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v3.23.03-Kratos

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@albertmena albertmena released this 08 Feb 10:55
v3.23.03-Kratos
75f74d6

Xmipp Programs

  • New programs: tomo_confidence_map, tomo_extract_particlestacks, tomo_extract_subtomograms, tomo_tiltseries_dose_filter, psd_estimatator

  • Deprecated programs (for more details visit the wiki):
    angular_distribution_show, apropos
    ctf_correct_idr, ctf_create_ctfdat , ctf_show , idr_xray_tomo , image_common_lines , metadata_convert_to_spider , metadata_selfile_create , mlf_refine_3d, ml_refine_3d, ml_tomo , mrc_create_metadata , pdb_construct_dictionary, pdb_restore_with_dictionary , reconstruct_admn , reconstruct_art_pseudo , resolution_ibw , resolution_ssnr , score_micrograph , reconstruct_fourier_starpu , tomo_align_tilt_series, tomo_align_dual_tilt_series, tomo_align_refinement, tomo_align_refinement, tomo_extract_subvolume, tomo_project_main, tomo_remove_fluctuations , tomo_align_tilt_series,transform_range_adjust , validation_tilt_pairs , volume_pca , volume_validate_pca , work_test , 6f4d983 , evaulate_coordinates , extract_subset , image_separate_objects , volume_enhance_contrast , volume_reslice , xray_import , xray_project , xray_psf_create , xray_reconstruct_art , gpu_correlation, gpu_utils, classify_significant, deepAlign.

  • volume_from_pdb: fixing input pdb file being overwritten when '-centerPDB' flag was set

  • xmipp_phantom_movie: adding support for fixed step shift & gain and dark image generation

  • CTF simulation allows astigmatism

  • xmipp_metadata_utility: Now join operations with an empty set will return a new empty set (previously no output file was generated).

  • xmipp_matrix_dimred: Program help improved. Exception is now thrown when the number of output dimensions is larger than the input dimensions

  • xmipp_angular_distance: Added itemId column to the output

Installation and user guide

  • Refactor and simplified Readme page.
  • Updating CUDA version compatibility
  • Updating gcc version availables
  • Fixed Matlab installation
  • Added missing array include to fix compilation error with g++12
  • Alert and not block compilation if gcc - CUDA are not compatible
  • Avoid compilation warnings
  • Required pyworkflow==3.0.31

Others

  • Maintenance: Recovered python binding tests
  • Maintenance: fixing dangling pointer in xmipp_error
  • Maintenance: Cleaned includes in xmipp_image_base
  • PSD estimation: templating function, improving performance
  • Flag cleanDeprecate in the installation; clean all deprecated executables programs
  • python binding: fixed bug when Numpy arrays created by slicing were badly interpretted
  • Removed "seed" library
  • Fixed memory pinning CUDA bug
  • Fixed compilation errors on CUDA 9
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