From 32427ebaa227c74fc99a218a2cb996c177fe9e49 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 10 Jun 2015 15:32:20 +0200
Subject: [PATCH] Updated fusion.bsh and fixed bug in export_output.bsh
BUG in export_output.bsh: took subsampling and chunk sizes from
resave hdf5. But these were not good.
Added new chunck size and subsampling option
---
spim_registration/timelapse/Snakefile | 15 +++++++-------
spim_registration/timelapse/export_output.bsh | 19 +++++++-----------
spim_registration/timelapse/fusion.bsh | 20 +++++++++++++------
.../timelapse/tomancak_test_cluster.yaml | 11 ++++++----
4 files changed, 36 insertions(+), 29 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index a0a6858..7b11770 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -21,6 +21,7 @@ xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
input: [ ds + "_output_hdf5" for ds in datasets ]
+ #input: [ ds + "_fusion" for ds in datasets ]
rule resave_prepared:
input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
@@ -288,7 +289,7 @@ rule fusion:
-- --no-splash {path_bsh}""",
config["common"],
config["fusion"],
- config["resave_czi_hdf5"],
+ config["resave_hdf5"],
path_bsh=config["common"]["bsh_directory"] + config["fusion"]["bsh_file"],
jdir=JOBDIR,
file_id_w="{wildcards.file_id}",
@@ -417,8 +418,8 @@ rule hdf5_xml_output:
-Dresave_channel={resave_channel} \
-Dresave_illumination={resave_illumination} \
-Dresave_timepoint={resave_timepoint} \
- -Dsubsampling_factors={subsampling_factors} \
- -Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
+ -Dsubsampling_factors={subsampling_output} \
+ -Dhdf5_chunk_sizes={chunk_sizes_output} \
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number=0 \
@@ -429,7 +430,7 @@ rule hdf5_xml_output:
config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
+ path_bsh=config["common"]["bsh_directory"] + config["hdf5_output"]["bsh_file_hdf5"])
part_string += " > {log} 2>&1 && touch {output}"
shell(part_string)
@@ -448,8 +449,8 @@ rule resave_hdf5_output:
-Dresave_channel={resave_channel} \
-Dresave_illumination={resave_illumination} \
-Dresave_timepoint={resave_timepoint} \
- -Dsubsampling_factors={subsampling_factors} \
- -Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
+ -Dsubsampling_factors={subsampling_output} \
+ -Dhdf5_chunk_sizes={chunk_sizes_output} \
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number={job_number} \
@@ -460,7 +461,7 @@ rule resave_hdf5_output:
config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
+ path_bsh=config["common"]["bsh_directory"] + config["hdf5_output"]["bsh_file_hdf5"],
input_xml_base="{wildcards.xml_base}",
job_number=int(wildcards.file_id)+1)
part_string += " > {log} 2>&1 && touch {output}"
diff --git a/spim_registration/timelapse/export_output.bsh b/spim_registration/timelapse/export_output.bsh
index af20191..2a16aed 100755
--- a/spim_registration/timelapse/export_output.bsh
+++ b/spim_registration/timelapse/export_output.bsh
@@ -54,26 +54,22 @@ System.out.println( "setups_per_partition=" + setups_per_partition );
System.out.println( "run_only_job_number=" + run_only_job_number );
// Add a switch for choosing between 16 or 32 bit
-
-
output_data_type = System.getProperty( "output_data_type" );
-
System.out.println( "Output Datatype = " + output_data_type );
+convert_32bit = System.getProperty( "convert_32bit" );
-if ( output_data_type.equalsIgnoreCase( "16Bit" ) )
+if ( output_data_type.equalsIgnoreCase( "32Bit" ) )
{
- data_string = "convert_32bit=convert_32bit";
+ data_string = "convert_32bit=" + convert_32bit;
}
-else if ( output_data_type.equalsIgnoreCase( "32Bit" ) )
+else if ( output_data_type.equalsIgnoreCase( "16Bit" ) )
{
data_string = "";
}
System.out.println( "Data string = " + data_string );
-
-
// Activate cluster processing
System.out.println("=========================================================");
System.out.println("Cluster setting:");
