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Merge pull request #795 from I2PC/ef_local_volAdjustment
New program: Local volume adjustment
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src/xmipp/applications/programs/local_volume_adjust/local_volume_adjust_main.cpp
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| /*************************************************************************** | ||
| * | ||
| * Authors: Estrella Fernandez Gimenez ([email protected]) | ||
| * | ||
| * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC | ||
| * | ||
| * This program 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 2 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program 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 this program; if not, write to the Free Software | ||
| * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA | ||
| * 02111-1307 USA | ||
| * | ||
| * All comments concerning this program package may be sent to the | ||
| * e-mail address '[email protected]' | ||
| ***************************************************************************/ | ||
|
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| #include <reconstruction/local_volume_adjust.cpp> | ||
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| RUN_XMIPP_PROGRAM(ProgLocalVolumeAdjust) |
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src/xmipp/libraries/reconstruction/local_volume_adjust.cpp
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| /*************************************************************************** | ||
| * | ||
| * Authors: Estrella Fernandez Gimenez ([email protected]) | ||
| * | ||
| * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC | ||
| * | ||
| * This program 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 2 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program 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 this program; if not, write to the Free Software | ||
| * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA | ||
| * 02111-1307 USA | ||
| * | ||
| * All comments concerning this program package may be sent to the | ||
| * e-mail address '[email protected]' | ||
| ***************************************************************************/ | ||
|
|
||
| #include "local_volume_adjust.h" | ||
| #include "core/transformations.h" | ||
| #include <core/histogram.h> | ||
| #include <core/xmipp_fftw.h> | ||
| #include <core/xmipp_program.h> | ||
| #include <data/fourier_filter.h> | ||
|
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|
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| // Usage =================================================================== | ||
| void ProgLocalVolumeAdjust::defineParams() { | ||
| // Usage | ||
| addUsageLine("This program modifies a volume in order to adjust its intensity locally to a reference volume"); | ||
| // Parameters | ||
| addParamsLine("--i1 <volume> : Reference volume"); | ||
| addParamsLine("--i2 <volume> : Volume to modify"); | ||
| addParamsLine("[-o <structure=\"\">]\t: Volume 2 modified or volume difference"); | ||
| addParamsLine("\t: If no name is given, then output_volume.mrc"); | ||
| addParamsLine("--mask <mask=\"\"> : Mask for volume 1"); | ||
| addParamsLine("[--sampling <sampling=1>]\t: Sampling rate (A/pixel)"); | ||
| addParamsLine("[--neighborhood <n=5>]\t: side length (in Angstroms) of a square which will define the region of adjustment"); | ||
| addParamsLine("[--sub]\t: Perform the subtraction of the volumes. Output will be the difference"); | ||
| } | ||
|
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| // Read arguments ========================================================== | ||
| void ProgLocalVolumeAdjust::readParams() { | ||
| fnVol1 = getParam("--i1"); | ||
| fnVol2 = getParam("--i2"); | ||
| fnOutVol = getParam("-o"); | ||
| if (fnOutVol.isEmpty()) | ||
| fnOutVol = "output_volume.mrc"; | ||
| performSubtraction = checkParam("--sub"); | ||
| fnMask = getParam("--mask"); | ||
| sampling = getDoubleParam("--sampling"); | ||
| neighborhood = getIntParam("--neighborhood"); | ||
| } | ||
|
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| // Show ==================================================================== | ||
| void ProgLocalVolumeAdjust::show() const { | ||
| std::cout << "Input volume 1 (reference):\t" << fnVol1 << std::endl | ||
| << "Input volume 2:\t" << fnVol2 << std::endl | ||
| << "Input mask:\t" << fnMask << std::endl | ||
| << "Output:\t" << fnOutVol << std::endl; | ||
| } | ||
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| void ProgLocalVolumeAdjust::run() { | ||
| show(); | ||
| // Read inputs | ||
| Image<double> Vref; | ||
| Vref.read(fnVol1); | ||
| MultidimArray<double> &mVref=Vref(); | ||
| mVref.setXmippOrigin(); | ||
| Image<double> V; | ||
| V.read(fnVol2); | ||
| MultidimArray<double> &mV=V(); | ||
| mV.setXmippOrigin(); | ||
| Image<double> M; | ||
| M.read(fnMask); | ||
| MultidimArray<double> &mM=M(); | ||
