From f75d0136d216224e98f241ed1e78b90eba328bde Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Mon, 25 Sep 2023 09:35:43 +0200
Subject: [PATCH] make crops
---
Snakefile | 12 +++++++++++-
make_crops.py | 41 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 52 insertions(+), 1 deletion(-)
create mode 100644 make_crops.py
diff --git a/Snakefile b/Snakefile
index c783a79..90b6a0e 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,7 +1,8 @@
rule combine_tables:
input:
table1="{folder}/day1/table.csv",
- table2="{folder}/day2/table.csv"
+ table2="{folder}/day2/table.csv",
+ crops = "{folder}/day2/BF_TRITC_aligned.crops.zarr"
params:
threshold="20" #minimum number of cells for day 2
@@ -26,6 +27,15 @@ rule align_and_count:
shell:
"python align.py {input.data} {output.zarr} {input.concentrations} {input.template} {input.labels} {output.table} 1"
+rule make_crops:
+ input:
+ data = "{folder}/day{day}/BF_TRITC_aligned.zarr"
+ output:
+ zarr = directory("{folder}/day{day}/BF_TRITC_aligned.crops.zarr")
+ shell:
+ "python make_crops.py {input.data} {output.zarr}"
+
+
rule correct_xy:
input:
zarr = "{folder}/day{day}/BF_TRITC_aligned-to-correct.zarr",
diff --git a/make_crops.py b/make_crops.py
new file mode 100644
index 0000000..f6de406
--- /dev/null
+++ b/make_crops.py
@@ -0,0 +1,41 @@
+import pandas as pd
+import os
+import dask.array as da
+import re
+import fire
+
+EXPECTED_SHAPE = (6, 3, 7152, 22192)
+
+def main(aligned_path, out_path, size=300):
+ centers = pd.read_csv(
+ "v3/centers_bin16.csv",
+ index_col=0
+ ).values * 8
+ _ = get_crops(aligned_path, out_path, centers=centers, size=size)
+ return 0
+
+def crop2d(img, center: tuple, size: int ):
+ im = img[
+ ...,
+ int(center[0]) - size // 2 : int(center[0]) + size // 2,
+ int(center[1]) - size // 2 : int(center[1]) + size // 2,
+ ]
+ return im
+
+def get_crops(path_to_zarr, out_path, centers, size):
+ if os.path.exists(out_path):
+ print(f"already exists, reading")
+ return da.from_zarr(out_path)
+ date = (re.compile("[0-9]{8}").findall(path_to_zarr)[0])
+ data = da.from_zarr(path_to_zarr+"/0/")
+ print(f"{date}: {data.shape} \n")
+ if not data.shape == EXPECTED_SHAPE:
+ return
+ crops = da.stack(map(lambda c: crop2d(data[:,:2], c, size), centers)).rechunk()
+ da.to_zarr(crops, out_path)
+ print(f"Saved {crops.shape} to {out_path}")
+ return crops
+
+
+if __name__ == "__main__":
+ fire.Fire(main)
--
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