Resaving uses now current Fiji version

At the moment only one z-stack size possible
compress not supported anymore

spim_registration/tools/compress/create-compress-jobs.sh

-#!/bin/bash
-
-# path of master file
-source ../master_preprocessing.sh
-
-# creates directory for job files if not present
-mkdir -p $jobs_compress
-
-echo $jobs_compress
-echo $czi_compress
-
-# splits up resaving into 1 job per .czi file and writes the given parameters
-# into the job file
-for i in $timepoints
-
-do
-	for a in $angle_prep
-	do
-		job="$jobs_compress/compress-$i-$a.job"
-		echo $job
-		echo "$XVFB_RUN $sysconfcpus $Fiji_resave \
-			-Ddir=$image_file_directory \
-			-Dtimepoint=$i \
-			-Dangle=$a \
-			-Dpad=$pad \
-			-- --no-splash $czi_compress" >> "$job"
-		chmod a+x "$job"
-	done
-done
-

spim_registration/tools/compress/for_czi.bsh

-// Loads Fiji dependencies
-import ij.IJ;
-import ij.ImagePlus;
-import java.lang.Runtime;
-import java.io.File;
-import java.io.FilenameFilter;
-
-runtime = Runtime.getRuntime();
-
-// Loads parameters form job file
-System.out.println( "=======================================================" );
-System.out.println( "Load Parameters" ) ;
-
-dir = System.getProperty( "dir" );
-int timepoint = Integer.parseInt( System.getProperty( "timepoint" ) );
-angle = System.getProperty( "angle" );
-int pad = Integer.parseInt( System.getProperty( "pad" ) );
-
-// Prints Parameters into output file
-System.out.println( "directory = " + dir );
-System.out.println( "timepoint = " + timepoint );
-System.out.println( "angle = " + angle );
-System.out.println( "pad = " + pad );
-
-
-// Executes Fiji Plugin "Bioformats Importer" to open .czi file
-System.out.println( "=======================================================" );
-System.out.println( "Opening Image" ) ;
-IJ.run("Bio-Formats Importer", 
-	"open=" + dir + "spim_TL" + IJ.pad( timepoint, pad ) + "_Angle" + angle + ".czi" + " " +
-	"autoscale " +
-	"color_mode=Default " +
-	"specify_range " +
-	"view=[Standard ImageJ] " +
-	"stack_order=Default " +
-	"t_begin=1000 " +
-	"t_end=1000 " +
-	"t_step=1");
-
-// Resaves .czi files as .zip file
-System.out.println( "Save as compressed image" ) ;
-IJ.saveAs("ZIP ", dir + "spim_TL" + IJ.pad( timepoint, pad ) + "_Angle" + angle + ".zip");
-
-/* shutdown */
-runtime.exit(0);
-

spim_registration/tools/compress/resubmit-failed-jobs.sh

-names=`grep "exit code 1" out.* -l`
-for name in $names; do
-	job=`sed -n '4,4p' $name | sed -n "s/Job <\([^>]*\)>.*/\1/p"`
-	echo bsub -q short -n 12 -R rusage[mem=110000] -R span[hosts=1] -o "out.%J" -e "err.%J" ${job}
-       bsub -q short -n 12 -R rusage[mem=110000] -R span[hosts=1] -o "out.%J" -e "err.%J" ${job}
-done

spim_registration/tools/compress/submit-jobs

-#!/bin/bash
-
-for file in `ls ${1} | grep ".job$"`
-do
-	bsub -q short -n 2 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
-done

spim_registration/tools/czi_resave/create-resaving-jobs.sh

@@ -8,19 +8,26 @@ mkdir -p $jobs_resaving
 
 # splits up resaving into 1 job per .czi file and writes the given parameters
 # into the job file
-for i in $timepoints
+tif_timepoint=${first_timepoint}
+
+for timepoint in ${timepoints}
 
 do
-	for a in $angle_prep
+	for angle in ${angles}
 	do
-		job="$jobs_resaving/resave-$i-$a.job"
+		job="$jobs_resaving/resave-${timepoint}-${angle}.job"
 		echo $job
-		echo "$XVFB_RUN $sysconfcpus $Fiji_resave \
-			-Ddir=$image_file_directory \
-			-Dtimepoint=$i \
-			-Dangle=$a \
-			-Dpad=$pad \
-			-- --no-splash $resaving" >> "$job"
-		chmod a+x "$job"
+		echo "${XVFB_RUN} ${sysconfcpus} ${Fiji} \
+			-Ddir=${image_file_directory} \
+			-Dfirst_czi_name=${first_czi_name} \
+			-Dtimepoint=${timepoint} \
+			-Dangle=${angle} \
+			-Dstack_size=${stack_size} \
+			-Dpad=${pad} \
+			-Dtif_timepoint=${tif_timepoint} \
+			-- --no-splash ${resaving}" >> "${job}"
+		chmod a+x "${job}"
 	done
+tif_timepoint=$((${tif_timepoint} + 1))
+
 done

spim_registration/tools/czi_resave/resaving.bsh

 // Loads Fiji dependencies
 import ij.IJ;
+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(2); 	// defines the number of threads allowed
+print("Threads: "+ Prefs.getThreads()); // prints thread setting in output
 
