From 1d9982f31f6866058b7537c1e66ae307f791874d Mon Sep 17 00:00:00 2001 From: David Strelak Date: Tue, 2 Jul 2019 14:29:31 +0200 Subject: [PATCH 1/2] changing the directory structure --- .gitignore | 18 +++++---- .travis.yml | 1 - scripts/travis_before_script.py | 35 ------------------ SConscript => src/xmipp/SConscript | 0 SConstruct => src/xmipp/SConstruct | 0 .../angular_accuracy_pca_main.cpp | 0 .../angular_break_symmetry_main.cpp | 0 .../angular_commonline_main.cpp | 0 .../angular_continuous_assign_main.cpp | 0 .../angular_continuous_assign_main2.cpp | 0 .../angular_discrete_assign_main.cpp | 0 .../angular_distance_main.cpp | 0 .../angular_distribution_show_main.cpp | 0 .../angular_estimate_tilt_axis_main.cpp | 0 .../angular_neighbourhood_main.cpp | 0 .../angular_project_library_main.cpp | 0 .../angular_projection_matching_main.cpp | 0 .../angular_rotate/angular_rotate_main.cpp | 0 .../classify_analyze_cluster_main.cpp | 0 .../classify_compare_classes_main.cpp | 0 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src/xmipp/resources}/test/sampling/ref_i3h_sampling.xmd (100%) rename {resources => src/xmipp/resources}/test/sampling/ref_sampling.xmd (100%) rename {resources => src/xmipp/resources}/test/sampling/refkk_sampling.xmd (100%) rename {resources => src/xmipp/resources}/test/sampling/test_sampling.xmd (100%) rename tar.py => src/xmipp/tar.py (100%) rename {tests => src/xmipp/tests}/__init__.py (100%) rename {tests => src/xmipp/tests}/_test_internal.py (100%) rename {tests => src/xmipp/tests}/_test_pythoninferface_xmipp.py (100%) rename {tests => src/xmipp/tests}/test.py (100%) rename {tests => src/xmipp/tests}/test_programs_xmipp.py (100%) diff --git a/.gitignore b/.gitignore index eae6f53df..284cc8eba 100644 --- a/.gitignore +++ b/.gitignore @@ -46,13 +46,17 @@ 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 -applications/programs/version +/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/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 b/src/xmipp/applications/tests/function_tests/test_transform_window.cpp similarity index 100% rename from applications/tests/function_tests/test_transform_window.cpp rename to src/xmipp/applications/tests/function_tests/test_transform_window.cpp diff --git a/applications/tests/function_tests/test_transformation_main.cpp b/src/xmipp/applications/tests/function_tests/test_transformation_main.cpp similarity index 100% rename from applications/tests/function_tests/test_transformation_main.cpp rename to src/xmipp/applications/tests/function_tests/test_transformation_main.cpp diff --git a/applications/tests/function_tests/test_wavelets_main.cpp b/src/xmipp/applications/tests/function_tests/test_wavelets_main.cpp similarity index 100% rename from applications/tests/function_tests/test_wavelets_main.cpp rename to src/xmipp/applications/tests/function_tests/test_wavelets_main.cpp diff --git a/bindings/matlab/README b/src/xmipp/bindings/matlab/README similarity index 100% rename from bindings/matlab/README rename to src/xmipp/bindings/matlab/README diff --git a/bindings/matlab/mirt3D_mexinterp.cpp b/src/xmipp/bindings/matlab/mirt3D_mexinterp.cpp similarity index 100% rename from bindings/matlab/mirt3D_mexinterp.cpp rename to src/xmipp/bindings/matlab/mirt3D_mexinterp.cpp diff --git a/bindings/matlab/mirt3D_mexinterp.m b/src/xmipp/bindings/matlab/mirt3D_mexinterp.m similarity index 100% rename from bindings/matlab/mirt3D_mexinterp.m rename to src/xmipp/bindings/matlab/mirt3D_mexinterp.m diff --git a/bindings/matlab/tom_calc_periodogram.m b/src/xmipp/bindings/matlab/tom_calc_periodogram.m similarity index 100% rename from bindings/matlab/tom_calc_periodogram.m rename to src/xmipp/bindings/matlab/tom_calc_periodogram.m diff --git a/bindings/matlab/tom_xmipp_adjust_ctf.cpp b/src/xmipp/bindings/matlab/tom_xmipp_adjust_ctf.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_adjust_ctf.