diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 149341ad04ec09c45ff0d8de032be24e86debf32..48bb4ad315d01d9815ac8f38e7ff983ba8062abd 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -35,7 +35,7 @@ rule done:
# defining xml for czi dataset
rule define_xml_czi:
input: glob.glob('*.czi')
- output: config["define_xml_czi"]["first_xml_filename"] + ".xml"
+ output: config["common"]["first_xml_filename"] + ".xml"
message: "Execute define_xml_czi on the following files {input}"
log: "define_xml_czi.log"
run:
@@ -71,7 +71,7 @@ rule resave_czi_hdf5:
input: rules.define_xml_czi.output, glob.glob('*.czi')
output: "hdf5_Stock68.h5", "hdf5_Stock68.xml"
message: "Execute resave_hdf5 on {input}"
- threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect
+# threads: int(config["resave_hdf5"]["parallel_timepoints"]) # parallel timepoints should tell me how many timepoints to expect
log: "export.log"
run:
part_string = produce_string("""{fiji-prefix} {fiji-app} \
@@ -99,21 +99,45 @@ rule resave_czi_hdf5:
shell(cmd_string)
+# defining xml for tif dataset
rule define_xml_tif:
-
-rule resave_tif_hdf5
-
-
-
-
-
+ input: glob.glob('*.tif')
+ output: config["common"]["first_xml_filename"] + ".xml"
+ message: "Execute define_xml_czi on the following files {input}"
+ log: "define_xml_tif.log"
+ run:
+ cmd_string = produce_string(
+ """{fiji-prefix} {fiji-app} \
+ -Dimage_file_directory={jdir} \
+ -Dtimepoints={timepoints} \
+ -Dacquisition_angles={acquisition_angles} \
+ -Dchannels={channels} \
+ -Dimage_file_pattern={image_file_pattern} \
+ -Dpixel_distance_x={pixel_distance_x} \
+ -Dpixel_distance_y={pixel_distance_y} \
+ -Dpixel_distance_z={pixel_distance_z} \
+ -Dpixel_unit={pixel_unit} \
+ -Dxml_filename={first_xml_filename} \
+ -Dtype_of_dataset={type_of_dataset} \
+ -Dmultiple_timepoints={multiple_timepoints} \
+ -Dmultiple_channels={multiple_channels} \
+ -Dmultiple_illumination_directions={multiple_illumination_directions} \
+ -Dmultiple_angles={multiple_angles} \
+ -Dimglib_container={imglib_container} \
+ -- --no-splash {path_bsh}""",
+ config["common"],
+ config["define_xml_tif"],
+ jdir=JOBDIR,
+ path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
+ cmd_string +="> {log} 2>&1 && touch {output}"
+ shell(cmd_string)
+rule resave_tif_hdf5
-
rule registration:
- # input: "{xml_base}-{file_id}-00.h5"
- input: rules.resave_hdf5.output, "{xml_base}-{file_id}-00.h5"
+ input: "{xml_base}-{file_id}-00.h5"
+ #input: rules.resave_hdf5.output, "{xml_base}-{file_id}-00.h5"
output: "{xml_base}-{file_id,\d+}-00.h5_registered", #"{xml_base}.job_{file_id,\d+}.xml"
log: "{xml_base}-{file_id}-registration.log"
run:
diff --git a/spim_registration/timelapse/define_tif_zip.bsh b/spim_registration/timelapse/define_tif_zip.bsh
new file mode 100755
index 0000000000000000000000000000000000000000..f03b52fec9445b4a3408983a8ade1af437162245
--- /dev/null
+++ b/spim_registration/timelapse/define_tif_zip.bsh
@@ -0,0 +1,87 @@
+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");
+
+Prefs.setThreads(1); // defines the number of threads allowed
+print("Threads: "+Prefs.getThreads()); // prints thread setting in output
+
+System.out.println("Start loading parameters");
+// Directory
+System.out.println("=========================================================");
+System.out.println("Directory:");
+image_file_directory = System.getProperty( "image_file_directory" );
+xml_filename = System.getProperty( "xml_filename" );
+
+System.out.println( "image_file_directory = " + image_file_directory );
+System.out.println( "xml_filename = " + xml_filename );
+
+// Dataset settings
+System.out.println("=========================================================");
+System.out.println("Dataset:");
+timepoints = System.getProperty( "timepoints" );
+channels = System.getProperty( "channels" );
+acquisition_angles = System.getProperty( "acquisition_angles" );
+image_file_pattern = System.getProperty( "image_file_pattern" );
+type_of_dataset = System.getProperty( "type_of_dataset" );
+multiple_timepoints = System.getProperty( "multiple_timepoints" );