| mM.setXmippOrigin(); | ||
| int iters; | ||
| int neighborhood_px; | ||
| neighborhood_px = round(neighborhood/sampling); | ||
| int cubic_neighborhood; | ||
| cubic_neighborhood = neighborhood_px*neighborhood_px*neighborhood_px; | ||
| iters = floor(ZYXSIZE(mV)/cubic_neighborhood); | ||
| int xsize = XSIZE(mV); | ||
| int ysize = YSIZE(mV); | ||
| int zsize = ZSIZE(mV); | ||
| int ki = 0; | ||
| int ii = 0; | ||
| int ji = 0; | ||
| for (size_t s=0; s < iters; s++) | ||
| { | ||
| sumV_Vref = 0; | ||
| sumVref2 = 0; | ||
| // Go over each subvolume | ||
| for (k=0; k < neighborhood_px; ++k) | ||
| { | ||
| for (i=0; i < neighborhood_px; ++i) | ||
| { | ||
| for (j=0; j < neighborhood_px; ++j) | ||
| { | ||
| if (DIRECT_A3D_ELEM(mM,ki+k,ii+i,ji+j) == 1) // Condition to check if we are inside mask | ||
| { | ||
| sumV_Vref += DIRECT_A3D_ELEM(mV,ki+k,ii+i,ji+j)*DIRECT_A3D_ELEM(mVref,ki+k,ii+i,ji+j); | ||
| sumVref2 += DIRECT_A3D_ELEM(mVref,ki+k,ii+i,ji+j)*DIRECT_A3D_ELEM(mVref,ki+k,ii+i,ji+j); | ||
| } | ||
| else | ||
| { | ||
| sumV_Vref += 0; | ||
| sumVref2 += 0; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| // Compute constant (c) | ||
| if (sumVref2 == 0) | ||
| c = 0; | ||
| else | ||
| c = sumV_Vref/sumVref2; | ||
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| // Apply adjustment TODO: per regions | ||
| for (k=0; k < neighborhood_px; ++k) | ||
| { | ||
| for (i=0; i < neighborhood_px; ++i) | ||
| { | ||
| for (j=0; j < neighborhood_px; ++j) | ||
| { | ||
| if (DIRECT_A3D_ELEM(mM,ki+k,ii+i,ji+j) == 1) // Condition to check if we are inside mask | ||
| { | ||
| DIRECT_A3D_ELEM(mV,ki+k,ii+i,ji+j) /= c; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| // Take the index to start in next subvolume | ||
| if (ji < (xsize-neighborhood_px)) | ||
| ji += neighborhood_px; | ||
| else | ||
| ji = 0; | ||
| if (ji == 0) | ||
| { | ||
| if (ii < (ysize-neighborhood_px)) | ||
| ii += neighborhood_px; | ||
| else | ||
| ii = 0; | ||
| } | ||
| if (ii == 0 && ji == 0) | ||
| { | ||
| if (ki < (zsize-neighborhood_px)) | ||
| ki += neighborhood_px; | ||
| else | ||
| ki = 0; | ||
| } | ||
| } | ||
| // The output of this program is a modified version of V (V') | ||
| if (performSubtraction) // Or the output is the subtraction V = Vref - V | ||
| { | ||
| FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV) | ||
| DIRECT_MULTIDIM_ELEM(mV, n) = DIRECT_MULTIDIM_ELEM(mVref, n) * (1 - DIRECT_MULTIDIM_ELEM(mM, n)) | ||
| + (DIRECT_MULTIDIM_ELEM(mVref, n) - std::min(DIRECT_MULTIDIM_ELEM(mV, n), DIRECT_MULTIDIM_ELEM(mVref, n))) | ||
| * DIRECT_MULTIDIM_ELEM(mM, n); | ||
| } | ||
| V.write(fnOutVol); | ||
| } |
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| /*************************************************************************** | ||
| * | ||
| * Authors: Estrella Fernandez Gimenez [email protected] (2023) | ||
| * | ||
| * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC | ||
| * | ||
| * This program 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 2 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program 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 this program; if not, write to the Free Software | ||
| * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA | ||
| * 02111-1307 USA | ||
| * | ||
| * All comments concerning this program package may be sent to the | ||
| * e-mail address '[email protected]' | ||
| ***************************************************************************/ | ||
| #ifndef LIBRARIES_RECONSTRUCTION_LOCAL_VOLUME_ADJUST_H_ | ||
| #define LIBRARIES_RECONSTRUCTION_LOCAL_VOLUME_ADJUST_H_ | ||
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| #include "core/xmipp_program.h" | ||
| #include <core/xmipp_fftw.h> | ||
| #include <data/fourier_filter.h> | ||
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| class ProgLocalVolumeAdjust: public XmippProgram { | ||
| /*This class contains methods that are use to adjust an input volume (V) to a another reference volume (V1) locally | ||
| by using a least squares solution in a sliding window*/ | ||
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| private: | ||
| FileName fnVol2; | ||
| FileName fnVol1; | ||
| FileName fnOutVol; | ||
| FileName fnMask; | ||
| bool performSubtraction; | ||
| int neighborhood; | ||
| float sampling; | ||
| double c; | ||
| double sumV_Vref; | ||
| double sumVref2; | ||
| size_t k; | ||
| size_t j; | ||
| size_t i; | ||
|
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| /// Read arguments | ||
| void readParams() override; | ||
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| /// Show | ||
| void show() const override; | ||
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| /// Define parameters | ||
| void defineParams() override; | ||
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| /** Run */ | ||
| void run() override; | ||
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| }; | ||
| //@} | ||
| #endif |