diff --git a/spim_registration/tools/czi_resave/create-resaving-jobs.sh b/spim_registration/tools/czi_resave/create-resaving-jobs.sh
index 2874a6089ae69b0ceb91cd77fae6aece30e23b4a..8f1e0229704ac0a2318af33d83b0b78572bb6397 100755
--- a/spim_registration/tools/czi_resave/create-resaving-jobs.sh
+++ b/spim_registration/tools/czi_resave/create-resaving-jobs.sh
@@ -22,7 +22,6 @@ do
-Dfirst_czi_name=${first_czi_name} \
-Dtimepoint=${timepoint} \
-Dangle=${angle} \
- -Dstack_size=${stack_size} \
-Dpad=${pad} \
-Dtif_timepoint=${tif_timepoint} \
-- --no-splash ${resaving}" >> "${job}"
diff --git a/spim_registration/tools/czi_resave/resaving.bsh b/spim_registration/tools/czi_resave/resaving.bsh
index 00bd0d7b7983e69782deac28abb97e00f9f8694c..25d97614ec7ce48923c900c8e8707d4012755096 100755
--- a/spim_registration/tools/czi_resave/resaving.bsh
+++ b/spim_registration/tools/czi_resave/resaving.bsh
@@ -39,15 +39,11 @@ System.out.println( "=======================================================" );
System.out.println( "Opening Image" ) ;
IJ.run("Bio-Formats Importer",
"open=" + dir + first_czi_name + " " +
- "autoscale " +
"color_mode=Default " +
"specify_range " +
"view=[Standard ImageJ] " +
"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");
diff --git a/spim_registration/tools/master_preprocessing.sh b/spim_registration/tools/master_preprocessing.sh
index 2bc2ed48ea71441f95abae0ccdeddac3a58f6f54..3ae3369970321129f830cb86ea89a14f3e332144 100755
--- a/spim_registration/tools/master_preprocessing.sh
+++ b/spim_registration/tools/master_preprocessing.sh
@@ -14,12 +14,10 @@
# REVISION: 2015-07-05
#
# Preprocessing
-# 1) rename .czi files
-# 2) resave .czi files into .tif or .zip
-# 3) resave ome.tiff files into .tif
-# 4) Splitting output for Channel is
-# c=0,1 etc
-# spim_TL{tt}_Angle{a}_Channel{c}.tif
+# resave single channel and dual channel .czi files into .tif
+# output: img_TL{t}_Angle{a}.tif
+# channels are 0,1 etc
+#
#===============================================================================
image_file_directory="/projects/pilot_spim/Christopher/cluster_test_HisYFP/2013-11-14_His-YFP_2/"
@@ -34,7 +32,6 @@ job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registr
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
first_timepoint="0" # Starts with 0
#-------------------------------------------------------------------------------
@@ -49,12 +46,4 @@ Fiji="/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64"
#--- Resaving .czi into .tif files----------------------------------------------
jobs_resaving=${job_directory}"czi_resave" # directory .czi resaving
resaving=${jobs_resaving}"/resaving.bsh" # script .czi resaving
-#--- Resaving ome.tiff into .tif files -----------------------------------------
-jobs_resaving_ometiff=${job_directory}"ometiff_resave" # directory .ome.tiff resaving
-resaving_ometiff=${jobs_resaving_ometiff}"/resaving-ometiff.bsh" # script .ome.tiff resaving
-#--- Compress dataset;----------------------------------------------------------
-jobs_compress=${job_directory}"compress" # directory .czi to .zip resaving
-czi_compress=${jobs_compress}"/for_czi.bsh" # script .czi to .zip resaving
-#--- Split channels-------------------------------------------------------------
-jobs_split=${job_directory}"split_channels" # directory
-split=${jobs_split}"/split.bsh" # script
+
diff --git a/spim_registration/tools/rename-zeiss-files.sh b/spim_registration/tools/rename-zeiss-files.sh
deleted file mode 100755
index b41a96f0d794eeb8109db681f172626e6aa91be3..0000000000000000000000000000000000000000
--- a/spim_registration/tools/rename-zeiss-files.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-# path of master file
-source master_preprocessing.sh
-
-# path of source and target files
-source_pattern=${image_file_directory}${source_pattern}
