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Commit 5111213d authored by Peter Steinbach's avatar Peter Steinbach
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added Christopher Schmied's pipeline to ghub repo

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spim_registration/timelapse/Snakefile 0 → 100644
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View file @ 5111213d
import os, glob, sys
#where are we
if "datadir" not in config.keys():
JOBDIR=os.path.abspath(os.path.curdir)
else:
if os.path.isdir(config['datadir']):
JOBDIR=config['datadir']
else:
print("given data dir does not exist {data}".format(data=config['datadir']))
sys.exit(1)
if JOBDIR[-1] != "/":
JOBDIR+="/"
datasets = glob.glob('*00.h5')
#data specific config file
configfile: "tomancak.json"
def produce_string(_fstring, *args, **kwargs):
contents = dict()
for item in args:
if type(item) == type(kwargs):
contents.update(item)
contents.update(kwargs)
return _fstring.format(**contents)
rule done:
input: [ ds+"-deconvolved" for ds in datasets ]
rule registration:
input: "{xml_base}-{file_id,\d+}-00.h5"
output: "{xml_base}-{file_id,\d+}-00.h5_registered", #convenience files
"{xml_base}.job_{file_id,\d+}.xml"
log: "{xml_base}-{file_id,\d+}-registration.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dparallel_timepoints={file_id_w} \
-Dimage_file_directory={jdir} \
-Dxml_filename={input_xml} \
-Dprocess_timepoint={timepoint} \
-Dprocess_channel={channel} \
-Dprocess_illumination={illuminations} \
-Dprocess_angle={angle} \
-Dprocessing_channel={proc-ch} \
-Dlabel_interest_points={label_interest_points} \
-Dtype_of_registration={type_of_registration} \
-Dtype_of_detection={type_of_detection} \
-Dsubpixel_localization={subpixel_localization} \
-Dimglib_container={imglib_container} \
-Dradius_1={radius_1} \
-Dradius_2={radius_2} \
-Dthreshold={threshold} \
-Dinitial_sigma={initial_sigma} \
-Dthreshold_gaussian={threshold_gaussian} \
-Dregistration_algorithm={algorithm} \
-Dinterest_points_channel_0={interest_points_channel_0} \
-Dinterest_points_channel_1={interest_points_channel_1} \
-Dfix_tiles={fix_tiles} \
-Dmap_back_tiles={map_back_tiles} \
-Dtransformation_model={transformation_model} \
-Dmodel_to_regularize_with={model_to_regularize_with} \
-Dlambda={lambda} \
-Dallowed_error_for_ransac={allowed_error_for_ransac} \
-Ddetection_min_max={detection_min_max} \
-- --no-splash {bsh_file}""",
config["common"],
config["registration"],
file_id_w="{wildcards.file_id}",
jdir=JOBDIR,
input_xml="{wildcards.xml_base}")
cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
#shell("touch {output}")
rule xml_merge:
input: [ item+"_registered" for item in datasets ]
output: "{xml_base}_merge.xml"
log: "{xml_base}_merge.log"
run:
cmd_string = produce_string("{fiji-prefix} {fiji-app} -Dimage_file_directory={jdir} -Dmerged_xml={merged_xml} -- --no-splash {bsh_file} > {log} 2>&1",
config["common"],
config["xml_merge"],
log="{log}",
jdir=JOBDIR)
shell(cmd_string)
rule external_trafo:
input: rules.xml_merge.output
output: rules.xml_merge.output[0] + "_external_trafo"
log: "external_trafo.log"
# message: "etrafo {input} -> {output}"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dmerged_xml={merged_xml} \
-Dtransform_angle={angle} \
-Dtransform_channel={channel} \
-Dtransform_illumination={illumination} \
-Dtransform_timepoint={timepoint} \
-Dtransformation={transformation} \
-Dapply_transformation={apply_transformation} \
-Ddefine_mode_transform={define_mode_transform} \
-Dmatrix_transform={matrix_transform} \
-- --no-splash {bsh_file}""",
config["common"],
config["external_transform"],
jdir=JOBDIR)
cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
rule deconvolution:
input: rules.external_trafo.output, "{xml_base}-{file_id,\d+}-00.h5"
output: "{xml_base}-{file_id,\d+}-00.h5-deconvolved"
log: "{xml_base}-{file_id,\d+}-00.h5-deconvolution.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Ddeco_output_file_directory={jdir} \
-Dmerged_xml={merged_xml} \
-Dparallel_timepoints={file_id_w} \
-Dprocess_timepoint={process_timepoint} \
-Dprocess_channel={process_channel} \
-Dprocess_illumination={process_illumination} \
-Dprocess_angle={process_angle} \
-Dminimal_x_deco={minimal_x} \
-Dminimal_y_deco={minimal_y} \
-Dminimal_z_deco={minimal_z} \
-Dmaximal_x_deco={maximal_x} \
-Dmaximal_y_deco={maximal_y} \
-Dmaximal_z_deco={maximal_z} \
-Dimglib2_container_deco={imglib2_container} \
-Dtype_of_iteration={type_of_iteration} \
-Dosem_acceleration={osem_acceleration} \
-DTikhonov_parameter={Tikhonov_parameter} \
-Dcompute={compute} \
-Dpsf_estimation={psf_estimation} \
-Ddirectory_cuda={directory_cuda} \
-Ddetections_to_extract_psf_for_channel_0={detections_to_extract_psf_for_channel_0} \
-Ddetections_to_extract_psf_for_channel_1={detections_to_extract_psf_for_channel_1} \