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_adjust_ctf.cpp diff --git a/bindings/matlab/tom_xmipp_adjust_ctf.m b/src/xmipp/bindings/matlab/tom_xmipp_adjust_ctf.m similarity index 100% rename from bindings/matlab/tom_xmipp_adjust_ctf.m rename to src/xmipp/bindings/matlab/tom_xmipp_adjust_ctf.m diff --git a/bindings/matlab/tom_xmipp_align2d.cpp b/src/xmipp/bindings/matlab/tom_xmipp_align2d.cpp similarity index 100% rename from bindings/matlab/tom_xmipp_align2d.cpp rename to src/xmipp/bindings/matlab/tom_xmipp_align2d.cpp diff --git a/bindings/matlab/tom_xmipp_align2d.m b/src/xmipp/bindings/matlab/tom_xmipp_align2d.m similarity 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a/libraries/reconstruction/ctf_correct_wiener3d.h b/src/xmipp/libraries/reconstruction/ctf_correct_wiener3d.h similarity index 100% rename from libraries/reconstruction/ctf_correct_wiener3d.h rename to src/xmipp/libraries/reconstruction/ctf_correct_wiener3d.h diff --git a/libraries/reconstruction/ctf_enhance_psd.cpp b/src/xmipp/libraries/reconstruction/ctf_enhance_psd.cpp similarity index 100% rename from libraries/reconstruction/ctf_enhance_psd.cpp rename to src/xmipp/libraries/reconstruction/ctf_enhance_psd.cpp diff --git a/libraries/reconstruction/ctf_enhance_psd.h b/src/xmipp/libraries/reconstruction/ctf_enhance_psd.h similarity index 100% rename from libraries/reconstruction/ctf_enhance_psd.h rename to src/xmipp/libraries/reconstruction/ctf_enhance_psd.h diff --git a/libraries/reconstruction/ctf_estimate_from_micrograph.cpp b/src/xmipp/libraries/reconstruction/ctf_estimate_from_micrograph.cpp similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_micrograph.cpp rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_micrograph.cpp diff --git a/libraries/reconstruction/ctf_estimate_from_micrograph.h b/src/xmipp/libraries/reconstruction/ctf_estimate_from_micrograph.h similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_micrograph.h rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_micrograph.h diff --git a/libraries/reconstruction/ctf_estimate_from_psd.cpp b/src/xmipp/libraries/reconstruction/ctf_estimate_from_psd.cpp similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_psd.cpp rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_psd.cpp diff --git a/libraries/reconstruction/ctf_estimate_from_psd.h b/src/xmipp/libraries/reconstruction/ctf_estimate_from_psd.h similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_psd.h rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_psd.h diff --git a/libraries/reconstruction/ctf_estimate_from_psd_base.cpp b/src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_base.cpp similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_psd_base.cpp rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_base.cpp diff --git a/libraries/reconstruction/ctf_estimate_from_psd_base.h b/src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_base.h similarity index 100% rename from libraries/reconstruction/ctf_estimate_from_psd_base.h rename to src/xmipp/libraries/reconstruction/ctf_estimate_from_psd_base.h diff --git 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 b/src/xmipp/libraries/reconstruction/ctf_estimate_psd_with_arma.h similarity index 100% rename from libraries/reconstruction/ctf_estimate_psd_with_arma.h rename to src/xmipp/libraries/reconstruction/ctf_estimate_psd_with_arma.h diff --git a/libraries/reconstruction/ctf_group.cpp b/src/xmipp/libraries/reconstruction/ctf_group.cpp similarity index 100% rename from libraries/reconstruction/ctf_group.cpp rename to src/xmipp/libraries/reconstruction/ctf_group.cpp diff --git a/libraries/reconstruction/ctf_group.h b/src/xmipp/libraries/reconstruction/ctf_group.h similarity index 100% rename from libraries/reconstruction/ctf_group.h rename to src/xmipp/libraries/reconstruction/ctf_group.h diff --git a/libraries/reconstruction/ctf_phase_flip.cpp b/src/xmipp/libraries/reconstruction/ctf_phase_flip.cpp similarity index 100% rename from libraries/reconstruction/ctf_phase_flip.cpp rename to src/xmipp/libraries/reconstruction/ctf_phase_flip.cpp diff --git a/libraries/reconstruction/ctf_phase_flip.h b/src/xmipp/libraries/reconstruction/ctf_phase_flip.h similarity index 100% rename from libraries/reconstruction/ctf_phase_flip.h rename to src/xmipp/libraries/reconstruction/ctf_phase_flip.h diff --git a/libraries/reconstruction/ctf_show.cpp b/src/xmipp/libraries/reconstruction/ctf_show.cpp similarity index 100% rename from libraries/reconstruction/ctf_show.cpp rename to src/xmipp/libraries/reconstruction/ctf_show.cpp diff --git a/libraries/reconstruction/ctf_show.h