Merge pull request #24 from catalystneuro/fix_custom_segmentation_int…

…erface

Fix Widefield segmentation file names change

src/pinto_lab_to_nwb/widefield/extractors/widefield_processed_segmentationextractor.py

@@ -2,7 +2,7 @@
 from typing import Tuple
 
 import numpy as np
-from neuroconv.utils import FolderPathType
+from neuroconv.utils import FolderPathType, FilePathType
 from pymatreader import read_mat
 from roiextractors import SegmentationExtractor
 
@@ -15,7 +15,10 @@ class WidefieldProcessedSegmentationExtractor(SegmentationExtractor):
 
     def __init__(
         self,
-        folder_path: FolderPathType,
+        info_mat_file_path: FilePathType,
+        roi_from_ref_mat_file_path: FilePathType,
+        vasculature_mask_file_path: FilePathType,
+        blue_pca_mask_file_path: FilePathType,
     ):
         """
         The SegmentationExtractor for the downsampled (binned) Widefield imaging data.
@@ -25,7 +28,6 @@ def __init__(
         - ROIfromRef.mat     : contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
         - vasculature_mask_2.mat : contains the vasculature mask on the downsampled (binned) session image.
         - blue_pca_vasculature_mask_2.mat : contains the PCA mask for the blue channel.
-        - violet_pca_vasculature_mask_2.mat.mat : contains the PCA mask for the violet channel.
 
          that contain the following variables:
         - The Allen area label for each binned pixel
@@ -34,33 +36,28 @@ def __init__(
 
         Parameters
         ----------
-        folder_path: FolderPathType
-            The path that points to the folder that contains the .mat files.
+        info_mat_file_path : FilePathType
+            The file path to the 'info.mat' file.
+        roi_from_ref_mat_file_path : FilePathType
+            The file that contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
+        vasculature_mask_file_path: FilePathType
+            The file that contains the vasculature mask on the downsampled (binned) session image.
+        blue_pca_mask_file_path: FilePathType
+            The file that contains the PCA mask for the blue channel.
         """
         super().__init__()
 
-        self.folder_path = Path(folder_path)
-
-        expected_files = [
-            "info.mat",
-            "ROIfromRef.mat",
-            "vasculature_mask_2.mat",
-            "blue_pca_vasculature_mask_2.mat",
-        ]
-        mat_file_paths = list(self.folder_path.glob("*.mat"))
-        assert mat_file_paths, f"The .mat files are missing from {folder_path}."
-        # assert all expected files are in the folder_path
-        for expected_file in expected_files:
-            assert (
-                self.folder_path / expected_file
-            ).exists(), f"The file {expected_file} is missing from {folder_path}."
-
-        info_mat = read_mat(self.folder_path / "info.mat")
+        info_mat_file_path = Path(info_mat_file_path)
+        assert info_mat_file_path.exists(), f"The file '{info_mat_file_path}' does not exist."
+
+        info_mat = read_mat(str(info_mat_file_path))
         assert "info" in info_mat, f"Could not find 'info' struct in 'info.mat'."
         self._num_frames = info_mat["info"]["numFrames"]
         self._sampling_frequency = info_mat["info"]["frameRate"]
 
-        roi_mat = read_mat(self.folder_path / "ROIfromRef.mat")
+        roi_from_ref_mat_file_path = Path(roi_from_ref_mat_file_path)
+        assert roi_from_ref_mat_file_path.exists(), f"The file '{roi_from_ref_mat_file_path}' does not exist."
+        roi_mat = read_mat(str(roi_from_ref_mat_file_path))
         assert "ROIcentroids" in roi_mat, f"Could not find 'ROIcentroids' in 'ROIfromRef.mat'."
         self._roi_locations = roi_mat[
             "ROIcentroids"
@@ -78,12 +75,16 @@ def __init__(
         self._dtype = self._image_masks.dtype
 
         # Contrast based vasculature mask
-        vasculature_mask = read_mat(self.folder_path / "vasculature_mask_2.mat")
-        assert "mask_binned" in vasculature_mask, f"Could not find 'mask_binned' in 'vasculature_mask_2.mat'."
+        vasculature_mask_file_path = Path(vasculature_mask_file_path)
+        assert vasculature_mask_file_path.exists(), f"The file '{vasculature_mask_file_path}' does not exist."
+        vasculature_mask = read_mat(str(vasculature_mask_file_path))
+        assert "mask_binned" in vasculature_mask, f"Could not find 'mask_binned' in '{vasculature_mask_file_path}'."
         self._image_vasculature = vasculature_mask["mask_binned"]
 
