- BUG: MetroPro info dictionary is now JSON serializable
- BUG: More robust catching of invalid values in AL3D reader
- ENH: Reader for the Zygo MetroPro
- ENH: analytical computation of scalar roughness parameters of ideal self-affine psd
- ENH: weighted integrals of the PSDs of containers
- ENH: scanning probe artefact simulations
- TST: remove dependency of test-suite on ContactMechanics
- MAINT: Switched from igor to igor2 which supports latest numpy
- BUG: Do not use
peek, since some stream objects do not support this operation - BUG: DI files sometimes report more data than they hold
- MAINT: Dropped Python 3.7 support (missing importlib)
- MAINT: Unified file naming schemes in file format examples
- ENH: Convenience decorator for creating simple pipeline functions
- ENH: Reader for NanoSurf easyScan (NID/EZD)
- ENH: Reader for BCR-STM/BCRF files
- BUG: Wrong data layout in AL3D reader
- BUG: Do not fail if SUR files have not acquisition time
- BUG: Fixed discover of version when in a git repository that is not the source directory of SurfaceTopography
- ENH: Pipeline function superpose
- BUG: Repair CompoundTopography and TranslatedTopography
- BUG: AL3D reader reported wrong unit in channel info (#276)
- BUG: SUR reader reported wrong info dictionary in channel info
- BUG: Increased numerical robustness of scanning probe artifact analysis (#275)
- BUILD: Replaced LAPACK with Eigen3, removing external dependency
- CI: Building and publishing of binary wheels (currently manylinux and Python 3.7, 3.8, 3.9 and 3.10 only)
- BUG: SUR reader reported wrong
height_scale_factorin channel info - BUILD: Yet another fix for version discovery when installing from source package
- BUILD: Another fix for version discovery when installing from source package
- BUILD: Fixed version discovery when installing from source package
- BUG: Make sure all readers return the same info dictionary for channels and the final topography
- MAINT: Automatic version discovery for Meson build
- MAINT: Switched build system to Meson
- BUG: Fixed multiple bugs in handling of
height_scale_factorby readers - BUG: Fixed handling of no scale factor in ASC reader
- TST: Added test for proper handling of
height_scale_factorby readers
- ENH: Extract X3P metadata
- MAINT: Converted X3P reader to new style
- MAINT: Bumped muFFT require to 0.24.0 - this avoids installation problems downstream, but disables automatic MPI detection
- BUG: X3P data was read in the wrong storage order
- ENH: Reader for Park Systems TIFF files
- ENH: Reader for Keyence VK3 and VK6 files
- ENH: Reader for Alicona Imaging AL3D files
- ENH: Reader for Digital Surf SUR files
- MAINT: Removed pandas dependency
- BUG: Fixed bug in VK4 reader
- API:
scale_dependent_statistical_propertyof aSurfaceContainernow returns eithernp.ndarrayornp.ma.masked_array - ENH: Reader for the Mitutoyo SurfTest Excel spread sheet format
- ENH: Reader for Keyence VK4
- MAINT: Added contact.engineering paper to bibliography
- BUG: Check for reentrant topographies in slope calculation
- BUG: Fixed aspect ratio used in convenience plotting function
- ENH: Generalized HDF5 reader
- MAINT: Removed
unitentry ofinfodictionary - MAINT: Removed
scale_factorproperty
- BUG: Ignore NaNs when suggesting units for data
- MAINT: Explicity convert to CSR matrix to suppress spsolve warning
- MAINT: Detect file corruption in DI reader when opening the file
- BUG: Ignore if analysis fails because of undefined data when computing averages
- API: ChannelInfo now has
is_uniformandhas_undefined_dataproperties that indicate the structure of the underlying data (if known after reading file headers)
- BUG: Allow manual specification of unit if IBW file does not provide unit information
- BUG: Missing
unitkeyword argument for HDF5 reader
- API: Add
has_undefined_dataproperty toNonuniformLineScan - MAINT: Avoid reading full file in Matlab reader
- MAINT: Avoid reading full file in OPD reader
- MAINT: Moved geometry analysis to separate module
- ENH: Filling undefined data points with harmonic functions
- BUG: Date format in OPDx can vary; use dateutil for parsing
- BUG: Date format in OPDx is month first
- BUG: Fixed unicode conversion issue in OPDx reader
- BUG: Always suggest a unit (#164)
