Updated external transformation and export output with new .bsh file

Started to update fusion

spim_registration/timelapse/Snakefile

@@ -306,6 +306,7 @@ rule external_transform:
         	"""{fiji-prefix} {fiji-app} \
         -Dimage_file_directory={jdir} \
 	-Dmerged_xml={merged_xml_file} \
+	-Dchannel_setting={channel_setting} \
 	-Dtransform_angle={transform_angle} \
 	-Dtransform_channel={transform_channel} \
 	-Dtransform_illumination={transform_illumination} \
@@ -405,7 +406,7 @@ rule hdf5_xml_output:
     input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
     output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
     	    [ item+"_output" for item in datasets ] 
-    log: "hdf5_xml.log"
+    log: "output_hdf5_xml.log"
     run:
         part_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \

spim_registration/timelapse/define_output.bsh

@@ -25,7 +25,6 @@ System.out.println( "xml_filename = " + xml_filename );
 System.out.println("=========================================================");
 System.out.println("Dataset:");
 timepoints = System.getProperty( "timepoints" );
-
 image_file_pattern = System.getProperty( "image_file_pattern" );
 type_of_dataset = System.getProperty( "type_of_dataset" );
 multiple_timepoints = System.getProperty( "multiple_timepoints" );
@@ -37,7 +36,6 @@ System.out.println( "timepoints = " + timepoints );
 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_illumination_directions = " + multiple_illumination_directions );
 System.out.println( "multiple_angles = " + multiple_angles );
 System.out.println( "imglib_container = " + imglib_container );
@@ -55,7 +53,7 @@ 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 );
 
-// Channel Switch
+// Channel switch
 System.out.println("=========================================================");
 System.out.println("Channel Switch:");
 multiple_channels = System.getProperty( "multiple_channels" );
@@ -63,7 +61,31 @@ System.out.println( "multiple_channels = " + multiple_channels );
 
 channels = System.getProperty( "channels" ); 
 
-IJ.run("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
+if ( multiple_channels.equalsIgnoreCase( "NO (one channel)" ) )
+
+{ 
+
+	channels="";
+
+}
+
+else if ( multiple_channels.equalsIgnoreCase( "YES (one file per channel)" ) )
+
+{
+
+	channels = "channels_=" + channels + " ";
+
+}
+
+else {
+
+	System.out.println( "Channel switch setting gibberish" );
+
+}
+
+System.out.println( "channels = " + channels );
+
+System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
 	"xml_filename=[" + xml_filename + ".xml] " +
 	"multiple_timepoints=[" + multiple_timepoints + "] " +
 	"multiple_channels=[" + multiple_channels + "] " +
@@ -78,8 +100,8 @@ IJ.run("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] "
 	"pixel_distance_x=" + pixel_distance_x + " " + 
 	"pixel_distance_y=" + pixel_distance_y + " " + 
 	"pixel_distance_z=" + pixel_distance_z + " " +
-	"pixel_unit=" + pixel_unit + "");	
-	
+	"pixel_unit=" + pixel_unit + "");
+
 // Executes Fiji plugin
 System.out.println("=========================================================");
 System.out.println("Start plugin:");

spim_registration/timelapse/fusion.bsh

@@ -20,15 +20,13 @@ System.out.println( "-------------------------------------------------------" );
 System.out.println( "Load xml 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";
 
 System.out.println( "xml_path=" + image_file_directory + merged_xml + ".xml" );
 
 // Load general Parameters
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "General parameters: " );
-int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoints" ));
+parallel_timepoints = System.getProperty( "parallel_timepoints" );
 process_timepoint = System.getProperty( "process_timepoint" );
 process_channel = System.getProperty( "process_channel" );
 process_illumination = System.getProperty( "process_illumination" );
@@ -75,9 +73,8 @@ System.out.println( "imglib2_data_container=" + imglib2_data_container );
 System.out.println( "=======================================================" );
 System.out.println( "Starting Fusion" );
 
-try{
 IJ.run("Fuse/Deconvolve Dataset", 
-	"select_xml=" + image_file_directory + merged_xml + " " +
+	"select_xml=" + image_file_directory + merged_xml + ".xml " +
 	"process_angle=[" + process_angle + "] " +	
         "process_illumination=[" + process_illumination + "] " +
         "process_timepoint=[" + process_timepoint + "] " +
@@ -103,12 +100,6 @@ IJ.run("Fuse/Deconvolve Dataset",
 	"output_file_directory=" + image_file_directory + " " +
 	"lossless " +
 	"imglib2_data_container=[" + imglib2_data_container + "]");
-}
-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_test_cluster.yaml

