chore: Scripts for segmentation dilation and max projection

examples/dilate_segmentation_mask.py

@@ -0,0 +1,93 @@
+"""Example script to dilate segmentation masks in image files."""
+
+import sys
+from argparse import ArgumentParser
+from glob import glob
+from itertools import chain
+from pathlib import Path
+
+import numpy as np
+
+from PartSegCore.image_operations import dilate, to_binary_image
+from PartSegCore.mask.io_functions import LoadROIImage, MaskProjectTuple, SaveROI, SaveROIOptions
+from PartSegCore.roi_info import ROIInfo
+from PartSegCore.segmentation.watershed import calculate_distances_array, get_neigh
+from PartSegCore_compiled_backend.sprawl_utils.find_split import euclidean_sprawl
+
+
+def convert_mask(file_path: Path, radius: float, suffix: str, only_selected: bool):
+    if radius <= 0:
+        raise ValueError("Radius must be positive")
+    print(f"Converting {file_path} to {suffix} with radius {radius}")
+
+    project = LoadROIImage.load([str(file_path)])
+
+    roi_ = project.roi_info.roi.squeeze()
+    selected_components = project.selected_components
+    if only_selected and selected_components is not None:
+        mask = np.isin(roi_, selected_components)
+        roi_ = roi_ * mask
+
+        unique_values = np.unique(roi_)
+        mapping = np.zeros(np.max(unique_values) + 1, dtype=roi_.dtype)
+        for new_val, old_val in enumerate(unique_values):
+            mapping[old_val] = new_val
+        roi_ = mapping[roi_]
+
+        selected_components = list(range(1, len(unique_values)))
+
+    bin_roi = to_binary_image(roi_)
+    sprawl_area = dilate(bin_roi, [radius, radius], True)
+    components_num = np.max(roi_)
+    neigh, dist = calculate_distances_array(project.image.spacing, get_neigh(True))
+    roi = project.image.fit_array_to_image(
+        euclidean_sprawl(
+            sprawl_area,
+            roi_,
+            components_num,
+            neigh,
+            dist,
+        )
+    )
+    new_file_path = file_path.with_name(file_path.stem + suffix + file_path.suffix)
+    print("Saving to ", new_file_path)
+    SaveROI.save(
+        str(new_file_path),
+        MaskProjectTuple(
+            file_path=str(new_file_path),
+            image=project.image,
+            roi_info=ROIInfo(roi),
+            spacing=project.spacing,
+            frame_thickness=project.frame_thickness,
+            selected_components=selected_components,
+        ),
+        SaveROIOptions(
+            relative_path=True,
+            mask_data=True,
+            frame_thickness=project.frame_thickness,
+            spacing=project.spacing,
+        ),
+    )
+
+
+def main():
+    parser = ArgumentParser()
+    parser.add_argument("project_files", nargs="+", type=str)
+    parser.add_argument("--dilate", type=int, default=1)
+    parser.add_argument("--suffix", type=str, default="_dilated")
+    parser.add_argument("--only-selected", action="store_true")
+
+    args = parser.parse_args()
+
+    files = list(chain.from_iterable(glob(x) for x in args.project_files))
+    if not files:
+        print("No files found")
+        return -1
+
+    for file_path in files:
+        convert_mask(Path(file_path).absolute(), args.dilate, args.suffix, args.only_selected)
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

examples/extract_components_from_project.py

@@ -0,0 +1,32 @@
+from argparse import ArgumentParser
+from glob import glob
+from itertools import chain
+from pathlib import Path
+
+from PartSegCore.mask.io_functions import LoadROIImage, SaveComponents, SaveComponentsOptions
+
+
+def cut_components(project_file: Path):
+    project = LoadROIImage.load([str(project_file)])
+    SaveComponents.save(
+        str(project_file.parent / (project_file.stem + "_components")),
+        project,
+        SaveComponentsOptions(
+            frame=0,
+            mask_data=True,
+        ),
+    )
+
+
+def main():
+    parser = ArgumentParser()
+    parser.add_argument("project_files", nargs="+", type=str)
+    args = parser.parse_args()
+    files = list(chain.from_iterable(glob(f) for f in args.project_files))
+    for file_path in files:
+        print(f"Processing {file_path}")
+        cut_components(Path(file_path))
+
+
+if __name__ == "__main__":
+    main()

examples/max_projection.py

@@ -0,0 +1,49 @@
+"""
+For collections of tiff files save a max projection of each file.
+"""
+
+from argparse import ArgumentParser
+from glob import glob
+from itertools import chain
+from pathlib import Path
+
+from PartSegImage import Image, ImageWriter, TiffImageReader
+
+
+def max_projection(file_path: Path, suffix: str = "_max", with_mask: bool = False):
+    if with_mask:
+        mask_path = str(file_path.parent / (file_path.stem + "_mask" + file_path.suffix))
+    else:
+        mask_path = None
+    image = TiffImageReader.read_image(str(file_path), mask_path)
+    if "Z" not in image.axis_order:
+        raise ValueError(f"Image {file_path} does not have Z axis")
+    max_proj = image.get_data().max(axis=image.axis_order.index("Z"))
+    if with_mask:
+        mask_projection = image.mask.max(axis=image.array_axis_order.index("Z"))
+    else:
+        mask_projection = None
+    image2 = Image(
+        max_proj, spacing=image.spacing[1:], axes_order=image.axis_order.replace("Z", ""), mask=mask_projection
+    )
+    ImageWriter.save(image2, str(file_path.with_name(file_path.stem + suffix + file_path.suffix)))
+    if with_mask:
+        ImageWriter.save_mask(image2, str(file_path.with_name(file_path.stem + suffix + "_mask" + file_path.suffix)))
+
+
+def main():
+    parser = ArgumentParser()
+    parser.add_argument("image_files", nargs="+", type=str)
+    parser.add_argument("--suffix", type=str, default="_max")
+    parser.add_argument("--with-mask", action="store_true")
+    args = parser.parse_args()
+    files = list(chain.from_iterable(glob(f) for f in args.image_files))
+    for file_path in files:
+        if args.with_mask and Path(file_path).stem.endswith("_mask"):
+            continue
+        print(f"Processing {file_path}")
+        max_projection(Path(file_path), args.suffix, args.with_mask)
+
+
+if __name__ == "__main__":
+    main()

package/PartSegImage/image_reader.py

@@ -276,7 +276,7 @@ def read_image(
         read image file with optional mask file
 
         :param image_path: path or opened file contains image
-        :param mask_path:
+        :param mask_path: path or opened file contains mask
         :param callback_function: function for provide information about progress in reading file (for progressbar)
         :param default_spacing: used if file do not contains information about spacing
             (or metadata format is not supported)