From db2406378650a60307ca41bd0b19c0124d3bdb0e Mon Sep 17 00:00:00 2001
From: Peter Steinbach <steinbach@scionics.de>
Date: Thu, 28 May 2015 23:01:03 +0200
Subject: [PATCH] various changes: removed dummy files between
registration->xml_merge; spotted problem in timepoint number for
registration; refactored padding
---
spim_registration/timelapse/Snakefile | 68 ++++++++++++++-------------
1 file changed, 35 insertions(+), 33 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 0e9744d..e04e8f9 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -9,9 +9,10 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
#data specific config file, expected to be inside JOBDIR
configfile: "tomancak_czi.json"
-padding_format = "-{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}-00.h5"
+padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
+ds_format = "-"+padding_format+"-00.h5"
# problematic needs padding of file_id
-datasets = [ config["common"]["hdf5_xml_filename"].strip('\"')+padding_format.format(item) for item in range(int(config["common"]["ntimepoints"])) ]
+datasets = [ str(config["common"]["hdf5_xml_filename"].strip('\"')+(ds_format.format(item))) for item in range(int(config["common"]["ntimepoints"])) ]
xml_merge_in = produce_xml_merge_job_files(datasets)
@@ -28,32 +29,32 @@ rule define_xml_czi:
output: config["common"]["first_xml_filename"] + ".xml"
log: "define_xml_czi.log"
run:
- cmd_string = produce_string(
- """{fiji-prefix} {fiji-app} \
+ cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
- -Dfirst_czi={first_czi} \
- -Dangle_1={angle_1} \
- -Dangle_2={angle_2} \
- -Dangle_3={angle_3} \
- -Dangle_4={angle_4} \
- -Dangle_5={angle_5} \
- -Dchannel_1={channel_1} \
- -Dchannel_2={channel_2} \
- -Dillumination_1={illumination_1} \
- -Drotation_around={rotation_around} \
- -Dpixel_distance_x={pixel_distance_x} \
- -Dpixel_distance_y={pixel_distance_y} \
- -Dpixel_distance_z={pixel_distance_z} \
- -Dpixel_unit={pixel_unit} \
- -Dfirst_xml_filename={first_xml_filename} \
- -- --no-splash {path_bsh}""",
- config["common"],
- config["define_xml_czi"],
- jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["define_xml_czi"]["bsh_file"])
-
- cmd_string += " > {log} 2>&1"
+ -Dfirst_czi={first_czi} \
+ -Dangle_1={angle_1} \
+ -Dangle_2={angle_2} \
+ -Dangle_3={angle_3} \
+ -Dangle_4={angle_4} \
+ -Dangle_5={angle_5} \
+ -Dchannel_1={channel_1} \
+ -Dchannel_2={channel_2} \
+ -Dillumination_1={illumination_1} \
+ -Drotation_around={rotation_around} \
+ -Dpixel_distance_x={pixel_distance_x} \
+ -Dpixel_distance_y={pixel_distance_y} \
+ -Dpixel_distance_z={pixel_distance_z} \
+ -Dpixel_unit={pixel_unit} \
+ -Dfirst_xml_filename={first_xml_filename} \
+ -- --no-splash {path_bsh}""",
+ config["common"],
+ config["define_xml_czi"],
+ jdir=JOBDIR,
+ path_bsh=config["common"]["bsh_directory"] + config["define_xml_czi"]["bsh_file"])
+ cmd_string += " > {log} 2>&1"
shell(cmd_string)
+
+
# defining xml for tif dataset
rule define_xml_tif:
@@ -80,10 +81,12 @@ rule define_xml_tif:
-Dmultiple_angles={multiple_angles} \
-Dimglib_container={imglib_container} \
-- --no-splash {path_bsh}""",
- config["common"],
- config["define_xml_tif"],
- jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
+ config["common"],
+ config["define_xml_tif"],
+ jdir=JOBDIR,
+ path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"],
+ timepoints="1-"+str(config["common"]["ntimepoints"])
+ )
cmd_string +=" > {log} 2>&1"
shell(cmd_string)
@@ -155,7 +158,7 @@ rule resave_hdf5:
rule registration:
input: "{xml_base}-{file_id}-00.h5"
- output: "{xml_base}-{file_id,\d+}-00.h5_registered", #"{xml_base}.job_{file_id,\d+}.xml"
+ output: "{xml_base}.job_{file_id,\d+}.xml"#, "{xml_base}-{file_id,\d+}-00.h5_registered",
log: "{xml_base}-{file_id}-registration.log"
run:
cmd_string = produce_string(
@@ -201,7 +204,7 @@ rule registration:
#shell("touch {output}")
rule xml_merge:
- input: [ item+"_registered" for item in datasets ] #xml_merge_in
+ input: [ str(config["common"]["hdf5_xml_filename"].strip('\"')+".job_"+(padding_format.format(item))+".xml") for item in range(int(config["common"]["ntimepoints"])) ] #[ item+"_registered" for item in datasets ]
output: "{xml_base}_merge.xml"
log: "{xml_base}_merge.log"
run:
@@ -212,7 +215,6 @@ rule xml_merge:
-- --no-splash {path_bsh}""",
config["common"],
config["xml_merge"],
- log="{log}",
path_bsh=config["common"]["bsh_directory"] + config["xml_merge"]["bsh_file"],
jdir=JOBDIR,
output="{output}")
--
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