Xmipp
v3.23.11-Nereus
xmipp
legacy
libraries
reconstruction
volume_pca.h
Go to the documentation of this file.
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/***************************************************************************
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*
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* Authors: Carlos Oscar coss@cnb.csic.es (2015)
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*
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* Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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* 02111-1307 USA
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*
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* All comments concerning this program package may be sent to the
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* e-mail address 'xmipp@cnb.csic.es'
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***************************************************************************/
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#ifndef _PROG_VOLUME_PCA
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#define _PROG_VOLUME_PCA
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#include "
core/xmipp_image.h
"
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#include "
core/xmipp_program.h
"
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#include "
core/metadata_vec.h
"
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#include "
data/basic_pca.h
"
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#include "
data/mask.h
"
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class
ProgVolumePCA
:
public
XmippProgram
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{
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public
:
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FileName
fnVols
;
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FileName
fnVolsOut
;
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int
NPCA
;
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Mask
mask
;
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FileName
fnBasis
;
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StringVector
listOfPercentiles
;
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FileName
fnAvgVol
;
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FileName
fnOutStack
;
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public
:
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// Metadata with volumes
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MetaDataVec
mdVols
;
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// Input volume
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Image<double>
V
;
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// PCA analyzer
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PCAMahalanobisAnalyzer
analyzer
;
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public
:
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void
readParams
();
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void
show
()
const
;
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void
defineParams
();
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void
produce_side_info
();
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void
run
();
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};
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#endif
PCAMahalanobisAnalyzer
Definition:
basic_pca.h:62
ProgVolumePCA::show
void show() const
Show.
Definition:
volume_pca.cpp:46
ProgVolumePCA
Definition:
volume_pca.h:38
metadata_vec.h
Mask
Definition:
mask.h:360
mask.h
ProgVolumePCA::fnVols
FileName fnVols
Input set of volumes.
Definition:
volume_pca.h:42
ProgVolumePCA::mdVols
MetaDataVec mdVols
Definition:
volume_pca.h:59
FileName
Definition:
xmipp_filename.h:65
StringVector
std::vector< String > StringVector
Definition:
xmipp_strings.h:35
ProgVolumePCA::produce_side_info
void produce_side_info()
Definition:
volume_pca.cpp:79
ProgVolumePCA::fnOutStack
FileName fnOutStack
Output PCA stack.
Definition:
volume_pca.h:56
MetaDataVec
Definition:
metadata_vec.h:46
ProgVolumePCA::analyzer
PCAMahalanobisAnalyzer analyzer
Definition:
volume_pca.h:65
xmipp_image.h
xmipp_program.h
basic_pca.h
ProgVolumePCA::fnBasis
FileName fnBasis
Output basis.
Definition:
volume_pca.h:50
ProgVolumePCA::defineParams
void defineParams()
Define parameters.
Definition:
volume_pca.cpp:65
ProgVolumePCA::readParams
void readParams()
Read arguments.
Definition:
volume_pca.cpp:31
ProgVolumePCA::mask
Mask mask
Mask.
Definition:
volume_pca.h:48
ProgVolumePCA::V
Image< double > V
Definition:
volume_pca.h:62
ProgVolumePCA::NPCA
int NPCA
Number of PCA bases.
Definition:
volume_pca.h:46
ProgVolumePCA::run
void run()
Definition:
volume_pca.cpp:95
Image< double >
ProgVolumePCA::fnAvgVol
FileName fnAvgVol
Average volume.
Definition:
volume_pca.h:54
ProgVolumePCA::fnVolsOut
FileName fnVolsOut
Output set of volumes.
Definition:
volume_pca.h:44
ProgVolumePCA::listOfPercentiles
StringVector listOfPercentiles
List of percentiles to generate volumes.
Definition:
volume_pca.h:52
XmippProgram
Definition:
xmipp_program.h:52
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