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#!/bin/bash
#===============================================================================
#
# FILE: master_preprocessing.sh
#
# 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
# 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/test_pipeline/dual_channel/tif_onefile/"
# --- 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)
#-------------------------------------------------------------------------------
first_czi_name="2015-02-20_LZ2_Stock48_Stock58.czi"
timepoints="`seq 0 1`" # number of time points format: "`seq 0 1`"
angles="1 2 3 4 5" # angles format: "1 2 3"
first_timepoint="0" # Starts with 0
#-------------------------------------------------------------------------------
# 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"
#-------------------------------------------------------------------------------
# Pre-processing
#-------------------------------------------------------------------------------
#--- Resaving .czi into .tif files----------------------------------------------
jobs_resaving=${job_directory}"czi_resave" # directory .czi resaving
resaving=${jobs_resaving}"/resaving.bsh" # script .czi resaving