From b1d34bb7c29ffaa1b8e7aa05abe33dad6e9c4aa8 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Sat, 23 May 2015 20:06:23 +0200
Subject: [PATCH] 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 | 52 +++++++-
.../timelapse/deconvolution_GPU.bsh | 3 +-
spim_registration/timelapse/fusion.bsh | 114 ++++++++++++++++++
spim_registration/timelapse/tomancak_czi.json | 26 +++-
4 files changed, 189 insertions(+), 6 deletions(-)
mode change 100644 => 100755 spim_registration/timelapse/deconvolution_GPU.bsh
create mode 100755 spim_registration/timelapse/fusion.bsh
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index ef53b60..2f71f0d 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/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(
diff --git a/spim_registration/timelapse/deconvolution_GPU.bsh b/spim_registration/timelapse/deconvolution_GPU.bsh
old mode 100644
new mode 100755
index ac80666..ec3d0d3
--- a/spim_registration/timelapse/deconvolution_GPU.bsh
+++ b/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 + " " +
diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh
new file mode 100755
index 0000000..5731ddb
--- /dev/null
+++ b/spim_registration/timelapse/fusion.bsh
@@ -0,0 +1,114 @@
+// 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);
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index 06d98a7..d173e9d 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/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" :
{
--
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