From 3f3996b9efe223248ecf3447b5ca48ad86fcd48c Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Wed, 8 Jul 2015 13:15:03 +0200
Subject: [PATCH] Tested and debugged rename-zeiss-files
---
spim_registration/tools/master_preprocessing.sh | 12 ++++++------
spim_registration/tools/rename-zeiss-files.sh | 11 +++++------
2 files changed, 11 insertions(+), 12 deletions(-)
diff --git a/spim_registration/tools/master_preprocessing.sh b/spim_registration/tools/master_preprocessing.sh
index be31db3..b0a2ca6 100755
--- a/spim_registration/tools/master_preprocessing.sh
+++ b/spim_registration/tools/master_preprocessing.sh
@@ -21,7 +21,7 @@
# c=0,1 etc
# spim_TL{tt}_Angle{a}_Channel{c}.tif
#===============================================================================
-image_file_directory="/projects/pilot_spim/Christopher/Test_pipeline_3.0/czi/"
+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/"
@@ -32,17 +32,17 @@ job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registr
# carry the index (0)
#-------------------------------------------------------------------------------
-pad="3" # for padded zeros
-angle_prep="1" # angles format: "1 2 3"
+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="391" # Last 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=2014-10-23_H2A_gsb_G3\(\{index\}\).czi # Name of .czi files
+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
#-------------------------------------------------------------------------------
@@ -50,7 +50,7 @@ target_pattern=spim_TL\{timepoint\}_Angle\{angle\}.czi # The output pattern of r
#-------------------------------------------------------------------------------
XVFB_RUN="/sw/bin/xvfb-run" # virtual frame buffer
-Fiji_resave="/sw/users/schmied/lifeline/Fiji.app.lifeline2/ImageJ-linux64" # Fiji that works for resaving
+Fiji_resave="/sw/users/schmied/packages/2014-06-02_Fiji.app_lifeline/ImageJ-linux64" # Fiji that works for resaving
#-------------------------------------------------------------------------------
# Pre-processing
#-------------------------------------------------------------------------------
diff --git a/spim_registration/tools/rename-zeiss-files.sh b/spim_registration/tools/rename-zeiss-files.sh
index fff0979..b41a96f 100755
--- a/spim_registration/tools/rename-zeiss-files.sh
+++ b/spim_registration/tools/rename-zeiss-files.sh
@@ -1,6 +1,6 @@
#!/bin/bash
# path of master file
-source ../master_preprocessing.sh
+source master_preprocessing.sh
# path of source and target files
source_pattern=${image_file_directory}${source_pattern}
@@ -15,19 +15,18 @@ 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}
+ 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
+ #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}"`
--
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