add readthedocs documentation and sphinx builder

.gitignore

@@ -3,3 +3,4 @@
 __pycache__/
 files/loaded-data/
 .vscode/
+docs/build/

.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+
+sphinx:
+  configuration: docs/source/conf.py
+
+formats:
+  - pdf
+  - epub

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx-rtd-theme
+sphinx-autodoc-typehints
+stingray

docs/source/DataLoading.rst

@@ -0,0 +1,21 @@
+DataLoading package
+===================
+
+Submodules
+----------
+
+DataLoading.DataIngestion module
+--------------------------------
+
+.. automodule:: modules.DataLoading.DataIngestion
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: modules.DataLoading
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/Home.rst

@@ -0,0 +1,21 @@
+Home package
+============
+
+Submodules
+----------
+
+Home.HomeContent module
+-----------------------
+
+.. automodule:: modules.Home.HomeContent
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: modules.Home
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/QuickLook.rst

@@ -0,0 +1,69 @@
+QuickLook package
+=================
+
+Submodules
+----------
+
+QuickLook.AverageCrossSpectrum module
+-------------------------------------
+
+.. automodule:: modules.QuickLook.AverageCrossSpectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+QuickLook.AveragePowerSpectrum module
+-------------------------------------
+
+.. automodule:: modules.QuickLook.AveragePowerSpectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+QuickLook.Bispectrum module
+---------------------------
+
+.. automodule:: modules.QuickLook.Bispectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+QuickLook.CrossSpectrum module
+------------------------------
+
+.. automodule:: modules.QuickLook.CrossSpectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+QuickLook.LightCurve module
+---------------------------
+
+.. automodule:: modules.QuickLook.LightCurve
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+QuickLook.PowerColors module
+----------------------------
+
+.. automodule:: modules.QuickLook.PowerColors
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+QuickLook.PowerSpectrum module
+------------------------------
+
+.. automodule:: modules.QuickLook.PowerSpectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: modules.QuickLook
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/conf.py

@@ -0,0 +1,39 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
+
+project = 'Stingray Explorer'
+copyright = '2024, Kartik Mandar'
+author = 'Kartik Mandar'
+release = '0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',       # For Google-style docstrings
+    'sphinx.ext.viewcode',       # Adds links to source code
+    'sphinx.ext.autosummary',    # Generate summaries automatically
+]
+autosummary_generate = True      # Enables automatic summary generation
+
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,28 @@
+.. StingrayExplorer documentation master file, created by
+   sphinx-quickstart on Fri Nov  8 15:00:39 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+StingrayExplorer documentation
+==============================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+   DataLoading
+   Home
+   QuickLook
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

@@ -0,0 +1,6 @@
+modules
+=======
+
+.. toctree::
+   :maxdepth: 4
+

modules/QuickLook/PowerSpectrum.py

@@ -42,6 +42,8 @@
     "#9edae5",
 ]
 
+log_binned = False
+
 # Create a warning handler
 def create_warning_handler():
     warning_handler = WarningHandler()
@@ -228,6 +230,62 @@ def create_holoviews_plots_no_colorbar(df, label, dt, norm, color_key=None):
             else:
                 return plot
 
+    def create_rebinned_holoviews_plots(df, label, dt, norm, color_key=None, log_binned=False):
+        """
+        Create a HoloViews plot for rebinned power spectrum data.
+        
+        Parameters:
+            df (pd.DataFrame): DataFrame containing rebinned frequency and power values.
+            label (str): Label for the plot.
+            dt (float): Time binning parameter.
+            norm (str): Normalization parameter.
+            color_key (str, optional): Color key for the plot.
+            log_binned (bool): If True, applies a logarithmic scale to the x-axis.
+        
+        Returns:
+            hv.Overlay or hv.DynamicMap: The generated HoloViews plot.
+        """
+        # Create the initial plot from the DataFrame
+        plot = df.hvplot(x="Frequency", y="Power", shared_axes=False, label=label)
+
+        # Check if color_key is provided for individual plot colors
+        if color_key:
+            if rasterize_checkbox.value:
+                return hd.rasterize(
+                    plot,
+                    aggregator=hd.ds.mean("Power"),
+                    color_key=color_key,
+                    line_width=3,
+                    pixel_ratio=2,
+                ).opts(
+                    tools=["hover"],
+                    cmap=[color_key],
+                    width=600,
+                    height=600,
+                    colorbar=True,
+                    logx=log_binned  # Apply log scale only if log_binned is True
+                )
+            else:
+                return plot.opts(logx=log_binned)  # Apply log scale only if log_binned is True
+        else:
+            if rasterize_checkbox.value:
+                return hd.rasterize(
+                    plot,
+                    aggregator=hd.ds.mean("Power"),
+                    line_width=3,
+                    pixel_ratio=2,
+                ).opts(
+                    tools=["hover"],
+                    width=600,
+                    height=600,
+                    cmap="Viridis",
+                    colorbar=True,
+                    logx=log_binned  # Apply log scale only if log_binned is True
+                )
+            else:
+                return plot.opts(logx=log_binned)  # Apply log scale only if log_binned is True
+
+
     def create_dataframe_panes(df, title):
         return pn.FlexBox(
             pn.pane.Markdown(f"**{title}**"),
@@ -258,12 +316,13 @@ def create_dataframe(selected_event_list_index, dt, norm):
 
     def rebin_powerspectrum(ps):
         rebin_size = rebin_size_input.value
-
+        log_binned = False  # Initialize flag for logarithmic rebinning
         if linear_rebin_checkbox.value:
             # Perform linear rebinning
             rebinned_ps = ps.rebin(rebin_size, method="mean")
             return rebinned_ps
         elif log_rebin_checkbox.value:
+            log_binned = True  # Set flag to indicate log rebinning
             # Perform logarithmic rebinning
             rebinned_ps = ps.rebin_log(f=rebin_size)
             return rebinned_ps
@@ -347,7 +406,7 @@ def generate_powerspectrum(event=None):
                     "Power": rebinned_ps.power,
                 })
                 rebinned_label = f"Rebinned {event_list_name} (dt={dt}, norm={norm})"
-                rebinned_plot_hv = create_holoviews_plots(rebinned_df, rebinned_label, dt, norm)
+                rebinned_plot_hv = create_rebinned_holoviews_plots(rebinned_df, rebinned_label, dt, norm, log_binned=log_binned)
 
                 # Check if the user wants to plot rebin with the original
                 if rebin_with_original_checkbox.value: