From 1cad3b4eb15b73d4aac3f3d29b070c9a00af94f2 Mon Sep 17 00:00:00 2001
From: Peter Steinbach <steinbach@scionics.de>
Date: Mon, 18 May 2015 13:49:04 +0200
Subject: [PATCH] added try-catch block to beanshell script, so that they
return exit status != 0 if exception is thrown
---
.../timelapse/deconvolution_CPU.bsh | 17 +++++--
.../timelapse/deconvolution_GPU.bsh | 18 +++++--
spim_registration/timelapse/registration.bsh | 50 +++++++++++--------
spim_registration/timelapse/transform.bsh | 15 +++++-
spim_registration/timelapse/xml_merge.bsh | 19 +++++--
5 files changed, 86 insertions(+), 33 deletions(-)
diff --git a/spim_registration/timelapse/deconvolution_CPU.bsh b/spim_registration/timelapse/deconvolution_CPU.bsh
index b2ba8ab..e38a7bc 100644
--- a/spim_registration/timelapse/deconvolution_CPU.bsh
+++ b/spim_registration/timelapse/deconvolution_CPU.bsh
@@ -13,10 +13,12 @@ System.out.println( "Start to load Parameters:" );
// Select xml
image_file_directory = System.getProperty( "image_file_directory" );
merged_xml = System.getProperty( "merged_xml" );
-
+if ( ! merged_xml.endsWith(".xml") )
+ merged_xml = merged.xml + ".xml";
+
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load xml file: " );
-System.out.println( "selected_xml = " + image_file_directory + merged_xml + ".xml");
+System.out.println( "selected_xml = " + image_file_directory + merged_xml);
// Load general Parameters
parallel_timepoints = System.getProperty( "parallel_timepoints" );
@@ -97,8 +99,9 @@ System.out.println( "psf_size_z = " + psf_size_z );
System.out.println( "=======================================================" );
System.out.println( "Starting Deconvolution" );
+try {
IJ.run("Fuse/Deconvolve Dataset",
- "select_xml=" + image_file_directory + merged_xml + ".xml " +
+ "select_xml=" + image_file_directory + merged_xml + " " +
"process_angle=[All angles] " +
"process_channel=[All channels] " +
"process_illumination=[All illuminations] " +
@@ -130,6 +133,14 @@ IJ.run("Fuse/Deconvolve Dataset",
"psf_size_x=" + psf_size_x + " " +
"psf_size_y=" + psf_size_y + " " +
"psf_size_z=" + psf_size_z + "");
+}
+catch ( e ) {
+
+ print( "[deconvolution-CPU] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/deconvolution_GPU.bsh b/spim_registration/timelapse/deconvolution_GPU.bsh
index f06b777..7ffb45b 100644
--- a/spim_registration/timelapse/deconvolution_GPU.bsh
+++ b/spim_registration/timelapse/deconvolution_GPU.bsh
@@ -13,10 +13,12 @@ System.out.println( "Start to load Parameters:" );
// Select xml
image_file_directory = System.getProperty( "image_file_directory" );
merged_xml = System.getProperty( "merged_xml" );
-
+if ( ! merged_xml.endsWith(".xml") )
+ merged_xml = merged.xml + ".xml";
+
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load xml file: " );
-System.out.println( "selected_xml = " + image_file_directory + merged_xml + ".xml");
+System.out.println( "selected_xml = " + image_file_directory + merged_xml);
// Load general Parameters
parallel_timepoints = System.getProperty( "parallel_timepoints" );
@@ -98,8 +100,9 @@ System.out.println( "psf_size_z = " + psf_size_z );
System.out.println( "=======================================================" );
System.out.println( "Starting Deconvolution" );
+try {
IJ.run("Fuse/Deconvolve Dataset",
- "select_xml=" + image_file_directory + merged_xml + ".xml " +
+ "select_xml=" + image_file_directory + merged_xml + " " +
"process_angle=[All angles] " +
"process_channel=[All channels] " +
"process_illumination=[All illuminations] " +
@@ -137,7 +140,14 @@ IJ.run("Fuse/Deconvolve Dataset",
"psf_size_x=" + psf_size_x + " " +
"psf_size_y=" + psf_size_y + " " +
"psf_size_z=" + psf_size_z + "");
-
+}
+catch ( e ) {
+
+ print( "[deconvolution-GPU] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/registration.bsh b/spim_registration/timelapse/registration.bsh
index ab21bba..4765129 100644
--- a/spim_registration/timelapse/registration.bsh
+++ b/spim_registration/timelapse/registration.bsh
@@ -131,26 +131,36 @@ IJ.run("Detect Interest Points for Registration",
//registration based on interest point detection
System.out.println( "=======================================================" );
System.out.println( "Starting Registration" );
-IJ.run("Register Dataset based on Interest Points",
- "select_xml=" + xml_path + xml_filename + ".job_" + parallel_timepoints + ".xml " +
- "process_angle=[" + process_angle + "] " +
- "process_channel=[" + process_channel + "] " +
- "process_illumination=[" + process_illumination + "] " +
- "process_timepoint=[" + process_timepoint + "] " +
- "xml_output=[Do not process on cluster] " +
- "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
- "registration_algorithm=[" + registration_algorithm + "] " +
- "type_of_registration=[" + type_of_registration + "] " +
- "interest_points_channel_0=" + interest_points_channel_0 + " " +
-// check? "interest_points_channel_0=[[DO NOT register this channel]] " +
-// "interest_points_channel_1=" + interest_points_channel_1 + " " + // Dual Channel
