wip: tadpole-script

examples/tadpole/downsample_source_images.py

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+import argparse
+from pathlib import Path
+
+from brainglobe_utils.IO.image import read_z_stack, save_any
+from loguru import logger
+
+from brainglobe_template_builder.preproc.transform_utils import (
+    downsample_anisotropic_image_stack,
+)
+
+# TODO: config for downsampling,
+# - make this `def downsample(config)` and tadpole-independent!
+# - be able to exclude hemisphere through the config
+# - generalise getting wavelength and sample id from folder name
+
+
+def downsample_tadpole(folder: Path) -> None:
+    logger.info(f"Downsampling {folder.name}...")
+    stack = read_z_stack(str(folder))
+
+    in_plane_resolution = 1
+    out_of_plane_resolution = 3
+    in_plane_factor = int(target_isotropic_resolution / in_plane_resolution)
+    axial_factor = int(target_isotropic_resolution / out_of_plane_resolution)
+    downsampled = downsample_anisotropic_image_stack(
+        stack, in_plane_factor=in_plane_factor, axial_factor=axial_factor
+    )
+
+    sample_id = str(folder).split("_")[1].lower()
+    channel = "blue" if str(folder).split("_")[2] == "488" else "orange"
+    sample_filename = (
+        f"sub-{sample_id}_res-{target_isotropic_resolution}"
+        f"um_channel-{channel}.tif"
+    )
+    save_any(downsampled, template_raw_data / sample_filename)
+
+    logger.info(f"{sample_filename} downsampled.")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Downsample source images")
+    parser.add_argument(
+        "--source_data",
+        type=str,
+        help="Path to the source data folder",
+        required=True,
+    )
+    parser.add_argument(
+        "--template_building_root",
+        type=str,
+        help="Path to the template-building root 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)
+    template_building_root = Path(args.template_building_root)
+    target_isotropic_resolution = int(args.target_isotropic_resolution)
+
+    for subfolder_name in [
+        "rawdata",
+        "logs",
+        "derivatives",
+        "scripts",
+        "templates",
+    ]:
+        subfolder = template_building_root / subfolder_name
+        subfolder.mkdir(exist_ok=True, parents=True)
+
+    template_raw_data = template_building_root / "rawdata"
+    for folder in source_data.iterdir():
+        downsample_tadpole(folder)