From c5af5c0e73d5e2fdf8a0b603e4c4197a328a5395 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 27 May 2015 20:02:40 +0200
Subject: [PATCH] Added and tested resaving of output files
---
spim_registration/timelapse/Snakefile | 47 ++++----
spim_registration/timelapse/define_output.bsh | 107 ++++++++++++++++++
spim_registration/timelapse/export.bsh | 3 -
spim_registration/timelapse/tomancak_czi.json | 5 +-
4 files changed, 133 insertions(+), 29 deletions(-)
create mode 100755 spim_registration/timelapse/define_output.bsh
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 66ddfed..36d8cfb 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -112,7 +112,6 @@ rule hdf5_xml:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number=0 \
- -Djob_type=xml \
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
@@ -148,7 +147,6 @@ rule resave_hdf5:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number={job_number} \
- -Djob_type=hdf5 \
-- --no-splash {path_bsh}""", # the & submits everyting at once
config["common"],
config["define_xml_czi"],
@@ -379,39 +377,38 @@ rule deconvolution:
rule define_output:
input: glob.glob('TP*')
- output: config["hdf5_output"]["output_xml"] + ".xml"
+ output: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
log: "define_xml_tif.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dtimepoints={output_timepoints} \
- -Dacquisition_angles={acquisition_angles} \
-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={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} \
+ -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} \
-- --no-splash {path_bsh}""",
config["common"],
- config["define_xml_tif"],
+ config["hdf5_output"],
jdir=JOBDIR,
- path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
+ path_bsh=config["common"]["bsh_directory"] + config["hdf5_output"]["bsh_file_define"])
cmd_string +=" > {log} 2>&1"
shell(cmd_string)
# create mother .xml/.h5
rule hdf5_xml_output:
- input: config["hdf5_output"]["output_xml"] + ".xml"
+ input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["hdf5_output"]["output_hdf5_xml"].strip('\"')], suffix=["xml","h5"]),
[ item+"_output" for item in datasets ]
log: "hdf5_xml.log"
@@ -419,8 +416,8 @@ rule hdf5_xml_output:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
- -Dfirst_xml_filename={first_xml_filename} \
- -Dhdf5_xml_filename={hdf5_xml_filename} \
+ -Dfirst_xml_filename={output_xml} \
+ -Dhdf5_xml_filename={output_hdf5_xml} \
-Dresave_angle={resave_angle} \
-Dresave_channel={resave_channel} \
-Dresave_illumination={resave_illumination} \
@@ -430,10 +427,11 @@ rule hdf5_xml_output:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number=0 \
- -Djob_type=xml \
+ -Doutput_data_type={output_data_type} \
+ -Dconvert_32bit={convert_32bit}\
-- --no-splash {path_bsh}""",
config["common"],
- config["define_xml_czi"],
+ config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
@@ -444,13 +442,13 @@ rule hdf5_xml_output:
rule resave_hdf5_output:
input: rules.hdf5_xml_output.output
output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
- log: "resave_hdf5-{file_id}.log"
+ log: "resave_output-{file_id}.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
- -Dfirst_xml_filename={first_xml_filename} \
- -Dhdf5_xml_filename={input_xml_base} \
+ -Dfirst_xml_filename={output_xml} \
+ -Dhdf5_xml_filename={output_hdf5_xml} \
-Dresave_angle={resave_angle} \
-Dresave_channel={resave_channel} \
-Dresave_illumination={resave_illumination} \
@@ -460,10 +458,11 @@ rule resave_hdf5_output:
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number={job_number} \
- -Djob_type=hdf5 \
- -- --no-splash {path_bsh}""", # the & submits everyting at once
+ -Doutput_data_type={output_data_type} \
+ -Dconvert_32bit={convert_32bit}\
+ -- --no-splash {path_bsh}""",
config["common"],
- config["define_xml_czi"],
+ config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
diff --git a/spim_registration/timelapse/define_output.bsh b/spim_registration/timelapse/define_output.bsh
new file mode 100755
index 0000000..aae8803
--- /dev/null
+++ b/spim_registration/timelapse/define_output.bsh
@@ -0,0 +1,107 @@
+import ij.IJ; // calls imagej
+import ij.Prefs; // calls imagej settings
+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");
+
+Prefs.setThreads(1); // defines the number of threads allowed
+print("Threads: "+Prefs.getThreads()); // prints thread setting in output
+
+System.out.println("Start loading parameters");
+// Directory
+System.out.println("=========================================================");
+System.out.println("Directory:");
+image_file_directory = System.getProperty( "image_file_directory" );
+xml_filename = System.getProperty( "xml_filename" );
+
+System.out.println( "image_file_directory = " + image_file_directory );
+System.out.println( "xml_filename = " + xml_filename );
+
+// Dataset settings
+System.out.println("=========================================================");
+System.out.println("Dataset:");
+timepoints = System.getProperty( "timepoints" );
+
+image_file_pattern = System.getProperty( "image_file_pattern" );
