CHANGELOG.md

Changelog

2.8.0

• Fixed element-wise variance accumulation in pylops.optimization.cls_basic.LSQR and pylops.lsqr, which previously assigned the same value to every entry of var (#639)

2.7.0

• Added cubic spline interpolation operator via pylops.signalprocessing.interpspline.InterpCubicSpline (also interfaceable via pylops.signalprocessing.interp.Interp(..., kind="cubic_spline")
• Added pylops.medical.MRI2D operator
• Added pylops.basicoperators.SmoothingND operator
• Added 3d extension to pylops.utils.signalprocessing.pwd_slope_estimate
• Fixed unwanted upcasting in pylops.avo.AVOLinearModelling, pylops.Laplacian, pylops.signalprocessing.Bilinear, pylops.signalprocessing.Interp, pylops.signalprocessing.NonStationaryFilters2D, pylops.signalprocessing.Seislet, pylops.signalprocessing.Sliding1D, pylops.signalprocessing.Sliding2D, pylops.signalprocessing.Sliding3D, pylops.basicoperators.Smoothing1D, pylops.basicoperators.Smoothing2D, and pylops.waveeqprocessing.Marchenko
• Improved typing annotations across all operators (and enforced use of Literal for parameters with multiple options)

2.6.0

• Added pylops.medical module and pylops.medical.CT2D operator
• Added pylops.utils.signalprocessing.pwd_slope_estimate and pylops.signalprocessing.PWSprayer2D and pylops.signalprocessing.PWSmoother2D operators
• Added support for multithreading to pylops.basicoperators.Block, pylops.basicoperators.BlockDiag, pylops.basicoperators.HStack, and pylops.basicoperators.VStack (and parallel_kind parameter)
• Added kwargs_fft to pylops.waveeqprocessing.BlendingContinuous, pylops.waveeqprocessing.BlendingGroup, and pylops.waveeqprocessing.BlendingHalf
• Added nttot to pylops.waveeqprocessing.BlendingContinuous
• Added fftengine to pylops.waveeqprocessing.PhaseShift
• Added mkl_fft engine to pylops.signalprocessing.FFT, pylops.signalprocessing.FFT2D, and pylops.signalprocessing.FFTND
• Added JAX backend to pylops.signalprocessing.ChirpRadon2D and pylops.signalprocessing.ChirpRadon3D operators.
• Added pylops.optimization.callback.CostNanInfCallback, pylops.optimization.callback.CostToDataCallback, and pylops.optimization.callback.CostToInitialCallback callbacks, and and rtol and rtol1 parameters in all solvers
• Optimized internal handling of pylops.basicoperators.Zero operators in pylops.basicoperators.BlockDiag, pylops.basicoperators.HStack, and pylops.basicoperators.VStack
• Homogenize error/warning/info messages across the library by switching to logging/warning
• Fixed initialization of r and rw in pylops.optimization.cls_sparsity.IRLS
• Fixed pylops.optimization.cls_sparsity._halfthreshold for complex valued CuPy arrays
• Fixed initialization of decay in sparse solvers to correctly solve complex-valued problems
• Fixed bug when calling __pow__ of a linear operator with CuPy arrays
• Fixed dtype handling in pylops.optimization.cls_sparsity.ISTA and pylops.optimization.cls_sparsity.FISTA

2.5.0

• Added cuda engine to pylops.waveeqprocessing.Kirchhoff operator
• Added Opbasis and optimal_coeff to pylops.optimization.cls_sparsity.OMP
• Added solver to the input parameters of the _oneshot internal methods of pylops.waveeqprocessing.AcousticWave2D to avoid recreating it for every shot
• Added kwargs_fft to pylops.signalprocessing.FFT, pylops.signalprocessing.FFT2D, and pylops.signalprocessing.FFTND
• Fixed bug in pylops.waveeqprocessing.MDD when using CuPy arrays for G and d with twosided=True and add_negative=True
• Fixed bug in pylops.signalprocessing.FourierRadon3D in the default choice of num_threads_per_blocks
• Fixed bug in pylops.signalprocessing.Convolve1D in the definition of pad and padd when applying the operator to a CuPy array
• Fixed bug in pylops.optimization.cls_sparsity.OMP avoiding passing explicit in the creation of _ColumnLinearOperator
• Fixed bug in pylops.optimization.cls_sparsity.OMP callback method as cols was not passed not allowing x to be properly reconstructed
• Fixed bug in pylops.waveeqprocessing.SeismicInterpolation in calculation of sampling when not passed

