From 7d7dbd9583171ffb0254b41cbbeaab9864742878 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Fri, 22 May 2015 18:49:31 +0200
Subject: [PATCH] Added resave czi as hdf5
---
spim_registration/timelapse/Snakefile | 43 ++++++++++++-------
spim_registration/timelapse/tomancak_czi.json | 8 ++--
2 files changed, 32 insertions(+), 19 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index d98baea..149341a 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -67,14 +67,14 @@ rule define_xml_czi:
shell(cmd_string)
# resave .czi dataset as hdf5
-rule resave_hdf5:
+rule resave_czi_hdf5:
input: rules.define_xml_czi.output, glob.glob('*.czi')
- output: glob.glob('*h5')
+ output: "hdf5_Stock68.h5", "hdf5_Stock68.xml"
message: "Execute resave_hdf5 on {input}"
+ threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect
log: "export.log"
- run:
- for i in config["resave_hdf5"]["parallel_timepoints"]:
- cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
+ run:
+ part_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={hdf5_xml_filename} \
@@ -86,17 +86,30 @@ rule resave_hdf5:
-Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
- -Drun_only_job_number=%i \
- -- --no-splash {path_bsh}""",
- config["common"],
- config["define_xml_czi"],
- config["resave_hdf5"],
- jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"]) % i
- i +=1
+ -Drun_only_job_number={job_number} \
+ -- --no-splash {path_bsh} > {log}-{job_number}.log 2>&1 &\n""", # the & submits everyting at once
+ config["common"],
+ config["define_xml_czi"],
+ config["resave_hdf5"],
+ jdir=JOBDIR,
+ path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
+ cmd_string = ""
+ for i in range(int(config["resave_hdf5"]["parallel_timepoints"])):
+ cmd_string += part_string.format(job_number=i)
+
+ shell(cmd_string)
+
+rule define_xml_tif:
+
+rule resave_tif_hdf5
+
+
+
+
+
+
+
- cmd_string += "> {log} 2>&1"
- shell(cmd_string)
rule registration:
# input: "{xml_base}-{file_id}-00.h5"
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 358cdff..b98a0ec 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -28,16 +28,16 @@
"bsh_file" : "define_czi.bsh"
},
- "resave_hdf5" :
+ "resave_czi_hdf5" :
{
- "parallel_timepoints" : "range(0,2)",
+ "parallel_timepoints" : "2",
"hdf5_xml_filename" : "\"hdf5_Stock68\"",
"resave_angle" : "\"All angles\"",
"resave_channel" : "\"All channels\"",
"resave_illumination" : "\"All illuminations\"",
"resave_timepoint" : "\"All Timepoints\"",
- "subsampling_factors" : "\"{ {1,1,1}, {2,2,1}, {4,4,1}, {8,8,1} }\"",
- "hdf5_chunk_sizes" : "\"{ {32,32,4}, {32,32,4}, {16,16,16}, {16,16,16} }\"",
+ "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
+ "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
"timepoints_per_partition" : "1",
"setups_per_partition" : "0",
"bsh_file" : "export.bsh"
--
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