         # PCA mask (separate for blue and violet)
-        pca_mask_blue = read_mat(self.folder_path / f"blue_pca_vasculature_mask_2.mat")
+        blue_pca_mask_file_path = Path(blue_pca_mask_file_path)
+        assert blue_pca_mask_file_path.exists(), f"The file '{blue_pca_mask_file_path}' does not exist."
+        pca_mask_blue = read_mat(str(blue_pca_mask_file_path))
         assert "mask" in pca_mask_blue, f"Could not find 'mask' in 'blue_pca_vasculature_mask_2.mat'."
         self._image_pca_blue = pca_mask_blue["mask"]
 
@@ -92,7 +93,8 @@ def _compute_image_masks(self, pixel_mask):
         num_rois = self.get_num_rois()
         image_mask = np.zeros(shape=(*self._image_size, num_rois), dtype=np.uint8)
         for roi_ind, pixel_mask_roi in enumerate(pixel_mask):
-            pixel_mask_roi = pixel_mask_roi[0]
+            if isinstance(pixel_mask_roi, list):
+                pixel_mask_roi = pixel_mask_roi[0]
             if len(pixel_mask_roi) == 0:
                 # there are rois with no pixels
                 continue

src/pinto_lab_to_nwb/widefield/interfaces/widefield_processed_segmentationinterface.py

@@ -2,7 +2,7 @@
 
 from neuroconv.datainterfaces.ophys.basesegmentationextractorinterface import BaseSegmentationExtractorInterface
 from neuroconv.tools import get_module
-from neuroconv.utils import FolderPathType
+from neuroconv.utils import FilePathType
 from pynwb import NWBFile
 
 from pinto_lab_to_nwb.widefield.extractors.widefield_processed_segmentationextractor import (
@@ -15,15 +15,34 @@ class WidefieldProcessedSegmentationinterface(BaseSegmentationExtractorInterface
 
     Extractor = WidefieldProcessedSegmentationExtractor
 
-    def __init__(self, folder_path: FolderPathType, verbose: bool = True):
+    def __init__(
+        self,
+        info_mat_file_path: FilePathType,
+        roi_from_ref_mat_file_path: FilePathType,
+        vasculature_mask_file_path: FilePathType,
+        blue_pca_mask_file_path: FilePathType,
+        verbose: bool = True,
+    ):
         """
 
         Parameters
         ----------
-        folder_path : FolderPathType
+        info_mat_file_path : FilePathType
+            The file path to the 'info.mat' file.
+        roi_from_ref_mat_file_path : FilePathType
+            The file that contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
+        vasculature_mask_file_path: FilePathType
+            The file that contains the vasculature mask on the downsampled (binned) session image.
+        blue_pca_mask_file_path: FilePathType
+            The file that contains the PCA mask for the blue channel.
         verbose : bool, default: True
         """
-        super().__init__(folder_path=folder_path)
+        super().__init__(
+            info_mat_file_path=info_mat_file_path,
+            roi_from_ref_mat_file_path=roi_from_ref_mat_file_path,
+            vasculature_mask_file_path=vasculature_mask_file_path,
+            blue_pca_mask_file_path=blue_pca_mask_file_path,
+        )
         self.verbose = verbose
 
     def get_metadata(self) -> dict:

src/pinto_lab_to_nwb/widefield/interfaces/widefield_segmentation_images_blue_datainterface.py

@@ -3,7 +3,7 @@
 import numpy as np
 from neuroconv import BaseDataInterface
 from neuroconv.tools import get_module
-from neuroconv.utils import FolderPathType
+from neuroconv.utils import FolderPathType, FilePathType
 from pymatreader import read_mat
 from pynwb import NWBFile
 from pynwb.base import Images
@@ -13,37 +13,57 @@
 class WidefieldSegmentationImagesBlueInterface(BaseDataInterface):
     """The custom interface to add the blue channel manual and vasculature mask to the NWBFile."""
 