+multiple_channels = System.getProperty( "multiple_channels" );
+multiple_illumination_directions = System.getProperty( "multiple_illumination_directions" );
+multiple_angles = System.getProperty( "multiple_angles" );
+imglib_container = System.getProperty( "imglib_container" );
+
+System.out.println( "timepoints = " + timepoints );
+System.out.println( "channels = " + channels );
+System.out.println( "acquisition_angles = " + acquisition_angles );
+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_channels = " + multiple_channels );
+System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
+System.out.println( "multiple_angles = " + multiple_angles );
+System.out.println( "imglib_container = " + imglib_container );
+
+// Calibaration
+System.out.println("=========================================================");
+System.out.println("Calibration:");
+float pixel_distance_x = Float.parseFloat( System.getProperty( "pixel_distance_x" ) );
+float pixel_distance_y = Float.parseFloat( System.getProperty( "pixel_distance_y" ) );
+float pixel_distance_z = Float.parseFloat( System.getProperty( "pixel_distance_z" ) );
+pixel_unit = System.getProperty( "pixel_unit" );
+
+System.out.println( "pixel_distance_x = " + pixel_distance_x );
+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 );
+
+// Executes Fiji plugin
+System.out.println("=========================================================");
+System.out.println("Start plugin:");
+IJ.run("Define Multi-View Dataset",
+ "type_of_dataset=[" + type_of_dataset + "] " +
+ "xml_filename=[" + xml_filename + ".xml] " +
+ "multiple_timepoints=[" + multiple_timepoints + "] " +
+ "multiple_channels=[" + multiple_channels + "] " +
+ "_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " +
+ "multiple_angles=[" + multiple_angles + "] " +
+ "image_file_directory=" + image_file_directory + " " +
+ "image_file_pattern=" + image_file_pattern + " " +
+ "timepoints_=" + timepoints + " " +
+// "channels_=" + channels + " " + // for dual channel comment out if single channel
+ "acquisition_angles_=" + acquisition_angles + " " +
+ "calibration_type=[Same voxel-size for all views] calibration_definition=[User define voxel-size(s)]" + " " +
+ "imglib2_data_container=[" + imglib_container + "] " +
+ "pixel_distance_x=" + pixel_distance_x + " " +
+ "pixel_distance_y=" + pixel_distance_y + " " +
+ "pixel_distance_z=" + pixel_distance_z + " " +
+ "pixel_unit=" + pixel_unit + "");
+
+/* shutdown */
+runtime.exit(0);
+
+
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
index b98a0ecb0e73f36adf29a59d7d46d90f6f7759e4..0a6d0d2aea9c12b6fe4b18fb65a76507aa9d386f 100755
--- a/spim_registration/timelapse/tomancak_czi.json
+++ b/spim_registration/timelapse/tomancak_czi.json
@@ -5,12 +5,12 @@
"fiji-prefix" : "/sw/bin/xvfb-run -a",
"directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
"merged_xml" : "hdf5_test_unicore_merge",
- "bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/"
+ "bsh_directory" : "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ "first_xml_filename" : "Stock68"
},
"define_xml_czi" :
{
- "first_xml_filename" : "Stock68",
"pixel_distance_x" : "0.2875535786151886",
"pixel_distance_y" : "0.2875535786151886",
"pixel_distance_z" : "1.50000",
@@ -43,6 +43,25 @@
"bsh_file" : "export.bsh"
},
+ "define_xml_tif" :
+ {
+ "timepoints" : "1-2",
+ "acquisition_angles" : "1,2,3,4,5",
+ "channels" : "0,1",
+ "image_file_pattern" : "spim_TL{{tt}}_Angle{{a}}.tif",
+ "pixel_distance_x" : "0.2875535786151886",
+ "pixel_distance_y" : "0.2875535786151886",
+ "pixel_distance_z" : "1.50000",
+ "pixel_unit" : "um",
+ "multiple_timepoints" : "\"YES (one file per time-point)\"",
+ "multiple_channels" : "\"YES (one file per channel)\"",
+ "multiple_illumination_directions" : "\"NO (one illumination direction)\"",
+ "multiple_angles" : "\"YES (one file per angle)\"",
+ "type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
+ "imglib_container" : "\"ArrayImg (faster)\"",
+ "bsh_file" : "define_tif_zip.bsh"
+ },
+
"registration" :
{
"timepoint" : "\"Single Timepoint (Select from List)\"",