1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
#!/bin/sh
#
#
# This file is part of MIA - a toolbox for medical image analysis
# Copyright (c) Leipzig, Madrid 1999-2015 Gert Wollny
#
# MIA is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# $1 input path
# $2 output path
median_width=3
mlv_width=4
mkdir -p $2
cd $2
number_pattern=`eva-filenumber-pattern $1`
if [ ! -e thresh.done ] ; then
thresh=`eva-multihisto -i $1 -V message -o pre_histo.dat`
mkdir -p bg_thresh
echo bg_thresh
eva-2dimagefilterstack -i $1 -t png -o bg_thresh/bg thresh:min=$thresh -V message && touch bg_thresh.done
fi
if [ ! -e filtered.done ] ; then
mkdir -p filtered
echo stack-process
eva-2dstackfilter -i bg_thresh/bg${number_pattern}.png -o filtered/f median:w=$median_width mlv:w=$mlv_width -V message && touch filtered.done
fi
|
