diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
old mode 100644
new mode 100755
index cafc9128152cf949d6fe15794451ee7f16b399d8..812dccc659d3b7bfd2aed5728f94dd2c1cf1ebf2
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -1,162 +1,475 @@
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}"
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
old mode 100644
new mode 100755
index 2807e94c521056fda295d81be4b2ee3a6954d42f..4b2be746447e0fbd6c2b2892b30e26c895b4b0dd
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -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]\""
}
}
diff --git a/spim_registration/timelapse/deconvolution_CPU.bsh b/spim_registration/timelapse/deconvolution_CPU.bsh
deleted file mode 100644
index f21f94d72529c6304592d7b59a592270ecfc550a..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/deconvolution_CPU.bsh
+++ /dev/null
@@ -1,146 +0,0 @@
-// 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);
diff --git a/spim_registration/timelapse/deconvolution_GPU.bsh b/spim_registration/timelapse/deconvolution_GPU.bsh
old mode 100644
new mode 100755
index ac8066689dd5d458ef6c48f4e362639626d5ddb5..32154c2c9986c8156073d169f1fa53071506cc35
--- a/spim_registration/timelapse/deconvolution_GPU.bsh
+++ b/spim_registration/timelapse/deconvolution_GPU.bsh
@@ -1,6 +1,6 @@
// 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 + "");
diff --git a/spim_registration/timelapse/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..e3e1d30e788e27aa6888ce5a4a7e352162aae4d5
--- /dev/null
+++ b/spim_registration/timelapse/define_czi.bsh
@@ -0,0 +1,174 @@
+// 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);
diff --git a/spim_registration/timelapse/define_output.bsh b/spim_registration/timelapse/define_output.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..e2469feb053fc3a11f2b2bf0169f2dbf699ffa15
--- /dev/null
+++ b/spim_registration/timelapse/define_output.bsh
@@ -0,0 +1,137 @@
+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);
+
+
diff --git a/spim_registration/timelapse/define_tif_zip.bsh b/spim_registration/timelapse/define_tif_zip.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..a5f401511eb4263335f9aa64b2ad8307d39ebee7
--- /dev/null
+++ b/spim_registration/timelapse/define_tif_zip.bsh
@@ -0,0 +1,179 @@
+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);
+
+
diff --git a/spim_registration/timelapse/export.bsh b/spim_registration/timelapse/export.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..1e928a8113f474ce8523b99124eb68f196db4a1b
--- /dev/null
+++ b/spim_registration/timelapse/export.bsh
@@ -0,0 +1,101 @@
+// 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);
+
diff --git a/spim_registration/timelapse/export_output.bsh b/spim_registration/timelapse/export_output.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..f05798a6b9e011e8d1b8737940a6a7cb08c5ca8e
--- /dev/null
+++ b/spim_registration/timelapse/export_output.bsh
@@ -0,0 +1,114 @@
+// 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);
+
diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..79f9d54911da2bef0b7b3f57e4d64ce62dbdf6d7
--- /dev/null
+++ b/spim_registration/timelapse/fusion.bsh
@@ -0,0 +1,113 @@
+// 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);
diff --git a/spim_registration/timelapse/registration.bsh b/spim_registration/timelapse/registration.bsh
old mode 100644
new mode 100755
index f7c6b26bb1edb96765c2da801b2c3f42da75e7e6..d6872232b191687a082c3e8f591979528318672e
--- a/spim_registration/timelapse/registration.bsh
+++ b/spim_registration/timelapse/registration.bsh
@@ -1,12 +1,18 @@
-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;
import java.io.FilenameFilter;
-
+import java.lang.Object;
+
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");
// select xml
@@ -18,24 +24,20 @@ xml_filename = System.getProperty( "xml_filename" );
System.out.println( "selected_xml = " + xml_path + xml_filename + ".xml");
-
// Load general Parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "General parameters: " );
-parallel_timepoints = 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" );
-processing_channel = System.getProperty( "processing_channel" );
+int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoints" ));
+unique_id = System.getProperty( "parallel_timepoints" );
+reg_process_timepoint = System.getProperty( "reg_process_timepoint" );
+reg_process_illumination = System.getProperty( "reg_process_illumination" );
+reg_process_angle = System.getProperty( "reg_process_angle" );
System.out.println( "parallel_timepoints = " + parallel_timepoints );
-System.out.println( "process_timepoints = " + process_timepoint );
-System.out.println( "process_channel = " + process_channel );
-System.out.println( "process_illumination = " + process_illumination );
-System.out.println( "process_angle = " + process_angle );
-System.out.println( "processing_channel = " + processing_channel );
+System.out.println( "process_timepoints = " + reg_process_timepoint );
+System.out.println( "process_illumination = " + reg_process_illumination );
+System.out.println( "process_angle = " + reg_process_angle );
// Interest point detection parameters
System.out.println( "-------------------------------------------------------" );
@@ -53,53 +55,215 @@ System.out.println( "type_of_detection = " + type_of_detection );
System.out.println( "subpixel_localization = " + subpixel_localization );
System.out.println( "imglib_container = " + imglib_container );
-// Parameters for difference of mean !!Comment out for Difference of Gaussian!!
