datajoint · ttngu207 · Feb 1, 2024 · Nov 16, 2023 · Dec 8, 2023 · Dec 19, 2023
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -4,9 +4,9 @@
     "editor.rulers": [
         88
     ],
-    "python.formatting.provider": "black",
+    "python.formatting.provider": "none",
     "[python]": {
-        "editor.defaultFormatter": null
+        "editor.defaultFormatter": "ms-python.black-formatter"
     },
     "[markdown]": {
         "editor.defaultFormatter": "disable"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,21 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.9.3] - 2024-01-29
+
++ Update - DataJoint Elements to install from GitHub instead of PyPI
++ Fix - `element-interface` required during package installation
++ Fix - apply formatting with `black` across the repository
+
+## [0.9.2] - 2024-01-10
+
++ Fix - Imports and attribute values in notebooks to resolve DataJoint errors
+
+## [0.9.1] - 2023-12-19
+
++ Update - Tutorial notebook
++ Fix - minor fixes in `setup.py` and `README`
+
 ## [0.9.0] - 2023-10-13
 
 + Add - Export to NWB and upload to DANDI
@@ -181,6 +196,10 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `scan` and `imaging` modules
 + Add - Readers for `ScanImage`, `ScanBox`, `Suite2p`, `CaImAn`
 
+[0.9.3]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.3
+[0.9.2]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.2
+[0.9.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.1
+[0.9.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.0
 [0.8.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.8.1
 [0.8.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.8.0
 [0.7.9]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.9

diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ documentation page.
 + Clone the repository to your computer
 
   ```bash
-  git clone https://github.com/<enter_github_username>/element-calcium-imaging
+  git clone https://github.com/<enter_github_username>/element-calcium-imaging.git
   ```
 
 + Install with `pip`

diff --git a/docs/src/.overrides/assets/stylesheets/extra.css b/docs/src/.overrides/assets/stylesheets/extra.css
@@ -96,7 +96,6 @@ html a[title="YouTube"].md-social__link svg {
     /* --md-footer-fg-color: var(--dj-white); */
 }
 
-[data-md-color-scheme="slate"] td,
-th {
+[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
     color: var(--dj-black)
 }
diff --git a/element_calcium_imaging/export/nwb/nwb.py b/element_calcium_imaging/export/nwb/nwb.py
@@ -192,9 +192,11 @@ def _add_scan_to_nwb(session_key, nwbfile):
                 name="ImagingPlane",
                 optical_channel=optical_channel,
                 imaging_rate=frame_rate,
-                description=scan_notes
-                if scan_notes != ""
-                else f"Imaging plane for field {field_no+1}, channel {channel+1}",
+                description=(
+                    scan_notes
+                    if scan_notes != ""
+                    else f"Imaging plane for field {field_no+1}, channel {channel+1}"
+                ),
                 device=device,
                 excitation_lambda=nan,
                 indicator="unknown",

diff --git a/element_calcium_imaging/imaging.py b/element_calcium_imaging/imaging.py
@@ -254,13 +254,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
                 e.g.: sub4/sess1/scan0/suite2p_0
         """
         acq_software = (scan.Scan & key).fetch1("acq_software")
-        filetypes = dict(
-            ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
-        )
-
         scan_dir = find_full_path(
             get_imaging_root_data_dir(),
-            get_calcium_imaging_files(key, filetypes[acq_software])[0],
+            get_calcium_imaging_files(key, acq_software)[0],
         ).parent
         root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)
 
@@ -1031,30 +1027,40 @@ def make(self, key):
                 }
                 for fkey, ref_image, ave_img, corr_img, max_img in zip(
                     field_keys,
-                    caiman_dataset.motion_correction["reference_image"].transpose(
-                        2, 0, 1
-                    )
-                    if is3D
-                    else caiman_dataset.motion_correction["reference_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["average_image"].transpose(2, 0, 1)
-                    if is3D
-                    else caiman_dataset.motion_correction["average_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["correlation_image"].transpose(
-                        2, 0, 1
-                    )
-                    if is3D
-                    else caiman_dataset.motion_correction["correlation_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["max_image"].transpose(2, 0, 1)
-                    if is3D
-                    else caiman_dataset.motion_correction["max_image"][...][
-                        np.newaxis, ...
-                    ],
+                    (
+                        caiman_dataset.motion_correction["reference_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["reference_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["average_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["average_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["correlation_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["correlation_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["max_image"].transpose(2, 0, 1)
+                        if is3D
+                        else caiman_dataset.motion_correction["max_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
                 )
             ]
             self.Summary.insert(summary_images)

diff --git a/element_calcium_imaging/imaging_no_curation.py b/element_calcium_imaging/imaging_no_curation.py
@@ -254,13 +254,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
                 e.g.: sub4/sess1/scan0/suite2p_0
         """
         acq_software = (scan.Scan & key).fetch1("acq_software")
-        filetypes = dict(
-            ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
-        )
-
         scan_dir = find_full_path(
             get_imaging_root_data_dir(),
-            get_calcium_imaging_files(key, filetypes[acq_software])[0],
+            get_calcium_imaging_files(key, acq_software)[0],
         ).parent
         root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)
 