b/src/xmipp/libraries/reconstruction/ctf_show.h similarity index 100% rename from libraries/reconstruction/ctf_show.h rename to src/xmipp/libraries/reconstruction/ctf_show.h diff --git a/libraries/reconstruction/ctf_sort_psds.cpp b/src/xmipp/libraries/reconstruction/ctf_sort_psds.cpp similarity index 100% rename from libraries/reconstruction/ctf_sort_psds.cpp rename to src/xmipp/libraries/reconstruction/ctf_sort_psds.cpp diff --git a/libraries/reconstruction/ctf_sort_psds.h b/src/xmipp/libraries/reconstruction/ctf_sort_psds.h similarity index 100% rename from libraries/reconstruction/ctf_sort_psds.h rename to src/xmipp/libraries/reconstruction/ctf_sort_psds.h diff --git a/libraries/reconstruction/denoise.cpp b/src/xmipp/libraries/reconstruction/denoise.cpp similarity index 100% rename from libraries/reconstruction/denoise.cpp rename to src/xmipp/libraries/reconstruction/denoise.cpp diff --git a/libraries/reconstruction/denoise.h b/src/xmipp/libraries/reconstruction/denoise.h similarity index 100% rename from libraries/reconstruction/denoise.h rename to src/xmipp/libraries/reconstruction/denoise.h diff --git a/libraries/reconstruction/directions.cpp b/src/xmipp/libraries/reconstruction/directions.cpp similarity index 100% rename from libraries/reconstruction/directions.cpp rename to src/xmipp/libraries/reconstruction/directions.cpp diff --git a/libraries/reconstruction/directions.h b/src/xmipp/libraries/reconstruction/directions.h similarity index 100% rename from libraries/reconstruction/directions.h rename to src/xmipp/libraries/reconstruction/directions.h diff --git a/libraries/reconstruction/eq_system_solver.cpp b/src/xmipp/libraries/reconstruction/eq_system_solver.cpp similarity index 100% rename from libraries/reconstruction/eq_system_solver.cpp rename to src/xmipp/libraries/reconstruction/eq_system_solver.cpp diff --git a/libraries/reconstruction/eq_system_solver.h b/src/xmipp/libraries/reconstruction/eq_system_solver.h similarity index 100% rename from libraries/reconstruction/eq_system_solver.h rename to src/xmipp/libraries/reconstruction/eq_system_solver.h diff --git a/libraries/reconstruction/evaluate_coordinates.cpp b/src/xmipp/libraries/reconstruction/evaluate_coordinates.cpp similarity index 100% rename from libraries/reconstruction/evaluate_coordinates.cpp rename to src/xmipp/libraries/reconstruction/evaluate_coordinates.cpp diff --git a/libraries/reconstruction/evaluate_coordinates.h b/src/xmipp/libraries/reconstruction/evaluate_coordinates.h similarity index 100% rename from libraries/reconstruction/evaluate_coordinates.h rename to src/xmipp/libraries/reconstruction/evaluate_coordinates.h diff --git a/libraries/reconstruction/fftwT.cpp b/src/xmipp/libraries/reconstruction/fftwT.cpp similarity index 100% rename from libraries/reconstruction/fftwT.cpp rename to src/xmipp/libraries/reconstruction/fftwT.cpp diff --git a/libraries/reconstruction/fftwT.h b/src/xmipp/libraries/reconstruction/fftwT.h similarity index 100% rename from libraries/reconstruction/fftwT.h rename to src/xmipp/libraries/reconstruction/fftwT.h diff --git a/libraries/reconstruction/flexible_alignment.cpp b/src/xmipp/libraries/reconstruction/flexible_alignment.cpp similarity index 100% rename from libraries/reconstruction/flexible_alignment.cpp rename to src/xmipp/libraries/reconstruction/flexible_alignment.cpp diff --git a/libraries/reconstruction/flexible_alignment.h b/src/xmipp/libraries/reconstruction/flexible_alignment.h similarity index 100% rename from libraries/reconstruction/flexible_alignment.h rename to src/xmipp/libraries/reconstruction/flexible_alignment.h diff --git a/libraries/reconstruction/fringe_processing.cpp b/src/xmipp/libraries/reconstruction/fringe_processing.cpp similarity index 100% rename from libraries/reconstruction/fringe_processing.cpp rename to src/xmipp/libraries/reconstruction/fringe_processing.cpp diff --git a/libraries/reconstruction/fringe_processing.h b/src/xmipp/libraries/reconstruction/fringe_processing.h similarity index 100% rename from libraries/reconstruction/fringe_processing.h rename to src/xmipp/libraries/reconstruction/fringe_processing.h diff --git a/libraries/reconstruction/gpu_geo_transformer_defines.h b/src/xmipp/libraries/reconstruction/gpu_geo_transformer_defines.h similarity index 