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Commit 27743163 authored by Peter Steinbach's avatar Peter Steinbach
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Merge pull request #1 from schmiedc/NewBshScripts 

New bsh scripts .. Thanks!
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import os, glob, sys, re
from timelaps_utils import produce_xml_merge_job_files, produce_string, padding_of_file_id
#where are we (can be configured through -d/--directory flag)
JOBDIR=os.path.abspath(os.path.curdir)
if JOBDIR[-1] != "/":
if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a slash
JOBDIR+="/"
#data specific config file, expected to be inside JOBDIR
configfile: "tomancak.json"
datasets = glob.glob('*00.h5')
#TODO: this should go into a python module in this path
fre = re.compile(r'(?P<xml_base>\w+)-(?P<file_id>\d+)-00.h5')
xml_merge_in = []
for ds in datasets:
bn = os.path.basename(ds)
bn_res = fre.search(bn)
xml_base,file_id = bn_res.group('xml_base'),bn_res.group('file_id')
xml_merge_in.append("{xbase}.job_{fid}.xml".format(xbase=xml_base, fid=int(file_id)))
#TODO: this should go into a python module in this path
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)
# configfile: "tomancak_test_cluster.json"
configfile: "tomancak_test_cluster.yaml"
padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
ds_format = "-"+padding_format+"-00.h5"
# problematic needs padding of file_id
datasets = [ str(config["common"]["hdf5_xml_filename"].strip('\"')+(ds_format.format(item))) for item in range(int(config["common"]["ntimepoints"])) ]
xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
input: [ ds+"_deconvolved" for ds in datasets ]
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"])
# defining xml for czi dataset
rule define_xml_czi:
input:glob.glob('*.czi'), config["define_xml_czi"]["first_czi"]
output: config["common"]["first_xml_filename"] + ".xml"
log: "define_xml_czi.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_czi={first_czi} \
-Dangles={angles} \
-Dchannels={channels} \
-Dillumination={illumination} \
-Dpixel_distance_x={pixel_distance_x} \
-Dpixel_distance_y={pixel_distance_y} \
-Dpixel_distance_z={pixel_distance_z} \
-Dpixel_unit={pixel_unit} \
-Dfirst_xml_filename={first_xml_filename} \
-Drotation_around={rotation_around} \
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["define_xml_czi"]["bsh_file"])
cmd_string += " > {log} 2>&1"
shell(cmd_string)
# defining xml for tif dataset
rule define_xml_tif:
input: glob.glob(re.sub("{{.}}","*",config["define_xml_tif"]['image_file_pattern'])) #replaces all occurrences of {{a}} (a can be any character) by * to use the string for globbing
output: config["common"]["first_xml_filename"] + ".xml"
log: "define_xml_tif.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dtimepoints={timepoints} \
-Dangles={angles} \
-Dchannels={channels} \
-Dillumination={illumination} \
-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["define_xml_tif"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"],
timepoints="0-"+str(int(config["common"]["ntimepoints"])-1)
)
cmd_string +=" > {log} 2>&1"
shell(cmd_string)
ruleorder: define_xml_czi > define_xml_tif
# create mother .xml/.h5
rule hdf5_xml:
input: config["common"]["first_xml_filename"] + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
[ item+"_xml" for item in datasets ]
log: "hdf5_xml.log"
run:
part_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dfirst_xml_filename={first_xml_filename} \
-Dhdf5_xml_filename={hdf5_xml_filename} \
-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 \
-- --no-splash {path_bsh}""",
config["common"],
config["define_xml_czi"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
part_string += " > {log} 2>&1 && touch {output}"
shell(part_string)
# resave .czi/.tif dataset as hdf5
rule resave_hdf5:
input: rules.hdf5_xml.output # "{xml_base}-{file_id,\d+}-00.h5_xml"
output: "{xml_base}-{file_id,\d+}-00.h5", "{xml_base}-{file_id,\d+}-00.h5_hdf5"
log: "resave_hdf5-{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} \
-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={job_number} \
-- --no-splash {path_bsh}""", # the & submits everyting at once
config["common"],
config["define_xml_czi"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
input_xml_base="{wildcards.xml_base}",
job_number=int(wildcards.file_id)+1)
part_string += " > {log} 2>&1 && touch {output}"
shell(part_string)
rule registration:
input: "{xml_base}-{file_id}-00.h5"
output: "{xml_base}-{file_id,\d+}-00.h5_registered", #"{xml_base}.job_{file_id,\d+}.xml"
input: "{xml_base}-{file_id}-00.h5"
output: "{xml_base}.job_{file_id,\d+}.xml"#, "{xml_base}-{file_id,\d+}-00.h5_registered",
log: "{xml_base}-{file_id}-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}""",
-Dparallel_timepoints={file_id_w} \
-Dimage_file_directory={jdir} \
-Dxml_filename={input_xml} \
-Dreg_process_timepoint={reg_process_timepoint} \
-Dreg_process_channel={reg_process_channel} \
-Dreg_process_illumination={reg_process_illumination} \
-Dreg_process_angle={reg_process_angle} \
-Dchannels={channels} \
-Dreg_processing_channel={reg_processing_channel} \
-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} \
-Dreg_radius_1={reg_radius_1} \
-Dreg_radius_2={reg_radius_2} \
-Dreg_threshold={reg_threshold} \
-Dinitial_sigma={initial_sigma} \
-Dthreshold_gaussian={threshold_gaussian} \
-Dregistration_algorithm={algorithm} \
-Dreg_interest_points_channel={reg_interest_points_channel} \
-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} \
-Dsignificance={significance} \
-- --no-splash {path_bsh}""",
config["common"],
config["registration"],
file_id_w="{wildcards.file_id}",
file_id_w=wildcards.file_id,
path_bsh=config["common"]["bsh_directory"] + config["registration"]["bsh_file"],
jdir=JOBDIR,
input_xml="{wildcards.xml_base}")
cmd_string += "> {log} 2>&1 && touch {output}"
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 ] #xml_merge_in
input: [ str(config["common"]["hdf5_xml_filename"].strip('\"')+".job_"+(padding_format.format(item))+".xml") for item in range(int(config["common"]["ntimepoints"])) ] #[ 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={output} -- --no-splash {bsh_file} > {log} 2>&1",
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dmerged_xml={output} \
-- --no-splash {path_bsh}""",
config["common"],
config["xml_merge"],
log="{log}",
path_bsh=config["common"]["bsh_directory"] + config["xml_merge"]["bsh_file"],
jdir=JOBDIR,
output="{output}")
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
rule external_trafo:
rule timelapse:
input: rules.xml_merge.output
output: rules.xml_merge.output[0] + "_external_trafo"
log: "external_trafo.log"
output: rules.xml_merge.output[0] + "_timelapse"
log: "{xml_base}_timelapse.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dmerged_xml={input} \
-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}""",
-Dtimelapse_process_timepoints={timelapse_process_timepoints} \
-Dreg_process_channel={reg_process_channel} \
-Dreg_process_illumination={reg_process_illumination} \
-Dreg_process_angle={reg_process_angle} \
-Dreference_timepoint={reference_timepoint} \
-Dchannels={channels} \
-Dtype_of_registration_timelapse={type_of_registration_timelapse} \
-Dregistration_algorithm={algorithm} \
-Dreg_interest_points_channel={reg_interest_points_channel} \
-Dtransformation_model={transformation_model} \
-Dmodel_to_regularize_with={model_to_regularize_with} \
-Dlambda={lambda} \
-Dallowed_error_for_ransac={allowed_error_for_ransac} \
