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
|
/*
//
// Copyright 1997-2010 Torsten Rohlfing
//
// Copyright 2004-2010, 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: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include "cmtkSimpleLevelsetCommandLineBase.h"
#include <System/cmtkConsole.h>
#include <IO/cmtkVolumeIO.h>
cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase()
: m_ScaleInitialSphere( 1.0 ),
m_FilterSigma( 2.0 ),
m_TimeDelta( 0.1 ),
m_LevelsetThreshold( 1.0 ),
m_NumberOfIterations( 100 ),
m_ForceIterations( false ),
m_Binarize( false ),
m_CommandLine( cmtk::CommandLine::PROPS_XML )
{
#ifdef CMTK_USE_SQLITE
this->m_UpdateDB = NULL;
#endif
this->m_CommandLine.SetProgramInfo( CommandLine::PRG_TITLE, "Levelset segmentation" );
this->m_CommandLine.SetProgramInfo( CommandLine::PRG_DESCR, "Levelset-type segmentation of foreground/background using minimum regional variance energy" );
this->m_CommandLine.SetProgramInfo( CommandLine::PRG_CATEG, "CMTK.Segmentation" );
typedef CommandLine::Key Key;
this->m_CommandLine.AddSwitch( Key( 'b', "binarize" ), &this->m_Binarize, true, "Binarize levelset and write as byte mask, rather than write floating-point levelset function itself." );
this->m_CommandLine.BeginGroup( "Levelset Initialization", "These parameters control the initialization of the levelset function" )->SetProperties( CommandLine::PROPS_ADVANCED );
this->m_CommandLine.AddOption( Key( "scale-initial-sphere" ), &this->m_ScaleInitialSphere, "Scale factor to reduce or increase the size of the initial foreground region sphere." );
this->m_CommandLine.EndGroup();
this->m_CommandLine.BeginGroup( "Levelset Evolution Parameters", "These parameters control the evolution of the levelset function" )->SetProperties( CommandLine::PROPS_ADVANCED );
this->m_CommandLine.AddOption( Key( 'n', "iterations" ), &this->m_NumberOfIterations, "Maximum number of iterations" );
this->m_CommandLine.AddSwitch( Key( 'f', "force-iterations" ), &this->m_ForceIterations, true, "Force given number of iterations, even when convergence has been detected" );
this->m_CommandLine.AddOption( Key( 's', "filter-sigma" ), &this->m_FilterSigma, "Gaussian filter sigma in world coordinate units (e.g., mm)" );
this->m_CommandLine.AddOption( Key( 'd', "delta" ), &this->m_TimeDelta, "Time constant for levelset evolution; must be > 0; larger is faster" );
this->m_CommandLine.AddOption( Key( 't', "levelset-threshold" ), &this->m_LevelsetThreshold, "Levelset threshold: levelset function is truncated at +/- this value" );
this->m_CommandLine.EndGroup();
#ifdef CMTK_USE_SQLITE
this->m_CommandLine.BeginGroup( "Database", "Image/Transformation Database" );
this->m_CommandLine.AddOption( Key( "db" ), &this->m_UpdateDB, "Path to image/transformation database that should be updated with the newly created image." );
this->m_CommandLine.EndGroup();
#endif
this->m_CommandLine.AddParameter( &this->m_InFile, "InputImage", "Input image path" )->SetProperties( CommandLine::PROPS_IMAGE );
this->m_CommandLine.AddParameter( &this->m_OutFile, "OutputImage", "Output image path" )->SetProperties( CommandLine::PROPS_IMAGE | CommandLine::PROPS_LABELS | CommandLine::PROPS_OUTPUT );
}
int
cmtk::SimpleLevelsetCommandLineBase::Init( const int argc, const char* argv[] )
{
try
{
this->m_CommandLine.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& ex )
{
cmtk::StdErr << ex;
return 1;
}
this->m_Volume = cmtk::VolumeIO::ReadOriented( this->m_InFile );
if ( !this->m_Volume )
return 1;
return 0;
}
|
