From 18da1ec182ddc5b2a2b18c44d4b61dfb0ca550c0 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 27 May 2015 19:06:14 +0200
Subject: [PATCH] Added resaving of output: define xml
---
spim_registration/timelapse/Snakefile | 85 ++++++-------------
spim_registration/timelapse/export.bsh | 15 ----
spim_registration/timelapse/export_output.bsh | 41 ++++++++-
spim_registration/timelapse/tomancak_czi.json | 4 +-
4 files changed, 66 insertions(+), 79 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 778c1e2..b912717 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -16,8 +16,10 @@ xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
#input: [ ds+"_fusion" for ds in datasets ]
- input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
-
+ #input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
+ #input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
+ input: config["hdf5_output"]["output_xml"] + ".xml"
+
rule resave_prepared:
input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
@@ -374,77 +376,42 @@ rule deconvolution:
)
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
-
-rule hdf5_output_define_xml:
- input: glob.glob('*.tif'), "{xml_base}-{file_id,\d+}-00.h5_" + config["common"]["fusion_switch"]
+
+rule define_output:
+ input: glob.glob('TP*')
output: config["hdf5_output"]["output_xml"] + ".xml"
- message: "Execute define_xml_tif on the following files {input}"
- log: "hdf5_output_define_xml.log"
+ log: "define_xml_tif.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
- -Dtimepoints={output_timepoints} \
- -Dchannels={output_channels} \
- -Dimage_file_pattern={output_image_file_pattern} \
- -Dpixel_distance_x={output_pixel_distance_x} \
- -Dpixel_distance_y={output_pixel_distance_y} \
- -Dpixel_distance_z={output_pixel_distance_z} \
- -Dpixel_unit={output_pixel_unit} \
- -Dxml_filename={output_xml} \
- -Dtype_of_dataset={output_type_of_dataset} \
- -Dmultiple_timepoints={output_multiple_timepoints} \
- -Dmultiple_channels={output_multiple_channels} \
- -Dmultiple_illumination_directions={output_illumination_directions} \
- -Dmultiple_angles={output_multiple_angles} \
- -Dimglib_container={output_imglib_container} \
+ -Dtimepoints={timepoints} \
+ -Dacquisition_angles={acquisition_angles} \
+ -Dchannels={channels} \
+ -Dimage_file_pattern={image_file_pattern} \
+ -Dpixel_distance_x={pixel_distance_x} \
+ -Dpixel_distance_y={pixel_distance_y} \
+ -Dpixel_distance_z={pixel_distance_z} \
+ -Dpixel_unit={pixel_unit} \
+ -Dxml_filename={first_xml_filename} \
+ -Dtype_of_dataset={type_of_dataset} \
+ -Dmultiple_timepoints={multiple_timepoints} \
+ -Dmultiple_channels={multiple_channels} \
+ -Dmultiple_illumination_directions={multiple_illumination_directions} \
+ -Dmultiple_angles={multiple_angles} \
+ -Dimglib_container={imglib_container} \
-- --no-splash {path_bsh}""",
config["common"],
- config["hdf5_output"],
+ config["define_xml_tif"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
- cmd_string +="> {log} 2>&1 && touch {output}"
+ cmd_string +=" > {log} 2>&1"
shell(cmd_string)
-ruleorder: define_xml_tif > define_xml_czi
-
-# create mother .xml/.h5
-rule hdf5_output_define_hdf5:
- input: config["hdf5_output"]["output_xml"] + ".xml"
- output: expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]),
- expand("{xml_base}-{file_id}-00.h5_empty", xml_base=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"') ],file_id=range(int(config["common"]["ntimepoints"]))) # problematic needs padding of file_id
- log: "hdf5_output_define_hdf5.log"
- run:
- part_string = produce_string(
- """{fiji-prefix} {fiji-app} \
- -Dimage_file_directory={jdir} \
- -Dfirst_xml_filename={output_xml} \
- -Dhdf5_xml_filename={output_hdf5_xml} \
- -Dresave_angle={resave_angle} \
- -Dresave_channel={resave_channel} \
- -Dresave_illumination={resave_illumination} \
- -Dresave_timepoint={resave_timepoint} \
- -Dsubsampling_factors={subsampling_factors} \
- -Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
- -Dtimepoints_per_partition={timepoints_per_partition} \
- -Dsetups_per_partition={setups_per_partition} \
- -Drun_only_job_number=0 \
- -Doutput_data_type={output_data_type} \
- -- --no-splash {path_bsh}""", # the & submits everyting at once
- config["common"],
