I2PC · DStrelak · Jul 17, 2019 · Jul 2, 2019 · Jul 8, 2019 · Jul 17, 2019
diff --git 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
@@ -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
diff --git a/SConscript → src/xmipp/SConscript b/SConscript → src/xmipp/SConscript
diff --git a/SConstruct → src/xmipp/SConstruct b/SConstruct → src/xmipp/SConstruct
diff --git a/...ccuracy_pca/angular_accuracy_pca_main.cpp → ...ccuracy_pca/angular_accuracy_pca_main.cpp b/...ccuracy_pca/angular_accuracy_pca_main.cpp → ...ccuracy_pca/angular_accuracy_pca_main.cpp
diff --git a/..._symmetry/angular_break_symmetry_main.cpp → ..._symmetry/angular_break_symmetry_main.cpp b/..._symmetry/angular_break_symmetry_main.cpp → ..._symmetry/angular_break_symmetry_main.cpp
diff --git a/...ar_commonline/angular_commonline_main.cpp → ...ar_commonline/angular_commonline_main.cpp b/...ar_commonline/angular_commonline_main.cpp → ...ar_commonline/angular_commonline_main.cpp
diff --git a/...assign/angular_continuous_assign_main.cpp → ...assign/angular_continuous_assign_main.cpp b/...assign/angular_continuous_assign_main.cpp → ...assign/angular_continuous_assign_main.cpp
diff --git a/...sign2/angular_continuous_assign_main2.cpp → ...sign2/angular_continuous_assign_main2.cpp b/...sign2/angular_continuous_assign_main2.cpp → ...sign2/angular_continuous_assign_main2.cpp
diff --git a/...e_assign/angular_discrete_assign_main.cpp → ...e_assign/angular_discrete_assign_main.cpp b/...e_assign/angular_discrete_assign_main.cpp → ...e_assign/angular_discrete_assign_main.cpp
diff --git a/...ngular_distance/angular_distance_main.cpp → ...ngular_distance/angular_distance_main.cpp b/...ngular_distance/angular_distance_main.cpp → ...ngular_distance/angular_distance_main.cpp
diff --git a/...n_show/angular_distribution_show_main.cpp → ...n_show/angular_distribution_show_main.cpp b/...n_show/angular_distribution_show_main.cpp → ...n_show/angular_distribution_show_main.cpp
diff --git a/..._axis/angular_estimate_tilt_axis_main.cpp → ..._axis/angular_estimate_tilt_axis_main.cpp b/..._axis/angular_estimate_tilt_axis_main.cpp → ..._axis/angular_estimate_tilt_axis_main.cpp
diff --git a/...ghbourhood/angular_neighbourhood_main.cpp → ...ghbourhood/angular_neighbourhood_main.cpp b/...ghbourhood/angular_neighbourhood_main.cpp → ...ghbourhood/angular_neighbourhood_main.cpp
diff --git a/..._library/angular_project_library_main.cpp → ..._library/angular_project_library_main.cpp b/..._library/angular_project_library_main.cpp → ..._library/angular_project_library_main.cpp
diff --git a/...hing/angular_projection_matching_main.cpp → ...hing/angular_projection_matching_main.cpp b/...hing/angular_projection_matching_main.cpp → ...hing/angular_projection_matching_main.cpp
diff --git a/...ms/angular_rotate/angular_rotate_main.cpp → ...ms/angular_rotate/angular_rotate_main.cpp b/...ms/angular_rotate/angular_rotate_main.cpp → ...ms/angular_rotate/angular_rotate_main.cpp
diff --git a/...cluster/classify_analyze_cluster_main.cpp → ...cluster/classify_analyze_cluster_main.cpp b/...cluster/classify_analyze_cluster_main.cpp → ...cluster/classify_analyze_cluster_main.cpp
diff --git a/...classes/classify_compare_classes_main.cpp → ...classes/classify_compare_classes_main.cpp b/...classes/classify_compare_classes_main.cpp → ...classes/classify_compare_classes_main.cpp
diff --git a/...lasses/classify_evaluate_classes_main.cpp → ...lasses/classify_evaluate_classes_main.cpp b/...lasses/classify_evaluate_classes_main.cpp → ...lasses/classify_evaluate_classes_main.cpp
diff --git a/...atures/classify_extract_features_main.cpp → ...atures/classify_extract_features_main.cpp b/...atures/classify_extract_features_main.cpp → ...atures/classify_extract_features_main.cpp
diff --git a/...first_split/classify_first_split_main.cpp → ...first_split/classify_first_split_main.cpp b/...first_split/classify_first_split_main.cpp → ...first_split/classify_first_split_main.cpp
diff --git a/...rst_split3/classify_first_split3_main.cpp → ...rst_split3/classify_first_split3_main.cpp b/...rst_split3/classify_first_split3_main.cpp → ...rst_split3/classify_first_split3_main.cpp
diff --git a/...ify_kerdensom/classify_kerdensom_main.cpp → ...ify_kerdensom/classify_kerdensom_main.cpp b/...ify_kerdensom/classify_kerdensom_main.cpp → ...ify_kerdensom/classify_kerdensom_main.cpp
diff --git a/...ify_kmeans_2d/classify_kmeans_2d_main.cpp → ...ify_kmeans_2d/classify_kmeans_2d_main.cpp b/...ify_kmeans_2d/classify_kmeans_2d_main.cpp → ...ify_kmeans_2d/classify_kmeans_2d_main.cpp
diff --git a/...significant/classify_significant_main.cpp → ...significant/classify_significant_main.cpp b/...significant/classify_significant_main.cpp → ...significant/classify_significant_main.cpp
diff --git a/...r/coordinates_noisy_zones_filter_main.cpp → ...r/coordinates_noisy_zones_filter_main.cpp b/...r/coordinates_noisy_zones_filter_main.cpp → ...r/coordinates_noisy_zones_filter_main.cpp
diff --git a/.../ctf_correct_idr/ctf_correct_idr_main.cpp → .../ctf_correct_idr/ctf_correct_idr_main.cpp b/.../ctf_correct_idr/ctf_correct_idr_main.cpp → .../ctf_correct_idr/ctf_correct_idr_main.cpp
diff --git a/...ct_wiener2d/ctf_correct_wiener2d_main.cpp → ...ct_wiener2d/ctf_correct_wiener2d_main.cpp b/...ct_wiener2d/ctf_correct_wiener2d_main.cpp → ...ct_wiener2d/ctf_correct_wiener2d_main.cpp
diff --git a/...ct_wiener3d/ctf_correct_wiener3d_main.cpp → ...ct_wiener3d/ctf_correct_wiener3d_main.cpp b/...ct_wiener3d/ctf_correct_wiener3d_main.cpp → ...ct_wiener3d/ctf_correct_wiener3d_main.cpp
diff --git a/..._create_ctfdat/ctf_create_ctfdat_main.cpp → ..._create_ctfdat/ctf_create_ctfdat_main.cpp b/..._create_ctfdat/ctf_create_ctfdat_main.cpp → ..._create_ctfdat/ctf_create_ctfdat_main.cpp
diff --git a/.../ctf_enhance_psd/ctf_enhance_psd_main.cpp → .../ctf_enhance_psd/ctf_enhance_psd_main.cpp b/.../ctf_enhance_psd/ctf_enhance_psd_main.cpp → .../ctf_enhance_psd/ctf_enhance_psd_main.cpp
diff --git a/...aph/ctf_estimate_from_micrograph_main.cpp → ...aph/ctf_estimate_from_micrograph_main.cpp b/...aph/ctf_estimate_from_micrograph_main.cpp → ...aph/ctf_estimate_from_micrograph_main.cpp
diff --git a/...e_from_psd/ctf_estimate_from_psd_main.cpp → ...e_from_psd/ctf_estimate_from_psd_main.cpp b/...e_from_psd/ctf_estimate_from_psd_main.cpp → ...e_from_psd/ctf_estimate_from_psd_main.cpp
diff --git a/..._fast/ctf_estimate_from_psd_fast_main.cpp → ..._fast/ctf_estimate_from_psd_fast_main.cpp b/..._fast/ctf_estimate_from_psd_fast_main.cpp → ..._fast/ctf_estimate_from_psd_fast_main.cpp
diff --git a/...ons/programs/ctf_group/ctf_group_main.cpp → ...ons/programs/ctf_group/ctf_group_main.cpp b/...ons/programs/ctf_group/ctf_group_main.cpp → ...ons/programs/ctf_group/ctf_group_main.cpp
diff --git a/...ms/ctf_phase_flip/ctf_phase_flip_main.cpp → ...ms/ctf_phase_flip/ctf_phase_flip_main.cpp b/...ms/ctf_phase_flip/ctf_phase_flip_main.cpp → ...ms/ctf_phase_flip/ctf_phase_flip_main.cpp
diff --git a/...tions/programs/ctf_show/ctf_show_main.cpp → ...tions/programs/ctf_show/ctf_show_main.cpp b/...tions/programs/ctf_show/ctf_show_main.cpp → ...tions/programs/ctf_show/ctf_show_main.cpp
diff --git a/...rams/ctf_sort_psds/ctf_sort_psds_main.cpp → ...rams/ctf_sort_psds/ctf_sort_psds_main.cpp b/...rams/ctf_sort_psds/ctf_sort_psds_main.cpp → ...rams/ctf_sort_psds/ctf_sort_psds_main.cpp
