Added define xml tif

spim_registration/timelapse/Snakefile

@@ -35,7 +35,7 @@ rule done:
 # defining xml for czi dataset
 rule define_xml_czi:
     input: glob.glob('*.czi')
-    output: config["define_xml_czi"]["first_xml_filename"] + ".xml"
+    output: config["common"]["first_xml_filename"] + ".xml"
     message: "Execute define_xml_czi on the following files {input}"
     log: "define_xml_czi.log"
     run: 
@@ -71,7 +71,7 @@ rule resave_czi_hdf5:
     input: rules.define_xml_czi.output, glob.glob('*.czi')
     output: "hdf5_Stock68.h5", "hdf5_Stock68.xml" 
     message: "Execute resave_hdf5 on {input}"
-    threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect 
+#    threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect 
     log: "export.log"
     run:
         part_string = produce_string("""{fiji-prefix} {fiji-app} \
@@ -99,21 +99,45 @@ rule resave_czi_hdf5:
         
         shell(cmd_string) 
 
+# defining xml for tif dataset
 rule define_xml_tif:
-
-rule resave_tif_hdf5
-        
-        
-        
-        
-        
+    input: glob.glob('*.tif')
+    output: config["common"]["first_xml_filename"] + ".xml"
+    message: "Execute define_xml_czi on the following files {input}"
+    log: "define_xml_tif.log"
+    run:
+        cmd_string = produce_string(
+        		"""{fiji-prefix} {fiji-app} \
+        	-Dimage_file_directory={jdir} \
+        	-Dtimepoints={timepoints} \
+        	-Dacquisition_angles={acquisition_angles} \
+        	-Dchannels={channels} \
+        	-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"])
+	cmd_string +="> {log} 2>&1 && touch {output}"
+	shell(cmd_string)
         
+rule resave_tif_hdf5
         
         
-
 rule registration:
-    # input: "{xml_base}-{file_id}-00.h5"
-    input: rules.resave_hdf5.output, "{xml_base}-{file_id}-00.h5"
+    input: "{xml_base}-{file_id}-00.h5"
+    #input: rules.resave_hdf5.output, "{xml_base}-{file_id}-00.h5"
     output: "{xml_base}-{file_id,\d+}-00.h5_registered", #"{xml_base}.job_{file_id,\d+}.xml"
     log: "{xml_base}-{file_id}-registration.log"
     run:

spim_registration/timelapse/define_tif_zip.bsh

+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" );
+channels = System.getProperty( "channels" ); 
+acquisition_angles = System.getProperty( "acquisition_angles" );
+image_file_pattern = System.getProperty( "image_file_pattern" );
+type_of_dataset = System.getProperty( "type_of_dataset" );
+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( "timepoints = " + timepoints );
+System.out.println( "channels = " + channels );
+System.out.println( "acquisition_angles = " + acquisition_angles );
+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_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 );
+
+// 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:");
+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_=" + channels	+ " " +		// for dual channel comment out if single channel
+	"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 + "");
+ 
+/* shutdown */
+runtime.exit(0);
+
+

spim_registration/timelapse/tomancak_czi.json

@@ -5,12 +5,12 @@
 	"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" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/"
+	"bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+	"first_xml_filename" : "Stock68"
     },
     
     "define_xml_czi" :
     {
-    	    "first_xml_filename" : "Stock68",
     	    "pixel_distance_x" : "0.2875535786151886",
     	    "pixel_distance_y" : "0.2875535786151886",
     	    "pixel_distance_z" : "1.50000", 
@@ -43,6 +43,25 @@
     	    "bsh_file" : "export.bsh"
     },
     
+    "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",
+	"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" : "\"YES (one file per 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" 
+    },
+    
     "registration" :
     {
 	"timepoint" : "\"Single Timepoint (Select from List)\"",