- config["define_xml_czi"],
- config["resave_hdf5"],
- config["hdf5_output"],
- jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
- part_string += "> {log} 2>&1"
- shell(part_string)
- #create dummy files according to the number of timepoints found
- for index in range(int(config["common"]["ntimepoints"])):
- shell("touch {basename}-{file_id}-00.h5_empty".format(basename=config["common"]["hdf5_xml_filename"], file_id="%02d" % index)) # problematic needs padding of file_id
+
rule distclean:
params : glob.glob(config["common"]["hdf5_xml_filename"].strip('\"')+"*"), glob.glob(config["common"]["first_xml_filename"].strip('\"')+"*"), glob.glob("*registered"), glob.glob("*log"), glob.glob("*_deconvolved"), glob.glob("*.xml~*"),"interestpoints", glob.glob("*empty"), expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"])# xml_merge_in,
diff --git a/spim_registration/timelapse/export.bsh b/spim_registration/timelapse/export.bsh
index 9905b6e..8666721 100755
--- a/spim_registration/timelapse/export.bsh
+++ b/spim_registration/timelapse/export.bsh
@@ -58,21 +58,6 @@ System.out.println( "setups_per_partition=" + setups_per_partition );
int run_only_job_number = Integer.parseInt( System.getProperty( "run_only_job_number" ) );
System.out.println( "run_only_job_number=" + run_only_job_number );
-job_type = System.getProperty( "job_type" );
-System.out.println( "Job type = " + job_type );
-
-//
-//if ( job_type.equalsIgnoreCase( "xml" ) )
-// {
-// job_number = 0;
-// }
-//else if ( job_type.equalsIgnoreCase( "hdf5" ) )
-// {
-// job_number = run_only_job_number + 1;
-// }
-//
-//System.out.println( "Job Number = " + job_number );
-
// Activate cluster processing
System.out.println("=========================================================");
try{
diff --git a/spim_registration/timelapse/export_output.bsh b/spim_registration/timelapse/export_output.bsh
index e43fe32..af20191 100755
--- a/spim_registration/timelapse/export_output.bsh
+++ b/spim_registration/timelapse/export_output.bsh
@@ -55,14 +55,41 @@ 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 );
+
+
+if ( output_data_type.equalsIgnoreCase( "16Bit" ) )
+ {
+ data_string = "convert_32bit=convert_32bit";
+ }
+else if ( output_data_type.equalsIgnoreCase( "32Bit" ) )
+ {
+ data_string = "";
+ }
+
+System.out.println( "Data string = " + data_string );
+
+
+
// Activate cluster processing
System.out.println("=========================================================");
System.out.println("Cluster setting:");
+try{
IJ.run("Toggle Cluster Processing", "display_cluster");
-
+}
+catch ( e ) {
+ print( "[deconvolution-GPU] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+}
+
// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
+try{
IJ.run("As HDF5",
"select_xml=" + image_file_directory + first_xml_filename + ".xml " +
"resave_angle=[" + resave_angle + "] " +
@@ -77,8 +104,16 @@ IJ.run("As HDF5",
"setups_per_partition=" + setups_per_partition + " " +
"run_only_job_number=" + run_only_job_number + " " +
"use_deflate_compression " +
- "export_path=" + image_file_directory + hdf5_xml_filename );
-
+ "export_path=" + image_file_directory + hdf5_xml_filename + " " +
+ data_string +
+ );
+}
+catch ( e ) {
+ print( "[deconvolution-GPU] caught exception: "+e );
+ //important to fail the process if exception occurs
+ runtime.exit(1);
+}
+
/* shutdown */
System.exit(0);
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index b1dbb8e..a21c0bc 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -176,7 +176,7 @@
"hdf5_output" :
{
"output_image_file_pattern" : "TP{t}_Ch{c}_Ill0_Ang0,72,144,216,288.tif",
- "output_data_type" : "16Bit",
+ "output_data_type" : "32Bit",
"output_xml" : "\"fused_Dual_Channel\"",
"output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
"output_multiple_channels" : "\"NO (one channel)\"",
@@ -191,7 +191,7 @@
"output_multiple_angles" : "\"NO (one angle)\"",
"output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"output_imglib_container" : "\"ArrayImg (faster)\"",
- "fusion_output_export" : "/export_output.bsh",
+ "bsh_file" : "/export_output.bsh",
"convert_32bit" : "\"[Use min/max of first image (might saturate intenities over time)]\""
}
--
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