-Dsignificance={significance} \
-- --no-splash {path_bsh}""",
config["common"],
config["registration"],
config["timelapse"],
input="{input}",
path_bsh=config["common"]["bsh_directory"] + config["timelapse"]["bsh_file"],
jdir=JOBDIR)
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
rule fusion:
input: rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
log: "{xml_base}-{file_id,\d+}-00-fusion.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dparallel_timepoints={file_id_w} \
-Dmerged_xml={merged_xml_file} \
-Dprocess_timepoint={process_timepoint} \
-Dprocess_channel={process_channel} \
-Dprocess_illumination={process_illumination} \
-Dprocess_angle={process_angle} \
-Dxml_output={xml_output} \
-Dfused_image={fused_image} \
-Dminimal_x={minimal_x} \
-Dminimal_y={minimal_y} \
-Dminimal_z={minimal_z} \
-Dmaximal_x={maximal_x} \
-Dmaximal_y={maximal_y} \
-Dmaximal_z={maximal_z} \
-Ddownsample={downsample} \
-Dpixel_type={pixel_type} \
-Dimglib2_container_fusion={imglib2_container_fusion} \
-Dprocess_views_in_paralell={process_views_in_paralell} \
-Dinterpolation={interpolation} \
-Dimglib2_data_container={imglib2_data_container} \
-Dsubsampling_factors={subsampling_factors} \
-Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-- --no-splash {path_bsh}""",
config["common"],
config["fusion"],
config["resave_hdf5"],
path_bsh=config["common"]["bsh_directory"] + config["fusion"]["bsh_file"],
jdir=JOBDIR,
file_id_w="{wildcards.file_id}",
merged_xml_file="{input.merged_xml}"
)
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
rule external_transform:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
output: rules.timelapse.output[0] + "_external_trafo"
log: "external_transform.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Dmerged_xml={merged_xml_file} \
-Dchannel_setting={channel_setting} \
-Dtransform_angle={transform_angle} \
-Dtransform_channel={transform_channel} \
-Dtransform_illumination={transform_illumination} \
-Dtransform_timepoint={transform_timepoint} \
-Dtransformation={transformation} \
-Dapply_transformation={apply_transformation} \
-Ddefine_mode_transform={define_mode_transform} \
-Dmatrix_transform={matrix_transform} \
-- --no-splash {path_bsh}""",
config["common"],
config["external_transform"],
path_bsh=config["common"]["bsh_directory"] + config["external_transform"]["bsh_file"],
jdir=JOBDIR,
input="{input}")
cmd_string += "> {log} 2>&1 && touch {output}"
merged_xml_file="{input.merged_xml}"
)
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
rule deconvolution:
input: rules.external_trafo.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_deconvolved"
input: rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
log: "{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Ddeco_output_file_directory={jdir} \
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
-Dimage_file_directory={jdir} \
-Ddeco_output_file_directory={jdir} \
-Dmerged_xml={merged_xml_file} \
-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}""",
-Dparallel_timepoints={file_id_w} \
-Dprocess_timepoint={process_timepoint} \
-Dprocess_channel={process_channel} \
-Dprocess_illumination={process_illumination} \
-Dprocess_angle={process_angle} \
-Dchannels={channels} \
-Dminimal_x_deco={minimal_x_deco} \
-Dminimal_y_deco={minimal_y_deco} \
-Dminimal_z_deco={minimal_z_deco} \
-Dmaximal_x_deco={maximal_x_deco} \
-Dmaximal_y_deco={maximal_y_deco} \
-Dmaximal_z_deco={maximal_z_deco} \
-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={detections_to_extract_psf_for_channel} \
-Dpsf_size_x={psf_size_x} \
-Dpsf_size_y={psf_size_y} \
-Dpsf_size_z={psf_size_z} \
-Diterations={iterations} \
-- --no-splash {path_bsh}""",
config["common"],
config["deconvolution"],
file_id_w="{wildcards.file_id}",
path_bsh=config["common"]["bsh_directory"] + config["deconvolution"]["bsh_file"],
jdir=JOBDIR,
merged_xml_file="{input.merged_xml}"
)
cmd_string += "> {log} 2>&1 && touch {output}"
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
rule define_output:
input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
output: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
log: "define_output.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} \
-- --no-splash {path_bsh}""",
config["common"],
config["hdf5_output"],
jdir=JOBDIR,
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"].strip('\"') + ".xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
[ item+"_output" for item in datasets ]
log: "output_hdf5_xml.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_output} \
-Dhdf5_chunk_sizes={chunk_sizes_output} \
-Dtimepoints_per_partition={timepoints_per_partition} \
-Dsetups_per_partition={setups_per_partition} \
-Drun_only_job_number=0 \
-Doutput_data_type={output_data_type} \
-Dconvert_32bit={convert_32bit}\
-- --no-splash {path_bsh}""",
config["common"],
config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
path_bsh=config["common"]["bsh_directory"] + config["hdf5_output"]["bsh_file_hdf5"])
part_string += " > {log} 2>&1 && touch {output}"
shell(part_string)
rule resave_hdf5_output:
input: rules.hdf5_xml_output.output
output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
log: "resave_output-{file_id}.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_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} \
-Doutput_data_type={output_data_type} \
-Dconvert_32bit={convert_32bit}\
-- --no-splash {path_bsh}""",
config["common"],
config["hdf5_output"],
config["resave_hdf5"],
jdir=JOBDIR,
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}"
shell(part_string)
rule distclean:
shell : "rm -rf *registered *tif *log *_deconvolved *.xml~* interestpoints "+str(" ".join(xml_merge_in))
params : glob.glob(config["common"]["hdf5_xml_filename"].strip('\"')+"*"), glob.glob(config["common"]["first_xml_filename"].strip('\"')+"*"), glob.glob("*registered"), glob.glob("*_fusion"), glob.glob("*_timelapse"), 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"]), glob.glob("*_output_hdf5"), glob.glob("*_output")# xml_merge_in,
message : os.path.abspath(os.path.curdir) + ": rm -rf {params}"
shell : "rm -rf {params}"
spim_registration/timelapse/cluster.json 100644 → 100755
+ 11
− 1
View file @ 27743163
......@@ -9,8 +9,13 @@
{
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=100000]\""
},
"timelapse" :
{
"lsf_extra" : "-n 6 -R \"span[hosts=1] rusage[mem=100000]\""
},
"external_trafo" :
"external_transfrom" :
{
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=10000]\""
},
......@@ -19,5 +24,10 @@
{
"lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\"",
"lsf_q" : "gpu"
},
"resave_hdf5_output" :
{
"lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\""
}
}
spim_registration/timelapse/deconvolution_CPU.bsh deleted 100644 → 0
+ 0
− 146
View file @ eb42acf0
// 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);
spim_registration/timelapse/deconvolution_GPU.bsh 100644 → 100755
+ 45
− 20
View file @ 27743163
// Load Fiji dependencies
import ij.IJ;
import ij.ImagePlus;
import ij.IJ; // calls imagej
import ij.Prefs; // calls imagej settings
import java.lang.Runtime;
import java.io.File;
import java.io.FilenameFilter;
......@@ -8,25 +8,28 @@ import java.io.FilenameFilter;
runtime = Runtime.getRuntime();
System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
System.out.println( "Start to load Parameters:" );
Prefs.setThreads(7); // defines the number of threads allowed
print("Threads: "+Prefs.getThreads()); // prints thread setting in output
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);