diff --git a/...uda_correlation/cuda_correlation_main.cpp → ...uda_correlation/cuda_correlation_main.cpp b/...uda_correlation/cuda_correlation_main.cpp → ...uda_correlation/cuda_correlation_main.cpp
diff --git a/...tion/cuda_movie_alignment_correlation.cpp → ...tion/cuda_movie_alignment_correlation.cpp b/...tion/cuda_movie_alignment_correlation.cpp → ...tion/cuda_movie_alignment_correlation.cpp
diff --git a/...fourier/cuda_reconstruct_fourier_main.cpp → ...fourier/cuda_reconstruct_fourier_main.cpp b/...fourier/cuda_reconstruct_fourier_main.cpp → ...fourier/cuda_reconstruct_fourier_main.cpp
diff --git a/...coordinates/evaluate_coordinates_main.cpp → ...coordinates/evaluate_coordinates_main.cpp b/...coordinates/evaluate_coordinates_main.cpp → ...coordinates/evaluate_coordinates_main.cpp
diff --git a/...ble_alignment/flexible_alignment_main.cpp → ...ble_alignment/flexible_alignment_main.cpp b/...ble_alignment/flexible_alignment_main.cpp → ...ble_alignment/flexible_alignment_main.cpp
diff --git a/...rams/idr_xray_tomo/idr_xray_tomo_main.cpp → ...rams/idr_xray_tomo/idr_xray_tomo_main.cpp b/...rams/idr_xray_tomo/idr_xray_tomo_main.cpp → ...rams/idr_xray_tomo/idr_xray_tomo_main.cpp
diff --git a/...programs/image_align/image_align_main.cpp → ...programs/image_align/image_align_main.cpp b/...programs/image_align/image_align_main.cpp → ...programs/image_align/image_align_main.cpp
diff --git a/...ign_tilt_pairs/image_align_tilt_pairs.cpp → ...ign_tilt_pairs/image_align_tilt_pairs.cpp b/...ign_tilt_pairs/image_align_tilt_pairs.cpp → ...ign_tilt_pairs/image_align_tilt_pairs.cpp
diff --git a/...t_tilt_pair/assignment_tilt_pair_main.cpp → ...t_tilt_pair/assignment_tilt_pair_main.cpp b/...t_tilt_pair/assignment_tilt_pair_main.cpp → ...t_tilt_pair/assignment_tilt_pair_main.cpp
diff --git a/..._common_lines/image_common_lines_main.cpp → ..._common_lines/image_common_lines_main.cpp b/..._common_lines/image_common_lines_main.cpp → ..._common_lines/image_common_lines_main.cpp
diff --git a/...rams/image_convert/image_convert_main.cpp → ...rams/image_convert/image_convert_main.cpp b/...rams/image_convert/image_convert_main.cpp → ...rams/image_convert/image_convert_main.cpp
diff --git a/.../image_eliminate_empty_particles_main.cpp → .../image_eliminate_empty_particles_main.cpp b/.../image_eliminate_empty_particles_main.cpp → .../image_eliminate_empty_particles_main.cpp
diff --git a/...ergy/image_eliminate_largeEnergy_main.cpp → ...ergy/image_eliminate_largeEnergy_main.cpp b/...ergy/image_eliminate_largeEnergy_main.cpp → ...ergy/image_eliminate_largeEnergy_main.cpp
diff --git a/...ge_find_center/image_find_center_main.cpp → ...ge_find_center/image_find_center_main.cpp b/...ge_find_center/image_find_center_main.cpp → ...ge_find_center/image_find_center_main.cpp
diff --git a/...ograms/image_header/image_header_main.cpp → ...ograms/image_header/image_header_main.cpp b/...ograms/image_header/image_header_main.cpp → ...ograms/image_header/image_header_main.cpp
diff --git a/.../image_histogram/image_histogram_main.cpp → .../image_histogram/image_histogram_main.cpp b/.../image_histogram/image_histogram_main.cpp → .../image_histogram/image_histogram_main.cpp
diff --git a/...rams/image_operate/image_operate_main.cpp → ...rams/image_operate/image_operate_main.cpp b/...rams/image_operate/image_operate_main.cpp → ...rams/image_operate/image_operate_main.cpp
diff --git a/.../image_residuals/image_residuals_main.cpp → .../image_residuals/image_residuals_main.cpp b/.../image_residuals/image_residuals_main.cpp → .../image_residuals/image_residuals_main.cpp
diff --git a/...ns/programs/image_resize/image_resize.cpp → ...ns/programs/image_resize/image_resize.cpp b/...ns/programs/image_resize/image_resize.cpp → ...ns/programs/image_resize/image_resize.cpp
diff --git a/...ational_pca/image_rotational_pca_main.cpp → ...ational_pca/image_rotational_pca_main.cpp b/...ational_pca/image_rotational_pca_main.cpp → ...ational_pca/image_rotational_pca_main.cpp
diff --git a/...spectra/image_rotational_spectra_main.cpp → ...spectra/image_rotational_spectra_main.cpp b/...spectra/image_rotational_spectra_main.cpp → ...spectra/image_rotational_spectra_main.cpp
diff --git a/...e_objects/image_separate_objects_main.cpp → ...e_objects/image_separate_objects_main.cpp b/...e_objects/image_separate_objects_main.cpp → ...e_objects/image_separate_objects_main.cpp
diff --git a/...tistics/image_sort_by_statistics_main.cpp → ...tistics/image_sort_by_statistics_main.cpp b/...tistics/image_sort_by_statistics_main.cpp → ...tistics/image_sort_by_statistics_main.cpp
diff --git a/...s/programs/image_ssnr/image_ssnr_main.cpp → ...s/programs/image_ssnr/image_ssnr_main.cpp b/...s/programs/image_ssnr/image_ssnr_main.cpp → ...s/programs/image_ssnr/image_ssnr_main.cpp
diff --git a/...mage_statistics/image_statistics_main.cpp → ...mage_statistics/image_statistics_main.cpp b/...mage_statistics/image_statistics_main.cpp → ...mage_statistics/image_statistics_main.cpp
diff --git a/.../image_vectorize/image_vectorize_main.cpp → .../image_vectorize/image_vectorize_main.cpp b/.../image_vectorize/image_vectorize_main.cpp → .../image_vectorize/image_vectorize_main.cpp
diff --git a/...rams/matrix_dimred/matrix_dimred_main.cpp → ...rams/matrix_dimred/matrix_dimred_main.cpp b/...rams/matrix_dimred/matrix_dimred_main.cpp → ...rams/matrix_dimred/matrix_dimred_main.cpp
diff --git a/...pider/metadata_convert_to_spider_main.cpp → ...pider/metadata_convert_to_spider_main.cpp b/...pider/metadata_convert_to_spider_main.cpp → ...pider/metadata_convert_to_spider_main.cpp
diff --git a/...ata_histogram/metadata_histogram_main.cpp → ...ata_histogram/metadata_histogram_main.cpp b/...ata_histogram/metadata_histogram_main.cpp → ...ata_histogram/metadata_histogram_main.cpp
diff --git a/.../metadata_import/metadata_import_main.cpp → .../metadata_import/metadata_import_main.cpp b/.../metadata_import/metadata_import_main.cpp → .../metadata_import/metadata_import_main.cpp
diff --git a/...ms/metadata_split/metadata_split_main.cpp → ...ms/metadata_split/metadata_split_main.cpp b/...ms/metadata_split/metadata_split_main.cpp → ...ms/metadata_split/metadata_split_main.cpp
diff --git a/...adata_split_3D/metadata_split_3D_main.cpp → ...adata_split_3D/metadata_split_3D_main.cpp b/...adata_split_3D/metadata_split_3D_main.cpp → ...adata_split_3D/metadata_split_3D_main.cpp
diff --git a/...ata_utilities/metadata_utilities_main.cpp → ...ata_utilities/metadata_utilities_main.cpp b/...ata_utilities/metadata_utilities_main.cpp → ...ata_utilities/metadata_utilities_main.cpp
diff --git a/...ograms/metadata_xml/metadata_xml_main.cpp → ...ograms/metadata_xml/metadata_xml_main.cpp b/...ograms/metadata_xml/metadata_xml_main.cpp → ...ograms/metadata_xml/metadata_xml_main.cpp
diff --git a/...ing/micrograph_automatic_picking_main.cpp → ...ing/micrograph_automatic_picking_main.cpp b/...ing/micrograph_automatic_picking_main.cpp → ...ing/micrograph_automatic_picking_main.cpp
diff --git a/...graph_scissor/micrograph_scissor_main.cpp → ...graph_scissor/micrograph_scissor_main.cpp b/...graph_scissor/micrograph_scissor_main.cpp → ...graph_scissor/micrograph_scissor_main.cpp
diff --git a/...s/programs/ml_align2d/ml_align2d_main.cpp → ...s/programs/ml_align2d/ml_align2d_main.cpp b/...s/programs/ml_align2d/ml_align2d_main.cpp → ...s/programs/ml_align2d/ml_align2d_main.cpp
