Merge pull request #7 from schmiedc/threadbug

Threadbug, cleaning up is good

spim_registration/tools/#master_preprocessing#

-#!/bin/bash
-#===============================================================================
-#
-#	  FILE: master
-#
-#  DESCRIPTION: source file for pre-processing of file formats
-#
-#       AUTHOR: Christopher Schmied, schmied@mpi-cbg.de
-#    INSTITUTE: Max Planck Institute for Molecular Cell Biology and Genetics
-#         BUGS:
-#        NOTES:
-#      Version: 1.0
-#      CREATED: 2015-07-05
-#     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
-#===============================================================================
-image_file_directory="/projects/pilot_spim/Christopher/Test_pipeline_3.0/czi/"
-
-# --- jobs directory -----------------------------------------------------------
-job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/tools/"
-#-------------------------------------------------------------------------------
-# Resaving, Renaming files and Splitting: General
-#
-# Important: For renaming and resaving .czi files the first .czi file has to
-# carry the index (0)
-#-------------------------------------------------------------------------------
-
-pad="3"		# for padded zeros
-angle_prep="1" # angles format: "1 2 3"
-
-#--- Renaming ------------------------------------------------------------------
-
-first_index="0"		# First index of czi files
-last_index="391"		# Last index of czi files
-first_timepoint="0"	# The first timepoint
-angles_renaming=(1)	# Angles format: (1 2 3)
-
-source_pattern=2014-10-23_H2A_gsb_G3\(\{index\}\).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"				 # virtual frame buffer
-# working Fiji
-#Fiji="/sw/users/schmied/packages/2015-05-21_Fiji.app.cuda/ImageJ-linux64"			# woriking Fiji
-Fiji="/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64"
-
-#Fiji for Dual Channel timelapse and Dual Channel Deconvolution
-FijiDualTimelapse="/sw/users/schmied/packages/2015-05-29_Fiji-2.3.9-SNAP.app.cuda/ImageJ-linux64"
-
-Fiji_resave="/sw/users/schmied/lifeline/Fiji.app.lifeline2/ImageJ-linux64" 	# Fiji that works for resaving
-Fiji_Deconvolution=${FijiDualTimelapse}		# Fiji that works for deconvolution
-
-#-------------------------------------------------------------------------------
-# Pre-processing
-#-------------------------------------------------------------------------------
-#--- Resaving .czi into .tif files----------------------------------------------
-jobs_resaving=${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} ${target} # alternatively copy source file and resave into target pattern
-                let i=i+1
-
-        done
-	t=$(( 10#${t} ))
-        let t=t+1
-        t=`printf "%0${pad}d" "${t}"`
-
-done