System.out.println( "selected_xml = " + image_file_directory + merged_xml + ".xml");
// Load general Parameters
parallel_timepoints = Integer.parseInt(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" );
process_angle = System.getProperty( "process_angle" );
System.out.println( "-------------------------------------------------------" );
System.out.println( "General parameters: " );
System.out.println( "timepoint_processed = " + parallel_timepoints );
......@@ -62,8 +65,7 @@ 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: " );
......@@ -75,14 +77,11 @@ 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: " );
directory_cuda = System.getProperty( "directory_cuda" );
System.out.println( "directory_cuda = " + directory_cuda );
// PSF Parameters
......@@ -96,19 +95,48 @@ 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 );
// Channel settings
System.out.println( "-------------------------------------------------------" );
System.out.println( "Channel Settings: " );
// Channel setting for Deconvolution
// parses channels and takes from there the number of channels
// parses detections_to_extract_psf_for_channel
channels = System.getProperty( "channels" );
System.out.println( "Channels = " + channels );
detections_to_extract_psf_for_channel = System.getProperty( "detections_to_extract_psf_for_channel" );
System.out.println( "PSF: " + detections_to_extract_psf_for_channel );
// Splits channels and detections_to_extract_psf_for_channel
String delims = "[,]";
String[] channel_token = channels.split(delims);
String[] psf_token = detections_to_extract_psf_for_channel.split(delims);
// Assembles channel_string
StringBuilder channel_string = new StringBuilder();
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "detections_to_extract_psf_for_channel_" + channel_token[channel] + "=" + psf_token[channel] + " ";
channel_string.append( channel_part );
channel_string.append(" ");
}
System.out.println( channel_string );
// Execute Fiji Plugin
System.out.println( "=======================================================" );
System.out.println( "Starting Deconvolution" );
try {
IJ.run("Fuse/Deconvolve Dataset",
"select_xml=" + image_file_directory + merged_xml + " " +
"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 + "] " +
// "processing_timepoint=[Timepoint 0] " +
"type_of_image_fusion=[Multi-view deconvolution] " +
"bounding_box=[Define manually] " +
"fused_image=[Save as TIFF stack] " +
......@@ -130,13 +158,10 @@ IJ.run("Fuse/Deconvolve Dataset",
"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 + "] " +
"cuda_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
channel_string +
"psf_size_x=" + psf_size_x + " " +
"psf_size_y=" + psf_size_y + " " +
"psf_size_z=" + psf_size_z + "");
......
spim_registration/timelapse/define_czi.bsh 0 → 100755
+ 174
− 0
View file @ 27743163
// Load Fiji dependencies
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(2); // defines the number of threads allowed
//print("Threads: "+Prefs.getThreads()); // prints thread setting in output
System.out.println("Start loading parameters");
// Directory, and first .czi
System.out.println("---------------------------------------------------------");
System.out.println("Directory:");
image_file_directory = System.getProperty( "image_file_directory" );
first_xml_filename = System.getProperty( "first_xml_filename" );
first_czi = System.getProperty( "first_czi" );
System.out.println( "xml_file_path = " + image_file_directory + first_xml_filename + ".xml" );
System.out.println( "first_czi_path = " + image_file_directory + first_czi );
// Dataset settings
System.out.println("---------------------------------------------------------");
System.out.println("Angle Settings:");
// Angle settings
// Parses angles and determines the number of angles
// uses tokens of string angles to assemble the string for angle_string
// via StringBuilder
angles = System.getProperty( "angles" );
System.out.println( "Angles = " + angles );
// Parses string angles
String delims = "[,]";
String[] angle_token = angles.split(delims);
// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder angle_string = new StringBuilder();
String angle_part;
for ( int angle = 0; angle < angle_token.length; angle++) {
int num_angles = angle + 1;
angle_part = "angle_" + num_angles + "=" + angle_token[angle];
angle_string.append(angle_part);
angle_string.append(" ");
}
System.out.println( angle_string );
System.out.println("---------------------------------------------------------");
System.out.println("Channel Settings:");
// Channel settings
// This parses channels and determines the number of channels
// then uses the tokens of channels to assemble the necessary string
// for channel_string via StringBuilder
channels = System.getProperty( "channels" );
System.out.println( "Channel Names = " + channels );
// Parses string channel_names
String delims = "[,]";
String[] channel_token = channels.split(delims);
// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder channel_string = new StringBuilder();
String channel_part;
for ( int channel = 0; channel < channel_token.length; channel++) {
int num_channel = channel + 1;
channel_part = "channel_" + num_channel + "=" + channel_token[channel];
channel_string.append(channel_part);
channel_string.append(" ");
}
System.out.println( "Channel String = " + channel_string );
System.out.println("---------------------------------------------------------");
System.out.println("Illumination Settings:");
// Illuminatin settings
// This parses illumination and determines the number of illuminations
// then uses the tokens of illuminations to assemble the string for
// illum_string via StringBuilder
illumination = System.getProperty( "illumination" );
System.out.println( "Illumination = " + illumination );
// Parses string illumination
String delims = "[,]";
String[] illum_token = illumination.split(delims);
// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder illum_string = new StringBuilder();
String illum_part;
for ( int illum= 0; illum< illum_token.length; illum++) {
int num_illum = illum + 1;
illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
illum_string.append(illum_part);
illum_string.append(" ");
}
System.out.println( illum_string );
System.out.println("---------------------------------------------------------");
System.out.println("Rotation setting:");
rotation_around = System.getProperty( "rotation_around" );
System.out.println( "rotation_around = " + rotation_around );
// 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 );
// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
System.out.println("Define Multi-View Dataset type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
"xml_filename=" + first_xml_filename + ".xml " +
"browse=" + image_file_directory + first_czi + " " +
"first_czi=" + image_file_directory + first_czi + " " +
angle_string +
channel_string +
illum_string +
"modify_calibration " +
"modify_rotation_axis " +
"pixel_distance_x=" + pixel_distance_x + " " +
"pixel_distance_y=" + pixel_distance_y + " " +
"pixel_distance_z=" + pixel_distance_z + " " +
"pixel_unit=" + pixel_unit + " " +
"rotation_around=" + rotation_around + "");
try {
IJ.run("Define Multi-View Dataset",
"type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
"xml_filename=" + first_xml_filename + ".xml " +
"browse=" + image_file_directory + first_czi + " " +
"first_czi=" + image_file_directory + first_czi + " " +
angle_string +
channel_string +
illum_string +
"modify_calibration " +
"modify_rotation_axis " +
