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
180
181
182
183
184
185
186
187
188
189
190
|
/*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 "BrainModelSurface.h"
#include "BrainModelSurfaceROIIntegratedFoldingIndexReport.h"
#include "BrainModelSurfaceROINodeSelection.h"
#include "BrainSet.h"
#include "CommandSurfaceRoiShapeMeasures.h"
#include "FileFilters.h"
#include "NodeRegionOfInterestFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TextFile.h"
/**
* constructor.
*/
CommandSurfaceRoiShapeMeasures::CommandSurfaceRoiShapeMeasures()
: CommandBase("-surface-shape-measures",
"SURFACE SHAPE MEASURES")
{
}
/**
* destructor.
*/
CommandSurfaceRoiShapeMeasures::~CommandSurfaceRoiShapeMeasures()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceRoiShapeMeasures::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Topology File", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Surface Shape File", FileFilters::getSurfaceShapeFileFilter());
paramsOut.addFile("Output Text File", FileFilters::getTextFileFilter(), "Folding.txt");
paramsOut.addFile("Region Of Interest File", FileFilters::getRegionOfInterestFileFilter(), "", "-roi");
}
/**
* get full help information.
*/
QString
CommandSurfaceRoiShapeMeasures::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<surface-shape-file-name>\n"
+ indent9 + "<output-text-report-file-name>\n"
+ indent9 + "[-roi region-of-interest-file-name]\n"
+ indent9 + "\n"
+ indent9 + "Generate a report of shape measurements on a surface.\n"
+ indent9 + "\n"
+ indent9 + "If an ROI is provided, the shape measurements are \n"
+ indent9 + "limited to that region of the surface.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceRoiShapeMeasures::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topoFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString surfaceShapeFileName =
parameters->getNextParameterAsString("Surface Shape File Name");
const QString textReportFileName =
parameters->getNextParameterAsString("Text Report File Name");
QString roiFileName;
while (parameters->getParametersAvailable()) {
const QString paramName =
parameters->getNextParameterAsString("Optional parameter");
if (paramName == "-roi") {
roiFileName =
parameters->getNextParameterAsString("Region of Interest File Name");
if (roiFileName.isEmpty()) {
throw CommandException("Region of Interest File Name is missing.");
}
}
else {
throw CommandException("Unrecognized parameter \""
+ paramName
+ "\".");
}
}
//
// Create a brain set
//
BrainSet brainSet(topoFileName,
coordinateFileName,
"");
//
// Find the surface
//
BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("Unable to find surface after reading files.");
}
if (bms->getTopologyFile() == NULL) {
throw CommandException("Unable to find topology after reading files.");
}
brainSet.readSurfaceShapeFile(surfaceShapeFileName, false, false);
//
// Get the ROI
//
BrainModelSurfaceROINodeSelection* surfaceROI =
brainSet.getBrainModelSurfaceRegionOfInterestNodeSelection();
if (roiFileName.isEmpty() == false) {
NodeRegionOfInterestFile nroi;
nroi.readFile(roiFileName);
surfaceROI->getRegionOfInterestFromFile(nroi);
}
else {
surfaceROI->selectAllNodes(bms);
}
//
// Run the report
//
BrainModelSurfaceROIIntegratedFoldingIndexReport
fmr(&brainSet,
bms,
surfaceROI,
brainSet.getSurfaceShapeFile(),
"",
true);
fmr.execute();
//
// File for text report
//
TextFile textReportFile;
textReportFile.setText(fmr.getReportText());
//
// Write the text file
//
textReportFile.writeFile(textReportFileName);
}
|
