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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
# 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/single_channel/resave_test/"
# --- 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="2" # for padded zeros
angle_prep="1 2 3 4 5" # angles format: "1 2 3"
#--- 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" # virtual frame buffer
Fiji_resave="/sw/users/schmied/packages/2014-06-02_Fiji.app_lifeline/ImageJ-linux64" # Fiji that works for resaving
#-------------------------------------------------------------------------------
# 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