"pixel_distance_x=" + pixel_distance_x + " " +
"pixel_distance_y=" + pixel_distance_y + " " +
"pixel_distance_z=" + pixel_distance_z + " " +
"pixel_unit=" + pixel_unit + " " +
"rotation_around=" + rotation_around + "");
}
catch ( e ) {
print( "[define_czi] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/define_output.bsh 0 → 100755
+ 137
− 0
View file @ 27743163
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" );
if ( multiple_channels.equalsIgnoreCase( "NO (one channel)" ) )
{
channels="";
}
else if ( multiple_channels.equalsIgnoreCase( "YES (one file per channel)" ) )
{
channels = "channels_=" + channels + " ";
}
else {
System.out.println( "Channel switch setting gibberish" );
}
System.out.println( "channels = " + channels );
System.out.println("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:");
try {
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 + "");
}
catch ( e ) {
print( "[define_output] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
/* shutdown */
runtime.exit(0);
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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:");
image_file_pattern = System.getProperty( "image_file_pattern" );
type_of_dataset = System.getProperty( "type_of_dataset" );
timepoints = System.getProperty( "timepoints" );
angles = System.getProperty( "angles" );
System.out.println( "image_file_pattern = " + image_file_pattern );
System.out.println( "type_of_dataset = " + type_of_dataset );
System.out.println( "timepoints = " + timepoints );
System.out.println( "angles = " + angles );
multiple_timepoints = System.getProperty( "multiple_timepoints" );
multiple_channels = System.getProperty( "multiple_channels" );
multiple_illumination_directions = System.getProperty( "multiple_illumination_directions" );
multiple_angles = System.getProperty( "multiple_angles" );
imglib_container = System.getProperty( "imglib_container" );
System.out.println( "multiple_timepoints = " + multiple_timepoints );
System.out.println( "multiple_channels = " + multiple_channels );
System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
System.out.println( "multiple_angles = " + multiple_angles );
System.out.println( "imglib_container = " + imglib_container );
System.out.println("---------------------------------------------------------");
System.out.println("Channel setting:");
// Channel switch: parses channels and determines if Single or Multi Channel
// assembles the appropriate string for the channel setting
channels = System.getProperty( "channels" );
String channel_string = null;
String delims = "[,]";
String[] channel_token = channels.split(delims);
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
else if ( channel_token.length == 1 )
{
channel_string="";
System.out.println("Single Channel");
}
else if ( channel_token.length > 1)
{
channel_string = "channels_=" + channels + " ";
System.out.println("Multi Channel");
}
System.out.println( "Channels = " + channel_string );
System.out.println("---------------------------------------------------------");
System.out.println("Illumination setting:");
// Illuminatin switch: parses illumination and determines if there is a single
// or multiple illumination sides and then assembles the illum_string
illumination = System.getProperty( "illumination" );
String illum_string = null;
String delims = "[,]";
String[] illum_token = illumination.split(delims);
if (illumination.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no illuminations set");
}
else if ( illum_token.length == 1 )
{
illum_string="";
System.out.println("One illumination side or fused illumination");
}
else if ( illum_token.length > 1)
{
illum_string = "illumination_=" + illumination + " ";
System.out.println("Dual Illumination sides");
}
System.out.println( "Illuminations = " + illum_string );
// 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 );
System.out.println("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 + " " +
channel_string +
illum_string +
"acquisition_angles_=" + acquisition_angles + " " +
"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:");
try {
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 + " " +
channel_string +
illum_string +
"acquisition_angles_=" + angles + " " +
"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 + "");
}
catch ( e ) {
print( "[define_tif_zip] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
/* shutdown */
runtime.exit(0);
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// Load Fiji dependencies
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, and first .czi
System.out.println("=========================================================");
System.out.println("Directory:");
image_file_directory = System.getProperty( "image_file_directory" );
first_xml_filename = System.getProperty( "first_xml_filename" );
hdf5_xml_filename = System.getProperty( "hdf5_xml_filename" );
System.out.println( "dir=" + image_file_directory );
System.out.println( "xml_filename=" + first_xml_filename );
System.out.println( "hdf5_xml_filename=" + hdf5_xml_filename );
// Dataset settings
System.out.println("=========================================================");
System.out.println("Dataset:");
resave_angle = System.getProperty( "resave_angle" );
resave_channel = System.getProperty( "resave_channel" );
resave_illumination = System.getProperty( "resave_illumination" );
resave_timepoint = System.getProperty( "resave_timepoint" );
System.out.println( "resave_angle=" + resave_angle );
System.out.println( "resave_channel=" + resave_channel );
System.out.println( "resave_illumination=" + resave_illumination );
System.out.println( "resave_timepoint=" + resave_timepoint);
// Hdf5 settings
System.out.println("=========================================================");
System.out.println("Hdf5 settings:");
subsampling_factors = System.getProperty( "subsampling_factors" );
hdf5_chunk_sizes = System.getProperty( "hdf5_chunk_sizes" );
timepoints_per_partition = System.getProperty( "timepoints_per_partition" );
setups_per_partition = System.getProperty( "setups_per_partition" );
run_only_job_number = System.getProperty( "run_only_job_number" );
System.out.println( "subsampling_factors=" + subsampling_factors);
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 );
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("=========================================================");
System.out.println("Start plugin:");
try {
IJ.run("As HDF5",
"select_xml=" + image_file_directory + first_xml_filename + ".xml " +
"resave_angle=[" + resave_angle + "] " +
"resave_channel=[" + resave_channel + "] " +
"resave_illumination=[" + resave_illumination + "] " +
"resave_timepoint=[" + resave_timepoint + "] " +
"manual_mipmap_setup " +
"subsampling_factors=[" + subsampling_factors + "] " +
"hdf5_chunk_sizes=[" + hdf5_chunk_sizes + "] " +
"split_hdf5 " +
"timepoints_per_partition=" + timepoints_per_partition + " " +
"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 );
}
catch ( e ) {
print( "[export::resaving] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
/* shutdown */
System.exit(0);
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// Load Fiji dependencies
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, and first .czi
System.out.println("=========================================================");
System.out.println("Directory:");
image_file_directory = System.getProperty( "image_file_directory" );
first_xml_filename = System.getProperty( "first_xml_filename" );
hdf5_xml_filename = System.getProperty( "hdf5_xml_filename" );
