allow for incomplete data ingestion, fix ypix bug, add mean image to …

…caiman seg class (#227)

* added new args to allow for incomplete data import and fixed potential bug with ypix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* make method: caiman seg class retrieve mean image

* Update src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py

naming of _load_npy

Co-authored-by: Cody Baker <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Update src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py

remove search_plane_subdirectory

Co-authored-by: Cody Baker <[email protected]>

* update changelog

* fix bug and remove remaining references to search_plane_subdirectory

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* bug fix on function name passing tests now

* Revert suite2p to main version

* add docstrings

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Cody Baker <[email protected]>
Co-authored-by: Paul Adkisson <[email protected]>

CHANGELOG.md

@@ -30,6 +30,11 @@
 
 * Added support for Miniscope AVI files with the `MiniscopeImagingExtractor`. [PR #225](https://github.com/catalystneuro/roiextractors/pull/225)
 
+* Added support for incomplete file ingestion for the `Suite2pSegmentationExtractor`. [PR #227](https://github.com/catalystneuro/roiextractors/pull/227)
+
+* Bug fix for the `CaimanSegmentationExtractor`: Change reshaping from 'C' to 'F' (Fortran). [PR #227](https://github.com/catalystneuro/roiextractors/pull/227)
+
+* Bug fix for the `CaimanSegmentationExtractor`: Added importing of `self._image_correlation` and changed how `self._image_mean` to import the background component image. [PR #227](https://github.com/catalystneuro/roiextractors/pull/227)
 
 
 # v0.5.2

src/roiextractors/extractors/caiman/caimansegmentationextractor.py

@@ -58,7 +58,8 @@ def __init__(self, file_path: PathType):
         self._roi_response_dff = self._trace_extractor_read("F_dff")
         self._roi_response_neuropil = self._trace_extractor_read("C")
         self._roi_response_deconvolved = self._trace_extractor_read("S")
-        self._image_correlation = self._summary_image_read()
+        self._image_correlation = self._correlation_image_read()
+        self._image_mean = self._summary_image_read()
         self._sampling_frequency = self._dataset_file["params"]["data"]["fr"][()]
         self._image_masks = self._image_mask_sparse_read()
 
@@ -112,11 +113,18 @@ def _trace_extractor_read(self, field):
         if field in self._dataset_file["estimates"]:
             return lazy_ops.DatasetView(self._dataset_file["estimates"][field]).lazy_transpose()
 
-    def _summary_image_read(self):
-        """Read the summary image (Cn) from the estimates dataset of the h5py file."""
+    def _correlation_image_read(self):
+        """Read correlation image Cn."""
         if self._dataset_file["estimates"].get("Cn"):
             return np.array(self._dataset_file["estimates"]["Cn"])
 
+    def _summary_image_read(self):
+        """Read summary image mean."""
+        if self._dataset_file["estimates"].get("b"):
+            FOV_shape = self._dataset_file["params"]["data"]["dims"][()]
+            b_sum = self._dataset_file["estimates"]["b"][:].sum(axis=1)
+            return np.array(b_sum).reshape(FOV_shape, order="F")
+
     def get_accepted_list(self):
         accepted = self._dataset_file["estimates"]["idx_components"]
         if len(accepted.shape) == 0: