diff --git a/.gitignore b/.gitignore index d42be9d74..3ed41e493 100644 --- a/.gitignore +++ b/.gitignore @@ -46,14 +46,18 @@ gmon.out .directory .settings -/config/*.conf -/bin -/lib -/models/* -/install/xmipp.conf -/tests/data +# ignore everything in src folder +/build/* +/src/* +# except xmipp folder +!/src/xmipp/* + +/src/xmipp/bin +/src/xmipp/lib +/src/xmipp/models/* +/src/xmipp/tests/data # Ignore version file .devel_version -/Debug/ -applications/programs/version +/src/xmipp/Debug/ +/src/xmipp/applications/programs/version diff --git a/.travis.yml b/.travis.yml index 40b4299db..19d9e3e4b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,7 +18,6 @@ before_install: - source scripts/install_cuda_travis.sh script: - | - python ./scripts/travis_before_script.py && \ build-wrapper-linux-x86-64 --out-dir bw-outputs ./xmipp && \ sonar-scanner && \ ccache -s diff --git a/README.md b/README.md index ee2e04e84..d468b673d 100644 --- a/README.md +++ b/README.md @@ -3,30 +3,30 @@ [![Technical debt](https://sonarcloud.io/api/project_badges/measure?project=Xmipp&metric=sqale_index)](https://sonarcloud.io/component_measures?id=Xmipp&metric=sqale_index) [![Bugs](https://sonarcloud.io/api/project_badges/measure?project=Xmipp&metric=bugs)](https://sonarcloud.io/project/issues?id=Xmipp&resolved=false&types=BUG) ---> -# xmipp +# Xmipp -If you want to use it as a **Scipion package for production proposes**, please visit [this](https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins). +Welcome to Xmipp. Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy. -If you want to use it as a **Scipion package for devel proposes**, please visit [this](https://github.com/I2PC/xmipp/wiki/Xmipp-bundle-installtion). -To install Xmipp in a certain place (e.g. in the `xmipp-bundle` directory) follow this instructions: +## Getting started +**Xmipp as a Scipion package** -``` -mkdir xmipp-bundle -cd xmipp-bundle -wget https://raw.githubusercontent.com/I2PC/xmipp/devel/xmipp -O xmipp -chmod 755 xmipp -./xmipp all N=4 br=devel -ln -sf src/xmipp/xmipp xmipp # optional, but VERY RECOMMENDED, to have always the last version of the xmipp script -``` -where you can replace `N=4` for `N=#processors` and `br=master` for `br=devel` if you want the development version of Xmipp. You can see the whole usage of the xmipp script with `./xmipp --help` +The recommended way to use Xmipp is via [Scipion](https://scipion-em.github.io/docs/index.html). +It can be easily installed using the [Plugin manager](https://scipion-em.github.io/docs/docs/user/plugin-manager.html). +**Xmipp as a standalone bundle (useful for developers)** -### Using Scipion libraries +Start by cloning the repository from GitHub. -If you want xmipp to pick up SCIPION libraries define SCIPION_HOME=\ +In case you don't want to import settings from Scipion, set XMIPP_NOSCIPION flag to true (`export XMIPP_NOSCIPION=True`). Otherwise, define SCIPION_HOME=\ -**Note**: If some program (like `nvcc`) is not visible from your terminal (`which nvcc` returns nothing), but it is visible by Scipion (`$SCIPION_HOME/scipion run which nvcc` returns the nvcc path). Then, you can use Scipion as wrapper to install Xmipp: -``` -$SCIPION_HOME/scipion run ./xmipp all N=8 br=devel -``` +Next, run `xmipp` script in the root folder (it might be necessary to add execute permission via `chmod +x xmipp`). This will checkout additional repositories and build Xmipp for you. + +You can see the whole usage of the script with `./xmipp --help`. The most useful options are `br=branch_name` to select a specific branch to be checkout-ed, and `N=#processors` to use for the build. + + +## FAQ + +If you want to use your specific version of Xmipp as a Scipion plugin, see following wiki [page](https://github.com/I2PC/xmipp/wiki/Migrating-branches-from-nonPluginized-Scipion-to-the-new-Scipion-Xmipp-structure#xmipp-plugin). + +Recently we have changed the directory structure. See this wiki [page](https://github.com/I2PC/xmipp/wiki/Transfer-to-new-directory-structure) for more information. diff --git a/applications/programs/angular_sph_alignment/angular_sph_alignment_main.cpp b/applications/programs/angular_sph_alignment/angular_sph_alignment_main.cpp deleted file mode 100644 index e3e812bd4..000000000 --- a/applications/programs/angular_sph_alignment/angular_sph_alignment_main.cpp +++ /dev/null @@ -1,28 +0,0 @@ -/*************************************************************************** - * - * Authors: Carlos Oscar S. Sorzano (coss@cnb.csic.es) - * - * 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 'xmipp@cnb.csic.es' - ***************************************************************************/ - -#include - -RUN_XMIPP_PROGRAM(ProgAngularSphAlignment) diff --git a/applications/programs/image_odd_even/image_odd_even_main.cpp b/applications/programs/image_odd_even/image_odd_even_main.cpp deleted file mode 100644 index 527753f4a..000000000 --- a/applications/programs/image_odd_even/image_odd_even_main.cpp +++ /dev/null @@ -1,33 +0,0 @@ -/*************************************************************************** - * Authors: Jose Luis Vilas (jlvilas@cnb.csic.es) - * - * - * 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 'xmipp@cnb.csic.es' - ***************************************************************************/ - -#include - -int main(int argc, char **argv) -{ - ProgOddEven program; - program.read(argc, argv); - return program.tryRun(); -} diff --git a/applications/programs/mpi_angular_sph_alignment/mpi_angular_sph_alignment_main.cpp b/applications/programs/mpi_angular_sph_alignment/mpi_angular_sph_alignment_main.cpp deleted file mode 100644 index 5eb624abd..000000000 --- a/applications/programs/mpi_angular_sph_alignment/mpi_angular_sph_alignment_main.cpp +++ /dev/null @@ -1,153 +0,0 @@ -/*************************************************************************** - * - * Authors: Carlos Oscar Sanchez Sorzano coss@cnb.csic.es - * - * 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 'xmipp@cnb.uam.es' - ***************************************************************************/ - -#include -#include -#include - - -class MpiProgAngularSphAlignment: public ProgAngularSphAlignment, public MpiMetadataProgram -{ - -//AJ new -private: - MpiFileMutex *fileMutex; -//END AJ - -public: - void defineParams() - { - ProgAngularSphAlignment::defineParams(); - MpiMetadataProgram::defineParams(); - } - void readParams() - { - MpiMetadataProgram::readParams(); - ProgAngularSphAlignment::readParams(); - } - void read(int argc, char **argv, bool reportErrors = true) - { - //AJ new - fileMutex = new MpiFileMutex(node); - //END AJ - MpiMetadataProgram::read(argc,argv); - } - void showProgress() - { - if (node->rank==1) - { - time_bar_done=first+1; - ProgAngularSphAlignment::showProgress(); - } - } - /*void preProcess() - { - ProgAngularSphAlignment::preProcess(); - MetaData &mdIn = *getInputMd(); - mdIn.addLabel(MDL_GATHER_ID); - mdIn.fillLinear(MDL_GATHER_ID,1,1); - createTaskDistributor(mdIn, blockSize); - }*/ - void createWorkFiles() - { - //Master node should prepare some stuff before start working - MetaData &mdIn = *getInputMd(); //get a reference to input metadata - - if (node->isMaster()) - { - ProgAngularSphAlignment::createWorkFiles(); - mdIn.write(fnOutDir + "/sphTodo.xmd"); - } - node->barrierWait();//Sync all before start working - mdIn.read(fnOutDir + "/sphTodo.xmd"); - mdIn.findObjects(imgsId);//get objects ids - distributor = new MpiTaskDistributor(mdIn.size(), 1, node); - } - void startProcessing() - { - if (node->rank==1) - { - verbose=1; - ProgAngularSphAlignment::startProcessing(); - } - node->barrierWait(); - } - bool getImageToProcess(size_t &objId, size_t &objIndex) - { - //return getTaskToProcess(objId, objIndex); - size_t first, last; - bool moreTasks = distributor->getTasks(first, last); - - if (moreTasks) - { - time_bar_done = first + 1; - objIndex = first; - objId = imgsId[first]; - return true; - } - time_bar_done = getInputMd()->size(); - objId = BAD_OBJID; - objIndex = BAD_INDEX; - return false; - } - /*void gatherMetadatas() - { - node->gatherMetadatas(*getOutputMd(), fn_out); - MetaData MDaux; - MDaux.sort(*getOutputMd(), MDL_GATHER_ID); - MDaux.removeLabel(MDL_GATHER_ID); - *getOutputMd()=MDaux; - } - void finishProcessing() - { - gatherMetadatas(); - if (node->isMaster()) - ProgAngularSphAlignment::finishProcessing(); - }*/ - void finishProcessing() - { - distributor->wait(); - - //All nodes wait for each other - node->barrierWait(); - if (node->isMaster()) - ProgAngularSphAlignment::finishProcessing(); - node->barrierWait(); - } - //AJ new - void writeImageParameters(const FileName &fnImg) - { - fileMutex->lock(); - ProgAngularSphAlignment::writeImageParameters(fnImg); - fileMutex->unlock(); - } - //END AJ - void wait() - { - distributor->wait(); - } -}; - -RUN_XMIPP_PROGRAM(MpiProgAngularSphAlignment) diff --git a/applications/scripts/deep_micrograph_cleaner/deep_micrograph_cleaner.py b/applications/scripts/deep_micrograph_cleaner/deep_micrograph_cleaner.py deleted file mode 100755 index d8b3e51c3..000000000 --- a/applications/scripts/deep_micrograph_cleaner/deep_micrograph_cleaner.py +++ /dev/null @@ -1,165 +0,0 @@ -#!/usr/bin/env python2 -"""/*************************************************************************** - * - * Authors: Ruben Sanchez Garcia rsanchez@cnb.csic.es - * - * 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 'xmipp@cnb.csic.es' - ***************************************************************************/ -""" - -import os -import sys -import xmipp_base -from xmipp3 import Plugin -import pyworkflow.em.metadata as md - -BAD_IMPORT_MSG=''' -Error, tensorflow/keras is probably not installed. Install it with:\n ./scipion installb deepLearnigToolkit -If gpu version of tensorflow desired, install cuda 8.0 or cuda 9.0 -We will try to automatically install cudnn, if unsucesfully, install cudnn and add to LD_LIBRARY_PATH -add to SCIPION_DIR/config/scipion.conf -CUDA = True -CUDA_VERSION = 8.0 or 9.0 -CUDA_HOME = /path/to/cuda-%(CUDA_VERSION) -CUDA_BIN = %(CUDA_HOME)s/bin -CUDA_LIB = %(CUDA_HOME)s/lib64 -CUDNN_VERSION = 6 or 7 -''' - -class ScriptMicrographCleanerEm(xmipp_base.XmippScript): - def __init__(self): - - xmipp_base.XmippScript.__init__(self) - - def getDoubleParamWithDefault(self, paramName, conditionFun= lambda x: False, defaultVal=None): - if self.checkParam(paramName): - x = self.getDoubleParam(paramName) - if conditionFun(x): - return defaultVal - return x - else: - return defaultVal - - def defineParams(self): - self.addUsageLine('Compute goodness score for picked coordinates. Rule out bad coordinates') - ## params - self.addParamsLine(' -i : metadata containing the micrograph(s) '+ - 'filenames where coordinates were picked (.mrc or .tif).\n') - - self.addParamsLine(' [ -c ] : input coordinates directory (.pos or tab separated x y). Filenames '+ - 'must agree with input micrographs except for file extension.') - - self.addParamsLine(' [ -o ] : output coordinates directory.') - self.addParamsLine(' [ -d ] : (optional) deep learning model filename. If not provided, default model will be used') - self.addParamsLine('-b : particles box size in pixels') - self.addParamsLine('-s : (optional) micrograph downsampling factor to scale coordinates, Default no scaling') - self.addParamsLine(' [ --deepThr ]: (optional) deep learning threshold to rule out a coordinate. The smaller the treshold '+ - 'the more coordiantes will be rule out. Ranges 0..1. Recommended 0.8') - self.addParamsLine(' [--sizeThr ]: Failure threshold. Fraction of the micrograph predicted as contamination to ignore predictions. '+ - '. Ranges 0..1. Default 0.8') - self.addParamsLine('[ --predictedMaskDir ] : directory to store the predicted masks. If a given mask already existed, it will be used instead'+ - ' of a new prediction') - self.addParamsLine('[ -g ] : GPU ids to employ. Comma separated list. E.g. "0,1". Default 0. ' - 'use -1 for CPU-only computation or "all" to use all devices found in CUDA_VISIBLE_DEVICES (option for slurm)') - - ## examples - self.addExampleLine('xmipp_deep_micrograph_cleaner -c path/to/inputCoords/ -o path/to/outputCoords -b $BOX_SIXE -i /path/to/micrographs/') - - def run(self): - - args={} - gpusToUse="0" - if self.checkParam('-g'): - gpusToUse= self.getParam('-g') - if "None" in gpusToUse or "-1" in gpusToUse: - gpusToUse=None - args["gpus"]=gpusToUse - - updateEnviron(gpusToUse) - - if self.checkParam('-i'): - mdObj= md.MetaData(os.path.expanduser( self.getParam('-i'))) - args["inputMicsPath"]= [] - for objId in mdObj: - args["inputMicsPath"]+= [mdObj.getValue(md.MDL_IMAGE, objId)] - else: - raise Exception("Error, input micrographs fnames are requried as argument") - - if self.checkParam('-b'): - args["boxSize"]= self.getIntParam('-b') - else: - raise Exception("Error, box size in pixels is required as argument") - - args["inputCoordsDir"], args["outputCoordsDir"], args["predictedMaskDir"]= None, None, None - if self.checkParam('-c'): - args["inputCoordsDir"]= os.path.expanduser( self.getParam('-c')) - if self.checkParam('-o'): - args["outputCoordsDir"]= os.path.expanduser( self.getParam('-o')) - if self.checkParam('--predictedMaskDir'): - args["predictedMaskDir"]= os.path.expanduser( self.getParam('--predictedMaskDir')) - - - args["downFactor"]= self.getDoubleParamWithDefault('-s', defaultVal=1.0) - args["deepThr"]= self.getDoubleParamWithDefault('--deepThr', conditionFun= lambda x: x <= 0 or x >= 1, - defaultVal=None) - - args["sizeThr"]= self.getDoubleParamWithDefault('--sizeThr', conditionFun= lambda x: x <= 0 or x >= 1, - defaultVal=0.8) - - if args["inputCoordsDir"] is None and args["predictedMaskDir"] is None: - raise Exception("Either inputCoordsDir or predictedMaskDir (or both) must be provided") - - if args["inputCoordsDir"] is not None and args["outputCoordsDir"] is None: - raise Exception("Error, if inputCoordsDir provided, then outputCoordsDir must also be provided") - - if args["outputCoordsDir"] is not None and args["inputCoordsDir"] is None: - raise Exception("Error, if outputCoordsDir provided, then inputCoordsDir must also be provided") - - - if self.checkParam('-d'): - args["deepLearningModel"]= self.getParam('-d') - else: - args["deepLearningModel"]=Plugin.getModel('deepMicrographCleaner', 'defaultModel.keras') - - try: - from xmippPyModules.micrograph_cleaner_em.cleanMics import main - except ImportError as e: - print(e) - raise ValueError(BAD_IMPORT_MSG) - main(** args) - - -def updateEnviron(gpus=None): - """ Create the needed environment for TensorFlow programs. """ - print("updating environ to select gpus: %s"%(gpus) ) - if gpus is not None and gpus.startswith("all"): return - if gpus is not None or gpus is not "": - os.environ['CUDA_VISIBLE_DEVICES']=str(gpus) - else: - os.environ['CUDA_VISIBLE_DEVICES']="-1" - -if __name__ == '__main__': - ''' -scipion python `which xmipp_deep_micrograph_cleaner` -g 0 - ''' - exitCode=ScriptMicrographCleanerEm().tryRun() - sys.exit(exitCode) - diff --git a/libraries/py_xmipp/deepResLearner/__init__.py b/libraries/py_xmipp/deepResLearner/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/libraries/py_xmipp/deepResLearner/cnn_deepRes_1_7.py b/libraries/py_xmipp/deepResLearner/cnn_deepRes_1_7.py deleted file mode 100644 index b537ebc9c..000000000 --- a/libraries/py_xmipp/deepResLearner/cnn_deepRes_1_7.py +++ /dev/null @@ -1,123 +0,0 @@ -from keras.models import Sequential -from keras.layers import Conv3D, MaxPooling3D, BatchNormalization, Dropout, Flatten, Dense -from keras.callbacks import ModelCheckpoint, TensorBoard -from keras.utils import Sequence, to_categorical -import glob -import numpy as np -import os -import random -import string -import sys -import xmipp -import xmippLib - -boxDim=13 -boxDim2 = boxDim//2 -fnDir = sys.argv[1] # /dataset/PDB/3Dcomplex_set/ - -allPDBs = glob.glob(fnDir+"/*pdb") - -# generator -def Gen(idx): - - while True: - - n = np.random.randint(0,len(allPDBs)) - - maxRes = round(np.random.uniform(0.9,7.0),1) - - #VOLUMENES - ok = False - fnRandom = ''.join([random.choice(string.ascii_letters + string.digits) for i in xrange(32)]) - fnHash = "tmp"+fnRandom - while not ok: - ok = True - ok = os.system("xmipp_volume_from_pdb -i %s -o %s --sampling 0.5 --centerPDB -v 0"%(allPDBs[n],fnHash))==0 - if ok: - ok = os.system("xmipp_transform_filter -i %s.vol -o %sFiltered.vol --fourier low_pass %f 0.02 --sampling 0.5 -v 0"%(fnHash,fnHash,maxRes))==0 - if ok: - ok = os.system("xmipp_transform_threshold -i %s.vol -o %sMask.vol --select below 0.2 --substitute binarize -v 0"%(fnHash,fnHash))==0 - n = np.random.randint(0,len(allPDBs)) - - Vf = xmipp.Image("%sFiltered.vol"%fnHash).getData() - Vmask = xmipp.Image("%sMask.vol"%fnHash).getData() - os.system("rm -f %s.vol %sFiltered.vol %sMask.vol"%(fnHash,fnHash,fnHash)) - - batchX = [] - batchY = [] - - - #BOX - Zdim, Ydim, Xdim = Vf.shape - boxDim2 = boxDim//2 - - cont1=0 - for z in range(boxDim2,Zdim-boxDim2, 2): - for y in range(boxDim2,Ydim-boxDim2, 2): - for x in range(boxDim2,Xdim-boxDim2, 2): - if Vmask[z,y,x]>0: - cont1=cont1+1 - - if cont1>1000: - batch_size=1000 - else: - batch_size=cont1 - - cont2=0 - for z in range(boxDim2,Zdim-boxDim2, 2): - for y in range(boxDim2,Ydim-boxDim2, 2): - for x in range(boxDim2,Xdim-boxDim2, 2): - if Vmask[z,y,x]>0: - - if (cont20: - cont1=cont1+1 - - if cont1>1000: - batch_size=1000 - else: - batch_size=cont1 - - cont2=0 - for z in range(boxDim2,Zdim-boxDim2, 2): - for y in range(boxDim2,Ydim-boxDim2, 2): - for x in range(boxDim2,Xdim-boxDim2, 2): - if Vmask[z,y,x]>0: - - if (cont2 -#include -#include -#include - -// Empty constructor ======================================================= -ProgAngularSphAlignment::ProgAngularSphAlignment() -{ - resume = false; - produces_a_metadata = true; - each_image_produces_an_output = false; - showOptimization = false; -// ctfImage = NULL; -} - -ProgAngularSphAlignment::~ProgAngularSphAlignment() -{ -// delete ctfImage; -} - -// Read arguments ========================================================== -void ProgAngularSphAlignment::readParams() -{ - XmippMetadataProgram::readParams(); - fnVolR = getParam("--ref"); - fnOutDir = getParam("--odir"); - maxShift = getDoubleParam("--max_shift"); - maxAngularChange = getDoubleParam("--max_angular_change"); - maxResol = getDoubleParam("--max_resolution"); - Ts = getDoubleParam("--sampling"); - Rmax = getIntParam("--Rmax"); - RmaxDef = getIntParam("--RDef"); - optimizeAlignment = checkParam("--optimizeAlignment"); - optimizeDeformation = checkParam("--optimizeDeformation"); - optimizeRadius = checkParam("--optimizeRadius"); - phaseFlipped = checkParam("--phaseFlipped"); - depth = getIntParam("--depth"); - lambda = getDoubleParam("--regularization"); - resume = checkParam("--resume"); -} - -// Show ==================================================================== -void ProgAngularSphAlignment::show() -{ - if (!verbose) - return; - XmippMetadataProgram::show(); - std::cout - << "Output directory: " << fnOutDir << std::endl - << "Reference volume: " << fnVolR << std::endl - << "Max. Shift: " << maxShift << std::endl - << "Max. Angular Change: " << maxAngularChange << std::endl - << "Max. Resolution: " << maxResol << std::endl - << "Sampling: " << Ts << std::endl - << "Max. Radius: " << Rmax << std::endl - << "Max. Radius Deform. " << RmaxDef << std::endl - << "Depth: " << depth << std::endl - << "Optimize alignment: " << optimizeAlignment << std::endl - << "Optimize deformation " << optimizeDeformation<< std::endl - << "Optimize radius " << optimizeRadius << std::endl - << "Phase flipped: " << phaseFlipped << std::endl - << "Regularization: " << lambda << std::endl - ; -} - -// usage =================================================================== -void ProgAngularSphAlignment::defineParams() -{ - addUsageLine("Make a continuous angular assignment with deformations"); - defaultComments["-i"].clear(); - defaultComments["-i"].addComment("Metadata with initial alignment"); - defaultComments["-o"].clear(); - defaultComments["-o"].addComment("Metadata with the angular alignment and deformation parameters"); - XmippMetadataProgram::defineParams(); - addParamsLine(" --ref : Reference volume"); - addParamsLine(" [--odir ] : Output directory"); - addParamsLine(" [--max_shift ] : Maximum shift allowed in pixels"); - addParamsLine(" [--max_angular_change ] : Maximum angular change allowed (in degrees)"); - addParamsLine(" [--max_resolution ] : Maximum resolution (A)"); - addParamsLine(" [--sampling ] : Sampling rate (A/pixel)"); - addParamsLine(" [--Rmax ] : Maximum radius (px). -1=Half of volume size"); - addParamsLine(" [--RDef ] : Maximum radius of the deformation (px). -1=Half of volume size"); - addParamsLine(" [--depth ] : Harmonical depth of the deformation=1,2,3,..."); - addParamsLine(" [--optimizeAlignment] : Optimize alignment"); - addParamsLine(" [--optimizeDeformation] : Optimize deformation"); - addParamsLine(" [--optimizeRadius] : Optimize the radius of each spherical harmonic"); - addParamsLine(" [--phaseFlipped] : Input images have been phase flipped"); - addParamsLine(" [--regularization ] : Regularization weight"); - addParamsLine(" [--resume] : Resume processing"); - addExampleLine("A typical use is:",false); - addExampleLine("xmipp_angular_sph_alignment -i anglesFromContinuousAssignment.xmd --ref reference.vol -o assigned_anglesAndDeformations.xmd --optimizeAlignment --optimizeDeformation --depth 1"); -} - -// Produce side information ================================================ -void ProgAngularSphAlignment::createWorkFiles() { - MetaData *pmdIn = getInputMd(); - MetaData mdTodo, mdDone; - mdTodo = *pmdIn; - FileName fn(fnOutDir+"/sphDone.xmd"); - if (fn.exists() && resume) { - mdDone.read(fn); - mdTodo.subtraction(mdDone, MDL_IMAGE); - } else //if not exists create metadata only with headers - { - mdDone.addLabel(MDL_IMAGE); - mdDone.addLabel(MDL_ENABLED); - mdDone.addLabel(MDL_ANGLE_ROT); - mdDone.addLabel(MDL_ANGLE_TILT); - mdDone.addLabel(MDL_ANGLE_PSI); - mdDone.addLabel(MDL_SHIFT_X); - mdDone.addLabel(MDL_SHIFT_Y); - mdDone.addLabel(MDL_FLIP); - mdDone.addLabel(MDL_SPH_DEFORMATION); - mdDone.addLabel(MDL_SPH_COEFFICIENTS); - mdDone.addLabel(MDL_COST); - mdDone.write(fn); - } - *pmdIn = mdTodo; -} - -void ProgAngularSphAlignment::preProcess() -{ - // Read the reference volume - V.read(fnVolR); - V().setXmippOrigin(); - Xdim=XSIZE(V()); - Vdeformed().initZeros(V()); - sumV=V().sum(); - - //Ip().initZeros(Xdim,Xdim); - Ifilteredp().initZeros(Xdim,Xdim); - Ifilteredp().setXmippOrigin(); - - // Construct mask - if (Rmax<0) - Rmax=Xdim/2; - Mask mask; - mask.type = BINARY_CIRCULAR_MASK; - mask.mode = INNER_MASK; - mask.R1 = Rmax; - mask.generate_mask(Xdim,Xdim); - mask2D=mask.get_binary_mask(); - - // Low pass filter - filter.FilterBand=LOWPASS; - filter.w1=Ts/maxResol; - filter.raised_w=0.02; - - // Transformation matrix - A.initIdentity(3); - - createWorkFiles(); -} - -void ProgAngularSphAlignment::finishProcessing() { - XmippMetadataProgram::finishProcessing(); - rename((fnOutDir+"/sphDone.xmd").c_str(), fn_out.c_str()); -} - -//#define DEBUG -double ProgAngularSphAlignment::tranformImageSph(double *pclnm, double rot, double tilt, double psi, - Matrix2D &A) -{ - const MultidimArray &mV=V(); - MultidimArray &mVD=Vdeformed(); - FOR_ALL_ELEMENTS_IN_MATRIX1D(clnm) - VEC_ELEM(clnm,i)=pclnm[i+1]; - double deformation=0.0; - totalDeformation=0.0; - deformVol(mVD, mV, deformation); - projectVolume(mVD, P, (int)XSIZE(I()), (int)XSIZE(I()), rot, tilt, psi); - double cost=0; - if (old_flip) - { - MAT_ELEM(A,0,0)*=-1; - MAT_ELEM(A,0,1)*=-1; - MAT_ELEM(A,0,2)*=-1; - } - - applyGeometry(LINEAR,Ifilteredp(),Ifiltered(),A,IS_NOT_INV,DONT_WRAP,0.); - const MultidimArray &mP=P(); - const MultidimArray &mMask2D=mask2D; - MultidimArray &mIfilteredp=Ifilteredp(); - double corr=correlationIndex(mIfilteredp,mP,&mMask2D); - cost=-corr; - -#ifdef DEBUG - std::cout << "A=" << A << std::endl; - Image save; - save()=prm->P(); - save.write("PPPtheo.xmp"); - save()=prm->Ifilteredp(); - save.write("PPPfilteredp.xmp"); - save()=prm->Ifiltered(); - save.write("PPPfiltered.xmp"); - Vdeformed.write("PPPVdeformed.vol"); - std::cout << "Cost=" << cost << " deformation=" << deformation << std::endl; - std::cout << "Press any key" << std::endl; - char c; std::cin >> c; -#endif - - if (showOptimization) - { - std::cout << "A=" << A << std::endl; - Image save; - save()=P(); - save.write("PPPtheo.xmp"); - save()=Ifilteredp(); - save.write("PPPfilteredp.xmp"); - save()=Ifiltered(); - save.write("PPPfiltered.xmp"); - Vdeformed.write("PPPVdeformed.vol"); - std::cout << "Cost=" << cost << " corr=" << corr << std::endl; - std::cout << "Deformation=" << totalDeformation << std::endl; - std::cout << "Press any key" << std::endl; - char c; std::cin >> c; - } - - double massDiff=std::abs(sumV-sumVd)/sumV*100; - double retval=cost+lambda*(deformation+massDiff*massDiff); - if (showOptimization) - std::cout << cost << " " << deformation << " " << lambda*deformation << " " << sumV << " " << sumVd << " " << massDiff << " " << retval << std::endl; - return retval; -} - -double continuousSphCost(double *x, void *_prm) -{ - ProgAngularSphAlignment *prm=(ProgAngularSphAlignment *)_prm; - double deltax=x[prm->pos+1]; - double deltay=x[prm->pos+2]; - double deltaRot=x[prm->pos+3]; - double deltaTilt=x[prm->pos+4]; - double deltaPsi=x[prm->pos+5]; - if (prm->maxShift>0 && deltax*deltax+deltay*deltay>prm->maxShift*prm->maxShift) - return 1e38; - if (prm->maxAngularChange>0 && (fabs(deltaRot)>prm->maxAngularChange || fabs(deltaTilt)>prm->maxAngularChange || fabs(deltaPsi)>prm->maxAngularChange)) - return 1e38; - - MAT_ELEM(prm->A,0,2)=prm->old_shiftX+deltax; - MAT_ELEM(prm->A,1,2)=prm->old_shiftY+deltay; - MAT_ELEM(prm->A,0,0)=1; - MAT_ELEM(prm->A,0,1)=0; - MAT_ELEM(prm->A,1,0)=0; - MAT_ELEM(prm->A,1,1)=1; - - return prm->tranformImageSph(x,prm->old_rot+deltaRot, prm->old_tilt+deltaTilt, prm->old_psi+deltaPsi, - prm->A); -} - -// Predict ================================================================= -//#define DEBUG -void ProgAngularSphAlignment::processImage(const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut) -{ - if (depth==0) - depth = 1; - Matrix1D nh; - nh.resize(depth+2); - nh.initConstant(0); - Numsph(nh); - - if (RmaxDef<0) - RmaxDef = Xdim/2; - - L = nh(2); - prevL = nh(1); - pos = 4*L; - p.resize(pos+5); - Matrix1D steps(pos+5); - clnm.initZeros(pos+5); - - rowOut=rowIn; - - flagEnabled=1; - - // Read input image and initial parameters -// ApplyGeoParams geoParams; -// geoParams.only_apply_shifts=false; -// geoParams.wrap=DONT_WRAP; - - rowIn.getValue(MDL_ANGLE_ROT,old_rot); - rowIn.getValue(MDL_ANGLE_TILT,old_tilt); - rowIn.getValue(MDL_ANGLE_PSI,old_psi); - rowIn.getValue(MDL_SHIFT_X,old_shiftX); - rowIn.getValue(MDL_SHIFT_Y,old_shiftY); - if (rowIn.containsLabel(MDL_FLIP)) - rowIn.getValue(MDL_FLIP,old_flip); - else - old_flip = false; - - if (verbose>=2) - std::cout << "Processing " << fnImg << std::endl; - I.read(fnImg); - I().setXmippOrigin(); - - Ifiltered()=I(); - filter.applyMaskSpace(Ifiltered()); - - for (int h=1;h=2) - { - std::cout<=2); - - if (verbose>=3) - { - showOptimization = true; - continuousSphCost(p.adaptForNumericalRecipes(),this); - showOptimization = false; - } - - if (cost>0) - { - //rowOut.setValue(MDL_ENABLED,-1); - flagEnabled=-1; - p.initZeros(); - } - cost=-cost; - correlation=cost; - if (verbose>=2) - { - std::cout< vectortemp; - for (int j = 0; j < VEC_XSIZE(clnm); j++) - { - vectortemp.push_back(clnm(j)); - } - md.setValue(MDL_SPH_COEFFICIENTS, vectortemp, objId); - md.setValue(MDL_COST, correlation, objId); - md.append(fnOutDir+"/sphDone.xmd"); -} - -void ProgAngularSphAlignment::Numsph(Matrix1D &sphD) -{ - for (int d=1;d<(VEC_XSIZE(sphD)-1);d++) - { - if (d%2==0) - { - sphD(d+1) = sphD(d)+((d/2)+1)*(2*d+1); - } - else - { - sphD(d+1) = sphD(d)+(((d-1)/2)+1)*(2*d+1); - } - } -} - -void ProgAngularSphAlignment::minimizepos(Matrix1D &vectpos) -{ - size_t groups = 4; - size_t olditems = (4*prevL)/groups; - size_t newitems = (4*L)/groups; - size_t initial = 3*newitems+olditems; - for (int i=initial;i &oldvect,Matrix1D &newvect) -{ - size_t groups = 4; - size_t olditems = (4*prevL)/groups; - size_t newitems = (4*L)/groups; - for (int g=0;g &mVD, const MultidimArray &mV, double &def) -{ - int l,n,m; - size_t idxY0=(VEC_XSIZE(clnm)-5)/4; - double Ncount=0.0; - double totalVal=0.0; - double voxModg=0.0; - double diff2=0.0; - - def=0.0; - size_t idxZ0=2*idxY0; - size_t idxR=3*idxY0; - sumVd=0.0; - for (int k=STARTINGZ(mV); k<=FINISHINGZ(mV); k++) - { - for (int i=STARTINGY(mV); i<=FINISHINGY(mV); i++) - { - for (int j=STARTINGX(mV); j<=FINISHINGX(mV); j++) - { - - double gx=0.0, gy=0.0, gz=0.0; - for (size_t idx=0; idx0 || l==0) - { - gx += VEC_ELEM(clnm,idx) *(zsph); - gy += VEC_ELEM(clnm,idx+idxY0) *(zsph); - gz += VEC_ELEM(clnm,idx+idxZ0) *(zsph); - } - } - mVD(k,i,j) = mV.interpolatedElement3D(j+gx,i+gy,k+gz); - double voxelR=A3D_ELEM(mV,k,i,j); - double absVoxelR=std::abs(voxelR); - voxModg += absVoxelR*(gx*gx+gy*gy+gz*gz); - totalVal += absVoxelR; - - double voxelI=A3D_ELEM(mVD,k,i,j); - double diff=voxelR-voxelI; - diff2+=absVoxelR*diff*diff; - sumVd+=voxelI; - } - } - } - - // COSS def=5e-3*sqrt(diff2/totalVal)+sqrt(voxModg/totalVal); - def=sqrt(voxModg/totalVal); - totalDeformation = sqrt(voxModg/totalVal); -} - diff --git a/libraries/reconstruction/angular_sph_alignment.h b/libraries/reconstruction/angular_sph_alignment.h deleted file mode 100644 index ff4b9be80..000000000 --- a/libraries/reconstruction/angular_sph_alignment.h +++ /dev/null @@ -1,171 +0,0 @@ -/*************************************************************************** - * - * Authors: Carlos Oscar Sanchez Sorzano coss@cnb.csic.es - * - * 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 'xmipp@cnb.csic.es' - ***************************************************************************/ - -#ifndef _PROG_ANGULAR_SPH_ALIGNMENT -#define _PROG_ANGULAR_SPH_ALIGNMENT - -#include -#include -#include -#include - -/**@defgroup AngularPredictContinuous2 angular_continuous_assign2 (Continuous angular assignment) - @ingroup ReconsLibrary */ -//@{ - -/** Predict Continuous Parameters. */ -class ProgAngularSphAlignment: public XmippMetadataProgram -{ -public: - /** Filename of the reference volume */ - FileName fnVolR; - /// Output directory - FileName fnOutDir; - /** Degree of Zernike polynomials and spherical harmonics */ - int depth; - /** Maximum shift allowed */ - double maxShift; - /** Maximum angular change allowed */ - double maxAngularChange; - /** Maximum frequency (A) */ - double maxResol; - /** Sampling rate */ - double Ts; - /** Maximum radius */ - int Rmax; - // Optimize alignment - bool optimizeAlignment; - //Optimize deformation - bool optimizeDeformation; - //Radius optimization - bool optimizeRadius; - // Phase Flipped - bool phaseFlipped; - // Regularization weight - double lambda; - // Maximum radius for the deformation - int RmaxDef; - - Matrix1D p; - int flagEnabled; - -public: - /** Resume computations */ - bool resume; - // 2D mask in real space - MultidimArray mask2D; - // Inverse of the sum of Mask2D -// double iMask2Dsum; - // Volume size - size_t Xdim; - // Input image - Image V, Vdeformed, I, Ip, Ifiltered, Ifilteredp; - // Theoretical projection - Projection P; - // Filter - FourierFilter filter; - // Transformation matrix - Matrix2D A; - // Original angles - double old_rot, old_tilt, old_psi; - // Original shift - double old_shiftX, old_shiftY; - // Original flip - bool old_flip; -// // CTF -// CTFDescription ctf; - // CTF image -// MultidimArray *ctfImage; - // Degree of the spherical harmonic - int prevL, L; - // Vector position - int pos; - // Vector containing the degree of the spherical harmonics - Matrix1D clnm; - //Total Deformation, sumV, sumVd - double totalDeformation, sumV, sumVd; - // Show optimization - bool showOptimization; - // Correlation - double correlation; - -public: - /// Empty constructor - ProgAngularSphAlignment(); - - /// Destructor - ~ProgAngularSphAlignment(); - - /// Read argument from command line - void readParams(); - - /// Show - void show(); - - /// Define parameters - void defineParams(); - - /** Produce side info. - An exception is thrown if any of the files is not found*/ - void preProcess(); - - /** Create the processing working files. - * The working files are: - * nmaTodo.xmd for images to process (nmaTodo = mdIn - nmaDone) - * nmaDone.xmd image already processed (could exists from a previous run) - */ - virtual void createWorkFiles(); - - /** Predict angles and shift. - At the input the pose parameters must have an initial guess of the - parameters. At the output they have the estimated pose.*/ - void processImage(const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut); - - ///Compute the number of spherical harmonics in l=0,1,...,depth - void Numsph(Matrix1D &sphD); - - // Determine the positions to be minimize of a vector containing spherical harmonic coefficients - void minimizepos(Matrix1D &vectpos); - - /// Copy the coefficients from harmonical depth n-1 vector to harmonical depth n vector - void copyvectors(Matrix1D &oldvect,Matrix1D &newvect); - - ///Deform a volumen using Zernike-Spherical harmonic basis - void deformVol(MultidimArray &mVD, const MultidimArray &mV, double &def); - - double tranformImageSph(double *pclnm, double rot, double tilt, double psi, - Matrix2D &A); - - //AJ new - /** Write the final parameters. */ - virtual void finishProcessing(); - - /** Write the parameters found for one image */ - virtual void writeImageParameters(const FileName &fnImg); - //END AJ - -}; -//@} -#endif diff --git a/libraries/reconstruction/image_odd_even.cpp b/libraries/reconstruction/image_odd_even.cpp deleted file mode 100644 index 543640461..000000000 --- a/libraries/reconstruction/image_odd_even.cpp +++ /dev/null @@ -1,151 +0,0 @@ -/*************************************************************************** - * - * Authors: Jose Luis Vilas, jlvilas@cnb.csic.es - * Carlos Oscar S. Sorzano coss@cnb.csic.es (2019) - * - * 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 'xmipp@cnb.csic.es' - ***************************************************************************/ - -#include "image_odd_even.h" -//#define DEBUG -//#define DEBUG_MASK - -void ProgOddEven::readParams() -{ - fnImg = getParam("--img"); - splitType = getParam("--type"); - sumFrames = checkParam("--sum_frames"); - fnOut_odd = getParam("-o"); - fnOut_even = getParam("-e"); -} - - -void ProgOddEven::defineParams() -{ - addUsageLine("This function splits a set of images or frames in two subsets named odd and even"); - addParamsLine(" --img : File of input images (movie or images tilt series)"); - addParamsLine(" --type : Type of splitting"); - addParamsLine(" :+ frames - If the frames will be split)"); - addParamsLine(" :+ images - If the images will be split)"); - addParamsLine("[ --sum_frames] : Sum the set of split frames"); - addParamsLine(" -o : File of odd images/frames)"); - addParamsLine(" -e : File of even images/frames)"); -} - - -void ProgOddEven::run() -{ - std::cout << "Starting..." << std::endl; - - - - if ((splitType != "frames") or (splitType != "frames")) - { - std::cout << "ERROR: Please specify the type of splitting in frames or images" << std::endl; - std::cout << " --type frames for splitting the set of frames or --type images for splitting" - "the set of images" << std::endl; - exit(0); - } - - MetaData movie; - movie.read(fnImg); - - if (splitType == "frames") - { - if (fnImg.isMetaData()) - { - movie.read(fnImg); - } - else - { - ImageGeneric movieStack; - movieStack.read(fnImg, HEADER); - size_t Xdim, Ydim, Zdim, Ndim; - movieStack.getDimensions(Xdim, Ydim, Zdim, Ndim); - if (fnImg.getExtension() == "mrc" and Ndim == 1) - Ndim = Zdim; - size_t id; - FileName fn; - for (size_t i = 0; i < Ndim; i++) { - id = movie.addObject(); - fn.compose(i + FIRST_IMAGE, fnImg); - movie.setValue(MDL_IMAGE, fn, id); - } - } - } -// -// if (splitType == "images") -// { -// std::cout << "TODO" << std::endl; -// } - - long n = 1; - MetaData movieOdd, movieEven; - - FileName fnFrame; - size_t objId, objId_odd, objId_even; - Image frame, imgOdd, imgEven; - - - int counter=0; - - FOR_ALL_OBJECTS_IN_METADATA(movie) - { - objId = __iter.objId; - movie.getValue(MDL_IMAGE, fnFrame, objId); - if (sumFrames) - frame.read(fnFrame); - - - if (objId%2 == 0) - { - objId_even = movieEven.addObject(); - movieEven.setValue(MDL_IMAGE, fnFrame, objId_even); - if (sumFrames) - if (counter > 1) - imgEven() += frame(); - else - imgEven() = frame(); - ++counter; - } - else - { - objId_odd = movieOdd.addObject(); - movieOdd.setValue(MDL_IMAGE, fnFrame, objId_odd); - if (sumFrames) - if (counter > 1) - imgOdd() += frame(); - else - imgOdd() = frame(); - ++counter; - } - } - - movieOdd.write(fnOut_odd); - movieEven.write(fnOut_even); - - if (sumFrames) - { - imgOdd.write(fnOut_odd.withoutExtension()+"_aligned.mrc"); - imgEven.write(fnOut_even.withoutExtension()+"_aligned.mrc"); - } -} - diff --git a/libraries/reconstruction/image_odd_even.h b/libraries/reconstruction/image_odd_even.h deleted file mode 100644 index c96d85994..000000000 --- a/libraries/reconstruction/image_odd_even.h +++ /dev/null @@ -1,59 +0,0 @@ -/*************************************************************************** - * - * Authors: Jose Luis Vilas, jlvilas@cnb.csic.es - * Carlos Oscar S. Sorzano coss@cnb.csic.es (2019) - * - * 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 'xmipp@cnb.csic.es' - ***************************************************************************/ - -#ifndef _PROG_SPLIT_ODD_EVEN -#define _PROG_SPLIT_ODD_EVEN - -#include -#include -#include -#include -#include -#include "core/metadata_extension.h" - -/**@defgroup Odd Even - @ingroup ReconsLibrary */ -//@{ -/** SSNR parameters. */ - -class ProgOddEven : public XmippProgram -{ -public: - /** Filenames */ - FileName fnOut_odd, fnOut_even, fnImg, splitType; - bool sumFrames; - -public: - void defineParams(); - void readParams(); - void produceSideInfo(); - void run(); - - -}; -//@} -#endif - diff --git a/scripts/travis_before_script.py b/scripts/travis_before_script.py deleted file mode 100755 index 09f00ad44..000000000 --- a/scripts/travis_before_script.py +++ /dev/null @@ -1,35 +0,0 @@ -#/usr/bin/env python -import os, shutil -from distutils.dir_util import copy_tree - -folder = './' -src_folder_name = 'src' -xmipp_folder_name = 'xmipp' -xmipp_folder = os.path.join(folder, src_folder_name, xmipp_folder_name) -xmipp_script = 'xmipp' -sonar_script = 'sonar-project.properties' -sync_script = 'sync_data.py' -git_folder = '.git' -# get folder relative to home dir and strip os.path separators -script_dir = os.path.dirname(os.path.realpath(__file__)).split(os.getcwd())[1][1:] -copy_list = [xmipp_script, script_dir, sonar_script, sync_script] -if 'TRAVIS' in os.environ: - # we need git folder so that SonarCloud can use it for PR decoration - copy_list.append(git_folder) -black_list = [src_folder_name] -os.makedirs(xmipp_folder) -for item in os.listdir(folder): - if item in black_list: - continue - item_path = os.path.join(folder, item) - try: - if item not in copy_list: - shutil.move(item_path, xmipp_folder) - else: - if os.path.isdir(item_path): - copy_tree(item_path, os.path.join(xmipp_folder, item)) - else: - shutil.copy(item_path, xmipp_folder) - except Exception as e: - print(e) - diff --git a/SConscript b/src/xmipp/SConscript similarity index 100% rename from SConscript rename to src/xmipp/SConscript diff --git a/SConstruct b/src/xmipp/SConstruct similarity index 100% rename from SConstruct rename to src/xmipp/SConstruct diff --git a/applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.cpp b/src/xmipp/applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.cpp similarity index 100% rename from applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.cpp rename to src/xmipp/applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.cpp diff --git a/applications/programs/angular_break_symmetry/angular_break_symmetry_main.cpp b/src/xmipp/applications/programs/angular_break_symmetry/angular_break_symmetry_main.cpp similarity index 100% rename from applications/programs/angular_break_symmetry/angular_break_symmetry_main.cpp rename to src/xmipp/applications/programs/angular_break_symmetry/angular_break_symmetry_main.cpp diff --git a/applications/programs/angular_commonline/angular_commonline_main.cpp b/src/xmipp/applications/programs/angular_commonline/angular_commonline_main.cpp similarity index 100% rename from applications/programs/angular_commonline/angular_commonline_main.cpp rename to src/xmipp/applications/programs/angular_commonline/angular_commonline_main.cpp diff --git a/applications/programs/angular_continuous_assign/angular_continuous_assign_main.cpp