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "Difference of Mean detection: " );
-
-int radius_1 = Integer.parseInt( System.getProperty( "radius_1" ) );
-int radius_2 = Integer.parseInt( System.getProperty( "radius_2" ) );
-float threshold = Float.parseFloat( System.getProperty( "threshold" ) );
-
-System.out.println( "radius_1 = " + radius_1 );
-System.out.println( "radius_2 = " + radius_2 );
-System.out.println( "threshold = " + threshold );
-
-//Parameters for difference of gaussian !!Comment out for Differnence of Mean!!
-//System.out.println( "-------------------------------------------------------" );
-//System.out.println( "Difference of Gaussian detection: " );
-//float initial_sigma = Float.parseFloat( System.getProperty( "initial_sigma" ) );
-//float threshold_gaussian = Float.parseFloat( System.getProperty( "threshold_gaussian" ) );
-//System.out.println( "initial_sigma = " + initial_sigma );
-//System.out.println( "threshold_gaussian = " + threshold_gaussian );
-
// Registration parameters
System.out.println( "-------------------------------------------------------" );
System.out.println( "Parameters for Registration: " );
registration_algorithm = System.getProperty( "registration_algorithm" );
-interest_points_channel_0 = System.getProperty( "interest_points_channel_0" );
-interest_points_channel_1 = System.getProperty( "interest_points_channel_1" );
+
fix_tiles = System.getProperty( "fix_tiles" );
map_back_tiles = System.getProperty( "map_back_tiles" );
transformation_model = System.getProperty( "transformation_model" );
model_to_regularize_with = System.getProperty( "model_to_regularize_with" );
float lambda = Float.parseFloat( System.getProperty( "lambda" ) );
int allowed_error_for_ransac = Integer.parseInt( System.getProperty( "allowed_error_for_ransac" ) );
-detection_min_max = System.getProperty( "detection_min_max" );
+significance = System.getProperty( "significance" );
System.out.println( "registration_algorithm = " + registration_algorithm );
-System.out.println( "interest_points_channel_0 = " + interest_points_channel_0 );
-System.out.println( "interest_points_channel_1 = " + interest_points_channel_1 );
System.out.println( "fix_tiles = " + fix_tiles );
System.out.println( "map_back_tiles = " + map_back_tiles );
System.out.println( "transformation = " + transformation_model);
System.out.println( "model_to_regularize_with = " + model_to_regularize_with );
System.out.println( "lambda = " + lambda );
System.out.println( "allowed_error_for_ransac = " + allowed_error_for_ransac );
-System.out.println( "detection_min_max = " + detection_min_max );
+System.out.println( "significance = " + significance );
+
+
+// detection_min_max = System.getProperty( "detection_min_max" );
+// System.out.println( "detection_min_max = " + detection_min_max );
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "Channel setting for Detection: " );
+
+// Channel setting for Difference-of-Mean detection
+// 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 );
+
+reg_processing_channel = System.getProperty( "reg_processing_channel" );
+System.out.println( "processing_channel = channel " + reg_processing_channel );
+
+channels = System.getProperty( "channels" );
+System.out.println( "Channels = " + channels );
+
+reg_radius_1 = System.getProperty( "reg_radius_1" );
+System.out.println( "reg_radius_1 = " + reg_radius_1 );
+
+reg_radius_2 = System.getProperty( "reg_radius_2" );
+System.out.println( "reg_radius_2 = " + reg_radius_2 );
+
+reg_threshold = System.getProperty( "reg_threshold" );
+System.out.println( "reg_threshold = " + reg_threshold);
+
+// Splits up channels, reg_radius_1, reg_radius_2 and reg_threshold
+String delims = "[,]";
+String[] channel_token = channels.split(delims);
+String[] radius_1_token = reg_radius_1.split(delims);
+String[] radius_2_token = reg_radius_2.split(delims);
+String[] threshold_token = reg_threshold.split(delims);
+
+String channel_string = "";
+String processing_channel_string = "";
+StringBuilder channel_string_multi = new StringBuilder();
+
+// If there are no channels set returns an error
+if (channels.equalsIgnoreCase(""))
+{
+ System.out.println("Warning: There are no channels set");
+}
+
+// Returns an Error if there is one channel in channels but multiple settings in radius and or threshold
+else if ( channel_token.length == 1 && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
