Downsample fly-wing-disc images using tif files as source

examples/drosophila/wing-disc.py

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+import argparse
+from pathlib import Path
+
+from loguru import logger
+
+from brainglobe_template_builder.preproc.transform_utils import downsample_anisotropic_image_stack
+from brainglobe_utils.IO.image import load_any, save_any
+from dask import array as da
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Download source image')
+    parser.add_argument(
+        '--source_data_root',
+        type=str,
+        help='Path to the source data folder. The source data should contain'
+             'a subfolder per subject, with picture files within it',
+        required=True,
+    )
+    parser.add_argument(
+        '--template_building_root',
+        type=str,
+        help='Path to the template-building root folder.Results will be '
+             'written to the rawdata folder.',
+        required=True
+    )
+    parser.add_argument(
+        '--target_isotropic_resolution',
+        type=int,
+        help='Target isotropic resolution',
+        required=True
+    )
+
+    args = parser.parse_args()
+
+    source_data = Path(args.source_data_root)
+    template_building_root = Path(args.template_building_root)
+    target_isotropic_resolution = int(args.target_isotropic_resolution)
+
+    in_plane_resolution=0.5
+    out_of_plane_resolution=1
+
+    in_plane_factor = int(target_isotropic_resolution/in_plane_resolution)
+    axial_factor = int(target_isotropic_resolution/in_plane_resolution)
+
+    template_raw_data = template_building_root/'rawdata'
+    template_raw_data.mkdir(exist_ok=True, parents=True)
+
+    for sample_folder in source_data.iterdir():
+        logger.info(f"Downsampling {sample_folder}...")
+        sample_id = str(sample_folder.name).split("_")[0].lower()
+        channel = 'membrane'
+        sample_filename = (
+            f"sub-{sample_id}_res-{target_isotropic_resolution}"
+            f"um_channel-{channel}.tif"
+        )
+        assert Path(sample_folder).exists(), f"{sample_folder} not found"
+        original_file_path = Path(sample_folder) / f"{sample_id}_overview-Airyscan-Processing-0{sample_id[-1]}_C1.tif"
+        assert Path(original_file_path).exists(), f"Filepath {original_file_path} not found"
+        original_image = load_any(original_file_path)
+        original_image_dask = da.from_array(original_image,chunks={0: 1, 1: -1, 2: -1})
+        down_sampled_image = downsample_anisotropic_image_stack(original_image_dask,in_plane_factor,axial_factor)
+        save_any(down_sampled_image,template_raw_data/sample_filename)
+        logger.info(f"{sample_filename} downsampled.")