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
|
/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET 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 2 of the License, or
* (at your option) any later version.
*
* CARET 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 CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "CommandVolumeFillBiggestObject.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeFillBiggestObject::CommandVolumeFillBiggestObject()
: CommandBase("-volume-fill-biggest-object",
"VOLUME FILL BIGGEST OBJECT")
{
}
/**
* destructor.
*/
CommandVolumeFillBiggestObject::~CommandVolumeFillBiggestObject()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeFillBiggestObject::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addInt("Min X", 1, 0, 100000);
paramsOut.addInt("Max X", 1, 0, 100000);
paramsOut.addInt("Min Y", 1, 0, 100000);
paramsOut.addInt("Max Y", 1, 0, 100000);
paramsOut.addInt("Min Z", 1, 0, 100000);
paramsOut.addInt("Max Z", 1, 0, 100000);
}
/**
* get full help information.
*/
QString
CommandVolumeFillBiggestObject::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-volume-file-name>\n"
+ indent9 + "<output-volume-file-name>\n"
+ indent9 + "<min-x> \n"
+ indent9 + "<max-x> \n"
+ indent9 + "<min-y> \n"
+ indent9 + "<max-y> \n"
+ indent9 + "<min-z> \n"
+ indent9 + "<max-z> \n"
+ indent9 + "\n"
+ indent9 + "Fill the biggest object with extent and remove all islands.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeFillBiggestObject::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Volume File Name");
QString outputVolumeFileName, outputVolumeFileLabel;
parameters->getNextParameterAsVolumeFileNameAndLabel("Output Volume File Name",
outputVolumeFileName,
outputVolumeFileLabel);
const int minX =
parameters->getNextParameterAsInt("Minimum X");
const int maxX =
parameters->getNextParameterAsInt("Maximum X");
const int minY =
parameters->getNextParameterAsInt("Minimum Y");
const int maxY =
parameters->getNextParameterAsInt("Maximum Y");
const int minZ =
parameters->getNextParameterAsInt("Minimum Z");
const int maxZ =
parameters->getNextParameterAsInt("Maximum Z");
checkForExcessiveParameters();
//
// Read the input volume file
//
VolumeFile vf;
vf.readFile(inputVolumeFileName);
//
// Find the biggest object and remove any islands.
//
const int extent[6] = {
minX, maxX, minY, maxY, minZ, maxZ
};
vf.fillBiggestObjectWithinMask(extent, 255.0, 255.0);
//
// Write the volume file
//
writeVolumeFile(vf, outputVolumeFileName, outputVolumeFileLabel);
}
|
