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
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
|
#!/bin/bash
#
#
# 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/>.
#
out_image_type="png"
blob_thresh=100
class=2
nclasses=3
prob_thresh=0.96
hist_thresh=1
verbosity=message
print_help() {
echo "This script runs the segmentation of one class from a series of gray "
echo "scale images. Parameters are"
echo " "
echo "Usage: mia-segment-class-from-stack [options]"
echo " "
echo "File IO:"
echo " --input Input images (give like e.g. input0000.png), Input images"
echo " are expected to be consecutively numbered"
echo " --output Output image base name"
echo " --output-type Output file type, (default=$out_image_type)"
echo " "
echo "Parameters:"
echo " --blop-thresh threshold for minimum size of blobs to be accepted (default=$blob_thresh)"
echo " --prob-thresh class probability to accept as class member (default=$prob_thresh)"
echo " --hist-thresh Percentage of pixels to merge into the extreme bins (default=$hist_thresh)"
echo " --class class Id to segment"
echo " --n-classes number of classes to use in the fuzzy c-means classification (default=$nclasses)"
echo " "
echo "Info:"
echo " --verbose -V verbosity of the output (info|message|warning|error|fatal)"
echo " "
exit 0
}
#
# read the command line
#
while [ -n "$1" ] ; do
case "$1" in
--blop-thresh)
blop_thresh="$2"
shift
;;
--class)
class="$2"
shift
;;
--n-classes)
nclasses="$2"
shift
;;
--prob-thresh)
prob_thresh="$2"
shift
;;
--hist-thresh)
hist_thresh="$2"
shift
;;
--input)
in_images="$2"
shift
;;
--output)
out_images="$2"
shift
;;
--output-type)
out_image_type="$2"
shift
;;
--verbose,-V)
verbosity="$2"
shift
;;
--help)
print_help
exit
;;
*)
echo "unknown option '$1' given, run with option --help to see supported options"
exit
;;
esac
shift
done
datestr=$(date +%y-%m-%d-%H-%m)
temp_dir=$(mktemp -d stackprocess-${datestr}.XXX)
echo mia-2dstack-cmeans-presegment -i $in_images -o "$temp_dir/class" \
-T $hist_thresh \
-S $prob_thresh \
-C "kmeans:nc=$nclasses" \
-L $class -V $verbosity
mia-2dstack-cmeans-presegment -i $in_images -o "$temp_dir/class" \
-T $hist_thresh \
-S $prob_thresh \
-C "kmeans:nc=$nclasses" \
-L $class -V $verbosity
number_pattern=$(mia-filenumberpattern -i "$in_images")
# label the images
mia-2dstackfilter -i "$temp_dir/class${number_pattern}.png" -t v -o "$temp_dir/labeled"\
"label:map=$temp_dir/labelmap.txt" -V $verbosity
#relabel joined labels
mia-2dimagefilterstack -i "$temp_dir/labeled${number_pattern}.v" -o $temp_dir/relabeled -t v \
"labelmap:map=$temp_dir/labelmap.txt" -V $verbosity
# evaluate the histogram
mia-multihist -i "$temp_dir/relabeled${number_pattern}.v" -o "$temp_dir/labelcount.txt" --max 1000000 --bins 1000000 -V $verbosity
# this can be done with awk
echo "MiaLabelmap" > "$temp_dir/labelbinarizationmap.txt"
awk -v thresh=$blob_thresh <"$temp_dir/labelcount.txt" \
'{if ($2 > thresh){ print $1 " 1"}else{ print $1 " 0"} }' \
>> "$temp_dir/labelbinarizationmap.txt"
mia-2dimagefilterstack -i "$temp_dir/relabeled${number_pattern}.v" -o "$temp_dir/inverse" -t v \
"labelmap:map=$temp_dir/labelbinarizationmap.txt" \
binarize:min=1 invert -V $verbosity
mia-2dstackfilter -i "$temp_dir/inverse${number_pattern}.v" -t v \
-o "$temp_dir/ilabeled" "label:map=$temp_dir/ilabelmap.txt" -V $verbosity
mia-2dimagefilterstack -i "$temp_dir/ilabeled${number_pattern}.v" -o $temp_dir/irelabeled -t v \
"labelmap:map=$temp_dir/ilabelmap.txt" -V $verbosity
mia-multihist -i "$temp_dir/irelabeled${number_pattern}.v" -o "$temp_dir/ilabelcount.txt" \
-V $verbosity --max 1000000 --bins 1000000
echo "MiaLabelmap" > "$temp_dir/ilabelbinarizationmap.txt"
awk -v thresh=$thresh <"$temp_dir/ilabelcount.txt" \
'{if ($2 > thresh){ print $1 " 1"}else{ print $1 " 0"} }'\
>> "$temp_dir/ilabelbinarizationmap.txt"
mia-2dimagefilterstack -i "$temp_dir/irelabeled${number_pattern}.v" -o "$out_images" -t png \
"labelmap:map=$temp_dir/ilabelbinarizationmap.txt" binarize:min=1 invert -V $verbosity
#rm -rf $temp_dir
|
