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Release notes
alberto edited this page Sep 23, 2022
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18 revisions
Release 3.22.07 - Helios Release 3.22.07 - Helios Release 3.22.07 - Helios Release 3.22.07 - Helios
- 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
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rotate_volume: New protocol
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subtract_projection: New implementation based on adjustment by regression instead of POCS and improved performance
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local_ctf: Add new sameDefocus option + formatting
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compare_reprojections & protocol_align_volume: Fast Fourier by default
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crop_resize: Allows input pointers
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resolution_deepres: Resize output to original size
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denoise_particles: Added setOfAverages as input option
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process: Change output from stk (spider) to mrcs (mrc)
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trigger_data: Bug fixed
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screen_deeplearning: Added descriptive help"
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center_particles: Added summary info
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align_volume_and_particles: Summary error fixed
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cl2d: Summary errors solved
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New tests: test_protocol_reconstruct_fourier, test_protocols_local_defocus, test_protocols_local_defocus, TestXmippAlignVolumeAndParticles, TestXmippRotateVolume
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Improved tests: test_protocols_deepVolPostprocessing, test_protocols_xmipp_3d, Test ProjSubtracion
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Excluded tests: test_protocols_zernike3d, test_protocols_metaprotocol_heterogeneity
- 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)
- 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
- 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
- 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
- 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
- CUDA-11 support
- New protocol: Deep align
- ChimeraX support
- Improvements of streaming process
- Several performance optimizations
- Build time optimization
- Multiple bug fixes
- Improved documentation
- 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
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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
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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.
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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.
Developed by xmipp team