- "fix_tiles=[" + fix_tiles + "] " +
- "map_back_tiles=[" + map_back_tiles + "] " +
- "transformation=" + transformation_model + " " +
- "regularize_model " +
- "model_to_regularize_with=" + model_to_regularize_with + " " +
- "lamba=" + lambda + " " +
- "allowed_error_for_ransac=" + allowed_error_for_ransac);
+
+try {
+ IJ.run("Register Dataset based on Interest Points",
+ "select_xml=" + xml_path + xml_filename + ".job_" + parallel_timepoints + ".xml " +
+ "process_angle=[" + process_angle + "] " +
+ "process_channel=[" + process_channel + "] " +
+ "process_illumination=[" + process_illumination + "] " +
+ "process_timepoint=[" + process_timepoint + "] " +
+ "xml_output=[Do not process on cluster] " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "registration_algorithm=[" + registration_algorithm + "] " +
+ "type_of_registration=[" + type_of_registration + "] " +
+ "interest_points_channel_0=" + interest_points_channel_0 + " " +
+ // check? "interest_points_channel_0=[[DO NOT register this channel]] " +
+ // "interest_points_channel_1=" + interest_points_channel_1 + " " + // Dual Channel
+ "fix_tiles=[" + fix_tiles + "] " +
+ "map_back_tiles=[" + map_back_tiles + "] " +
+ "transformation=" + transformation_model + " " +
+ "regularize_model " +
+ "model_to_regularize_with=" + model_to_regularize_with + " " +
+ "lamba=" + lambda + " " +
+ "allowed_error_for_ransac=" + allowed_error_for_ransac);
+}
+catch ( e ) {
+
+ print( "[registration] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/transform.bsh b/spim_registration/timelapse/transform.bsh
index 3a1cb2e..839a085 100644
--- a/spim_registration/timelapse/transform.bsh
+++ b/spim_registration/timelapse/transform.bsh
@@ -11,6 +11,9 @@ System.out.println(runtime.availableProcessors() + " cores available for multi-t
// Load Parameters form job file
image_file_directory = System.getProperty( "image_file_directory" );
merged_xml = System.getProperty( "merged_xml" );
+if ( ! merged_xml.endsWith(".xml") )
+ merged_xml = merged.xml + ".xml";
+
transform_angle = System.getProperty( "transform_angle" );
transform_channel = System.getProperty( "transform_channel" );
transform_illumination = System.getProperty( "transform_illumination" );
@@ -23,7 +26,7 @@ matrix_transform = System.getProperty( "matrix_transform" );
// Print Parameters into output file
System.out.println( "browse = " + image_file_directory );
-System.out.println( "select_xml = " + image_file_directory + merged_xml + ".xml" );
+System.out.println( "select_xml = " + image_file_directory + merged_xml );
System.out.println( "apply_to_angle = " + transform_angle );
System.out.println( "apply_to_channel = " + transform_channel );
System.out.println( "apply_to_illumination = " + transform_illumination );
@@ -34,9 +37,10 @@ System.out.println( "define = " + define_mode_transform );
System.out.println( "all_timepoints_channel_0_illumination_0_all_angles = " + matrix_transform );
// Execute Fiji Plugin
+try {
IJ.run("Apply Transformations",
"browse=" + image_file_directory + " " +
- "select_xml=" + image_file_directory + merged_xml + ".xml " +
+ "select_xml=" + image_file_directory + merged_xml + " " +
"apply_to_angle=[" + transform_angle + "] " +
"apply_to_channel=[" + transform_channel + "] " +
"apply_to_illumination=[" + transform_illumination + "] " +
@@ -48,7 +52,14 @@ IJ.run("Apply Transformations",
"same_transformation_for_all_angles " +
// "all_timepoints_channel_0_illumination_0_all_angles=[0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0]");
"all_timepoints_channel_0_illumination_0_all_angles=[" + matrix_transform + "]");
+}
+catch ( e ) {
+ print( "[transform] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/xml_merge.bsh b/spim_registration/timelapse/xml_merge.bsh
index 99925e7..a3ab7da 100644
--- a/spim_registration/timelapse/xml_merge.bsh
+++ b/spim_registration/timelapse/xml_merge.bsh
@@ -12,8 +12,11 @@ System.out.println( "Load Parameters:");
// Getting parameters from job file
image_file_directory = System.getProperty( "image_file_directory" );
-merged_xml = System.getProperty( "merged_xml" );
+merged_xml = System.getProperty( "merged_xml" );
+if ( ! merged_xml.endsWith(".xml") )
+ merged_xml = merged.xml + ".xml";
+
// Printing parameters into output file
System.out.println( "directory=" + image_file_directory );
System.out.println( "merged_xml=" + merged_xml );
@@ -22,13 +25,21 @@ System.out.println( "=======================================================" );
System.out.println( "Start to merge .xml files" );
// Executing Fiji plugin
+try {
IJ.run("Merge Cluster Jobs",
"directory=" + image_file_directory + " " +
"filename_contains=job_ " +
"filename_also_contains=.xml " +
"display " +
-// "delete_xml's " +
- "merged_xml=" + merged_xml + ".xml");
-
+ "merged_xml=" + merged_xml);
+}
+catch ( e ) {
+
+ print( "[xml_merge] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
+
/* shutdown */
runtime.exit(0);
--
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