-    def __init__(self, folder_path: FolderPathType, verbose: bool = True):
+    def __init__(
+        self,
+        vasculature_mask_file_path: FilePathType,
+        manual_mask_file_path: FilePathType,
+        manual_mask_struct_name: str,
+        verbose: bool = True,
+    ):
         """
         The interface to add the summary images to the NWBFile.
 
         Parameters
         ----------
-        folder_path : FolderPathType
+        vasculature_mask_file_path : FilePathType
+            The file path to the vasculature mask file.
+        manual_mask_file_path : FilePathType
+            The file path to the manual mask file.
+        manual_mask_struct_name: str
+            The name of the struct in the manual mask file that contains the manual mask (e.g. "regMask" or "reg_manual_mask").
         verbose : bool, default: True
         """
-        super().__init__(folder_path=folder_path)
-        self.folder_path = Path(folder_path)
+        super().__init__(vasculature_mask_file_path=vasculature_mask_file_path)
+        self.vasculature_mask_file_path = Path(vasculature_mask_file_path)
+        assert (
+            self.vasculature_mask_file_path.exists()
+        ), f"The vasculature mask file '{vasculature_mask_file_path}' does not exist."
+
+        self.manual_mask_file_path = Path(manual_mask_file_path)
+        assert self.manual_mask_file_path.exists(), f"The manual mask file '{manual_mask_file_path}' does not exist."
+
+        self.manual_mask_struct_name = manual_mask_struct_name
+
         self.verbose = verbose
 
         self._image_vasculature = self._load_vasculature_mask()
         self._image_manual = self._load_manual_mask()
 
     def _load_vasculature_mask(self) -> np.ndarray:
-        vasculature_mask_file_path = self.folder_path / "vasculature_mask_2.mat"
-        assert vasculature_mask_file_path.exists(), f"The vasculature mask file is missing from {self.folder_path}."
-        vasculature_mask_mat = read_mat(str(vasculature_mask_file_path))
-        assert "mask" in vasculature_mask_mat, f"The vasculature mask is missing from {vasculature_mask_file_path}."
+        vasculature_mask_mat = read_mat(str(self.vasculature_mask_file_path))
+        assert (
+            "mask" in vasculature_mask_mat
+        ), f"The vasculature mask is missing from {self.vasculature_mask_file_path}."
         vasculature_mask = vasculature_mask_mat["mask"]
 
         return vasculature_mask
 
     def _load_manual_mask(self):
-        manual_mask_file_path = Path(self.folder_path) / "regManualMask.mat"
-        assert manual_mask_file_path.exists(), f"The manual mask file is missing from {self.folder_path}."
-        manual_mask_mat = read_mat(str(manual_mask_file_path))
-        assert "regMask" in manual_mask_mat, f"The manual mask is missing from {manual_mask_file_path}."
-        manual_mask = manual_mask_mat["regMask"]
+        manual_mask_mat = read_mat(self.manual_mask_file_path)
+        assert (
+            self.manual_mask_struct_name in manual_mask_mat
+        ), f"The manual mask is missing from {self.manual_mask_file_path}."
+        manual_mask = manual_mask_mat[self.manual_mask_struct_name]
 
         return manual_mask
 

src/pinto_lab_to_nwb/widefield/interfaces/widefield_segmentation_images_violet_datainterface.py

@@ -3,7 +3,7 @@
 import numpy as np
 from neuroconv import BaseDataInterface
 from neuroconv.tools import get_module
-from neuroconv.utils import FolderPathType
+from neuroconv.utils import FilePathType
 from pymatreader import read_mat
 from pynwb import NWBFile
 from pynwb.base import Images
@@ -13,28 +13,28 @@
 class WidefieldSegmentationImagesVioletInterface(BaseDataInterface):
     """The custom interface to add the violet channel PCA mask to the NWBFile."""
 
-    def __init__(self, folder_path: FolderPathType, verbose: bool = True):
+    def __init__(self, violet_pca_mask_file_path: FilePathType, verbose: bool = True):
         """
         The interface to add the summary images to the NWBFile.
 
