Added content based multiview fusion.

Build in a switch to decide witch fusion method should be used.
Tested workflow and works.

spim_registration/timelapse/Snakefile

@@ -30,7 +30,8 @@ def produce_string(_fstring, *args, **kwargs):
    return _fstring.format(**contents)
 
 rule done:
-    input: [ ds+"_deconvolved" for ds in datasets ]
+    #input: [ ds+"_fusion" for ds in datasets ]
+    input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
 
 # defining xml for czi dataset
 rule define_xml_czi:
@@ -236,6 +237,50 @@ rule timelapse:
         cmd_string += "> {log} 2>&1 && touch {output}"
         shell(cmd_string)
         
+rule fusion:
+    input: rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
+    output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
+    log: "{xml_base}-{file_id,\d+}-00-fusion.log"
+    run:
+        cmd_string = produce_string(
+        	"""{fiji-prefix} {fiji-app} \
+        -Dimage_file_directory={jdir} \
+    	-Dparallel_timepoints={file_id_w} \
+    	-Dmerged_xml={merged_xml_file} \
+    	-Dprocess_timepoint={process_timepoint} \
+    	-Dprocess_channel={process_channel} \
+    	-Dprocess_illumination={process_illumination} \
+    	-Dprocess_angle={process_angle} \
+    	-Dxml_output={xml_output} \
+    	-Dfused_image={fused_image} \
+    	-Dminimal_x={minimal_x} \
+    	-Dminimal_y={minimal_y} \
+    	-Dminimal_z={minimal_z} \
+    	-Dmaximal_x={maximal_x} \
+    	-Dmaximal_y={maximal_y} \
+    	-Dmaximal_z={maximal_z} \
+    	-Ddownsample={downsample} \
+    	-Dpixel_type={pixel_type} \
+    	-Dimglib2_container_fusion={imglib2_container_fusion} \
+    	-Dprocess_views_in_paralell={process_views_in_paralell} \
+    	-Dinterpolation={interpolation} \
+    	-Dimglib2_data_container={imglib2_data_container} \
+    	-Dsubsampling_factors={subsampling_factors} \
+    	-Dhdf5_chunk_sizes={hdf5_chunk_sizes} \
+    	-Dtimepoints_per_partition={timepoints_per_partition} \
+    	-Dsetups_per_partition={setups_per_partition} \
+    		-- --no-splash {path_bsh}""",
+                                    config["common"],
+                                    config["fusion"],
+                                    config["resave_czi_hdf5"],
+                                    path_bsh=config["common"]["bsh_directory"] + config["fusion"]["bsh_file"],
+                                    jdir=JOBDIR,
+                                    file_id_w="{wildcards.file_id}",
+                                    merged_xml_file="{input.merged_xml}"
+        )
+        cmd_string += "> {log} 2>&1 && touch {output}"
+        shell(cmd_string)
+
 rule external_transform:
     input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
     output: rules.timelapse.output[0] + "_external_trafo"
@@ -258,13 +303,14 @@ rule external_transform:
                                     config["external_transform"],
                                     path_bsh=config["common"]["bsh_directory"] + config["external_transform"]["bsh_file"],
                                     jdir=JOBDIR,
-                                    merged_xml_file="{input.merged_xml}")
+                                    merged_xml_file="{input.merged_xml}"
+        )
         cmd_string += "> {log} 2>&1 && touch {output}"
         shell(cmd_string)
 
 rule deconvolution:
     input: rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
-    output: "{xml_base}-{file_id,\d+}-00.h5_deconvolved"
+    output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
     log: "{xml_base}-{file_id,\d+}-00-deconvolution.log"
     run:
         cmd_string = produce_string(

spim_registration/timelapse/deconvolution_GPU.bsh

@@ -21,7 +21,7 @@ System.out.println( "Load xml file: " );
 System.out.println( "selected_xml = " + image_file_directory + merged_xml);
 
 // Load general Parameters
-parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoints" ));
+int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoints" ));
 process_timepoint = System.getProperty( "process_timepoint" );
 process_channel = System.getProperty( "process_channel" );
 process_illumination = System.getProperty( "process_illumination" );
@@ -134,7 +134,6 @@ IJ.run("Fuse/Deconvolve Dataset",
 	"directory=[" + directory_cuda + "] " +
 	"select_native_library_for_cudafourierconvolution=libFourierConvolutionCUDALib.so " + 
 	"gpu_1 " +
-//	"gpu_2 " + 
 	"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
 	"psf_size_x=" + psf_size_x + " " +

