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
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
|
/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#include "transformixlib.h"
#include "elastix.h" // For ConvertSecondsToDHMS and GetCurrentDateAndTime.
#ifdef _ELASTIX_USE_MEVISDICOMTIFF
# include "itkUseMevisDicomTiff.h"
#endif
#include "elxTransformixMain.h"
#include <iostream>
#include <string>
#include <vector>
#include <queue>
#include <ctime>
#include "itkObject.h"
#include "itkDataObject.h"
#include <itksys/SystemTools.hxx>
#include <itksys/SystemInformation.hxx>
#include "itkTimeProbe.h"
namespace transformix
{
/**
* ******************* Constructor ***********************
*/
TRANSFORMIX::TRANSFORMIX()
: m_ResultImage(nullptr)
{} // end Constructor
/**
* ******************* Destructor ***********************
*/
TRANSFORMIX::~TRANSFORMIX()
{
this->m_ResultImage = nullptr;
} // end Destructor
/**
* ******************* GetResultImage ***********************
*/
TRANSFORMIX::ConstImagePointer
TRANSFORMIX::GetResultImage() const
{
return this->m_ResultImage;
} // end GetResultImage()
TRANSFORMIX::ImagePointer
TRANSFORMIX::GetResultImage()
{
return this->m_ResultImage;
} // end GetResultImage()
/**
* ******************* TransformImage ***********************
*/
int
TRANSFORMIX::TransformImage(ImagePointer inputImage,
std::vector<ParameterMapType> & parameterMaps,
const std::string & outputPath,
bool performLogging,
bool performCout)
{
/** Some typedef's.*/
using TransformixMainType = elx::TransformixMain;
using TransformixMainPointer = TransformixMainType::Pointer;
using ArgumentMapType = TransformixMainType::ArgumentMapType;
using ArgumentMapEntryType = ArgumentMapType::value_type;
using DataObjectContainerType = elx::MainBase::DataObjectContainerType;
using DataObjectContainerPointer = elx::MainBase::DataObjectContainerPointer;
/** Declare an instance of the Transformix class. */
TransformixMainPointer transformix;
DataObjectContainerPointer movingImageContainer = nullptr;
;
DataObjectContainerPointer resultImageContainer = nullptr;
/** Initialize. */
int returndummy = 0;
ArgumentMapType argMap;
bool outFolderPresent = false;
std::string outFolder = "";
std::string logFileName = "";
std::string key;
std::string value;
if (!outputPath.empty())
{
key = "-out";
value = outputPath;
/** Make sure that last character of the output folder equals a '/'. */
if (outputPath.back() != '/')
{
value.append("/");
}
outFolderPresent = true;
}
else
{
/** Put command line parameters into parameterFileList. */
// there must be an "-out", this is checked later in code!!
key = "-out";
value = "";
}
/** Save this information. */
outFolder = value;
/** Attempt to save the arguments in the ArgumentMap. */
if (argMap.count(key) == 0)
{
argMap.insert(ArgumentMapEntryType(key, value));
}
else if (performCout)
{
/** Duplicate arguments. */
std::cerr << "WARNING!\n"
<< "Argument " << key << "is only required once.\n"
<< "Arguments " << key << " " << value << "are ignored" << std::endl;
}
if (performLogging)
{
/** Check if the output directory exists. */
bool outFolderExists = itksys::SystemTools::FileIsDirectory(outFolder);
if (!outFolderExists)
{
if (performCout)
{
std::cerr << "ERROR: the output directory does not exist.\n"
<< "You are responsible for creating it." << std::endl;
}
return (-2);
}
else
{
if (performLogging)
{
logFileName = outFolder + "transformix.log";
}
}
}
/** The argv0 argument, required for finding the component.dll/so's. */
argMap.insert(ArgumentMapEntryType("-argv0", "transformix"));
/** Setup the log system. */
const elx::log::guard logGuard{};
int returndummy2 = elx::log::setup(logFileName, performLogging, performCout) ? 0 : 1;
if (returndummy2 && performCout)
{
if (performCout)
{
std::cerr << "ERROR while setting up the log system." << std::endl;
}
return (returndummy2);
}
elx::log::info("");
/** Declare a timer, start it and print the start time. */
itk::TimeProbe totaltimer;
totaltimer.Start();
elx::log::info(std::ostringstream{} << "transformix is started at " << GetCurrentDateAndTime() << ".\n");
/**
* ********************* START TRANSFORMATION *******************
*/
/** Set transformix. */
transformix = TransformixMainType::New();
/** Set stuff from input or needed for output */
movingImageContainer = DataObjectContainerType::New();
movingImageContainer->CreateElementAt(0) = inputImage;
transformix->SetMovingImageContainer(movingImageContainer);
transformix->SetResultImageContainer(resultImageContainer);
/** Run transformix. */
returndummy = transformix->Run(argMap, parameterMaps);
/** Check if transformix run without errors. */
if (returndummy != 0)
{
elx::log::error("Errors occurred");
return returndummy;
}
/** Get the result image */
resultImageContainer = transformix->GetModifiableResultImageContainer();
/** Stop timer and print it. */
totaltimer.Stop();
elx::log::info(std::ostringstream{} << "\nTransformix has finished at " << GetCurrentDateAndTime() << ".\n"
<< "Elapsed time: " << ConvertSecondsToDHMS(totaltimer.GetMean(), 1) << ".\n");
this->m_ResultImage = resultImageContainer->ElementAt(0);
/** Clean up. */
transformix = nullptr;
/** Exit and return the error code. */
return returndummy;
} // end TransformImage()
/**
* ******************* TransformImage ***********************
*/
int
TRANSFORMIX::TransformImage(ImagePointer inputImage,
ParameterMapType & parameterMap,
std::string outputPath,
bool performLogging,
bool performCout)
{
// Transform single parameter map to a one-sized vector of parameter maps and call other
// transform method.
std::vector<ParameterMapType> parameterMaps;
parameterMaps.push_back(parameterMap);
return TransformImage(inputImage, parameterMaps, outputPath, performLogging, performCout);
} // end TransformImage()
} // namespace transformix
|