- ENH: Self-report citations (#135)
- ENH: Raise exception if missing data points are unsupported (#106)
- ENH: Parallel implementation of scalar roughness parameters (#55)
- ENH: DZI writer has option to write metadata as JSON
- ENH: DZI writer dumps colorbar information into metadata file
- ENH: Support for line scans in OPDx files
- BUG: eq for topographies did not compare height information (#96)
- BUG: NetCDF reader checks consistency of units (#82)
- BUG: Storing topographies with undefined data to NetCDF files was broken in some cases; now an explicit mask is stored to the NetCDF file
- MAINT: Compute Fourier derivative with muFFT (#111)
- MAINT: Refactored OPDx reader (attention: height scale factor differs from old reader)
- MAINT: Variable bandwidth raises
UndefinedDataErrorwhen topography has undefined data points
- BUG: Raise NoReliableDataError for container only if none of the topographies contribute data (#152)
- MAINT: DZI writer return list of written files
- ENH: Allow specification of a minimum number of data points for scale-dependent statistical properties
- BUG: Properly raise
NoReliableDataErrorfor variable bandwidth method and scale-dependent statistical properties - BUG: Multiple bug fixes for corner cases
- BUG: Fixed shape of return array for derivatives
- API: Analysis function now raise errors upon encountering reentrant topographies or topographies with no reliable data
- ENH: Added kilometers to units
- ENH: Interpret 'resolution' instrument entry as reliability cutoff
- ENH: Apply reliability cutoff to scale-dependent statistical analysis
- BUG: Filtered wrong end of autocorrelation for reliability cutoff
- BUG: Fix segmentation faults due to integer overflow for large bicubic interpolation
- BUG: Prefer micrometer with Greek 'mu' sign
- BUG: Surface is already reentrant if two x values are identical
- ENH:
bandwidthfunction for containers - ENH: Suggesting ideal length units for containers
- ENH: Progress callbacks for some analysis functions
- ENH: Gaussian process regression for resampling noisy data onto an arbitrary grid
- ENH: Added
is_reentrantproperty - ENH: Computing averaged scale-dependent roughness parameteras, autocorrelation, power spectrum and variable bandwidth analysis for containers
- BUG: Multiple bugs fixed in scale-dependent analyses
- API: Reconciled radial averages into its own regression module; default behavior has changed
- API: All analysis functions now resample data onto a reasonable grid
- API: Resampling methods no longer discard bins with no data; those are filled with NaNs
- ENH: Generic scale-dependent statistical properties for containers (#116)
- ENH: Linear interpolation for derivatives at arbitrary distances (#128)
- ENH: Tip radius reliability analysis (#116)
- ENH: Third derivatives
- DOC: Include description for PyPI package (#102)
- API:
to_nonuniformnow only works with nonperiodic uniform line scans
- ENH: Read instrument name from DI files (#124)
- ENH: Specify PSD as a function in Fourier synthesis
- BUG: Avoid loosing mask information when reading/writing NetCDF (#126)
- DOC: Mention .spm file extension in doc string of DI reader (#123)
- DOC: Clearer error message for reentrant topographies (#108)
- DOC: Updated docstring of
bandwidth(#109) - DOC: Converted docstrings to numpydoc (#5)
- Fixed missing dependency for matplotlib in setup.py (#120)
- Fixed building wheel when numpy is not installed yet (#119)
- API: Changed the meaning of
distancein scale dependent derivative. A distance is now the width of the stencil of lowest truncation order of a certain derivative, i.e. n * dx where n is the order of the derivative - API:
variable_bandwidthis nowvariable_bandwidth_from_areaand an additionalvariable_bandwidth_from_profilewas added for a line-by-line analysis - API:
checkerboard_detrendis nowcheckerboard_detrend_areaand an additionalcheckerboard_detrend_profilewas added for a line-by-line analysis - API: Topographies now have a
unitproperty. For backwards compatibility, this information is still returned in theinfodictionary but this behavior will be deprecated in version 1.0. (#83) - API:
physical_sizescan no longer be set after the topography has been created - API: Renamed
ninterpolatekeyword argument tonb_interpolate - API:
