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
|
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: itkTransformFileReader.cxx,v $
Language: C++
Date: $Date: 2007-08-09 15:15:39 $
Version: $Revision: 1.24 $
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkTransformFileReader_cxx
#define __itkTransformFileReader_cxx
#include "itkTransformFileReader.h"
#include "itkTransformBase.h"
#include "itkTransformFactoryBase.h"
#include <itksys/ios/sstream>
namespace itk
{
std::string trim(std::string const& source, char const* delims = " \t\r\n") {
std::string result(source);
std::string::size_type index = result.find_last_not_of(delims);
if(index != std::string::npos)
{
result.erase(++index);
}
index = result.find_first_not_of(delims);
if(index != std::string::npos)
{
result.erase(0, index);
}
else
{
result.erase();
}
return result;
}
/** Constructor */
TransformFileReader
::TransformFileReader()
{
m_FileName = "";
TransformFactoryBase::RegisterDefaultTransforms();
}
/** Destructor */
TransformFileReader
::~TransformFileReader()
{
}
/** Update the Reader */
void TransformFileReader
::Update()
{
TransformPointer transform;
std::ifstream in;
in.open ( m_FileName.c_str(), std::ios::in | std::ios::binary );
if( in.fail() )
{
in.close();
itkExceptionMacro ( "The file could not be opened for read access "
<< std::endl << "Filename: \"" << m_FileName << "\"" );
}
OStringStream InData;
// in.get ( InData );
std::filebuf *pbuf;
pbuf=in.rdbuf();
// get file size using buffer's members
int size=pbuf->pubseekoff (0,std::ios::end,std::ios::in);
pbuf->pubseekpos (0,std::ios::in);
// allocate memory to contain file data
char* buffer=new char[size+1];
// get file data
pbuf->sgetn (buffer,size);
buffer[size]='\0';
itkDebugMacro ( "Read file transform Data" );
InData << buffer;
delete[] buffer;
std::string data = InData.str();
in.close();
// Read line by line
vnl_vector<double> VectorBuffer;
std::string::size_type position = 0;
Array<double> TmpParameterArray;
Array<double> TmpFixedParameterArray;
TmpParameterArray.clear();
TmpFixedParameterArray.clear();
bool haveFixedParameters = false;
bool haveParameters = false;
while ( position < data.size() )
{
// Find the next string
std::string::size_type end = data.find ( "\n", position );
std::string line = trim ( data.substr ( position, end - position ) );
position = end+1;
itkDebugMacro ("Found line: \"" << line << "\"" );
if ( line.length() == 0 )
{
continue;
}
if ( line[0] == '#' || std::string::npos == line.find_first_not_of ( " \t" ) )
{
// Skip lines beginning with #, or blank lines
continue;
}
// Get the name
end = line.find ( ":" );
if ( end == std::string::npos )
{
// Throw an error
itkExceptionMacro ( "Tags must be delimited by :" );
}
std::string Name = trim ( line.substr ( 0, end ) );
std::string Value = trim ( line.substr ( end + 1, line.length() ) );
// Push back
itkDebugMacro ( "Name: \"" << Name << "\"" );
itkDebugMacro ( "Value: \"" << Value << "\"" );
itksys_ios::istringstream parse ( Value );
VectorBuffer.clear();
if ( Name == "Transform" )
{
// Instantiate the transform
itkDebugMacro ( "About to call ObjectFactory" );
LightObject::Pointer i;
i = ObjectFactoryBase::CreateInstance ( Value.c_str() );
itkDebugMacro ( "After call ObjectFactory");
TransformType* ptr = dynamic_cast<TransformBase*> ( i.GetPointer() );
if ( ptr == NULL )
{
OStringStream msg;
msg << "Could not create an instance of " << Value << std::endl
<< "The usual cause of this error is not registering the "
<< "transform with TransformFactory" << std::endl;
msg << "Currently registered Transforms: " << std::endl;
std::list<std::string> names = TransformFactoryBase::GetFactory()->GetClassOverrideWithNames();
std::list<std::string>::iterator it;
for ( it = names.begin(); it != names.end(); it++ )
{
msg << "\t\"" << *it << "\"" << std::endl;
}
itkExceptionMacro ( << msg.str() );
return;
}
transform = ptr;
m_TransformList.push_back ( transform );
}
else if ( Name == "Parameters" || Name == "FixedParameters" )
{
VectorBuffer.clear();
// Read them
parse >> VectorBuffer;
itkDebugMacro ( "Parsed: " << VectorBuffer );
if ( Name == "Parameters" )
{
TmpParameterArray = VectorBuffer;
itkDebugMacro ( "Setting Parameters: " << TmpParameterArray );
if ( haveFixedParameters )
{
transform->SetFixedParameters ( TmpFixedParameterArray );
itkDebugMacro ( "Set Transform Fixed Parameters" );
transform->SetParametersByValue ( TmpParameterArray );
itkDebugMacro ( "Set Transform Parameters" );
TmpParameterArray.clear();
TmpFixedParameterArray.clear();
haveFixedParameters = false;
haveParameters = false;
}
else
{
haveParameters = true;
}
}
else if ( Name == "FixedParameters" )
{
TmpFixedParameterArray = VectorBuffer;
itkDebugMacro ( "Setting Fixed Parameters: " << TmpFixedParameterArray );
if ( !transform )
{
itkExceptionMacro ( "Please set the transform before parameters or fixed parameters" );
}
if ( haveParameters )
{
transform->SetFixedParameters ( TmpFixedParameterArray );
itkDebugMacro ( "Set Transform Fixed Parameters" );
transform->SetParametersByValue ( TmpParameterArray );
itkDebugMacro ( "Set Transform Parameters" );
TmpParameterArray.clear();
TmpFixedParameterArray.clear();
haveFixedParameters = false;
haveParameters = false;
}
else
{
haveFixedParameters = true;
}
}
}
}
}
} // namespace itk
#endif
|
