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
|
/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2013 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit 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 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit 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 the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 386 $
//
// $LastChangedDate: 2009-08-04 14:31:09 -0700 (Tue, 04 Aug 2009) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkConsole.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <Base/cmtkTypedArray.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkSplineWarpXform.h>
#include <Base/cmtkDeformationField.h>
#include <Base/cmtkXformList.h>
#include <IO/cmtkVolumeIO.h>
#include <IO/cmtkXformListIO.h>
#ifdef CMTK_USE_GCD
# include <dispatch/dispatch.h>
#endif
bool WarpOnly = false;
namespace
cmtk
{
/// Mode for scalar value extraction.
typedef enum {
/// Extract x component.
X2S_EXTRACT_X,
/// Extract y component.
X2S_EXTRACT_Y,
/// Extract z component.
X2S_EXTRACT_Z,
/// Extract Jacobian determinant.
X2S_MAGNITUDE
} XformToScalarMode;
}
/// Mode for scalar value extraction.
cmtk::XformToScalarMode Mode = cmtk::X2S_MAGNITUDE;
/// Data type for scalar data.
cmtk::ScalarDataType DataType = cmtk::TYPE_DOUBLE;
std::string InputGridPath;
std::string OutImagePath;
std::vector<std::string> InputXformPaths;
int
doMain ( const int argc, const char* argv[] )
{
cmtk::Threads::GetNumberOfThreads();
try
{
cmtk::CommandLine cl( cmtk::CommandLine::PROPS_XML );
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Extract scalar measures from transformations and deformation fields" );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool extracts scalar measures from transformations and deformation fields, sampled at grid locations, and writes the results to an image. "
"Examples of supported scalar measures are: x,y,z component of the transformation, magnitude of the transformation, and Jacobian determinants." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_CATEG, "CMTK.Data Processing" );
typedef cmtk::CommandLine::Key Key;
cl.BeginGroup( "operation", "Operating Options" );
cmtk::CommandLine::EnumGroup<cmtk::XformToScalarMode>::SmartPtr modeGroup = cl.AddEnum( "mode", &Mode, "Mode of operation: type of scalar measure to be extracted." );
modeGroup->AddSwitch( Key( "x-component" ), cmtk::X2S_EXTRACT_X, "X component of transformation vector." );
modeGroup->AddSwitch( Key( "y-component" ), cmtk::X2S_EXTRACT_Y, "Y component of transformation vector." );
modeGroup->AddSwitch( Key( "z-component" ), cmtk::X2S_EXTRACT_Z, "Z component of transformation vector." );
modeGroup->AddSwitch( Key( "magnitude" ), cmtk::X2S_MAGNITUDE, "Magnitude of the transformation vector." );
cl.AddSwitch( Key( 'w', "warp-only" ), &WarpOnly, true, "Output warp component only (excluding affine)." );
cl.EndGroup();
cl.BeginGroup( "output", "Output Options" );
cmtk::CommandLine::EnumGroup<cmtk::ScalarDataType>::SmartPtr
typeGroup = cl.AddEnum( "type", &DataType, "Scalar data type of output image." );
typeGroup->AddSwitch( Key( "float" ), cmtk::TYPE_FLOAT, "Single-precision float." );
typeGroup->AddSwitch( Key( "double" ), cmtk::TYPE_DOUBLE, "Double-precision float." );
cl.AddOption( Key( 'o', "output" ), &OutImagePath, "Output path for image with extracted scalar data." )->SetProperties( cmtk::CommandLine::PROPS_IMAGE | cmtk::CommandLine::PROPS_OUTPUT );
cl.AddParameter( &InputGridPath, "InputImage", "Input grid path" )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.AddParameterVector( &InputXformPaths, "XformList", "List of concatenated transformations. Insert '--inverse' to use the inverse of the transformation listed next. "
"(If the first transformation in the sequence is inverted, then '--inverse' must be preceded by '--', i.e., use '-- --inverse xform.path')." )->SetProperties( cmtk::CommandLine::PROPS_XFORM );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::UniformVolume::SmartPtr scalarImage( cmtk::VolumeIO::ReadGridOriented( InputGridPath ) );
if ( ! scalarImage )
{
cmtk::StdErr << "Could not read grid from image " << InputGridPath << "\n";
throw cmtk::ExitException(1);
}
scalarImage->CreateDataArray( DataType );
const cmtk::XformList xformList = cmtk::XformListIO::MakeFromStringList( InputXformPaths );
const cmtk::XformList& xformListRef = xformList; // workaround for GCD segfaults
const cmtk::XformList xformListAffine = xformList.MakeAllAffine();
const cmtk::XformList& xformListAffineRef = xformListAffine; // workaround for GCD segfaults
cmtk::UniformVolume* image = scalarImage.GetPtr();
const cmtk::DataGrid::IndexType& dims = image->GetDims();
#ifdef CMTK_USE_GCD
dispatch_apply( dims[2], dispatch_get_global_queue(0, 0), ^(size_t z){
#else
#pragma omp parallel for
for ( int z = 0; z < dims[2]; ++z )
{
#endif
size_t offset = z * dims[0] * dims[1];
for ( int y = 0; y < dims[1]; ++y )
{
for ( int x = 0; x < dims[0]; ++x, ++offset )
{
// Get current grid location.
cmtk::UniformVolume::CoordinateVectorType v = scalarImage->GetGridLocation( x, y, z );
const cmtk::UniformVolume::CoordinateVectorType v0( v );
// Apply transformation and subtract original coordinate
if ( xformListRef.ApplyInPlace( v ) )
{
v -= v0;
// Is this is a B-spline warp and we're only interesting in the nonrigid component?
if ( WarpOnly )
{
// Transform current location also using affine transformation
cmtk::Vector3D vAffine( v0 );
if ( ! xformListAffineRef.ApplyInPlace( vAffine ) )
{
cmtk::StdErr << "ERROR: applying affine transformation sequence failed.\n";
throw cmtk::ExitException( 1 );
}
vAffine -= v0;
// subtract affine-transformed from total transformed
v -= vAffine;
}
switch ( Mode )
{
case cmtk::X2S_EXTRACT_X: image->SetDataAt( v[0], offset ); break;
case cmtk::X2S_EXTRACT_Y: image->SetDataAt( v[1], offset ); break;
case cmtk::X2S_EXTRACT_Z: image->SetDataAt( v[2], offset ); break;
case cmtk::X2S_MAGNITUDE: image->SetDataAt( v.RootSumOfSquares(), offset ); break;
default: break;
}
}
else
{
image->GetData()->SetPaddingAt( offset );
}
}
}
}
#ifdef CMTK_USE_GCD
);
#endif
if ( !OutImagePath.empty() )
{
cmtk::VolumeIO::Write( *scalarImage, OutImagePath );
}
return 0;
}
#include "cmtkSafeMain"
|
