlation moving window analysis...') + output_filename = f"{column_name}" + filename_suffix + ".png" + collection_prefix = column_name.split("_")[0] + print(f"Plotting {collection_prefix} correlation moving window analysis...") plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) plt.close(fig) for column in df.columns: - if 'precip' in column and ('corr' in column or 'lag' in column): + if "precip" in column and ("corr" in column or "lag" in column): make_plot(df, column, output_dir, filename_suffix) @@ -778,9 +985,10 @@ def plot_ews_resiliance(series_name, EWSmetrics_df, Kendalltau_df, dates, output output_dir: str Output dir to save plot in. """ + def zoom_out(ys): - ymin = ys.mean() - 2*((ys.mean() - ys).abs().max()) - ymax = ys.mean() + 2*((ys.mean() - ys).abs().max()) + ymin = ys.mean() - 2 * ((ys.mean() - ys).abs().max()) + ymax = ys.mean() + 2 * ((ys.mean() - ys).abs().max()) if np.isnan(ymin): ymin = -1 if np.isnan(ymax): @@ -788,36 +996,39 @@ def zoom_out(ys): return [ymin, ymax] - def annotate(text, xy=(6 , 70), size=10): - if 'Kendall' in text: + def annotate(text, xy=(6, 70), size=10): + if "Kendall" in text: xy = (xy[0], 60) - plt.gca().annotate(text, xy=xy, xycoords='axes points', - size=size, ha='left', va='top') + plt.gca().annotate( + text, xy=xy, xycoords="axes points", size=size, ha="left", va="top" + ) dates = get_datetime_xs(pd.DataFrame(dates).dropna()) - fig, _ = plt.subplots(figsize=(4,8), sharex='col') + fig, _ = plt.subplots(figsize=(4, 8), sharex="col") ax1 = plt.subplot(611) - ys = EWSmetrics_df['State variable'] + ys = EWSmetrics_df["State variable"] - plt.plot(dates[-len(ys):], ys, color='black') - plt.plot(dates[-len(ys):], EWSmetrics_df['Smoothing'], color='red', linestyle='dashed') + plt.plot(dates[-len(ys) :], ys, color="black") + plt.plot( + dates[-len(ys) :], EWSmetrics_df["Smoothing"], color="red", linestyle="dashed" + ) plt.ylim(zoom_out(ys)) annotate(series_name) ax2 = plt.subplot(612, sharex=ax1) - ys = EWSmetrics_df['Residuals'] - plt.plot(dates[-len(ys):], ys, color='black', label='Time Series') + ys = EWSmetrics_df["Residuals"] + plt.plot(dates[-len(ys) :], ys, color="black", label="Time Series") plt.ylim(zoom_out(ys)) - annotate('Residuals') + annotate("Residuals") ax3 = plt.subplot(613, sharex=ax1) - ys = EWSmetrics_df['Lag-1 AC'] - plt.plot(dates[-len(ys):], ys, color='black') + ys = EWSmetrics_df["Lag-1 AC"] + plt.plot(dates[-len(ys) :], ys, color="black") plt.ylim(zoom_out(ys)) - annotate('Lag-1 AC') - tau = Kendalltau_df['Lag-1 AC'].iloc[0] - annotate(f'Kendall $\\tau = {tau:.2f}$', size=8) + annotate("Lag-1 AC") + tau = Kendalltau_df["Lag-1 AC"].iloc[0] + annotate(f"Kendall $\\tau = {tau:.2f}$", size=8) """ys = EWSmetrics_df['Lag-2 AC'] plt.plot(ys, color='navy') @@ -827,30 +1038,30 @@ def annotate(text, xy=(6 , 70), size=10): annotate(f'Kendall $\\tau = {tau:.2f}$', xy=(8, 55), size=8)""" ax4 = plt.subplot(614, sharex=ax1) - ys = EWSmetrics_df['Standard deviation'] - plt.plot(dates[-len(ys):], ys, color='black') + ys = EWSmetrics_df["Standard deviation"] + plt.plot(dates[-len(ys) :], ys, color="black") plt.ylim(zoom_out(ys)) - annotate('Standard deviation') - tau = Kendalltau_df['Standard deviation'].iloc[0] - annotate(f'Kendall $\\tau = {tau:.2f}$', size=8) + annotate("Standard deviation") + tau = Kendalltau_df["Standard deviation"].iloc[0] + annotate(f"Kendall $\\tau = {tau:.2f}$", size=8) ax5 = plt.subplot(615, sharex=ax1) - ys = EWSmetrics_df['Skewness'] - plt.plot(dates[-len(ys):], ys, color='black') + ys = EWSmetrics_df["Skewness"] + plt.plot(dates[-len(ys) :], ys, color="black") plt.ylim(zoom_out(ys)) - annotate('Skewness') - tau = Kendalltau_df['Skewness'].iloc[0] - annotate(f'Kendall $\\tau = {tau:.2f}$', size=8) + annotate("Skewness") + tau = Kendalltau_df["Skewness"].iloc[0] + annotate(f"Kendall $\\tau = {tau:.2f}$", size=8) ax6 = plt.subplot(616, sharex=ax1) - ys = EWSmetrics_df['Kurtosis'] - plt.plot(dates[-len(ys):], ys, color='black') + ys = EWSmetrics_df["Kurtosis"] + plt.plot(dates[-len(ys) :], ys, color="black") plt.ylim(zoom_out(ys)) - annotate('Kurtosis') - tau = Kendalltau_df['Kurtosis'].iloc[0] - annotate(f'Kendall $\\tau = {tau:.2f}$', size=8) + annotate("Kurtosis") + tau = Kendalltau_df["Kurtosis"].iloc[0] + annotate(f"Kendall $\\tau = {tau:.2f}$", size=8) - plt.xlabel('Time') + plt.xlabel("Time") # remove vertical space between plots plt.subplots_adjust(hspace=0.0) @@ -883,9 +1094,9 @@ def annotate(text, xy=(6 , 70), size=10): ) # save the plot - output_filename = series_name.replace(' ', '-') + '-ews.png' - print(f'Plotting {series_name} ews plots...') - plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI, bbox_inches='tight') + output_filename = series_name.replace(" ", "-") + "-ews.png" + print(f"Plotting {series_name} ews plots...") + plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI, bbox_inches="tight") plt.close(fig) @@ -903,19 +1114,23 @@ def plot_sensitivity_heatmap(series_name, df, output_dir): """ for column in df.columns: - if column == "smooth" or column=="winsize": + if column == "smooth" or column == "winsize": continue else: fig, ax = plt.subplots(figsize=(5, 5)) - piv = pd.pivot_table(df, values=column, index=["smooth"], columns=["winsize"], fill_value=0) - ax = sns.heatmap(piv, square=True,cmap='viridis',vmin=-1, vmax=1) - ax.set_title('Sensitivity for '+ column) + piv = pd.pivot_table( + df, values=column, index=["smooth"], columns=["winsize"], fill_value=0 + ) + ax = sns.heatmap(piv, square=True, cmap="viridis", vmin=-1, vmax=1) + ax.set_title("Sensitivity for " + column) plt.setp(ax.xaxis.get_majorticklabels(), rotation=90) plt.tight_layout() - plt.xlabel('Rolling Window') - plt.ylabel('Smoothing') - output_filename = series_name.replace(' ', '-') + '-' + column + '-sensitivity.png' - print(f'Plotting {series_name} {column} sensitivity plot...') + plt.xlabel("Rolling Window") + plt.ylabel("Smoothing") + output_filename = ( + series_name.replace(" ", "-") + "-" + column + "-sensitivity.png" + ) + print(f"Plotting {series_name} {column} sensitivity plot...") plt.savefig(os.path.join(output_dir, output_filename), dpi=DPI) plt.close(fig) diff --git a/pyveg/src/processor_modules.py b/pyveg/src/processor_modules.py index f84c5e10..9ae72033 100644 --- a/pyveg/src/processor_modules.py +++ b/pyveg/src/processor_modules.py @@ -3,48 +3,45 @@ that can be chained together to build a sequence. """ +import datetime import os import re import shutil import tempfile -import datetime import time +from multiprocessing import Pool +import cv2 as cv import numpy as np - from PIL import Image -import cv2 as cv - -from multiprocessing import Pool +from pyveg.src import azure_utils, batch_utils +from pyveg.src.coordinate_utils import find_coords_string +from pyveg.src.date_utils import assign_dates_to_tasks +from pyveg.src.file_utils import consolidate_json_to_list, save_image, save_json from pyveg.src.image_utils import ( - convert_to_rgb, check_image_ok, + convert_to_rgb, + create_count_heatmap, crop_image_npix, - scale_tif, - process_and_threshold, pillow_to_numpy, - create_count_heatmap -) -from pyveg.src.file_utils import ( - save_image, - save_json, - consolidate_json_to_list -) -from pyveg.src.coordinate_utils import ( - find_coords_string -) -from pyveg.src.date_utils import ( - assign_dates_to_tasks + process_and_threshold, + scale_tif, ) -from pyveg.src.subgraph_centrality import ( - subgraph_centrality, - feature_vector_metrics, -) -from pyveg.src import azure_utils -from pyveg.src import batch_utils +# from pyveg.src.coordinate_utils import find_coords_string +# from pyveg.src.date_utils import assign_dates_to_tasks +# from pyveg.src.file_utils import consolidate_json_to_list, save_image, save_json +# from pyveg.src.image_utils import ( +# check_image_ok,y +# convert_to_rgb,y +# crop_image_npix,y +# pillow_to_numpy,y +# process_and_threshold,y +# scale_tif,y +# ) from pyveg.src.pyveg_pipeline import BaseModule, logger +from pyveg.src.subgraph_centrality import feature_vector_metrics, subgraph_centrality class ProcessorModule(BaseModule): @@ -62,7 +59,7 @@ def __init__(self, name): ("dates_to_process", [list, tuple]), ("run_mode", [str]), # batch or local ("n_batch_tasks", [int]), - ("timeout", [int]) # timeout in mins for waiting for batch jobs + ("timeout", [int]), # timeout in mins for waiting for batch jobs ] def set_default_parameters(self): @@ -84,11 +81,11 @@ def set_default_parameters(self): if not "run_mode" in vars(self): self.run_mode = "local" if not "n_batch_tasks" in vars(self): - self.n_batch_tasks = -1 # as many as we need + self.n_batch_tasks = -1 # as many as we need if not "batch_task_dict" in vars(self): self.batch_task_dict = {} if not "timeout" in vars(self): - self.timeout = 30 # 1/2 hour, with nothing changing + self.timeout = 30 # 1/2 hour, with nothing changing def check_input_data_exists(self, date_string): """ @@ -275,7 +272,9 @@ def get_dependent_batch_tasks(self): sys.stdout.flush() time.sleep(1) task_dependencies.update(dependency_module.batch_task_dict) - logger.info("{} return task_dependencies {}".format(self.name, task_dependencies)) + logger.info( + "{} return task_dependencies {}".format(self.name, task_dependencies) + ) return task_dependencies def create_task_dict(self, task_id, date_list, dependencies=[]): @@ -288,7 +287,7 @@ def create_task_dict(self, task_id, date_list, dependencies=[]): return task_dict def run_batch(self): - """" + """ " Write a config json file for each set of dates. If this module depends on another module running in batch, we first get the tasks on which this modules tasks will depend on. @@ -317,7 +316,9 @@ def run_batch(self): date_strings = [ ds for ds in date_strings if self.check_input_data_exists(ds) ] - logger.info("number of date strings with input data {}".format(len(date_strings))) + logger.info( + "number of date strings with input data {}".format(len(date_strings)) + ) date_strings = [ ds for ds in date_strings if not self.check_output_data_exists(ds) ] @@ -339,7 +340,9 @@ def run_batch(self): task_dict = self.create_task_dict( "{}_{}".format(self.name, i), dates_per_task[i] ) - logger.debug("{} adding task_dict {} to list".format(self.name, task_dict)) + logger.debug( + "{} adding task_dict {} to list".format(self.name, task_dict) + ) task_dicts.append(task_dict) else: # we have a bunch of tasks from the previous Module in the Sequence @@ -377,8 +380,9 @@ def check_timeout(self, task_status): """ See how long since task_status last changed. """ - if not ("previous_task_status" in vars(self) \ - and "previous_task_status_change") in vars(self): + if not ( + "previous_task_status" in vars(self) and "previous_task_status_change" + ) in vars(self): self.previous_task_status = task_status self.previous_task_status_change = datetime.datetime.now() return False @@ -386,11 +390,11 @@ def check_timeout(self, task_status): # task status has not changed # see how long it has been since last change time_now = datetime.datetime.now() - if time_now > self.previous_task_status_change \ - + datetime.timedelta(minutes=self.timeout): + if time_now > self.previous_task_status_change + datetime.timedelta( + minutes=self.timeout + ): logger.info( - "{}: reached timeout of {} minutes since last change. Aborting"\ - .format( + "{}: reached timeout of {} minutes since last change. Aborting".format( self.name, self.timeout ) ) @@ -401,15 +405,12 @@ def check_timeout(self, task_status): self.previous_task_status_change = datetime.datetime.now() return False - def check_if_finished(self): if self.run_mode == "local": return self.is_finished elif self.parent and self.parent.batch_job_id: job_id = self.parent.batch_job_id - task_status = batch_utils.check_tasks_status( - job_id, self.name - ) + task_status = batch_utils.check_tasks_status(job_id, self.name) logger.info( "{} job status: success: {} failed: {} running: {} waiting: {} cannot_run: {}".format( @@ -418,14 +419,16 @@ def