b/src/xmipp/applications/programs/angular_continuous_assign/angular_continuous_assign_main.cpp similarity index 100% rename from applications/programs/angular_continuous_assign/angular_continuous_assign_main.cpp rename to src/xmipp/applications/programs/angular_continuous_assign/angular_continuous_assign_main.cpp diff --git a/applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.cpp b/src/xmipp/applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.cpp similarity index 100% rename from applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.cpp rename to src/xmipp/applications/programs/angular_continuous_assign2/angular_continuous_assign_main2.cpp diff --git a/applications/programs/angular_discrete_assign/angular_discrete_assign_main.cpp b/src/xmipp/applications/programs/angular_discrete_assign/angular_discrete_assign_main.cpp similarity index 100% rename from applications/programs/angular_discrete_assign/angular_discrete_assign_main.cpp rename to src/xmipp/applications/programs/angular_discrete_assign/angular_discrete_assign_main.cpp diff --git a/applications/programs/angular_distance/angular_distance_main.cpp b/src/xmipp/applications/programs/angular_distance/angular_distance_main.cpp similarity index 100% rename from applications/programs/angular_distance/angular_distance_main.cpp rename to src/xmipp/applications/programs/angular_distance/angular_distance_main.cpp diff --git a/applications/programs/angular_distribution_show/angular_distribution_show_main.cpp b/src/xmipp/applications/programs/angular_distribution_show/angular_distribution_show_main.cpp similarity index 100% rename from applications/programs/angular_distribution_show/angular_distribution_show_main.cpp rename to src/xmipp/applications/programs/angular_distribution_show/angular_distribution_show_main.cpp diff --git a/applications/programs/angular_estimate_tilt_axis/angular_estimate_tilt_axis_main.cpp b/src/xmipp/applications/programs/angular_estimate_tilt_axis/angular_estimate_tilt_axis_main.cpp similarity index 100% rename from applications/programs/angular_estimate_tilt_axis/angular_estimate_tilt_axis_main.cpp rename to src/xmipp/applications/programs/angular_estimate_tilt_axis/angular_estimate_tilt_axis_main.cpp diff --git a/applications/programs/angular_neighbourhood/angular_neighbourhood_main.cpp b/src/xmipp/applications/programs/angular_neighbourhood/angular_neighbourhood_main.cpp similarity index 100% rename from applications/programs/angular_neighbourhood/angular_neighbourhood_main.cpp rename to src/xmipp/applications/programs/angular_neighbourhood/angular_neighbourhood_main.cpp diff --git a/applications/programs/angular_project_library/angular_project_library_main.cpp b/src/xmipp/applications/programs/angular_project_library/angular_project_library_main.cpp similarity index 100% rename from applications/programs/angular_project_library/angular_project_library_main.cpp rename to src/xmipp/applications/programs/angular_project_library/angular_project_library_main.cpp diff --git a/applications/programs/angular_projection_matching/angular_projection_matching_main.cpp b/src/xmipp/applications/programs/angular_projection_matching/angular_projection_matching_main.cpp similarity index 100% rename from applications/programs/angular_projection_matching/angular_projection_matching_main.cpp rename to src/xmipp/applications/programs/angular_projection_matching/angular_projection_matching_main.cpp diff --git a/applications/programs/angular_rotate/angular_rotate_main.cpp b/src/xmipp/applications/programs/angular_rotate/angular_rotate_main.cpp similarity index 100% rename from applications/programs/angular_rotate/angular_rotate_main.cpp rename to src/xmipp/applications/programs/angular_rotate/angular_rotate_main.cpp diff --git a/applications/programs/classify_analyze_cluster/classify_analyze_cluster_main.cpp b/src/xmipp/applications/programs/classify_analyze_cluster/classify_analyze_cluster_main.cpp similarity index 100% rename from applications/programs/classify_analyze_cluster/classify_analyze_cluster_main.cpp rename to src/xmipp/applications/programs/classify_analyze_cluster/classify_analyze_cluster_main.cpp diff --git a/applications/programs/classify_compare_classes/classify_compare_classes_main.cpp b/src/xmipp/applications/programs/classify_compare_classes/classify_compare_classes_main.cpp similarity index 100% rename from applications/programs/classify_compare_classes/classify_compare_classes_main.cpp rename to src/xmipp/applications/programs/classify_compare_classes/classify_compare_classes_main.cpp diff --git a/applications/programs/classify_evaluate_classes/classify_evaluate_classes_main.cpp b/src/xmipp/applications/programs/classify_evaluate_classes/classify_evaluate_classes_main.cpp similarity index 100% rename from applications/programs/classify_evaluate_classes/classify_evaluate_classes_main.cpp rename to src/xmipp/applications/programs/classify_evaluate_classes/classify_evaluate_classes_main.cpp diff --git a/applications/programs/classify_extract_features/classify_extract_features_main.cpp b/src/xmipp/applications/programs/classify_extract_features/classify_extract_features_main.cpp similarity index 100% rename from applications/programs/classify_extract_features/classify_extract_features_main.cpp rename to src/xmipp/applications/programs/classify_extract_features/classify_extract_features_main.cpp diff --git a/applications/programs/classify_first_split/classify_first_split_main.cpp b/src/xmipp/applications/programs/classify_first_split/classify_first_split_main.cpp similarity index 100% rename from applications/programs/classify_first_split/classify_first_split_main.cpp rename to src/xmipp/applications/programs/classify_first_split/classify_first_split_main.cpp diff --git a/applications/programs/classify_first_split3/classify_first_split3_main.cpp b/src/xmipp/applications/programs/classify_first_split3/classify_first_split3_main.cpp similarity index 100% rename from applications/programs/classify_first_split3/classify_first_split3_main.cpp rename to src/xmipp/applications/programs/classify_first_split3/classify_first_split3_main.cpp diff --git a/applications/programs/classify_kerdensom/classify_kerdensom_main.cpp b/src/xmipp/applications/programs/classify_kerdensom/classify_kerdensom_main.cpp similarity index 100% rename from applications/programs/classify_kerdensom/classify_kerdensom_main.cpp rename to src/xmipp/applications/programs/classify_kerdensom/classify_kerdensom_main.cpp diff --git a/applications/programs/classify_kmeans_2d/classify_kmeans_2d_main.cpp b/src/xmipp/applications/programs/classify_kmeans_2d/classify_kmeans_2d_main.cpp similarity index 100% rename from applications/programs/classify_kmeans_2d/classify_kmeans_2d_main.cpp rename to src/xmipp/applications/programs/classify_kmeans_2d/classify_kmeans_2d_main.cpp diff --git a/applications/programs/classify_significant/classify_significant_main.cpp b/src/xmipp/applications/programs/classify_significant/classify_significant_main.cpp similarity index 100% rename from applications/programs/classify_significant/classify_significant_main.cpp rename to src/xmipp/applications/programs/classify_significant/classify_significant_main.cpp diff --git a/applications/programs/coordinates_noisy_zones_filter/coordinates_noisy_zones_filter_main.cpp b/src/xmipp/applications/programs/coordinates_noisy_zones_filter/coordinates_noisy_zones_filter_main.cpp similarity index 100% rename from applications/programs/coordinates_noisy_zones_filter/coordinates_noisy_zones_filter_main.cpp rename to src/xmipp/applications/programs/coordinates_noisy_zones_filter/coordinates_noisy_zones_filter_main.cpp diff --git a/applications/programs/ctf_correct_idr/ctf_correct_idr_main.cpp b/src/xmipp/applications/programs/ctf_correct_idr/ctf_correct_idr_main.cpp similarity index 100% rename from applications/programs/ctf_correct_idr/ctf_correct_idr_main.cpp rename to src/xmipp/applications/programs/ctf_correct_idr/ctf_correct_idr_main.cpp diff --git a/applications/programs/ctf_correct_wiener2d/ctf_correct_wiener2d_main.cpp b/src/xmipp/applications/programs/ctf_correct_wiener2d/ctf_correct_wiener2d_main.cpp similarity index 100% rename from applications/programs/ctf_correct_wiener2d/ctf_correct_wiener2d_main.cpp rename to src/xmipp/applications/programs/ctf_correct_wiener2d/ctf_correct_wiener2d_main.cpp diff --git a/applications/programs/ctf_correct_wiener3d/ctf_correct_wiener3d_main.cpp b/src/xmipp/applications/programs/ctf_correct_wiener3d/ctf_correct_wiener3d_main.cpp similarity index 100% rename from applications/programs/ctf_correct_wiener3d/ctf_correct_wiener3d_main.cpp rename to src/xmipp/applications/programs/ctf_correct_wiener3d/ctf_correct_wiener3d_main.cpp diff --git a/applications/programs/ctf_create_ctfdat/ctf_create_ctfdat_main.cpp b/src/xmipp/applications/programs/ctf_create_ctfdat/ctf_create_ctfdat_main.cpp similarity index 100% rename from applications/programs/ctf_create_ctfdat/ctf_create_ctfdat_main.cpp rename to src/xmipp/applications/programs/ctf_create_ctfdat/ctf_create_ctfdat_main.cpp diff --git a/applications/programs/ctf_enhance_psd/ctf_enhance_psd_main.cpp b/src/xmipp/applications/programs/ctf_enhance_psd/ctf_enhance_psd_main.cpp similarity index 100% rename from applications/programs/ctf_enhance_psd/ctf_enhance_psd_main.cpp rename to src/xmipp/applications/programs/ctf_enhance_psd/ctf_enhance_psd_main.cpp diff --git a/applications/programs/ctf_estimate_from_micrograph/ctf_estimate_from_micrograph_main.cpp b/src/xmipp/applications/programs/ctf_estimate_from_micrograph/ctf_estimate_from_micrograph_main.cpp similarity index 100% rename from applications/programs/ctf_estimate_from_micrograph/ctf_estimate_from_micrograph_main.cpp rename to src/xmipp/applications/programs/ctf_estimate_from_micrograph/ctf_estimate_from_micrograph_main.cpp diff --git a/applications/programs/ctf_estimate_from_psd/ctf_estimate_from_psd_main.cpp b/src/xmipp/applications/programs/ctf_estimate_from_psd/ctf_estimate_from_psd_main.cpp similarity index 100% rename from applications/programs/ctf_estimate_from_psd/ctf_estimate_from_psd_main.cpp rename to src/xmipp/applications/programs/ctf_estimate_from_psd/ctf_estimate_from_psd_main.cpp diff --git a/applications/programs/ctf_estimate_from_psd_fast/ctf_estimate_from_psd_fast_main.cpp b/src/xmipp/applications/programs/ctf_estimate_from_psd_fast/ctf_estimate_from_psd_fast_main.cpp similarity index 100% rename from applications/programs/ctf_estimate_from_psd_fast/ctf_estimate_from_psd_fast_main.cpp rename to src/xmipp/applications/programs/ctf_estimate_from_psd_fast/ctf_estimate_from_psd_fast_main.cpp diff --git a/applications/programs/ctf_group/ctf_group_main.cpp b/src/xmipp/applications/programs/ctf_group/ctf_group_main.cpp similarity index 100% rename from applications/programs/ctf_group/ctf_group_main.cpp rename to src/xmipp/applications/programs/ctf_group/ctf_group_main.cpp diff --git a/applications/programs/ctf_phase_flip/ctf_phase_flip_main.cpp b/src/xmipp/applications/programs/ctf_phase_flip/ctf_phase_flip_main.cpp similarity index 100% rename from applications/programs/ctf_phase_flip/ctf_phase_flip_main.cpp rename to src/xmipp/applications/programs/ctf_phase_flip/ctf_phase_flip_main.cpp diff --git a/applications/programs/ctf_show/ctf_show_main.cpp b/src/xmipp/applications/programs/ctf_show/ctf_show_main.cpp similarity index 100% rename from applications/programs/ctf_show/ctf_show_main.cpp rename to src/xmipp/applications/programs/ctf_show/ctf_show_main.cpp diff --git a/applications/programs/ctf_sort_psds/ctf_sort_psds_main.cpp b/src/xmipp/applications/programs/ctf_sort_psds/ctf_sort_psds_main.cpp similarity index 100% rename from applications/programs/ctf_sort_psds/ctf_sort_psds_main.cpp rename to src/xmipp/applications/programs/ctf_sort_psds/ctf_sort_psds_main.cpp diff --git a/applications/programs/cuda_correlation/cuda_correlation_main.cpp b/src/xmipp/applications/programs/cuda_correlation/cuda_correlation_main.cpp similarity index 100% rename from applications/programs/cuda_correlation/cuda_correlation_main.cpp rename to src/xmipp/applications/programs/cuda_correlation/cuda_correlation_main.cpp diff --git a/applications/programs/cuda_movie_alignment_correlation/cuda_movie_alignment_correlation.cpp b/src/xmipp/applications/programs/cuda_movie_alignment_correlation/cuda_movie_alignment_correlation.cpp similarity index 100% rename from applications/programs/cuda_movie_alignment_correlation/cuda_movie_alignment_correlation.cpp rename to src/xmipp/applications/programs/cuda_movie_alignment_correlation/cuda_movie_alignment_correlation.cpp diff --git a/applications/programs/cuda_reconstruct_fourier/cuda_reconstruct_fourier_main.cpp b/src/xmipp/applications/programs/cuda_reconstruct_fourier/cuda_reconstruct_fourier_main.cpp similarity index 100% rename from applications/programs/cuda_reconstruct_fourier/cuda_reconstruct_fourier_main.cpp rename to src/xmipp/applications/programs/cuda_reconstruct_fourier/cuda_reconstruct_fourier_main.cpp diff --git a/applications/programs/evaluate_coordinates/evaluate_coordinates_main.cpp b/src/xmipp/applications/programs/evaluate_coordinates/evaluate_coordinates_main.cpp similarity index 100% rename from applications/programs/evaluate_coordinates/evaluate_coordinates_main.cpp rename to src/xmipp/applications/programs/evaluate_coordinates/evaluate_coordinates_main.cpp diff --git a/applications/programs/flexible_alignment/flexible_alignment_main.cpp b/src/xmipp/applications/programs/flexible_alignment/flexible_alignment_main.cpp similarity index 100% rename from applications/programs/flexible_alignment/flexible_alignment_main.cpp rename to src/xmipp/applications/programs/flexible_alignment/flexible_alignment_main.cpp diff --git a/applications/programs/idr_xray_tomo/idr_xray_tomo_main.cpp b/src/xmipp/applications/programs/idr_xray_tomo/idr_xray_tomo_main.cpp similarity index 100% rename from applications/programs/idr_xray_tomo/idr_xray_tomo_main.cpp rename to src/xmipp/applications/programs/idr_xray_tomo/idr_xray_tomo_main.cpp diff --git a/applications/programs/image_align/image_align_main.cpp b/src/xmipp/applications/programs/image_align/image_align_main.cpp similarity index 100% rename from applications/programs/image_align/image_align_main.cpp rename to src/xmipp/applications/programs/image_align/image_align_main.cpp diff --git a/applications/programs/image_align_tilt_pairs/image_align_tilt_pairs.cpp b/src/xmipp/applications/programs/image_align_tilt_pairs/image_align_tilt_pairs.cpp similarity index 100% rename from applications/programs/image_align_tilt_pairs/image_align_tilt_pairs.cpp rename to src/xmipp/applications/programs/image_align_tilt_pairs/image_align_tilt_pairs.cpp diff --git a/applications/programs/image_assignment_tilt_pair/assignment_tilt_pair_main.cpp b/src/xmipp/applications/programs/image_assignment_tilt_pair/assignment_tilt_pair_main.cpp similarity index 100% rename from applications/programs/image_assignment_tilt_pair/assignment_tilt_pair_main.cpp rename to src/xmipp/applications/programs/image_assignment_tilt_pair/assignment_tilt_pair_main.cpp diff --git a/applications/programs/image_common_lines/image_common_lines_main.cpp b/src/xmipp/applications/programs/image_common_lines/image_common_lines_main.cpp similarity index 100% rename from applications/programs/image_common_lines/image_common_lines_main.cpp rename to src/xmipp/applications/programs/image_common_lines/image_common_lines_main.cpp diff --git a/applications/programs/image_convert/image_convert_main.cpp b/src/xmipp/applications/programs/image_convert/image_convert_main.cpp similarity index 100% rename from applications/programs/image_convert/image_convert_main.cpp rename to src/xmipp/applications/programs/image_convert/image_convert_main.cpp diff --git a/applications/programs/image_eliminate_empty_particles/image_eliminate_empty_particles_main.cpp b/src/xmipp/applications/programs/image_eliminate_empty_particles/image_eliminate_empty_particles_main.cpp similarity index 100% rename from applications/programs/image_eliminate_empty_particles/image_eliminate_empty_particles_main.cpp rename to src/xmipp/applications/programs/image_eliminate_empty_particles/image_eliminate_empty_particles_main.cpp diff --git a/applications/programs/image_eliminate_largeEnergy/image_eliminate_largeEnergy_main.cpp b/src/xmipp/applications/programs/image_eliminate_largeEnergy/image_eliminate_largeEnergy_main.cpp similarity index 100% rename from applications/programs/image_eliminate_largeEnergy/image_eliminate_largeEnergy_main.cpp rename to src/xmipp/applications/programs/image_eliminate_largeEnergy/image_eliminate_largeEnergy_main.cpp diff --git a/applications/programs/image_find_center/image_find_center_main.cpp b/src/xmipp/applications/programs/image_find_center/image_find_center_main.cpp similarity index 100% rename from applications/programs/image_find_center/image_find_center_main.cpp rename to src/xmipp/applications/programs/image_find_center/image_find_center_main.cpp diff --git a/applications/programs/image_header/image_header_main.cpp b/src/xmipp/applications/programs/image_header/image_header_main.cpp similarity index 100% rename from applications/programs/image_header/image_header_main.cpp rename to src/xmipp/applications/programs/image_header/image_header_main.cpp diff --git a/applications/programs/image_histogram/image_histogram_main.cpp b/src/xmipp/applications/programs/image_histogram/image_histogram_main.cpp similarity index 100% rename from applications/programs/image_histogram/image_histogram_main.cpp rename to src/xmipp/applications/programs/image_histogram/image_histogram_main.cpp diff --git a/applications/programs/image_operate/image_operate_main.cpp b/src/xmipp/applications/programs/image_operate/image_operate_main.cpp similarity index 100% rename from applications/programs/image_operate/image_operate_main.cpp rename to src/xmipp/applications/programs/image_operate/image_operate_main.cpp diff --git a/applications/programs/image_residuals/image_residuals_main.cpp b/src/xmipp/applications/programs/image_residuals/image_residuals_main.cpp similarity index 100% rename from applications/programs/image_residuals/image_residuals_main.cpp rename to src/xmipp/applications/programs/image_residuals/image_residuals_main.cpp diff --git a/applications/programs/image_resize/image_resize.cpp b/src/xmipp/applications/programs/image_resize/image_resize.cpp similarity index 100% rename from applications/programs/image_resize/image_resize.cpp rename to src/xmipp/applications/programs/image_resize/image_resize.cpp diff --git a/applications/programs/image_rotational_pca/image_rotational_pca_main.cpp b/src/xmipp/applications/programs/image_rotational_pca/image_rotational_pca_main.cpp similarity index 100% rename from applications/programs/image_rotational_pca/image_rotational_pca_main.cpp rename to src/xmipp/applications/programs/image_rotational_pca/image_rotational_pca_main.cpp diff --git a/applications/programs/image_rotational_spectra/image_rotational_spectra_main.cpp b/src/xmipp/applications/programs/image_rotational_spectra/image_rotational_spectra_main.cpp similarity index 100% rename from applications/programs/image_rotational_spectra/image_rotational_spectra_main.cpp rename to src/xmipp/applications/programs/image_rotational_spectra/image_rotational_spectra_main.cpp diff --git a/applications/programs/image_separate_objects/image_separate_objects_main.cpp b/src/xmipp/applications/programs/image_separate_objects/image_separate_objects_main.cpp similarity index 100% rename from applications/programs/image_separate_objects/image_separate_objects_main.cpp rename to src/xmipp/applications/programs/image_separate_objects/image_separate_objects_main.cpp diff --git a/applications/programs/image_sort_by_statistics/image_sort_by_statistics_main.cpp b/src/xmipp/applications/programs/image_sort_by_statistics/image_sort_by_statistics_main.cpp similarity index 100% rename from applications/programs/image_sort_by_statistics/image_sort_by_statistics_main.cpp rename to src/xmipp/applications/programs/image_sort_by_statistics/image_sort_by_statistics_main.cpp diff --git a/applications/programs/image_ssnr/image_ssnr_main.cpp b/src/xmipp/applications/programs/image_ssnr/image_ssnr_main.cpp similarity index 100% rename from applications/programs/image_ssnr/image_ssnr_main.cpp rename to src/xmipp/applications/programs/image_ssnr/image_ssnr_main.cpp diff --git a/applications/programs/image_statistics/image_statistics_main.cpp