From 68bc626c36beccd1296b5979308c6301a22b5334 Mon Sep 17 00:00:00 2001
From: Peter Steinbach <steinbach@scionics.de>
Date: Mon, 18 May 2015 16:55:36 +0200
Subject: [PATCH] * updated beanshell file to throw away padded 0 in file_id *
updated Snakefile accordingly
---
spim_registration/timelapse/Snakefile | 12 +++++------
spim_registration/timelapse/registration.bsh | 21 ++++++++++++++++++--
2 files changed, 25 insertions(+), 8 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 3edf065..cafc912 100644
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -17,7 +17,7 @@ for ds in datasets:
bn = os.path.basename(ds)
bn_res = fre.search(bn)
xml_base,file_id = bn_res.group('xml_base'),bn_res.group('file_id')
- xml_merge_in.append("{xbase}.job_{fid}.xml".format(xbase=xml_base, fid=file_id))
+ xml_merge_in.append("{xbase}.job_{fid}.xml".format(xbase=xml_base, fid=int(file_id)))
#TODO: this should go into a python module in this path
def produce_string(_fstring, *args, **kwargs):
@@ -33,9 +33,9 @@ rule done:
input: [ ds+"_deconvolved" for ds in datasets ]
rule registration:
- input: "{xml_base}-{file_id,\d+}-00.h5"
- output: "{xml_base}.job_{file_id,\d+}.xml"
- log: "{xml_base}-{file_id,\d+}-registration.log"
+ input: "{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"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -79,7 +79,7 @@ rule registration:
#shell("touch {output}")
rule xml_merge:
- input: xml_merge_in
+ input: [ item+"_registered" for item in datasets ] #xml_merge_in
output: "{xml_base}_merge.xml"
log: "{xml_base}_merge.log"
run:
@@ -159,4 +159,4 @@ rule deconvolution:
shell(cmd_string)
rule distclean:
- shell : "rm -rf *registered *tif "+str(" ".join(xml_merge_in))
+ shell : "rm -rf *registered *tif *log *_deconvolved *.xml~* interestpoints "+str(" ".join(xml_merge_in))
diff --git a/spim_registration/timelapse/registration.bsh b/spim_registration/timelapse/registration.bsh
index 4765129..f7c6b26 100644
--- a/spim_registration/timelapse/registration.bsh
+++ b/spim_registration/timelapse/registration.bsh
@@ -23,7 +23,7 @@ System.out.println( "selected_xml = " + xml_path + xml_filename + ".xml");
System.out.println( "-------------------------------------------------------" );
System.out.println( "General parameters: " );
-parallel_timepoints = System.getProperty( "parallel_timepoints" );
+parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoints" ));
process_timepoint = System.getProperty( "process_timepoint" );
process_channel = System.getProperty( "process_channel" );
process_illumination = System.getProperty( "process_illumination" );
@@ -101,13 +101,23 @@ System.out.println( "detection_min_max = " + detection_min_max );
//activate cluster processing
System.out.println( "=======================================================" );
+try {
IJ.run("Toggle Cluster Processing", "display_cluster");
+}
+catch ( e ) {
+
+ print( "[registration::activate_cluster_processing] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
System.out.println( "Activated Cluster Processing" );
//interest point detection
System.out.println( "=======================================================" );
System.out.println( "Starting Detection of Interest Points" );
+try {
IJ.run("Detect Interest Points for Registration",
"select_xml=" + xml_path + xml_filename + ".xml " +
"unique_id=" + parallel_timepoints + " " +
@@ -127,7 +137,14 @@ IJ.run("Detect Interest Points for Registration",
"radius_2=" + radius_2 + " " +
"threshold=" + threshold + " " +
"find_maxima");
+}
+catch ( e ) {
+ print( "[registration::interest_points] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
//registration based on interest point detection
System.out.println( "=======================================================" );
System.out.println( "Starting Registration" );
@@ -156,7 +173,7 @@ try {
}
catch ( e ) {
- print( "[registration] caught exception: "+e );
+ print( "[registration::based_on_interestpoints] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
--
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