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
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
|
/*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 <algorithm>
#include <QDir>
#include "Category.h"
#include "CommandSpecFileCreate.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SpecFile.h"
#include "Species.h"
#include "StereotaxicSpace.h"
#include "Structure.h"
/**
* constructor.
*/
CommandSpecFileCreate::CommandSpecFileCreate()
: CommandBase("-spec-file-create",
"SPEC FILE CREATE")
{
}
/**
* destructor.
*/
CommandSpecFileCreate::~CommandSpecFileCreate()
{
}
/**
* get the script builder parameters.
*/
void
CommandSpecFileCreate::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<StereotaxicSpace> allSpaces;
StereotaxicSpace::getAllStereotaxicSpaces(allSpaces);
std::vector<QString> spaceNames;
for (unsigned int i = 0; i < allSpaces.size(); i++) {
spaceNames.push_back(allSpaces[i].getName());
}
std::vector<Species::TYPE> speciesTypes;
std::vector<QString> speciesNames;
Species::getAllSpeciesTypesAndNames(speciesTypes, speciesNames);
std::vector<Structure::STRUCTURE_TYPE> structureTypes;
std::vector<QString> structureNames;
Structure::getAllTypesAndNames(structureTypes, structureNames, false);
paramsOut.clear();
paramsOut.addListOfItems("Species", speciesNames, speciesNames);
paramsOut.addString("Subject", "");
paramsOut.addListOfItems("Structure", structureNames, structureNames);
paramsOut.addListOfItems("Stereotaxic Space", spaceNames, spaceNames);
paramsOut.addVariableListOfParameters("Create Spec Options");
}
/**
* get full help information.
*/
QString
CommandSpecFileCreate::getHelpInformation() const
{
std::vector<StereotaxicSpace> allSpaces;
StereotaxicSpace::getAllStereotaxicSpaces(allSpaces);
std::vector<QString> spaceNames;
for (int i = 0; i < static_cast<int>(allSpaces.size()); i++) {
spaceNames.push_back(allSpaces[i].getName());
}
std::sort(spaceNames.begin(), spaceNames.end());
std::vector<Species::TYPE> speciesTypes;
std::vector<QString> speciesNames;
Species::getAllSpeciesTypesAndNames(speciesTypes, speciesNames);
std::sort(speciesNames.begin(), speciesNames.end());
std::vector<Structure::STRUCTURE_TYPE> structureTypes;
std::vector<QString> structureNames;
Structure::getAllTypesAndNames(structureTypes, structureNames, false);
std::sort(structureNames.begin(), structureNames.end());
std::vector<Category::TYPE> categoryTypes;
std::vector<QString> categoryNames;
Category::getAllCategoryTypesAndNames(categoryTypes, categoryNames);
std::sort(structureNames.begin(), structureNames.end());
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<species>\n"
+ indent9 + "<subject>\n"
+ indent9 + "<structure>\n"
+ indent9 + "<stereotaxic-space>\n"
+ indent9 + "[-add-files-in-directory]\n"
+ indent9 + "[-category category-name]\n"
+ indent9 + "[-spec-file-name spec-file-name]\n"
+ indent9 + "\n"
+ indent9 + "Create a Spec File\n"
+ indent9 + "\n"
+ indent9 + "If \"-add-files-in-directory\" is specified, all files in \n"
+ indent9 + "the directory that end with caret data file extensions are\n"
+ indent9 + "added to the spec file.\n"
+ indent9 + "\n"
+ indent9 + "The \"spec-file-name\" is optional and should only be specified\n"
+ indent9 + "if you must name the spec file. If the \"spec-file-name\" is not\n"
+ indent9 + "specified, the spec file name will be created using the Caret \n"
+ indent9 + "standard which composes the spec file name using the species,\n"
+ indent9 + "subject, and structure.\n"
+ indent9 + "\n"
+ indent9 + "Valid species for \"species\" are: \n");
for (int i = 0; i < static_cast<int>(speciesNames.size()); i++) {
helpInfo += (indent9 + " " + speciesNames[i] + "\n");
}
helpInfo += "\n";
helpInfo += (indent9 + "Valid structures for \"structure\" are: \n");
for (int i = 0; i < static_cast<int>(structureNames.size()); i++) {
helpInfo += (indent9 + " " + structureNames[i] + "\n");
}
helpInfo += "\n";
helpInfo += (indent9 + "Valid stereotaxic spaces for \"stereotaxic-space\" are: \n");
for (int i = 0; i < static_cast<int>(spaceNames.size()); i++) {
helpInfo += (indent9 + " " + spaceNames[i] + "\n");
}
helpInfo += "\n";
helpInfo += (indent9 + "Valid categories for \"category\" are: \n");
for (int i = 0; i < static_cast<int>(categoryNames.size()); i++) {
helpInfo += (indent9 + " " + categoryNames[i] + "\n");
}
helpInfo += "\n";
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSpecFileCreate::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString speciesName =
parameters->getNextParameterAsString("Species Name");
const QString subjectName =
parameters->getNextParameterAsString("Subject Name");
const Structure structure =
parameters->getNextParameterAsStructure("Structure");
const QString spaceName =
parameters->getNextParameterAsString("Stereotaxic Space Name");
//
// Optional parameters
//
QString categoryName;
QString specFileName;
bool addFilesInCurrentDirectoryFlag = false;
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("Spec File Create Option");
if (paramName == "-add-files-in-directory") {
addFilesInCurrentDirectoryFlag = true;
}
else if (paramName == "-category") {
categoryName = parameters->getNextParameterAsString("Category");
}
else if (paramName == "-spec-file-name") {
specFileName = parameters->getNextParameterAsString("Spec File Name");
}
else {
throw CommandException("Invalid parameter \""
+ paramName
+ "\"");
}
}
SpecFile sf;
if (specFileName.isEmpty()) {
specFileName = speciesName + "."
+ subjectName + "."
+ structure.getTypeAsAbbreviatedString()
+ SpecFile::getSpecFileExtension();
}
sf.setSpecies(speciesName);
sf.setSubject(subjectName);
sf.setSpace(spaceName);
sf.setStructure(structure.getTypeAsString());
sf.setCategory(categoryName);
if (addFilesInCurrentDirectoryFlag) {
addFilesInCurrentDirectory(sf);
}
sf.writeFile(specFileName);
}
/**
* add all files in the current directory.
*/
void
CommandSpecFileCreate::addFilesInCurrentDirectory(SpecFile& sf)
{
QDir dir(QDir::currentPath());
QFileInfoList list = dir.entryInfoList(QDir::Files);
for (int i = 0; i < list.size(); i++) {
sf.addUnknownTypeOfFileToSpecFile(list.at(i).fileName());
}
}
|