diff --git a/...programs/ml_refine3d/ml_refine3d_main.cpp → ...programs/ml_refine3d/ml_refine3d_main.cpp b/...programs/ml_refine3d/ml_refine3d_main.cpp → ...programs/ml_refine3d/ml_refine3d_main.cpp
diff --git a/...cations/programs/ml_tomo/ml_tomo_main.cpp → ...cations/programs/ml_tomo/ml_tomo_main.cpp b/...cations/programs/ml_tomo/ml_tomo_main.cpp → ...cations/programs/ml_tomo/ml_tomo_main.cpp
diff --git a/...programs/mlf_align2d/mlf_align2d_main.cpp → ...programs/mlf_align2d/mlf_align2d_main.cpp b/...programs/mlf_align2d/mlf_align2d_main.cpp → ...programs/mlf_align2d/mlf_align2d_main.cpp
diff --git a/...ograms/mlf_refine3d/mlf_refine3d_main.cpp → ...ograms/mlf_refine3d/mlf_refine3d_main.cpp b/...ograms/mlf_refine3d/mlf_refine3d_main.cpp → ...ograms/mlf_refine3d/mlf_refine3d_main.cpp
diff --git a/...rrelation/movie_alignment_correlation.cpp → ...rrelation/movie_alignment_correlation.cpp b/...rrelation/movie_alignment_correlation.cpp → ...rrelation/movie_alignment_correlation.cpp
diff --git a/...stimate_gain/movie_estimate_gain_main.cpp → ...stimate_gain/movie_estimate_gain_main.cpp b/...stimate_gain/movie_estimate_gain_main.cpp → ...stimate_gain/movie_estimate_gain_main.cpp
diff --git a/...s/movie_filter_dose/movie_filter_dose.cpp → ...s/movie_filter_dose/movie_filter_dose.cpp b/...s/movie_filter_dose/movie_filter_dose.cpp → ...s/movie_filter_dose/movie_filter_dose.cpp
diff --git a/...ograms/movie_optical_alignment_cpu/README → ...ograms/movie_optical_alignment_cpu/README b/...ograms/movie_optical_alignment_cpu/README → ...ograms/movie_optical_alignment_cpu/README
diff --git a/...nment_cpu/movie_optical_alignment_cpu.cpp → ...nment_cpu/movie_optical_alignment_cpu.cpp b/...nment_cpu/movie_optical_alignment_cpu.cpp → ...nment_cpu/movie_optical_alignment_cpu.cpp
diff --git a/...ograms/movie_optical_alignment_gpu/README → ...ograms/movie_optical_alignment_gpu/README b/...ograms/movie_optical_alignment_gpu/README → ...ograms/movie_optical_alignment_gpu/README
diff --git a/...nment_gpu/movie_optical_alignment_gpu.cpp → ...nment_gpu/movie_optical_alignment_gpu.cpp b/...nment_gpu/movie_optical_alignment_gpu.cpp → ...nment_gpu/movie_optical_alignment_gpu.cpp
diff --git a/...acy_pca/mpi_angular_accuracy_pca_main.cpp → ...acy_pca/mpi_angular_accuracy_pca_main.cpp b/...acy_pca/mpi_angular_accuracy_pca_main.cpp → ...acy_pca/mpi_angular_accuracy_pca_main.cpp
diff --git a/...verage/mpi_angular_class_average_main.cpp → ...verage/mpi_angular_class_average_main.cpp b/...verage/mpi_angular_class_average_main.cpp → ...verage/mpi_angular_class_average_main.cpp
diff --git a/...gn/mpi_angular_continuous_assign_main.cpp → ...gn/mpi_angular_continuous_assign_main.cpp b/...gn/mpi_angular_continuous_assign_main.cpp → ...gn/mpi_angular_continuous_assign_main.cpp
diff --git a/...2/mpi_angular_continuous_assign_main2.cpp → ...2/mpi_angular_continuous_assign_main2.cpp b/...2/mpi_angular_continuous_assign_main2.cpp → ...2/mpi_angular_continuous_assign_main2.cpp
diff --git a/...sign/mpi_angular_discrete_assign_main.cpp → ...sign/mpi_angular_discrete_assign_main.cpp b/...sign/mpi_angular_discrete_assign_main.cpp → ...sign/mpi_angular_discrete_assign_main.cpp
diff --git a/...rary/mpi_angular_project_library_main.cpp → ...rary/mpi_angular_project_library_main.cpp b/...rary/mpi_angular_project_library_main.cpp → ...rary/mpi_angular_project_library_main.cpp
diff --git a/.../mpi_angular_projection_matching_main.cpp → .../mpi_angular_projection_matching_main.cpp b/.../mpi_angular_projection_matching_main.cpp → .../mpi_angular_projection_matching_main.cpp
diff --git a/...ams/mpi_classify_CL2D/mpi_classify_CL2D.h → ...ams/mpi_classify_CL2D/mpi_classify_CL2D.h b/...ams/mpi_classify_CL2D/mpi_classify_CL2D.h → ...ams/mpi_classify_CL2D/mpi_classify_CL2D.h
diff --git a/..._classify_CL2D/mpi_classify_CL2D_main.cpp → ..._classify_CL2D/mpi_classify_CL2D_main.cpp b/..._classify_CL2D/mpi_classify_CL2D_main.cpp → ..._classify_CL2D/mpi_classify_CL2D_main.cpp
diff --git a/.../mpi_classify_CL2D_core_analysis_main.cpp → .../mpi_classify_CL2D_core_analysis_main.cpp b/.../mpi_classify_CL2D_core_analysis_main.cpp → .../mpi_classify_CL2D_core_analysis_main.cpp
diff --git a/...lassify_CLTomo_prog/mpi_classify_CLTomo.h → ...lassify_CLTomo_prog/mpi_classify_CLTomo.h b/...lassify_CLTomo_prog/mpi_classify_CLTomo.h → ...lassify_CLTomo_prog/mpi_classify_CLTomo.h
diff --git a/...mo_prog/mpi_classify_CLTomo_prog_main.cpp → ...mo_prog/mpi_classify_CLTomo_prog_main.cpp b/...mo_prog/mpi_classify_CLTomo_prog_main.cpp → ...mo_prog/mpi_classify_CLTomo_prog_main.cpp
diff --git a/...lassify_FTTRI/mpi_classify_FTTRI_main.cpp → ...lassify_FTTRI/mpi_classify_FTTRI_main.cpp b/...lassify_FTTRI/mpi_classify_FTTRI_main.cpp → ...lassify_FTTRI/mpi_classify_FTTRI_main.cpp
diff --git a/..._correct_idr/mpi_ctf_correct_idr_main.cpp → ..._correct_idr/mpi_ctf_correct_idr_main.cpp b/..._correct_idr/mpi_ctf_correct_idr_main.cpp → ..._correct_idr/mpi_ctf_correct_idr_main.cpp
diff --git a/...iener2d/mpi_ctf_correct_wiener2d_main.cpp → ...iener2d/mpi_ctf_correct_wiener2d_main.cpp b/...iener2d/mpi_ctf_correct_wiener2d_main.cpp → ...iener2d/mpi_ctf_correct_wiener2d_main.cpp
diff --git a/..._ctf_sort_psds/mpi_ctf_sort_psds_main.cpp → ..._ctf_sort_psds/mpi_ctf_sort_psds_main.cpp b/..._ctf_sort_psds/mpi_ctf_sort_psds_main.cpp → ..._ctf_sort_psds/mpi_ctf_sort_psds_main.cpp
diff --git a/...ier/mpi_cuda_reconstruct_fourier_main.cpp → ...ier/mpi_cuda_reconstruct_fourier_main.cpp b/...ier/mpi_cuda_reconstruct_fourier_main.cpp → ...ier/mpi_cuda_reconstruct_fourier_main.cpp
diff --git a/.../mpi_image_eliminate_largeEnergy_main.cpp → .../mpi_image_eliminate_largeEnergy_main.cpp b/.../mpi_image_eliminate_largeEnergy_main.cpp → .../mpi_image_eliminate_largeEnergy_main.cpp
diff --git a/..._image_operate/mpi_image_operate_main.cpp → ..._image_operate/mpi_image_operate_main.cpp b/..._image_operate/mpi_image_operate_main.cpp → ..._image_operate/mpi_image_operate_main.cpp
diff --git a/...pi_image_resize/mpi_image_resize_main.cpp → ...pi_image_resize/mpi_image_resize_main.cpp b/...pi_image_resize/mpi_image_resize_main.cpp → ...pi_image_resize/mpi_image_resize_main.cpp
diff --git a/...nal_pca/mpi_image_rotational_pca_main.cpp → ...nal_pca/mpi_image_rotational_pca_main.cpp b/...nal_pca/mpi_image_rotational_pca_main.cpp → ...nal_pca/mpi_image_rotational_pca_main.cpp
diff --git a/...ms/mpi_image_sort/mpi_image_sort_main.cpp → ...ms/mpi_image_sort/mpi_image_sort_main.cpp b/...ms/mpi_image_sort/mpi_image_sort_main.cpp → ...ms/mpi_image_sort/mpi_image_sort_main.cpp
diff --git a/...ms/mpi_image_ssnr/mpi_image_ssnr_main.cpp → ...ms/mpi_image_ssnr/mpi_image_ssnr_main.cpp b/...ms/mpi_image_ssnr/mpi_image_ssnr_main.cpp → ...ms/mpi_image_ssnr/mpi_image_ssnr_main.cpp
diff --git a/...ms/mpi_ml_align2d/mpi_ml_align2d_main.cpp → ...ms/mpi_ml_align2d/mpi_ml_align2d_main.cpp b/...ms/mpi_ml_align2d/mpi_ml_align2d_main.cpp → ...ms/mpi_ml_align2d/mpi_ml_align2d_main.cpp
diff --git a/.../mpi_ml_refine3d/mpi_ml_refine3d_main.cpp → .../mpi_ml_refine3d/mpi_ml_refine3d_main.cpp b/.../mpi_ml_refine3d/mpi_ml_refine3d_main.cpp → .../mpi_ml_refine3d/mpi_ml_refine3d_main.cpp
diff --git a/...programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp → ...programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp b/...programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp → ...programs/mpi_ml_tomo/mpi_ml_tomo_main.cpp