System.out.println( "dir=" + image_file_directory );
System.out.println( "xml_filename=" + first_xml_filename );
System.out.println( "hdf5_xml_filename=" + hdf5_xml_filename );
// Dataset settings
System.out.println("=========================================================");
System.out.println("Dataset:");
resave_angle = System.getProperty( "resave_angle" );
resave_channel = System.getProperty( "resave_channel" );
resave_illumination = System.getProperty( "resave_illumination" );
resave_timepoint = System.getProperty( "resave_timepoint" );
System.out.println( "resave_angle=" + resave_angle );
System.out.println( "resave_channel=" + resave_channel );
System.out.println( "resave_illumination=" + resave_illumination );
System.out.println( "resave_timepoint=" + resave_timepoint);
// Hdf5 settings
System.out.println("=========================================================");
System.out.println("Hdf5 settings:");
subsampling_factors = System.getProperty( "subsampling_factors" );
hdf5_chunk_sizes = System.getProperty( "hdf5_chunk_sizes" );
timepoints_per_partition = System.getProperty( "timepoints_per_partition" );
setups_per_partition = System.getProperty( "setups_per_partition" );
run_only_job_number = System.getProperty( "run_only_job_number" );
System.out.println( "subsampling_factors=" + subsampling_factors);
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 );
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( "32Bit" ) )
{
data_string = "convert_32bit=" + convert_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:");
try{
IJ.run("Toggle Cluster Processing", "display_cluster");
}
catch ( e ) {
print( "[export_output::cluster setting] 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 + "] " +
"resave_channel=[" + resave_channel + "] " +
"resave_illumination=[" + resave_illumination + "] " +
"resave_timepoint=[" + resave_timepoint + "] " +
"manual_mipmap_setup " +
"subsampling_factors=[" + subsampling_factors + "] " +
"hdf5_chunk_sizes=[" + hdf5_chunk_sizes + "] " +
"split_hdf5 " +
"timepoints_per_partition=" + timepoints_per_partition + " " +
"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 + " " +
data_string + "");
}
catch ( e ) {
print( "[export_output::resaving] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
/* shutdown */
System.exit(0);
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// Load Fiji dependencies
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");
System.out.println( "Start to load Parameters:" );
Prefs.setThreads(6); // defines the number of threads allowed
print("Threads: "+Prefs.getThreads()); // prints thread setting in output
System.out.println( "Start to load Parameters:" );
// select xml
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: " );
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" );
process_angle = System.getProperty( "process_angle" );
System.out.println( process_timepoint );
System.out.println( "timepoint = " + parallel_timepoints);
System.out.println( "illuminations = " + process_illumination );
System.out.println( "angles = " + process_angle );
//Load bounding box
System.out.println( "-------------------------------------------------------" );
System.out.println( "Load bounding box: " );
minimal_x = System.getProperty( "minimal_x" );
minimal_y = System.getProperty( "minimal_y" );
minimal_z = System.getProperty( "minimal_z" );
maximal_x = System.getProperty( "maximal_x" );
maximal_y = System.getProperty( "maximal_y" );
maximal_z = System.getProperty( "maximal_z" );
downsample = System.getProperty( "downsample" );
System.out.println( "minimal_x=" + minimal_x );
System.out.println( "minimal_y=" + minimal_y );
System.out.println( "minimal_z=" + minimal_z );
System.out.println( "maximal_x=" + maximal_x );
System.out.println( "maximal_y=" + maximal_y );
System.out.println( "maximal_z=" + maximal_z );
System.out.println( "downsample=" + downsample );
// Load fusion parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "Fusion parameters: " );
pixel_type = System.getProperty( "pixel_type" );
imglib2_container_fusion = System.getProperty( "imglib2_container_fusion" );
interpolation = System.getProperty( "interpolation" );
imglib2_data_container = System.getProperty( "imglib2_data_container" );
System.out.println( "pixel_type=" + pixel_type );
System.out.println( "imglib2_container_fusion=" + imglib2_container_fusion );
System.out.println( "interpolation=" + interpolation );
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 + " " +
"process_angle=[" + process_angle + "] " +
"process_illumination=[" + process_illumination + "] " +
"process_timepoint=[" + process_timepoint + "] " +
"processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
// "xml_output=[Do not process on cluster] " +
"processing_timepoint=[Timepoint "+ parallel_timepoints +"] " +
"type_of_image_fusion=[Weighted-average fusion] " +
"bounding_box=[Define manually] " +
"fused_image=[Save as TIFF stack] " + // works but does not create xml file
"minimal_x=" + minimal_x + " " +
"minimal_y=" + minimal_y + " " +
"minimal_z=" + minimal_z + " " +
"maximal_x=" + maximal_x + " " +
"maximal_y=" + maximal_y + " " +
"maximal_z=" + maximal_z + " " +
"downsample=" + downsample + " " +
"pixel_type=[" + pixel_type + "] " +
"imglib2_container=" + imglib2_container_fusion + " " +
"process_views_in_paralell=All " +
"interpolation=[" + interpolation + "] " +
//"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);
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spim_registration/timelapse/timelaps_utils.py 0 → 100644
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import re
import os
import math
def produce_xml_merge_job_files(_datasets):
fre = re.compile(r'(?P<xml_base>\w+)-(?P<file_id>\d+)-00.h5')
value = []
for ds in _datasets:
bn = os.path.basename(ds)
bn_res = fre.search(bn)
if bn_res:
xml_base,file_id = bn_res.group('xml_base'),bn_res.group('file_id')
value.append("{xbase}.job_{fid}.xml".format(xbase=xml_base, fid=int(file_id)))
return value
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)
def padding_of_file_id(_n_timepoints):
value = math.ceil(math.log10(_n_timepoints))
if value < 2:
return 2
else:
return value
spim_registration/timelapse/timelapse_registration.bsh 0 → 100755
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// Load Fiji dependencies
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
// Load xml file
System.out.println("---------------------------------------------------------");
System.out.println("Xml file:");
xml_path = System.getProperty( "image_file_directory" );
xml_path = System.getProperty( "image_file_directory" );
merged_xml = System.getProperty( "merged_xml" );
if ( ! merged_xml.endsWith(".xml") )
merged_xml = merged.xml + ".xml";
System.out.println( "selected_xml = " + xml_path + merged_xml );
// General Registration Parameters and Channel Settings
System.out.println("---------------------------------------------------------");
System.out.println( "General parameters: " );
timelapse_process_timepoints = System.getProperty( "timelapse_process_timepoints" );
reg_process_illumination = System.getProperty( "reg_process_illumination" );
reg_process_angle = System.getProperty( "reg_process_angle" );
System.out.println( "process_timepoints = " + timelapse_process_timepoints );
System.out.println( "process_illumination = " + reg_process_illumination );
System.out.println( "process_angle = " + reg_process_angle );
// Timelapse registration Parameter
System.out.println("---------------------------------------------------------");