+{
+ System.out.println( "Error: Only one channel detected but multiple channel settings for radius or threshold" );
+}
+
+// Assembles String for Singel Channel
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 )
+{
+ processing_channel_string = "";
+ channel_string_multi.append("");
+ channel_string = "interest_point_specification=[Advanced ...] " +
+ "radius_1=" + reg_radius_1 + " " +
+ "radius_2=" + reg_radius_2 + " " +
+ "threshold=" + reg_threshold + " " +
+ "find_maxima";
+}
+
+// Dual Channels both Channels contain beads
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
+{
+ // Assembles String using StringBuilder for 2 Channels
+ for (int channel=0; channel < channel_token.length; channel++ )
+ {
+ String channel_part = "interest_point_specification_(channel_" + channel_token[channel] + ")=[Advanced ...] " +
+ "radius_1_" + channel_token[channel] + "=" + radius_1_token[channel] + " " +
+ "radius_2_" + channel_token[channel] + "=" + radius_2_token[channel] + " " +
+ "threshold_" + channel_token[channel] + "=" + threshold_token[channel] + " " +
+ "find_maxima_" + channel_token[channel];
+ channel_string_multi.append(channel_part);
+ channel_string_multi.append(" ");
+ }
+
+}
+
+// Returns an Error if set to Dual Channel one Channel contains beads but there is only one channel in channels
+else if ( reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length == 1 )
+{
+ System.out.println( "Error: reg_process_channel or channels set incorrectly" );
+}
+
+// Returns and Error if set to Dual Channel processing one channel contains the beads but there are multiple settings in radius and or threshold
+else if ( reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
+{
+ System.out.println( "Error: You said you wanted to process only one channel but there are multiple settings for radius or threshold" );
+}
+
+// Assembles String for Dual Channel but only one Channel contains beads
+else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1)
+{
+ channel_string_multi.append("");
+ processing_channel_string = "processing_channel=[channel " + reg_processing_channel + "] ";
+ channel_string = "interest_point_specification=[Advanced ...] " +
+ "radius_1=" + reg_radius_1 + " " +
+ "radius_2=" + reg_radius_2 + " " +
+ "threshold=" + reg_threshold + " " +
+ "find_maxima";
+}
+
+// Returns and Error if no conditions above are met
+else
+{
+ System.out.println( "Error: Incorrect settings" );
+}
+
+System.out.println( "Processing Channel = " + processing_channel_string );
+System.out.println( "Channel String: " + channel_string );
+System.out.println( reg_process_channel );
+System.out.println( "Multi channel String: " + channel_string_multi );
+
+// Channel Setting Registration
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "Channel Setting for 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_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);
+// Splits up channels, reg_interest_points_channel
+String[] interest_token = reg_interest_points_channel.split(delims);
+String reg_single_channel_string ="";
+StringBuilder reg_multi_channel_string = new StringBuilder();
+
+// If there are no channels set returns an error
+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 && interest_token.length == 1 )
+{
+ reg_multi_channel_string.append( "" );
+ reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
+}
+
+// Returns error if Multi Channels are selected but not enough settings in channels or reg_interest_points_channel
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && ( channel_token.length < 1 || interest_token.length < 1) )
+{
+ System.out.println( "Error: Multi Channel selected but only one setting in channels or 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 );
-//activate cluster processing
+// activate cluster processing
System.out.println( "=======================================================" );
try {
IJ.run("Toggle Cluster Processing", "display_cluster");
@@ -111,73 +275,107 @@ catch ( e ) {
runtime.exit(1);
}
-System.out.println( "Activated Cluster Processing" );
+System.out.println( "Activated Cluster Processing" );
-//interest point detection
+// interest point detection
System.out.println( "=======================================================" );
System.out.println( "Starting Detection of Interest Points" );
+