100% rename from libraries/reconstruction/gpu_geo_transformer_defines.h rename to src/xmipp/libraries/reconstruction/gpu_geo_transformer_defines.h diff --git a/libraries/reconstruction/idr_xray_tomo.cpp b/src/xmipp/libraries/reconstruction/idr_xray_tomo.cpp similarity index 100% rename from libraries/reconstruction/idr_xray_tomo.cpp rename to src/xmipp/libraries/reconstruction/idr_xray_tomo.cpp diff --git a/libraries/reconstruction/idr_xray_tomo.h b/src/xmipp/libraries/reconstruction/idr_xray_tomo.h similarity index 100% rename from libraries/reconstruction/idr_xray_tomo.h rename to src/xmipp/libraries/reconstruction/idr_xray_tomo.h diff --git a/libraries/reconstruction/image_assignment_tilt_pair.cpp b/src/xmipp/libraries/reconstruction/image_assignment_tilt_pair.cpp similarity index 100% rename from libraries/reconstruction/image_assignment_tilt_pair.cpp rename to src/xmipp/libraries/reconstruction/image_assignment_tilt_pair.cpp diff --git a/libraries/reconstruction/image_assignment_tilt_pair.h b/src/xmipp/libraries/reconstruction/image_assignment_tilt_pair.h similarity index 100% rename from libraries/reconstruction/image_assignment_tilt_pair.h rename to src/xmipp/libraries/reconstruction/image_assignment_tilt_pair.h diff --git a/libraries/reconstruction/image_eliminate_empty_particles.cpp b/src/xmipp/libraries/reconstruction/image_eliminate_empty_particles.cpp similarity index 100% rename from libraries/reconstruction/image_eliminate_empty_particles.cpp rename to src/xmipp/libraries/reconstruction/image_eliminate_empty_particles.cpp diff --git a/libraries/reconstruction/image_eliminate_empty_particles.h b/src/xmipp/libraries/reconstruction/image_eliminate_empty_particles.h similarity index 100% rename from libraries/reconstruction/image_eliminate_empty_particles.h rename to src/xmipp/libraries/reconstruction/image_eliminate_empty_particles.h diff --git a/libraries/reconstruction/image_eliminate_largeEnergy.cpp b/src/xmipp/libraries/reconstruction/image_eliminate_largeEnergy.cpp similarity index 100% rename from libraries/reconstruction/image_eliminate_largeEnergy.cpp rename to src/xmipp/libraries/reconstruction/image_eliminate_largeEnergy.cpp diff --git a/libraries/reconstruction/image_eliminate_largeEnergy.h b/src/xmipp/libraries/reconstruction/image_eliminate_largeEnergy.h similarity index 100% rename from libraries/reconstruction/image_eliminate_largeEnergy.h rename to src/xmipp/libraries/reconstruction/image_eliminate_largeEnergy.h diff --git a/libraries/reconstruction/image_rotational_pca.cpp b/src/xmipp/libraries/reconstruction/image_rotational_pca.cpp similarity index 100% rename from libraries/reconstruction/image_rotational_pca.cpp rename to src/xmipp/libraries/reconstruction/image_rotational_pca.cpp diff --git a/libraries/reconstruction/image_rotational_pca.h b/src/xmipp/libraries/reconstruction/image_rotational_pca.h similarity index 100% rename from libraries/reconstruction/image_rotational_pca.h rename to src/xmipp/libraries/reconstruction/image_rotational_pca.h diff --git 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 similarity index 100% rename from libraries/reconstruction/image_sort_by_statistics.h rename to src/xmipp/libraries/reconstruction/image_sort_by_statistics.h diff --git a/libraries/reconstruction/mean_shift.cpp b/src/xmipp/libraries/reconstruction/mean_shift.cpp similarity index 100% rename from libraries/reconstruction/mean_shift.cpp rename to src/xmipp/libraries/reconstruction/mean_shift.cpp diff --git a/libraries/reconstruction/mean_shift.h b/src/xmipp/libraries/reconstruction/mean_shift.h similarity index 100% rename from libraries/reconstruction/mean_shift.h rename to src/xmipp/libraries/reconstruction/mean_shift.h diff --git a/libraries/reconstruction/metadata_split_3D.cpp b/src/xmipp/libraries/reconstruction/metadata_split_3D.cpp similarity index 100% rename from libraries/reconstruction/metadata_split_3D.cpp rename to src/xmipp/libraries/reconstruction/metadata_split_3D.cpp diff --git a/libraries/reconstruction/metadata_split_3D.h b/src/xmipp/libraries/reconstruction/metadata_split_3D.h similarity index 100% rename from libraries/reconstruction/metadata_split_3D.h rename to src/xmipp/libraries/reconstruction/metadata_split_3D.h diff --git