check_if_finished(self): task_status["num_failed"], task_status["num_running"], task_status["num_waiting"], - task_status["num_cannot_run"] + task_status["num_cannot_run"], ) ) self.run_status["succeeded"] = task_status["num_success"] - self.run_status["failed"] = task_status["num_failed"] + task_status["num_cannot_run"] + self.run_status["failed"] = ( + task_status["num_failed"] + task_status["num_cannot_run"] + ) num_incomplete = task_status["num_running"] + task_status["num_waiting"] self.run_status["incomplete"] = num_incomplete - self.is_finished = (num_incomplete == 0) + self.is_finished = num_incomplete == 0 # if we have exceeded timeout, say that we are finished. if self.check_timeout(task_status): @@ -459,7 +462,7 @@ def __init__(self, name=None): ("region_size", [float]), ("RGB_bands", [list]), ("split_RGB_images", [bool]), - ("ndvi",[bool]) + ("ndvi", [bool]), ] def set_default_parameters(self): @@ -651,14 +654,17 @@ def process_single_date(self, date_string): if self.ndvi: # save the NDVI image ndvi_tif = self.get_file( - self.join_path(input_filepath, "download.NDVI.tif"), self.input_location_type + self.join_path(input_filepath, "download.NDVI.tif"), + self.input_location_type, ) ndvi_image = scale_tif(ndvi_tif) ndvi_filepath = self.construct_image_savepath( date_string, coords_string, "NDVI" ) self.save_image( - ndvi_image, os.path.dirname(ndvi_filepath), os.path.basename(ndvi_filepath) + ndvi_image, + os.path.dirname(ndvi_filepath), + os.path.basename(ndvi_filepath), ) # preprocess and threshold the NDVI image @@ -673,7 +679,9 @@ def process_single_date(self, date_string): ) # split and save sub-images - self.split_and_save_sub_images(ndvi_image, date_string, coords_string, "NDVI") + self.split_and_save_sub_images( + ndvi_image, date_string, coords_string, "NDVI" + ) self.split_and_save_sub_images( processed_ndvi, date_string, coords_string, "BWNDVI" @@ -682,7 +690,8 @@ def process_single_date(self, date_string): if self.count: # save the COUNT image count_tif = self.get_file( - self.join_path(input_filepath, "download.COUNT.tif"), self.input_location_type + self.join_path(input_filepath, "download.COUNT.tif"), + self.input_location_type, ) count_image = create_count_heatmap(count_tif) @@ -690,13 +699,15 @@ def process_single_date(self, date_string): date_string, coords_string, "COUNT" ) self.save_image( - count_image, os.path.dirname(count_filepath), os.path.basename(count_filepath) + count_image, + os.path.dirname(count_filepath), + os.path.basename(count_filepath), ) # split and save sub-images - self.split_and_save_sub_images(count_image, date_string, coords_string, "COUNT") - - + self.split_and_save_sub_images( + count_image, date_string, coords_string, "COUNT" + ) return True @@ -744,7 +755,8 @@ def process_single_date(self, date_string): name_variable = (filename.split("."))[1] variable_array = cv.imread( self.get_file( - self.join_path(input_location, filename), self.input_location_type + self.join_path(input_location, filename), + self.input_location_type, ), cv.IMREAD_ANYDEPTH, ) diff --git a/pyveg/src/pyveg_pipeline.py b/pyveg/src/pyveg_pipeline.py index 2464361d..da4dbe6a 100644 --- a/pyveg/src/pyveg_pipeline.py +++ b/pyveg/src/pyveg_pipeline.py @@ -13,13 +13,15 @@ the results of the different SEQUENCES into one output file. """ -import os import json +import logging +import os import subprocess import time - -import logging from logging.handlers import RotatingFileHandler +from shutil import copyfile + +from pyveg.src.file_utils import save_json logger = logging.getLogger("pyveg_logger") formatter = logging.Formatter("%(asctime)s [%(levelname)s] %(message)s") @@ -29,7 +31,8 @@ c_handler.setFormatter(formatter) f_handler = RotatingFileHandler( "pyveg_{}.log".format(time.strftime("%Y-%m-%d_%H-%M-%S")), - maxBytes=5 * 1024 * 1024, backupCount=10 + maxBytes=5 * 1024 * 1024, + backupCount=10, ) f_handler.setFormatter(formatter) @@ -37,15 +40,8 @@ logger.addHandler(c_handler) - - -from pyveg.src.file_utils import save_json - -from shutil import copyfile - try: - from pyveg.src import azure_utils - from pyveg.src import batch_utils + from pyveg.src import azure_utils, batch_utils except: print("Azure utils could not be imported - is Azure SDK installed?") @@ -146,7 +142,6 @@ def cleanup(self): sequence.cleanup() - class Sequence(object): """ A Sequence is a collection of Modules where the output of one module is @@ -271,15 +266,14 @@ def run(self): dependencies_finished = num_seq_finished == len(self.depends_on) logger.info( "{}: {} / {} dependencies finished".format( - self.name, - num_seq_finished, len(self.depends_on) + self.name, num_seq_finished, len(self.depends_on) ) ) time.sleep(10) self.create_batch_job_if_needed() for module in self.modules: - self.run_status[module.name] = module.run() + self.run_status[module.name] = module.run() def __repr__(self): if not self.is_configured: @@ -527,8 +521,10 @@ def copy_to_output_location(self, tmpdir, output_location, file_endings=[]): for ending in file_endings: if filename.endswith(ending): - copyfile(os.path.join(root,filename), - os.path.join(output_location,filename)) + copyfile( + os.path.join(root, filename), + os.path.join(output_location, filename), + ) else: subprocess.run( [ @@ -651,7 +647,6 @@ def save_config(self, config_location): json.dump(config_dict, output_json) logger.info("{}: wrote config to {}".format(self.name, config_location)) - def print_run_status(self): """ Print out how many jobs succeeded or failed @@ -661,6 +656,6 @@ def print_run_status(self): self.name, self.run_status["succeeded"], self.run_status["failed"], - self.run_status["incomplete"] - ) + self.run_status["incomplete"], ) + ) diff --git a/pyveg/src/subgraph_centrality.py b/pyveg/src/subgraph_centrality.py index 7a3654bd..49b0300a 100644 --- a/pyveg/src/subgraph_centrality.py +++ b/pyveg/src/subgraph_centrality.py @@ -14,13 +14,14 @@ https://arxiv.org/pdf/cond-mat/0504730.pdf """ +import argparse + +import igraph import