+System.out.println("Detect Interest Points for Registration , select_xml=" + xml_path + xml_filename + ".xml " +
+ "unique_id=" + unique_id + " " +
+ "process_angle=[" + reg_process_angle + "] " +
+ "process_channel=[" + reg_process_channel + "] " +
+ "process_illumination=[" + reg_process_illumination + "] " +
+ "process_timepoint=[" + reg_process_timepoint + "] " +
+ processing_channel_string +
+ "xml_output=[Save every XML with user-provided unique id]" + " " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "type_of_interest_point_detection=[" + type_of_detection + "] " +
+ "label_interest_points=" + label_interest_points + " " +
+ "subpixel_localization=[" + subpixel_localization + "] " +
+ channel_string + "" +
+ channel_string_multi + "" +
+ "");
+
try {
IJ.run("Detect Interest Points for Registration",
"select_xml=" + xml_path + xml_filename + ".xml " +
- "unique_id=" + parallel_timepoints + " " +
- "process_angle=[" + process_angle + "] " +
- "process_channel=[" + process_channel + "] " +
- "process_illumination=[" + process_illumination + "] " +
- "process_timepoint=[" + process_timepoint + "] " +
- "processing_channel=[" + processing_channel + "] " + // Dual Channel: 1 Channel contains the beads
+ "unique_id=" + unique_id + " " +
+ "process_angle=[" + reg_process_angle + "] " +
+ "process_channel=[" + reg_process_channel + "] " +
+ "process_illumination=[" + reg_process_illumination + "] " +
+ "process_timepoint=[" + reg_process_timepoint + "] " +
+ processing_channel_string +
"xml_output=[Save every XML with user-provided unique id]" + " " +
"processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
"type_of_interest_point_detection=[" + type_of_detection + "] " +
"label_interest_points=" + label_interest_points + " " +
"subpixel_localization=[" + subpixel_localization + "] " +
- "interest_point_specification_(channel_0)=[Advanced ...] " +
-// "interest_point_specification_(channel_1)=[Advanced ...] " + // Dual Channel
- "radius_1=" + radius_1 + " " +
- "radius_2=" + radius_2 + " " +
- "threshold=" + threshold + " " +
- "find_maxima");
+ channel_string + "" +
+ channel_string_multi + "" +
+ "");
}
catch ( e ) {
- print( "[registration::interest_points] caught exception: "+e );
+ print( "[registration::detection of interest_points] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
-//registration based on interest point detection
+
+// registration based on interest point detection
System.out.println( "=======================================================" );
System.out.println( "Starting Registration" );
+System.out.println("Register Dataset based on Interest Points , select_xml=" + xml_path + xml_filename + ".job_" + unique_id + ".xml " +
+ "process_angle=[" + reg_process_angle + "] " +
+ "process_channel=[" + reg_process_channel + "] " +
+ "process_illumination=[" + reg_process_illumination + "] " +
+ "process_timepoint=[" + reg_process_timepoint + "] " +
+ "xml_output=[Do not process on cluster] " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "registration_algorithm=[" + registration_algorithm + "] " +
+ "type_of_registration=[" + type_of_registration + "] " +
+ reg_single_channel_string +
+ reg_multi_channel_string +
+ "fix_tiles=[" + fix_tiles + "] " +
+ "map_back_tiles=[" + map_back_tiles + "] " +
+ "transformation=" + transformation_model + " " +
+ "regularize_model " +
+ "model_to_regularize_with=" + model_to_regularize_with + " " +
+ "lamba=" + lambda + " " +
+ "allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
+ "significance=" + significance + "");
+
try {
- IJ.run("Register Dataset based on Interest Points",
- "select_xml=" + xml_path + xml_filename + ".job_" + parallel_timepoints + ".xml " +
- "process_angle=[" + process_angle + "] " +
- "process_channel=[" + process_channel + "] " +
- "process_illumination=[" + process_illumination + "] " +
- "process_timepoint=[" + process_timepoint + "] " +
- "xml_output=[Do not process on cluster] " +
- "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
- "registration_algorithm=[" + registration_algorithm + "] " +
- "type_of_registration=[" + type_of_registration + "] " +
- "interest_points_channel_0=" + interest_points_channel_0 + " " +
- // check? "interest_points_channel_0=[[DO NOT register this channel]] " +
- // "interest_points_channel_1=" + interest_points_channel_1 + " " + // Dual Channel
- "fix_tiles=[" + fix_tiles + "] " +