@@ -81,7 +77,7 @@ try{
IJ.run("Toggle Cluster Processing", "display_cluster");
}
catch ( e ) {
- print( "[deconvolution-GPU] caught exception: "+e );
+ print( "[export output: cluster setting] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
@@ -105,11 +101,10 @@ IJ.run("As HDF5",
"run_only_job_number=" + run_only_job_number + " " +
"use_deflate_compression " +
"export_path=" + image_file_directory + hdf5_xml_filename + " " +
- data_string +
- );
+ data_string + "");
}
catch ( e ) {
- print( "[deconvolution-GPU] 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/fusion.bsh b/spim_registration/timelapse/fusion.bsh
index f88eff8..79f9d54 100755
--- a/spim_registration/timelapse/fusion.bsh
+++ b/spim_registration/timelapse/fusion.bsh
@@ -19,14 +19,17 @@ System.out.println( "Start to load Parameters:" );
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load xml 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";
System.out.println( "xml_path=" + image_file_directory + merged_xml + ".xml" );
// Load general Parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "General parameters: " );
-parallel_timepoints = System.getProperty( "parallel_timepoints" );
+int 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" );
@@ -72,9 +75,9 @@ System.out.println( "imglib2_data_container=" + imglib2_data_container );
// Execute Fiji Plugin
System.out.println( "=======================================================" );
System.out.println( "Starting Fusion" );
-
+try{
IJ.run("Fuse/Deconvolve Dataset",
- "select_xml=" + image_file_directory + merged_xml + ".xml " +
+ "select_xml=" + image_file_directory + merged_xml + " " +
"process_angle=[" + process_angle + "] " +
"process_illumination=[" + process_illumination + "] " +
"process_timepoint=[" + process_timepoint + "] " +
@@ -95,11 +98,16 @@ IJ.run("Fuse/Deconvolve Dataset",
"imglib2_container=" + imglib2_container_fusion + " " +
"process_views_in_paralell=All " +
"interpolation=[" + interpolation + "] " +
- "blend " +
- "content-based " +
+ //"blend " +
+ //"content-based " +
"output_file_directory=" + image_file_directory + " " +
"lossless " +
"imglib2_data_container=[" + imglib2_data_container + "]");
-
+}
+catch ( e ) {
+ print( "[Contentbased multiview fusion] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index bab766e..817e3c1 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -15,7 +15,8 @@ common: {
pixel_distance_y: '0.28590106964',
pixel_distance_z: '1.50000',
pixel_unit: "um",
- fusion_switch: "deconvolution"
+ # fusion_switch: "deconvolution"
+ fusion_switch: "fusion"
}
define_xml_czi: {
@@ -96,7 +97,7 @@ Dublicate_transformations: {
fusion: {
bsh_file: "fusion.bsh",
- downsample: '1',
+ downsample: '4',
fused_image: '"Append to current XML Project"',
imglib2_container_fusion: '"ArrayImg"',
imglib2_data_container: '"ArrayImg (faster)"',
@@ -160,7 +161,7 @@ deconvolution: {
hdf5_output: {
output_image_file_pattern: 'TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
output_xml: '"fused_Single_Channel"',
- output_hdf5_xml: '"hdf5_fused_Stock68"',
+ output_hdf5_xml: '"hdf5_fused_Single_Channel"',
output_multiple_channels: '"NO (one channel)"',
output_timepoints: '0-4',
output_pixel_distance_x: 0.5718,
@@ -168,13 +169,15 @@ hdf5_output: {
output_pixel_distance_z: 0.5718,
output_pixel_unit: 'um',
output_channels: "green",
- output_data_type: "32Bit",
+ output_data_type: "16Bit",
convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
output_multiple_timepoints: '"YES (one file per time-point)"',
output_multiple_angles: '"NO (one angle)"',
output_illumination_directions: '"NO (one illumination direction)"',
output_imglib_container: '"ArrayImg (faster)"',
+ subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+ chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
bsh_file_define: "define_output.bsh",
bsh_file_hdf5: "export_output.bsh"
}
--
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