Integrate BrainGlobe Atlas API to download atlases from within the GUI

.github/workflows/main.yml

@@ -19,15 +19,17 @@ jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
 
     steps:
       - name: Check out repo
         uses: actions/checkout@v2
       - name: Install VTK dependencies
+        if: ${{ runner.os == 'Linux' }}
         run: |
           sudo apt-get update
           sudo apt-get install libsm6 libgl1-mesa-glx
@@ -43,11 +45,12 @@ jobs:
           # check for cache from the corresponding requirements file
           key: ${{ env.pythonLocation }}-pip-${{ hashFiles('envs/requirements.txt') }}
       - name: Install dependencies
+        env:
+          QT_QPA_PLATFORM: offscreen
         run: |
           python -m pip install --upgrade pip setuptools wheel
           pip install flake8
-          export QT_QPA_PLATFORM=offscreen
-          if [ -f envs/requirements.txt ]; then pip install -r envs/requirements.txt; fi
+          pip install -r envs/requirements.txt
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -56,6 +59,10 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude stitch
       - name: Test with pytest
         run: |
-          # TODO: add image artifact
-          #python -u -m magmap.tests.unit_testing
+          python -u -m magmap.tests.test_chunking
           python -u -m magmap.tests.test_libmag
+          # TODO: add UI testing
+          #python -u -m magmap.tests.test_visualizer
+          # TODO: add image artifacts
+          #python -u -m magmap.tests.test_img_equality
+          #python -u -m magmap.tests.unit_testing

docs/release/release_v1.5.md

@@ -158,4 +158,7 @@ See the [table of CLI changes](../cli.md#changes-in-magellanmapper-v15) for a su
 - Python-Bioformats has been upgraded to 4.0.5 and uses a custom package that uses the existing Javabridge rather than Python-Javabridge to avoid a higher NumPy version requirement
 - Workaround for failure to install Mayavi because of a newer VTK, now pinned to 9.0.1
 - Matplotlib >= 3.2 is now required
-- 
+
+#### R Dependency Changes
+
+#### Server dependency Changes

docs/release/release_v1.6.md

@@ -16,6 +16,7 @@
 - "Help" buttons added to open the online documentation (#109)
 - Default confirmation labels can be set before detection (#115)
 - Resets the labels reference file path when reloading an image in the GUI (#139)
+- BrainGlobe panel: access atlases hosted by BrainGlobe directly from the GUI (#75)
 - Registered image suffixes with variable endings (eg `annotationEdgeLevel<n>`) now show up in the dropdown boxes (#142)
 - Registered image and region names are truncated in the middle to prevent expanding the sidebar for long names (#147)
 - "Show all" in the Regions section of the ROI panel shows names for all labels (#145)
@@ -117,6 +118,7 @@
 #### Python Dependency Changes
 
 - Python 3.8 is the default version now that Python 3.6 has reached End-of-Life
+- The BrainGlobe Atlas API package (`bg-atlasapi`) dependency has been added to access a suite of cloud-based atlases (#75)
 - The `dataclasses` backport is installed for Python < 3.7
 - `Tifffile` is now a direct dependency, previously already installed as a sub-dependency of other required packages
 - Updated to use the `axis_channel` parameter in Scikit-image's `transform.rescale` function (#115)

environment.yml

@@ -25,3 +25,4 @@ dependencies:
     - simpleitk==2.0.2rc2.dev785+g8ac4f
     - javabridge==1.0.19.post4+gbebed64
     - python-bioformats==4.0.5.post2+g51eb88a
+    - "https://github.com/brainglobe/bg-atlasapi/archive/refs/heads/master.zip"