- "map_back_tiles=[" + map_back_tiles + "] " +
- "transformation=" + transformation_model + " " +
- "regularize_model " +
- "model_to_regularize_with=" + model_to_regularize_with + " " +
- "lamba=" + lambda + " " +
- "allowed_error_for_ransac=" + allowed_error_for_ransac);
+IJ.run("Register Dataset based on Interest Points",
+ "select_xml=" + xml_path + xml_filename + ".job_" + unique_id + ".xml " +
+ "process_angle=[" + reg_process_angle + "] " +
+ "process_channel=[" + reg_process_channel + "] " +
+ "process_illumination=[" + reg_process_illumination + "] " +
+ "process_timepoint=[" + reg_process_timepoint + "] " +
+ "xml_output=[Do not process on cluster] " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "registration_algorithm=[" + registration_algorithm + "] " +
+ "type_of_registration=[" + type_of_registration + "] " +
+ reg_single_channel_string +
+ reg_multi_channel_string +
+ "fix_tiles=[" + fix_tiles + "] " +
+ "map_back_tiles=[" + map_back_tiles + "] " +
+ "transformation=" + transformation_model + " " +
+ "regularize_model " +
+ "model_to_regularize_with=" + model_to_regularize_with + " " +
+ "lamba=" + lambda + " " +
+ "allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
+ "significance=" + significance + "");
}
catch ( e ) {
- print( "[registration::based_on_interestpoints] caught exception: "+e );
+ print( "[registration::registration of interest points] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
}
-
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/timelaps_utils.py b/spim_registration/timelapse/timelaps_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..6a2bebe5395e172fe6c6cb394da4e3efff4ee3e1
--- /dev/null
+++ b/spim_registration/timelapse/timelaps_utils.py
@@ -0,0 +1,33 @@
+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
diff --git a/spim_registration/timelapse/timelapse_registration.bsh b/spim_registration/timelapse/timelapse_registration.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..82c051815af93ceee782daab02e48dd8c0f7abc2
--- /dev/null
+++ b/spim_registration/timelapse/timelapse_registration.bsh
@@ -0,0 +1,193 @@
+// 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);
diff --git a/spim_registration/timelapse/tomancak.json b/spim_registration/timelapse/tomancak.json
index b1a87ba51d43edd2bb5a778b1680030c116c3688..021578435e6439631f55fdcb0780d5de97888993 100644
--- a/spim_registration/timelapse/tomancak.json
+++ b/spim_registration/timelapse/tomancak.json
@@ -1,7 +1,7 @@
{
"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"
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
new file mode 100644
index 0000000000000000000000000000000000000000..9a2445f03860cec92dec550035d55edcc38ada2e
--- /dev/null
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -0,0 +1,204 @@
+{
+ "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)]\""
+
+ }
+
+
+
+
+
+}
diff --git a/spim_registration/timelapse/tomancak_test_cluster.json b/spim_registration/timelapse/tomancak_test_cluster.json
new file mode 100644
index 0000000000000000000000000000000000000000..44899c53b1b4dca63946a6b2a9d852faa25c9909
--- /dev/null
+++ b/spim_registration/timelapse/tomancak_test_cluster.json
@@ -0,0 +1,202 @@
+{
+ "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)]\""
+
+ }
+
+
+
+
+
+}
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
new file mode 100755
index 0000000000000000000000000000000000000000..77c76210cd21385a3cbff9cf250fd1a697657831
--- /dev/null
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -0,0 +1,186 @@
+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"
+ }
+
diff --git a/spim_registration/timelapse/transform.bsh b/spim_registration/timelapse/transform.bsh
old mode 100644
new mode 100755
index 839a08521875b663810ef80a37742f9131c30a80..3e87082b23b8619a2efb4842681d3033e8b3bbf7
--- a/spim_registration/timelapse/transform.bsh
+++ b/spim_registration/timelapse/transform.bsh
@@ -1,3 +1,5 @@
+// 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);
diff --git a/spim_registration/timelapse/xml_merge.bsh b/spim_registration/timelapse/xml_merge.bsh
old mode 100644
new mode 100755
index a3ab7dab127d6d4fad3f9d841f029aaa65630d5b..74949e34558d49d5ea8d1dea815d5e183cd0e9fe
--- a/spim_registration/timelapse/xml_merge.bsh
+++ b/spim_registration/timelapse/xml_merge.bsh
@@ -1,4 +1,6 @@
-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 ) {