Updated xml merge, timelapse registration and transform

Added dual channel processing for these parts
updated .bsh file

spim_registration/timelapse/Snakefile

@@ -230,15 +230,14 @@ rule timelapse:
         -Dimage_file_directory={jdir} \
         -Dmerged_xml={input} \
         -Dtimelapse_process_timepoints={timelapse_process_timepoints} \
-        -Dprocess_channel_timelapse={channel} \
-        -Dprocess_illumination={illuminations} \
-        -Dprocess_angle={angle} \
+        -Dreg_process_channel={reg_process_channel} \
+        -Dreg_process_illumination={reg_process_illumination} \
+        -Dreg_process_angle={reg_process_angle} \
         -Dreference_timepoint={reference_timepoint} \
-        -Dchannel_1={proc-ch} \
+        -Dchannels={channels} \
         -Dtype_of_registration_timelapse={type_of_registration_timelapse} \
         -Dregistration_algorithm={algorithm} \
-        -Dreg_1_interest_points_channel={interest_points_channel_0} \
-        -Dreg_2_interest_points_channel={interest_points_channel_1} \
+        -Dreg_interest_points_channel={reg_interest_points_channel} \
         -Dtransformation_model={transformation_model} \
         -Dmodel_to_regularize_with={model_to_regularize_with} \
         -Dlambda={lambda} \
@@ -307,10 +306,10 @@ rule external_transform:
         	"""{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} \
+	-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} \

spim_registration/timelapse/registration.bsh

@@ -28,7 +28,8 @@ System.out.println( "selected_xml = " + xml_path + xml_filename + ".xml");
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "General parameters: " );
 
-parallel_timepoints = System.getProperty( "parallel_timepoints" );
+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" ); 
@@ -290,7 +291,7 @@ 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=" + parallel_timepoints + " " +
+	"unique_id=" + unique_id + " " +
 	"process_angle=[" + reg_process_angle + "] " + 
 	"process_channel=[" + reg_process_channel + "] " +
 	"process_illumination=[" + reg_process_illumination + "] " + 
@@ -308,7 +309,7 @@ System.out.println("Detect Interest Points for Registration , select_xml=" + xml
 try {
 IJ.run("Detect Interest Points for Registration", 
 	"select_xml=" + xml_path + xml_filename + ".xml " +  
-	"unique_id=" + parallel_timepoints + " " +
+	"unique_id=" + unique_id + " " +
 	"process_angle=[" + reg_process_angle + "] " + 
 	"process_channel=[" + reg_process_channel + "] " +
 	"process_illumination=[" + reg_process_illumination + "] " + 
@@ -325,7 +326,7 @@ IJ.run("Detect Interest Points for Registration",
 }
 catch ( e ) { 
 
-    print( "[registration::activate_cluster_processing] caught exception: "+e );
+    print( "[registration::interest_points] caught exception: "+e );
     //important to fail the process if exception occurs
     runtime.exit(1);
     
@@ -335,7 +336,7 @@ catch ( e ) {
 System.out.println( "=======================================================" );
 System.out.println( "Starting Registration" );
 
-System.out.println("Register Dataset based on Interest Points , select_xml=" + xml_path + xml_filename + ".job_" + parallel_timepoints + ".xml " +
+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 + "] " +
@@ -357,7 +358,7 @@ System.out.println("Register Dataset based on Interest Points , select_xml=" + x
 
 try {
 IJ.run("Register Dataset based on Interest Points",
-	"select_xml=" + xml_path + xml_filename + ".job_" + parallel_timepoints + ".xml " +
+	"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 + "] " +
@@ -379,7 +380,7 @@ IJ.run("Register Dataset based on Interest Points",
 }
 catch ( e ) { 
 
-    print( "[registration::activate_cluster_processing] caught exception: "+e );
+    print( "[registration::based_on_interestpoints] caught exception: "+e );
     //important to fail the process if exception occurs
     runtime.exit(1);
     

spim_registration/timelapse/timelapse_registration.bsh

@@ -16,30 +16,27 @@ print("Threads: "+Prefs.getThreads()); // prints thread setting in output
 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 + ".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" );
-process_channel_timelapse = System.getProperty( "process_channel_timelapse" );
-process_illumination = System.getProperty( "process_illumination" );
-process_angle = System.getProperty( "process_angle" ); 
-channel_1 = System.getProperty( "channel_1" );
-channel_2 = System.getProperty( "channel_2" );
+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_channel = " + process_channel_timelapse );
-System.out.println( "process_illumination = " + process_illumination );
-System.out.println( "process_angle = " + process_angle );
-System.out.println( "channel_1 = " + channel_1 );
-System.out.println( "channel_2 = " + channel_2 );
-	
+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: " );
@@ -49,13 +46,11 @@ System.out.println( "reference_timepoint=" + reference_timepoint );
 
 type_of_registration_timelapse = System.getProperty( "type_of_registration_timelapse" );
 registration_algorithm = System.getProperty( "registration_algorithm" );
-reg_1_interest_points_channel = System.getProperty( "reg_1_interest_points_channel" );
-reg_2_interest_points_channel = System.getProperty( "reg_2_interest_points_channel" ); // Dual Channel 
+
 