+type_of_dataset = System.getProperty( "type_of_dataset" );
+multiple_timepoints = System.getProperty( "multiple_timepoints" );
+multiple_illumination_directions = System.getProperty( "multiple_illumination_directions" );
+multiple_angles = System.getProperty( "multiple_angles" );
+imglib_container = System.getProperty( "imglib_container" );
+
+System.out.println( "timepoints = " + timepoints );
+System.out.println( "image_file_pattern = " + image_file_pattern );
+System.out.println( "type_of_dataset = " + type_of_dataset );
+System.out.println( "multiple_timepoints = " + multiple_timepoints );
+
+System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
+System.out.println( "multiple_angles = " + multiple_angles );
+System.out.println( "imglib_container = " + imglib_container );
+
+// Calibaration
+System.out.println("=========================================================");
+System.out.println("Calibration:");
+float pixel_distance_x = Float.parseFloat( System.getProperty( "pixel_distance_x" ) );
+float pixel_distance_y = Float.parseFloat( System.getProperty( "pixel_distance_y" ) );
+float pixel_distance_z = Float.parseFloat( System.getProperty( "pixel_distance_z" ) );
+pixel_unit = System.getProperty( "pixel_unit" );
+
+System.out.println( "pixel_distance_x = " + pixel_distance_x );
+System.out.println( "pixel_distance_y = " + pixel_distance_y );
+System.out.println( "pixel_distance_z = " + pixel_distance_z );
+System.out.println( "pixel_unit = " + pixel_unit );
+
+// Channel Switch
+System.out.println("=========================================================");
+System.out.println("Channel Switch:");
+multiple_channels = System.getProperty( "multiple_channels" );
+System.out.println( "multiple_channels = " + multiple_channels );
+
+channels = System.getProperty( "channels" );
+
+IJ.run("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
+ "xml_filename=[" + xml_filename + ".xml] " +
+ "multiple_timepoints=[" + multiple_timepoints + "] " +
+ "multiple_channels=[" + multiple_channels + "] " +
+ "_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " +
+ "multiple_angles=[" + multiple_angles + "] " +
+ "image_file_directory=" + image_file_directory + " " +
+ "image_file_pattern=" + image_file_pattern + " " +
+ "timepoints_=" + timepoints + " " +
+ channels +
+ "calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " +
+ "imglib2_data_container=[" + imglib_container + "] " +
+ "pixel_distance_x=" + pixel_distance_x + " " +
+ "pixel_distance_y=" + pixel_distance_y + " " +
+ "pixel_distance_z=" + pixel_distance_z + " " +
+ "pixel_unit=" + pixel_unit + "");
+
+// Executes Fiji plugin
+System.out.println("=========================================================");
+System.out.println("Start plugin:");
+IJ.run("Define Multi-View Dataset",
+ "type_of_dataset=[" + type_of_dataset + "] " +
+ "xml_filename=[" + xml_filename + ".xml] " +
+ "multiple_timepoints=[" + multiple_timepoints + "] " +
+ "multiple_channels=[" + multiple_channels + "] " +
+ "_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " +
+ "multiple_angles=[" + multiple_angles + "] " +
+ "image_file_directory=" + image_file_directory + " " +
+ "image_file_pattern=" + image_file_pattern + " " +
+ "timepoints_=" + timepoints + " " +
+ channels +
+ "calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " +
+ "imglib2_data_container=[" + imglib_container + "] " +
+ "pixel_distance_x=" + pixel_distance_x + " " +
+ "pixel_distance_y=" + pixel_distance_y + " " +
+ "pixel_distance_z=" + pixel_distance_z + " " +
+ "pixel_unit=" + pixel_unit + "");
+
+/* shutdown */
+runtime.exit(0);
+
+
diff --git a/spim_registration/timelapse/export.bsh b/spim_registration/timelapse/export.bsh
index 8666721..d7d064b 100755
--- a/spim_registration/timelapse/export.bsh
+++ b/spim_registration/timelapse/export.bsh
@@ -52,9 +52,6 @@ System.out.println( "hdf5_chunk_sizes=" + hdf5_chunk_sizes );
System.out.println( "timepoints_per_partition=" + timepoints_per_partition );
System.out.println( "setups_per_partition=" + setups_per_partition );
-
-// job switch
-
int run_only_job_number = Integer.parseInt( System.getProperty( "run_only_job_number" ) );
System.out.println( "run_only_job_number=" + run_only_job_number );
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index a21c0bc..317466f 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -175,7 +175,7 @@
"hdf5_output" :
{
- "output_image_file_pattern" : "TP{t}_Ch{c}_Ill0_Ang0,72,144,216,288.tif",
+ "output_image_file_pattern" : "TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif",
"output_data_type" : "32Bit",
"output_xml" : "\"fused_Dual_Channel\"",
"output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
@@ -191,7 +191,8 @@
"output_multiple_angles" : "\"NO (one angle)\"",
"output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"output_imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "/export_output.bsh",
+ "bsh_file_define" : "/define_output.bsh",
+ "bsh_file_hdf5" : "/export_output.bsh",
"convert_32bit" : "\"[Use min/max of first image (might saturate intenities over time)]\""
}
--
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