diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 5faec2cf7f7fc810f44db01f2adbf48b5281ed2d..ef53b60fc310e4748117d190d3d82c980189a55c 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -205,7 +205,7 @@ rule xml_merge:
rule timelapse:
input: rules.xml_merge.output
output: rules.xml_merge.output[0] + "_timelapse"
- log: "timelapse.log"
+ log: "{xml_base}_timelapse.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -218,7 +218,7 @@ rule timelapse:
-Dreference_timepoint={reference_timepoint} \
-Dchannel_1={proc-ch} \
-Dtype_of_registration_timelapse={type_of_registration_timelapse} \
- -Dregistration_algorithm={registration_algorithm} \
+ -Dregistration_algorithm={algorithm} \
-Dreg_1_interest_points_channel={interest_points_channel_0} \
-Dreg_2_interest_points_channel={interest_points_channel_1} \
-Dtransformation_model={transformation_model} \
@@ -233,66 +233,69 @@ rule 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 external_trafo:
- input: rules.timelapse.output
+rule external_transform:
+ input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
output: rules.timelapse.output[0] + "_external_trafo"
- log: "external_trafo.log"
+ log: "external_transform.log"
run:
- 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 {path_bsh}""",
+ cmd_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dmerged_xml={merged_xml_file} \
+ -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 {path_bsh}""",
config["common"],
config["external_transform"],
- path_bsh=config["common"]["bsh_directory"] + config["external_trafo"]["bsh_file"],
+ path_bsh=config["common"]["bsh_directory"] + config["external_transform"]["bsh_file"],
jdir=JOBDIR,
- input="{input}")
+ 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"
+ input: 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_deconvolved"
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} \
+ -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 {path_bsh}""",
config["common"],
config["deconvolution"],
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
old mode 100644
new mode 100755
index 2807e94c521056fda295d81be4b2ee3a6954d42f..cb47db9c31910bf7f679d661b0a6a00fa177949e
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -9,6 +9,11 @@
{
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=100000]\""
},
+
+ "timelapse" :
+ {
+ "lsf_extra" : "-n 6 -R \"span[hosts=1] rusage[mem=100000]\""
+ },
"external_trafo" :
{
diff --git a/spim_registration/timelapse/timelapse_registration.bsh b/spim_registration/timelapse/timelapse_registration.bsh
index e27c1fbb018bc512c33d13eff552cdaf15a8cb68..76290e3288480b86bdb3f95aa30304c4b14f4ef3 100755
--- a/spim_registration/timelapse/timelapse_registration.bsh
+++ b/spim_registration/timelapse/timelapse_registration.bsh
@@ -18,6 +18,8 @@ System.out.println("Xml file:");
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 + ".xml");
@@ -69,8 +71,10 @@ System.out.println( "significance = " + significance );
System.out.println( "=======================================================" );
System.out.println( "Starting Timelapse Registration" );
+
+try {
IJ.run("Register Dataset based on Interest Points",
- "select_xml=" + xml_path + merged_xml + ".xml " +
+ "select_xml=" + xml_path + merged_xml + " " +
"process_angle=[" + process_angle + "] " +
"process_channel=[" + process_channel_timelapse + "] " +
"process_illumination=[" + process_illumination + "] " +
@@ -87,6 +91,14 @@ IJ.run("Register Dataset based on Interest Points",
"lamba=" + lambda + " " +
"allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
"significance=" + significance + "");
+}
+catch ( e ) {
+
+ print( "[deconvolution-GPU] 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_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 7a5d46f710ed22805805c561d4bc47df4754a50d..06d98a778a1b5caf76fa605d08e5bfa3e8fa7909 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -6,8 +6,8 @@
"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
"merged_xml" : "hdf5_test_unicore_merge",
"bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
- "first_xml_filename" : "Stock68",
- "hdf5_xml_filename" : "\"hdf5_Stock68\""
+ "first_xml_filename" : "test_unicore",
+ "hdf5_xml_filename" : "\"hdf5_test_unicore\""
},
"define_xml_czi" :
@@ -79,13 +79,14 @@
"radius_2" : "3",
"threshold" : "0.005",
"interest_points_channel_0" : "\"beads\"",
- "interest_points_channel_1" : "\"[DO NOT register this channel]\"",
+ "interest_points_channel_1" : "\"beads\"",
"fix_tiles" : "\"Fix first tile\"",
"map_back_tiles" : "\"Map back to first tile using rigid model\"",
"transformation_model" : "Affine",
"model_to_regularize_with" : "Rigid",
"lambda" : "0.10" ,
"allowed_error_for_ransac" : "5",
+ "significance" : "10",
"detection_min_max" : "find_maxima",
"initial_sigma" : "1.8",
"threshold_gaussian" : "0.0080",