From b8bc0db9b50b771de31a6fdfe2818f4cf89c5b0a Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 21 May 2024 13:27:59 -0400
Subject: [PATCH] BaseSegmentation class improvements (#327)

* prepopulate private attribute for image mask; rearrange abstract method

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

for more information, see https://pre-commit.ci

* Update CHANGELOG.md

* Update CHANGELOG.md

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Paul Adkisson <paul.wesley.adkisson@gmail.com>
---
 CHANGELOG.md                               |  3 ++-
 src/roiextractors/segmentationextractor.py | 25 +++++++++++-----------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ece49f53..c7ee71ed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,12 +11,13 @@
 
 ### Fixes
 
-* Remove unecessary scipy import error handling: [#315](https://github.com/catalystneuro/roiextractors/pull/315)
+* Remove unnecessary `scipy` import error handling: [#315](https://github.com/catalystneuro/roiextractors/pull/315)
 * Fixed the typing returned by the `InscopixImagingExtractor.get_dtype` method: [#326](https://github.com/catalystneuro/roiextractors/pull/326)
 
 ### Improvements
 
 * The `Suite2PSegmentationExtractor` now produces an error when a required sub-file is missin: [#330](https://github.com/catalystneuro/roiextractors/pull/330)
+* Added `_image_mask` initialization in `BaseSegmentationExtractor`; combined `abstractmethod`s into top of file: [#327](https://github.com/catalystneuro/roiextractors/pull/327)
 
 ### Testing
 
diff --git a/src/roiextractors/segmentationextractor.py b/src/roiextractors/segmentationextractor.py
index 856c62f9..40502c08 100644
--- a/src/roiextractors/segmentationextractor.py
+++ b/src/roiextractors/segmentationextractor.py
@@ -32,7 +32,7 @@ class SegmentationExtractor(ABC):
     """
 
     def __init__(self):
-        """Create a new SegmentationExtractor from specified data type (unique to each child SegmentationExtractor)."""
+        """Create a new SegmentationExtractor for a specific data format (unique to each child SegmentationExtractor)."""
         self._sampling_frequency = None
         self._times = None
         self._channel_names = ["OpticalChannel"]
@@ -44,6 +44,7 @@ def __init__(self):
         self._roi_response_deconvolved = None
         self._image_correlation = None
         self._image_mean = None
+        self._image_mask = None
 
     @abstractmethod
     def get_accepted_list(self) -> list:
@@ -67,6 +68,17 @@ def get_rejected_list(self) -> list:
         """
         pass
 
+    @abstractmethod
+    def get_image_size(self) -> ArrayType:
+        """Get frame size of movie (height, width).
+
+        Returns
+        -------
+        no_rois: array_like
+            2-D array: image height x image width
+        """
+        pass
+
     def get_num_frames(self) -> int:
         """Get the number of frames in the recording (duration of recording).
 
@@ -204,17 +216,6 @@ def get_background_pixel_masks(self, background_ids=None) -> np.array:
 
         return _pixel_mask_extractor(self.get_background_image_masks(background_ids=background_ids), background_ids)
 
-    @abstractmethod
-    def get_image_size(self) -> ArrayType:
-        """Get frame size of movie (height, width).
-
-        Returns
-        -------
-        no_rois: array_like
-            2-D array: image height x image width
-        """
-        pass
-
     def frame_slice(self, start_frame: Optional[int] = None, end_frame: Optional[int] = None):
         """Return a new SegmentationExtractor ranging from the start_frame to the end_frame.