From 84b09a5cd9f9cacc46406a99ec903420479a76ea Mon Sep 17 00:00:00 2001
From: alessandrofelder <alessandrofelder@users.noreply.github.com>
Date: Thu, 21 Nov 2024 10:27:21 +0000
Subject: [PATCH] simple crab downsampling

---
 examples/crab/downsample_source_images.py | 64 +++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 examples/crab/downsample_source_images.py

diff --git a/examples/crab/downsample_source_images.py b/examples/crab/downsample_source_images.py
new file mode 100644
index 0000000..18230b9
--- /dev/null
+++ b/examples/crab/downsample_source_images.py
@@ -0,0 +1,64 @@
+import argparse
+from pathlib import Path
+
+from loguru import logger
+
+from brainglobe_template_builder.preproc.transform_utils import downsample
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Downsample source images")
+    parser.add_argument(
+        "--source_data",
+        type=str,
+        help="Path to the source data folder. The source data should "
+        "contain a subfolder per subject, and tiffs 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 subfolder.",
+        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)
+
+    in_plane_resolution = 0.43
+    out_of_plane_resolution = 5
+    in_plane_factor = round(target_isotropic_resolution / in_plane_resolution)
+    axial_factor = round(target_isotropic_resolution / out_of_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():
+        if (
+            not str(sample_folder)[-6:-1] == "Crab_"
+        ):  # find folders like Crab_3
+            logger.info(f"{str(sample_folder)[-6:-1]} is not a crab folder")
+            continue
+        logger.info(f"Downsampling {sample_folder.name}...")
+        sample_id = str(sample_folder).split("_")[-1].lower()
+        stain = "Nuclear"
+        sample_filename = (
+            f"sub-{sample_id}_res-{target_isotropic_resolution}"
+            f"um_stain-{stain}.tif"
+        )
+        downsample(
+            sample_folder / "Nuclear/",
+            template_raw_data / sample_filename,
+            in_plane_factor,
+            axial_factor,
+        )
+        logger.info(f"{sample_filename} downsampled.")