diff --git a/.../mpi_mlf_align2d/mpi_mlf_align2d_main.cpp → .../mpi_mlf_align2d/mpi_mlf_align2d_main.cpp b/.../mpi_mlf_align2d/mpi_mlf_align2d_main.cpp → .../mpi_mlf_align2d/mpi_mlf_align2d_main.cpp
diff --git a/...pi_mlf_refine3d/mpi_mlf_refine3d_main.cpp → ...pi_mlf_refine3d/mpi_mlf_refine3d_main.cpp b/...pi_mlf_refine3d/mpi_mlf_refine3d_main.cpp → ...pi_mlf_refine3d/mpi_mlf_refine3d_main.cpp
diff --git a/...mpi_multireference_aligneability_main.cpp → ...mpi_multireference_aligneability_main.cpp b/...mpi_multireference_aligneability_main.cpp → ...mpi_multireference_aligneability_main.cpp
diff --git a/..._nma_alignment/mpi_nma_alignment_main.cpp → ..._nma_alignment/mpi_nma_alignment_main.cpp b/..._nma_alignment/mpi_nma_alignment_main.cpp → ..._nma_alignment/mpi_nma_alignment_main.cpp
diff --git a/...rmance_test/mpi_performance_test_main.cpp → ...rmance_test/mpi_performance_test_main.cpp b/...rmance_test/mpi_performance_test_main.cpp → ...rmance_test/mpi_performance_test_main.cpp
diff --git a/...struct_admm/mpi_reconstruct_admm_main.cpp → ...struct_admm/mpi_reconstruct_admm_main.cpp b/...struct_admm/mpi_reconstruct_admm_main.cpp → ...struct_admm/mpi_reconstruct_admm_main.cpp
diff --git a/...onstruct_art/mpi_reconstruct_art_main.cpp → ...onstruct_art/mpi_reconstruct_art_main.cpp b/...onstruct_art/mpi_reconstruct_art_main.cpp → ...onstruct_art/mpi_reconstruct_art_main.cpp
diff --git a/..._fourier/mpi_reconstruct_fourier_main.cpp → ..._fourier/mpi_reconstruct_fourier_main.cpp b/..._fourier/mpi_reconstruct_fourier_main.cpp → ..._fourier/mpi_reconstruct_fourier_main.cpp
diff --git a/...el/mpi_reconstruct_fourier_accel_main.cpp → ...el/mpi_reconstruct_fourier_accel_main.cpp b/...el/mpi_reconstruct_fourier_accel_main.cpp → ...el/mpi_reconstruct_fourier_accel_main.cpp
diff --git a/...cant/mpi_reconstruct_significant_main.cpp → ...cant/mpi_reconstruct_significant_main.cpp b/...cant/mpi_reconstruct_significant_main.cpp → ...cant/mpi_reconstruct_significant_main.cpp
diff --git a/...onstruct_wbp/mpi_reconstruct_wbp_main.cpp → ...onstruct_wbp/mpi_reconstruct_wbp_main.cpp b/...onstruct_wbp/mpi_reconstruct_wbp_main.cpp → ...onstruct_wbp/mpi_reconstruct_wbp_main.cpp
diff --git a/...cations/programs/mpi_run/mpi_run_main.cpp → ...cations/programs/mpi_run/mpi_run_main.cpp b/...cations/programs/mpi_run/mpi_run_main.cpp → ...cations/programs/mpi_run/mpi_run_main.cpp
diff --git a/..._subvolume/mpi_tomo_extract_subvolume.cpp → ..._subvolume/mpi_tomo_extract_subvolume.cpp b/..._subvolume/mpi_tomo_extract_subvolume.cpp → ..._subvolume/mpi_tomo_extract_subvolume.cpp
diff --git a/...ansform_adjust_image_grey_levels_main.cpp → ...ansform_adjust_image_grey_levels_main.cpp b/...ansform_adjust_image_grey_levels_main.cpp → ...ansform_adjust_image_grey_levels_main.cpp
diff --git a/...form_filter/mpi_transform_filter_main.cpp → ...form_filter/mpi_transform_filter_main.cpp b/...form_filter/mpi_transform_filter_main.cpp → ...form_filter/mpi_transform_filter_main.cpp
diff --git a/..._geometry/mpi_transform_geometry_main.cpp → ..._geometry/mpi_transform_geometry_main.cpp b/..._geometry/mpi_transform_geometry_main.cpp → ..._geometry/mpi_transform_geometry_main.cpp
diff --git a/...ransform_mask/mpi_transform_mask_main.cpp → ...ransform_mask/mpi_transform_mask_main.cpp b/...ransform_mask/mpi_transform_mask_main.cpp → ...ransform_mask/mpi_transform_mask_main.cpp
diff --git a/...ormalize/mpi_transform_normalize_main.cpp → ...ormalize/mpi_transform_normalize_main.cpp b/...ormalize/mpi_transform_normalize_main.cpp → ...ormalize/mpi_transform_normalize_main.cpp
diff --git a/...m_symmetrize/mpi_transform_symmetrize.cpp → ...m_symmetrize/mpi_transform_symmetrize.cpp b/...m_symmetrize/mpi_transform_symmetrize.cpp → ...m_symmetrize/mpi_transform_symmetrize.cpp
diff --git a/...hreshold/mpi_transform_threshold_main.cpp → ...hreshold/mpi_transform_threshold_main.cpp b/...hreshold/mpi_transform_threshold_main.cpp → ...hreshold/mpi_transform_threshold_main.cpp
diff --git a/...n_nontilt/mpi_validation_nontilt_main.cpp → ...n_nontilt/mpi_validation_nontilt_main.cpp b/...n_nontilt/mpi_validation_nontilt_main.cpp → ...n_nontilt/mpi_validation_nontilt_main.cpp
diff --git a/...me_homogenizer/mpi_volume_homogenizer.cpp → ...me_homogenizer/mpi_volume_homogenizer.cpp b/...me_homogenizer/mpi_volume_homogenizer.cpp → ...me_homogenizer/mpi_volume_homogenizer.cpp
diff --git a/...lume_homogenizer/mpi_volume_homogenizer.h → ...lume_homogenizer/mpi_volume_homogenizer.h b/...lume_homogenizer/mpi_volume_homogenizer.h → ...lume_homogenizer/mpi_volume_homogenizer.h
diff --git a/...mogenizer/mpi_volume_homogenizer_main.cpp → ...mogenizer/mpi_volume_homogenizer_main.cpp b/...mogenizer/mpi_volume_homogenizer_main.cpp → ...mogenizer/mpi_volume_homogenizer_main.cpp
diff --git a/...volume_homogenizer/volume_homogenizer.cpp → ...volume_homogenizer/volume_homogenizer.cpp b/...volume_homogenizer/volume_homogenizer.cpp → ...volume_homogenizer/volume_homogenizer.cpp
diff --git a/...i_volume_homogenizer/volume_homogenizer.h → ...i_volume_homogenizer/volume_homogenizer.h b/...i_volume_homogenizer/volume_homogenizer.h → ...i_volume_homogenizer/volume_homogenizer.h
diff --git a/...rograms/mpi_write_test/mpi_write_test.cpp → ...rograms/mpi_write_test/mpi_write_test.cpp b/...rograms/mpi_write_test/mpi_write_test.cpp → ...rograms/mpi_write_test/mpi_write_test.cpp
diff --git a/...pi_xray_project/mpi_xray_project_main.cpp → ...pi_xray_project/mpi_xray_project_main.cpp b/...pi_xray_project/mpi_xray_project_main.cpp → ...pi_xray_project/mpi_xray_project_main.cpp
diff --git a/...ate_metadata/mrc_create_metadata_main.cpp → ...ate_metadata/mrc_create_metadata_main.cpp b/...ate_metadata/mrc_create_metadata_main.cpp → ...ate_metadata/mrc_create_metadata_main.cpp
diff --git a/...ty/multireference_aligneabililty_main.cpp → ...ty/multireference_aligneabililty_main.cpp b/...ty/multireference_aligneabililty_main.cpp → ...ty/multireference_aligneabililty_main.cpp
diff --git a/...rams/nma_alignment/nma_alignment_main.cpp → ...rams/nma_alignment/nma_alignment_main.cpp b/...rams/nma_alignment/nma_alignment_main.cpp → ...rams/nma_alignment/nma_alignment_main.cpp
diff --git a/..._alignment_vol/nma_alignment_vol_main.cpp → ..._alignment_vol/nma_alignment_vol_main.cpp b/..._alignment_vol/nma_alignment_vol_main.cpp → ..._alignment_vol/nma_alignment_vol_main.cpp
diff --git a/...ograms/pdb_analysis/pdb_analysis_main.cpp → ...ograms/pdb_analysis/pdb_analysis_main.cpp b/...ograms/pdb_analysis/pdb_analysis_main.cpp → ...ograms/pdb_analysis/pdb_analysis_main.cpp
diff --git a/...tionary/pdb_construct_dictionary_main.cpp → ...tionary/pdb_construct_dictionary_main.cpp b/...tionary/pdb_construct_dictionary_main.cpp → ...tionary/pdb_construct_dictionary_main.cpp
diff --git a/...ms/pdb_nma_deform/pdb_nma_deform_main.cpp → ...ms/pdb_nma_deform/pdb_nma_deform_main.cpp b/...ms/pdb_nma_deform/pdb_nma_deform_main.cpp → ...ms/pdb_nma_deform/pdb_nma_deform_main.cpp
diff --git a/...eudoatoms/pdb_reduce_pseudoatoms_main.cpp → ...eudoatoms/pdb_reduce_pseudoatoms_main.cpp b/...eudoatoms/pdb_reduce_pseudoatoms_main.cpp → ...eudoatoms/pdb_reduce_pseudoatoms_main.cpp