to_uniformfor nonuniform line scans now accepts annb_interpolateargument specifying the number of grid points put between closest points. - ENH: Writing Deep Zoom Image (DZI) files
- ENH: Checkerboard detrending can now be carried out to arbitrary polynomial order
- ENH:
scalepipeline function is now able to rescale lateral dimensions (positions) - ENH: Add
to_unitpipeline function for unit conversion - ENH:
SurfaceContainerclass including pipeline functions for collections of topographies - ENH: Reading and writing of surface containers
- ENH: Retrieving surface containers from https://contact.engineering
- ENH: Added analysis functions for scale-dependent statistical properties of containers
- ENH: Added
scanning_probe_reliability_cutoffpipeline function to estimate a lateral length scale below which scanning probe data become unreliable because of tip artifacts (see arXiv:2106.16013) - ENH: Support for Digital Instruments Nanoscope (DI) files with 32-bit integer data
- ENH: Added API tests for checking existence of functions and properties for different kinds of topographies (#100)
- ENH: Added height_scale_factor to reader channels (#98)
- ENH: Disallow to provide physical_sizes or height_scale_factor as argument to .topography() if fixed by file contents
- BUG: Fixed missing function for RMS curvature for uniform line scans (#95)
- BUG: Make sure that .topography(height_scale_factor=..) is effective
- BUG: Fixed loading of 2D measurements from xyz data (#93)
- API: Replace
_1Dsuffix with_from_profileand_2Dsuffix with_from_area - API:
saveis now calledto_matrix - ENH: Reader for Keyence ZON files
- ENH: Derivative can be computed for different scales
- ENH: Scale-dependent slope and curvature
- ENH: Pipeline function for windowing
- ENH: Reader for NetCDF can read from streams
- BUG: Fixes that info dict was not always taken when topography was initialized from a reader's channel
- Drop support for python3.5
- ENH: rms_slope, rms_curvature and rms_laplace can now filter short wavelength roughness
- MAINT: Filters follow pipeline model
- MAINT: Derivatives now use muFFT derivative operators
- MAINT: Bumped muFFT dependency to v0.12.0
- API: Return nonuniform PSD only up to a reasonable wavevector
- BUG: Fixed differing versions in setup.py and requirements
- BUG: Fixed issue with reading npy from binary stream
- BUG: Fixed periodic flag for npy files in some cases
- BUG: UniformLineScan.area_per_pt is now a scalar, not a tuple
- BUG: supress assertion that discarded imaginary part in fourier derivative is small
- BUG: Memory leak in Python bindings for bicubic interpolation
- MAINT: Bumped muFFT dependency to v0.10.0
- ENH: return topography with undefined (masked) data filled (#19)
- ENH: make_sphere has option to put undefined data in standoff or not
- BUG: Fixed missing dependencies when installed as package (#15)
- BUG: Fixed error when loading text file with trailing newline (#16)
- BUG: Fixed wrong error message when loading unknown text file format (#14)
- BUG: renamed CompoundTopography.array to CompoundTopography.heights (#18)
- Refactored PyCo code into three separate Python modules: SurfaceTopography, ContactMechanics and Adhesion
- muFFT dependency updated to muFFT-0.9.1
- Moved documentation from README.md to the docs folder
- MAINT: Support for new, rewritten muFFT bindings
- ENH: Bicubic interpolation of two-dimensional topography maps
- ENH: Fourier derivative of topography
- BUG: Computation of plastic area is now parallelized (#303)
- BUG: Info dictionary mutable from user
- ENH: Change orientation of some readers such that all topographies look like the image in Gwyddion when plotted with "pcolormesh(t.heights().T)" (#295)
- BUG: Fixes unknown unit "um" when reading mi file (#296)
- BUG: Fixes missing channel name for mi files (#294)
- ENH: generate self-affine random surfaces by specifying the self-affine prefactor (#261, #278, #279)
- BUG: now fourier synthesis can generate Linescans again (#277, #279)
- API: Readers now report channel info in ChannelInfo class, fixes inconsistencies in reporting channel information (#190, #192, #236)
- ENH: Readers report format identifier and are self-documented (#229, #238)
- ENH: Readers now support Gwyddion's text export format for English and German locale (#230)
