1. successful trial run

spim_registration/timelapse/Snakefile

@@ -93,7 +93,7 @@ ruleorder: define_xml_tif > define_xml_czi
 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+"_empty" for item in datasets ]
+            [ item+"_xml" for item in datasets ]
     log: "hdf5_xml.log"
     run:
         part_string = produce_string(
@@ -128,8 +128,8 @@ rule hdf5_xml:
 
 # resave  .czi/.tif dataset as hdf5	
 rule resave_hdf5:
-    input: "{xml_base}-{file_id,\d+}-00.h5_empty" # rules.hdf5_xml.output
-    output: "{xml_base}-{file_id,\d+}-00.h5"
+    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(
@@ -154,8 +154,8 @@ rule 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) # problematic calculation not possible in cannot deal wiht wildcards file_id
-   	part_string += " > {log} 2>&1"
+           job_number=int(wildcards.file_id)+1) 
+   	part_string += " > {log} 2>&1 && touch {output}"
         shell(part_string) 
        	       	
 rule registration:

spim_registration/timelapse/export.bsh

@@ -61,16 +61,18 @@ System.out.println( "run_only_job_number=" + run_only_job_number );
 job_type = System.getProperty( "job_type" );
 System.out.println( "Job type = " + job_type );
 
-if ( job_type.equalsIgnoreCase( "xml" ) )
-	{
-		job_number = 0;
-	}
-else if ( job_type.equalsIgnoreCase( "hdf5" ) )
-	{
-		job_number = run_only_job_number + 1;
-	}
-
-System.out.println( "Job Number = " + job_number );
+//
+//if ( job_type.equalsIgnoreCase( "xml" ) )
+//	{
+//		job_number = 0;
+//	}
+//else if ( job_type.equalsIgnoreCase( "hdf5" ) )
+//	{
+//		job_number = run_only_job_number + 1;
+//	}
+//
+//System.out.println( "Job Number = " + job_number );
+
 // Activate cluster processing
 System.out.println("=========================================================");
 try{
@@ -98,7 +100,7 @@ IJ.run("As HDF5",
 	"split_hdf5 " +
 	"timepoints_per_partition=" + timepoints_per_partition + " " +
 	"setups_per_partition=" + setups_per_partition + " " +
-	"run_only_job_number=" + job_number + " " +
+	"run_only_job_number=" + run_only_job_number + " " +
 	"use_deflate_compression " +
 	"export_path=" + image_file_directory + hdf5_xml_filename );
 }

spim_registration/timelapse/tomancak_czi.json

@@ -33,10 +33,10 @@
     
     "define_xml_tif" :
     {
-	"timepoints" : "1-2",
-	"acquisition_angles" : "1,2,3,4,5",
-	"channels" : "0,1",
-	"image_file_pattern" : "spim_TL{{tt}}_Angle{{a}}.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",
@@ -70,7 +70,7 @@
 	"illuminations" : "\"All illuminations\"",
 	"angle" : "\"All angles\"",
 	"channel" : "\"All channels\"",
-	"proc-ch" : "\"channel 1\"",
+	"proc-ch" : "\"channel 0\"",
 	"algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
 	"label_interest_points" : "\"beads\"",
 	"type_of_registration" : "\"Register timepoints individually\"",