diff --git a/spim_registration/tools/compress/create-compress-jobs.sh b/spim_registration/tools/compress/create-compress-jobs.sh
deleted file mode 100755
index e4e869b39b0546f9c128d3791f33c10bd7137c09..0000000000000000000000000000000000000000
--- a/spim_registration/tools/compress/create-compress-jobs.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/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
-
diff --git a/spim_registration/tools/compress/for_czi.bsh b/spim_registration/tools/compress/for_czi.bsh
deleted file mode 100755
index e860cf53e8038a8a241c844fb8935b6a4a219162..0000000000000000000000000000000000000000
--- a/spim_registration/tools/compress/for_czi.bsh
+++ /dev/null
@@ -1,46 +0,0 @@
-// 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);
-
diff --git a/spim_registration/tools/compress/resubmit-failed-jobs.sh b/spim_registration/tools/compress/resubmit-failed-jobs.sh
deleted file mode 100755
index 7f2b0eff00cefb3c37d98211532199914fb10b01..0000000000000000000000000000000000000000
--- a/spim_registration/tools/compress/resubmit-failed-jobs.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-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
diff --git a/spim_registration/tools/compress/submit-jobs b/spim_registration/tools/compress/submit-jobs
deleted file mode 100755
index 626449c2bfc64732d0467b6f20cff8cb6060d2a7..0000000000000000000000000000000000000000
--- a/spim_registration/tools/compress/submit-jobs
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/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
diff --git a/spim_registration/tools/czi_resave/create-resaving-jobs.sh b/spim_registration/tools/czi_resave/create-resaving-jobs.sh
index 200bc1a50935f74af511382c9c7aba46d9f1fa20..2874a6089ae69b0ceb91cd77fae6aece30e23b4a 100755
--- a/spim_registration/tools/czi_resave/create-resaving-jobs.sh
+++ b/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
diff --git a/spim_registration/tools/czi_resave/resaving.bsh b/spim_registration/tools/czi_resave/resaving.bsh
index eb3c14e4ee60fd67c2b22c77ee3e62a259e4220a..00bd0d7b7983e69782deac28abb97e00f9f8694c 100755
--- a/spim_registration/tools/czi_resave/resaving.bsh
+++ b/spim_registration/tools/czi_resave/resaving.bsh
@@ -1,44 +1,60 @@
// 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);
diff --git a/spim_registration/tools/czi_resave/submit-jobs b/spim_registration/tools/czi_resave/submit-jobs
index 626449c2bfc64732d0467b6f20cff8cb6060d2a7..00fbd7fbd40dbde0f81d508bb2448fa754414f52 100755
--- a/spim_registration/tools/czi_resave/submit-jobs
+++ b/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
diff --git a/spim_registration/tools/master_preprocessing.sh b/spim_registration/tools/master_preprocessing.sh
index 74a9ba09898ba51ed24de4a04f5aafba420629d9..2bc2ed48ea71441f95abae0ccdeddac3a58f6f54 100755
--- a/spim_registration/tools/master_preprocessing.sh
+++ b/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
#-------------------------------------------------------------------------------