Releases xmipp program
3.24.06 - Oceanus
Xmipp Programs
- New programs
xtomo tigre reconstruction: This program provides a variety of algorithms to reconstruct tomogram from a set of tilt series
graph_max_cut: split volume program
tomo_simulate_tilt_series: simualtion of ts, tomograms and coordinates
- Programs updated
Deep_center: interface simplified, calculate shift for particles
deep_misalignment_detection: update model
pdb_label_from_volume:Added CIF format support
resolution_monotomo: Fast subtomo extraction
resolution_monotomo: accelarating monotomo with float
tomogram_reconstruction: tigre reconstruction added
tomo_extract_subtomograms: solving some bugs and enhancing performance
tomo_extract_particlestacks: solving some bugs and enhancing performance
- Programs fixed
movie_estimate_gain: Initialize sigma values
resolution_localfilter: double not integer
movie_estimate_gain: Initialize sigma values
project_tomography: internal loop
pdb: Fixed PDB write function when no categories are present
fourier_filter:Fix WEDGE option in FourierFilter
resolution_pdb_bfactor:fix unaccounted column in res bfac pdb
fourier_filter: Fixing missing cone
Installation and user guide
Fixed PyXmipp installation
Update pythorch version on DLTK pyTorch enviroment
Fix DLTK installation
Removed force flag on conda installations (new conda version)
More Xmipp
API for collecting xmipp installation statistics
Local average added: Now the micrograph scissor annotates the local intensity value around the particles in the original micrographs.
Added support for half precision float micrographs
Wipe out memory ouptut in cuFFT
Deprecated deep_denoising
Fix for rare axis orderings in MRC/MAP files
Adding fixed extension to tomo
3.23.11 - Nereus
Xmipp Programs
- New programs
local_volume_adjustment: This program modifies a volume in order to adjust its intensity locally to a reference volume
subtomo_subtraction: New program with mpi version
- Programs updated
tomo_extract_subtomogram: Accept target box size
convert_from_pdb: Added cif support
phantom_movies: Adding more options: circle and cross
angular_neighbourhood: Modified to output the result in the best symmetry group
batch_deep_misalignment: Detection: GPU option
- Programs fixed
volume_from_pdb: Bug fix in dealing with orig=0, Detection of contrast inverted maps
tomo_extract_particles: Stack fixes, dose fixes
image_convert: Fixed issue when providing a metadata file as input
volume_substraction: Change NaNs generated by a division between 0 by 0s.
Installation and user guide
Disabled downloading 380MB file not required
Clarifying the requirements
More robust thread execution in the installator
Fixed bug collecting versions
Removed auto updater from libcifpp
More Xmipp
Upgraded CUDA toolkit in DLTK 1.0
Fix PDB read: This fixes a bug where pdbs whose atom name start in position 12 (in base 0)
CUDA 12.2 supported (not full tested)
Fixed PDB reading for shorter PDBs
Allow not compiling xmipp to debug changes in python scripts
Xmipp will now be able to read any volume with any values of those fields correctly.
Fixed pixel size not being properly stored
Fixed MetaData to avoid dangling references
Added compatibility for undefined axis sequences in MRC files
Added option to write mirrors in angularDistance
3.23.07 - Morpheus
Xmipp Programs
New programs: image_peak_high_contrast(for detecting high contrast regions in tomographic reconstruction)
misaligment_detection (to detect misalignment in tomographic reconstructions from high-contrast regions)
deep_global_assignment
deep_center
Programs updated
xmipp_angular_distance: new features - tomo_extract_particles: new features
subtract_projection: parallelization with mpi
tomo_extract_subtomograms: allow downsampling of features
angular_resolution_alignment: Detect misalignment with resolution
Programs fixed
align_volume_and_particles: Fixed error
angular_project_library: Removed deterministic behaviour (mpi)
volumen_subtraction: fixed bug - Deprecated programs (For more details visit)
classify_kmeans_2D - rotational_spectra - particle_boxsize
Installation and user guide
New clearer, more intuitive and informative installer. It also creates a file to facilitate user support.
Refactored the deep learning toolkit, more robust and new environment with updated tensorflow.
Updated requirement.
More Xmipp
Added half precission suport to numpy
Added the ability to read and write CIF files
Modular design of winner filter
Decoupling XmippTomo from XmippSPA
Fix Zernike equation - Removed all occurrences of non base-class default destructors
Improved MultidimArray performance
Added support for half precision floating point numbers in MRCs
Assign tiff to gain files - adding half maps labels
3.23.03 - Kratos
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
3.22.11 - Iris
Xmipp Programs
Speeding up iterations in some xmipp programs (xmipp_ctf_group, xmipp_image_histogram, xmipp_mpi_angular_class_average, xmipp_angular_distance, xmipp_angular_estimate_tilt_axis, xmipp_ctf_create_ctfdat, xmipp_resolution_ssnr)
New Zernike3D programs
angular_project_library: Reported some error if there are no images in the range
angular_discrete_assign.cpp: Removed memory leak and uninitialized values
angular_distance: Fixing condition to avoid iteration behind the end of the MD in cases when input data have different sizes. Optimized performance
Pdb_reduce_pseudoatoms: Produced pdb is one-based indexed - xmipp_micrograph_automatic_picking: Fixing memory leak
subtract_projection: Fixed several bugs (improved results), added circular mask to avoid edge artifacts, added option to boost particles instead of subtract
Installation and user guide
Various bug fixing
More information about hdf5 library
Updating CUDA
GCC compatibility. Added CUDA 11.7 (not tested)
Updating Readme
Others
Performance optimization (metadata binding)
Python binding: adding methods to directly set / get entire MD row
g++ >= 8 required
In viewers used pwutils
The pdb data library now has all the right fields and should write the record type (“ATOM” or “HETATM”) correctly at the beginning of the line and the atomType (element) and charge (if applicable) correctly at the end of the line.
Removal of anartifact of symmetrization related to the z pitch (symmetries.cpp)
Using the same identical Deprecated param from pyworkflow.
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
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
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
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
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
3.20.07 - Boreas
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