numpy as np from PIL import Image from scipy import spatial -import argparse -import igraph -from .image_utils import image_from_array, image_file_to_array +from .image_utils import image_file_to_array, image_from_array def make_graph(adj_matrix): diff --git a/pyveg/src/zenodo_utils.py b/pyveg/src/zenodo_utils.py index 837fbfce..8626dea8 100644 --- a/pyveg/src/zenodo_utils.py +++ b/pyveg/src/zenodo_utils.py @@ -15,20 +15,23 @@ with "sandbox.zenodo.org" in the URLs, and put the token into a file named "zenodo_test_api_token" then call the functions in this module with the "test" argument set to True. """ -import os -import shutil import json +import os import re -import requests +import shutil import tempfile -from zipfile import ZipFile, BadZipFile +from zipfile import BadZipFile, ZipFile + +import requests -from pyveg.src.file_utils import get_filepath_after_directory from pyveg.src.coordinate_utils import find_coords_string -ZENODO_CONFIG_FOUND=False +from pyveg.src.file_utils import get_filepath_after_directory + +ZENODO_CONFIG_FOUND = False try: import pyveg.zenodo_config as config - ZENODO_CONFIG_FOUND=True + + ZENODO_CONFIG_FOUND = True except: pass @@ -47,7 +50,9 @@ def get_base_url_and_token(test=False): api_token: str, the personal access token, read from a file. """ if not ZENODO_CONFIG_FOUND: - raise RuntimeError("File zenodo_config.py not found - will not be able to access the Zenodo API") + raise RuntimeError( + "File zenodo_config.py not found - will not be able to access the Zenodo API" + ) if test: base_url = config.test_api_credentials["base_url"] token = config.test_api_credentials["api_token"] @@ -66,7 +71,7 @@ def get_deposition_id(json_or_csv="json", test=False): credentials = config.test_api_credentials else: - credentials = config.prod_api_credentials + credentials = config.prod_api_credentials if json_or_csv == "json": return credentials["deposition_id_summary_json"] else: @@ -86,8 +91,9 @@ def list_depositions(test=False): r: list of dicts, response from the API with info about the depositions """ base_url, api_token = get_base_url_and_token(test) - r = requests.get('{}/deposit/depositions'.format(base_url), - params={'access_token': api_token}) + r = requests.get( + "{}/deposit/depositions".format(base_url), params={"access_token": api_token} + ) if r.status_code != 200: print("Error retrieving depositions", r.content) return False @@ -108,11 +114,13 @@ def create_deposition(test=False): """ headers = {"Content-Type": "application/json"} base_url, api_token = get_base_url_and_token(test) - params = {'access_token': api_token} - r = requests.post('{}/deposit/depositions'.format(base_url), - params=params, - json={}, - headers=headers) + params = {"access_token": api_token} + r = requests.post( + "{}/deposit/depositions".format(base_url), + params=params, + json={}, + headers=headers, + ) if r.status_code != 201: print("Error creating deposition", r.content) return None @@ -134,11 +142,13 @@ def get_deposition_info(deposition_id, test=False): """ headers = {"Content-Type": "application/json"} base_url, api_token = get_base_url_and_token(test) - params = {'access_token': api_token} - r = requests.get('{}/deposit/depositions/{}'.format(base_url, deposition_id), - params=params, - json={}, - headers=headers) + params = {"access_token": api_token} + r = requests.get( + "{}/deposit/depositions/{}".format(base_url, deposition_id), + params=params, + json={}, + headers=headers, + ) if r.status_code != 200: print("Error getting deposition", r.content) return {} @@ -183,9 +193,11 @@ def upload_file(filename, deposition_id, test=False): bucket_url = get_bucket_url(deposition_id, test) with open(filename, "rb") as f: - r = requests.put("{}/{}".format(bucket_url, os.path.basename(filename)), - data=f, - params = {'access_token': api_token}) + r = requests.put( + "{}/{}".format(bucket_url, os.path.basename(filename)), + data=f, + params={"access_token": api_token}, + ) if r.status_code != 200: print("Error uploading file", r.content) return False @@ -210,8 +222,10 @@ def list_files(deposition_id, json_or_csv="json", test=False): base_url, api_token = get_base_url_and_token(test) deposition_id = get_deposition_id(json_or_csv, test=test) - r = requests.get("{}/deposit/depositions/{}/files".format(base_url, deposition_id), - params={"access_token": api_token}) + r = requests.get( + "{}/deposit/depositions/{}/files".format(base_url, deposition_id), + params={"access_token": api_token}, + ) if r.status_code != 200: print("Error getting file list for deposition {}".format(deposition_id)) return [f["filename"] for f in r.json()] @@ -234,8 +248,10 @@ def download_file(filename, deposition_id, destination_path=".", test=False): """ base_url, api_token = get_base_url_and_token(test) bucket_url = get_bucket_url(deposition_id, test) - r = requests.get("{}/{}".format(bucket_url, os.path.basename(filename)), - params = {'access_token': api_token}) + r = requests.get( + "{}/{}".format(bucket_url, os.path.basename(filename)), + params={"access_token": api_token}, + ) if r.status_code != 200: print("Error downloading file", r.content) return {} @@ -261,8 +277,10 @@ def delete_file(filename, deposition_id, test=False): True if file was deleted OK, False otherwise. """ base_url, api_token = get_base_url_and_token(test) - r = requests.delete("{}/deposit/depositions/{}/files/{}".format(base_url, deposition_id, filename), - params = {'access_token': api_token}) + r = requests.delete( + "{}/deposit/depositions/{}/files/{}".format(base_url, deposition_id, filename), + params={"access_token": api_token}, + ) if r.status_code != 204: print("Error deleting file", r.content) @@ -291,16 +309,20 @@ def upload_standard_metadata(deposition_id, json_or_csv="json", test=False): else: metadata_dict = config.metadata_dict_ts_csv base_url, api_token = get_base_url_and_token(test) - r = requests.put("{}/deposit/depositions/{}".format(base_url, deposition_id), - params={"access_token": api_token}, - json=metadata_dict) + r = requests.put( + "{}/deposit/depositions/{}".format(base_url, deposition_id), + params={"access_token": api_token}, + json=metadata_dict, + ) if r.status_code != 200: print("Error uploading metadata", r.content) return False return r.json() -def upload_custom_metadata(title, upload_type, description, creators, deposition_id, test=False): +def upload_custom_metadata( + title, upload_type, description, creators, deposition_id, test=False +): """ Upload a dict to the deposition containing metadata with the format: @@ -331,13 +353,15 @@ def upload_custom_metadata(title, upload_type, description, creators, deposition "title": title, "upload_type": upload_type, "description": description, - "creators": creators - } + "creators": creators, + } } base_url, api_token = get_base_url_and_token(test) - r = requests.put("{}/deposit/depositions/{}".format(base_url, deposition_id), - params={"access_token": api_token}, - json=metadata_dict) + r = requests.put( + "{}/deposit/depositions/{}".format(base_url, deposition_id), + params={"access_token": api_token}, + json=metadata_dict, + ) if r.status_code != 200: print("Error uploading metadata", r.content) return False @@ -349,8 +373,10 @@ def publish_deposition(deposition_id, test=False): Submit the deposition, so it will be findable on Zenodo and have a DOI. """ base_url, api_token = get_base_url_and_token(test) - r = requests.post("{}/deposit/depositions/{}/actions/publish".format(base_url, deposition_id), - params={"access_token": api_token}) + r = requests.post( + "{}/deposit/depositions/{}/actions/publish".format(base_url, deposition_id), + params={"access_token": api_token}, + ) if r.status_code != 202: print("Error publishing", r.content) return False @@ -362,19 +388,23 @@ def unlock_deposition(deposition_id, test=False): Unlock a previously submitted deposition, so we can add to it. """ base_url, api_token = get_base_url_and_token(test) - r = requests.post("{}/deposit/depositions/{}/actions/edit".format(base_url, deposition_id), - params={"access_token": api_token}) + r = requests.post( + "{}/deposit/depositions/{}/actions/edit".format(base_url, deposition_id), + params={"access_token": api_token}, + ) if r.status_code != 201: print("Error unlocking", r.content) return False return r.json() -def prepare_results_zipfile(collection_name, - png_location, - png_location_type="local", - json_location=None, - json_location_type="local"): +def prepare_results_zipfile( + collection_name, + png_location, + png_location_type="local", + json_location=None, + json_location_type="local", +): """ Create a zipfile called containing the 'results_summary.json', and the outputs of the analysis. @@ -393,7 +423,7 @@ def prepare_results_zipfile(collection_name, zip_filename: str, location of the produced zipfile """ tmpdir = tempfile.mkdtemp() - zip_filename = os.path.join(tmpdir,"results_") + zip_filename = os.path.join(tmpdir, "results_") if find_coords_string(png_location): zip_filename += find_coords_string(png_location) + "_" zip_filename += collection_name + ".zip" @@ -406,13 +436,19 @@ def prepare_results_zipfile(collection_name, raise RuntimeError("{} is not a directory".format(json_location)) dir_contents = os.listdir(json_location) if not os.path.exists(os.path.join(json_location, "results_summary.json")): - raise RuntimeError("Could not find results_summary.json in {}".format(json_location)) - zf.write(os.path.join(json_location, "results_summary.json"), - arcname="results_summary.json") + raise RuntimeError( + "Could not find results_summary.json in {}".format(json_location) + ) + zf.write( + os.path.join(json_location, "results_summary.json"), + arcname="results_summary.json", + ) if png_location_type == "local": if not os.path.exists(os.path.join(png_location, "analysis")): raise RuntimeError("Could not find analysis dir in {}".format(png_location)) - for root, dirnames, filenames in os.walk(os.path.join(png_location, "analysis")): + for root, dirnames, filenames in os.walk( + os.path.join(png_location, "analysis") + ): for filename in filenames: full_filepath = os.path.join(root, filename) short_filepath = get_filepath_after_directory(full_filepath, "analysis") @@ -420,6 +456,7 @@ def prepare_results_zipfile(collection_name, zf.close() return zip_filename + def get_results_summary_json(coords_string, collection, deposition_id, test=False): """ Assuming the zipfile is named following the convention @@ -429,7 +466,11 @@ def get_results_summary_json(coords_string, collection, deposition_id, test=Fals """ zip_filename = "results_{}_{}.zip".format(coords_string, collection) if not zip_filename in list_files(deposition_id, test): - print("Unable to find file {} in deposition {}".format(zip_filename, deposition_id)) + print( + "Unable to find file {} in deposition {}".format( + zip_filename, deposition_id + ) + ) return None data = {} @@ -444,8 +485,9 @@ def get_results_summary_json(coords_string, collection, deposition_id, test=Fals return json.loads(data) - -def download_results_by_coord_id(coords_id, json_or_csv="json", destination_path=None, deposition_id=None, test=False): +def download_results_by_coord_id( + coords_id, json_or_csv="json", destination_path=None, deposition_id=None, test=False +): """ Search the deposition (defined by the deposition_id in zenodo_config.py) for results_summary json or summary_stats csv files beginning with 'coord_id' @@ -460,7 +502,7 @@ def download_results_by_coord_id(coords_id, json_or_csv="json", destination_path test: bool, if True, use the sandbox Zenodo repository """ # coords_id should be two digits, e.g. '00' - if not re.search('[\d]{2}', coords_id): + if not re.search("[\d]{2}", coords_id): raise RuntimeError("coords_id should be a 2-digit string") if not deposition_id: deposition_id = get_deposition_id(json_or_csv, test=test) @@ -469,9 +511,12 @@ def download_results_by_coord_id(coords_id, json_or_csv="json", destination_path elif not