From 1a3e1caebcf9c94e331a3e5c58d3a44b1319dd80 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 10 Jun 2015 21:08:48 +0200
Subject: [PATCH] Added hooks for ImagJ exceptions
---
.../timelapse/deconvolution_CPU.bsh | 146 ------------------
spim_registration/timelapse/define_czi.bsh | 2 +-
spim_registration/timelapse/define_output.bsh | 10 +-
.../timelapse/define_tif_zip.bsh | 2 +-
spim_registration/timelapse/export.bsh | 11 +-
spim_registration/timelapse/export_output.bsh | 4 +-
spim_registration/timelapse/registration.bsh | 4 +-
7 files changed, 25 insertions(+), 154 deletions(-)
delete mode 100644 spim_registration/timelapse/deconvolution_CPU.bsh
diff --git a/spim_registration/timelapse/deconvolution_CPU.bsh b/spim_registration/timelapse/deconvolution_CPU.bsh
deleted file mode 100644
index f21f94d..0000000
--- a/spim_registration/timelapse/deconvolution_CPU.bsh
+++ /dev/null
@@ -1,146 +0,0 @@
-// Load Fiji dependencies
-import ij.IJ;
-import ij.ImagePlus;
-import java.lang.Runtime;
-import java.io.File;
-import java.io.FilenameFilter;
-
-runtime = Runtime.getRuntime();
-System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
-
-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);
-
-// Load general Parameters
-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" );
-process_angle = System.getProperty( "process_angle" );
-
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "General parameters: " );
-System.out.println( "timepoint_processed = " + parallel_timepoints );
-System.out.println( "process_timepoints = " + process_timepoint );
-System.out.println( "process_channel = " + process_channel );
-System.out.println( "process_illumination = " + process_illumination );
-System.out.println( "process_angle = " + process_angle );
-
-// Load bounding box
-minimal_x_deco = System.getProperty( "minimal_x_deco" );
-minimal_y_deco = System.getProperty( "minimal_y_deco" );
-minimal_z_deco = System.getProperty( "minimal_z_deco" );
-maximal_x_deco = System.getProperty( "maximal_x_deco" );
-maximal_y_deco = System.getProperty( "maximal_y_deco" );
-maximal_z_deco = System.getProperty( "maximal_z_deco" );
-
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "Bounding box: " );
-System.out.println( "minimal_x_deco = " + minimal_x_deco );
-System.out.println( "minimal_y_deco = " + minimal_y_deco );
-System.out.println( "minimal_z_deco = " + minimal_z_deco );
-System.out.println( "maximal_x_deco = " + maximal_x_deco );
-System.out.println( "maximal_y_deco = " + maximal_y_deco );
-System.out.println( "maximal_z_deco = " + maximal_z_deco );
-
-// Load deconvolution Parameters
-imglib2_container_deco = System.getProperty( "imglib2_container_deco" );
-type_of_iteration = System.getProperty( "type_of_iteration" );
-osem_acceleration = System.getProperty( "osem_acceleration" );
-Tikhonov_parameter = System.getProperty( "Tikhonov_parameter" );
-//float Tikhonov_parameter = Float.parseFloat( System.getProperty( "Tikhonov_parameter" ) );
-compute = System.getProperty( "compute" );
-psf_estimation = System.getProperty( "psf_estimation" );
-iterations = System.getProperty( "iterations" );
-deco_output_file_directory = System.getProperty( "deco_output_file_directory" );
-detections_to_extract_psf_for_channel_0 = System.getProperty( "detections_to_extract_psf_for_channel_0" );
-detections_to_extract_psf_for_channel_1 = System.getProperty( " detections_to_extract_psf_for_channel_1" );
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "Deconvolution settings: " );
-System.out.println( "imglib2_container = " + imglib2_container_deco );
-System.out.println( "type_of_iteration = "+ type_of_iteration );
-System.out.println( "osem_acceleration = " + osem_acceleration );
-System.out.println( "Tikhonov_parameter = " + Tikhonov_parameter );
-System.out.println( "compute = " + compute );
-System.out.println( "psf_estimation = " + psf_estimation );
-System.out.println( "number_of_iterations = " + iterations );
-System.out.println( "deco_output_file_directory = " + deco_output_file_directory );
-System.out.println( "detections_to_extract_psf_for_channel_0 = " + detections_to_extract_psf_for_channel_0 );
-System.out.println( "detections_to_extract_psf_for_channel_1 = " + detections_to_extract_psf_for_channel_1 );
-
-// Search for CUDA
-directory_cuda = System.getProperty( "directory_cuda" );
-
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "Loading CUDA directory: " );
-System.out.println( "directory_cuda = " + directory_cuda );
-
-// PSF Parameters
-psf_size_x = System.getProperty( "psf_size_x" );
-psf_size_y = System.getProperty( "psf_size_y" );
-psf_size_z = System.getProperty( "psf_size_z" );
-
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "PSF Parameters: " );
-System.out.println( "psf_size_x = " + psf_size_x );
-System.out.println( "psf_size_y = " + psf_size_y );
-System.out.println( "psf_size_z = " + psf_size_z );
-
-// Execute Fiji Plugin
-System.out.println( "=======================================================" );
-System.out.println( "Starting Deconvolution" );
-
-try {
-IJ.run("Fuse/Deconvolve Dataset",
- "select_xml=" + image_file_directory + merged_xml + " " +
- "process_angle=[All angles] " +
- "process_channel=[All channels] " +
- "process_illumination=[All illuminations] " +
- "process_timepoint=[" + process_timepoint + "] " +