a/libraries/reconstruction/micrograph_automatic_picking2.cpp b/src/xmipp/libraries/reconstruction/micrograph_automatic_picking2.cpp similarity index 100% rename from libraries/reconstruction/micrograph_automatic_picking2.cpp rename to src/xmipp/libraries/reconstruction/micrograph_automatic_picking2.cpp diff --git a/libraries/reconstruction/micrograph_automatic_picking2.h b/src/xmipp/libraries/reconstruction/micrograph_automatic_picking2.h similarity index 100% rename from libraries/reconstruction/micrograph_automatic_picking2.h rename to src/xmipp/libraries/reconstruction/micrograph_automatic_picking2.h diff --git a/libraries/reconstruction/ml2d.cpp b/src/xmipp/libraries/reconstruction/ml2d.cpp similarity index 100% rename from libraries/reconstruction/ml2d.cpp rename to src/xmipp/libraries/reconstruction/ml2d.cpp diff --git a/libraries/reconstruction/ml2d.h b/src/xmipp/libraries/reconstruction/ml2d.h similarity index 100% rename from libraries/reconstruction/ml2d.h rename to src/xmipp/libraries/reconstruction/ml2d.h diff --git a/libraries/reconstruction/ml_align2d.cpp b/src/xmipp/libraries/reconstruction/ml_align2d.cpp similarity index 100% rename from libraries/reconstruction/ml_align2d.cpp rename to 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a/libraries/reconstruction/ml_tomo.h b/src/xmipp/libraries/reconstruction/ml_tomo.h similarity index 100% rename from libraries/reconstruction/ml_tomo.h rename to src/xmipp/libraries/reconstruction/ml_tomo.h diff --git a/libraries/reconstruction/mlf_align2d.cpp b/src/xmipp/libraries/reconstruction/mlf_align2d.cpp similarity index 100% rename from libraries/reconstruction/mlf_align2d.cpp rename to src/xmipp/libraries/reconstruction/mlf_align2d.cpp diff --git a/libraries/reconstruction/mlf_align2d.h b/src/xmipp/libraries/reconstruction/mlf_align2d.h similarity index 100% rename from libraries/reconstruction/mlf_align2d.h rename to src/xmipp/libraries/reconstruction/mlf_align2d.h diff --git a/libraries/reconstruction/movie_alignment_correlation.cpp b/src/xmipp/libraries/reconstruction/movie_alignment_correlation.cpp similarity index 100% rename from libraries/reconstruction/movie_alignment_correlation.cpp rename to src/xmipp/libraries/reconstruction/movie_alignment_correlation.cpp diff --git a/libraries/reconstruction/movie_alignment_correlation.h b/src/xmipp/libraries/reconstruction/movie_alignment_correlation.h similarity index 100% rename from libraries/reconstruction/movie_alignment_correlation.h rename to src/xmipp/libraries/reconstruction/movie_alignment_correlation.h diff --git a/libraries/reconstruction/movie_alignment_correlation_base.cpp b/src/xmipp/libraries/reconstruction/movie_alignment_correlation_base.cpp similarity index 100% rename from libraries/reconstruction/movie_alignment_correlation_base.cpp rename to src/xmipp/libraries/reconstruction/movie_alignment_correlation_base.cpp diff --git a/libraries/reconstruction/movie_alignment_correlation_base.h b/src/xmipp/libraries/reconstruction/movie_alignment_correlation_base.h similarity index 100% rename from libraries/reconstruction/movie_alignment_correlation_base.h rename to src/xmipp/libraries/reconstruction/movie_alignment_correlation_base.h diff --git a/libraries/reconstruction/movie_alignment_gpu_defines.h b/src/xmipp/libraries/reconstruction/movie_alignment_gpu_defines.h similarity index 100% rename from libraries/reconstruction/movie_alignment_gpu_defines.h rename to src/xmipp/libraries/reconstruction/movie_alignment_gpu_defines.h diff --git a/libraries/reconstruction/movie_estimate_gain.cpp b/src/xmipp/libraries/reconstruction/movie_estimate_gain.cpp similarity index 100% rename from libraries/reconstruction/movie_estimate_gain.cpp rename to src/xmipp/libraries/reconstruction/movie_estimate_gain.cpp diff --git a/libraries/reconstruction/movie_estimate_gain.h b/src/xmipp/libraries/reconstruction/movie_estimate_gain.h similarity index 100% rename from libraries/reconstruction/movie_estimate_gain.h rename to src/xmipp/libraries/reconstruction/movie_estimate_gain.h diff --git a/libraries/reconstruction/movie_filter_dose.cpp b/src/xmipp/libraries/reconstruction/movie_filter_dose.cpp similarity index 100% rename from libraries/reconstruction/movie_filter_dose.cpp rename to src/xmipp/libraries/reconstruction/movie_filter_dose.cpp