envs/requirements.txt

@@ -6,71 +6,65 @@ apptools==5.1.0
 async-timeout==4.0.2
 asynctest==0.13.0
 attrs==21.4.0
-awscli==1.22.37
-boto3==1.20.37
-botocore==1.23.37
-charset-normalizer==2.0.10
-colorama==0.4.3
+bg-atlasapi @ git+https://github.com/brainglobe/bg-atlasapi.git@cc980143c88e71202d09cbbd0f1bcfa491ea759d
+bg-space==0.6.0
+boto3==1.23.10
+botocore==1.26.10
+certifi==2022.6.15
+charset-normalizer==2.0.12
+click==8.0.4
+commonmark==0.9.1
 configobj==5.0.6
 cycler==0.11.0
-docutils==0.15.2
+dataclasses==0.8;python_version<"3.7"
+decorator==4.4.2
 envisage==6.0.1
-et-xmlfile==1.1.0
-fonttools==4.28.5
 frozenlist==1.2.0
 future==0.18.2
 idna==3.3
-imageio==2.13.5
-importlib-metadata==4.10.1
+idna-ssl==1.1.0
+imageio==2.15.0
+importlib-metadata==4.8.3
 importlib-resources==5.4.0
-iniconfig==1.1.1
 javabridge==1.0.19.post4+gbebed64
-Jinja2==3.0.3
 jmespath==0.10.0
-joblib==1.1.0
-kiwisolver==1.3.2
-MarkupSafe==2.0.1
-matplotlib==3.5.1
-matplotlib-scalebar==0.8.0
-mayavi==4.7.4
+kiwisolver==1.3.1
+matplotlib==3.3.4
+matplotlib-scalebar==0.7.2
+mayavi==4.8.0
+meshio==4.4.6
 multidict==5.2.0
-networkx==2.6.3
-numpy==1.21.5
-openpyxl==3.0.9
-packaging==21.3
-pandas==1.3.5
-Pillow==9.0.1
-pluggy==1.0.0
-py==1.11.0
-pyamg==4.2.1
-pyasn1==0.4.8
-pyface==7.3.0
-Pygments==2.11.2
-pyparsing==3.0.6
+networkx==2.5.1
+numpy==1.19.5
+pandas==1.1.5
+Pillow==8.4.0
+pyamg==4.2.3
+pyface==7.4.2
+Pygments==2.12.0
+pyparsing==3.0.9
 PyQt5==5.15.6
 PyQt5-Qt5==5.15.2
-PyQt5-sip==12.9.0
-pytest==6.2.5
+PyQt5-sip==12.9.1
 python-bioformats==4.0.5.post2+g51eb88a
 python-dateutil==2.8.2
-pytz==2021.3
-PyWavelets==1.2.0
-PyYAML==5.4.1
-rsa==4.7.2
-s3transfer==0.5.0
-scikit-image==0.19.1
-scikit-learn==1.0.2
-scipy==1.7.3
+pytz==2022.1
+PyWavelets==1.1.1
+PyYAML==6.0
+requests==2.27.1
+rich==12.5.1
+s3transfer==0.5.2
+scikit-image==0.17.2;python_version<"3.9"
+scikit-image==0.19.3;python_version>="3.9"
+scipy==1.5.4
 SimpleITK==2.0.2rc2.dev785+g8ac4f
 six==1.16.0
-threadpoolctl==3.0.0
-tifffile==2021.11.2
-toml==0.10.2
+tifffile==2020.9.3
 traits==6.3.2
-traitsui==7.2.1
-typing_extensions==4.0.1
-urllib3==1.26.8
+traitsui==7.4.0
+treelib==1.6.1
+typing_extensions==4.1.1
+urllib3==1.26.11
 vtk==9.1.0
-wslink==1.3.1
+wslink==1.6.6
 yarl==1.7.2
-zipp==3.7.0
+zipp==3.6.0

magmap/atlas/ontology.py

@@ -185,15 +185,17 @@ def create_reverse_lookup(
             print(e)
         return id_dict
 
-    def create_lookup_pd(self, df: pd.DataFrame) -> Dict[int, Any]:
+    def create_lookup_pd(
+            self, df: Optional[pd.DataFrame] = None) -> Dict[int, Any]:
         """Create a lookup dictionary from a Pandas data frame.
 
         Args:
             df: Pandas data frame, assumed to have at
                 least columns corresponding to :const:``config.ABAKeys.ABA_ID``
                 or :const:``config.AtlasMetrics.REGION`` and 
                 :const:``config.ABAKeys.ABA_NAME`` or
-                :const:``config.AtlasMetrics.REGION_NAME``.
+                :const:``config.AtlasMetrics.REGION_NAME``. Defaults to None,
+                in which case :attr:`loaded_ref` is used.
 
         Returns:
             Dictionary similar to that generated from 
@@ -297,7 +299,7 @@ def get_ref_lookup_as_df(self) -> Optional[pd.DataFrame]:
         return df_regions
 
     def create_ref_lookup(
-            self, labels_ref: Union[pd.DataFrame, Dict] = None
+            self, labels_ref: Optional[Union[pd.DataFrame, Dict]] = None
     ) -> Dict[int, Any]:
         """Wrapper to create a reference lookup from different sources.
 
@@ -306,7 +308,8 @@ def create_ref_lookup(
 
         Args:
             labels_ref: Reference dictionary or data frame, typically loaded
-                from :meth:`load_labels`.
+                from :meth:`load_labels`. Defaults to None, in which case
+                :attr:`loads_ref` is used.
 
         Returns:
             Ordered dictionary for looking up by ID.