Updated deconvolution

spim_registration/timelapse/Snakefile

@@ -89,7 +89,7 @@ rule define_xml_tif:
 	cmd_string +=" > {log} 2>&1"
 	shell(cmd_string)
 
-ruleorder: define_xml_tif > define_xml_czi
+ruleorder: define_xml_czi > define_xml_tif 
 
 # create mother .xml/.h5
 rule hdf5_xml:
@@ -339,12 +339,13 @@ rule deconvolution:
         -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} \
+        -Dchannels={channels} \
+        -Dminimal_x_deco={minimal_x_deco} \
+        -Dminimal_y_deco={minimal_y_deco} \
+        -Dminimal_z_deco={minimal_z_deco} \
+        -Dmaximal_x_deco={maximal_x_deco} \
+        -Dmaximal_y_deco={maximal_y_deco} \
+        -Dmaximal_z_deco={maximal_z_deco} \
         -Dimglib2_container_deco={imglib2_container} \
         -Dtype_of_iteration={type_of_iteration} \
         -Dosem_acceleration={osem_acceleration} \
@@ -352,8 +353,7 @@ rule deconvolution:
         -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} \
+        -Ddetections_to_extract_psf_for_channel={detections_to_extract_psf_for_channel} \
         -Dpsf_size_x={psf_size_x} \
         -Dpsf_size_y={psf_size_y} \
         -Dpsf_size_z={psf_size_z} \

spim_registration/timelapse/deconvolution_GPU.bsh

 // Load Fiji dependencies
-import ij.IJ;
-import ij.ImagePlus;
+import ij.IJ; 		// calls imagej
+import ij.Prefs; 	// calls imagej settings
 import java.lang.Runtime;
 import java.io.File;
 import java.io.FilenameFilter;
@@ -8,17 +8,19 @@ import java.io.FilenameFilter;
 runtime = Runtime.getRuntime();
 System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
 
-System.out.println( "Start to load Parameters:" );
+Prefs.setThreads(7); 	// defines the number of threads allowed 
+print("Threads: "+Prefs.getThreads()); // prints thread setting in output
 
+System.out.println( "Start to load Parameters:" );
 // Select xml
 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( "-------------------------------------------------------" );
 System.out.println( "Load xml file: " );
-System.out.println( "selected_xml = " + image_file_directory + merged_xml);
+System.out.println( "selected_xml = " + image_file_directory + merged_xml + ".xml");
 
 // Load general Parameters
 int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoints" ));
@@ -27,6 +29,7 @@ process_channel = System.getProperty( "process_channel" );
 process_illumination = System.getProperty( "process_illumination" );
 process_angle = System.getProperty( "process_angle" ); 
 
+
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "General parameters: " );
 System.out.println( "timepoint_processed = " + parallel_timepoints );
@@ -62,8 +65,7 @@ compute = System.getProperty( "compute" );
 psf_estimation = System.getProperty( "psf_estimation" );
 iterations = System.getProperty( "iterations" );
 deco_output_file_directory = System.getProperty( "deco_output_file_directory" );
-detections_to_extract_psf_for_channel_0 = System.getProperty( "detections_to_extract_psf_for_channel_0" );
-detections_to_extract_psf_for_channel_1 = System.getProperty( "detections_to_extract_psf_for_channel_1" );
+
 
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "Deconvolution settings: " );
@@ -75,14 +77,11 @@ System.out.println( "compute = " + compute );
 System.out.println( "psf_estimation = " + psf_estimation );
 System.out.println( "number_of_iterations = " + iterations );
 System.out.println( "deco_output_file_directory = " + deco_output_file_directory );
-System.out.println( "detections_to_extract_psf_for_channel_0 = " + detections_to_extract_psf_for_channel_0 );
-System.out.println( "detections_to_extract_psf_for_channel_1 = " + detections_to_extract_psf_for_channel_1 );
 
 // Search for CUDA
-directory_cuda = System.getProperty( "directory_cuda" );
-
 System.out.println( "-------------------------------------------------------" );
 System.out.println( "Loading CUDA directory: " );
+directory_cuda = System.getProperty( "directory_cuda" );
 System.out.println( "directory_cuda = " + directory_cuda );
 
 // PSF Parameters
@@ -96,19 +95,48 @@ System.out.println( "psf_size_x = " + psf_size_x );
 System.out.println( "psf_size_y = " + psf_size_y );
 System.out.println( "psf_size_z = " + psf_size_z );
 