-Dpsf_size_x={psf_size_x} \
-Dpsf_size_y={psf_size_y} \
-Dpsf_size_z={psf_size_z} \
-Diterations={iterations} \
-- --no-splash {bsh_file}""",
config["common"],
config["deconvolution"],
file_id_w="{wildcards.file_id}",
jdir=JOBDIR)
cmd_string += "> {log} 2>&1 && touch {output}"
shell(cmd_string)
rule clean:
shell : "rm -rf *registered"
spim_registration/timelapse/cluster.json 0 → 100644
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{
"__default__" :
{
"fiji-app" : "/projects/pilot_spim/Christopher/Test_pipeline_3.0/test_unicore/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-good-4-resave" : "/sw/users/schmied/lifeline/Fiji.app.lifeline2/ImageJ-linux64",
"fiji-good-4-deconv" : "/projects/pilot_spim/Christopher/Test_pipeline_3.0/test_unicore/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-prefix" : "/sw/bin/xvfb-run -a",
"lsf_extra" : "-R span[hosts=1]",
"lsf_queue" : "short"
},
"registration" :
{
"lsf_extra" : "-R span[hosts=1] -R rusage[mem=100000]",
"lsf_queue" : "gpu"
},
"produce" :
{
"lsf_queue" : "short"
}
}
spim_registration/timelapse/deconvolution_CPU.bsh 0 → 100644
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// 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" );
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load xml file: " );
System.out.println( "selected_xml = " + image_file_directory + merged_xml + ".xml");
// Load general Parameters
parallel_timepoints = 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" );
IJ.run("Fuse/Deconvolve Dataset",
"select_xml=" + image_file_directory + merged_xml + ".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 + "");
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/deconvolution_GPU.bsh 0 → 100644
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// 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" );
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load xml file: " );
System.out.println( "selected_xml = " + image_file_directory + merged_xml + ".xml");
// Load general Parameters
parallel_timepoints = 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" );
IJ.run("Fuse/Deconvolve Dataset",
"select_xml=" + image_file_directory + merged_xml + ".xml " +
"process_angle=[All angles] " +
"process_channel=[All channels] " +
"process_illumination=[All illuminations] " +
"process_timepoint=[" + process_timepoint + "] " +
"processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
// "processing_timepoint=[Timepoint 0] " +
"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=[GPU (Nvidia CUDA via JNA)] " +
"psf_estimation=[" + psf_estimation + "] " +
"psf_display=[Do not show PSFs] " +
"output_file_directory=" + deco_output_file_directory + " " +
// "directory=[/sw/users/schmied/packages/Fiji.app.cuda_new/lib/] " +
"directory=[" + directory_cuda + "] " +
"select_native_library_for_cudafourierconvolution=libFourierConvolutionCUDALib.so " +
"gpu_1 " +
// "gpu_2 " +
"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 + "");
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/registration.bsh 0 → 100644
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View file @ 5111213d
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 loading parameters");
// select xml
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load xml file: " );
xml_path = System.getProperty( "image_file_directory" );
xml_filename = System.getProperty( "xml_filename" );
System.out.println( "selected_xml = " + xml_path + xml_filename + ".xml");
// Load general Parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "General parameters: " );
parallel_timepoints = 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" );
processing_channel = System.getProperty( "processing_channel" );
System.out.println( "parallel_timepoints = " + 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 );
System.out.println( "processing_channel = " + processing_channel );
// Interest point detection parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "Detection of Interest Points: " );
label_interest_points= System.getProperty( "label_interest_points" );
type_of_registration = System.getProperty( "type_of_registration" );
type_of_detection = System.getProperty( "type_of_detection" );
subpixel_localization = System.getProperty( "subpixel_localization" );
imglib_container = System.getProperty( "imglib_container" );
System.out.println( "label_interest_points = " + label_interest_points );
System.out.println( "type_of_registration = " + type_of_registration );
System.out.println( "type_of_detection = " + type_of_detection );
System.out.println( "subpixel_localization = " + subpixel_localization );
System.out.println( "imglib_container = " + imglib_container );
// Parameters for difference of mean !!Comment out for Difference of Gaussian!!