diff --git a/libraries/reconstruction/movie_filter_dose.h b/src/xmipp/libraries/reconstruction/movie_filter_dose.h similarity index 100% rename from libraries/reconstruction/movie_filter_dose.h rename to src/xmipp/libraries/reconstruction/movie_filter_dose.h diff --git a/libraries/reconstruction/multireference_aligneability.cpp b/src/xmipp/libraries/reconstruction/multireference_aligneability.cpp 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 b/src/xmipp/libraries/reconstruction/reconstruct_fourier_projection_traverse_space.h similarity index 100% rename from libraries/reconstruction/reconstruct_fourier_projection_traverse_space.h rename to src/xmipp/libraries/reconstruction/reconstruct_fourier_projection_traverse_space.h diff --git a/libraries/reconstruction/reconstruct_significant.cpp b/src/xmipp/libraries/reconstruction/reconstruct_significant.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_significant.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_significant.cpp diff --git a/libraries/reconstruction/reconstruct_significant.h b/src/xmipp/libraries/reconstruction/reconstruct_significant.h similarity index 100% rename from libraries/reconstruction/reconstruct_significant.h rename to src/xmipp/libraries/reconstruction/reconstruct_significant.h diff --git a/libraries/reconstruction/reconstruct_wbp.cpp b/src/xmipp/libraries/reconstruction/reconstruct_wbp.cpp similarity index 100% rename from libraries/reconstruction/reconstruct_wbp.cpp rename to src/xmipp/libraries/reconstruction/reconstruct_wbp.cpp diff --git a/libraries/reconstruction/reconstruct_wbp.h b/src/xmipp/libraries/reconstruction/reconstruct_wbp.h similarity index 100% rename from libraries/reconstruction/reconstruct_wbp.h rename to src/xmipp/libraries/reconstruction/reconstruct_wbp.h diff --git a/libraries/reconstruction/refinement.cpp b/src/xmipp/libraries/reconstruction/refinement.cpp similarity index 100% rename from libraries/reconstruction/refinement.cpp rename to src/xmipp/libraries/reconstruction/refinement.cpp diff --git a/libraries/reconstruction/refinement.h b/src/xmipp/libraries/reconstruction/refinement.h similarity index 100% rename from libraries/reconstruction/refinement.h rename to src/xmipp/libraries/reconstruction/refinement.h diff --git a/libraries/reconstruction/resolution_directional.cpp b/src/xmipp/libraries/reconstruction/resolution_directional.cpp similarity index 100% rename from libraries/reconstruction/resolution_directional.cpp rename to src/xmipp/libraries/reconstruction/resolution_directional.cpp diff --git a/libraries/reconstruction/resolution_directional.h b/src/xmipp/libraries/reconstruction/resolution_directional.h similarity index 100% rename from libraries/reconstruction/resolution_directional.h rename to src/xmipp/libraries/reconstruction/resolution_directional.h diff --git a/libraries/reconstruction/resolution_ibw.cpp b/src/xmipp/libraries/reconstruction/resolution_ibw.cpp similarity index 100% rename from libraries/reconstruction/resolution_ibw.cpp rename to src/xmipp/libraries/reconstruction/resolution_ibw.cpp diff --git a/libraries/reconstruction/resolution_ibw.h b/src/xmipp/libraries/reconstruction/resolution_ibw.h similarity index 100% rename from libraries/reconstruction/resolution_ibw.h rename to src/xmipp/libraries/reconstruction/resolution_ibw.h diff --git a/libraries/reconstruction/resolution_localfilter.cpp b/src/xmipp/libraries/reconstruction/resolution_localfilter.cpp similarity index 100% rename from libraries/reconstruction/resolution_localfilter.cpp rename to src/xmipp/libraries/reconstruction/resolution_localfilter.cpp diff --git a/libraries/reconstruction/resolution_localfilter.h b/src/xmipp/libraries/reconstruction/resolution_localfilter.h similarity index 100% rename from libraries/reconstruction/resolution_localfilter.h rename to src/xmipp/libraries/reconstruction/resolution_localfilter.h diff --git a/libraries/reconstruction/resolution_monogenic_signal.cpp b/src/xmipp/libraries/reconstruction/resolution_monogenic_signal.cpp similarity index 100% rename from libraries/reconstruction/resolution_monogenic_signal.cpp rename to src/xmipp/libraries/reconstruction/resolution_monogenic_signal.cpp diff --git a/libraries/reconstruction/resolution_monogenic_signal.h