From c38292d6003898c14f54a0f2f0555d9cf096628a Mon Sep 17 00:00:00 2001
From: alessandrofelder <alessandrofelder@users.noreply.github.com>
Date: Thu, 15 Aug 2024 17:40:40 +0100
Subject: [PATCH 1/3] implement downsampling script for tadpoles.

---
 examples/tadpole/downsample_source_images.py | 74 ++++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 examples/tadpole/downsample_source_images.py

diff --git a/examples/tadpole/downsample_source_images.py b/examples/tadpole/downsample_source_images.py
new file mode 100644
index 0000000..777a2cd
--- /dev/null
+++ b/examples/tadpole/downsample_source_images.py
@@ -0,0 +1,74 @@
+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,
+)
+
+
+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)

From 62e221e2b764085b25232a884486291f260e6501 Mon Sep 17 00:00:00 2001
From: Alessandro Felder <alessandrofelder@users.noreply.github.com>
Date: Fri, 30 Aug 2024 13:47:01 +0100
Subject: [PATCH 2/3] expand help strings

---
 examples/tadpole/downsample_source_images.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/examples/tadpole/downsample_source_images.py b/examples/tadpole/downsample_source_images.py
index 777a2cd..e88423f 100644
--- a/examples/tadpole/downsample_source_images.py
+++ b/examples/tadpole/downsample_source_images.py
@@ -37,13 +37,15 @@ def downsample_tadpole(folder: Path) -> None:
     parser.add_argument(
         "--source_data",
         type=str,
-        help="Path to the source data folder",
+        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",
+        help="Path to the template-building root folder. Results will " \
+        "be written to the rawdata subfolder.",
         required=True,
     )
     parser.add_argument(

From 6cce8c9a9aec9d9941031ed668932016727b3785 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 30 Aug 2024 12:47:13 +0000
Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 examples/tadpole/downsample_source_images.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/tadpole/downsample_source_images.py b/examples/tadpole/downsample_source_images.py
index e88423f..e5e4662 100644
--- a/examples/tadpole/downsample_source_images.py
+++ b/examples/tadpole/downsample_source_images.py
@@ -37,14 +37,14 @@ def downsample_tadpole(folder: Path) -> None:
     parser.add_argument(
         "--source_data",
         type=str,
-        help="Path to the source data folder. The source data should " \
+        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 " \
+        help="Path to the template-building root folder. Results will "
         "be written to the rawdata subfolder.",
         required=True,
     )