 // Loads parameters form job file
 System.out.println( "=======================================================" );
 System.out.println( "Load Parameters" ) ;
 
 dir = System.getProperty( "dir" );
+first_czi_name = System.getProperty( "first_czi_name" );
+	
 int timepoint = Integer.parseInt( System.getProperty( "timepoint" ) );
 angle = System.getProperty( "angle" );
+stack_size = System.getProperty( "stack_size" );
 int pad = Integer.parseInt( System.getProperty( "pad" ) );
+int tif_timepoint = Integer.parseInt( System.getProperty( "tif_timepoint" ) );
 
 // Prints Parameters into output file
 System.out.println( "directory = " + dir );
+System.out.println( "first_czi_name = " + first_czi_name );
 System.out.println( "timepoint = " + timepoint );
 System.out.println( "angle = " + angle );
+System.out.println( "stack_size = " + stack_size );
 System.out.println( "pad = " + pad );
+System.out.println( "timepoint = " + tif_timepoint );
 
 // Executes Fiji Plugin "Bioformats Importer" to open .czi file
 System.out.println( "=======================================================" );
 System.out.println( "Opening Image" ) ;
 IJ.run("Bio-Formats Importer", 
-	"open=" + dir + "spim_TL" + IJ.pad( timepoint, pad ) + "_Angle" + angle + ".czi" + " " +
+	"open=" + dir + first_czi_name + " " + 
 	"autoscale " +
 	"color_mode=Default " +
 	"specify_range " +
 	"view=[Standard ImageJ] " +
-	"stack_order=Default " +
-	"t_begin=1000 " +
-	"t_end=1000 " +
-	"t_step=1");
+	"stack_order=XYCZT " +
+	"series_" + angle + " " +
+	"z_begin_" + angle + "=1 " +
+	"z_end_" + angle + "=" + stack_size + " " +
+	"z_step_" + angle + "=1 " +
+	"t_begin_" + angle + "=" + timepoint + " " +
+	"t_end_" + angle + "=" + timepoint + " " +
+	"t_step_" + angle + "=1");
 
 // Resaves .czi files as .tif file
 System.out.println( "Save as  .tif" ) ;
-IJ.saveAs("Tiff ", dir + "spim_TL" + IJ.pad( timepoint, pad ) + "_Angle" + angle + ".tif");
+IJ.saveAs("Tiff ", dir + "img_TL" + IJ.pad( tif_timepoint, pad ) + "_Angle" + angle + ".tif");
 
 /* shutdown */
 runtime.exit(0);

spim_registration/tools/czi_resave/submit-jobs

@@ -2,5 +2,5 @@
 
 for file in `ls ${1} | grep ".job$"`
 do
-	bsub -q short -n 2 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
+	bsub -q short -n 2 -R span[hosts=1] -R rusage[mem=10000] -o "out.%J" -e "err.%J" ${1}/$file
 done

spim_registration/tools/master_preprocessing.sh

@@ -21,7 +21,7 @@
 #		c=0,1 etc
 #		spim_TL{tt}_Angle{a}_Channel{c}.tif
 #===============================================================================
-image_file_directory="/projects/pilot_spim/Christopher/test_pipeline/single_channel/resave_test/"
+image_file_directory="/projects/pilot_spim/Christopher/cluster_test_HisYFP/2013-11-14_His-YFP_2/"
 
 # --- jobs directory -----------------------------------------------------------
 job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/tools/"
@@ -31,27 +31,18 @@ job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registr
 # Important: For renaming and resaving .czi files the first .czi file has to
 # carry the index (0)
 #-------------------------------------------------------------------------------
-timepoints="`seq 0 1`" # number of time points format: "`seq 0 1`"
-angle_prep="1 2 3 4 5" # angles format: "1 2 3"
+first_czi_name="2013-11-14_His-YFP_2.czi"
+timepoints="`seq 1 2`" # number of time points format: "`seq 0 1`"
+angles="1 2 3 4 5" # angles format: "1 2 3"
+stack_size="142"
 pad="2"		# for padded zeros
-num_angles="5"
-#--- Renaming ------------------------------------------------------------------
-
-first_index="0"		# First index of czi files
-last_index="9"	# Last index of czi files
 first_timepoint="0"	# Starts with 0
-angles_renaming=(1 2 3 4 5)	# Angles format: (1 2 3)
-
-source_pattern=2015-02-21_LZ1_Stock68_3\(\{index\}\).czi # Name of .czi files
-target_pattern=spim_TL\{timepoint\}_Angle\{angle\}.czi	# The output pattern of renaming
-
 #-------------------------------------------------------------------------------
 # Fiji settings
 #-------------------------------------------------------------------------------
 XVFB_RUN="/sw/bin/xvfb-run -a" # virtual frame buffer
 sysconfcpus="sysconfcpus -n 2"
-Fiji: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64"
-Fiji_resave="/sw/users/schmied/packages/2014-06-02_Fiji.app_lifeline/ImageJ-linux64" # Fiji that works for resaving
+Fiji="/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64"
 #-------------------------------------------------------------------------------
 # Pre-processing
 #-------------------------------------------------------------------------------