System.out.println( "-------------------------------------------------------" );
System.out.println( "Difference of Mean detection: " );
int radius_1 = Integer.parseInt( System.getProperty( "radius_1" ) );
int radius_2 = Integer.parseInt( System.getProperty( "radius_2" ) );
float threshold = Float.parseFloat( System.getProperty( "threshold" ) );
System.out.println( "radius_1 = " + radius_1 );
System.out.println( "radius_2 = " + radius_2 );
System.out.println( "threshold = " + threshold );
//Parameters for difference of gaussian !!Comment out for Differnence of Mean!!
//System.out.println( "-------------------------------------------------------" );
//System.out.println( "Difference of Gaussian detection: " );
//float initial_sigma = Float.parseFloat( System.getProperty( "initial_sigma" ) );
//float threshold_gaussian = Float.parseFloat( System.getProperty( "threshold_gaussian" ) );
//System.out.println( "initial_sigma = " + initial_sigma );
//System.out.println( "threshold_gaussian = " + threshold_gaussian );
// Registration parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "Parameters for Registration: " );
registration_algorithm = System.getProperty( "registration_algorithm" );
interest_points_channel_0 = System.getProperty( "interest_points_channel_0" );
interest_points_channel_1 = System.getProperty( "interest_points_channel_1" );
fix_tiles = System.getProperty( "fix_tiles" );
map_back_tiles = System.getProperty( "map_back_tiles" );
transformation_model = System.getProperty( "transformation_model" );
model_to_regularize_with = System.getProperty( "model_to_regularize_with" );
float lambda = Float.parseFloat( System.getProperty( "lambda" ) );
int allowed_error_for_ransac = Integer.parseInt( System.getProperty( "allowed_error_for_ransac" ) );
detection_min_max = System.getProperty( "detection_min_max" );
System.out.println( "registration_algorithm = " + registration_algorithm );
System.out.println( "interest_points_channel_0 = " + interest_points_channel_0 );
System.out.println( "interest_points_channel_1 = " + interest_points_channel_1 );
System.out.println( "fix_tiles = " + fix_tiles );
System.out.println( "map_back_tiles = " + map_back_tiles );
System.out.println( "transformation = " + transformation_model);
System.out.println( "model_to_regularize_with = " + model_to_regularize_with );
System.out.println( "lambda = " + lambda );
System.out.println( "allowed_error_for_ransac = " + allowed_error_for_ransac );
System.out.println( "detection_min_max = " + detection_min_max );
//activate cluster processing
System.out.println( "=======================================================" );
IJ.run("Toggle Cluster Processing", "display_cluster");
System.out.println( "Activated Cluster Processing" );
//interest point detection
System.out.println( "=======================================================" );
System.out.println( "Starting Detection of Interest Points" );
IJ.run("Detect Interest Points for Registration",
"select_xml=" + xml_path + xml_filename + ".xml " +
"unique_id=" + parallel_timepoints + " " +
"process_angle=[" + process_angle + "] " +
"process_channel=[" + process_channel + "] " +
"process_illumination=[" + process_illumination + "] " +
"process_timepoint=[" + process_timepoint + "] " +
"processing_channel=[" + processing_channel + "] " + // Dual Channel: 1 Channel contains the beads
"xml_output=[Save every XML with user-provided unique id]" + " " +
"processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
"type_of_interest_point_detection=[" + type_of_detection + "] " +
"label_interest_points=" + label_interest_points + " " +
"subpixel_localization=[" + subpixel_localization + "] " +
"interest_point_specification_(channel_0)=[Advanced ...] " +
// "interest_point_specification_(channel_1)=[Advanced ...] " + // Dual Channel
"radius_1=" + radius_1 + " " +
"radius_2=" + radius_2 + " " +
"threshold=" + threshold + " " +
"find_maxima");
//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);
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/tomancak.json 0 → 100644
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{
"common" :
{
"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher-sandbox/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-prefix" : "/sw/bin/xvfb-run -a",
"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
"merged_xml" : "hdf5_test_unicore_merge"
},
"registration" :
{
"timepoint" : "\"Single Timepoint (Select from List)\"",
"illuminations" : "\"All illuminations\"",
"angle" : "\"All angles\"",
"channel" : "\"All channels\"",
"proc-ch" : "\"channel 1\"",
"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
"label_interest_points" : "\"beads\"",
"type_of_registration" : "\"Register timepoints individually\"",
"type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
