From 0bc8aba325d675c45e22ba64de80d5a470b5b0fa Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Sun, 24 May 2015 17:44:43 +0200
Subject: [PATCH] resave hdf5
---
spim_registration/timelapse/Snakefile | 19 ++++++++++---------
spim_registration/timelapse/tomancak_czi.json | 6 +++---
2 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 2f71f0d..d61c139 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -71,7 +71,7 @@ rule define_xml_czi:
rule define_xml_tif:
input: glob.glob('*.tif')
output: config["common"]["first_xml_filename"] + ".xml"
- message: "Execute define_xml_czi on the following files {input}"
+ message: "Execute define_xml_tif on the following files {input}"
log: "define_xml_tif.log"
run:
cmd_string = produce_string(
@@ -97,18 +97,17 @@ rule define_xml_tif:
config["define_xml_tif"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
+
cmd_string +="> {log} 2>&1 && touch {output}"
shell(cmd_string)
# resave .czi dataset as hdf5
-rule resave_czi_hdf5:
-# input: config["common"]["first_xml_filename"] + ".xml"
+rule resave_hdf5:
input: rules.define_xml_tif.output, glob.glob('*.tif')
-# output: "hdf5_Stock68.h5", "hdf5_Stock68.xml"
- output: config["common"]["hdf5_xml_filename"] + ".xml", config["common"]["hdf5_xml_filename"] + ".h5"
+ output: "hdf5_test_unicore.xml", "hdf5_test_unicore.h5"
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_czi.log"
+ threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect
+ log: "resave_hdf5.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -130,14 +129,16 @@ rule resave_czi_hdf5:
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)
-
+
+ #cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
rule registration:
- input: "{xml_base}-{file_id}-00.h5"
+ input: "{xml_base}-{file_id}-00.h5", rules.resave_hdf5.output
#input: rules.resave_hdf5.output, "{xml_base}-{file_id}-00.h5"
output: "{xml_base}-{file_id,\d+}-00.h5_registered", #"{xml_base}.job_{file_id,\d+}.xml"
log: "{xml_base}-{file_id}-registration.log"
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index d173e9d..21c30f1 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -8,7 +8,7 @@
"bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
"first_xml_filename" : "test_unicore",
"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
- "fusion_switch" : "fusion"
+ "fusion_switch" : "deconvolution"
},
"define_xml_czi" :
@@ -49,9 +49,9 @@
"bsh_file" : "define_tif_zip.bsh"
},
- "resave_czi_hdf5" :
+ "resave_hdf5" :
{
- "parallel_timepoints" : "2",
+ "parallel_timepoints" : "3",
"resave_angle" : "\"All angles\"",
"resave_channel" : "\"All channels\"",
"resave_illumination" : "\"All illuminations\"",
--
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