+
+// Channel settings
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "Channel Settings: " );
+// Channel setting for Deconvolution
+// parses channels and takes from there the number of channels
+// parses detections_to_extract_psf_for_channel 
+channels = System.getProperty( "channels" );
+System.out.println( "Channels = " + channels ); 
+
+detections_to_extract_psf_for_channel = System.getProperty( "detections_to_extract_psf_for_channel" );
+System.out.println( "PSF: " + detections_to_extract_psf_for_channel );
+
+// Splits channels and detections_to_extract_psf_for_channel 
+String delims = "[,]";
+String[] channel_token = channels.split(delims);
+String[] psf_token = detections_to_extract_psf_for_channel.split(delims);
+		
+// Assembles channel_string 
+StringBuilder channel_string = new StringBuilder();
+
+for (int channel=0; channel < channel_token.length; channel++ )
+
+{	
+	String channel_part = "detections_to_extract_psf_for_channel_" + channel_token[channel] + "=" + psf_token[channel] + " ";
+	channel_string.append( channel_part );
+	channel_string.append(" ");
+}
+
+System.out.println( channel_string );
+
 // Execute Fiji Plugin
 System.out.println( "=======================================================" );
 System.out.println( "Starting Deconvolution" );
-
 try {
 IJ.run("Fuse/Deconvolve Dataset", 
-	"select_xml=" + image_file_directory + merged_xml + " " +
+	"select_xml=" + image_file_directory + merged_xml + " " + 
 	"process_angle=[All angles] " +
 	"process_channel=[All channels] " + 
 	"process_illumination=[All illuminations] " +
 	"process_timepoint=[" + process_timepoint + "] " +
 	"processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
-//	"processing_timepoint=[Timepoint 0] " + 
 	"type_of_image_fusion=[Multi-view deconvolution] " +
 	"bounding_box=[Define manually] " +
 	"fused_image=[Save as TIFF stack] " +
@@ -130,12 +158,10 @@ IJ.run("Fuse/Deconvolve Dataset",
 	"psf_estimation=[" + psf_estimation + "] " +
 	"psf_display=[Do not show PSFs] " +
 	"output_file_directory=" + deco_output_file_directory + " " +
-//	"directory=[/sw/users/schmied/packages/Fiji.app.cuda_new/lib/] " +
-	"directory=[" + directory_cuda + "] " +
+	"cuda_directory=[" + directory_cuda + "] " +
 	"select_native_library_for_cudafourierconvolution=libFourierConvolutionCUDALib.so " + 
 	"gpu_1 " +
-	"detections_to_extract_psf_for_channel_0=" + detections_to_extract_psf_for_channel_0 + " " +
-//	"detections_to_extract_psf_for_channel_1=" + detections_to_extract_psf_for_channel_1 + " " + // Dual Channel
+	channel_string +
 	"psf_size_x=" + psf_size_x + " " +
 	"psf_size_y=" + psf_size_y + " " +
 	"psf_size_z=" + psf_size_z + "");

spim_registration/timelapse/tomancak_test_cluster.yaml

 common: {
   # directory that contains the bean shell scripts
   bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
-  directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/lib/",
+  directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/",
   fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
   fiji-prefix: "/sw/bin/xvfb-run -a",
   first_xml_filename: "test_unicore",
@@ -128,30 +128,31 @@ external_transform: {
   }
 
 deconvolution: {
+  iterations: '5',
+  maximal_x_deco: '509',
+  maximal_y_deco: '970',
+  maximal_z_deco: '243',
+  minimal_x_deco: '95',
+  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"',
+  process_illumination: '"All illuminations"',
   Tikhonov_parameter: '0.0006',
-  bsh_file: "deconvolution_GPU.bsh",
   compute: '"in 512x512x512 blocks"',
   compute_on: '"GPU (Nvidia CUDA via JNA)"',
-  detections_to_extract_psf_for_channel_0: '"beads"',
-  detections_to_extract_psf_for_channel_1: '"beads"',
   imglib2_container: '"ArrayImg"',
-  iterations: '5',
-  maximal_x: '509',
-  maximal_y: '970',
-  maximal_z: '243',
-  minimal_x: '95',
-  minimal_y: '-8',
-  minimal_z: '-174',
   osem_acceleration: '"1 (balanced)"',
-  process_angle: '"All angles"',
-  process_channel: '"All channels"',
-  process_illumination: '"All illuminations"',
-  process_timepoint: '"Single Timepoint (Select from List)"',
   psf_estimation: '"Extract from beads"',
   psf_size_x: '19',
   psf_size_y: '19',
   psf_size_z: '25',
-  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"'
+  type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+  bsh_file: "deconvolution_GPU.bsh"
   }
   
 hdf5_output: {