b/src/xmipp/applications/programs/image_statistics/image_statistics_main.cpp similarity index 100% rename from applications/programs/image_statistics/image_statistics_main.cpp rename to src/xmipp/applications/programs/image_statistics/image_statistics_main.cpp diff --git a/applications/programs/image_vectorize/image_vectorize_main.cpp b/src/xmipp/applications/programs/image_vectorize/image_vectorize_main.cpp similarity index 100% rename from applications/programs/image_vectorize/image_vectorize_main.cpp rename to src/xmipp/applications/programs/image_vectorize/image_vectorize_main.cpp diff --git a/applications/programs/matrix_dimred/matrix_dimred_main.cpp b/src/xmipp/applications/programs/matrix_dimred/matrix_dimred_main.cpp similarity index 100% rename from applications/programs/matrix_dimred/matrix_dimred_main.cpp rename to src/xmipp/applications/programs/matrix_dimred/matrix_dimred_main.cpp diff --git a/applications/programs/metadata_convert_to_spider/metadata_convert_to_spider_main.cpp b/src/xmipp/applications/programs/metadata_convert_to_spider/metadata_convert_to_spider_main.cpp similarity index 100% rename from applications/programs/metadata_convert_to_spider/metadata_convert_to_spider_main.cpp rename to src/xmipp/applications/programs/metadata_convert_to_spider/metadata_convert_to_spider_main.cpp diff --git a/applications/programs/metadata_histogram/metadata_histogram_main.cpp b/src/xmipp/applications/programs/metadata_histogram/metadata_histogram_main.cpp similarity index 100% rename from applications/programs/metadata_histogram/metadata_histogram_main.cpp rename to src/xmipp/applications/programs/metadata_histogram/metadata_histogram_main.cpp diff --git a/applications/programs/metadata_import/metadata_import_main.cpp b/src/xmipp/applications/programs/metadata_import/metadata_import_main.cpp similarity index 100% rename from applications/programs/metadata_import/metadata_import_main.cpp rename to src/xmipp/applications/programs/metadata_import/metadata_import_main.cpp diff --git a/applications/programs/metadata_split/metadata_split_main.cpp b/src/xmipp/applications/programs/metadata_split/metadata_split_main.cpp similarity index 100% rename from applications/programs/metadata_split/metadata_split_main.cpp rename to src/xmipp/applications/programs/metadata_split/metadata_split_main.cpp diff --git a/applications/programs/metadata_split_3D/metadata_split_3D_main.cpp b/src/xmipp/applications/programs/metadata_split_3D/metadata_split_3D_main.cpp similarity index 100% rename from applications/programs/metadata_split_3D/metadata_split_3D_main.cpp rename to src/xmipp/applications/programs/metadata_split_3D/metadata_split_3D_main.cpp diff --git a/applications/programs/metadata_utilities/metadata_utilities_main.cpp b/src/xmipp/applications/programs/metadata_utilities/metadata_utilities_main.cpp similarity index 100% rename from applications/programs/metadata_utilities/metadata_utilities_main.cpp rename to src/xmipp/applications/programs/metadata_utilities/metadata_utilities_main.cpp diff --git a/applications/programs/metadata_xml/metadata_xml_main.cpp b/src/xmipp/applications/programs/metadata_xml/metadata_xml_main.cpp similarity index 100% rename from applications/programs/metadata_xml/metadata_xml_main.cpp rename to src/xmipp/applications/programs/metadata_xml/metadata_xml_main.cpp diff --git a/applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.cpp b/src/xmipp/applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.cpp similarity index 100% rename from applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.cpp rename to src/xmipp/applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.cpp diff --git a/applications/programs/micrograph_scissor/micrograph_scissor_main.cpp b/src/xmipp/applications/programs/micrograph_scissor/micrograph_scissor_main.cpp similarity index 100% rename from applications/programs/micrograph_scissor/micrograph_scissor_main.cpp rename to src/xmipp/applications/programs/micrograph_scissor/micrograph_scissor_main.cpp diff --git a/applications/programs/ml_align2d/ml_align2d_main.cpp b/src/xmipp/applications/programs/ml_align2d/ml_align2d_main.cpp similarity index 100% rename from applications/programs/ml_align2d/ml_align2d_main.cpp rename to src/xmipp/applications/programs/ml_align2d/ml_align2d_main.cpp diff --git a/applications/programs/ml_refine3d/ml_refine3d_main.cpp b/src/xmipp/applications/programs/ml_refine3d/ml_refine3d_main.cpp similarity index 100% rename from applications/programs/ml_refine3d/ml_refine3d_main.cpp rename to src/xmipp/applications/programs/ml_refine3d/ml_refine3d_main.cpp diff --git a/applications/programs/ml_tomo/ml_tomo_main.cpp b/src/xmipp/applications/programs/ml_tomo/ml_tomo_main.cpp similarity index 100% rename from applications/programs/ml_tomo/ml_tomo_main.cpp rename to src/xmipp/applications/programs/ml_tomo/ml_tomo_main.cpp diff --git a/applications/programs/mlf_align2d/mlf_align2d_main.cpp b/src/xmipp/applications/programs/mlf_align2d/mlf_align2d_main.cpp similarity index 100% rename from applications/programs/mlf_align2d/mlf_align2d_main.cpp rename to src/xmipp/applications/programs/mlf_align2d/mlf_align2d_main.cpp diff --git a/applications/programs/mlf_refine3d/mlf_refine3d_main.cpp b/src/xmipp/applications/programs/mlf_refine3d/mlf_refine3d_main.cpp similarity index 100% rename from applications/programs/mlf_refine3d/mlf_refine3d_main.cpp rename to src/xmipp/applications/programs/mlf_refine3d/mlf_refine3d_main.cpp diff --git a/applications/programs/movie_alignment_correlation/movie_alignment_correlation.cpp b/src/xmipp/applications/programs/movie_alignment_correlation/movie_alignment_correlation.cpp similarity index 100% rename from applications/programs/movie_alignment_correlation/movie_alignment_correlation.cpp rename to src/xmipp/applications/programs/movie_alignment_correlation/movie_alignment_correlation.cpp diff --git a/applications/programs/movie_estimate_gain/movie_estimate_gain_main.cpp b/src/xmipp/applications/programs/movie_estimate_gain/movie_estimate_gain_main.cpp similarity index 100% rename from applications/programs/movie_estimate_gain/movie_estimate_gain_main.cpp rename to src/xmipp/applications/programs/movie_estimate_gain/movie_estimate_gain_main.cpp diff --git a/applications/programs/movie_filter_dose/movie_filter_dose.cpp b/src/xmipp/applications/programs/movie_filter_dose/movie_filter_dose.cpp similarity index 100% rename from applications/programs/movie_filter_dose/movie_filter_dose.cpp rename to src/xmipp/applications/programs/movie_filter_dose/movie_filter_dose.cpp diff --git a/applications/programs/movie_optical_alignment_cpu/README b/src/xmipp/applications/programs/movie_optical_alignment_cpu/README similarity index 100% rename from applications/programs/movie_optical_alignment_cpu/README rename to src/xmipp/applications/programs/movie_optical_alignment_cpu/README diff --git a/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp b/src/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp similarity index 100% rename from applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp rename to src/xmipp/applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.cpp diff --git a/applications/programs/movie_optical_alignment_gpu/README b/src/xmipp/applications/programs/movie_optical_alignment_gpu/README similarity index 100% rename from applications/programs/movie_optical_alignment_gpu/README rename to src/xmipp/applications/programs/movie_optical_alignment_gpu/README diff --git a/applications/programs/movie_optical_alignment_gpu/movie_optical_alignment_gpu.cpp b/src/xmipp/applications/programs/movie_optical_alignment_gpu/movie_optical_alignment_gpu.cpp similarity index 100% rename from applications/programs/movie_optical_alignment_gpu/movie_optical_alignment_gpu.cpp rename to src/xmipp/applications/programs/movie_optical_alignment_gpu/movie_optical_alignment_gpu.cpp diff --git a/applications/programs/mpi_angular_accuracy_pca/mpi_angular_accuracy_pca_main.cpp b/src/xmipp/applications/programs/mpi_angular_accuracy_pca/mpi_angular_accuracy_pca_main.cpp similarity index 100% rename from applications/programs/mpi_angular_accuracy_pca/mpi_angular_accuracy_pca_main.cpp rename to src/xmipp/applications/programs/mpi_angular_accuracy_pca/mpi_angular_accuracy_pca_main.cpp diff --git a/applications/programs/mpi_angular_class_average/mpi_angular_class_average_main.cpp b/src/xmipp/applications/programs/mpi_angular_class_average/mpi_angular_class_average_main.cpp similarity index 100% rename from applications/programs/mpi_angular_class_average/mpi_angular_class_average_main.cpp rename to src/xmipp/applications/programs/mpi_angular_class_average/mpi_angular_class_average_main.cpp diff --git a/applications/programs/mpi_angular_continuous_assign/mpi_angular_continuous_assign_main.cpp b/src/xmipp/applications/programs/mpi_angular_continuous_assign/mpi_angular_continuous_assign_main.cpp similarity index 100% rename from applications/programs/mpi_angular_continuous_assign/mpi_angular_continuous_assign_main.cpp rename to src/xmipp/applications/programs/mpi_angular_continuous_assign/mpi_angular_continuous_assign_main.cpp diff --git a/applications/programs/mpi_angular_continuous_assign2/mpi_angular_continuous_assign_main2.cpp b/src/xmipp/applications/programs/mpi_angular_continuous_assign2/mpi_angular_continuous_assign_main2.cpp similarity index 100% rename from applications/programs/mpi_angular_continuous_assign2/mpi_angular_continuous_assign_main2.cpp rename to src/xmipp/applications/programs/mpi_angular_continuous_assign2/mpi_angular_continuous_assign_main2.cpp diff --git a/applications/programs/mpi_angular_discrete_assign/mpi_angular_discrete_assign_main.cpp b/src/xmipp/applications/programs/mpi_angular_discrete_assign/mpi_angular_discrete_assign_main.cpp similarity index 100% rename from applications/programs/mpi_angular_discrete_assign/mpi_angular_discrete_assign_main.cpp rename to src/xmipp/applications/programs/mpi_angular_discrete_assign/mpi_angular_discrete_assign_main.cpp diff --git a/applications/programs/mpi_angular_project_library/mpi_angular_project_library_main.cpp b/src/xmipp/applications/programs/mpi_angular_project_library/mpi_angular_project_library_main.cpp similarity index 100% rename from applications/programs/mpi_angular_project_library/mpi_angular_project_library_main.cpp rename to src/xmipp/applications/programs/mpi_angular_project_library/mpi_angular_project_library_main.cpp diff --git a/applications/programs/mpi_angular_projection_matching/mpi_angular_projection_matching_main.cpp b/src/xmipp/applications/programs/mpi_angular_projection_matching/mpi_angular_projection_matching_main.cpp similarity index 100% rename from applications/programs/mpi_angular_projection_matching/mpi_angular_projection_matching_main.cpp rename to src/xmipp/applications/programs/mpi_angular_projection_matching/mpi_angular_projection_matching_main.cpp diff --git a/applications/programs/mpi_classify_CL2D/mpi_classify_CL2D.h b/src/xmipp/applications/programs/mpi_classify_CL2D/mpi_classify_CL2D.h similarity index 100% rename from applications/programs/mpi_classify_CL2D/mpi_classify_CL2D.h rename to src/xmipp/applications/programs/mpi_classify_CL2D/mpi_classify_CL2D.h diff --git a/applications/programs/mpi_classify_CL2D/mpi_classify_CL2D_main.cpp b/src/xmipp/applications/programs/mpi_classify_CL2D/mpi_classify_CL2D_main.cpp similarity index 100% rename from applications/programs/mpi_classify_CL2D/mpi_classify_CL2D_main.cpp rename to src/xmipp/applications/programs/mpi_classify_CL2D/mpi_classify_CL2D_main.cpp diff --git a/applications/programs/mpi_classify_CL2D_core_analysis/mpi_classify_CL2D_core_analysis_main.cpp b/src/xmipp/applications/programs/mpi_classify_CL2D_core_analysis/mpi_classify_CL2D_core_analysis_main.cpp similarity index 100% rename from applications/programs/mpi_classify_CL2D_core_analysis/mpi_classify_CL2D_core_analysis_main.cpp rename to src/xmipp/applications/programs/mpi_classify_CL2D_core_analysis/mpi_classify_CL2D_core_analysis_main.cpp diff --git a/applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo.h b/src/xmipp/applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo.h similarity index 100% rename from applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo.h rename to src/xmipp/applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo.h diff --git a/applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo_prog_main.cpp b/src/xmipp/applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo_prog_main.cpp similarity index 100% rename from applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo_prog_main.cpp rename to src/xmipp/applications/programs/mpi_classify_CLTomo_prog/mpi_classify_CLTomo_prog_main.cpp diff --git a/applications/programs/mpi_classify_FTTRI/mpi_classify_FTTRI_main.cpp b/src/xmipp/applications/programs/mpi_classify_FTTRI/mpi_classify_FTTRI_main.cpp similarity index 100% rename from applications/programs/mpi_classify_FTTRI/mpi_classify_FTTRI_main.cpp rename to src/xmipp/applications/programs/mpi_classify_FTTRI/mpi_classify_FTTRI_main.cpp diff --git a/applications/programs/mpi_ctf_correct_idr/mpi_ctf_correct_idr_main.cpp b/src/xmipp/applications/programs/mpi_ctf_correct_idr/mpi_ctf_correct_idr_main.cpp similarity index 100% rename from applications/programs/mpi_ctf_correct_idr/mpi_ctf_correct_idr_main.cpp rename to src/xmipp/applications/programs/mpi_ctf_correct_idr/mpi_ctf_correct_idr_main.cpp diff --git a/applications/programs/mpi_ctf_correct_wiener2d/mpi_ctf_correct_wiener2d_main.cpp b/src/xmipp/applications/programs/mpi_ctf_correct_wiener2d/mpi_ctf_correct_wiener2d_main.cpp similarity index 100% rename from applications/programs/mpi_ctf_correct_wiener2d/mpi_ctf_correct_wiener2d_main.cpp rename to src/xmipp/applications/programs/mpi_ctf_correct_wiener2d/mpi_ctf_correct_wiener2d_main.cpp diff --git a/applications/programs/mpi_ctf_sort_psds/mpi_ctf_sort_psds_main.cpp b/src/xmipp/applications/programs/mpi_ctf_sort_psds/mpi_ctf_sort_psds_main.cpp similarity index 100% rename from applications/programs/mpi_ctf_sort_psds/mpi_ctf_sort_psds_main.cpp rename to src/xmipp/applications/programs/mpi_ctf_sort_psds/mpi_ctf_sort_psds_main.cpp diff --git a/applications/programs/mpi_cuda_reconstruct_fourier/mpi_cuda_reconstruct_fourier_main.cpp b/src/xmipp/applications/programs/mpi_cuda_reconstruct_fourier/mpi_cuda_reconstruct_fourier_main.cpp similarity index 100% rename from applications/programs/mpi_cuda_reconstruct_fourier/mpi_cuda_reconstruct_fourier_main.cpp rename to src/xmipp/applications/programs/mpi_cuda_reconstruct_fourier/mpi_cuda_reconstruct_fourier_main.cpp diff --git a/applications/programs/mpi_image_eliminate_largeEnergy/mpi_image_eliminate_largeEnergy_main.cpp b/src/xmipp/applications/programs/mpi_image_eliminate_largeEnergy/mpi_image_eliminate_largeEnergy_main.cpp similarity index 100% rename from applications/programs/mpi_image_eliminate_largeEnergy/mpi_image_eliminate_largeEnergy_main.cpp rename to src/xmipp/applications/programs/mpi_image_eliminate_largeEnergy/mpi_image_eliminate_largeEnergy_main.cpp diff --git a/applications/programs/mpi_image_operate/mpi_image_operate_main.cpp b/src/xmipp/applications/programs/mpi_image_operate/mpi_image_operate_main.cpp similarity index 100% rename from applications/programs/mpi_image_operate/mpi_image_operate_main.cpp rename to src/xmipp/applications/programs/mpi_image_operate/mpi_image_operate_main.cpp diff --git a/applications/programs/mpi_image_resize/mpi_image_resize_main.cpp b/src/xmipp/applications/programs/mpi_image_resize/mpi_image_resize_main.cpp similarity index 100% rename from applications/programs/mpi_image_resize/mpi_image_resize_main.cpp rename to src/xmipp/applications/programs/mpi_image_resize/mpi_image_resize_main.cpp diff --git a/applications/programs/mpi_image_rotational_pca/mpi_image_rotational_pca_main.cpp b/src/xmipp/applications/programs/mpi_image_rotational_pca/mpi_image_rotational_pca_main.cpp similarity index 100% rename from applications/programs/mpi_image_rotational_pca/mpi_image_rotational_pca_main.cpp rename to src/xmipp/applications/programs/mpi_image_rotational_pca/mpi_image_rotational_pca_main.cpp diff --git a/applications/programs/mpi_image_sort/mpi_image_sort_main.cpp b/src/xmipp/applications/programs/mpi_image_sort/mpi_image_sort_main.cpp similarity index 100% rename from applications/programs/mpi_image_sort/mpi_image_sort_main.cpp rename to src/xmipp/applications/programs/mpi_image_sort/mpi_image_sort_main.cpp diff --git a/applications/programs/mpi_image_ssnr/mpi_image_ssnr_main.cpp b/src/xmipp/applications/programs/mpi_image_ssnr/mpi_image_ssnr_main.cpp similarity index 100% rename from applications/programs/mpi_image_ssnr/mpi_image_ssnr_main.cpp rename to src/xmipp/applications/programs/mpi_image_ssnr/mpi_image_ssnr_main.cpp diff --git a/applications/programs/mpi_ml_align2d/mpi_ml_align2d_main.cpp b/src/xmipp/applications/programs/mpi_ml_align2d/mpi_ml_align2d_main.cpp similarity index 100% rename from applications/programs/mpi_ml_align2d/mpi_ml_align2d_main.cpp rename to src/xmipp/applications/programs/mpi_ml_align2d/mpi_ml_align2d_main.cpp diff --git a/applications/programs/mpi_ml_refine3d/mpi_ml_refine3d_main.cpp b/src/xmipp/applications/programs/mpi_ml_refine3d/mpi_ml_refine3d_main.cpp similarity index 100% rename from applications/programs/mpi_ml_refine3d/mpi_ml_refine3d_main.cpp rename to src/xmipp/applications/programs/mpi_ml_refine3d/mpi_ml_refine3d_main.cpp diff --git a/applications/programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp b/src/xmipp/applications/programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp similarity index 100% rename from applications/programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp rename to src/xmipp/applications/programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp diff --git a/applications/programs/mpi_mlf_align2d/mpi_mlf_align2d_main.cpp b/src/xmipp/applications/programs/mpi_mlf_align2d/mpi_mlf_align2d_main.cpp similarity index 100% rename from applications/programs/mpi_mlf_align2d/mpi_mlf_align2d_main.cpp rename to src/xmipp/applications/programs/mpi_mlf_align2d/mpi_mlf_align2d_main.cpp diff --git a/applications/programs/mpi_mlf_refine3d/mpi_mlf_refine3d_main.cpp b/src/xmipp/applications/programs/mpi_mlf_refine3d/mpi_mlf_refine3d_main.cpp similarity index 100% rename from applications/programs/mpi_mlf_refine3d/mpi_mlf_refine3d_main.cpp rename to src/xmipp/applications/programs/mpi_mlf_refine3d/mpi_mlf_refine3d_main.cpp diff --git a/applications/programs/mpi_multireference_aligneability/mpi_multireference_aligneability_main.cpp b/src/xmipp/applications/programs/mpi_multireference_aligneability/mpi_multireference_aligneability_main.cpp similarity index 100% rename from applications/programs/mpi_multireference_aligneability/mpi_multireference_aligneability_main.cpp rename to src/xmipp/applications/programs/mpi_multireference_aligneability/mpi_multireference_aligneability_main.cpp diff --git a/applications/programs/mpi_nma_alignment/mpi_nma_alignment_main.cpp b/src/xmipp/applications/programs/mpi_nma_alignment/mpi_nma_alignment_main.cpp similarity index 100% rename from applications/programs/mpi_nma_alignment/mpi_nma_alignment_main.cpp rename to src/xmipp/applications/programs/mpi_nma_alignment/mpi_nma_alignment_main.cpp diff --git a/applications/programs/mpi_performance_test/mpi_performance_test_main.cpp b/src/xmipp/applications/programs/mpi_performance_test/mpi_performance_test_main.cpp similarity index 100% rename from applications/programs/mpi_performance_test/mpi_performance_test_main.cpp rename to src/xmipp/applications/programs/mpi_performance_test/mpi_performance_test_main.cpp diff --git a/applications/programs/mpi_reconstruct_admm/mpi_reconstruct_admm_main.cpp b/src/xmipp/applications/programs/mpi_reconstruct_admm/mpi_reconstruct_admm_main.cpp similarity index 100% rename from applications/programs/mpi_reconstruct_admm/mpi_reconstruct_admm_main.cpp rename to src/xmipp/applications/programs/mpi_reconstruct_admm/mpi_reconstruct_admm_main.cpp diff --git a/applications/programs/mpi_reconstruct_art/mpi_reconstruct_art_main.cpp b/src/xmipp/applications/programs/mpi_reconstruct_art/mpi_reconstruct_art_main.cpp similarity index 100% rename from applications/programs/mpi_reconstruct_art/mpi_reconstruct_art_main.cpp rename to src/xmipp/applications/programs/mpi_reconstruct_art/mpi_reconstruct_art_main.cpp diff --git