os.path.exists(destination_path): os.makedirs(destination_path) # list the files in the deposition - file_list = [f for f in list_files(deposition_id, test=test) \ - if f.startswith(coords_id) and "results_summary" in f] - if len(file_list)==0: + file_list = [ + f + for f in list_files(deposition_id, test=test) + if f.startswith(coords_id) and "results_summary" in f + ] + if len(file_list) == 0: print("No files for coords_id {} found.".format(coords_id)) return "" # files should follow the same naming convention, and have the date at the end. diff --git a/pyveg/testdata/ERA5/test_json/2018-03-01/JSON/WEATHER/weather_data.json b/pyveg/testdata/ERA5/test_json/2018-03-01/JSON/WEATHER/weather_data.json index 1cce38b4..383f74af 100644 --- a/pyveg/testdata/ERA5/test_json/2018-03-01/JSON/WEATHER/weather_data.json +++ b/pyveg/testdata/ERA5/test_json/2018-03-01/JSON/WEATHER/weather_data.json @@ -3,4 +3,4 @@ "mean_2m_air_temperature": 295.2695617675781, "total_precipitation": 0.0 } -} \ No newline at end of file +} diff --git a/pyveg/testdata/Sentinel2/test_json/2018-03-01/JSON/NC/network_centralities.json b/pyveg/testdata/Sentinel2/test_json/2018-03-01/JSON/NC/network_centralities.json index c8aa9d3b..a9b8df2a 100644 --- a/pyveg/testdata/Sentinel2/test_json/2018-03-01/JSON/NC/network_centralities.json +++ b/pyveg/testdata/Sentinel2/test_json/2018-03-01/JSON/NC/network_centralities.json @@ -373,4 +373,4 @@ "veg_ndvi_mean": 22.5017, "veg_ndvi_std": 4.3913 } -] \ No newline at end of file +] diff --git a/pyveg/testdata/gee_labyrinths_summary.json b/pyveg/testdata/gee_labyrinths_summary.json index 4e00a1e9..89474633 100644 --- a/pyveg/testdata/gee_labyrinths_summary.json +++ b/pyveg/testdata/gee_labyrinths_summary.json @@ -189048,4 +189048,4 @@ } } } -} \ No newline at end of file +} diff --git a/pyveg/testdata/network_json_data/analysis_report_-5.92_15.57_Sentinel2.md b/pyveg/testdata/network_json_data/analysis_report_-5.92_15.57_Sentinel2.md new file mode 100644 index 00000000..9e0be8aa --- /dev/null +++ b/pyveg/testdata/network_json_data/analysis_report_-5.92_15.57_Sentinel2.md @@ -0,0 +1,38 @@ + +Results for Sentinel2 and coordinates -5.92 (longitude) and 15.57 (latitude) +============================================================================ + +Contents +======== + +* [Time series](#time-series) +* [STL decomposition](#stl-decomposition) +* [Early warnings analysis](#early-warnings-analysis) +* [Average annual time series CB fit](#average-annual-time-series-cb-fit) +* [RGB images through time](#rgb-images-through-time) + +# Time series + +![Time series Offset50](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/time-series/S2-time-series_smooth.png) +![Time series NDVI](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/time-series/S2-ndvi-time-series.png) + +# STL decomposition + +![STL Offset50](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/detrended/STL/S2_offset50_mean_STL_decomposition.png) +![STL NDVI](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/detrended/STL/S2_ndvi_mean_STL_decomposition.png) + +# Early warnings analysis + +![EWS Offset50](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/resiliance/deseasonalised/ewstools/S2-offset50-mean-ews.png) + +![EWS NDVI](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/resiliance/deseasonalised/ewstools/S2-ndvi-mean-ews.png) + +# Average annual time series CB fit + +![Offset50 CB fit](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/fit_ts_CB_S2_offset50_mean.png) + +![NDVI CB fit](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/fit_ts_CB_S2_ndvi_mean.png) + +![total precipitation CB fit](/Users/a.smith/Library/CloudStorage/OneDrive-TheAlanTuringInstitute/Documents/code/urbangrammarai/gee_pipeline/pyveg/tests/../testdata/network_json_data/analysis/fit_ts_CB_total_precipitation.png) + +# RGB images through time diff --git a/pyveg/testdata/network_json_data/results_summary.json b/pyveg/testdata/network_json_data/results_summary.json index 41eba7be..60df6624 100644 --- a/pyveg/testdata/network_json_data/results_summary.json +++ b/pyveg/testdata/network_json_data/results_summary.json @@ -1 +1 @@ -{"metadata": {"start_date": "2015-01-01", "end_date": "2020-09-02", "time_per_point": "1m", "longitude": -5.92, "latitude": 15.57, "collection": "COPERNICUS/S2", "num_data_points": 56, "config_filename": "config_49_Sentinel2_15.57N_-5.92E_Mauritania_2015-01-01_2020-09-02_1m_batch.py"}, "COPERNICUS/S2": {"type": "vegetation", "time-series-data": {"2015-07-15": [{"slope": -54.1, "offset": -1082.0, "offset50": -640.0, "mean": -456.7, "std": 343.61389669220307, "latitude": 2.6377, "longitude": 13.1086, "date": "2015-07-15", "feature_vec": [0.0, -31.0, -59.0, -71.0, -116.0, -130.0, -221.0, -293.0, -311.0, -362.0, -442.0, -490.0, -539.0, -638.0, -734.0, -808.0, -874.0, -927.0, -1006.0, -1082.0]}, {"slope": -51.3, 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0.124627485871315}, "2018-08-28": {"total_precipitation": 0.06945662200450897, "mean_2m_air_temperature": 302.12506103515625}, "2018-09-27": {"total_precipitation": 0.013370160013437271, "mean_2m_air_temperature": 304.2967834472656}, "2018-10-27": {"mean_2m_air_temperature": 301.0340576171875, "total_precipitation": 1.7881393432617188e-07}, "2018-11-26": {"total_precipitation": 0.0, "mean_2m_air_temperature": 297.1903076171875}, "2018-12-26": {"mean_2m_air_temperature": 297.2773132324219, "total_precipitation": 0.0}, "2019-01-25": {"total_precipitation": 0.0, "mean_2m_air_temperature": 299.10546875}, "2019-02-24": {"total_precipitation": 0.0, "mean_2m_air_temperature": 304.4804382324219}, "2019-03-26": {"mean_2m_air_temperature": 307.6292724609375, "total_precipitation": 0.00036898069083690643}, "2019-04-25": {"total_precipitation": 0.016424482688307762, "mean_2m_air_temperature": 307.8606872558594}, "2019-05-25": {"mean_2m_air_temperature": 305.1732482910156, "total_precipitation": 0.03664827346801758}, "2019-06-24": {"total_precipitation": 0.05319624021649361, "mean_2m_air_temperature": 