         Parameters
         ----------
-        folder_path : FolderPathType
+        violet_pca_mask_file_path : FilePathType
+            The file path to the violet channel PCA mask file.
         verbose : bool, default: True
         """
-        super().__init__(folder_path=folder_path)
-        self.folder_path = Path(folder_path)
+        super().__init__(violet_pca_mask_file_path=violet_pca_mask_file_path)
+        self.violet_pca_mask_file_path = Path(violet_pca_mask_file_path)
+        assert (
+            self.violet_pca_mask_file_path.exists()
+        ), f"The violet channel PCA mask file '{violet_pca_mask_file_path}' does not exist."
         self.verbose = verbose
 
         self._image_pca_violet = self._load_pca_mask()
 
     def _load_pca_mask(self) -> np.ndarray:
-        pca_mask_file_path = self.folder_path / "violet_pca_vasculature_mask_2.mat"
-        assert (
-            pca_mask_file_path.exists()
-        ), f"The PCA mask file for the violet channel is missing from {self.folder_path}."
-        pca_mask_violet = read_mat(str(pca_mask_file_path))
-        assert "vasc_mask" in pca_mask_violet, f"Could not find 'vasc_mask' in 'violet_pca_vasculature_mask_2.mat'."
+        pca_mask_violet = read_mat(str(self.violet_pca_mask_file_path))
+        assert "vasc_mask" in pca_mask_violet, f"Could not find 'vasc_mask' in '{self.violet_pca_mask_file_path}'."
         pca_mask = pca_mask_violet["vasc_mask"]
 
         return pca_mask

src/pinto_lab_to_nwb/widefield/widefield_convert_session.py

@@ -21,6 +21,13 @@ def session_to_nwb(
     strobe_sequence_file_path: FilePathType,
     processed_imaging_file_path: FilePathType,
     info_file_path: FilePathType,
+    vasculature_mask_file_path: FilePathType,
+    manual_mask_file_path: FilePathType,
+    manual_mask_struct_name: str,
+    roi_from_ref_mat_file_path: FilePathType,
+    binned_vasculature_mask_file_path: FilePathType,
+    binned_blue_pca_mask_file_path: FilePathType,
+    binned_violet_pca_mask_file_path: FilePathType,
     subject_metadata_file_path: Optional[FilePathType] = None,
     stub_test: bool = False,
 ):
@@ -34,9 +41,23 @@ def session_to_nwb(
     widefield_imaging_folder_path: FolderPathType
         The folder path that contains the Micro-Manager OME-TIF imaging output (.ome.tif files).
     strobe_sequence_file_path: FilePathType
-            The file path to the strobe sequence file. This file should contain the 'strobe_session_key' key.
+        The file path to the strobe sequence file. This file should contain the 'strobe_session_key' key.
     info_file_path: FilePathType
         The file path to the Matlab file with information about the imaging session (e.g. 'frameRate').
+    vasculature_mask_file_path: FilePathType
+        The file path that contains the contrast based vasculature mask on the full size session image (blue channel).
+    manual_mask_file_path: FilePathType
+        The file path that contains the manual mask on the full size session image (blue channel).
+    manual_mask_struct_name: str
+        The name of the struct in the manual mask file that contains the manual mask (e.g. "regMask" or "reg_manual_mask").
+    roi_from_ref_mat_file_path: FilePathType
+        The file path that contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
+    binned_vasculature_mask_file_path: FilePathType
+        The file path that contains the contrast based vasculature mask on the downsampled (binned) session image (blue channel).
+    binned_blue_pca_mask_file_path: FilePathType
+        The file path that contains the PCA mask for the blue channel.
+    binned_violet_pca_mask_file_path: FilePathType
+        The file path that contains the PCA mask for the violet channel.
     subject_metadata_file_path: FilePathType, optional
         The file path to the subject metadata file. This file should contain the 'metadata' key.
     stub_test: bool, optional
@@ -106,13 +127,18 @@ def session_to_nwb(
     source_data.update(
         dict(
             SegmentationProcessedBlue=dict(
-                folder_path=str(widefield_imaging_folder_path),
+                info_mat_file_path=str(info_file_path),
+                roi_from_ref_mat_file_path=str(roi_from_ref_mat_file_path),
+                vasculature_mask_file_path=str(binned_vasculature_mask_file_path),
+                blue_pca_mask_file_path=str(binned_blue_pca_mask_file_path),
             ),
             SummaryImagesBlue=dict(
-                folder_path=str(widefield_imaging_folder_path),
+                vasculature_mask_file_path=str(vasculature_mask_file_path),
+                manual_mask_file_path=str(manual_mask_file_path),
+                manual_mask_struct_name=manual_mask_struct_name,
             ),
             SummaryImagesViolet=dict(
-                folder_path=str(widefield_imaging_folder_path),
+                violet_pca_mask_file_path=str(binned_violet_pca_mask_file_path),
             ),
         )
     )
@@ -156,13 +182,39 @@ def session_to_nwb(
     # Parameters for conversion
 
