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@@ -68,14 +68,10 @@ def apply_transform(segmentation, fixed, index, out_dir, temporary_directory):
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return post_transform_loc
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def generate_segmentation(slice_path, segment_path, template_path, approx_index, dapi, output_directory):
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-
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+ tools.create_dir(output_directory)
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+
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if slice_path.endswith('.tiff') or slice_path.endswith('.tif'):
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Image.MAX_IMAGE_PIXELS = None
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- # tif_image = Image.open(slice_path)
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- # ch_nm = (list(tif_image.tag_v2[270].split('='))[2])
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- # if int(ch_nm[0]) < dapi:
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- # print(f'DAPI channel out of range, max range is {ch_nm[0]} channels')
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- # sys.exit()
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tif_path = preprocess.tiff_to_nii(slice_path, output_directory)
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slice_path = tif_path[0]
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elif not slice_path.endswith(".nii"):
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@@ -84,15 +80,17 @@ def generate_segmentation(slice_path, segment_path, template_path, approx_index,
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out_subdir = Path(output_directory) / Path(slice_path).stem.replace(' ', '_').replace(',','_').replace('.','')
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tools.create_dir(out_subdir)
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- temporary_directory = Path(output_directory) / Path(out_subdir) / 'tmp'
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+ temporary_directory = Path(out_subdir) / 'tmp'
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tools.create_dir(temporary_directory)
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channel_paths = preprocess.split_nii_channels(slice_path, out_subdir, True, dapi-1)
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optimal_index = find_optimal_index(channel_paths[dapi-1], template_path, approx_index, temporary_directory)
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seg_loc = apply_transform(segment_path, channel_paths[dapi-1], optimal_index, out_subdir, temporary_directory)
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+
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tools.remove_dir(temporary_directory)
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os.remove(Path(out_subdir) / 'segment_slice.nii')
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os.rename(Path(out_subdir) / 'TemplateSlice_Composite.h5', Path(out_subdir) / 'Transformation_Composite.h5')
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os.rename(Path(out_subdir) / 'TemplateSlice_InverseComposite.h5', Path(out_subdir) / 'Transformation_InverseComposite.h5')
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+
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return seg_loc
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if __name__ == "__main__":
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