@@ -48,7 +48,8 @@ resave_hdf5: {
   }
 
 registration: {
-  reg_process_channel: '"Single Channel"',
+  # "Single Channel" is not a valid choice for "Process_channel"
+  reg_process_channel: '"Single Channel"', 
   reg_processing_channel: '"green"',
   reg_interest_points_channel: '"beads"',
   reg_radius_1: '2',
@@ -116,9 +117,12 @@ fusion: {
   }
 
 external_transform: {
+  # channel setting: '"all_channels"'
+  channel_setting: '"green"',
   transform_timepoint: '"All Timepoints"',
   transform_angle: '"All angles"',
   transform_channel: '"All channels"',
+  # illumination setting only one illumination side
   transform_illumination: '"All illuminations"',
   apply_transformation: '"Current view transformations (appends to current transforms)"',
   define_mode_transform: '"Matrix"',
@@ -128,7 +132,7 @@ external_transform: {
   }
 
 deconvolution: {
-  iterations: '5',
+  iterations: '1',
   maximal_x_deco: '509',
   maximal_y_deco: '970',
   maximal_z_deco: '243',
@@ -136,8 +140,6 @@ deconvolution: {
   minimal_y_deco: '-8',
   minimal_z_deco: '-174',
   detections_to_extract_psf_for_channel: '"beads"',
-  #detections_to_extract_psf_for_channel_0: '"beads"',
-  #detections_to_extract_psf_for_channel_1: '"beads"',
   process_timepoint: '"Single Timepoint (Select from List)"',
   process_angle: '"All angles"',
   process_channel: '"All channels"',
@@ -156,24 +158,24 @@ deconvolution: {
   }
   
 hdf5_output: {
-  bsh_file_define: "define_output.bsh",
-  bsh_file_hdf5: "export_output.bsh",
-  convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
-  output_channels: "green",
-  output_data_type: "32Bit",
+  output_image_file_pattern: 'TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
+  output_xml: '"fused_Single_Channel"',
   output_hdf5_xml: '"hdf5_fused_Stock68"',
-  output_illumination_directions: '"NO (one illumination direction)"',
-  output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
-  output_imglib_container: '"ArrayImg (faster)"',
-  output_multiple_angles: '"NO (one angle)"',
   output_multiple_channels: '"NO (one channel)"',
-  output_multiple_timepoints: '"YES (one file per time-point)"',
+  output_timepoints: '0-4',
   output_pixel_distance_x: 0.5718,
   output_pixel_distance_y: 0.5718,
   output_pixel_distance_z: 0.5718,
   output_pixel_unit: 'um',
-  output_timepoints: '0-4',
+  output_channels: "green",
+  output_data_type: "32Bit",
+  convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
   output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
-  output_xml: '"fused_Dual_Channel"'
+  output_multiple_timepoints: '"YES (one file per time-point)"',
+  output_multiple_angles: '"NO (one angle)"',
+  output_illumination_directions: '"NO (one illumination direction)"',
+  output_imglib_container: '"ArrayImg (faster)"',
+  bsh_file_define: "define_output.bsh",
+  bsh_file_hdf5: "export_output.bsh"
   }
 

spim_registration/timelapse/transform.bsh

+// is problematic needs to be adjusted for
+// multi channel and multi illumination datasets
 import ij.IJ;
 import ij.ImagePlus;
 import java.lang.Runtime;
@@ -15,8 +17,7 @@ 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" );
+channel_setting = System.getProperty( "channel_setting" );
 transformation = System.getProperty( "transformation" );
 apply_transformation  = System.getProperty( "apply_transformation" );
 define_mode_transform = System.getProperty( "define_mode_transform" );
@@ -30,12 +31,11 @@ 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( "Channel_setting = " + channel_setting );
 System.out.println( "transformation = " + transformation );
 System.out.println( "apply = " + apply_transformation );
 System.out.println( "define = " + define_mode_transform );
-System.out.println( "all_timepoints_channel_" + channel_1 + "_illumination_0_all_angles = " + matrix_transform );
+System.out.println( "all_timepoints_channel_" + channel_setting + "_illumination_0_all_angles = " + matrix_transform );
 
 // Execute Fiji Plugin
 try {
@@ -51,11 +51,11 @@ IJ.run("Apply Transformations",
 	"define=" + define_mode_transform + " " + 
 	"same_transformation_for_all_timepoints " + 
 	"same_transformation_for_all_angles " +
-	"all_timepoints_channel_" + channel_1 + "_illumination_0_all_angles=[" + matrix_transform + "]");
+	"all_timepoints_channel_" + channel_setting + "_illumination_0_all_angles=[" + matrix_transform + "]");
 }
 catch ( e ) { 
 
-    print( "[registration::interest_points] caught exception: "+e );
+    print( "[external transformation] caught exception: "+e );
     //important to fail the process if exception occurs
     runtime.exit(1);