Add Two backgrounds option

.github/workflows/actions.yml

@@ -9,42 +9,24 @@ on:
 
 jobs:
   tests:
-    runs-on: self-hosted
+    runs-on: ubuntu-22.04
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v2
     - name: Set up Miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
-        channels: conda-forge,defaults,mantid
         auto-update-conda: true
         miniforge-version: latest
-        python-version: "3.8"
         environment-file: environment.yml
-        activate-environment: liquid-ref
-    - name: Restore cached conda environment
-      id: cache-load
-      uses: actions/cache/restore@v3
-      with:
-        path: /usr/share/miniconda/envs/liquid-ref
-        key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
-    - name: Load Environment
-      if: steps.cache-load.outputs.cache-hit != 'true'
-      run: |
-        mamba env update --file environment.yml  --prune
-    - name: Start xvfb daemon
-      run: |
-        /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -ac -screen 0 1280x1024x16
     - name: Test with pytest
       working-directory: ./reduction
       run: |
-        echo datasearch.directories=/home/cloud/_work/LiquidsReflectometer/LiquidsReflectometer/reduction/tests/data/liquidsreflectometer-data/nexus/ >> ~/.mantid/Mantid.user.properties
-        cat ~/.mantid/Mantid.user.properties
         git submodule add --force https://code.ornl.gov/sns-hfir-scse/infrastructure/test-data/liquidsreflectometer-data.git tests/data/liquidsreflectometer-data
         git submodule update --init
-        python -m pytest --cov=. --cov-report=xml --cov-report=term test
+        python -m pytest -vv --cov=. --cov-report=xml --cov-report=term test
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:

environment.yml

@@ -1,15 +1,14 @@
 name: liquid-ref
 channels:
+  - mantid/label/main
   - conda-forge
-  - default
-  - mantid
+  - defaults
 dependencies:
   - pre-commit
   - pytest
   - pytest-cov
   - numpy
   - lmfit
-  - python=3.8
   - mantidworkbench>=6.7.0
   - codecov
   - conda-build

reduction/data/template_fbck.xml

@@ -14,6 +14,7 @@
    <to_peak_pixels>147</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>133</back_roi1_from>
    <back_roi1_to>150</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>
@@ -61,6 +62,7 @@
    <to_peak_pixels>147</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>133</back_roi1_from>
    <back_roi1_to>150</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>
@@ -108,6 +110,7 @@
    <to_peak_pixels>147</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>133</back_roi1_from>
    <back_roi1_to>150</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>
@@ -155,6 +158,7 @@
    <to_peak_pixels>147</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>133</back_roi1_from>
    <back_roi1_to>150</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>
@@ -202,6 +206,7 @@
    <to_peak_pixels>147</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>133</back_roi1_from>
    <back_roi1_to>150</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>
@@ -249,6 +254,7 @@
    <to_peak_pixels>147</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>126</back_roi1_from>
    <back_roi1_to>131</back_roi1_to>
    <back_roi2_from>153</back_roi2_from>
@@ -296,6 +302,7 @@
    <to_peak_pixels>148</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>131</back_roi1_from>
    <back_roi1_to>151</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>
@@ -343,6 +350,7 @@
    <to_peak_pixels>148</to_peak_pixels>
    <peak_discrete_selection>N/A</peak_discrete_selection>
    <background_flag>True</background_flag>
+   <two_backgrounds_flag>True</two_backgrounds_flag>
    <back_roi1_from>131</back_roi1_from>
    <back_roi1_to>151</back_roi1_to>
    <back_roi2_from>0</back_roi2_from>

reduction/lr_reduction/reduction_template_reader.py

@@ -21,6 +21,7 @@ def __init__(self):
         # Signal selection
         self.data_peak_range = [140, 150]
         self.subtract_background = True
+        self.two_backgrounds: bool = False
         self.background_roi = [137, 153, 0, 0]
         self.tof_range = [9600., 21600.]
         self.select_tof_range = True
@@ -65,6 +66,20 @@ def __init__(self):
         self.incident_medium_index_selected = 0
 
     def from_dict(self, data_dict):
+        r"""
+        Update object's attributes with a dictionary with entries of the type  attribute_name: attribute_value.
+
+        Raises
+        ------
+        ValueError
+            if one entry of the dictionary is not an attribute of this object
+        """
+
+        # check all keys are data_dict are attributes of object `self`
+        attribute_names = list(vars(self))
+        if not all(key in attribute_names for key in data_dict):
+            raise ValueError("data_dir contains invalid entries")
+        # update attribute values
         for k, v in data_dict.items():
             setattr(self, k, v)
 
@@ -78,6 +93,7 @@ def to_xml(self):
         _xml += "<to_peak_pixels>%s</to_peak_pixels>\n" % str(self.data_peak_range[1])
         _xml += "<peak_discrete_selection>N/A</peak_discrete_selection>\n"
         _xml += "<background_flag>%s</background_flag>\n" % str(self.subtract_background)
+        _xml += "<two_backgrounds_flag>%s</two_backgrounds_flag>\n" % str(self.two_backgrounds)
         _xml += "<back_roi1_from>%s</back_roi1_from>\n" % str(self.background_roi[0])
         _xml += "<back_roi1_to>%s</back_roi1_to>\n" % str(self.background_roi[1])
         _xml += "<back_roi2_from>%s</back_roi2_from>\n" % str(self.background_roi[2])
@@ -162,11 +178,15 @@ def from_xml_element(self, instrument_dom):
         self.norm_x_range = [getIntElement(instrument_dom, "norm_x_min"),
                              getIntElement(instrument_dom, "norm_x_max")]
 