@@ -369,6 +365,7 @@ def make(self, key):
         task_mode, output_dir = (ProcessingTask & key).fetch1(
             "task_mode", "processing_output_dir"
         )
+        acq_software = (scan.Scan & key).fetch1("acq_software")
 
         if not output_dir:
             output_dir = ProcessingTask.infer_output_dir(key, relative=True, mkdir=True)
@@ -452,8 +449,8 @@ def make(self, key):
                         "Caiman pipeline is not yet capable of analyzing 3D scans."
                     )
 
-                # handle multi-channel tiff image before running CaImAn
-                if nchannels > 1:
+                if acq_software == "ScanImage" and nchannels > 1:
+                    # handle multi-channel tiff image before running CaImAn
                     channel_idx = caiman_params.get("channel_to_process", 0)
                     tmp_dir = pathlib.Path(output_dir) / "channel_separated_tif"
                     tmp_dir.mkdir(exist_ok=True)
@@ -958,30 +955,40 @@ def make(self, key):
                 }
                 for fkey, ref_image, ave_img, corr_img, max_img in zip(
                     field_keys,
-                    caiman_dataset.motion_correction["reference_image"].transpose(
-                        2, 0, 1
-                    )
-                    if is3D
-                    else caiman_dataset.motion_correction["reference_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["average_image"].transpose(2, 0, 1)
-                    if is3D
-                    else caiman_dataset.motion_correction["average_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["correlation_image"].transpose(
-                        2, 0, 1
-                    )
-                    if is3D
-                    else caiman_dataset.motion_correction["correlation_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["max_image"].transpose(2, 0, 1)
-                    if is3D
-                    else caiman_dataset.motion_correction["max_image"][...][
-                        np.newaxis, ...
-                    ],
+                    (
+                        caiman_dataset.motion_correction["reference_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["reference_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["average_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["average_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["correlation_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["correlation_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["max_image"].transpose(2, 0, 1)
+                        if is3D
+                        else caiman_dataset.motion_correction["max_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
                 )
             ]
             self.Summary.insert(summary_images)

diff --git a/element_calcium_imaging/imaging_preprocess.py b/element_calcium_imaging/imaging_preprocess.py
@@ -444,13 +444,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
                 e.g.: sub4/sess1/scan0/suite2p_0
         """
         acq_software = (scan.Scan & key).fetch1("acq_software")
-        filetypes = dict(
-            ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
-        )
-
         scan_dir = find_full_path(
             get_imaging_root_data_dir(),
-            get_calcium_imaging_files(key, filetypes[acq_software])[0],
+            get_calcium_imaging_files(key, acq_software)[0],
         ).parent
         root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)
 
@@ -1244,30 +1240,40 @@ def make(self, key):
                 }
                 for fkey, ref_image, ave_img, corr_img, max_img in zip(
                     field_keys,
-                    caiman_dataset.motion_correction["reference_image"].transpose(
-                        2, 0, 1
-                    )
-                    if is3D
-                    else caiman_dataset.motion_correction["reference_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["average_image"].transpose(2, 0, 1)
-                    if is3D
-                    else caiman_dataset.motion_correction["average_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["correlation_image"].transpose(
-                        2, 0, 1
-                    )
-                    if is3D
-                    else caiman_dataset.motion_correction["correlation_image"][...][
-                        np.newaxis, ...
-                    ],
-                    caiman_dataset.motion_correction["max_image"].transpose(2, 0, 1)
-                    if is3D
-                    else caiman_dataset.motion_correction["max_image"][...][
-                        np.newaxis, ...
-                    ],
+                    (
+                        caiman_dataset.motion_correction["reference_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["reference_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["average_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["average_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["correlation_image"].transpose(
+                            2, 0, 1
+                        )
+                        if is3D
+                        else caiman_dataset.motion_correction["correlation_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
+                    (
+                        caiman_dataset.motion_correction["max_image"].transpose(2, 0, 1)
+                        if is3D
+                        else caiman_dataset.motion_correction["max_image"][...][
+                            np.newaxis, ...
+                        ]
+                    ),
                 )
             ]
             self.Summary.insert(summary_images)