spim_registration/timelapse/fusion.bsh

+// 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;
+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(6); 	// defines the number of threads allowed 
+print("Threads: "+Prefs.getThreads()); // prints thread setting in output
+
+System.out.println( "Start to load Parameters:" );
+// select xml
+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" ));
+process_timepoint = System.getProperty( "process_timepoint" );
+process_channel = System.getProperty( "process_channel" );
+process_illumination = System.getProperty( "process_illumination" );
+process_angle = System.getProperty( "process_angle" ); 
+
+System.out.println( process_timepoint );
+System.out.println( "timepoint = " + parallel_timepoints);
+System.out.println( "illuminations = " + process_illumination );
+System.out.println( "angles = " + process_angle );
+
+//Load bounding box
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "Load bounding box: " );
+minimal_x = System.getProperty( "minimal_x" );
+minimal_y = System.getProperty( "minimal_y" );
+minimal_z = System.getProperty( "minimal_z" );
+maximal_x = System.getProperty( "maximal_x" );
+maximal_y = System.getProperty( "maximal_y" );
+maximal_z = System.getProperty( "maximal_z" );
+downsample = System.getProperty( "downsample" );
+
+System.out.println( "minimal_x=" + minimal_x );
+System.out.println( "minimal_y=" + minimal_y );
+System.out.println( "minimal_z=" + minimal_z );
+System.out.println( "maximal_x=" + maximal_x );
+System.out.println( "maximal_y=" + maximal_y );
+System.out.println( "maximal_z=" + maximal_z );
+System.out.println( "downsample=" + downsample );
+
+// Load fusion parameters
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "Fusion parameters: " );
+pixel_type = System.getProperty( "pixel_type" );
+imglib2_container_fusion = System.getProperty( "imglib2_container_fusion" );
+interpolation = System.getProperty( "interpolation" );
+imglib2_data_container = System.getProperty( "imglib2_data_container" );
+
+System.out.println( "pixel_type=" + pixel_type );
+System.out.println( "imglib2_container_fusion=" + imglib2_container_fusion );
+System.out.println( "interpolation=" + interpolation );
+System.out.println( "imglib2_data_container=" + imglib2_data_container );
+
+// Execute Fiji Plugin
+System.out.println( "=======================================================" );
+System.out.println( "Starting Fusion" );
+
+try{
+IJ.run("Fuse/Deconvolve Dataset", 
+	"select_xml=" + image_file_directory + merged_xml + " " +
+	"process_angle=[" + process_angle + "] " +	
+        "process_illumination=[" + process_illumination + "] " +
+        "process_timepoint=[" + process_timepoint + "] " +
+	"processing_timepoint=[Timepoint " + parallel_timepoints + "] " + 
+//	"xml_output=[Do not process on cluster] " +
+	"processing_timepoint=[Timepoint "+ parallel_timepoints +"] " +
+	"type_of_image_fusion=[Weighted-average fusion] " +
+	"bounding_box=[Define manually] " +
+	"fused_image=[Save as TIFF stack] " + // works but does not create xml file
+	"minimal_x=" + minimal_x + " " +
+	"minimal_y=" + minimal_y + " " +
+	"minimal_z=" + minimal_z + " " +
+	"maximal_x=" + maximal_x + " " +
+	"maximal_y=" + maximal_y + " " +
+	"maximal_z=" + maximal_z + " " +
+	"downsample=" + downsample + " " +
+	"pixel_type=[" + pixel_type + "] " + 
+	"imglib2_container=" + imglib2_container_fusion + " " + 
+	"process_views_in_paralell=All " +
+	"interpolation=[" + interpolation + "] " + 
+	"blend " +
+	"content-based " +
+	"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_czi.json

@@ -7,7 +7,8 @@
 	"merged_xml" : "hdf5_test_unicore_merge",
 	"bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
 	"first_xml_filename" : "test_unicore",
-	"hdf5_xml_filename" : "\"hdf5_test_unicore\""
+	"hdf5_xml_filename" : "\"hdf5_test_unicore\"",
+	"fusion_switch" : "fusion"
     },
     
     "define_xml_czi" :
@@ -118,6 +119,29 @@
 	"define_mode_transform" : "\"Matrix\"",
 	"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\""
     },
+    
+    "fusion" :
+    {
+    	    "minimal_x" : "128",	
+    	    "minimal_y" : "-13",
+    	    "minimal_z" : "-407",
+    	    "maximal_x" : "986",
+    	    "maximal_y" : "1927",
+    	    "maximal_z" : "498",
+    	    "downsample" : "1",
+    	    "process_timepoint" : "\"Single Timepoint (Select from List)\"",
+    	    "process_channel" : "\"All channels\"",
+    	    "process_illumination" : "\"All illuminations\"",
+    	    "process_angle" : "\"All angles\"",
+    	    "xml_output" : "\"Save every XML with user-provided unique id\"", 
+    	    "fused_image" : "\"Append to current XML Project\"",
+    	    "pixel_type" : "\"16-bit unsigned integer\"",
+    	    "imglib2_container_fusion" : "\"ArrayImg\"",
+    	    "process_views_in_paralell" : "\"All\"",
+    	    "interpolation" : "\"Linear Interpolation\"",
+    	    "imglib2_data_container" : "\"ArrayImg (faster)\"",
+    	    "bsh_file" : "fusion.bsh"
+    },
 
     "deconvolution" :
     {