-        #background flag
+        # background flag
         self.subtract_background = getBoolElement(instrument_dom, "background_flag",
                                                  default=self.subtract_background)
 
-        #background from/to pixels
+        # use two backgrounds flag
+        self.two_backgrounds = getBoolElement(instrument_dom, "two_backgrounds_flag",
+                                              default=self.two_backgrounds)
+
+        # background from/to pixels
         self.background_roi = [getIntElement(instrument_dom, "back_roi1_from"),
                                getIntElement(instrument_dom, "back_roi1_to"),
                                getIntElement(instrument_dom, "back_roi2_from"),
@@ -191,6 +211,7 @@ def from_xml_element(self, instrument_dom):
         # Background subtraction option
         self.subtract_norm_background = getBoolElement(instrument_dom, "norm_background_flag",
                                                        default=self.subtract_norm_background)
+
         self.norm_background_roi = [getIntElement(instrument_dom, "norm_from_back_pixels"),
                                     getIntElement(instrument_dom, "norm_to_back_pixels")]
 
@@ -312,7 +333,7 @@ def from_xml(xml_str):
                 data_set.from_xml_element(item)
                 data_sets.append(data_set)
 
-    if len(data_sets)==0:
+    if len(data_sets) == 0:
         data_sets = [ReductionParameters()]
 
     return data_sets

reduction/lr_reduction/template.py

@@ -185,6 +185,8 @@ def process_from_template_ws(ws_sc, template_data, q_summing=False,
     peak = template_data.data_peak_range
     if template_data.subtract_background:
         peak_bck = template_data.background_roi
+        if template_data.two_backgrounds is False:
+            peak_bck = peak_bck[0: 2]  # retain only the first background
     else:
         peak_bck = None
 
@@ -202,7 +204,7 @@ def process_from_template_ws(ws_sc, template_data, q_summing=False,
     else:
         norm_low_res = None
 
-    # We are not subtrating background for the direct beam
+    # We are not subtracting background for the direct beam
     if template_data.subtract_norm_background:
         norm_bck = template_data.norm_background_roi
     else:

reduction/lr_reduction/utils.py

@@ -0,0 +1,68 @@
+# standard imports
+from contextlib import contextmanager
+from copy import deepcopy
+from pathlib import Path
+from typing import Union
+
+# third-party libraries
+from mantid.kernel import ConfigService
+
+
+@contextmanager
+def amend_config(
+    new_config: dict = None, data_dir: Union[str, list] = None, data_dir_insert_mode: str = "prepend"
+) -> None:
+    r"""
+    Context manager to safely modify Mantid Configuration Service while
+    the function is executed.
+
+    Parameters
+    ----------
+    new_config
+        (key, value) pairs to substitute in the configuration service
+    data_dir
+        prepend one (when passing a string) or more (when passing a list)
+        directories to the list of data search directories. Alternatively, replace instead of prepend.
+    data_dir_insert_mode
+        How to insert the data directories. Options are: "prepend" (default) and "replace".
+    """
+    modified_keys = list()
+    backup = dict()
+    config = ConfigService.Instance()
+    if new_config is not None:
+        SEARCH_ARCHIVE = "datasearch.searcharchive"
+        if SEARCH_ARCHIVE not in new_config:
+            new_config[SEARCH_ARCHIVE] = "hfir, sns"
+        DEFAULT_FACILITY = "default.facility"
+        if DEFAULT_FACILITY not in new_config:
+            new_config[DEFAULT_FACILITY] = "SNS"
+        for key, val in new_config.items():
+            backup[key] = config[key]
+            config[key] = val  # config does not have an 'update' method
+            modified_keys.append(key)
+    if data_dir is not None:
+        data_dirs = (
+            [
+                data_dir,
+            ]
+            if isinstance(data_dir, str)
+            else data_dir
+        )
+        # make sure the data_dirs exists and are directories
+        for path in data_dirs:
+            if Path(path).is_dir() is False:
+                raise ValueError(f"Data directory: {path} does not exist or is not a directory")
+        key = "datasearch.directories"
+        backup[key] = deepcopy(config[key])
+        # prepend or replace our custom data directories to the list of data search directories
+        if data_dir_insert_mode == "prepend":
+            config.setDataSearchDirs(data_dirs + list(config.getDataSearchDirs()))
+        elif data_dir_insert_mode == "replace":
+            config.setDataSearchDirs(data_dirs)
+        else:
+            raise ValueError(f"Invalid data_dir_insert_mode: {data_dir_insert_mode}")
+    try:
+        yield
+    finally:
+        for key in modified_keys:
+            config[key] = backup[key]

reduction/test/conftest.py

@@ -0,0 +1,17 @@
+# standard imports
+from pathlib import Path
+
+# third-party imports
+import pytest
+
+
+@pytest.fixture(scope="session")
+def nexus_dir() -> str:
+    r"""Absolute path to the event nexus files"""
+    return str(Path(__file__).parent.parent / "tests/data/liquidsreflectometer-data/nexus")
+
+
+@pytest.fixture(scope="session")
+def template_dir() -> str:
+    r"""Absolute path to reduction/data/ directory"""
+    return str(Path(__file__).parent.parent / "data")