From 0ff77eccbdad4560214692eebaa0854d202f88cc Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Mon, 13 Mar 2023 13:43:04 +0100
Subject: [PATCH] remove conversion, combine directly nd2
---
Snakefile | 14 +++++++++++---
combine.py | 7 ++++---
2 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index 2ed2a08..c783a79 100644
--- a/Snakefile
+++ b/Snakefile
@@ -18,7 +18,7 @@ rule align_and_count:
input:
data="{folder}/day{day}/BF_TRITC_maxZ.zarr",
concentrations="{folder}/concentrations.yaml",
- template="template16_pad100-adj-sm2.tif",
+ template="v3/template_bin16_v3.tif",
labels="v3/labels_bin2_v4.tif"
output:
zarr = directory("{folder}/day{day}/BF_TRITC_aligned.zarr"),
@@ -26,6 +26,14 @@ rule align_and_count:
shell:
"python align.py {input.data} {output.zarr} {input.concentrations} {input.template} {input.labels} {output.table} 1"
+rule correct_xy:
+ input:
+ zarr = "{folder}/day{day}/BF_TRITC_aligned-to-correct.zarr",
+ table = "{folder}/day{day}/correction.csv"
+ output:
+ zarr = directory("{folder}/day{day}/BF_TRITC_aligned-corrected.zarr")
+ shell:
+ "python correct.py {input.zarr} {input.table} {output.zarr}"
rule align_and_count_2D:
input:
@@ -50,8 +58,8 @@ rule get_sizes_nd2:
rule combine_BF_TRITC_3D_maxZ:
input:
- bf="{folder}/day{day}/BF-2D.zarr",
- fluo="{folder}/day{day}/TRITC-3D.zarr"
+ bf="{folder}/day{day}/BF-2D.nd2",
+ fluo="{folder}/day{day}/TRITC-3D.nd2"
output:
directory("{folder}/day{day}/BF_TRITC_maxZ.zarr")
shell:
diff --git a/combine.py b/combine.py
index b50dd92..10b142e 100644
--- a/combine.py
+++ b/combine.py
@@ -2,11 +2,12 @@ import dask.array as da
import os
from zarr_tools.convert import to_zarr
import fire
+import nd2
-def combine(BF_zarr_2D_path:str, TRITC_zarr_3D_path:str, out_zarr_path:str):
- bd2d = da.from_zarr(os.path.join(BF_zarr_2D_path,'0/'))
+def combine(BF_2D_path:str, TRITC_3D_path:str, out_zarr_path:str):
+ bd2d = nd2.ND2File(BF_2D_path).to_dask()
print('Opened BF:', bd2d)
- fd3d = da.from_zarr(os.path.join(TRITC_zarr_3D_path,'0/'))
+ fd3d = nd2.ND2File(TRITC_3D_path).to_dask()
print('Opened TRITC:', fd3d)
fd2d = fd3d.max(axis=1)
bd2d = da.stack([bd2d, fd2d], axis=1)
--
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