b/src/xmipp/libraries/reconstruction/resolution_monogenic_signal.h similarity index 100% rename from libraries/reconstruction/resolution_monogenic_signal.h rename to src/xmipp/libraries/reconstruction/resolution_monogenic_signal.h diff --git a/libraries/reconstruction/resolution_monotomo.cpp b/src/xmipp/libraries/reconstruction/resolution_monotomo.cpp similarity index 100% rename from libraries/reconstruction/resolution_monotomo.cpp rename to src/xmipp/libraries/reconstruction/resolution_monotomo.cpp diff --git a/libraries/reconstruction/resolution_monotomo.h b/src/xmipp/libraries/reconstruction/resolution_monotomo.h similarity index 100% rename from libraries/reconstruction/resolution_monotomo.h rename to src/xmipp/libraries/reconstruction/resolution_monotomo.h diff --git a/libraries/reconstruction/resolution_ssnr.cpp b/src/xmipp/libraries/reconstruction/resolution_ssnr.cpp similarity index 100% rename from libraries/reconstruction/resolution_ssnr.cpp rename to src/xmipp/libraries/reconstruction/resolution_ssnr.cpp diff --git a/libraries/reconstruction/resolution_ssnr.h b/src/xmipp/libraries/reconstruction/resolution_ssnr.h similarity index 100% rename from libraries/reconstruction/resolution_ssnr.h rename to src/xmipp/libraries/reconstruction/resolution_ssnr.h diff --git a/libraries/reconstruction/score_micrograph.cpp b/src/xmipp/libraries/reconstruction/score_micrograph.cpp similarity index 100% rename from libraries/reconstruction/score_micrograph.cpp rename to src/xmipp/libraries/reconstruction/score_micrograph.cpp diff --git a/libraries/reconstruction/score_micrograph.h b/src/xmipp/libraries/reconstruction/score_micrograph.h similarity index 100% rename from libraries/reconstruction/score_micrograph.h rename to src/xmipp/libraries/reconstruction/score_micrograph.h diff --git a/libraries/reconstruction/shift_corr_estimator.cpp b/src/xmipp/libraries/reconstruction/shift_corr_estimator.cpp similarity index 100% rename from libraries/reconstruction/shift_corr_estimator.cpp rename to src/xmipp/libraries/reconstruction/shift_corr_estimator.cpp diff --git a/libraries/reconstruction/shift_corr_estimator.h b/src/xmipp/libraries/reconstruction/shift_corr_estimator.h similarity index 100% rename from libraries/reconstruction/shift_corr_estimator.h rename to src/xmipp/libraries/reconstruction/shift_corr_estimator.h diff --git a/libraries/reconstruction/symmetrize.cpp b/src/xmipp/libraries/reconstruction/symmetrize.cpp similarity index 100% rename from libraries/reconstruction/symmetrize.cpp rename to src/xmipp/libraries/reconstruction/symmetrize.cpp diff --git a/libraries/reconstruction/symmetrize.h b/src/xmipp/libraries/reconstruction/symmetrize.h similarity index 100% rename from libraries/reconstruction/symmetrize.h rename to src/xmipp/libraries/reconstruction/symmetrize.h diff --git a/libraries/reconstruction/threshold.cpp b/src/xmipp/libraries/reconstruction/threshold.cpp similarity index 100% rename from libraries/reconstruction/threshold.cpp rename to src/xmipp/libraries/reconstruction/threshold.cpp diff --git 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 src/xmipp/libraries/reconstruction/transform_adjust_image_grey_levels.cpp diff --git a/libraries/reconstruction/transform_adjust_image_grey_levels.h b/src/xmipp/libraries/reconstruction/transform_adjust_image_grey_levels.h similarity index 100% rename from libraries/reconstruction/transform_adjust_image_grey_levels.h rename to src/xmipp/libraries/reconstruction/transform_adjust_image_grey_levels.h diff --git a/libraries/reconstruction/validation_nontilt.cpp 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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 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b/src/xmipp/libraries/reconstruction/volume_initial_simulated_annealing.cpp similarity index 100% rename from libraries/reconstruction/volume_initial_simulated_annealing.cpp rename to src/xmipp/libraries/reconstruction/volume_initial_simulated_annealing.cpp diff --git a/libraries/reconstruction/volume_initial_simulated_annealing.h b/src/xmipp/libraries/reconstruction/volume_initial_simulated_annealing.h similarity index 100% rename from libraries/reconstruction/volume_initial_simulated_annealing.h rename to 