Release notes - I2PC/xmipp Wiki


Release 3.22.07 - Helios

Scripts Xmipp

  • xmipp_image_operate: taked into account non existing files
  • angular_continuous_assign2: Bug fixed
  • volume_consensus: Bug fixed
  • ctf.h and angular_continuous_assign_2: Changes for local defocus estimation #578

Protocols scipion-em-xmipp

  • rotate_volume: New protocol

  • subtract_projection: New implementation based on adjustment by regression instead of POCS and improved performance

  • local_ctf: Add new sameDefocus option + formatting

  • compare_reprojections & protocol_align_volume: Fast Fourier by default

  • crop_resize: Allows input pointers

  • resolution_deepres: Resize output to original size

  • denoise_particles: Added setOfAverages as input option

  • process: Change output from stk (spider) to mrcs (mrc)

  • trigger_data: Bug fixed

  • screen_deeplearning: Added descriptive help"

  • center_particles: Added summary info

  • align_volume_and_particles: Summary error fixed

  • cl2d: Summary errors solved

  • New tests: test_protocol_reconstruct_fourier, test_protocols_local_defocus, test_protocols_local_defocus, TestXmippAlignVolumeAndParticles, TestXmippRotateVolume

  • Improved tests: test_protocols_deepVolPostprocessing, test_protocols_xmipp_3d, Test ProjSubtracion

  • Excluded tests: test_protocols_zernike3d, test_protocols_metaprotocol_heterogeneity

Installation and user guide

  • Version info printed at the end of the installation
  • Removed empty folder with cleanBin command
  • Clarifing linking to Scipion and removed a bug with the build link
  • New flag (OPENCV_VERSION) in xmipp.config
  • Updated Readme (explain OpenCV-CUDA support)

Others

  • Validation server: Merged what remains
  • Replaced sincos to sin and cos
  • Handling of pointers in MPI programs
  • "nullptr" used to denote the null pointer not "NULL"
  • Check if nvidiaDriverVer is None

Release 3.22.04 - Gaia

Installation and user guide

  • Updated readme
    • Updated hdf5 info troubleshoting
    • Updated Standalone installation
    • Updated Scons installation
  • xmipp get_models: fixing the run and download path
  • Updating xmipp links for Scipion on installation
  • Removed fatal message in installation
  • Reported error if happen on installation - runjob
  • Ensuring that target directory for the libraries exists

Protocols scipion-em-xmipp

  • protocol_core_analysis: New protocol
  • protocol_compare_angles: Bug fix in compare angles under some conditions
  • protocol_center_particles: protocol simplified (removed setofCoordinates as output)
  • protocol_CTF_consensus: concurrency error fixed
  • protocol_convert_pdb: remove size if deactivated
  • protocol_resolution_deepres: binary masked not stored in Extra folder and avoiding memory problems on GPUs
  • protocol_add_noise: fixes
  • protocol_compare_reprojections: improve computation of residuals + tests + fix + formatting
  • protocol_screen_deepConsensus: multiple fixes in batch processing, trainging and streaming mode
  • protocol_shift_particles: apply transform is now optional

Others

  • New XMIPP logo
  • subtract_projection: adding new flag + fix
  • Add intersection size metadata (bindings/python)
  • Fixed unitialized unique pointers (bindings/python)
  • Bug fixing: Resolution directional and anisotropic filtering fixing the test
  • Removed SonarCloud issues
    • Replaced defines with constexpr
    • Removing Unused funtion parameters
    • Division by zero
    • Memory management
    • Removed field shadowing
    • Destructors should not throw exceptions

Release 3.22.01 - Eris

  • Updating to C++17
  • Support newer versions of CUDA and gcc
  • Zernike programs compatible with Cuda 8.x
  • Fixed Sonar Cloud issues and bugs
  • Matlab compilation Fixed
  • Fixed importing pwem.metadata
  • nma_alignment: Fixed arguments for the xmipp_angular_projection_matching invocation
  • Fixed test fails: ResolutionSsnr, ReconstructArtMpi, ReconstructArt, MlfRefine3dMpi, MlfRefine3d, MlRefine3dMpi, MlRefine3d, xmipp_test_pocs_main & volume_subtraction
  • xmipp_micrograph_automatic_picking: Fixed tests, avoid possible memory corruption
  • resolution_pdb_bfactor: bug fixed - error with multiple chains
  • FlexAlign: Fixed crash when binning > 1
  • Bug fixed and allowed controlling high sampling rate
  • Volume consensus: Fixed number of levels in the wavelet transform
  • Compilation: Fixed compilation of starpu programs
  • xmipp_transform_dimred: Fixed output metadata in append mode, adding MDL_DIMRED label
  • Config file generation: Fixed config version detection outside of the git repo, refactored check_CUDA and managed gcc compiler if it is installed out of /usr/bin/, check and exit if xmipp.conf does not exist
  • Compilation: Fixed detection of the last commit changed the config script
  • Resolution_fso: Bingham test implemented
  • Opencv not detected. Added include to user/include/opencv4 folder on config file
  • Compilation: asking whether to continue with compilation even though the config file is outdated
  • XMIPP install: Linked libsvm to scipion
  • Installation: Referenced 'global' xmipp.conf instead of using local copy of it
  • Multiple MPI programs: replaced CREATE_MPI_METADATA_PROGRAM macro by templated class
  • python_constants: add defocus labels
  • Metadata: added new nmaEigenval label
  • Python binding: added new function - correlationAfterAlignment, MDL_RESOLUTION_ANISOTROPY, MDL_RESOLUTION_ANISOTROPY
  • Matlab binding dependencies: set XMIPP as a hard dependency
  • Projections subtraction: new program
  • FFTwT: added mutex for plan handling
  • Multiple programs: Added a common implementation of the rerun
  • Phantom_create: update info link
  • Multiple programs: Added a common implementation of the rerun
  • Transform Geometry: save new shifted coordinates in option "shift to" + enterOfMass to python binding
  • Readme info: add virtual machine info
  • Removal of the SVM from inside the XMIPP repository and downloading it as an external dependence
  • Solved a configuration problem with CUDA
  • ml_tomo: Using .mrc instead of .vol ; volume_align: Addded wrapping during alignment