-target_pattern=${image_file_directory}${target_pattern}
-
-# ------------------------------------------------------------------------------
-
-i=${first_index}
-t=${first_timepoint}
-t=`printf "%0${pad}d" "${t}"`
-
-while [ $i -le $last_index ]; do
-
- for a in "${angles_renaming[@]}"; do
-
- source=${source_pattern/\{index\}/${i}}
- tmp=${target_pattern/\{timepoint\}/${t}}
- target=${tmp/\{angle\}/${a}}
-
- echo ${source} ${target} # displays source file and target file with path
-
- #mv ${source} ${target} # renames source file into target pattern
- cp ${source} ${target} # alternatively copy source file and resave into target pattern
- let i=i+1
-
- done
- let t=t+1
- t=`printf "%0${pad}d" "${t}"`
-
-done
diff --git a/spim_registration/tools/split_channels/create-split-jobs.sh b/spim_registration/tools/split_channels/create-split-jobs.sh
deleted file mode 100755
index 1491121f8a77251244c68d2fb5016a269e9ec1db..0000000000000000000000000000000000000000
--- a/spim_registration/tools/split_channels/create-split-jobs.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/bin/bash
-
-source ../master_preprocessing.sh
-
-mkdir -p ${jobs_split}
-
-for i in $parallel_timepoints
-
- do
- for a in $angle_prep
-
- do
- job="$jobs_split/split-$i-$a.job"
- echo $job
- echo "#!/bin/bash" > "$job"
- echo "$XVFB_RUN $sysconfcpus $Fiji \
- -Dimage_file_directory=$image_file_directory \
- -Dparallel_timepoints=$i \
- -Dangle_prep=$a \
- -Dpad=$pad \
- -Dtarget_split=$image_file_directory \
- -- --no-splash \
- $split" >> "$job"
-chmod a+x "$job"
- done
-done
-
diff --git a/spim_registration/tools/split_channels/split.bsh b/spim_registration/tools/split_channels/split.bsh
deleted file mode 100755
index e562f2c0a2cd1e7a21f26ec124dda0fd18e80365..0000000000000000000000000000000000000000
--- a/spim_registration/tools/split_channels/split.bsh
+++ /dev/null
@@ -1,44 +0,0 @@
-import ij.IJ;
-import ij.ImagePlus;
-import ij.ImageStack;
-import java.lang.Runtime;
-import java.io.File;
-import java.io.FilenameFilter;
-
-
-runtime = Runtime.getRuntime();
-
-image_file_directory = System.getProperty( "image_file_directory" );
-int parallel_timepoints = Integer.parseInt( System.getProperty( "parallel_timepoints" ) );
-angle_prep = System.getProperty( "angle_prep" );
-target_split = System.getProperty( "target_split" );
-int pad = Integer.parseInt( System.getProperty( "pad" ) );
-
-System.out.println( "directory = " + image_file_directory );
-System.out.println( "timpoint = " + parallel_timepoints );
-System.out.println( "angles = " + angle_prep );
-System.out.println( "target_split = " + target_split );
-System.out.println( "pad = " + pad );
-
-//open image
-
-imp = new ImagePlus( image_file_directory + "spim_TL" + IJ.pad( parallel_timepoints , pad ) + "_Angle" + angle_prep + ".tif" );
-System.out.println( imp.getTitle() );
-
-/* split channels */
-stack = imp.getStack();
-for ( c = 0; c < imp.getNChannels(); ++c )
-{
- channelStack = new ImageStack( imp.getWidth(), imp.getHeight() );
- for ( z = 0; z < imp.getNSlices(); ++z )
- channelStack.addSlice(
- "",
- stack.getProcessor(
- imp.getStackIndex( c + 1, z + 1, 1 ) ) );
- impc = new ImagePlus( imp.getTitle() + " #" + ( c + 1 ), channelStack );
- IJ.save( impc, target_split + imp.getTitle().replaceFirst( ".tif$", "_Channel" + ( c ) + ".tif" ) );
-}
-
-/* shutdown */
-runtime.exit(0);
-
diff --git a/spim_registration/tools/split_channels/submit-jobs b/spim_registration/tools/split_channels/submit-jobs
deleted file mode 100755
index d631b4efa2d22f1174da389ee8da22662df47c55..0000000000000000000000000000000000000000
--- a/spim_registration/tools/split_channels/submit-jobs
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-for file in `ls ${1} | grep ".job$"`
-do
- bsub -q short -n 3 -R span[hosts=1] -o "out.%J" -e "err.%J" ${1}/$file
-done