 System.out.println( "type_of_registration = " + type_of_registration_timelapse );
 System.out.println( "registration_algorithm = " + registration_algorithm );
-System.out.println( "interest_points_channel_" + channel_1 + " = " + reg_1_interest_points_channel );
-System.out.println( "interest_points_channel_" + channel_2 + " = " + reg_2_interest_points_channel );
+
 
 transformation_model = System.getProperty( "transformation_model" );
 model_to_regularize_with = System.getProperty( "model_to_regularize_with" );
@@ -63,25 +58,132 @@ 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 );
+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");
+	}
+		
+	// Returns Error if Single Channel selected but multiple settings in channels or reg_interest_points_channel
+	else if ( reg_process_channel.equalsIgnoreCase( "Single Channel" ) && (channel_token.length > 1 || interest_token.length > 1 ))
+	{
+		System.out.println( "Error: Single Channel selected but multiple settings in channls or reg_interest_points_channel" );
+	}
+	
+	// Assembles string for Single Channel registration
+	else if (reg_process_channel.equalsIgnoreCase( "Single channel" ) && channel_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 );
+
+
 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=[" + process_angle + "] " + 
-	"process_channel=[" + process_channel_timelapse + "] " +
-	"process_illumination=[" + process_illumination + "] " +  
+	"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 + "] " +
-	"interest_points_channel_" + channel_1 + "=" + reg_1_interest_points_channel + " " +
+	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 " +
@@ -94,11 +196,10 @@ IJ.run("Register Dataset based on Interest Points",
 }
 catch ( e ) { 
 
-    print( "[deconvolution-GPU] caught exception: "+e );
+    print( "[registration::timelapse] caught exception: "+e );
     //important to fail the process if exception occurs
     runtime.exit(1);
     
 }
-
 /* shutdown */
 runtime.exit(0);

spim_registration/timelapse/tomancak_test_cluster.yaml

@@ -72,7 +72,6 @@ registration: {
   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"
   }
@@ -82,10 +81,16 @@ xml_merge: {
   }
   
 timelapse: {
-  bsh_file: "timelapse_registration.bsh",
   reference_timepoint: '0',
+  type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
   timelapse_process_timepoints: '"All Timepoints"',
-  type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"'
+  bsh_file: "timelapse_registration.bsh"
+  }
+  
+Dublicate_transformations: {
+  source_dublication: "red",
+  target_dublication: "green",
+  bsh_file: "dublicate_channel.bsh"
   }
   
 fusion: {
@@ -111,16 +116,15 @@ fusion: {
   }
 
 external_transform: {
-  angle: '"All angles"',
-  apply_transformation: '"Current view transformations
-  (appends to current transforms)"',
-  bsh_file: "transform.bsh",
-  channel: '"All channels"',
+  transform_timepoint: '"All Timepoints"',
+  transform_angle: '"All angles"',
+  transform_channel: '"All channels"',
+  transform_illumination: '"All illuminations"',
+  apply_transformation: '"Current view transformations (appends to current transforms)"',
   define_mode_transform: '"Matrix"',
-  illumination: '"All illuminations"',
   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"',
-  timepoint: '"All Timepoints"',
-  transformation: '"Rigid"'
+  transformation: '"Rigid"',
+  bsh_file: "transform.bsh"
   }
 
 deconvolution: {

spim_registration/timelapse/transform.bsh

@@ -11,13 +11,12 @@ 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_1 = System.getProperty( "channel_1" );
+channel_2 = System.getProperty( "channel_2" );
 transformation = System.getProperty( "transformation" );
 apply_transformation  = System.getProperty( "apply_transformation" );
 define_mode_transform = System.getProperty( "define_mode_transform" );
@@ -26,15 +25,17 @@ 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_1 = " + channel_1 ); 
+System.out.println( "channel_2 = " + channel_2 ); 
 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_1 + "_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_1 + "_illumination_0_all_angles=[" + matrix_transform + "]");
 }
 catch ( e ) { 
 
-    print( "[transform] caught exception: "+e );
+    print( "[registration::interest_points] caught exception: "+e );
     //important to fail the process if exception occurs
     runtime.exit(1);
     

spim_registration/timelapse/xml_merge.bsh

-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 ) {