a/applications/programs/mpi_reconstruct_fourier/mpi_reconstruct_fourier_main.cpp b/src/xmipp/applications/programs/mpi_reconstruct_fourier/mpi_reconstruct_fourier_main.cpp similarity index 100% rename from applications/programs/mpi_reconstruct_fourier/mpi_reconstruct_fourier_main.cpp rename to src/xmipp/applications/programs/mpi_reconstruct_fourier/mpi_reconstruct_fourier_main.cpp diff --git a/applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.cpp b/src/xmipp/applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.cpp similarity index 100% rename from applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.cpp rename to src/xmipp/applications/programs/mpi_reconstruct_fourier_accel/mpi_reconstruct_fourier_accel_main.cpp diff --git a/applications/programs/mpi_reconstruct_significant/mpi_reconstruct_significant_main.cpp b/src/xmipp/applications/programs/mpi_reconstruct_significant/mpi_reconstruct_significant_main.cpp similarity index 100% rename from applications/programs/mpi_reconstruct_significant/mpi_reconstruct_significant_main.cpp rename to src/xmipp/applications/programs/mpi_reconstruct_significant/mpi_reconstruct_significant_main.cpp diff --git a/applications/programs/mpi_reconstruct_wbp/mpi_reconstruct_wbp_main.cpp b/src/xmipp/applications/programs/mpi_reconstruct_wbp/mpi_reconstruct_wbp_main.cpp similarity index 100% rename from applications/programs/mpi_reconstruct_wbp/mpi_reconstruct_wbp_main.cpp rename to src/xmipp/applications/programs/mpi_reconstruct_wbp/mpi_reconstruct_wbp_main.cpp diff --git a/applications/programs/mpi_run/mpi_run_main.cpp b/src/xmipp/applications/programs/mpi_run/mpi_run_main.cpp similarity index 100% rename from applications/programs/mpi_run/mpi_run_main.cpp rename to src/xmipp/applications/programs/mpi_run/mpi_run_main.cpp diff --git a/applications/programs/mpi_tomo_extract_subvolume/mpi_tomo_extract_subvolume.cpp b/src/xmipp/applications/programs/mpi_tomo_extract_subvolume/mpi_tomo_extract_subvolume.cpp similarity index 100% rename from applications/programs/mpi_tomo_extract_subvolume/mpi_tomo_extract_subvolume.cpp rename to src/xmipp/applications/programs/mpi_tomo_extract_subvolume/mpi_tomo_extract_subvolume.cpp diff --git a/applications/programs/mpi_transform_adjust_image_grey_levels/mpi_transform_adjust_image_grey_levels_main.cpp b/src/xmipp/applications/programs/mpi_transform_adjust_image_grey_levels/mpi_transform_adjust_image_grey_levels_main.cpp similarity index 100% rename from applications/programs/mpi_transform_adjust_image_grey_levels/mpi_transform_adjust_image_grey_levels_main.cpp rename to src/xmipp/applications/programs/mpi_transform_adjust_image_grey_levels/mpi_transform_adjust_image_grey_levels_main.cpp diff --git a/applications/programs/mpi_transform_filter/mpi_transform_filter_main.cpp b/src/xmipp/applications/programs/mpi_transform_filter/mpi_transform_filter_main.cpp similarity index 100% rename from applications/programs/mpi_transform_filter/mpi_transform_filter_main.cpp rename to src/xmipp/applications/programs/mpi_transform_filter/mpi_transform_filter_main.cpp diff --git a/applications/programs/mpi_transform_geometry/mpi_transform_geometry_main.cpp b/src/xmipp/applications/programs/mpi_transform_geometry/mpi_transform_geometry_main.cpp similarity index 100% rename from applications/programs/mpi_transform_geometry/mpi_transform_geometry_main.cpp rename to src/xmipp/applications/programs/mpi_transform_geometry/mpi_transform_geometry_main.cpp diff --git a/applications/programs/mpi_transform_mask/mpi_transform_mask_main.cpp b/src/xmipp/applications/programs/mpi_transform_mask/mpi_transform_mask_main.cpp similarity index 100% rename from applications/programs/mpi_transform_mask/mpi_transform_mask_main.cpp rename to src/xmipp/applications/programs/mpi_transform_mask/mpi_transform_mask_main.cpp diff --git a/applications/programs/mpi_transform_normalize/mpi_transform_normalize_main.cpp b/src/xmipp/applications/programs/mpi_transform_normalize/mpi_transform_normalize_main.cpp similarity index 100% rename from applications/programs/mpi_transform_normalize/mpi_transform_normalize_main.cpp rename to src/xmipp/applications/programs/mpi_transform_normalize/mpi_transform_normalize_main.cpp diff --git a/applications/programs/mpi_transform_symmetrize/mpi_transform_symmetrize.cpp b/src/xmipp/applications/programs/mpi_transform_symmetrize/mpi_transform_symmetrize.cpp similarity index 100% rename from applications/programs/mpi_transform_symmetrize/mpi_transform_symmetrize.cpp rename to src/xmipp/applications/programs/mpi_transform_symmetrize/mpi_transform_symmetrize.cpp diff --git a/applications/programs/mpi_transform_threshold/mpi_transform_threshold_main.cpp b/src/xmipp/applications/programs/mpi_transform_threshold/mpi_transform_threshold_main.cpp similarity index 100% rename from applications/programs/mpi_transform_threshold/mpi_transform_threshold_main.cpp rename to src/xmipp/applications/programs/mpi_transform_threshold/mpi_transform_threshold_main.cpp diff --git a/applications/programs/mpi_validation_nontilt/mpi_validation_nontilt_main.cpp b/src/xmipp/applications/programs/mpi_validation_nontilt/mpi_validation_nontilt_main.cpp similarity index 100% rename from applications/programs/mpi_validation_nontilt/mpi_validation_nontilt_main.cpp rename to src/xmipp/applications/programs/mpi_validation_nontilt/mpi_validation_nontilt_main.cpp diff --git a/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.cpp b/src/xmipp/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.cpp similarity index 100% rename from applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.cpp rename to src/xmipp/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.cpp diff --git a/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.h b/src/xmipp/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.h similarity index 100% rename from applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.h rename to src/xmipp/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer.h diff --git a/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer_main.cpp b/src/xmipp/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer_main.cpp similarity index 100% rename from applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer_main.cpp rename to src/xmipp/applications/programs/mpi_volume_homogenizer/mpi_volume_homogenizer_main.cpp diff --git a/applications/programs/mpi_volume_homogenizer/volume_homogenizer.cpp b/src/xmipp/applications/programs/mpi_volume_homogenizer/volume_homogenizer.cpp similarity index 100% rename from applications/programs/mpi_volume_homogenizer/volume_homogenizer.cpp rename to src/xmipp/applications/programs/mpi_volume_homogenizer/volume_homogenizer.cpp diff --git a/applications/programs/mpi_volume_homogenizer/volume_homogenizer.h b/src/xmipp/applications/programs/mpi_volume_homogenizer/volume_homogenizer.h similarity index 100% rename from applications/programs/mpi_volume_homogenizer/volume_homogenizer.h rename to src/xmipp/applications/programs/mpi_volume_homogenizer/volume_homogenizer.h diff --git a/applications/programs/mpi_write_test/mpi_write_test.cpp b/src/xmipp/applications/programs/mpi_write_test/mpi_write_test.cpp similarity index 100% rename from applications/programs/mpi_write_test/mpi_write_test.cpp rename to src/xmipp/applications/programs/mpi_write_test/mpi_write_test.cpp diff --git a/applications/programs/mpi_xray_project/mpi_xray_project_main.cpp b/src/xmipp/applications/programs/mpi_xray_project/mpi_xray_project_main.cpp similarity index 100% rename from applications/programs/mpi_xray_project/mpi_xray_project_main.cpp rename to src/xmipp/applications/programs/mpi_xray_project/mpi_xray_project_main.cpp diff --git a/applications/programs/mrc_create_metadata/mrc_create_metadata_main.cpp b/src/xmipp/applications/programs/mrc_create_metadata/mrc_create_metadata_main.cpp similarity index 100% rename from applications/programs/mrc_create_metadata/mrc_create_metadata_main.cpp rename to src/xmipp/applications/programs/mrc_create_metadata/mrc_create_metadata_main.cpp diff --git a/applications/programs/multireference_aligneability/multireference_aligneabililty_main.cpp b/src/xmipp/applications/programs/multireference_aligneability/multireference_aligneabililty_main.cpp similarity index 100% rename from applications/programs/multireference_aligneability/multireference_aligneabililty_main.cpp rename to src/xmipp/applications/programs/multireference_aligneability/multireference_aligneabililty_main.cpp diff --git a/applications/programs/nma_alignment/nma_alignment_main.cpp b/src/xmipp/applications/programs/nma_alignment/nma_alignment_main.cpp similarity index 100% rename from applications/programs/nma_alignment/nma_alignment_main.cpp rename to src/xmipp/applications/programs/nma_alignment/nma_alignment_main.cpp diff --git a/applications/programs/nma_alignment_vol/nma_alignment_vol_main.cpp b/src/xmipp/applications/programs/nma_alignment_vol/nma_alignment_vol_main.cpp similarity index 100% rename from applications/programs/nma_alignment_vol/nma_alignment_vol_main.cpp rename to src/xmipp/applications/programs/nma_alignment_vol/nma_alignment_vol_main.cpp diff --git a/applications/programs/pdb_analysis/pdb_analysis_main.cpp b/src/xmipp/applications/programs/pdb_analysis/pdb_analysis_main.cpp similarity index 100% rename from applications/programs/pdb_analysis/pdb_analysis_main.cpp rename to src/xmipp/applications/programs/pdb_analysis/pdb_analysis_main.cpp diff --git a/applications/programs/pdb_construct_dictionary/pdb_construct_dictionary_main.cpp b/src/xmipp/applications/programs/pdb_construct_dictionary/pdb_construct_dictionary_main.cpp similarity index 100% rename from applications/programs/pdb_construct_dictionary/pdb_construct_dictionary_main.cpp rename to src/xmipp/applications/programs/pdb_construct_dictionary/pdb_construct_dictionary_main.cpp diff --git a/applications/programs/pdb_nma_deform/pdb_nma_deform_main.cpp b/src/xmipp/applications/programs/pdb_nma_deform/pdb_nma_deform_main.cpp similarity index 100% rename from applications/programs/pdb_nma_deform/pdb_nma_deform_main.cpp rename to src/xmipp/applications/programs/pdb_nma_deform/pdb_nma_deform_main.cpp diff --git a/applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.cpp b/src/xmipp/applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.cpp similarity index 100% rename from applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.cpp rename to src/xmipp/applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.cpp diff --git a/applications/programs/pdb_restore_with_dictionary/pdb_restore_with_dictionary_main.cpp b/src/xmipp/applications/programs/pdb_restore_with_dictionary/pdb_restore_with_dictionary_main.cpp similarity index 100% rename from applications/programs/pdb_restore_with_dictionary/pdb_restore_with_dictionary_main.cpp rename to src/xmipp/applications/programs/pdb_restore_with_dictionary/pdb_restore_with_dictionary_main.cpp diff --git a/applications/programs/phantom_create/phantom_create_main.cpp b/src/xmipp/applications/programs/phantom_create/phantom_create_main.cpp similarity index 100% rename from applications/programs/phantom_create/phantom_create_main.cpp rename to src/xmipp/applications/programs/phantom_create/phantom_create_main.cpp diff --git a/applications/programs/phantom_movie/phantom_movie_main.cpp b/src/xmipp/applications/programs/phantom_movie/phantom_movie_main.cpp similarity index 100% rename from applications/programs/phantom_movie/phantom_movie_main.cpp rename to src/xmipp/applications/programs/phantom_movie/phantom_movie_main.cpp diff --git a/applications/programs/phantom_project/phantom_project_main.cpp b/src/xmipp/applications/programs/phantom_project/phantom_project_main.cpp similarity index 100% rename from applications/programs/phantom_project/phantom_project_main.cpp rename to src/xmipp/applications/programs/phantom_project/phantom_project_main.cpp diff --git a/applications/programs/phantom_simulate_microscope/phantom_simulate_microscope_main.cpp b/src/xmipp/applications/programs/phantom_simulate_microscope/phantom_simulate_microscope_main.cpp similarity index 100% rename from applications/programs/phantom_simulate_microscope/phantom_simulate_microscope_main.cpp rename to src/xmipp/applications/programs/phantom_simulate_microscope/phantom_simulate_microscope_main.cpp diff --git a/applications/programs/phantom_transform/phantom_transform_main.cpp b/src/xmipp/applications/programs/phantom_transform/phantom_transform_main.cpp similarity index 100% rename from applications/programs/phantom_transform/phantom_transform_main.cpp rename to src/xmipp/applications/programs/phantom_transform/phantom_transform_main.cpp diff --git a/applications/programs/reconstruct_admm/reconstruct_admm_main.cpp b/src/xmipp/applications/programs/reconstruct_admm/reconstruct_admm_main.cpp similarity index 100% rename from applications/programs/reconstruct_admm/reconstruct_admm_main.cpp rename to src/xmipp/applications/programs/reconstruct_admm/reconstruct_admm_main.cpp diff --git a/applications/programs/reconstruct_art/reconstruct_art_main.cpp b/src/xmipp/applications/programs/reconstruct_art/reconstruct_art_main.cpp similarity index 100% rename from applications/programs/reconstruct_art/reconstruct_art_main.cpp rename to src/xmipp/applications/programs/reconstruct_art/reconstruct_art_main.cpp diff --git a/applications/programs/reconstruct_art_pseudo/reconstruct_art_pseudo_main.cpp b/src/xmipp/applications/programs/reconstruct_art_pseudo/reconstruct_art_pseudo_main.cpp similarity index 100% rename from applications/programs/reconstruct_art_pseudo/reconstruct_art_pseudo_main.cpp rename to src/xmipp/applications/programs/reconstruct_art_pseudo/reconstruct_art_pseudo_main.cpp diff --git a/applications/programs/reconstruct_art_xray/reconstruct_art_xray_main.cpp b/src/xmipp/applications/programs/reconstruct_art_xray/reconstruct_art_xray_main.cpp similarity index 100% rename from applications/programs/reconstruct_art_xray/reconstruct_art_xray_main.cpp rename to src/xmipp/applications/programs/reconstruct_art_xray/reconstruct_art_xray_main.cpp diff --git a/applications/programs/reconstruct_fourier/reconstruct_fourier_main.cpp b/src/xmipp/applications/programs/reconstruct_fourier/reconstruct_fourier_main.cpp similarity index 100% rename from applications/programs/reconstruct_fourier/reconstruct_fourier_main.cpp rename to src/xmipp/applications/programs/reconstruct_fourier/reconstruct_fourier_main.cpp diff --git a/applications/programs/reconstruct_fourier_accel/reconstruct_fourier_accel_main.cpp b/src/xmipp/applications/programs/reconstruct_fourier_accel/reconstruct_fourier_accel_main.cpp similarity index 100% rename from applications/programs/reconstruct_fourier_accel/reconstruct_fourier_accel_main.cpp rename to src/xmipp/applications/programs/reconstruct_fourier_accel/reconstruct_fourier_accel_main.cpp diff --git a/applications/programs/reconstruct_significant/reconstruct_significant_main.cpp b/src/xmipp/applications/programs/reconstruct_significant/reconstruct_significant_main.cpp similarity index 100% rename from applications/programs/reconstruct_significant/reconstruct_significant_main.cpp rename to src/xmipp/applications/programs/reconstruct_significant/reconstruct_significant_main.cpp diff --git a/applications/programs/reconstruct_wbp/reconstruct_wbp_main.cpp b/src/xmipp/applications/programs/reconstruct_wbp/reconstruct_wbp_main.cpp similarity index 100% rename from applications/programs/reconstruct_wbp/reconstruct_wbp_main.cpp rename to src/xmipp/applications/programs/reconstruct_wbp/reconstruct_wbp_main.cpp diff --git a/applications/programs/resolution_directional/resolution_directional_main.cpp b/src/xmipp/applications/programs/resolution_directional/resolution_directional_main.cpp similarity index 100% rename from applications/programs/resolution_directional/resolution_directional_main.cpp rename to src/xmipp/applications/programs/resolution_directional/resolution_directional_main.cpp diff --git a/applications/programs/resolution_fsc/resolution_fsc_main.cpp b/src/xmipp/applications/programs/resolution_fsc/resolution_fsc_main.cpp similarity index 100% rename from applications/programs/resolution_fsc/resolution_fsc_main.cpp rename to src/xmipp/applications/programs/resolution_fsc/resolution_fsc_main.cpp diff --git a/applications/programs/resolution_ibw/resolution_ibw_main.cpp b/src/xmipp/applications/programs/resolution_ibw/resolution_ibw_main.cpp similarity index 100% rename from applications/programs/resolution_ibw/resolution_ibw_main.cpp rename to src/xmipp/applications/programs/resolution_ibw/resolution_ibw_main.cpp diff --git a/applications/programs/resolution_localfilter/resolution_localfilter_main.cpp b/src/xmipp/applications/programs/resolution_localfilter/resolution_localfilter_main.cpp similarity index 100% rename from applications/programs/resolution_localfilter/resolution_localfilter_main.cpp rename to src/xmipp/applications/programs/resolution_localfilter/resolution_localfilter_main.cpp diff --git a/applications/programs/resolution_monogenic_signal/resolution_monogenic_signal_main.cpp b/src/xmipp/applications/programs/resolution_monogenic_signal/resolution_monogenic_signal_main.cpp similarity index 100% rename from applications/programs/resolution_monogenic_signal/resolution_monogenic_signal_main.cpp rename to src/xmipp/applications/programs/resolution_monogenic_signal/resolution_monogenic_signal_main.cpp diff --git a/applications/programs/resolution_monotomo/resolution_monotomo_main.cpp b/src/xmipp/applications/programs/resolution_monotomo/resolution_monotomo_main.cpp similarity index 100% rename from applications/programs/resolution_monotomo/resolution_monotomo_main.cpp rename to src/xmipp/applications/programs/resolution_monotomo/resolution_monotomo_main.cpp diff --git a/applications/programs/resolution_ssnr/resolution_ssnr_main.cpp b/src/xmipp/applications/programs/resolution_ssnr/resolution_ssnr_main.cpp similarity index 100% rename from applications/programs/resolution_ssnr/resolution_ssnr_main.cpp rename to src/xmipp/applications/programs/resolution_ssnr/resolution_ssnr_main.cpp diff --git a/applications/programs/score_micrograph/score_micrograph_main.cpp b/src/xmipp/applications/programs/score_micrograph/score_micrograph_main.cpp similarity index 100% rename from applications/programs/score_micrograph/score_micrograph_main.cpp rename to src/xmipp/applications/programs/score_micrograph/score_micrograph_main.cpp diff --git a/applications/programs/tomo_align_dual_tilt_series/tomo_align_dual_tilt_series_main.cpp b/src/xmipp/applications/programs/tomo_align_dual_tilt_series/tomo_align_dual_tilt_series_main.cpp similarity index 100% rename from applications/programs/tomo_align_dual_tilt_series/tomo_align_dual_tilt_series_main.cpp rename to src/xmipp/applications/programs/tomo_align_dual_tilt_series/tomo_align_dual_tilt_series_main.cpp diff --git a/applications/programs/tomo_align_refinement/tomo_align_refinement_main.cpp b/src/xmipp/applications/programs/tomo_align_refinement/tomo_align_refinement_main.cpp similarity index 100% rename from applications/programs/tomo_align_refinement/tomo_align_refinement_main.cpp rename to src/xmipp/applications/programs/tomo_align_refinement/tomo_align_refinement_main.cpp diff --git a/applications/programs/tomo_align_tilt_series/tomo_align_tilt_series_main.cpp b/src/xmipp/applications/programs/tomo_align_tilt_series/tomo_align_tilt_series_main.cpp similarity index 100% rename from applications/programs/tomo_align_tilt_series/tomo_align_tilt_series_main.cpp rename to src/xmipp/applications/programs/tomo_align_tilt_series/tomo_align_tilt_series_main.cpp diff --git a/applications/programs/tomo_detect_missing_wedge/tomo_detect_missing_wedge_main.cpp b/src/xmipp/applications/programs/tomo_detect_missing_wedge/tomo_detect_missing_wedge_main.cpp similarity index 100% rename from applications/programs/tomo_detect_missing_wedge/tomo_detect_missing_wedge_main.cpp rename to src/xmipp/applications/programs/tomo_detect_missing_wedge/tomo_detect_missing_wedge_main.cpp diff --git a/applications/programs/tomo_extract_subvolume/tomo_extract_volume_main.cpp b/src/xmipp/applications/programs/tomo_extract_subvolume/tomo_extract_volume_main.cpp similarity index 100% rename from applications/programs/tomo_extract_subvolume/tomo_extract_volume_main.cpp rename to src/xmipp/applications/programs/tomo_extract_subvolume/tomo_extract_volume_main.cpp diff --git a/applications/programs/tomo_project/tomo_project_main.cpp