     # The folder path that contains the raw imaging data in Micro-Manager OME-TIF format (.ome.tif files).
-    imaging_folder_path = Path("/Users/weian/data/DrChicken_20230419_20hz")
+    # imaging_folder_path = Path("/Users/weian/data/Cherry/20230802/Cherry_20230802_20hz_1")
+    imaging_folder_path = Path("/Volumes/t7-ssd/Pinto/DrChicken_20230419_20hz")
     # The file path to the strobe sequence file.
     strobe_sequence_file_path = imaging_folder_path / "strobe_seq_1_2.mat"
     # The file path to the downsampled imaging data in Matlab format (.mat file).
     processed_imaging_path = imaging_folder_path / "rawf_full.mat"
     # The file path to the Matlab file with information about the imaging session (e.g. 'frameRate').
     info_file_path = imaging_folder_path / "info.mat"
+
+    # Parameters for custom segmentation and summary images
+    # The file path that contains the contrast based vasculature mask on the full size session image (blue channel).
+    vasculature_mask_file_path = imaging_folder_path / "vasculature_mask_2.mat"
+
+    # The file path that contains the manual mask on the full size session image (blue channel).
+    # manual_mask_file_path = imaging_folder_path / "reg_manual_mask_jlt6316_Cherry_20230802_1_1_1.mat"
+    manual_mask_file_path = imaging_folder_path / "regManualMask.mat"
+    # The name of the struct in the manual mask file that contains the manual mask (e.g. "regMask" or "reg_manual_mask").
+    # manual_mask_struct_name = "reg_manual_mask"
+    manual_mask_struct_name = "regMask"
+
+    # The file path that contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
+    # roi_from_ref_mat_file_path = imaging_folder_path / "ROIfromRef_1.mat"
+    roi_from_ref_mat_file_path = imaging_folder_path / "ROIfromRef.mat"
+
+    # The file path that contains the contrast based vasculature mask on the downsampled (binned) session image (blue channel).
+    binned_vasculature_mask_file_path = imaging_folder_path / "vasculature_mask_2.mat"
+
+    # The file path that contains the PCA mask for the blue channel.
+    binned_blue_pca_mask_file_path = imaging_folder_path / "blue_pca_vasculature_mask_2.mat"
+
+    # The file path that contains the PCA mask for the violet channel.
+    binned_violet_pca_mask_file_path = imaging_folder_path / "violet_pca_vasculature_mask_2.mat"
+
     subject_metadata_file_path = "/Volumes/t7-ssd/Pinto/Behavior/subject_metadata.mat"
     # The file path to the NWB file that will be created.
     nwbfile_path = Path("/Volumes/t7-ssd/Pinto/nwbfiles/widefield/DrChicken_20230419_20hz.nwb")
@@ -175,6 +227,13 @@ def session_to_nwb(
         strobe_sequence_file_path=strobe_sequence_file_path,
         processed_imaging_file_path=processed_imaging_path,
         info_file_path=info_file_path,
+        vasculature_mask_file_path=vasculature_mask_file_path,
+        manual_mask_file_path=manual_mask_file_path,
+        manual_mask_struct_name=manual_mask_struct_name,
+        roi_from_ref_mat_file_path=roi_from_ref_mat_file_path,
+        binned_vasculature_mask_file_path=binned_vasculature_mask_file_path,
+        binned_blue_pca_mask_file_path=binned_blue_pca_mask_file_path,
+        binned_violet_pca_mask_file_path=binned_violet_pca_mask_file_path,
         subject_metadata_file_path=subject_metadata_file_path,
         stub_test=stub_test,
     )