- ENH: DI reader now read acquisition date and stores it in the info dictionary
- BUG: DI reader autodetection did not work (#258)
- BUG: Fixes orientation for DI files (#291)
- DOC: Added notebook showing how 2D topographies can be plotted
- TST: Added demo notebook which shows how to plot 2D topographies
- ENH: adhesive ideal plastic simulations with Softwall system (#260, #283)
- BUG: Fixes missing 'nb_grid_pts' key in channels from IBW reader
- BUG: Fixes assertion because of wrong number of channel names (#252)
- BUG: fix rms_laplacian for periodic topographies (#247)
- ENH: higher order derivative for periodic surface (#234,#227)
- ENH: new reader for Igor Binary Wave files (IBW) (#224)
- BUG: opdx reader can now handle binary filestreams (#209)
- BUG: store and restore periodic flag in NonuniformTopography (#240)
- MAINT: correct installation problems because Eigen repository has moved
- ENH: anisotropic cubic Green's Functions
- BUG: NPY reader can now handle filestreams (#209, NUMPI/#24)
- BUG: opdx reader can now handle filestreams (#209)
- API: Detrended Topographies with mode "center" keep is_periodic property. Other modes lead to is_periodic=False. See pastewka/TopoBank/#347
- API: ability to set periodic property of HeightContainer in reader.topography (#198)
- API: default window for computing PSD is choosen according to topography.is_periodic (#217)
- Feature: interpolate_fourier pipeline function
- API: Default of check_boundaries in FreeSystem is False
- Bug fix: fourier synthesis had a padding line in the generation of topographies with odd number of points (#202)
- Bug fix:
topography.rms_curvatureno returns rms_curvature, previously rms_laplacian (#200) - gnuplot scripts to plot logger output
- API: Return contact map (the 'active set') from constrained conjugate gradient
- Bug fix:
assign_patch_numberswas broken on some configurations since v0.51.2
- Bug fix:
assign_patch_numberscrashed for maps larger that 64k x 64k (#191)
- Bug fix: Setting physical_sizes argument in readers (#188)
- Bug fix: physical_sizes should be None for surfacs without a physical size (#189)
- Bug fix: Running and testing without mpi4py is now possible (#179)
- Bug fix: Multiple calls to
topographymethod of readers (#187) - Method to inspect pipeline (#175)
- CI: All tests (serial and MPI parallel) pass in Travis CI
- Cleanup of new reader API
- Bug fix: Missing
channelargument fortopographymethod ofWrappedReader(#181) WrappedReadernow uses 'Default' as channel name
- Bug fix: Running without an MPI installation
- Bug fix: Reading DI files with non-topographic data (#338)
Overview:
- MPI parallelization of topographies, substrates and interaction.
- Updated reader framework that supports loading files in parallel. This requires to peek at the files (without loading them) to understand the number of grid points to decide on a domain decomposition strategy.
Technical:
- Use MPI wrapper provided by NuMPI (https://github.com/IMTEK-Simulation/NuMPI) for serial calculations.
- Switch to parallel L-BFGS of NuMPI.
- Removed Cython dependencies. (Parallel) FFT is now handled by muFFT (https://gitlab.com/muspectre/muspectre).
- Tests have been partially converted to pytest. Parallel tests are run through run-tests (https://github.com/AntoineSIMTEK/runtests).
- Autocorrelation and power-spectrum updates. Both now have an option 'algorithm' that let's the user select between a (fast) FFT and a (slow) brute-force implementation.
- Removed check for existing forces on boundaries (nonperiodic calculations only).
- Bug fix: Contact calculations now also run with detrended/scaled topographies.
- Updated hard wall command line script to new topography interface.
- Added height-difference autocorrelation and variable bandwidth analysis for nonuniform line scans.
- Added wrapper 'to_nonuniform' function that turns uniform into nonuniform line scans.
- Bug fix: 'center' detrend mode for nonunform line scans now minimizes rms height.
Overview:
- Added non-uniform line scans, which can be loaded from text files or constructed from arrays.
- New class structure for topographies and line scans (for easier maintenance).
- Major API changes and several bug fixes (see below).