diff --git a/...nary/pdb_restore_with_dictionary_main.cpp → ...nary/pdb_restore_with_dictionary_main.cpp b/...nary/pdb_restore_with_dictionary_main.cpp → ...nary/pdb_restore_with_dictionary_main.cpp
diff --git a/...ms/phantom_create/phantom_create_main.cpp → ...ms/phantom_create/phantom_create_main.cpp b/...ms/phantom_create/phantom_create_main.cpp → ...ms/phantom_create/phantom_create_main.cpp
diff --git a/...rams/phantom_movie/phantom_movie_main.cpp → ...rams/phantom_movie/phantom_movie_main.cpp b/...rams/phantom_movie/phantom_movie_main.cpp → ...rams/phantom_movie/phantom_movie_main.cpp
diff --git a/.../phantom_project/phantom_project_main.cpp → .../phantom_project/phantom_project_main.cpp b/.../phantom_project/phantom_project_main.cpp → .../phantom_project/phantom_project_main.cpp
diff --git a/...cope/phantom_simulate_microscope_main.cpp → ...cope/phantom_simulate_microscope_main.cpp b/...cope/phantom_simulate_microscope_main.cpp → ...cope/phantom_simulate_microscope_main.cpp
diff --git a/...ntom_transform/phantom_transform_main.cpp → ...ntom_transform/phantom_transform_main.cpp b/...ntom_transform/phantom_transform_main.cpp → ...ntom_transform/phantom_transform_main.cpp
diff --git a/...econstruct_admm/reconstruct_admm_main.cpp → ...econstruct_admm/reconstruct_admm_main.cpp b/...econstruct_admm/reconstruct_admm_main.cpp → ...econstruct_admm/reconstruct_admm_main.cpp
diff --git a/.../reconstruct_art/reconstruct_art_main.cpp → .../reconstruct_art/reconstruct_art_main.cpp b/.../reconstruct_art/reconstruct_art_main.cpp → .../reconstruct_art/reconstruct_art_main.cpp
diff --git a/...rt_pseudo/reconstruct_art_pseudo_main.cpp → ...rt_pseudo/reconstruct_art_pseudo_main.cpp b/...rt_pseudo/reconstruct_art_pseudo_main.cpp → ...rt_pseudo/reconstruct_art_pseudo_main.cpp
diff --git a/...ct_art_xray/reconstruct_art_xray_main.cpp → ...ct_art_xray/reconstruct_art_xray_main.cpp b/...ct_art_xray/reconstruct_art_xray_main.cpp → ...ct_art_xray/reconstruct_art_xray_main.cpp
diff --git a/...ruct_fourier/reconstruct_fourier_main.cpp → ...ruct_fourier/reconstruct_fourier_main.cpp b/...ruct_fourier/reconstruct_fourier_main.cpp → ...ruct_fourier/reconstruct_fourier_main.cpp
diff --git a/..._accel/reconstruct_fourier_accel_main.cpp → ..._accel/reconstruct_fourier_accel_main.cpp b/..._accel/reconstruct_fourier_accel_main.cpp → ..._accel/reconstruct_fourier_accel_main.cpp
diff --git a/...nificant/reconstruct_significant_main.cpp → ...nificant/reconstruct_significant_main.cpp b/...nificant/reconstruct_significant_main.cpp → ...nificant/reconstruct_significant_main.cpp
diff --git a/.../reconstruct_wbp/reconstruct_wbp_main.cpp → .../reconstruct_wbp/reconstruct_wbp_main.cpp b/.../reconstruct_wbp/reconstruct_wbp_main.cpp → .../reconstruct_wbp/reconstruct_wbp_main.cpp
diff --git a/...rectional/resolution_directional_main.cpp → ...rectional/resolution_directional_main.cpp b/...rectional/resolution_directional_main.cpp → ...rectional/resolution_directional_main.cpp
diff --git a/...ms/resolution_fsc/resolution_fsc_main.cpp → ...ms/resolution_fsc/resolution_fsc_main.cpp b/...ms/resolution_fsc/resolution_fsc_main.cpp → ...ms/resolution_fsc/resolution_fsc_main.cpp
diff --git a/...ms/resolution_ibw/resolution_ibw_main.cpp → ...ms/resolution_ibw/resolution_ibw_main.cpp b/...ms/resolution_ibw/resolution_ibw_main.cpp → ...ms/resolution_ibw/resolution_ibw_main.cpp
diff --git a/...calfilter/resolution_localfilter_main.cpp → ...calfilter/resolution_localfilter_main.cpp b/...calfilter/resolution_localfilter_main.cpp → ...calfilter/resolution_localfilter_main.cpp
diff --git a/...gnal/resolution_monogenic_signal_main.cpp → ...gnal/resolution_monogenic_signal_main.cpp b/...gnal/resolution_monogenic_signal_main.cpp → ...gnal/resolution_monogenic_signal_main.cpp
diff --git a/...ion_monotomo/resolution_monotomo_main.cpp → ...ion_monotomo/resolution_monotomo_main.cpp b/...ion_monotomo/resolution_monotomo_main.cpp → ...ion_monotomo/resolution_monotomo_main.cpp
diff --git a/.../resolution_ssnr/resolution_ssnr_main.cpp → .../resolution_ssnr/resolution_ssnr_main.cpp b/.../resolution_ssnr/resolution_ssnr_main.cpp → .../resolution_ssnr/resolution_ssnr_main.cpp
diff --git a/...core_micrograph/score_micrograph_main.cpp → ...core_micrograph/score_micrograph_main.cpp b/...core_micrograph/score_micrograph_main.cpp → ...core_micrograph/score_micrograph_main.cpp
diff --git a/...ries/tomo_align_dual_tilt_series_main.cpp → ...ries/tomo_align_dual_tilt_series_main.cpp b/...ries/tomo_align_dual_tilt_series_main.cpp → ...ries/tomo_align_dual_tilt_series_main.cpp
diff --git a/...refinement/tomo_align_refinement_main.cpp → ...refinement/tomo_align_refinement_main.cpp b/...refinement/tomo_align_refinement_main.cpp → ...refinement/tomo_align_refinement_main.cpp
diff --git a/...lt_series/tomo_align_tilt_series_main.cpp → ...lt_series/tomo_align_tilt_series_main.cpp b/...lt_series/tomo_align_tilt_series_main.cpp → ...lt_series/tomo_align_tilt_series_main.cpp
diff --git a/..._wedge/tomo_detect_missing_wedge_main.cpp → ..._wedge/tomo_detect_missing_wedge_main.cpp b/..._wedge/tomo_detect_missing_wedge_main.cpp → ..._wedge/tomo_detect_missing_wedge_main.cpp
diff --git a/...ct_subvolume/tomo_extract_volume_main.cpp → ...ct_subvolume/tomo_extract_volume_main.cpp b/...ct_subvolume/tomo_extract_volume_main.cpp → ...ct_subvolume/tomo_extract_volume_main.cpp
diff --git a/...ograms/tomo_project/tomo_project_main.cpp → ...ograms/tomo_project/tomo_project_main.cpp b/...ograms/tomo_project/tomo_project_main.cpp → ...ograms/tomo_project/tomo_project_main.cpp
diff --git a/...uations/tomo_remove_fluctuations_main.cpp → ...uations/tomo_remove_fluctuations_main.cpp b/...uations/tomo_remove_fluctuations_main.cpp → ...uations/tomo_remove_fluctuations_main.cpp
diff --git a/...rm_add_noise/transform_add_noise_main.cpp → ...rm_add_noise/transform_add_noise_main.cpp b/...rm_add_noise/transform_add_noise_main.cpp → ...rm_add_noise/transform_add_noise_main.cpp
diff --git a/...ansform_adjust_image_grey_levels_main.cpp → ...ansform_adjust_image_grey_levels_main.cpp b/...ansform_adjust_image_grey_levels_main.cpp → ...ansform_adjust_image_grey_levels_main.cpp
diff --git a/...nsform_adjust_volume_grey_levels_main.cpp → ...nsform_adjust_volume_grey_levels_main.cpp b/...nsform_adjust_volume_grey_levels_main.cpp → ...nsform_adjust_volume_grey_levels_main.cpp
diff --git a/...ter_image/transform_center_image_main.cpp → ...ter_image/transform_center_image_main.cpp b/...ter_image/transform_center_image_main.cpp → ...ter_image/transform_center_image_main.cpp
diff --git a/...ransform_dimred/transform_dimred_main.cpp → ...ransform_dimred/transform_dimred_main.cpp b/...ransform_dimred/transform_dimred_main.cpp → ...ransform_dimred/transform_dimred_main.cpp
diff --git a/..._downsample/transform_downsample_main.cpp → ..._downsample/transform_downsample_main.cpp b/..._downsample/transform_downsample_main.cpp → ..._downsample/transform_downsample_main.cpp
diff --git a/...ransform_filter/transform_filter_main.cpp → ...ransform_filter/transform_filter_main.cpp b/...ransform_filter/transform_filter_main.cpp → ...ransform_filter/transform_filter_main.cpp
diff --git a/...form_geometry/transform_geometry_main.cpp → ...form_geometry/transform_geometry_main.cpp b/...form_geometry/transform_geometry_main.cpp → ...form_geometry/transform_geometry_main.cpp