System.out.println( "Timelapse Registration: " );
reference_timepoint = System.getProperty( "reference_timepoint" );
System.out.println( "reference_timepoint=" + reference_timepoint );
type_of_registration_timelapse = System.getProperty( "type_of_registration_timelapse" );
registration_algorithm = System.getProperty( "registration_algorithm" );
System.out.println( "type_of_registration = " + type_of_registration_timelapse );
System.out.println( "registration_algorithm = " + registration_algorithm );
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" ) );
significance = System.getProperty( "significance" );
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( "significance = " + significance );
// Timelapse registration Parameter
System.out.println("---------------------------------------------------------");
System.out.println( "Channel Settings: " );
// Channel Setting Registration
// parses channels and takes from there the number of channels
// takes from reg_process_channel if it is Single Channel, Dual Channel or Dual Channel
// were one Channel contains the beads
// from this it decides which string to assemble
reg_process_channel = System.getProperty( "reg_process_channel" );
System.out.println( "process_channel = " + reg_process_channel );
channels = System.getProperty( "channels" );
System.out.println( "Channels = " + channels );
reg_interest_points_channel = System.getProperty( "reg_interest_points_channel" );
System.out.println( "reg_interest_points_channel = " + reg_interest_points_channel );
// Splits up channels, reg_interest_points_channel
String delims = "[,]";
String[] channel_token = channels.split(delims);
String[] interest_token = reg_interest_points_channel.split(delims);
String reg_single_channel_string = "";
StringBuilder reg_multi_channel_string = new StringBuilder();
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
// Assembles string for Single Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 )
{
reg_multi_channel_string.append( "" );
reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
}
// Assembles string for Multi Channel registration
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
// Returns error of Multi Channels one Channel contains the beads is selected but not enough settings in channels or reg_interest_points_channel
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && ( channel_token.length < 1 || interest_token.length < 1 ))
{
System.out.println( "Error: Multi Channel one Channel contains beads selected but only one setting in channls or reg_interest_points_channel" );
}
// Assembles string for Multi Channel Processing one Channel Contains the beads
else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
{
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
}
}
System.out.println( "reg_single_channel_string = " + reg_single_channel_string );
System.out.println( "reg_multi_channel_string = " + reg_multi_channel_string );
System.out.println( "=======================================================" );
System.out.println( "Starting Timelapse Registration" );
System.out.println( "Register Dataset based on Interest Points , select_xml=" + xml_path + merged_xml + " " +
"process_angle=[" + reg_process_angle + "] " +
"process_channel=[" + reg_process_channel + "] " +
"process_illumination=[" + reg_process_illumination + "] " +
"process_timepoint=[" + timelapse_process_timepoints + "] " +
"registration_algorithm=[" + registration_algorithm + "] " +
"type_of_registration=[" + type_of_registration_timelapse + "] " +
reg_multi_channel_string +
reg_single_channel_string +
// "interest_points_channel_" + channel_1 + "=" + reg_1_interest_points_channel + " " +
// "interest_points_channel_" + channel_2 + "=" + reg_2_interest_points_channel + " " + // Dual Channel
"reference=" + reference_timepoint + " " +
"consider_each_timepoint_as_rigid_unit " +
"transformation=" + transformation_model + " " +
"regularize_model " +
"model_to_regularize_with=" + model_to_regularize_with + " " +
"lamba=" + lambda + " " +
"allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
"significance=" + significance + "");
try {
IJ.run("Register Dataset based on Interest Points",
"select_xml=" + xml_path + merged_xml + " " +
"process_angle=[" + reg_process_angle + "] " +
"process_channel=[" + reg_process_channel + "] " +
"process_illumination=[" + reg_process_illumination + "] " +
"process_timepoint=[" + timelapse_process_timepoints + "] " +
"registration_algorithm=[" + registration_algorithm + "] " +
"type_of_registration=[" + type_of_registration_timelapse + "] " +
reg_multi_channel_string +
reg_single_channel_string +
// "interest_points_channel_" + channel_1 + "=" + reg_1_interest_points_channel + " " +
// "interest_points_channel_" + channel_2 + "=" + reg_2_interest_points_channel + " " + // Dual Channel
"reference=" + reference_timepoint + " " +
"consider_each_timepoint_as_rigid_unit " +
"transformation=" + transformation_model + " " +
"regularize_model " +
"model_to_regularize_with=" + model_to_regularize_with + " " +
"lamba=" + lambda + " " +
"allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
"significance=" + significance + "");
}
catch ( e ) {
print( "[registration::timelapse] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
/* shutdown */
runtime.exit(0);
spim_registration/timelapse/tomancak.json
+ 1
− 1
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{
"common" :
{
"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher-sandbox/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/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"
......
spim_registration/timelapse/tomancak_czi.json 0 → 100644
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View file @ 27743163
{
"common" :
{
"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/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",
"bsh_directory" : "/home/steinbac/development/cschmied-snakemake-workflows/spim_registration/timelapse/",
"first_xml_filename" : "test_unicore",
"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
"fusion_switch" : "deconvolution",
"ntimepoints" : 3
},
"define_xml_czi" :
{
"pixel_distance_x" : "0.2875535786151886",
"pixel_distance_y" : "0.2875535786151886",
"pixel_distance_z" : "1.50000",
"pixel_unit" : "um",
"first_czi" : "2015-02-21_LZ1_Stock68_3.czi",
"channel_1" : "green",
"channel_2" : "red",
"angle_1" : "0",
"angle_2" : "72",
"angle_3" :"144",
"angle_4" :"216",
"angle_5" : "288",
"illumination_1" : "0",
"rotation_around" : "X-Axis",
"bsh_file" : "define_czi.bsh"
},
"define_xml_tif" :
{
"timepoints" : "0-1",
"acquisition_angles" : "0,72,144,216,288",
"channels" : "0",
"image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
"pixel_distance_x" : "0.2875535786151886",
"pixel_distance_y" : "0.2875535786151886",
"pixel_distance_z" : "1.50000",
"pixel_unit" : "um",
"multiple_timepoints" : "\"YES (one file per time-point)\"",
"multiple_channels" : "\"NO (one channel)\"",
"multiple_illumination_directions" : "\"NO (one illumination direction)\"",
"multiple_angles" : "\"YES (one file per angle)\"",
"type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"imglib_container" : "\"ArrayImg (faster)\"",
"bsh_file" : "define_tif_zip.bsh"
},
"resave_hdf5" :
{
"parallel_timepoints" : "3",
"resave_angle" : "\"All angles\"",
"resave_channel" : "\"All channels\"",
"resave_illumination" : "\"All illuminations\"",
"resave_timepoint" : "\"All Timepoints\"",
"subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
"hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