b/src/xmipp/applications/programs/tomo_project/tomo_project_main.cpp similarity index 100% rename from applications/programs/tomo_project/tomo_project_main.cpp rename to src/xmipp/applications/programs/tomo_project/tomo_project_main.cpp diff --git a/applications/programs/tomo_remove_fluctuations/tomo_remove_fluctuations_main.cpp b/src/xmipp/applications/programs/tomo_remove_fluctuations/tomo_remove_fluctuations_main.cpp similarity index 100% rename from applications/programs/tomo_remove_fluctuations/tomo_remove_fluctuations_main.cpp rename to src/xmipp/applications/programs/tomo_remove_fluctuations/tomo_remove_fluctuations_main.cpp diff --git a/applications/programs/transform_add_noise/transform_add_noise_main.cpp b/src/xmipp/applications/programs/transform_add_noise/transform_add_noise_main.cpp similarity index 100% rename from applications/programs/transform_add_noise/transform_add_noise_main.cpp rename to src/xmipp/applications/programs/transform_add_noise/transform_add_noise_main.cpp diff --git a/applications/programs/transform_adjust_image_grey_levels/transform_adjust_image_grey_levels_main.cpp b/src/xmipp/applications/programs/transform_adjust_image_grey_levels/transform_adjust_image_grey_levels_main.cpp similarity index 100% rename from applications/programs/transform_adjust_image_grey_levels/transform_adjust_image_grey_levels_main.cpp rename to src/xmipp/applications/programs/transform_adjust_image_grey_levels/transform_adjust_image_grey_levels_main.cpp diff --git a/applications/programs/transform_adjust_volume_grey_levels/transform_adjust_volume_grey_levels_main.cpp b/src/xmipp/applications/programs/transform_adjust_volume_grey_levels/transform_adjust_volume_grey_levels_main.cpp similarity index 100% rename from applications/programs/transform_adjust_volume_grey_levels/transform_adjust_volume_grey_levels_main.cpp rename to src/xmipp/applications/programs/transform_adjust_volume_grey_levels/transform_adjust_volume_grey_levels_main.cpp diff --git a/applications/programs/transform_center_image/transform_center_image_main.cpp b/src/xmipp/applications/programs/transform_center_image/transform_center_image_main.cpp similarity index 100% rename from applications/programs/transform_center_image/transform_center_image_main.cpp rename to src/xmipp/applications/programs/transform_center_image/transform_center_image_main.cpp diff --git a/applications/programs/transform_dimred/transform_dimred_main.cpp b/src/xmipp/applications/programs/transform_dimred/transform_dimred_main.cpp similarity index 100% rename from applications/programs/transform_dimred/transform_dimred_main.cpp rename to src/xmipp/applications/programs/transform_dimred/transform_dimred_main.cpp diff --git a/applications/programs/transform_downsample/transform_downsample_main.cpp b/src/xmipp/applications/programs/transform_downsample/transform_downsample_main.cpp similarity index 100% rename from applications/programs/transform_downsample/transform_downsample_main.cpp rename to src/xmipp/applications/programs/transform_downsample/transform_downsample_main.cpp diff --git a/applications/programs/transform_filter/transform_filter_main.cpp b/src/xmipp/applications/programs/transform_filter/transform_filter_main.cpp similarity index 100% rename from applications/programs/transform_filter/transform_filter_main.cpp rename to src/xmipp/applications/programs/transform_filter/transform_filter_main.cpp diff --git a/applications/programs/transform_geometry/transform_geometry_main.cpp b/src/xmipp/applications/programs/transform_geometry/transform_geometry_main.cpp similarity index 100% rename from applications/programs/transform_geometry/transform_geometry_main.cpp rename to src/xmipp/applications/programs/transform_geometry/transform_geometry_main.cpp diff --git a/applications/programs/transform_mask/transform_mask_main.cpp b/src/xmipp/applications/programs/transform_mask/transform_mask_main.cpp similarity index 100% rename from applications/programs/transform_mask/transform_mask_main.cpp rename to src/xmipp/applications/programs/transform_mask/transform_mask_main.cpp diff --git a/applications/programs/transform_mirror/transform_mirror_main.cpp b/src/xmipp/applications/programs/transform_mirror/transform_mirror_main.cpp similarity index 100% rename from applications/programs/transform_mirror/transform_mirror_main.cpp rename to src/xmipp/applications/programs/transform_mirror/transform_mirror_main.cpp diff --git a/applications/programs/transform_morphology/transform_morphology_main.cpp b/src/xmipp/applications/programs/transform_morphology/transform_morphology_main.cpp similarity index 100% rename from applications/programs/transform_morphology/transform_morphology_main.cpp rename to src/xmipp/applications/programs/transform_morphology/transform_morphology_main.cpp diff --git a/applications/programs/transform_normalize/transform_normalize_main.cpp b/src/xmipp/applications/programs/transform_normalize/transform_normalize_main.cpp similarity index 100% rename from applications/programs/transform_normalize/transform_normalize_main.cpp rename to src/xmipp/applications/programs/transform_normalize/transform_normalize_main.cpp diff --git a/applications/programs/transform_randomize_phases/transform_randomize_phases_main.cpp b/src/xmipp/applications/programs/transform_randomize_phases/transform_randomize_phases_main.cpp similarity index 100% rename from applications/programs/transform_randomize_phases/transform_randomize_phases_main.cpp rename to src/xmipp/applications/programs/transform_randomize_phases/transform_randomize_phases_main.cpp diff --git a/applications/programs/transform_range_adjust/transform_range_adjust_main.cpp b/src/xmipp/applications/programs/transform_range_adjust/transform_range_adjust_main.cpp similarity index 100% rename from applications/programs/transform_range_adjust/transform_range_adjust_main.cpp rename to src/xmipp/applications/programs/transform_range_adjust/transform_range_adjust_main.cpp diff --git a/applications/programs/transform_symmetrize/transform_symmetrize_main.cpp b/src/xmipp/applications/programs/transform_symmetrize/transform_symmetrize_main.cpp similarity index 100% rename from applications/programs/transform_symmetrize/transform_symmetrize_main.cpp rename to src/xmipp/applications/programs/transform_symmetrize/transform_symmetrize_main.cpp diff --git a/applications/programs/transform_threshold/transform_threshold_main.cpp b/src/xmipp/applications/programs/transform_threshold/transform_threshold_main.cpp similarity index 100% rename from applications/programs/transform_threshold/transform_threshold_main.cpp rename to src/xmipp/applications/programs/transform_threshold/transform_threshold_main.cpp diff --git a/applications/programs/transform_window/transform_window_main.cpp b/src/xmipp/applications/programs/transform_window/transform_window_main.cpp similarity index 100% rename from applications/programs/transform_window/transform_window_main.cpp rename to src/xmipp/applications/programs/transform_window/transform_window_main.cpp diff --git a/applications/programs/validation_nontilt/validation_nontilt_main.cpp b/src/xmipp/applications/programs/validation_nontilt/validation_nontilt_main.cpp similarity index 100% rename from applications/programs/validation_nontilt/validation_nontilt_main.cpp rename to src/xmipp/applications/programs/validation_nontilt/validation_nontilt_main.cpp diff --git a/applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.cpp b/src/xmipp/applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.cpp similarity index 100% rename from applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.cpp rename to src/xmipp/applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.cpp diff --git a/applications/programs/volume_align_prog/volume_align_prog_main.cpp b/src/xmipp/applications/programs/volume_align_prog/volume_align_prog_main.cpp similarity index 100% rename from applications/programs/volume_align_prog/volume_align_prog_main.cpp rename to src/xmipp/applications/programs/volume_align_prog/volume_align_prog_main.cpp diff --git a/applications/programs/volume_center/volume_center_main.cpp b/src/xmipp/applications/programs/volume_center/volume_center_main.cpp similarity index 100% rename from applications/programs/volume_center/volume_center_main.cpp rename to src/xmipp/applications/programs/volume_center/volume_center_main.cpp diff --git a/applications/programs/volume_correct_bfactor/volume_correct_bfactor_main.cpp b/src/xmipp/applications/programs/volume_correct_bfactor/volume_correct_bfactor_main.cpp similarity index 100% rename from applications/programs/volume_correct_bfactor/volume_correct_bfactor_main.cpp rename to src/xmipp/applications/programs/volume_correct_bfactor/volume_correct_bfactor_main.cpp diff --git a/applications/programs/volume_deform_sph/volume_deform_sph_main.cpp b/src/xmipp/applications/programs/volume_deform_sph/volume_deform_sph_main.cpp similarity index 100% rename from applications/programs/volume_deform_sph/volume_deform_sph_main.cpp rename to src/xmipp/applications/programs/volume_deform_sph/volume_deform_sph_main.cpp diff --git a/applications/programs/volume_enhance_contrast/volume_enhance_contrast_main.cpp b/src/xmipp/applications/programs/volume_enhance_contrast/volume_enhance_contrast_main.cpp similarity index 100% rename from applications/programs/volume_enhance_contrast/volume_enhance_contrast_main.cpp rename to src/xmipp/applications/programs/volume_enhance_contrast/volume_enhance_contrast_main.cpp diff --git a/applications/programs/volume_find_symmetry/volume_find_symmetry_main.cpp b/src/xmipp/applications/programs/volume_find_symmetry/volume_find_symmetry_main.cpp similarity index 100% rename from applications/programs/volume_find_symmetry/volume_find_symmetry_main.cpp rename to src/xmipp/applications/programs/volume_find_symmetry/volume_find_symmetry_main.cpp diff --git a/applications/programs/volume_from_pdb/volume_from_pdb_main.cpp b/src/xmipp/applications/programs/volume_from_pdb/volume_from_pdb_main.cpp similarity index 100% rename from applications/programs/volume_from_pdb/volume_from_pdb_main.cpp rename to src/xmipp/applications/programs/volume_from_pdb/volume_from_pdb_main.cpp diff --git a/applications/programs/volume_halves_restoration/volume_halves_restoration_main.cpp b/src/xmipp/applications/programs/volume_halves_restoration/volume_halves_restoration_main.cpp similarity index 100% rename from applications/programs/volume_halves_restoration/volume_halves_restoration_main.cpp rename to src/xmipp/applications/programs/volume_halves_restoration/volume_halves_restoration_main.cpp diff --git a/applications/programs/volume_initial_simulated_annealing/volume_initial_simulated_annealing_main.cpp b/src/xmipp/applications/programs/volume_initial_simulated_annealing/volume_initial_simulated_annealing_main.cpp similarity index 100% rename from applications/programs/volume_initial_simulated_annealing/volume_initial_simulated_annealing_main.cpp rename to src/xmipp/applications/programs/volume_initial_simulated_annealing/volume_initial_simulated_annealing_main.cpp diff --git a/applications/programs/volume_local_sharpening/volume_local_sharpening_main.cpp b/src/xmipp/applications/programs/volume_local_sharpening/volume_local_sharpening_main.cpp similarity index 100% rename from applications/programs/volume_local_sharpening/volume_local_sharpening_main.cpp rename to src/xmipp/applications/programs/volume_local_sharpening/volume_local_sharpening_main.cpp diff --git a/applications/programs/volume_pca/volume_pca_main.cpp b/src/xmipp/applications/programs/volume_pca/volume_pca_main.cpp similarity index 100% rename from applications/programs/volume_pca/volume_pca_main.cpp rename to src/xmipp/applications/programs/volume_pca/volume_pca_main.cpp diff --git a/applications/programs/volume_reslice/volume_reslice_main.cpp b/src/xmipp/applications/programs/volume_reslice/volume_reslice_main.cpp similarity index 100% rename from applications/programs/volume_reslice/volume_reslice_main.cpp rename to src/xmipp/applications/programs/volume_reslice/volume_reslice_main.cpp diff --git a/applications/programs/volume_segment/volume_segment_main.cpp b/src/xmipp/applications/programs/volume_segment/volume_segment_main.cpp similarity index 100% rename from applications/programs/volume_segment/volume_segment_main.cpp rename to src/xmipp/applications/programs/volume_segment/volume_segment_main.cpp diff --git a/applications/programs/volume_structure_factor/volume_structure_factor_main.cpp b/src/xmipp/applications/programs/volume_structure_factor/volume_structure_factor_main.cpp similarity index 100% rename from applications/programs/volume_structure_factor/volume_structure_factor_main.cpp rename to src/xmipp/applications/programs/volume_structure_factor/volume_structure_factor_main.cpp diff --git a/applications/programs/volume_to_pseudoatoms/volume_to_pseudoatoms_main.cpp b/src/xmipp/applications/programs/volume_to_pseudoatoms/volume_to_pseudoatoms_main.cpp similarity index 100% rename from applications/programs/volume_to_pseudoatoms/volume_to_pseudoatoms_main.cpp rename to src/xmipp/applications/programs/volume_to_pseudoatoms/volume_to_pseudoatoms_main.cpp diff --git a/applications/programs/volume_to_web/volume_to_web_main.cpp b/src/xmipp/applications/programs/volume_to_web/volume_to_web_main.cpp similarity index 100% rename from applications/programs/volume_to_web/volume_to_web_main.cpp rename to src/xmipp/applications/programs/volume_to_web/volume_to_web_main.cpp diff --git a/applications/programs/volume_validate_pca/volume_validate_pca_main.cpp b/src/xmipp/applications/programs/volume_validate_pca/volume_validate_pca_main.cpp similarity index 100% rename from applications/programs/volume_validate_pca/volume_validate_pca_main.cpp rename to src/xmipp/applications/programs/volume_validate_pca/volume_validate_pca_main.cpp diff --git a/applications/programs/work_test/work_test.cpp b/src/xmipp/applications/programs/work_test/work_test.cpp similarity index 100% rename from applications/programs/work_test/work_test.cpp rename to src/xmipp/applications/programs/work_test/work_test.cpp diff --git a/applications/programs/xray_import/xray_import_main.cpp b/src/xmipp/applications/programs/xray_import/xray_import_main.cpp similarity index 100% rename from applications/programs/xray_import/xray_import_main.cpp rename to src/xmipp/applications/programs/xray_import/xray_import_main.cpp diff --git a/applications/programs/xray_project/xray_project_main.cpp b/src/xmipp/applications/programs/xray_project/xray_project_main.cpp similarity index 100% rename from applications/programs/xray_project/xray_project_main.cpp rename to src/xmipp/applications/programs/xray_project/xray_project_main.cpp diff --git a/applications/programs/xray_psf_create/xray_psf_create_main.cpp b/src/xmipp/applications/programs/xray_psf_create/xray_psf_create_main.cpp similarity index 100% rename from applications/programs/xray_psf_create/xray_psf_create_main.cpp rename to src/xmipp/applications/programs/xray_psf_create/xray_psf_create_main.cpp diff --git a/applications/scripts/apropos/batch_apropos.py b/src/xmipp/applications/scripts/apropos/batch_apropos.py similarity index 100% rename from applications/scripts/apropos/batch_apropos.py rename to src/xmipp/applications/scripts/apropos/batch_apropos.py diff --git a/applications/scripts/compile/batch_compile.py b/src/xmipp/applications/scripts/compile/batch_compile.py similarity index 100% rename from applications/scripts/compile/batch_compile.py rename to src/xmipp/applications/scripts/compile/batch_compile.py diff --git a/applications/scripts/coordinates_consensus/coordinates_consensus.py b/src/xmipp/applications/scripts/coordinates_consensus/coordinates_consensus.py similarity index 100% rename from applications/scripts/coordinates_consensus/coordinates_consensus.py rename to src/xmipp/applications/scripts/coordinates_consensus/coordinates_consensus.py diff --git a/applications/scripts/deepRes_resolution/batch_deepRes_resolution.py b/src/xmipp/applications/scripts/deepRes_resolution/batch_deepRes_resolution.py similarity index 100% rename from applications/scripts/deepRes_resolution/batch_deepRes_resolution.py rename to src/xmipp/applications/scripts/deepRes_resolution/batch_deepRes_resolution.py diff --git a/applications/scripts/deep_consensus/deep_consensus.py b/src/xmipp/applications/scripts/deep_consensus/deep_consensus.py similarity index 100% rename from applications/scripts/deep_consensus/deep_consensus.py rename to src/xmipp/applications/scripts/deep_consensus/deep_consensus.py diff --git a/applications/scripts/deep_consensus/helpers/howToPretrainDeepConsensus.txt b/src/xmipp/applications/scripts/deep_consensus/helpers/howToPretrainDeepConsensus.txt similarity index 100% rename from applications/scripts/deep_consensus/helpers/howToPretrainDeepConsensus.txt rename to src/xmipp/applications/scripts/deep_consensus/helpers/howToPretrainDeepConsensus.txt diff --git a/applications/scripts/deep_consensus/helpers/protocol_prepare_deepConsensus.py b/src/xmipp/applications/scripts/deep_consensus/helpers/protocol_prepare_deepConsensus.py similarity index 100% rename from applications/scripts/deep_consensus/helpers/protocol_prepare_deepConsensus.py rename to src/xmipp/applications/scripts/deep_consensus/helpers/protocol_prepare_deepConsensus.py diff --git a/applications/scripts/extract_particles/extract_particles.py b/src/xmipp/applications/scripts/extract_particles/extract_particles.py similarity index 100% rename from applications/scripts/extract_particles/extract_particles.py rename to src/xmipp/applications/scripts/extract_particles/extract_particles.py diff --git a/applications/scripts/metadata_selfile_create/batch_metadata_selfile_create.py b/src/xmipp/applications/scripts/metadata_selfile_create/batch_metadata_selfile_create.py similarity index 100% rename from applications/scripts/metadata_selfile_create/batch_metadata_selfile_create.py rename to src/xmipp/applications/scripts/metadata_selfile_create/batch_metadata_selfile_create.py diff --git a/applications/scripts/mpi_classify_CLTomo/batch_mpi_classify_CLTomo.sh b/src/xmipp/applications/scripts/mpi_classify_CLTomo/batch_mpi_classify_CLTomo.sh similarity index 100% rename from applications/scripts/mpi_classify_CLTomo/batch_mpi_classify_CLTomo.sh rename to src/xmipp/applications/scripts/mpi_classify_CLTomo/batch_mpi_classify_CLTomo.sh diff --git a/applications/scripts/particle_boxsize/batch_particle_boxsize.py b/src/xmipp/applications/scripts/particle_boxsize/batch_particle_boxsize.py similarity index 100% rename from applications/scripts/particle_boxsize/batch_particle_boxsize.py rename to src/xmipp/applications/scripts/particle_boxsize/batch_particle_boxsize.py diff --git a/applications/scripts/pdb_center/batch_pdb_center.py b/src/xmipp/applications/scripts/pdb_center/batch_pdb_center.py similarity index 100% rename from applications/scripts/pdb_center/batch_pdb_center.py rename to src/xmipp/applications/scripts/pdb_center/batch_pdb_center.py diff --git a/applications/scripts/pdb_select/batch_pdb_select.py b/src/xmipp/applications/scripts/pdb_select/batch_pdb_select.py similarity index 100% rename from applications/scripts/pdb_select/batch_pdb_select.py rename to src/xmipp/applications/scripts/pdb_select/batch_pdb_select.py diff --git a/applications/scripts/pick_noise/pick_noise.py b/src/xmipp/applications/scripts/pick_noise/pick_noise.py similarity index 100% rename from applications/scripts/pick_noise/pick_noise.py rename to src/xmipp/applications/scripts/pick_noise/pick_noise.py diff --git a/applications/scripts/preprocess_mics/preprocess_mics.py b/src/xmipp/applications/scripts/preprocess_mics/preprocess_mics.py similarity index 100% rename from applications/scripts/preprocess_mics/preprocess_mics.py rename to src/xmipp/applications/scripts/preprocess_mics/preprocess_mics.py diff --git a/applications/scripts/sync_data/batch_sync_data.py b/src/xmipp/applications/scripts/sync_data/batch_sync_data.py similarity index 100% rename from applications/scripts/sync_data/batch_sync_data.py rename to src/xmipp/applications/scripts/sync_data/batch_sync_data.py diff --git a/applications/scripts/test_script_importing_module/batch_test_script_importing_module.py b/src/xmipp/applications/scripts/test_script_importing_module/batch_test_script_importing_module.py similarity index 100% rename from applications/scripts/test_script_importing_module/batch_test_script_importing_module.py