diff --git a/...ms/transform_mask/transform_mask_main.cpp → ...ms/transform_mask/transform_mask_main.cpp b/...ms/transform_mask/transform_mask_main.cpp → ...ms/transform_mask/transform_mask_main.cpp
diff --git a/...ransform_mirror/transform_mirror_main.cpp → ...ransform_mirror/transform_mirror_main.cpp b/...ransform_mirror/transform_mirror_main.cpp → ...ransform_mirror/transform_mirror_main.cpp
diff --git a/..._morphology/transform_morphology_main.cpp → ..._morphology/transform_morphology_main.cpp b/..._morphology/transform_morphology_main.cpp → ..._morphology/transform_morphology_main.cpp
diff --git a/...rm_normalize/transform_normalize_main.cpp → ...rm_normalize/transform_normalize_main.cpp b/...rm_normalize/transform_normalize_main.cpp → ...rm_normalize/transform_normalize_main.cpp
diff --git a/...hases/transform_randomize_phases_main.cpp → ...hases/transform_randomize_phases_main.cpp b/...hases/transform_randomize_phases_main.cpp → ...hases/transform_randomize_phases_main.cpp
diff --git a/...ge_adjust/transform_range_adjust_main.cpp → ...ge_adjust/transform_range_adjust_main.cpp b/...ge_adjust/transform_range_adjust_main.cpp → ...ge_adjust/transform_range_adjust_main.cpp
diff --git a/..._symmetrize/transform_symmetrize_main.cpp → ..._symmetrize/transform_symmetrize_main.cpp b/..._symmetrize/transform_symmetrize_main.cpp → ..._symmetrize/transform_symmetrize_main.cpp
diff --git a/...rm_threshold/transform_threshold_main.cpp → ...rm_threshold/transform_threshold_main.cpp b/...rm_threshold/transform_threshold_main.cpp → ...rm_threshold/transform_threshold_main.cpp
diff --git a/...ransform_window/transform_window_main.cpp → ...ransform_window/transform_window_main.cpp b/...ransform_window/transform_window_main.cpp → ...ransform_window/transform_window_main.cpp
diff --git a/...ation_nontilt/validation_nontilt_main.cpp → ...ation_nontilt/validation_nontilt_main.cpp b/...ation_nontilt/validation_nontilt_main.cpp → ...ation_nontilt/validation_nontilt_main.cpp
diff --git a/...tilt_pairs/validation_tilt_pairs_main.cpp → ...tilt_pairs/validation_tilt_pairs_main.cpp b/...tilt_pairs/validation_tilt_pairs_main.cpp → ...tilt_pairs/validation_tilt_pairs_main.cpp
diff --git a/...ume_align_prog/volume_align_prog_main.cpp → ...ume_align_prog/volume_align_prog_main.cpp b/...ume_align_prog/volume_align_prog_main.cpp → ...ume_align_prog/volume_align_prog_main.cpp
diff --git a/...rams/volume_center/volume_center_main.cpp → ...rams/volume_center/volume_center_main.cpp b/...rams/volume_center/volume_center_main.cpp → ...rams/volume_center/volume_center_main.cpp
diff --git a/...t_bfactor/volume_correct_bfactor_main.cpp → ...t_bfactor/volume_correct_bfactor_main.cpp b/...t_bfactor/volume_correct_bfactor_main.cpp → ...t_bfactor/volume_correct_bfactor_main.cpp
diff --git a/...ume_deform_sph/volume_deform_sph_main.cpp → ...ume_deform_sph/volume_deform_sph_main.cpp b/...ume_deform_sph/volume_deform_sph_main.cpp → ...ume_deform_sph/volume_deform_sph_main.cpp
diff --git a/...contrast/volume_enhance_contrast_main.cpp → ...contrast/volume_enhance_contrast_main.cpp b/...contrast/volume_enhance_contrast_main.cpp → ...contrast/volume_enhance_contrast_main.cpp
diff --git a/...nd_symmetry/volume_find_symmetry_main.cpp → ...nd_symmetry/volume_find_symmetry_main.cpp b/...nd_symmetry/volume_find_symmetry_main.cpp → ...nd_symmetry/volume_find_symmetry_main.cpp
diff --git a/.../volume_from_pdb/volume_from_pdb_main.cpp → .../volume_from_pdb/volume_from_pdb_main.cpp b/.../volume_from_pdb/volume_from_pdb_main.cpp → .../volume_from_pdb/volume_from_pdb_main.cpp
diff --git a/...ration/volume_halves_restoration_main.cpp → ...ration/volume_halves_restoration_main.cpp b/...ration/volume_halves_restoration_main.cpp → ...ration/volume_halves_restoration_main.cpp
diff --git a/...lume_initial_simulated_annealing_main.cpp → ...lume_initial_simulated_annealing_main.cpp b/...lume_initial_simulated_annealing_main.cpp → ...lume_initial_simulated_annealing_main.cpp
diff --git a/...arpening/volume_local_sharpening_main.cpp → ...arpening/volume_local_sharpening_main.cpp b/...arpening/volume_local_sharpening_main.cpp → ...arpening/volume_local_sharpening_main.cpp
diff --git a/...s/programs/volume_pca/volume_pca_main.cpp → ...s/programs/volume_pca/volume_pca_main.cpp b/...s/programs/volume_pca/volume_pca_main.cpp → ...s/programs/volume_pca/volume_pca_main.cpp
diff --git a/...ms/volume_reslice/volume_reslice_main.cpp → ...ms/volume_reslice/volume_reslice_main.cpp b/...ms/volume_reslice/volume_reslice_main.cpp → ...ms/volume_reslice/volume_reslice_main.cpp
diff --git a/...ms/volume_segment/volume_segment_main.cpp → ...ms/volume_segment/volume_segment_main.cpp b/...ms/volume_segment/volume_segment_main.cpp → ...ms/volume_segment/volume_segment_main.cpp
diff --git a/...e_factor/volume_structure_factor_main.cpp → ...e_factor/volume_structure_factor_main.cpp b/...e_factor/volume_structure_factor_main.cpp → ...e_factor/volume_structure_factor_main.cpp
diff --git a/...seudoatoms/volume_to_pseudoatoms_main.cpp → ...seudoatoms/volume_to_pseudoatoms_main.cpp b/...seudoatoms/volume_to_pseudoatoms_main.cpp → ...seudoatoms/volume_to_pseudoatoms_main.cpp
diff --git a/...rams/volume_to_web/volume_to_web_main.cpp → ...rams/volume_to_web/volume_to_web_main.cpp b/...rams/volume_to_web/volume_to_web_main.cpp → ...rams/volume_to_web/volume_to_web_main.cpp
diff --git a/...validate_pca/volume_validate_pca_main.cpp → ...validate_pca/volume_validate_pca_main.cpp b/...validate_pca/volume_validate_pca_main.cpp → ...validate_pca/volume_validate_pca_main.cpp
diff --git a/...ications/programs/work_test/work_test.cpp → ...ications/programs/work_test/work_test.cpp b/...ications/programs/work_test/work_test.cpp → ...ications/programs/work_test/work_test.cpp
diff --git a/...programs/xray_import/xray_import_main.cpp → ...programs/xray_import/xray_import_main.cpp b/...programs/xray_import/xray_import_main.cpp → ...programs/xray_import/xray_import_main.cpp
diff --git a/...ograms/xray_project/xray_project_main.cpp → ...ograms/xray_project/xray_project_main.cpp b/...ograms/xray_project/xray_project_main.cpp → ...ograms/xray_project/xray_project_main.cpp
diff --git a/.../xray_psf_create/xray_psf_create_main.cpp → .../xray_psf_create/xray_psf_create_main.cpp b/.../xray_psf_create/xray_psf_create_main.cpp → .../xray_psf_create/xray_psf_create_main.cpp
diff --git a/...ications/scripts/apropos/batch_apropos.py → ...ications/scripts/apropos/batch_apropos.py b/...ications/scripts/apropos/batch_apropos.py → ...ications/scripts/apropos/batch_apropos.py
diff --git a/...ications/scripts/compile/batch_compile.py → ...ications/scripts/compile/batch_compile.py b/...ications/scripts/compile/batch_compile.py → ...ications/scripts/compile/batch_compile.py
diff --git a/...inates_consensus/coordinates_consensus.py → ...inates_consensus/coordinates_consensus.py b/...inates_consensus/coordinates_consensus.py → ...inates_consensus/coordinates_consensus.py
diff --git a/...es_resolution/batch_deepRes_resolution.py → ...es_resolution/batch_deepRes_resolution.py b/...es_resolution/batch_deepRes_resolution.py → ...es_resolution/batch_deepRes_resolution.py
diff --git a/.../scripts/deep_consensus/deep_consensus.py → .../scripts/deep_consensus/deep_consensus.py b/.../scripts/deep_consensus/deep_consensus.py → .../scripts/deep_consensus/deep_consensus.py