"timepoints_per_partition" : "1",
"setups_per_partition" : "0",
"bsh_file" : "export.bsh"
},
"registration" :
{
"timepoint" : "\"Single Timepoint (Select from List)\"",
"illuminations" : "\"All illuminations\"",
"angle" : "\"All angles\"",
"channel" : "\"All channels\"",
"proc-ch" : "\"channel 0\"",
"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
"label_interest_points" : "\"beads\"",
"type_of_registration" : "\"Register timepoints individually\"",
"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" : "\"beads\"",
"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",
"significance" : "10",
"detection_min_max" : "find_maxima",
"initial_sigma" : "1.8",
"threshold_gaussian" : "0.0080",
"bsh_file" : "registration.bsh"
},
"xml_merge" :
{
"bsh_file" : "xml_merge.bsh"
},
"timelapse" :
{
"reference_timepoint" : "0",
"timelapse_process_timepoints" : "\"All Timepoints\"",
"type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
"bsh_file" : "timelapse_registration.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\""
},
"fusion" :
{
"minimal_x" : "128",
"minimal_y" : "-13",
"minimal_z" : "-407",
"maximal_x" : "986",
"maximal_y" : "1927",
"maximal_z" : "498",
"downsample" : "1",
"process_timepoint" : "\"Single Timepoint (Select from List)\"",
"process_channel" : "\"All channels\"",
"process_illumination" : "\"All illuminations\"",
"process_angle" : "\"All angles\"",
"xml_output" : "\"Save every XML with user-provided unique id\"",
"fused_image" : "\"Append to current XML Project\"",
"pixel_type" : "\"16-bit unsigned integer\"",
"imglib2_container_fusion" : "\"ArrayImg\"",
"process_views_in_paralell" : "\"All\"",
"interpolation" : "\"Linear Interpolation\"",
"imglib2_data_container" : "\"ArrayImg (faster)\"",
"bsh_file" : "fusion.bsh"
},
"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"
},
"hdf5_output" :
{
"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\"",
"output_multiple_channels" : "\"NO (one channel)\"",
"output_timepoints" : "0-1",
"output_channels" : "green",
"output_pixel_distance_x" : "0.5718",
"output_pixel_distance_y" : "0.5718",
"output_pixel_distance_z" : "0.5718",
"output_pixel_unit" : "um",
"output_multiple_timepoints" : "\"YES (one file per time-point)\"",
"output_illumination_directions" : "\"NO (one illumination direction)\"",
"output_multiple_angles" : "\"NO (one angle)\"",
"output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"output_imglib_container" : "\"ArrayImg (faster)\"",
"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)]\""
}
}
spim_registration/timelapse/tomancak_test_cluster.json 0 → 100644
+ 202
− 0
View file @ 27743163
{
"common" :
{
"fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/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",
"bsh_directory" : "/home/steinbac/development/schmied-snakemake-workflows/spim_registration/timelapse/",
"first_xml_filename" : "test_unicore",
"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
"fusion_switch" : "deconvolution",
"ntimepoints" : 5
},
"define_xml_czi" :
{
"pixel_distance_x" : "0.28590106964",
"pixel_distance_y" : "0.28590106964",
"pixel_distance_z" : "1.50000",
"pixel_unit" : "um",
"first_czi" : "2015-04-11_LZ2_Stock68_3.czi",
"channel_1" : "green",
"channel_2" : "red",
"angle_1" : "0",
"angle_2" : "72",
"angle_3" : "144",
"angle_4" : "216",
"angle_5" : "288",
"illumination_1" : "0",
"rotation_around" : "X-Axis",
"bsh_file" : "define_czi.bsh"
},
"define_xml_tif" :
{
"acquisition_angles" : "0,72,144,216,288",
"channels" : "0",
"image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
"pixel_distance_x" : "0.28590106964",
"pixel_distance_y" : "0.28590106964",
"pixel_distance_z" : "1.50000",
"pixel_unit" : "um",
"multiple_timepoints" : "\"YES (one file per time-point)\"",
"multiple_channels" : "\"NO (one channel)\"",
"multiple_illumination_directions" : "\"NO (one illumination direction)\"",
"multiple_angles" : "\"YES (one file per angle)\"",
"type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"imglib_container" : "\"ArrayImg (faster)\"",
"bsh_file" : "define_tif_zip.bsh"
},
"resave_hdf5" :
{
"resave_angle" : "\"All angles\"",
"resave_channel" : "\"All channels\"",
"resave_illumination" : "\"All illuminations\"",
"resave_timepoint" : "\"All Timepoints\"",
"subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
"hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
"timepoints_per_partition" : "1",
"setups_per_partition" : "0",
"bsh_file" : "export.bsh"
},
"registration" :
{
"timepoint" : "\"Single Timepoint (Select from List)\"",
"illuminations" : "\"All illuminations\"",
"angle" : "\"All angles\"",
"channel" : "\"All channels\"",
"proc-ch" : "\"channel 0\"",
"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
"label_interest_points" : "\"beads\"",
"type_of_registration" : "\"Register timepoints individually\"",
"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" : "\"beads\"",
"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",
"significance" : "10",
"detection_min_max" : "find_maxima",
"initial_sigma" : "1.8",
"threshold_gaussian" : "0.0080",
"bsh_file" : "registration.bsh"
},
"xml_merge" :
{
"bsh_file" : "xml_merge.bsh"
},
"timelapse" :
{
"reference_timepoint" : "0",
"timelapse_process_timepoints" : "\"All Timepoints\"",
"type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
"bsh_file" : "timelapse_registration.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\""
},
"fusion" :
{
"minimal_x" : "190",
"minimal_y" : "-16",
"minimal_z" : "-348",
"maximal_x" : "1019",
"maximal_y" : "1941",
"maximal_z" : "486",
"downsample" : "1",
"process_timepoint" : "\"Single Timepoint (Select from List)\"",
"process_channel" : "\"All channels\"",
"process_illumination" : "\"All illuminations\"",
"process_angle" : "\"All angles\"",
"xml_output" : "\"Save every XML with user-provided unique id\"",
"fused_image" : "\"Append to current XML Project\"",
"pixel_type" : "\"16-bit unsigned integer\"",
"imglib2_container_fusion" : "\"ArrayImg\"",
"process_views_in_paralell" : "\"All\"",
"interpolation" : "\"Linear Interpolation\"",
"imglib2_data_container" : "\"ArrayImg (faster)\"",
"bsh_file" : "fusion.bsh"
},
"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" : "95",
"minimal_y" : "-8",
"minimal_z" : "-174",
"maximal_x" : "509",
"maximal_y" : "970",
"maximal_z" : "243",
"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"
},
"hdf5_output" :
{
"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\"",
"output_multiple_channels" : "\"NO (one channel)\"",
"output_timepoints" : "0-4",
"output_channels" : "green",
"output_pixel_distance_x" : "0.5718",
"output_pixel_distance_y" : "0.5718",
"output_pixel_distance_z" : "0.5718",
"output_pixel_unit" : "um",
"output_multiple_timepoints" : "\"YES (one file per time-point)\"",
"output_illumination_directions" : "\"NO (one illumination direction)\"",
"output_multiple_angles" : "\"NO (one angle)\"",
"output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
"output_imglib_container" : "\"ArrayImg (faster)\"",
"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)]\""
}
}
spim_registration/timelapse/tomancak_test_cluster.yaml 0 → 100755
+ 186
− 0
View file @ 27743163
common: {
# directory that contains the bean shell scripts
bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/",
fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
fiji-prefix: "/sw/bin/xvfb-run -a",
first_xml_filename: "test_unicore",
hdf5_xml_filename: '"hdf5_test_unicore"',
merged_xml: "hdf5_test_unicore_merge",
ntimepoints: 5,
angles: "0,72,144,216,288",
channels: "green",
