Merge branch 'master' into contour-nan-fix

.github/workflows/linux-conda.yml

@@ -27,7 +27,7 @@ jobs:
         
     - name: Install mamba
       run: |
-        conda install -c conda-forge mamba
+        conda install -c conda-forge mamba python=3.10
         conda clean -a
         
         #   - name: install caiman

.github/workflows/macos-conda.yml

@@ -16,32 +16,21 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python '3.10'
-      uses: actions/setup-python@v3
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.10'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-        
-    - name: Install mamba
-      run: |
-        conda install -c conda-forge mamba
-        conda clean -a
-        
-        #   - name: install caiman
-        #     run: |
-        #       mamba install -c conda-forge caiman
+        mamba-version: "*"
+        channels: conda-forge,defaults
+        channel-priority: true
+        activate-environment: mescore
+        environment-file: environment.yml
 
-    - name: install mesmerize-core
+    - name: Test mesmerize-core with pytest
+      shell: bash -el {0}
       run: |
-        mamba env update -n base --file environment.yml
+        conda activate mescore
+        mamba install pytest
         caimanmanager install
         pip install .
-        
-    - name: Test with pytest
-      run: |
-        mamba install pytest
         DOWNLOAD_GROUND_TRUTHS=1 pytest -s .
 

.github/workflows/windows-conda.yml

@@ -14,9 +14,9 @@ jobs:
     runs-on: "windows-latest"
     steps:
       - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: 3.9
+          python-version: '3.10'
           mamba-version: "*"
           channels: conda-forge,defaults
           channel-priority: true

environment.yml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
 dependencies:
-  - caiman >= 1.9.10
+  - caiman >= 1.11.2
   - pandas >= 1.5.0
   - requests
   - click

environment_rtd.yml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
 dependencies:
-  - caiman >= 1.9.10
+  - caiman >= 1.11.2
   - pandas >= 1.5.0
   - requests
   - click

mesmerize_core/algorithms/cnmf.py

@@ -99,7 +99,7 @@ def run_algo(batch_path, uuid, data_path: str = None):
 
         cnm.save(str(output_path))
 
-        Cn = cm.local_correlations(images.transpose(1, 2, 0))
+        Cn = cm.local_correlations(images, swap_dim=False)
         Cn[np.isnan(Cn)] = 0
 
         corr_img_path = output_dir.joinpath(f"{uuid}_cn.npy").resolve()

mesmerize_core/algorithms/mcorr.py

@@ -90,7 +90,7 @@ def run_algo(batch_path, uuid, data_path: str = None):
 
         print("Computing correlation image")
         Cns = local_correlations_movie_offline(
-            [str(mcorr_memmap_path)],
+            str(mcorr_memmap_path),
             remove_baseline=True,
             window=1000,
             stride=1000,
@@ -102,24 +102,27 @@ def run_algo(batch_path, uuid, data_path: str = None):
         Cn[np.isnan(Cn)] = 0
         cn_path = output_dir.joinpath(f"{uuid}_cn.npy")
         np.save(str(cn_path), Cn, allow_pickle=False)
-
-        # output dict for pandas series for dataframe row
-        d = dict()
-
+
         print("finished computing correlation image")
 
+
         # Compute shifts
         if opts.motion["pw_rigid"] == True:
             x_shifts = mc.x_shifts_els
             y_shifts = mc.y_shifts_els
             shifts = [x_shifts, y_shifts]
+            if hasattr(mc, 'z_shifts_els'):
+                shifts += mc.z_shifts_els
             shift_path = output_dir.joinpath(f"{uuid}_shifts.npy")
             np.save(str(shift_path), shifts)
         else:
             shifts = mc.shifts_rig
             shift_path = output_dir.joinpath(f"{uuid}_shifts.npy")
             np.save(str(shift_path), shifts)
 
+        # output dict for pandas series for dataframe row
+        d = dict()
+
         # save paths as relative path strings with forward slashes
         cn_path = str(PurePosixPath(cn_path.relative_to(output_dir.parent)))
         mcorr_memmap_path = str(PurePosixPath(mcorr_memmap_path.relative_to(output_dir.parent)))