diff --git a/...us/helpers/howToPretrainDeepConsensus.txt → ...us/helpers/howToPretrainDeepConsensus.txt b/...us/helpers/howToPretrainDeepConsensus.txt → ...us/helpers/howToPretrainDeepConsensus.txt
diff --git a/...helpers/protocol_prepare_deepConsensus.py → ...helpers/protocol_prepare_deepConsensus.py b/...helpers/protocol_prepare_deepConsensus.py → ...helpers/protocol_prepare_deepConsensus.py
diff --git a/...ts/extract_particles/extract_particles.py → ...ts/extract_particles/extract_particles.py b/...ts/extract_particles/extract_particles.py → ...ts/extract_particles/extract_particles.py
diff --git a/...e_create/batch_metadata_selfile_create.py → ...e_create/batch_metadata_selfile_create.py b/...e_create/batch_metadata_selfile_create.py → ...e_create/batch_metadata_selfile_create.py
diff --git a/...ssify_CLTomo/batch_mpi_classify_CLTomo.sh → ...ssify_CLTomo/batch_mpi_classify_CLTomo.sh b/...ssify_CLTomo/batch_mpi_classify_CLTomo.sh → ...ssify_CLTomo/batch_mpi_classify_CLTomo.sh
diff --git a/...article_boxsize/batch_particle_boxsize.py → ...article_boxsize/batch_particle_boxsize.py b/...article_boxsize/batch_particle_boxsize.py → ...article_boxsize/batch_particle_boxsize.py
diff --git a/...ns/scripts/pdb_center/batch_pdb_center.py → ...ns/scripts/pdb_center/batch_pdb_center.py b/...ns/scripts/pdb_center/batch_pdb_center.py → ...ns/scripts/pdb_center/batch_pdb_center.py
diff --git a/...ns/scripts/pdb_select/batch_pdb_select.py → ...ns/scripts/pdb_select/batch_pdb_select.py b/...ns/scripts/pdb_select/batch_pdb_select.py → ...ns/scripts/pdb_select/batch_pdb_select.py
diff --git a/...ications/scripts/pick_noise/pick_noise.py → ...ications/scripts/pick_noise/pick_noise.py b/...ications/scripts/pick_noise/pick_noise.py → ...ications/scripts/pick_noise/pick_noise.py
diff --git a/...cripts/preprocess_mics/preprocess_mics.py → ...cripts/preprocess_mics/preprocess_mics.py b/...cripts/preprocess_mics/preprocess_mics.py → ...cripts/preprocess_mics/preprocess_mics.py
diff --git a/...ions/scripts/sync_data/batch_sync_data.py → ...ions/scripts/sync_data/batch_sync_data.py b/...ions/scripts/sync_data/batch_sync_data.py → ...ions/scripts/sync_data/batch_sync_data.py
diff --git a/...ule/batch_test_script_importing_module.py → ...ule/batch_test_script_importing_module.py b/...ule/batch_test_script_importing_module.py → ...ule/batch_test_script_importing_module.py
diff --git a/...cripts/volume_align/batch_volume_align.sh → ...cripts/volume_align/batch_volume_align.sh b/...cripts/volume_align/batch_volume_align.sh → ...cripts/volume_align/batch_volume_align.sh
diff --git a/...ications/tests/function_tests/aft_tests.h → ...ications/tests/function_tests/aft_tests.h b/...ications/tests/function_tests/aft_tests.h → ...ications/tests/function_tests/aft_tests.h
diff --git a/...ction_tests/ashift_corr_estimator_tests.h → ...ction_tests/ashift_corr_estimator_tests.h b/...ction_tests/ashift_corr_estimator_tests.h → ...ction_tests/ashift_corr_estimator_tests.h
diff --git a/...s/function_tests/ashift_estimator_tests.h → ...s/function_tests/ashift_estimator_tests.h b/...s/function_tests/ashift_estimator_tests.h → ...s/function_tests/ashift_estimator_tests.h
diff --git a/...ns/tests/function_tests/test_ctf_main.cpp → ...ns/tests/function_tests/test_ctf_main.cpp b/...ns/tests/function_tests/test_ctf_main.cpp → ...ns/tests/function_tests/test_ctf_main.cpp
diff --git a/...ns/tests/function_tests/test_cuda_fft.cpp → ...ns/tests/function_tests/test_cuda_fft.cpp b/...ns/tests/function_tests/test_cuda_fft.cpp → ...ns/tests/function_tests/test_cuda_fft.cpp
diff --git a/...o_transformer_apply_bspline_transform.cpp → ...o_transformer_apply_bspline_transform.cpp b/...o_transformer_apply_bspline_transform.cpp → ...o_transformer_apply_bspline_transform.cpp
diff --git a/...o_transformer_produce_and_load_coeffs.cpp → ...o_transformer_produce_and_load_coeffs.cpp b/...o_transformer_produce_and_load_coeffs.cpp → ...o_transformer_produce_and_load_coeffs.cpp
diff --git a/..._cuda_movie_alignment_correlation_gpu.cpp → ..._cuda_movie_alignment_correlation_gpu.cpp b/..._cuda_movie_alignment_correlation_gpu.cpp → ..._cuda_movie_alignment_correlation_gpu.cpp
diff --git a/..._tests/test_cuda_shift_corr_estimator.cpp → ..._tests/test_cuda_shift_corr_estimator.cpp b/..._tests/test_cuda_shift_corr_estimator.cpp → ..._tests/test_cuda_shift_corr_estimator.cpp
diff --git a/...tests/function_tests/test_dimred_main.cpp → ...tests/function_tests/test_dimred_main.cpp b/...tests/function_tests/test_dimred_main.cpp → ...tests/function_tests/test_dimred_main.cpp
diff --git a/.../tests/function_tests/test_euler_main.cpp → .../tests/function_tests/test_euler_main.cpp b/.../tests/function_tests/test_euler_main.cpp → .../tests/function_tests/test_euler_main.cpp
diff --git a/...s/tests/function_tests/test_fftw_main.cpp → ...s/tests/function_tests/test_fftw_main.cpp b/...s/tests/function_tests/test_fftw_main.cpp → ...s/tests/function_tests/test_fftw_main.cpp
diff --git a/...tions/tests/function_tests/test_fftwt.cpp → ...tions/tests/function_tests/test_fftwt.cpp b/...tions/tests/function_tests/test_fftwt.cpp → ...tions/tests/function_tests/test_fftwt.cpp
diff --git a/...sts/function_tests/test_filename_main.cpp → ...sts/function_tests/test_filename_main.cpp b/...sts/function_tests/test_filename_main.cpp → ...sts/function_tests/test_filename_main.cpp
diff --git a/...ests/function_tests/test_filters_main.cpp → ...ests/function_tests/test_filters_main.cpp b/...ests/function_tests/test_filters_main.cpp → ...ests/function_tests/test_filters_main.cpp
diff --git a/...ion_tests/test_fringe_processing_main.cpp → ...ion_tests/test_fringe_processing_main.cpp b/...ion_tests/test_fringe_processing_main.cpp → ...ion_tests/test_fringe_processing_main.cpp
diff --git a/.../tests/function_tests/test_funcs_main.cpp → .../tests/function_tests/test_funcs_main.cpp b/.../tests/function_tests/test_funcs_main.cpp → .../tests/function_tests/test_funcs_main.cpp
diff --git a/...sts/function_tests/test_geometry_main.cpp → ...sts/function_tests/test_geometry_main.cpp b/...sts/function_tests/test_geometry_main.cpp → ...sts/function_tests/test_geometry_main.cpp
diff --git a/...unction_tests/test_image_generic_main.cpp → ...unction_tests/test_image_generic_main.cpp b/...unction_tests/test_image_generic_main.cpp → ...unction_tests/test_image_generic_main.cpp
diff --git a/.../tests/function_tests/test_image_main.cpp → .../tests/function_tests/test_image_main.cpp b/.../tests/function_tests/test_image_main.cpp → .../tests/function_tests/test_image_main.cpp
diff --git a/...tests/function_tests/test_matrix_main.cpp → ...tests/function_tests/test_matrix_main.cpp b/...tests/function_tests/test_matrix_main.cpp → ...tests/function_tests/test_matrix_main.cpp
diff --git a/...sts/function_tests/test_metadata_main.cpp → ...sts/function_tests/test_metadata_main.cpp b/...sts/function_tests/test_metadata_main.cpp → ...sts/function_tests/test_metadata_main.cpp
diff --git a/...function_tests/test_movie_filter_dose.cpp → ...function_tests/test_movie_filter_dose.cpp b/...function_tests/test_movie_filter_dose.cpp → ...function_tests/test_movie_filter_dose.cpp
diff --git a/...sts/function_tests/test_multidim_main.cpp → ...sts/function_tests/test_multidim_main.cpp b/...sts/function_tests/test_multidim_main.cpp → ...sts/function_tests/test_multidim_main.cpp