- Added Hardwall simulation tutorial.
- Added calculation for second derivative and RMS curvature for nonuniform topographies.
- Added coordination counting for contact patches.
- Simplified computation of perimeter using coordination counting.
- Started Sphinx documentation with notes how to use the package.
API Changes:
- New API for generating topographies and line scans (height containers) from data, please use "from PyCo Topography import Topography, NonlinearLineScan, UniformLineScan" now.
- New API for building pipelines using methods on height containers, e.g. "topography.scale(2).detrend()".
- Uniform topographies and line scans can be periodic.
- Removed unit property from height containers. Units are now stored in the info dictionary, which has to be set on generation of the height container.
- All topographies must have a physical_sizes. Readers use the resolution as the default physical_sizes if the files contain no physical_sizes information.
- Removed 'shape' alias to 'resolution' property for height containers.
- Size + shape are now always tuples, physical_sizes is also always set as tuple.
- Topographies can now be pickled and unpickled.
- Replaced class 'Sphere' with generator function 'make_sphere'.
- Contact with "FreeFFTElasticHalfSpace": Now an error is raised when points at the outer ring of the surface are interacting. See notebook "examples/Hardwall_Simulation.ipynb".
Bug fixes:
- periodicity was ignored in calculation of the distance between contact patches in
distance_map - computation of energy in fourier space didn't match the computation of energy in real space (however it is not used in actual simulation)
- Removed keyword "full_output" from shift_and_tilt().
- Text files without spaces at beginning of line can be read now.
- Enable reading topography data from memory buffers and from binary streams.
- Calculation of 2D autocorrelation function was broken, e.g. radial average.
- 1D autocorrelation was broken for nonperiodic calculations.
- Refactored "Surface" to "Topography".
- Bug fix: Corrected computation of attractive contact area in Smooth contact system.
- Bug fix: Corrected computation of inflexion point in LJ93 and VW82 smoothed potentials.
- Height-difference autocorrelation function.
- PyCo now licensed under MIT license.
- Implemented substrates of finite thickness.
- Support for additional DI file formats.
- More clever unit conversion in DI files.
- macOS compatibility fixes.
- Automatic conversion from hardness value (given in units of pressure) into internal units in constrained CG solver.
- Added penetration hardness model for simple plastic calculations.
- Bug fix: Periodic Green's function offset by one lattice constant.
- Added further adhesive reference models (Maugis-Dugdale type models for cylinder and wedge).
- Added callback option for Polonsky & Keer optimizer.
- setup.py now has '--openmp' option that triggers compilation of shared-memory (OpenMP) parallel code.
- Main enhancement: Support for masked_arrays in NumpySurface. This allows to have undefined (missing) data points in surfaces. Polonsky & Keer can handle this now.
- Polonsky & Keer can now optimize at constant pressure (in addition to constant displacement)
- Updated hard wall script to accept command line arguments.
- Moved scripts to new 'commandline' folder.
- Added plotmap.py, tool for plotting surfaces from the command line.
- Added plotpsd.py, tool for plotting the PSD of a surface from the command line.
- Renamed TiltedSurface to DetrendedSurface.
- Added reader for HGT files (topography data from NASA Shuttle Radar Topography Mission).
- Bug fix in deprecated 'set_size' that broke hard wall example.
- Added reader for MATLAB files.
- Added 'center' detrending mode which just subtracts the mean value.
- Added getter and setter for detrend_mode.
- Added function to return string representation of subtracted plane.
- Added area_per_pt property to Surface object.
- Exponential adhesion potential from Martin's contact mechanics challenge, to be used in combination with hard-wall (bounded L-BFGS). Added tests for this potential. Thanks go to Joe Monty for implementing this.
- Surfaces now have a unit property, that can be any object but will likely be a string in many cases.
- Readers now create NumpySurface with raw data and wrap it into a ScaledSurface to convert to proper unit.
- Travis-CI integration
- Greenwood-Tripp reference solution
- Many bug fixes in topography file readers
- Wyko OPD reader (.opd)
- Digital Instruments Nanoscope reader (.di)
- Igor Binary Wave reader (.ibw)
- Detrending
- X3P reader (.x3p)
- Automatic file format detection