rename to src/xmipp/applications/scripts/test_script_importing_module/batch_test_script_importing_module.py diff --git a/applications/scripts/volume_align/batch_volume_align.sh b/src/xmipp/applications/scripts/volume_align/batch_volume_align.sh similarity index 100% rename from applications/scripts/volume_align/batch_volume_align.sh rename to src/xmipp/applications/scripts/volume_align/batch_volume_align.sh diff --git a/applications/tests/function_tests/aft_tests.h b/src/xmipp/applications/tests/function_tests/aft_tests.h similarity index 100% rename from applications/tests/function_tests/aft_tests.h rename to src/xmipp/applications/tests/function_tests/aft_tests.h diff --git a/applications/tests/function_tests/ashift_corr_estimator_tests.h b/src/xmipp/applications/tests/function_tests/ashift_corr_estimator_tests.h similarity index 100% rename from applications/tests/function_tests/ashift_corr_estimator_tests.h rename to src/xmipp/applications/tests/function_tests/ashift_corr_estimator_tests.h diff --git a/applications/tests/function_tests/ashift_estimator_tests.h b/src/xmipp/applications/tests/function_tests/ashift_estimator_tests.h similarity index 100% rename from applications/tests/function_tests/ashift_estimator_tests.h rename to src/xmipp/applications/tests/function_tests/ashift_estimator_tests.h diff --git a/applications/tests/function_tests/test_ctf_main.cpp b/src/xmipp/applications/tests/function_tests/test_ctf_main.cpp similarity index 100% rename from applications/tests/function_tests/test_ctf_main.cpp rename to src/xmipp/applications/tests/function_tests/test_ctf_main.cpp diff --git a/applications/tests/function_tests/test_cuda_fft.cpp b/src/xmipp/applications/tests/function_tests/test_cuda_fft.cpp similarity index 100% rename from applications/tests/function_tests/test_cuda_fft.cpp rename to src/xmipp/applications/tests/function_tests/test_cuda_fft.cpp diff --git a/applications/tests/function_tests/test_cuda_geo_transformer_apply_bspline_transform.cpp b/src/xmipp/applications/tests/function_tests/test_cuda_geo_transformer_apply_bspline_transform.cpp similarity index 100% rename from applications/tests/function_tests/test_cuda_geo_transformer_apply_bspline_transform.cpp rename to src/xmipp/applications/tests/function_tests/test_cuda_geo_transformer_apply_bspline_transform.cpp diff --git a/applications/tests/function_tests/test_cuda_geo_transformer_produce_and_load_coeffs.cpp b/src/xmipp/applications/tests/function_tests/test_cuda_geo_transformer_produce_and_load_coeffs.cpp similarity index 100% rename from applications/tests/function_tests/test_cuda_geo_transformer_produce_and_load_coeffs.cpp rename to src/xmipp/applications/tests/function_tests/test_cuda_geo_transformer_produce_and_load_coeffs.cpp diff --git a/applications/tests/function_tests/test_cuda_movie_alignment_correlation_gpu.cpp b/src/xmipp/applications/tests/function_tests/test_cuda_movie_alignment_correlation_gpu.cpp similarity index 100% rename from applications/tests/function_tests/test_cuda_movie_alignment_correlation_gpu.cpp rename to src/xmipp/applications/tests/function_tests/test_cuda_movie_alignment_correlation_gpu.cpp diff --git a/applications/tests/function_tests/test_cuda_shift_corr_estimator.cpp b/src/xmipp/applications/tests/function_tests/test_cuda_shift_corr_estimator.cpp similarity index 100% rename from applications/tests/function_tests/test_cuda_shift_corr_estimator.cpp rename to src/xmipp/applications/tests/function_tests/test_cuda_shift_corr_estimator.cpp diff --git a/applications/tests/function_tests/test_dimred_main.cpp b/src/xmipp/applications/tests/function_tests/test_dimred_main.cpp similarity index 100% rename from applications/tests/function_tests/test_dimred_main.cpp rename to src/xmipp/applications/tests/function_tests/test_dimred_main.cpp diff --git a/applications/tests/function_tests/test_euler_main.cpp b/src/xmipp/applications/tests/function_tests/test_euler_main.cpp similarity index 100% rename from applications/tests/function_tests/test_euler_main.cpp rename to src/xmipp/applications/tests/function_tests/test_euler_main.cpp diff --git a/applications/tests/function_tests/test_fftw_main.cpp b/src/xmipp/applications/tests/function_tests/test_fftw_main.cpp similarity index 100% rename from applications/tests/function_tests/test_fftw_main.cpp rename to src/xmipp/applications/tests/function_tests/test_fftw_main.cpp diff --git a/applications/tests/function_tests/test_fftwt.cpp b/src/xmipp/applications/tests/function_tests/test_fftwt.cpp similarity index 100% rename from applications/tests/function_tests/test_fftwt.cpp rename to src/xmipp/applications/tests/function_tests/test_fftwt.cpp diff --git a/applications/tests/function_tests/test_filename_main.cpp b/src/xmipp/applications/tests/function_tests/test_filename_main.cpp similarity index 100% rename from applications/tests/function_tests/test_filename_main.cpp rename to src/xmipp/applications/tests/function_tests/test_filename_main.cpp diff --git a/applications/tests/function_tests/test_filters_main.cpp b/src/xmipp/applications/tests/function_tests/test_filters_main.cpp similarity index 100% rename from applications/tests/function_tests/test_filters_main.cpp rename to src/xmipp/applications/tests/function_tests/test_filters_main.cpp diff --git a/applications/tests/function_tests/test_fringe_processing_main.cpp b/src/xmipp/applications/tests/function_tests/test_fringe_processing_main.cpp similarity index 100% rename from applications/tests/function_tests/test_fringe_processing_main.cpp rename to src/xmipp/applications/tests/function_tests/test_fringe_processing_main.cpp diff --git a/applications/tests/function_tests/test_funcs_main.cpp b/src/xmipp/applications/tests/function_tests/test_funcs_main.cpp similarity index 100% rename from applications/tests/function_tests/test_funcs_main.cpp rename to src/xmipp/applications/tests/function_tests/test_funcs_main.cpp diff --git a/applications/tests/function_tests/test_geometry_main.cpp b/src/xmipp/applications/tests/function_tests/test_geometry_main.cpp similarity index 100% rename from applications/tests/function_tests/test_geometry_main.cpp rename to src/xmipp/applications/tests/function_tests/test_geometry_main.cpp diff --git a/applications/tests/function_tests/test_image_generic_main.cpp b/src/xmipp/applications/tests/function_tests/test_image_generic_main.cpp similarity index 100% rename from applications/tests/function_tests/test_image_generic_main.cpp rename to src/xmipp/applications/tests/function_tests/test_image_generic_main.cpp diff --git a/applications/tests/function_tests/test_image_main.cpp b/src/xmipp/applications/tests/function_tests/test_image_main.cpp similarity index 100% rename from applications/tests/function_tests/test_image_main.cpp rename to src/xmipp/applications/tests/function_tests/test_image_main.cpp diff --git a/applications/tests/function_tests/test_matrix_main.cpp b/src/xmipp/applications/tests/function_tests/test_matrix_main.cpp similarity index 100% rename from applications/tests/function_tests/test_matrix_main.cpp rename to src/xmipp/applications/tests/function_tests/test_matrix_main.cpp diff --git a/applications/tests/function_tests/test_metadata_main.cpp b/src/xmipp/applications/tests/function_tests/test_metadata_main.cpp similarity index 100% rename from applications/tests/function_tests/test_metadata_main.cpp rename to src/xmipp/applications/tests/function_tests/test_metadata_main.cpp diff --git a/applications/tests/function_tests/test_movie_filter_dose.cpp b/src/xmipp/applications/tests/function_tests/test_movie_filter_dose.cpp similarity index 100% rename from applications/tests/function_tests/test_movie_filter_dose.cpp rename to src/xmipp/applications/tests/function_tests/test_movie_filter_dose.cpp diff --git a/applications/tests/function_tests/test_multidim_main.cpp b/src/xmipp/applications/tests/function_tests/test_multidim_main.cpp similarity index 100% rename from applications/tests/function_tests/test_multidim_main.cpp rename to src/xmipp/applications/tests/function_tests/test_multidim_main.cpp diff --git a/applications/tests/function_tests/test_polar_main.cpp b/src/xmipp/applications/tests/function_tests/test_polar_main.cpp similarity index 100% rename from applications/tests/function_tests/test_polar_main.cpp rename to src/xmipp/applications/tests/function_tests/test_polar_main.cpp diff --git a/applications/tests/function_tests/test_polynomials_main.cpp b/src/xmipp/applications/tests/function_tests/test_polynomials_main.cpp similarity index 100% rename from applications/tests/function_tests/test_polynomials_main.cpp rename to src/xmipp/applications/tests/function_tests/test_polynomials_main.cpp diff --git a/applications/tests/function_tests/test_psd_estimator.cpp b/src/xmipp/applications/tests/function_tests/test_psd_estimator.cpp similarity index 100% rename from applications/tests/function_tests/test_psd_estimator.cpp rename to src/xmipp/applications/tests/function_tests/test_psd_estimator.cpp diff --git a/applications/tests/function_tests/test_resolution_frc.cpp b/src/xmipp/applications/tests/function_tests/test_resolution_frc.cpp similarity index 100% rename from applications/tests/function_tests/test_resolution_frc.cpp rename to src/xmipp/applications/tests/function_tests/test_resolution_frc.cpp diff --git a/applications/tests/function_tests/test_sampling_main.cpp b/src/xmipp/applications/tests/function_tests/test_sampling_main.cpp similarity index 100% rename from applications/tests/function_tests/test_sampling_main.cpp rename to src/xmipp/applications/tests/function_tests/test_sampling_main.cpp diff --git a/applications/tests/function_tests/test_shift_corr_estimator.cpp b/src/xmipp/applications/tests/function_tests/test_shift_corr_estimator.cpp similarity index 100% rename from applications/tests/function_tests/test_shift_corr_estimator.cpp rename to src/xmipp/applications/tests/function_tests/test_shift_corr_estimator.cpp diff --git a/applications/tests/function_tests/test_symmetries_main.cpp b/src/xmipp/applications/tests/function_tests/test_symmetries_main.cpp similarity index 100% rename from applications/tests/function_tests/test_symmetries_main.cpp rename to src/xmipp/applications/tests/function_tests/test_symmetries_main.cpp diff --git a/applications/tests/function_tests/test_transform_window.cpp 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b/src/xmipp/bindings/matlab/tom_xmipp_ctf_correct_phase.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_ctf_correct_phase.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_ctf_correct_phase.cpp diff --git a/bindings/matlab/tom_xmipp_ctf_correct_phase.m b/src/xmipp/bindings/matlab/tom_xmipp_ctf_correct_phase.m similarity index 100% rename from bindings/matlab/tom_xmipp_ctf_correct_phase.m rename to src/xmipp/bindings/matlab/tom_xmipp_ctf_correct_phase.m diff --git a/bindings/matlab/tom_xmipp_helpers.h b/src/xmipp/bindings/matlab/tom_xmipp_helpers.h similarity index 100% rename from bindings/matlab/tom_xmipp_helpers.h rename to src/xmipp/bindings/matlab/tom_xmipp_helpers.h diff --git a/bindings/matlab/tom_xmipp_mask.cpp b/src/xmipp/bindings/matlab/tom_xmipp_mask.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_mask.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_mask.cpp diff --git a/bindings/matlab/tom_xmipp_mask.m 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to src/xmipp/bindings/matlab/tom_xmipp_psd_enhance.m diff --git a/bindings/matlab/tom_xmipp_resolution.cpp b/src/xmipp/bindings/matlab/tom_xmipp_resolution.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_resolution.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_resolution.cpp diff --git a/bindings/matlab/tom_xmipp_resolution.m b/src/xmipp/bindings/matlab/tom_xmipp_resolution.m similarity index 100% rename from bindings/matlab/tom_xmipp_resolution.m rename to src/xmipp/bindings/matlab/tom_xmipp_resolution.m diff --git a/bindings/matlab/tom_xmipp_rotate.cpp b/src/xmipp/bindings/matlab/tom_xmipp_rotate.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_rotate.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_rotate.cpp diff --git a/bindings/matlab/tom_xmipp_rotate.m b/src/xmipp/bindings/matlab/tom_xmipp_rotate.m similarity index 100% rename from bindings/matlab/tom_xmipp_rotate.m rename to src/xmipp/bindings/matlab/tom_xmipp_rotate.m diff --git a/bindings/matlab/tom_xmipp_scale.cpp b/src/xmipp/bindings/matlab/tom_xmipp_scale.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_scale.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_scale.cpp diff --git a/bindings/matlab/tom_xmipp_scale.m b/src/xmipp/bindings/matlab/tom_xmipp_scale.m similarity index 100% rename from bindings/matlab/tom_xmipp_scale.m rename to src/xmipp/bindings/matlab/tom_xmipp_scale.m diff --git a/bindings/matlab/tom_xmipp_scale_pyramid.cpp b/src/xmipp/bindings/matlab/tom_xmipp_scale_pyramid.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_scale_pyramid.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_scale_pyramid.cpp diff --git a/bindings/matlab/tom_xmipp_scale_pyramid.m b/src/xmipp/bindings/matlab/tom_xmipp_scale_pyramid.m similarity index 100% rename from bindings/matlab/tom_xmipp_scale_pyramid.m rename to src/xmipp/bindings/matlab/tom_xmipp_scale_pyramid.m diff --git a/bindings/matlab/tom_xmipp_volume_segment.cpp 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a/libraries/reconstruction/ctf_correct_idr.cpp b/src/xmipp/libraries/reconstruction/ctf_correct_idr.cpp similarity index 100% rename from libraries/reconstruction/ctf_correct_idr.cpp rename to src/xmipp/libraries/reconstruction/ctf_correct_idr.cpp diff --git a/libraries/reconstruction/ctf_correct_idr.h b/src/xmipp/libraries/reconstruction/ctf_correct_idr.h similarity index 100% rename from libraries/reconstruction/ctf_correct_idr.h rename to src/xmipp/libraries/reconstruction/ctf_correct_idr.h diff --git a/libraries/reconstruction/ctf_correct_wiener2d.cpp b/src/xmipp/libraries/reconstruction/ctf_correct_wiener2d.cpp similarity index 100% rename from libraries/reconstruction/ctf_correct_wiener2d.cpp rename to src/xmipp/libraries/reconstruction/ctf_correct_wiener2d.cpp diff --git a/libraries/reconstruction/ctf_correct_wiener2d.h b/src/xmipp/libraries/reconstruction/ctf_correct_wiener2d.h similarity index 100% rename from libraries/reconstruction/ctf_correct_wiener2d.h rename to 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a/libraries/reconstruction/ctf_estimate_from_psd_fast.cpp b/src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_fast.cpp similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_psd_fast.cpp rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_fast.cpp diff --git a/libraries/reconstruction/ctf_estimate_from_psd_fast.h b/src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_fast.h similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_psd_fast.h rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_fast.h diff --git a/libraries/reconstruction/ctf_estimate_psd_with_arma.cpp b/src/xmipp/libraries/reconstruction/ctf_estimate_psd_with_arma.cpp similarity index 100% rename from libraries/reconstruction/ctf_estimate_psd_with_arma.cpp rename to src/xmipp/libraries/reconstruction/ctf_estimate_psd_with_arma.cpp diff --git a/libraries/reconstruction/ctf_estimate_psd_with_arma.h 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a/libraries/reconstruction/image_rotational_spectra.cpp b/src/xmipp/libraries/reconstruction/image_rotational_spectra.cpp similarity index 100% rename from libraries/reconstruction/image_rotational_spectra.cpp rename to src/xmipp/libraries/reconstruction/image_rotational_spectra.cpp diff --git a/libraries/reconstruction/image_rotational_spectra.h b/src/xmipp/libraries/reconstruction/image_rotational_spectra.h similarity index 100% rename from libraries/reconstruction/image_rotational_spectra.h rename to src/xmipp/libraries/reconstruction/image_rotational_spectra.h diff --git a/libraries/reconstruction/image_sort_by_statistics.cpp b/src/xmipp/libraries/reconstruction/image_sort_by_statistics.cpp similarity index 100% rename from libraries/reconstruction/image_sort_by_statistics.cpp rename to src/xmipp/libraries/reconstruction/image_sort_by_statistics.cpp diff --git a/libraries/reconstruction/image_sort_by_statistics.h b/src/xmipp/libraries/reconstruction/image_sort_by_statistics.h 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similarity index 100% rename from libraries/reconstruction/multireference_aligneability.cpp rename to src/xmipp/libraries/reconstruction/multireference_aligneability.cpp diff --git a/libraries/reconstruction/multireference_aligneability.h b/src/xmipp/libraries/reconstruction/multireference_aligneability.h similarity index 100% rename from libraries/reconstruction/multireference_aligneability.h rename to src/xmipp/libraries/reconstruction/multireference_aligneability.h diff --git a/libraries/reconstruction/nma_alignment.cpp b/src/xmipp/libraries/reconstruction/nma_alignment.cpp similarity index 100% rename from libraries/reconstruction/nma_alignment.cpp rename to src/xmipp/libraries/reconstruction/nma_alignment.cpp diff --git a/libraries/reconstruction/nma_alignment.h b/src/xmipp/libraries/reconstruction/nma_alignment.h similarity index 100% rename from libraries/reconstruction/nma_alignment.h rename to src/xmipp/libraries/reconstruction/nma_alignment.h diff --git a/libraries/reconstruction/nma_alignment_vol.cpp b/src/xmipp/libraries/reconstruction/nma_alignment_vol.cpp similarity index 100% rename from libraries/reconstruction/nma_alignment_vol.cpp rename to src/xmipp/libraries/reconstruction/nma_alignment_vol.cpp diff --git a/libraries/reconstruction/nma_alignment_vol.h b/src/xmipp/libraries/reconstruction/nma_alignment_vol.h similarity index 100% rename from libraries/reconstruction/nma_alignment_vol.h rename to src/xmipp/libraries/reconstruction/nma_alignment_vol.h diff --git a/libraries/reconstruction/pdb_analysis.cpp b/src/xmipp/libraries/reconstruction/pdb_analysis.cpp similarity index 100% rename from libraries/reconstruction/pdb_analysis.cpp rename to src/xmipp/libraries/reconstruction/pdb_analysis.cpp diff --git a/libraries/reconstruction/pdb_analysis.h b/src/xmipp/libraries/reconstruction/pdb_analysis.h similarity index 100% rename from libraries/reconstruction/pdb_analysis.h rename to src/xmipp/libraries/reconstruction/pdb_analysis.h diff --git a/libraries/reconstruction/pdb_construct_dictionary.cpp b/src/xmipp/libraries/reconstruction/pdb_construct_dictionary.cpp similarity index 100% rename from libraries/reconstruction/pdb_construct_dictionary.cpp rename to src/xmipp/libraries/reconstruction/pdb_construct_dictionary.cpp diff --git a/libraries/reconstruction/pdb_construct_dictionary.h b/src/xmipp/libraries/reconstruction/pdb_construct_dictionary.h similarity index 100% rename from libraries/reconstruction/pdb_construct_dictionary.h rename to src/xmipp/libraries/reconstruction/pdb_construct_dictionary.h diff --git a/libraries/reconstruction/pdb_nma_deform.cpp b/src/xmipp/libraries/reconstruction/pdb_nma_deform.cpp similarity index 100% rename from libraries/reconstruction/pdb_nma_deform.cpp rename to src/xmipp/libraries/reconstruction/pdb_nma_deform.cpp diff --git a/libraries/reconstruction/pdb_nma_deform.h b/src/xmipp/libraries/reconstruction/pdb_nma_deform.h similarity index 100% rename from libraries/reconstruction/pdb_nma_deform.h rename to src/xmipp/libraries/reconstruction/pdb_nma_deform.h diff --git a/libraries/reconstruction/pdb_reduce_pseudoatoms.cpp b/src/xmipp/libraries/reconstruction/pdb_reduce_pseudoatoms.cpp similarity index 100% rename from libraries/reconstruction/pdb_reduce_pseudoatoms.cpp rename to src/xmipp/libraries/reconstruction/pdb_reduce_pseudoatoms.cpp diff --git a/libraries/reconstruction/pdb_reduce_pseudoatoms.h b/src/xmipp/libraries/reconstruction/pdb_reduce_pseudoatoms.h similarity index 100% rename from libraries/reconstruction/pdb_reduce_pseudoatoms.h rename to src/xmipp/libraries/reconstruction/pdb_reduce_pseudoatoms.h diff --git a/libraries/reconstruction/pdb_restore_with_dictionary.cpp b/src/xmipp/libraries/reconstruction/pdb_restore_with_dictionary.cpp similarity index 100% rename from libraries/reconstruction/pdb_restore_with_dictionary.cpp rename to src/xmipp/libraries/reconstruction/pdb_restore_with_dictionary.cpp diff --git a/libraries/reconstruction/pdb_restore_with_dictionary.h