Made timelapse registration stable in workflow

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"],

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" :
     {

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);

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",