diff --git a/.../tests/function_tests/test_polar_main.cpp → .../tests/function_tests/test_polar_main.cpp b/.../tests/function_tests/test_polar_main.cpp → .../tests/function_tests/test_polar_main.cpp
diff --git a/.../function_tests/test_polynomials_main.cpp → .../function_tests/test_polynomials_main.cpp b/.../function_tests/test_polynomials_main.cpp → .../function_tests/test_polynomials_main.cpp
diff --git a/...sts/function_tests/test_psd_estimator.cpp → ...sts/function_tests/test_psd_estimator.cpp b/...sts/function_tests/test_psd_estimator.cpp → ...sts/function_tests/test_psd_estimator.cpp
diff --git a/...ts/function_tests/test_resolution_frc.cpp → ...ts/function_tests/test_resolution_frc.cpp b/...ts/function_tests/test_resolution_frc.cpp → ...ts/function_tests/test_resolution_frc.cpp
diff --git a/...sts/function_tests/test_sampling_main.cpp → ...sts/function_tests/test_sampling_main.cpp b/...sts/function_tests/test_sampling_main.cpp → ...sts/function_tests/test_sampling_main.cpp
diff --git a/...ction_tests/test_shift_corr_estimator.cpp → ...ction_tests/test_shift_corr_estimator.cpp b/...ction_tests/test_shift_corr_estimator.cpp → ...ction_tests/test_shift_corr_estimator.cpp
diff --git a/...s/function_tests/test_symmetries_main.cpp → ...s/function_tests/test_symmetries_main.cpp b/...s/function_tests/test_symmetries_main.cpp → ...s/function_tests/test_symmetries_main.cpp
diff --git a/.../function_tests/test_transform_window.cpp → .../function_tests/test_transform_window.cpp b/.../function_tests/test_transform_window.cpp → .../function_tests/test_transform_window.cpp
diff --git a/...nction_tests/test_transformation_main.cpp → ...nction_tests/test_transformation_main.cpp b/...nction_tests/test_transformation_main.cpp → ...nction_tests/test_transformation_main.cpp
diff --git a/...sts/function_tests/test_wavelets_main.cpp → ...sts/function_tests/test_wavelets_main.cpp b/...sts/function_tests/test_wavelets_main.cpp → ...sts/function_tests/test_wavelets_main.cpp
diff --git a/bindings/matlab/README → src/xmipp/bindings/matlab/README b/bindings/matlab/README → src/xmipp/bindings/matlab/README
diff --git a/bindings/matlab/mirt3D_mexinterp.cpp → ...mipp/bindings/matlab/mirt3D_mexinterp.cpp b/bindings/matlab/mirt3D_mexinterp.cpp → ...mipp/bindings/matlab/mirt3D_mexinterp.cpp
diff --git a/bindings/matlab/mirt3D_mexinterp.m → src/xmipp/bindings/matlab/mirt3D_mexinterp.m b/bindings/matlab/mirt3D_mexinterp.m → src/xmipp/bindings/matlab/mirt3D_mexinterp.m
diff --git a/bindings/matlab/tom_calc_periodogram.m → ...pp/bindings/matlab/tom_calc_periodogram.m b/bindings/matlab/tom_calc_periodogram.m → ...pp/bindings/matlab/tom_calc_periodogram.m
diff --git a/bindings/matlab/tom_xmipp_adjust_ctf.cpp → .../bindings/matlab/tom_xmipp_adjust_ctf.cpp b/bindings/matlab/tom_xmipp_adjust_ctf.cpp → .../bindings/matlab/tom_xmipp_adjust_ctf.cpp
diff --git a/bindings/matlab/tom_xmipp_adjust_ctf.m → ...pp/bindings/matlab/tom_xmipp_adjust_ctf.m b/bindings/matlab/tom_xmipp_adjust_ctf.m → ...pp/bindings/matlab/tom_xmipp_adjust_ctf.m
diff --git a/bindings/matlab/tom_xmipp_align2d.cpp → ...ipp/bindings/matlab/tom_xmipp_align2d.cpp b/bindings/matlab/tom_xmipp_align2d.cpp → ...ipp/bindings/matlab/tom_xmipp_align2d.cpp
diff --git a/bindings/matlab/tom_xmipp_align2d.m → ...xmipp/bindings/matlab/tom_xmipp_align2d.m b/bindings/matlab/tom_xmipp_align2d.m → ...xmipp/bindings/matlab/tom_xmipp_align2d.m
diff --git a/bindings/matlab/tom_xmipp_align2d_stack.m → ...bindings/matlab/tom_xmipp_align2d_stack.m b/bindings/matlab/tom_xmipp_align2d_stack.m → ...bindings/matlab/tom_xmipp_align2d_stack.m
diff --git a/...gs/matlab/tom_xmipp_ctf_correct_phase.cpp → ...gs/matlab/tom_xmipp_ctf_correct_phase.cpp b/...gs/matlab/tom_xmipp_ctf_correct_phase.cpp → ...gs/matlab/tom_xmipp_ctf_correct_phase.cpp
diff --git a/...ings/matlab/tom_xmipp_ctf_correct_phase.m → ...ings/matlab/tom_xmipp_ctf_correct_phase.m b/...ings/matlab/tom_xmipp_ctf_correct_phase.m → ...ings/matlab/tom_xmipp_ctf_correct_phase.m
diff --git a/bindings/matlab/tom_xmipp_helpers.h → ...xmipp/bindings/matlab/tom_xmipp_helpers.h b/bindings/matlab/tom_xmipp_helpers.h → ...xmipp/bindings/matlab/tom_xmipp_helpers.h
diff --git a/bindings/matlab/tom_xmipp_mask.cpp → src/xmipp/bindings/matlab/tom_xmipp_mask.cpp b/bindings/matlab/tom_xmipp_mask.cpp → src/xmipp/bindings/matlab/tom_xmipp_mask.cpp
diff --git a/bindings/matlab/tom_xmipp_mask.m → src/xmipp/bindings/matlab/tom_xmipp_mask.m b/bindings/matlab/tom_xmipp_mask.m → src/xmipp/bindings/matlab/tom_xmipp_mask.m
diff --git a/bindings/matlab/tom_xmipp_mirror.cpp → ...mipp/bindings/matlab/tom_xmipp_mirror.cpp b/bindings/matlab/tom_xmipp_mirror.cpp → ...mipp/bindings/matlab/tom_xmipp_mirror.cpp
diff --git a/bindings/matlab/tom_xmipp_mirror.m → src/xmipp/bindings/matlab/tom_xmipp_mirror.m b/bindings/matlab/tom_xmipp_mirror.m → src/xmipp/bindings/matlab/tom_xmipp_mirror.m
diff --git a/bindings/matlab/tom_xmipp_morphology.cpp → .../bindings/matlab/tom_xmipp_morphology.cpp b/bindings/matlab/tom_xmipp_morphology.cpp → .../bindings/matlab/tom_xmipp_morphology.cpp
diff --git a/bindings/matlab/tom_xmipp_morphology.m → ...pp/bindings/matlab/tom_xmipp_morphology.m b/bindings/matlab/tom_xmipp_morphology.m → ...pp/bindings/matlab/tom_xmipp_morphology.m
diff --git a/bindings/matlab/tom_xmipp_normalize.cpp → ...p/bindings/matlab/tom_xmipp_normalize.cpp b/bindings/matlab/tom_xmipp_normalize.cpp → ...p/bindings/matlab/tom_xmipp_normalize.cpp
diff --git a/bindings/matlab/tom_xmipp_normalize.m → ...ipp/bindings/matlab/tom_xmipp_normalize.m b/bindings/matlab/tom_xmipp_normalize.m → ...ipp/bindings/matlab/tom_xmipp_normalize.m
diff --git a/bindings/matlab/tom_xmipp_psd_enhance.cpp → ...bindings/matlab/tom_xmipp_psd_enhance.cpp b/bindings/matlab/tom_xmipp_psd_enhance.cpp → ...bindings/matlab/tom_xmipp_psd_enhance.cpp
diff --git a/bindings/matlab/tom_xmipp_psd_enhance.m → ...p/bindings/matlab/tom_xmipp_psd_enhance.m b/bindings/matlab/tom_xmipp_psd_enhance.m → ...p/bindings/matlab/tom_xmipp_psd_enhance.m
diff --git a/bindings/matlab/tom_xmipp_resolution.cpp → .../bindings/matlab/tom_xmipp_resolution.cpp b/bindings/matlab/tom_xmipp_resolution.cpp → .../bindings/matlab/tom_xmipp_resolution.cpp
diff --git a/bindings/matlab/tom_xmipp_resolution.m → ...pp/bindings/matlab/tom_xmipp_resolution.m b/bindings/matlab/tom_xmipp_resolution.m → ...pp/bindings/matlab/tom_xmipp_resolution.m
diff --git a/bindings/matlab/tom_xmipp_rotate.cpp → ...mipp/bindings/matlab/tom_xmipp_rotate.cpp b/bindings/matlab/tom_xmipp_rotate.cpp → ...mipp/bindings/matlab/tom_xmipp_rotate.cpp
diff --git a/bindings/matlab/tom_xmipp_rotate.m → src/xmipp/bindings/matlab/tom_xmipp_rotate.m b/bindings/matlab/tom_xmipp_rotate.m → src/xmipp/bindings/matlab/tom_xmipp_rotate.m
diff --git a/bindings/matlab/tom_xmipp_scale.cpp → ...xmipp/bindings/matlab/tom_xmipp_scale.cpp b/bindings/matlab/tom_xmipp_scale.cpp → ...xmipp/bindings/matlab/tom_xmipp_scale.cpp
diff --git a/bindings/matlab/tom_xmipp_scale.m → src/xmipp/bindings/matlab/tom_xmipp_scale.m b/bindings/matlab/tom_xmipp_scale.m → src/xmipp/bindings/matlab/tom_xmipp_scale.m
diff --git a/bindings/matlab/tom_xmipp_scale_pyramid.cpp → ...ndings/matlab/tom_xmipp_scale_pyramid.cpp b/bindings/matlab/tom_xmipp_scale_pyramid.cpp → ...ndings/matlab/tom_xmipp_scale_pyramid.cpp