b/src/xmipp/libraries/reconstruction/pdb_restore_with_dictionary.h similarity index 100% rename from libraries/reconstruction/pdb_restore_with_dictionary.h rename to src/xmipp/libraries/reconstruction/pdb_restore_with_dictionary.h diff --git a/libraries/reconstruction/phantom_movie.cpp b/src/xmipp/libraries/reconstruction/phantom_movie.cpp similarity index 100% rename from libraries/reconstruction/phantom_movie.cpp rename to src/xmipp/libraries/reconstruction/phantom_movie.cpp diff --git a/libraries/reconstruction/phantom_movie.h b/src/xmipp/libraries/reconstruction/phantom_movie.h similarity index 100% rename from libraries/reconstruction/phantom_movie.h rename to src/xmipp/libraries/reconstruction/phantom_movie.h diff --git a/libraries/reconstruction/phantom_movie_param_estimator.m b/src/xmipp/libraries/reconstruction/phantom_movie_param_estimator.m similarity index 100% rename from libraries/reconstruction/phantom_movie_param_estimator.m rename to src/xmipp/libraries/reconstruction/phantom_movie_param_estimator.m diff --git a/libraries/reconstruction/phantom_simulate_microscope.cpp b/src/xmipp/libraries/reconstruction/phantom_simulate_microscope.cpp similarity index 100% rename from libraries/reconstruction/phantom_simulate_microscope.cpp rename to src/xmipp/libraries/reconstruction/phantom_simulate_microscope.cpp diff --git a/libraries/reconstruction/phantom_simulate_microscope.h b/src/xmipp/libraries/reconstruction/phantom_simulate_microscope.h similarity index 100% rename from libraries/reconstruction/phantom_simulate_microscope.h rename to src/xmipp/libraries/reconstruction/phantom_simulate_microscope.h diff --git a/libraries/reconstruction/precompute_sampling.cpp b/src/xmipp/libraries/reconstruction/precompute_sampling.cpp similarity index 100% rename from libraries/reconstruction/precompute_sampling.cpp rename to src/xmipp/libraries/reconstruction/precompute_sampling.cpp diff --git a/libraries/reconstruction/precompute_sampling.h b/src/xmipp/libraries/reconstruction/precompute_sampling.h similarity index 100% rename from libraries/reconstruction/precompute_sampling.h rename to src/xmipp/libraries/reconstruction/precompute_sampling.h diff --git a/libraries/reconstruction/program_extension.cpp b/src/xmipp/libraries/reconstruction/program_extension.cpp similarity index 100% rename from libraries/reconstruction/program_extension.cpp rename to src/xmipp/libraries/reconstruction/program_extension.cpp diff --git a/libraries/reconstruction/program_extension.h b/src/xmipp/libraries/reconstruction/program_extension.h similarity index 100% rename from libraries/reconstruction/program_extension.h rename to src/xmipp/libraries/reconstruction/program_extension.h diff --git a/libraries/reconstruction/program_filter.cpp b/src/xmipp/libraries/reconstruction/program_filter.cpp similarity index 100% rename from libraries/reconstruction/program_filter.cpp rename to src/xmipp/libraries/reconstruction/program_filter.cpp diff --git a/libraries/reconstruction/program_filter.h b/src/xmipp/libraries/reconstruction/program_filter.h similarity index 100% rename from libraries/reconstruction/program_filter.h rename to src/xmipp/libraries/reconstruction/program_filter.h diff --git a/libraries/reconstruction/program_image_residuals.cpp b/src/xmipp/libraries/reconstruction/program_image_residuals.cpp similarity index 100% rename from libraries/reconstruction/program_image_residuals.cpp rename to src/xmipp/libraries/reconstruction/program_image_residuals.cpp diff --git a/libraries/reconstruction/program_image_residuals.h b/src/xmipp/libraries/reconstruction/program_image_residuals.h similarity index 100% rename from libraries/reconstruction/program_image_residuals.h rename to src/xmipp/libraries/reconstruction/program_image_residuals.h diff --git a/libraries/reconstruction/program_image_ssnr.cpp b/src/xmipp/libraries/reconstruction/program_image_ssnr.cpp similarity index 100% rename from libraries/reconstruction/program_image_ssnr.cpp rename to src/xmipp/libraries/reconstruction/program_image_ssnr.cpp diff --git a/libraries/reconstruction/program_image_ssnr.h b/src/xmipp/libraries/reconstruction/program_image_ssnr.h similarity index 100% rename from libraries/reconstruction/program_image_ssnr.h rename to src/xmipp/libraries/reconstruction/program_image_ssnr.h diff --git a/libraries/reconstruction/project.cpp b/src/xmipp/libraries/reconstruction/project.cpp similarity index 100% rename from libraries/reconstruction/project.cpp rename to src/xmipp/libraries/reconstruction/project.cpp diff --git a/libraries/reconstruction/project.h b/src/xmipp/libraries/reconstruction/project.h similarity index 100% rename from libraries/reconstruction/project.h rename to src/xmipp/libraries/reconstruction/project.h diff --git a/libraries/reconstruction/project_crystal.cpp b/src/xmipp/libraries/reconstruction/project_crystal.cpp similarity index 100% rename from libraries/reconstruction/project_crystal.cpp rename to src/xmipp/libraries/reconstruction/project_crystal.cpp diff --git a/libraries/reconstruction/project_crystal.h b/src/xmipp/libraries/reconstruction/project_crystal.h similarity index 100% rename from libraries/reconstruction/project_crystal.h rename to src/xmipp/libraries/reconstruction/project_crystal.h diff --git a/libraries/reconstruction/project_real_shears.cpp b/src/xmipp/libraries/reconstruction/project_real_shears.cpp similarity index 100% rename from libraries/reconstruction/project_real_shears.cpp rename to src/xmipp/libraries/reconstruction/project_real_shears.cpp diff --git a/libraries/reconstruction/project_real_shears.h b/src/xmipp/libraries/reconstruction/project_real_shears.h similarity index 100% rename from libraries/reconstruction/project_real_shears.h rename to src/xmipp/libraries/reconstruction/project_real_shears.h diff --git a/libraries/reconstruction/project_tomography.cpp b/src/xmipp/libraries/reconstruction/project_tomography.cpp similarity index 100% rename from libraries/reconstruction/project_tomography.cpp rename to src/xmipp/libraries/reconstruction/project_tomography.cpp diff --git a/libraries/reconstruction/project_tomography.h b/src/xmipp/libraries/reconstruction/project_tomography.h similarity index 100% rename from libraries/reconstruction/project_tomography.h rename to src/xmipp/libraries/reconstruction/project_tomography.h diff --git a/libraries/reconstruction/project_xray.cpp b/src/xmipp/libraries/reconstruction/project_xray.cpp similarity index 100% rename from libraries/reconstruction/project_xray.cpp rename to src/xmipp/libraries/reconstruction/project_xray.cpp diff --git a/libraries/reconstruction/project_xray.h b/src/xmipp/libraries/reconstruction/project_xray.h similarity index 100% rename from libraries/reconstruction/project_xray.h rename to src/xmipp/libraries/reconstruction/project_xray.h diff --git a/libraries/reconstruction/psd_estimator.cpp b/src/xmipp/libraries/reconstruction/psd_estimator.cpp similarity index 100% rename from libraries/reconstruction/psd_estimator.cpp rename to src/xmipp/libraries/reconstruction/psd_estimator.cpp diff --git a/libraries/reconstruction/psd_estimator.h b/src/xmipp/libraries/reconstruction/psd_estimator.h similarity index 100% rename from libraries/reconstruction/psd_estimator.h rename to src/xmipp/libraries/reconstruction/psd_estimator.h diff --git a/libraries/reconstruction/radon.cpp b/src/xmipp/libraries/reconstruction/radon.cpp similarity index 100% rename from libraries/reconstruction/radon.cpp rename to src/xmipp/libraries/reconstruction/radon.cpp diff --git a/libraries/reconstruction/radon.h b/src/xmipp/libraries/reconstruction/radon.h similarity index 100% rename from libraries/reconstruction/radon.h rename to src/xmipp/libraries/reconstruction/radon.h diff --git a/libraries/reconstruction/recons.cpp b/src/xmipp/libraries/reconstruction/recons.cpp similarity index 100% rename from libraries/reconstruction/recons.cpp rename to src/xmipp/libraries/reconstruction/recons.cpp diff --git a/libraries/reconstruction/recons.h b/src/xmipp/libraries/reconstruction/recons.h similarity index 100% rename from libraries/reconstruction/recons.h rename to src/xmipp/libraries/reconstruction/recons.h diff --git a/libraries/reconstruction/recons_misc.cpp b/src/xmipp/libraries/reconstruction/recons_misc.cpp similarity index 100% rename from libraries/reconstruction/recons_misc.cpp rename to src/xmipp/libraries/reconstruction/recons_misc.cpp diff --git a/libraries/reconstruction/recons_misc.h b/src/xmipp/libraries/reconstruction/recons_misc.h similarity index 100% rename from libraries/reconstruction/recons_misc.h rename to src/xmipp/libraries/reconstruction/recons_misc.h diff --git a/libraries/reconstruction/reconstruct_ADMM.cpp b/src/xmipp/libraries/reconstruction/reconstruct_ADMM.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_ADMM.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_ADMM.cpp diff --git a/libraries/reconstruction/reconstruct_ADMM.h b/src/xmipp/libraries/reconstruction/reconstruct_ADMM.h similarity index 100% rename from libraries/reconstruction/reconstruct_ADMM.h rename to src/xmipp/libraries/reconstruction/reconstruct_ADMM.h diff --git a/libraries/reconstruction/reconstruct_art.cpp b/src/xmipp/libraries/reconstruction/reconstruct_art.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_art.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_art.cpp diff --git a/libraries/reconstruction/reconstruct_art.h b/src/xmipp/libraries/reconstruction/reconstruct_art.h similarity index 100% rename from libraries/reconstruction/reconstruct_art.h rename to src/xmipp/libraries/reconstruction/reconstruct_art.h diff --git a/libraries/reconstruction/reconstruct_art_pseudo.cpp b/src/xmipp/libraries/reconstruction/reconstruct_art_pseudo.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_art_pseudo.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_art_pseudo.cpp diff --git a/libraries/reconstruction/reconstruct_art_pseudo.h b/src/xmipp/libraries/reconstruction/reconstruct_art_pseudo.h similarity index 100% rename from libraries/reconstruction/reconstruct_art_pseudo.h rename to src/xmipp/libraries/reconstruction/reconstruct_art_pseudo.h diff --git a/libraries/reconstruction/reconstruct_art_xray.cpp b/src/xmipp/libraries/reconstruction/reconstruct_art_xray.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_art_xray.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_art_xray.cpp diff --git a/libraries/reconstruction/reconstruct_art_xray.h b/src/xmipp/libraries/reconstruction/reconstruct_art_xray.h similarity index 100% rename from libraries/reconstruction/reconstruct_art_xray.h rename to src/xmipp/libraries/reconstruction/reconstruct_art_xray.h diff --git a/libraries/reconstruction/reconstruct_fourier.cpp b/src/xmipp/libraries/reconstruction/reconstruct_fourier.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_fourier.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_fourier.cpp diff --git a/libraries/reconstruction/reconstruct_fourier.h b/src/xmipp/libraries/reconstruction/reconstruct_fourier.h similarity index 100% rename from libraries/reconstruction/reconstruct_fourier.h rename to src/xmipp/libraries/reconstruction/reconstruct_fourier.h diff --git a/libraries/reconstruction/reconstruct_fourier_accel.cpp b/src/xmipp/libraries/reconstruction/reconstruct_fourier_accel.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_fourier_accel.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_fourier_accel.cpp diff --git a/libraries/reconstruction/reconstruct_fourier_accel.h b/src/xmipp/libraries/reconstruction/reconstruct_fourier_accel.h similarity index 100% rename from libraries/reconstruction/reconstruct_fourier_accel.h rename to src/xmipp/libraries/reconstruction/reconstruct_fourier_accel.h diff --git a/libraries/reconstruction/reconstruct_fourier_buffer_data.h b/src/xmipp/libraries/reconstruction/reconstruct_fourier_buffer_data.h similarity index 100% rename from libraries/reconstruction/reconstruct_fourier_buffer_data.h rename to src/xmipp/libraries/reconstruction/reconstruct_fourier_buffer_data.h diff --git a/libraries/reconstruction/reconstruct_fourier_defines.h b/src/xmipp/libraries/reconstruction/reconstruct_fourier_defines.h similarity index 100% rename from libraries/reconstruction/reconstruct_fourier_defines.h rename to src/xmipp/libraries/reconstruction/reconstruct_fourier_defines.h diff --git a/libraries/reconstruction/reconstruct_fourier_projection_traverse_space.h 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a/libraries/reconstruction/threshold.h b/src/xmipp/libraries/reconstruction/threshold.h similarity index 100% rename from libraries/reconstruction/threshold.h rename to src/xmipp/libraries/reconstruction/threshold.h diff --git a/libraries/reconstruction/tomo_align_dual_tilt_series.cpp b/src/xmipp/libraries/reconstruction/tomo_align_dual_tilt_series.cpp similarity index 100% rename from libraries/reconstruction/tomo_align_dual_tilt_series.cpp rename to src/xmipp/libraries/reconstruction/tomo_align_dual_tilt_series.cpp diff --git a/libraries/reconstruction/tomo_align_dual_tilt_series.h b/src/xmipp/libraries/reconstruction/tomo_align_dual_tilt_series.h similarity index 100% rename from libraries/reconstruction/tomo_align_dual_tilt_series.h rename to src/xmipp/libraries/reconstruction/tomo_align_dual_tilt_series.h diff --git a/libraries/reconstruction/tomo_align_refinement.cpp b/src/xmipp/libraries/reconstruction/tomo_align_refinement.cpp similarity index 100% rename from libraries/reconstruction/tomo_align_refinement.cpp rename to src/xmipp/libraries/reconstruction/tomo_align_refinement.cpp diff --git a/libraries/reconstruction/tomo_align_refinement.h b/src/xmipp/libraries/reconstruction/tomo_align_refinement.h similarity index 100% rename from libraries/reconstruction/tomo_align_refinement.h rename to src/xmipp/libraries/reconstruction/tomo_align_refinement.h diff --git a/libraries/reconstruction/tomo_align_tilt_series.cpp b/src/xmipp/libraries/reconstruction/tomo_align_tilt_series.cpp similarity index 100% rename from libraries/reconstruction/tomo_align_tilt_series.cpp rename to src/xmipp/libraries/reconstruction/tomo_align_tilt_series.cpp diff --git a/libraries/reconstruction/tomo_align_tilt_series.h b/src/xmipp/libraries/reconstruction/tomo_align_tilt_series.h similarity index 100% rename from libraries/reconstruction/tomo_align_tilt_series.h rename to src/xmipp/libraries/reconstruction/tomo_align_tilt_series.h diff --git a/libraries/reconstruction/tomo_detect_missing_wedge.cpp b/src/xmipp/libraries/reconstruction/tomo_detect_missing_wedge.cpp similarity index 100% rename from libraries/reconstruction/tomo_detect_missing_wedge.cpp rename to src/xmipp/libraries/reconstruction/tomo_detect_missing_wedge.cpp diff --git a/libraries/reconstruction/tomo_detect_missing_wedge.h b/src/xmipp/libraries/reconstruction/tomo_detect_missing_wedge.h similarity index 100% rename from libraries/reconstruction/tomo_detect_missing_wedge.h rename to src/xmipp/libraries/reconstruction/tomo_detect_missing_wedge.h diff --git a/libraries/reconstruction/tomo_extract_subvolume.cpp b/src/xmipp/libraries/reconstruction/tomo_extract_subvolume.cpp similarity index 100% rename from libraries/reconstruction/tomo_extract_subvolume.cpp rename to src/xmipp/libraries/reconstruction/tomo_extract_subvolume.cpp diff --git a/libraries/reconstruction/tomo_extract_subvolume.h b/src/xmipp/libraries/reconstruction/tomo_extract_subvolume.h similarity index 100% rename from libraries/reconstruction/tomo_extract_subvolume.h rename to src/xmipp/libraries/reconstruction/tomo_extract_subvolume.h diff --git a/libraries/reconstruction/tomo_remove_fluctuations.cpp b/src/xmipp/libraries/reconstruction/tomo_remove_fluctuations.cpp similarity index 100% rename from libraries/reconstruction/tomo_remove_fluctuations.cpp rename to src/xmipp/libraries/reconstruction/tomo_remove_fluctuations.cpp diff --git a/libraries/reconstruction/tomo_remove_fluctuations.h b/src/xmipp/libraries/reconstruction/tomo_remove_fluctuations.h similarity index 100% rename from libraries/reconstruction/tomo_remove_fluctuations.h rename to src/xmipp/libraries/reconstruction/tomo_remove_fluctuations.h diff --git a/libraries/reconstruction/transform_adjust_image_grey_levels.cpp b/src/xmipp/libraries/reconstruction/transform_adjust_image_grey_levels.cpp similarity index 100% rename from libraries/reconstruction/transform_adjust_image_grey_levels.cpp rename to 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b/src/xmipp/libraries/reconstruction/validation_tilt_pairs.cpp similarity index 100% rename from libraries/reconstruction/validation_tilt_pairs.cpp rename to src/xmipp/libraries/reconstruction/validation_tilt_pairs.cpp diff --git a/libraries/reconstruction/validation_tilt_pairs.h b/src/xmipp/libraries/reconstruction/validation_tilt_pairs.h similarity index 100% rename from libraries/reconstruction/validation_tilt_pairs.h rename to src/xmipp/libraries/reconstruction/validation_tilt_pairs.h diff --git a/libraries/reconstruction/volume_correct_bfactor.cpp b/src/xmipp/libraries/reconstruction/volume_correct_bfactor.cpp similarity index 100% rename from libraries/reconstruction/volume_correct_bfactor.cpp rename to src/xmipp/libraries/reconstruction/volume_correct_bfactor.cpp diff --git a/libraries/reconstruction/volume_correct_bfactor.h b/src/xmipp/libraries/reconstruction/volume_correct_bfactor.h similarity index 100% rename from libraries/reconstruction/volume_correct_bfactor.h rename to src/xmipp/libraries/reconstruction/volume_correct_bfactor.h diff --git a/libraries/reconstruction/volume_deform_sph.cpp b/src/xmipp/libraries/reconstruction/volume_deform_sph.cpp similarity index 100% rename from libraries/reconstruction/volume_deform_sph.cpp rename to src/xmipp/libraries/reconstruction/volume_deform_sph.cpp diff --git a/libraries/reconstruction/volume_deform_sph.h b/src/xmipp/libraries/reconstruction/volume_deform_sph.h similarity index 100% rename from libraries/reconstruction/volume_deform_sph.h rename to src/xmipp/libraries/reconstruction/volume_deform_sph.h diff --git a/libraries/reconstruction/volume_enhance_contrast.cpp b/src/xmipp/libraries/reconstruction/volume_enhance_contrast.cpp similarity index 100% rename from libraries/reconstruction/volume_enhance_contrast.cpp rename to src/xmipp/libraries/reconstruction/volume_enhance_contrast.cpp diff --git a/libraries/reconstruction/volume_enhance_contrast.h b/src/xmipp/libraries/reconstruction/volume_enhance_contrast.h similarity index 100% rename from libraries/reconstruction/volume_enhance_contrast.h rename to src/xmipp/libraries/reconstruction/volume_enhance_contrast.h diff --git a/libraries/reconstruction/volume_from_pdb.cpp b/src/xmipp/libraries/reconstruction/volume_from_pdb.cpp similarity index 100% rename from libraries/reconstruction/volume_from_pdb.cpp rename to src/xmipp/libraries/reconstruction/volume_from_pdb.cpp diff --git a/libraries/reconstruction/volume_from_pdb.h b/src/xmipp/libraries/reconstruction/volume_from_pdb.h similarity index 100% rename from libraries/reconstruction/volume_from_pdb.h rename to src/xmipp/libraries/reconstruction/volume_from_pdb.h diff --git a/libraries/reconstruction/volume_halves_restoration.cpp b/src/xmipp/libraries/reconstruction/volume_halves_restoration.cpp similarity index 100% rename from libraries/reconstruction/volume_halves_restoration.cpp rename to 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src/xmipp/libraries/reconstruction/volume_initial_simulated_annealing.h diff --git a/libraries/reconstruction/volume_local_sharpening.cpp b/src/xmipp/libraries/reconstruction/volume_local_sharpening.cpp similarity index 100% rename from libraries/reconstruction/volume_local_sharpening.cpp rename to src/xmipp/libraries/reconstruction/volume_local_sharpening.cpp diff --git a/libraries/reconstruction/volume_local_sharpening.h b/src/xmipp/libraries/reconstruction/volume_local_sharpening.h similarity index 100% rename from libraries/reconstruction/volume_local_sharpening.h rename to src/xmipp/libraries/reconstruction/volume_local_sharpening.h diff --git a/libraries/reconstruction/volume_pca.cpp b/src/xmipp/libraries/reconstruction/volume_pca.cpp similarity index 100% rename from libraries/reconstruction/volume_pca.cpp rename to src/xmipp/libraries/reconstruction/volume_pca.cpp diff --git a/libraries/reconstruction/volume_pca.h b/src/xmipp/libraries/reconstruction/volume_pca.h similarity 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