Tested for single channel and dual channel

Varying z-slices should be possible now, loads them automatically
But not tested yet

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}"

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");

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
+

spim_registration/tools/rename-zeiss-files.sh

-#!/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

spim_registration/tools/split_channels/create-split-jobs.sh

-#!/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
-

spim_registration/tools/split_channels/split.bsh

-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);
-

spim_registration/tools/split_channels/submit-jobs

-#!/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