Release 3.21.06 - Caerus

  • CUDA-11 support
  • New protocol: Deep align
  • ChimeraX support
  • Improvements of streaming process
  • Several performance optimizations
  • Build time optimization
  • Multiple bug fixes
  • Improved documentation

Release 3.20.07 -

  • Fast CTF estimation
  • CTF includes phase shifts now
  • Selection of alpha helices or beta sheets from a PDB (xmipp_pdb_select)
  • Centering a PDB (xmipp_pdb_center)
  • New Protocol: MicrographCleaner is a new algorithm that removes coordinates picked from carbon edges, aggregations, ice crystals and other contaminations
  • New functionality: The protocol compare reprojections can now compute the residuals after alignment
  • New protocol: Split frames divide input movies into odd and even movies so that they can be processed independently
  • New protocol: Continuous heterogeneity analysis using spherical harmonics (not ready to be used)
  • Bug fixing when some micrograph has no coordinates in the consensus-picking.
  • New functionalities: Different architectures and training modes
  • Normal Mode Analysis protocols have been moved to the plugin ContinuousFlex
  • Fixing MPI version of the Fourier Reconstruction
  • New protocol: local CTF integration and consensus protocol for local ctf (also the viewers)
  • Local CTF analysis tools: Not yet ready for general public
  • New functionallity: Introducing the posibility of automatic estimation of the gain orientation.
  • Bugs fixings regarding stability on streaming processing
  • Support of heterogeneous movie sets
  • New protocol: Clustering of subtomogram coordinates into connected components that can be processed independently
  • New Protocol: Removing duplicated coordinates
  • New protocol: Subtomograms can be projected in several ways to 2D images so that 2D clustering tools can be used
  • New protocol: Regions of Interest can be defined in tomograms (e.g., membranes)
  • Bug fixing in mask3d protocol
  • Bug fix: in helical search symmetry protocol
  • Enhanced precision of the FlexAlign program
  • Now, deepLearningToolkit is under its own conda environment
  • Multiple protocols accelerated using GPU
  • New functionality: Xmipp CTF estimation can now take a previous defocus and do not change it
  • New functionallity: CTF-consensus is able to take the primary main values or an average of the two.
  • New functionallity: CTF-consensus is able to append metadata from the secondary input
  • New functionality: Xmipp Highres can now work with non-phase flipped images
  • New functionality: Xmipp Preprocess particles can now phase flip the images
  • New protocol: Tool to evaluate the quality of a map-model fitting
  • Allowing multi-GPU processing using FlexAlign
  • Improvement in monores and localdeblur
  • Randomize phases also available for images
  • Change the plugin to the new Scipion structure
  • Migrating the code to python3

Release 3.19.04 - Boreas

  • New protocols:

    • New protocol: 3D bionotes
    • New protocol: Align volume and particles
    • New protocol: Center particles
    • New protocols: GL2D, GL2D streaming and GL2D static
    • New protocol: 2D kmeans clustering
    • New protocol: compare angles
    • New protocol: consensus 3D classes
    • New protocol: CTF consensus
    • New protocol: deep denoising
    • New protocols: Eliminate empty particles and eliminate empty classes
    • New protocol: Extract unit cell
    • New protocol: Generate reprojections
    • New protocol: metaprotocol heterogenety output, metaprotocol heterogeneity subset and metaprotocol heterogeneity
    • New protocol: Movie Max Shift
    • New protocol: particle boxsize
    • New protocol: pick noise
    • New protocol: significant heterogeneity
    • New protocol: swarm consensus intial volumes
    • New protocol: directional ResDir
    • New protocol: local monoTomo
    • New protocol: deep consensus picking
    • New protocol: screen deep learning
    • New protocol: split volume hierarchical
    • New protocol: trigger data
  • New features:

    • Highres can now take a global alignment performed by any other method
    • A short presentation with some of the new algorithms can be seen here.
  • New code structure:

This release is the first one after a big re-factorization of the code in several repositories. The previous Xmipp version was inside the Scipion's repository. However, we have now splited the code in 4 Xmipp repositories:

  • Xmipp Core: This repository contains the most basic software for cryo-EM (coded in C++), such us multidimensional matrices, image definition, Fast Fourier Transform, metadata management, symmetry groups, Xmipp programs...
  • Xmipp Software: This repository contains image processing methods for cryo-EM, data management... (mostly coded in C++)
  • Xmipp Viz: This repository contains visualizations programs for cryo-EM data, such us Movies, Micrographs, Particles, Coordinates, stack of images... (coded in java).
  • Xmipp plugin: This is the plugin to be installed in Scipion.