"type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
"subpixel_localization" : "\"3-dimensional quadratic fit\"",
"imglib_container" : "\"ArrayImg (faster)\"",
"radius_1" : "2",
"radius_2" : "3",
"threshold" : "0.005",
"interest_points_channel_0" : "\"[DO NOT register this channel]\"" ,
"interest_points_channel_1" : "\"beads\"",
"fix_tiles" : "\"Fix first tile\"" ,
"map_back_tiles" : "\"Map back to first tile using rigid model\"",
"transformation_model" : "Affine",
"model_to_regularize_with" : "Rigid",
"lambda" : "0.10" ,
"allowed_error_for_ransac" : "5",
"detection_min_max" : "find_maxima",
"initial_sigma" : "1.8",
"threshold_gaussian" : "0.0080",
"bsh_file" : "registration.bsh"
},
"xml_merge" :
{
"bsh_file" : "xml_merge.bsh"
},
"external_transform" :
{
"bsh_file" : "transform.bsh",
"angle" : "\"All angles\"",
"channel" : "\"All channels\"",
"illumination" : "\"All illuminations\"",
"timepoint" : "\"All Timepoints\"",
"transformation" : "\"Rigid\"",
"apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
"define_mode_transform" : "\"Matrix\"",
"matrix_transform" : "\"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0\""
},
"deconvolution" :
{
"bsh_file" : "deconvolution_GPU.bsh",
"process_timepoint" : "\"Single Timepoint (Select from List)\"",
"process_channel" : "\"All channels\"",
"process_illumination" : "\"All illuminations\"",
"process_angle" : "\"All angles\"",
"minimal_x" : "76",
"minimal_y" : "4",
"minimal_z" : "-192",
"maximal_x" : "488",
"maximal_y" : "956",
"maximal_z" : "214",
"imglib2_container" : "\"ArrayImg \"",
"type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
"osem_acceleration" : "\"1 (balanced)\"",
"Tikhonov_parameter" : "0.0006",
"compute" : "\"in 512x512x512 blocks\"",
"compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
"psf_estimation" : "\"Extract from beads\"",
"iterations" : "5",
"detections_to_extract_psf_for_channel_0" : "\"beads\"",
"detections_to_extract_psf_for_channel_1" : "\"beads\"",
"psf_size_x" : "19",
"psf_size_y" : "19",
"psf_size_z" : "25"
}
}
spim_registration/timelapse/transform.bsh 0 → 100644
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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");
// Load Parameters form job file
image_file_directory = System.getProperty( "image_file_directory" );
merged_xml = System.getProperty( "merged_xml" );
transform_angle = System.getProperty( "transform_angle" );
transform_channel = System.getProperty( "transform_channel" );
transform_illumination = System.getProperty( "transform_illumination" );
transform_timepoint = System.getProperty( "transform_timepoint" );
transformation = System.getProperty( "transformation" );
apply_transformation = System.getProperty( "apply_transformation" );
define_mode_transform = System.getProperty( "define_mode_transform" );
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( "apply_to_angle = " + transform_angle );
System.out.println( "apply_to_channel = " + transform_channel );
System.out.println( "apply_to_illumination = " + transform_illumination );
System.out.println( "apply_to_timepoint = " + transform_timepoint );
System.out.println( "transformation = " + transformation );
System.out.println( "apply = " + apply_transformation );
System.out.println( "define = " + define_mode_transform );
System.out.println( "all_timepoints_channel_0_illumination_0_all_angles = " + matrix_transform );
// Execute Fiji Plugin
IJ.run("Apply Transformations",
"browse=" + image_file_directory + " " +
"select_xml=" + image_file_directory + merged_xml + ".xml " +
"apply_to_angle=[" + transform_angle + "] " +
"apply_to_channel=[" + transform_channel + "] " +
"apply_to_illumination=[" + transform_illumination + "] " +
"apply_to_timepoint=[" + transform_timepoint + "] " +
"transformation=" + transformation + " " +
"apply=[" + apply_transformation + "] " +
"define=" + define_mode_transform + " " +
"same_transformation_for_all_timepoints " +
"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 + "]");
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/xml_merge.bsh 0 → 100644
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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( "Load Parameters:");
// Getting parameters from job file
image_file_directory = System.getProperty( "image_file_directory" );
merged_xml = System.getProperty( "merged_xml" );
// Printing parameters into output file
System.out.println( "directory=" + image_file_directory );
System.out.println( "merged_xml=" + merged_xml );
System.out.println( "=======================================================" );
System.out.println( "Start to merge .xml files" );
// Executing Fiji plugin
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");
/* shutdown */
runtime.exit(0);
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