- "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
- "type_of_image_fusion=[Multi-view deconvolution] " +
- "bounding_box=[Define manually] " +
- "fused_image=[Save as TIFF stack] " +
- "minimal_x=" + minimal_x_deco + " " +
- "minimal_y=" + minimal_y_deco + " " +
- "minimal_z=" + minimal_z_deco + " " +
- "maximal_x=" + maximal_x_deco + " " +
- "maximal_y=" + maximal_y_deco + " " +
- "maximal_z=" + maximal_z_deco + " " +
- "imglib2_container=" + imglib2_container_deco + " " +
- "type_of_iteration=[" + type_of_iteration + "] " +
- "osem_acceleration=[" + osem_acceleration + "] " +
- "number_of_iterations=" + iterations + " " +
-// "adjust_blending_parameters " +
- "use_tikhonov_regularization " +
- "tikhonov_parameter=" + Tikhonov_parameter + " " +
- "compute=[" + compute + "] " +
- "compute_on=[CPU (Java)] " +
- "psf_estimation=[" + psf_estimation + "] " +
- "psf_display=[Do not show PSFs] " +
- "output_file_directory=" + deco_output_file_directory + " " +
- "detections_to_extract_psf_for_channel_0=" + detections_to_extract_psf_for_channel_0 + " " +
- "detections_to_extract_psf_for_channel_1=" + detections_to_extract_psf_for_channel_1 + " " + // Dual Channel
- "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/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
index 0b9b1ee..e3e1d30 100755
--- a/spim_registration/timelapse/define_czi.bsh
+++ b/spim_registration/timelapse/define_czi.bsh
@@ -165,7 +165,7 @@ IJ.run("Define Multi-View Dataset",
}
catch ( e ) {
- print( "[registration::interest_points] caught exception: "+e );
+ print( "[define_czi] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
diff --git a/spim_registration/timelapse/define_output.bsh b/spim_registration/timelapse/define_output.bsh
index da8a3ce..e2469fe 100755
--- a/spim_registration/timelapse/define_output.bsh
+++ b/spim_registration/timelapse/define_output.bsh
@@ -105,6 +105,7 @@ System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dat
// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
+try {
IJ.run("Define Multi-View Dataset",
"type_of_dataset=[" + type_of_dataset + "] " +
"xml_filename=[" + xml_filename + ".xml] " +
@@ -122,7 +123,14 @@ IJ.run("Define Multi-View Dataset",
"pixel_distance_y=" + pixel_distance_y + " " +
"pixel_distance_z=" + pixel_distance_z + " " +
"pixel_unit=" + pixel_unit + "");
-
+}
+catch ( e ) {
+
+ print( "[define_output] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/define_tif_zip.bsh b/spim_registration/timelapse/define_tif_zip.bsh
index 32ab010..a5f4015 100755
--- a/spim_registration/timelapse/define_tif_zip.bsh
+++ b/spim_registration/timelapse/define_tif_zip.bsh
@@ -168,7 +168,7 @@ IJ.run("Define Multi-View Dataset",
}
catch ( e ) {
- print( "[registration::interest_points] caught exception: "+e );
+ print( "[define_tif_zip] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
diff --git a/spim_registration/timelapse/export.bsh b/spim_registration/timelapse/export.bsh
index 6d620ad..1e928a8 100755
--- a/spim_registration/timelapse/export.bsh
+++ b/spim_registration/timelapse/export.bsh
@@ -56,7 +56,16 @@ System.out.println( "run_only_job_number=" + run_only_job_number );
// Activate cluster processing
System.out.println("=========================================================");
System.out.println("Cluster setting:");
+try {
IJ.run("Toggle Cluster Processing", "display_cluster");
+}
+catch ( e ) {
+
+ print( "[export::cluster setting] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+
+}
// Executes Fiji plugin
System.out.println("=========================================================");
@@ -81,7 +90,7 @@ IJ.run("As HDF5",
}
catch ( e ) {
- print( "[registration::interest_points] caught exception: "+e );
+ print( "[export::resaving] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
diff --git a/spim_registration/timelapse/export_output.bsh b/spim_registration/timelapse/export_output.bsh
index 2a16aed..f05798a 100755
--- a/spim_registration/timelapse/export_output.bsh
+++ b/spim_registration/timelapse/export_output.bsh
@@ -77,7 +77,7 @@ try{
IJ.run("Toggle Cluster Processing", "display_cluster");
}
catch ( e ) {
- print( "[export output: cluster setting] caught exception: "+e );
+ print( "[export_output::cluster setting] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
@@ -104,7 +104,7 @@ IJ.run("As HDF5",
data_string + "");
}
catch ( e ) {
- print( "[export output: resaving caught exception: "+e );
+ print( "[export_output::resaving] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
diff --git a/spim_registration/timelapse/registration.bsh b/spim_registration/timelapse/registration.bsh
index 0998046..0031b54 100755
--- a/spim_registration/timelapse/registration.bsh
+++ b/spim_registration/timelapse/registration.bsh
@@ -329,7 +329,7 @@ IJ.run("Detect Interest Points for Registration",
}
catch ( e ) {
- print( "[registration::interest_points] caught exception: "+e );
+ print( "[registration::detection of interest_points] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
@@ -383,7 +383,7 @@ IJ.run("Register Dataset based on Interest Points",
}
catch ( e ) {
- print( "[registration::based_on_interestpoints] caught exception: "+e );
+ print( "[registration::registration of interest points] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
--
GitLab