illumination: "0",
pixel_distance_x: '0.28590106964',
pixel_distance_y: '0.28590106964',
pixel_distance_z: '1.50000',
pixel_unit: "um",
fusion_switch: "deconvolution"
# fusion_switch: "fusion"
}
define_xml_czi: {
first_czi: "2015-04-11_LZ2_Stock68_3.czi",
rotation_around: "X-Axis",
bsh_file: "define_czi.bsh"
}
define_xml_tif: {
image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
imglib_container: '"ArrayImg (faster)"',
multiple_angles: '"YES (one file per angle)"',
multiple_channels: '"NO (one channel)"',
multiple_illumination_directions: '"NO (one illumination direction)"',
multiple_timepoints: '"YES (one file per time-point)"',
type_of_dataset: '"Image Stacks (ImageJ Opener)"',
bsh_file: "define_tif_zip.bsh"
}
resave_hdf5: {
hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
resave_angle: '"All angles"',
resave_channel: '"All channels"',
resave_illumination: '"All illuminations"',
resave_timepoint: '"All Timepoints"',
setups_per_partition: '0',
subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
timepoints_per_partition: '1',
bsh_file: "export.bsh"
}
registration: {
# "Single Channel" is not a valid choice for "Process_channel"
reg_process_channel: '"All channels"',
reg_processing_channel: '"green"',
reg_interest_points_channel: '"beads"',
reg_radius_1: '2',
reg_radius_2: '3',
reg_threshold: '0.005',
initial_sigma: '1.8',
threshold_gaussian: '0.0080',
type_of_detection: '"Difference-of-Mean (Integral image based)"',
label_interest_points: '"beads"',
reg_process_timepoint: '"Single Timepoint (Select from List)"',
reg_process_angle: '"All angles"',
reg_process_illumination: '"All illuminations"',
subpixel_localization: '"3-dimensional quadratic fit"',
detection_min_max: "find_maxima",
type_of_registration: '"Register timepoints individually"',
algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
transformation_model: "Affine",
allowed_error_for_ransac: '5',
significance: '10',
fix_tiles: '"Fix first tile"',
map_back_tiles: '"Map back to first tile using rigid model"',
model_to_regularize_with: "Rigid",
lambda: '0.10',
imglib_container: '"ArrayImg (faster)"',
bsh_file: "registration.bsh"
}
xml_merge: {
bsh_file: "xml_merge.bsh"
}
timelapse: {
reference_timepoint: '0',
type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
timelapse_process_timepoints: '"All Timepoints"',
bsh_file: "timelapse_registration.bsh"
}
Dublicate_transformations: {
source_dublication: "red",
target_dublication: "green",
bsh_file: "dublicate_channel.bsh"
}
fusion: {
bsh_file: "fusion.bsh",
downsample: '4',
fused_image: '"Append to current XML Project"',
imglib2_container_fusion: '"ArrayImg"',
imglib2_data_container: '"ArrayImg (faster)"',
interpolation: '"Linear Interpolation"',
minimal_x: '190',
minimal_y: '-16',
minimal_z: '-348',
maximal_x: '1019',
maximal_y: '1941',
maximal_z: '486',
pixel_type: '"16-bit unsigned integer"',
process_angle: '"All angles"',
process_channel: '"All channels"',
process_illumination: '"All illuminations"',
process_timepoint: '"Single Timepoint (Select from List)"',
process_views_in_paralell: '"All"',
xml_output: '"Save every XML with user-provided unique id"'
}
external_transform: {
# channel setting: '"all_channels"'
channel_setting: '"green"',
transform_timepoint: '"All Timepoints"',
transform_angle: '"All angles"',
transform_channel: '"All channels"',
# illumination setting only one illumination side
transform_illumination: '"All illuminations"',
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"',
transformation: '"Rigid"',
bsh_file: "transform.bsh"
}
deconvolution: {
iterations: '1',
minimal_x_deco: '190',
minimal_y_deco: '-16',
minimal_z_deco: '-348',
maximal_x_deco: '1019',
maximal_y_deco: '1941',
maximal_z_deco: '486',
detections_to_extract_psf_for_channel: '"beads"',
process_timepoint: '"Single Timepoint (Select from List)"',
process_angle: '"All angles"',
process_channel: '"All channels"',
process_illumination: '"All illuminations"',
Tikhonov_parameter: '0.0006',
compute: '"in 512x512x512 blocks"',
compute_on: '"GPU (Nvidia CUDA via JNA)"',
imglib2_container: '"ArrayImg"',
osem_acceleration: '"1 (balanced)"',
psf_estimation: '"Extract from beads"',
psf_size_x: '19',
psf_size_y: '19',
psf_size_z: '25',
type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
bsh_file: "deconvolution_GPU.bsh"
}
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_Single_Channel"',
output_multiple_channels: '"NO (one channel)"',
output_timepoints: '0-4',
output_pixel_distance_x: 0.5718,
output_pixel_distance_y: 0.5718,
output_pixel_distance_z: 0.5718,
output_pixel_unit: 'um',
output_channels: "green",
output_data_type: "32Bit",
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}}, {{4,4,4}}, {{8,8,8}} }}"',
chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"',
# 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"
}
spim_registration/timelapse/transform.bsh 100644 → 100755
+ 8
− 8
View file @ 27743163
// is problematic needs to be adjusted for
// multi channel and multi illumination datasets
import ij.IJ;
import ij.ImagePlus;
import java.lang.Runtime;
......@@ -11,13 +13,11 @@ System.out.println(runtime.availableProcessors() + " cores available for multi-t
// Load Parameters form job 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";
transform_angle = System.getProperty( "transform_angle" );
transform_channel = System.getProperty( "transform_channel" );
transform_illumination = System.getProperty( "transform_illumination" );
transform_timepoint = System.getProperty( "transform_timepoint" );
channel_setting = System.getProperty( "channel_setting" );
transformation = System.getProperty( "transformation" );
apply_transformation = System.getProperty( "apply_transformation" );
define_mode_transform = System.getProperty( "define_mode_transform" );
......@@ -26,15 +26,16 @@ 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 );
System.out.println( "select_xml = " + image_file_directory + merged_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( "Channel_setting = " + channel_setting );
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 );
System.out.println( "all_timepoints_channel_" + channel_setting + "_illumination_0_all_angles = " + matrix_transform );
// Execute Fiji Plugin
try {
......@@ -50,12 +51,11 @@ IJ.run("Apply Transformations",
"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 + "]");
"all_timepoints_channel_" + channel_setting + "_illumination_0_all_angles=[" + matrix_transform + "]");
}
catch ( e ) {
print( "[transform] caught exception: "+e );
print( "[external transformation] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
......
spim_registration/timelapse/xml_merge.bsh 100644 → 100755
+ 9
− 4
View file @ 27743163
import ij.IJ;
// Load Fiji dependencies
import ij.IJ; // calls imagej
import ij.Prefs; // calls imagej settings
import ij.ImagePlus;
import java.lang.Runtime;
import java.io.File;
......@@ -7,16 +9,18 @@ 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( "Load Parameters:");
// Getting parameters from job file
// Getting parameters from job 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";
// Printing parameters into output file
System.out.println( "directory=" + image_file_directory );
System.out.println( "merged_xml=" + merged_xml );
......@@ -31,7 +35,8 @@ IJ.run("Merge Cluster Jobs",
"filename_contains=job_ " +
"filename_also_contains=.xml " +
"display " +
"merged_xml=" + merged_xml);
// "delete_xml's " +
"merged_xml=" + merged_xml + "");
}
catch ( e ) {
......
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