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 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b/src/xmipp/libraries/reconstruction/volume_segment.h similarity index 100% rename from libraries/reconstruction/volume_segment.h rename to src/xmipp/libraries/reconstruction/volume_segment.h diff --git a/libraries/reconstruction/volume_to_pseudoatoms.cpp b/src/xmipp/libraries/reconstruction/volume_to_pseudoatoms.cpp similarity index 100% rename from libraries/reconstruction/volume_to_pseudoatoms.cpp rename to src/xmipp/libraries/reconstruction/volume_to_pseudoatoms.cpp diff --git a/libraries/reconstruction/volume_to_pseudoatoms.h b/src/xmipp/libraries/reconstruction/volume_to_pseudoatoms.h similarity index 100% rename from libraries/reconstruction/volume_to_pseudoatoms.h rename to src/xmipp/libraries/reconstruction/volume_to_pseudoatoms.h diff --git a/libraries/reconstruction/volume_validate_pca.cpp b/src/xmipp/libraries/reconstruction/volume_validate_pca.cpp similarity index 100% rename from libraries/reconstruction/volume_validate_pca.cpp rename to 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a/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.cpp b/src/xmipp/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.cpp similarity index 100% rename from libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.cpp rename to src/xmipp/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.cpp diff --git a/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.h b/src/xmipp/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.h similarity index 100% rename from libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.h rename to src/xmipp/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.h diff --git a/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation_kernels.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation_kernels.cu similarity index 100% rename from libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation_kernels.cu 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rename to src/xmipp/resources/test/sampling/test_sampling.xmd diff --git a/tar.py b/src/xmipp/tar.py similarity index 100% rename from tar.py rename to src/xmipp/tar.py diff --git a/tests/__init__.py b/src/xmipp/tests/__init__.py similarity index 100% rename from tests/__init__.py rename to src/xmipp/tests/__init__.py diff --git a/tests/_test_internal.py b/src/xmipp/tests/_test_internal.py similarity index 100% rename from tests/_test_internal.py rename to src/xmipp/tests/_test_internal.py diff --git a/tests/_test_pythoninferface_xmipp.py b/src/xmipp/tests/_test_pythoninferface_xmipp.py similarity index 100% rename from tests/_test_pythoninferface_xmipp.py rename to src/xmipp/tests/_test_pythoninferface_xmipp.py diff --git a/tests/test.py b/src/xmipp/tests/test.py similarity index 100% rename from tests/test.py rename to src/xmipp/tests/test.py diff --git a/tests/test_programs_xmipp.py b/src/xmipp/tests/test_programs_xmipp.py similarity index 100% rename from tests/test_programs_xmipp.py rename to src/xmipp/tests/test_programs_xmipp.py From 5f9bb98ada3b097bd5ac893ea5ff56f416bb0245 Mon Sep 17 00:00:00 2001 From: DStrelak Date: Mon, 8 Jul 2019 12:27:00 +0200 Subject: [PATCH 2/2] Update README.md --- README.md | 35 +++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index d888b2de1..d468b673d 100644 --- a/README.md +++ b/README.md @@ -3,23 +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**, please visit [this](https://github.com/I2PC/xmipp/wiki/Migrating-branches-from-nonPluginized-Scipion-to-the-new-Scipion-Xmipp-structure#xmipp-plugin). +Welcome to Xmipp. Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy. -To install Xmipp in a certain place (e.g. in the `xmipp-bundle` directory) follow this instructions: -``` -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` +## Getting started +**Xmipp as a Scipion package** +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). -### Using Scipion libraries +**Xmipp as a standalone bundle (useful for developers)** -If you want xmipp to pick up SCIPION libraries define SCIPION_HOME=\ +Start by cloning the repository from GitHub. + +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=\ + +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.