302.4949645996094}, "2019-07-24": {"total_precipitation": 0.19292894005775452, "mean_2m_air_temperature": 300.8216247558594}, "2019-08-23": {"mean_2m_air_temperature": 302.8372802734375, "total_precipitation": 0.04268037527799606}, "2019-09-22": {"total_precipitation": 0.043634213507175446, "mean_2m_air_temperature": 303.1981506347656}, "2019-10-22": {"total_precipitation": -1.7881393432617188e-07, "mean_2m_air_temperature": 302.6445007324219}, "2019-12-04": {"mean_2m_air_temperature": 298.11328125, "total_precipitation": 0.0}}}} diff --git a/pyveg/testdata/network_json_data/test-results-summary.json b/pyveg/testdata/network_json_data/test-results-summary.json index 77d3b4b7..a3141c71 100644 --- a/pyveg/testdata/network_json_data/test-results-summary.json +++ b/pyveg/testdata/network_json_data/test-results-summary.json @@ -3918,4 +3918,4 @@ } } } -} \ No newline at end of file +} diff --git a/pyveg/testdata/test.gif b/pyveg/testdata/test.gif index a81f483f..424f2d06 100644 Binary files a/pyveg/testdata/test.gif and b/pyveg/testdata/test.gif differ diff --git a/pyveg/tests/test_analyse_gee_data.py b/pyveg/tests/test_analyse_gee_data.py index b35fb413..3132b1e8 100644 --- a/pyveg/tests/test_analyse_gee_data.py +++ b/pyveg/tests/test_analyse_gee_data.py @@ -1,9 +1,10 @@ """ Test the functions in analyse_gee_data.py """ +import json import os import shutil -import json + from pyveg.scripts.analyse_gee_data import analyse_gee_data diff --git a/pyveg/tests/test_analysis_preprocessing.py b/pyveg/tests/test_analysis_preprocessing.py index 8ff0e1d7..440013d3 100644 --- a/pyveg/tests/test_analysis_preprocessing.py +++ b/pyveg/tests/test_analysis_preprocessing.py @@ -1,12 +1,12 @@ """ Test the functions in analysis_preprocessing.py """ -import os import json +import os from pyveg.src.analysis_preprocessing import ( - read_results_summary, read_json_to_dataframes, + read_results_summary, ) diff --git a/pyveg/tests/test_azure_utils.py b/pyveg/tests/test_azure_utils.py index c3eb4396..df99c987 100644 --- a/pyveg/tests/test_azure_utils.py +++ b/pyveg/tests/test_azure_utils.py @@ -1,7 +1,7 @@ import unittest -import pytest -import PIL +import PIL +import pytest from pyveg.src.azure_utils import * diff --git a/pyveg/tests/test_combiner_modules.py b/pyveg/tests/test_combiner_modules.py index 0ad5456c..d2730323 100644 --- a/pyveg/tests/test_combiner_modules.py +++ b/pyveg/tests/test_combiner_modules.py @@ -3,9 +3,10 @@ e.g. vegetation images and weather, to produce one output json file. """ +import json import os import shutil -import json +import unittest from pyveg.src.combiner_modules import VegAndWeatherJsonCombiner @@ -15,6 +16,11 @@ def test_instantiate_combiner(): assert VegAndWeatherJsonCombiner +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a CI - waiting on a fix for #19. " + "https://github.com/urbangrammarai/gee_pipeline/issues/19", +) def test_combine(): input_veg_dir = os.path.join( os.path.dirname(__file__), "..", "testdata", "Sentinel2", "test_json" diff --git a/pyveg/tests/test_data_analysis_utils.py b/pyveg/tests/test_data_analysis_utils.py index b35c3855..7b3b309c 100644 --- a/pyveg/tests/test_data_analysis_utils.py +++ b/pyveg/tests/test_data_analysis_utils.py @@ -2,12 +2,12 @@ Test the functions in data_analysis_utils.py """ +import json import os import shutil -import json -from pyveg.src.data_analysis_utils import * from pyveg.src.analysis_preprocessing import * +from pyveg.src.data_analysis_utils import * def test_coarse_dataframe(): diff --git a/pyveg/tests/test_download_modules.py b/pyveg/tests/test_download_modules.py index 53ea1ef5..d278e9dd 100644 --- a/pyveg/tests/test_download_modules.py +++ b/pyveg/tests/test_download_modules.py @@ -1,39 +1,51 @@ import os import shutil +import unittest import pytest -import unittest if os.name == "posix": TMPDIR = "/tmp/" else: TMPDIR = "%TMP%" -if not os.environ.get("TRAVIS") == "true": +if not os.environ.get("CI") == "true": from pyveg.src.download_modules import VegetationDownloader, WeatherDownloader -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_instantiate_vegetation_downloader(): veg_downloader = VegetationDownloader("Sentinel2") assert isinstance(veg_downloader, VegetationDownloader) -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_veg_downloader_unconfigured_exception(): veg_downloader = VegetationDownloader("Sentinel2") with pytest.raises(RuntimeError): veg_downloader.run() -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_veg_downloader_variables_not_set_exception(): veg_downloader = VegetationDownloader("Sentinel2") with pytest.raises(RuntimeError): veg_downloader.configure() -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_veg_downloader_configure_sentinel2(): veg_downloader = VegetationDownloader("Sentinel2") veg_downloader.data_type = "vegetation" @@ -51,7 +63,10 @@ def test_veg_downloader_configure_sentinel2(): assert veg_downloader.is_configured == True -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_veg_downloader_run_sentinel2(): veg_downloader = VegetationDownloader("Sentinel2") veg_downloader.data_type = "vegetation" @@ -79,27 +94,39 @@ def test_veg_downloader_run_sentinel2(): shutil.rmtree(tif_dir, ignore_errors=True) -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_instantiate_weather_downloader(): weather_downloader = WeatherDownloader("ERA5") assert isinstance(weather_downloader, WeatherDownloader) -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_weather_downloader_unconfigured_exception(): weather_downloader = WeatherDownloader("ERA5") with pytest.raises(RuntimeError): weather_downloader.run() -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_weather_downloader_variables_not_set_exception(): weather_downloader = WeatherDownloader("ERA5") with pytest.raises(RuntimeError): weather_downloader.configure() -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_weather_downloader_configure_era5(): weather_downloader = WeatherDownloader("ERA5") weather_downloader.data_type = "weather" @@ -113,7 +140,10 @@ def test_weather_downloader_configure_era5(): assert weather_downloader.is_configured == True -@unittest.skipIf(os.environ.get("TRAVIS") == "true", "Skipping this test on Travis CI.") +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a Continuous Integration environment.", +) def test_weather_downloader_run_era5(): weather_downloader = WeatherDownloader("ERA5") weather_downloader.data_type = "weather" diff --git a/pyveg/tests/test_image_utils.py b/pyveg/tests/test_image_utils.py index 5172f29e..4d78e53e 100644 --- a/pyveg/tests/test_image_utils.py +++ b/pyveg/tests/test_image_utils.py @@ -3,9 +3,11 @@ """ import os + +import igraph import numpy as np + from pyveg.src.image_utils import * -import igraph def test_image_all_white(): diff --git a/pyveg/tests/test_pattern_gen.py b/pyveg/tests/test_pattern_gen.py index b78f2aa9..d1b87dd3 100644 --- a/pyveg/tests/test_pattern_gen.py +++ b/pyveg/tests/test_pattern_gen.py @@ -2,8 +2,9 @@ Tests for the functions and methods in pattern_generation.py """ import os -import pytest + import numpy as np +import pytest from pyveg.src.pattern_generation import PatternGenerator as PG diff --git a/pyveg/tests/test_pipeline_core.py b/pyveg/tests/test_pipeline_core.py index 90b2d76d..d4ad41ca 100644 --- a/pyveg/tests/test_pipeline_core.py +++ b/pyveg/tests/test_pipeline_core.py @@ -2,7 +2,7 @@ Tests of the core functionality of pipelines, sequences, and modules. """ -from pyveg.src.pyveg_pipeline import Pipeline, Sequence, BaseModule +from pyveg.src.pyveg_pipeline import BaseModule, Pipeline, Sequence def test_instantiate_pipeline(): diff --git a/pyveg/tests/test_processor_modules.py b/pyveg/tests/test_processor_modules.py index 27fb3cfe..f0120c57 100644 --- a/pyveg/tests/test_processor_modules.py +++ b/pyveg/tests/test_processor_modules.py @@ -2,19 +2,24 @@ Tests for the modules that process the images downloaded from GEE """ -import os -import pytest import json +import os import shutil +import unittest from pyveg.src.processor_modules import ( - VegetationImageProcessor, - NetworkCentralityCalculator, NDVICalculator, + NetworkCentralityCalculator, + VegetationImageProcessor, WeatherImageToJSON, ) +@unittest.skipIf( + os.environ.get("CI") == "true", + "Skipping this test in a CI - waiting on a fix for #20. " + "https://github.com/urbangrammarai/gee_pipeline/issues/20", +) def test_Sentinel2_image_processor(): """ Should combine tif files into RGB, NDVI, and BWNDVI diff --git a/pyveg/tests/test_sc.py b/pyveg/tests/test_sc.py index 80201f98..e5c64da5 100644 --- a/pyveg/tests/test_sc.py +++ b/pyveg/tests/test_sc.py @@ -3,9 +3,11 @@ """ import os + +import igraph import numpy as np + from pyveg.src.subgraph_centrality import * -import igraph IMG_FILE = os.path.join(os.path.dirname(__file__), "..", "testdata", "binary_image.txt") FULL_IMG = text_file_to_array(IMG_FILE) diff --git a/pyveg/zenodo_config_template.py b/pyveg/zenodo_config_template.py index b7c86998..12dc9394 100644 --- a/pyveg/zenodo_config_template.py +++ b/pyveg/zenodo_config_template.py @@ -13,24 +13,24 @@ metadata_dict = { - "metadata": { - "title": - "upload_type": "dataset", - "description": <description>, - "creators": [ - {"name": <name>, "affiliation": <affiliation>}, - ] - } + "metadata": { + "title": < title > + "upload_type": "dataset", + "description": < description > , + "creators": [ + {"name": < name > , "affiliation": < affiliation >}, + ] + } } test_api_credentials = { "base_url": "https://sandbox.zenodo.org/api/", - "api_token": <api_token>, + "api_token": < api_token > , "deposition_id": None } prod_api_credentials = { "base_url": "https://zenodo.org/api/", - "api_token": <api_token> + "api_token": < api_token > "deposition_id": None } diff --git a/setup.py b/setup.py index bb170fd7..e7bf97bd 100644 --- a/setup.py +++ b/setup.py @@ -11,23 +11,21 @@ author="Nick Barlow, Camila Rangel Smith and Samuel Van Stroud", license="MIT", include_package_data=True, - packages=["pyveg", - "pyveg.src", - "pyveg.scripts", - "pyveg.configs"], + packages=["pyveg", "pyveg.src", "pyveg.scripts", "pyveg.configs"], install_requires=REQUIRED_PACKAGES, scripts=["pyveg/scripts/batch_commands.sh"], - entry_points={"console_scripts": [ - "pyveg_calc_EC=pyveg.scripts.calc_euler_characteristic:main", - "pyveg_gen_pattern=pyveg.scripts.generate_pattern:main", - "pyveg_gee_analysis=pyveg.scripts.analyse_gee_data:main", - "pyveg_run_pipeline=pyveg.scripts.run_pyveg_pipeline:main", - "pyveg_run_module=pyveg.scripts.run_pyveg_module:main", - "pyveg_azure_download=pyveg.scripts.download_from_azure:main", - "pyveg_zenodo_upload=pyveg.scripts.upload_to_zenodo:main", - "pyveg_generate_config=pyveg.scripts.generate_config_file:main", - "pyveg_create_analysis_report=pyveg.scripts.create_analysis_report:main", - "pyveg_analysis_summary_data=pyveg.scripts.analyse_pyveg_summary_data:main" - - ]}, + entry_points={ + "console_scripts": [ + "pyveg_calc_EC=pyveg.scripts.calc_euler_characteristic:main", + "pyveg_gen_pattern=pyveg.scripts.generate_pattern:main", + "pyveg_gee_analysis=pyveg.scripts.analyse_gee_data:main", + "pyveg_run_pipeline=pyveg.scripts.run_pyveg_pipeline:main", + "pyveg_run_module=pyveg.scripts.run_pyveg_module:main", + "pyveg_azure_download=pyveg.scripts.download_from_azure:main", + "pyveg_zenodo_upload=pyveg.scripts.upload_to_zenodo:main", + "pyveg_generate_config=pyveg.scripts.generate_config_file:main", + "pyveg_create_analysis_report=pyveg.scripts.create_analysis_report:main", + "pyveg_analysis_summary_data=pyveg.scripts.analyse_pyveg_summary_data:main", + ] + }, ) diff --git a/.travis.yml b/travis.yml.legacy similarity index 97% rename from .travis.yml rename to travis.yml.legacy index 016222e8..f59359d0 100644 --- a/.travis.yml +++ b/travis.yml.legacy @@ -32,4 +32,4 @@ after_failure: - cat config.log after_success: - - echo "All tests passed!" \ No newline at end of file + - echo "All tests passed!"