2.4.0

• Added pylops.signalprocessing.FourierRadon2d and pylops.signalprocessing.FourierRadon3d operators
• Added pylops.PyTensorOperator operator
• Added pylops.ToCupy operator
• Added pylops.utils.seismicevents.parabolic3d method
• Fixed bug in pylops.Restriction when passing iava as cupy array

2.3.1

• Fixed bug in pylops.utils.backend (see Issue #606)

2.3.0

• Added pylops.JaxOperator, pylops.signalprocessing.DWTND, and pylops.signalprocessing.DTCWT operators.
• Added updatesrc method to pylops.waveeqprocessing.AcousticWave2D.
• Added verb to pylops.signalprocessing.Sliding1D.sliding1d_design, pylops.signalprocessing.Sliding2D.sliding2d_design, pylops.signalprocessing.Sliding3D.sliding3d_design, pylops.signalprocessing.Patch2D.patch2d_design, and pylops.signalprocessing.Patch3D.patch3d_design.
• Added kwargs_fft to pylops.signalprocessing.FFTND.
• Added cosinetaper to pylops.utils.tapers.cosinetaper.
• Added kind to pylops.waveeqprocessing.Deghosting.
• Modified all methods in pylops.utils.backend to enable jax integration.
• Modified implementations of pylops.signalprocessing.Sliding1D, pylops.signalprocessing.Sliding2D, pylops.signalprocessing.Sliding3D, pylops.signalprocessing.Patch2D, and pylops.signalprocessing.Patch3D to being directly implemented instead of relying on other PyLops operators. Added also savetaper parameter and an option to apply the operator Op simultaneously to all windows.
• Modified pylops.waveeqprocessing.AcousticWave2D._born_oneshot and pylops.waveeqprocessing.AcousticWave2D._born_allshots to avoid recreating the devito solver for each shot (and enabling internal caching...)
• Modified dtype of pylops.signalprocessing.Shift to be that of the input vector.
• Modified pylops.waveeqprocessing.BlendingContinuous to use matvec/rmatvec instead of @/.H @ for compatibility with pylops solvers.
• Removed cusignal as optional dependency and cupy's equivalent methods (since the library is now unmantained and merged into cupy).
• Fixed ImportError of optional dependencies when installed but not correctly functioning (see Issue #548)
• Fixed bug in pylops.utils.deps.to_cupy_conditional (see Issue #579)
• Fixed bug in the definition of nttot in pylops.waveeqprocessing.BlendingContinuous
• Fixed bug in pylops.utils.signalprocessing.dip_estimate (see Issue #572)

2.2.0

• Added pylops.signalprocessing.NonStationaryConvolve3D operator
• Added nd-array capabilities to pylops.basicoperators.Identity and pylops.basicoperators.Zero
• Added second implementation in pylops.waveeqprocessing.BlendingContinuous which is more performant when dealing with small number of receivers
• Added forceflat property to operators with ambiguous rmatvec (pylops.basicoperators.Block, pylops.basicoperators.Bilinear, pylops.basicoperators.BlockDiag, pylops.basicoperators.HStack, pylops.basicoperators.MatrixMult, pylops.basicoperators.VStack, and pylops.basicoperators.Zero)
• Improved dynamic mode of pylops.waveeqprocessing.Kirchhoff operator
• Modified pylops.signalprocessing.Convolve1D to allow both filters that are both shorter and longer of the input vector
• Modified all solvers to use matvec/rmatvec instead of @/.H @ to improve performance

2.1.0

• Added pylops.signalprocessing.DCT, pylops.signalprocessing.NonStationaryConvolve1D, pylops.signalprocessing.NonStationaryConvolve2D, pylops.signalprocessing.NonStationaryFilters1D, and pylops.signalprocessing.NonStationaryFilters2D operators
• Added pylops.waveeqprocessing.BlendingContinuous, pylops.waveeqprocessing.BlendingGroup, and pylops.waveeqprocessing.BlendingHalf operators
• Added kind='datamodel' to pylops.optimization.cls_sparsity.IRLS
• Improved inner working of pylops.waveeqprocessing.Kirchhoff operator significantly reducing the memory usage related to storing traveltime, angle, and amplitude tables.
• Improved handling of haxes in pylops.signalprocessing.Radon2D and pylops.signalprocessing.Radon3D operators
• Added possibility to feed ND-arrays to pylops.TorchOperator
• Removed pylops.LinearOperator inheritance and added __call__ method to pylops.TorchOperator
• Removed scipy.sparse.linalg.LinearOperator and added abc.ABC inheritance to pylops.LinearOperator
• All operators are now classes of pylops.LinearOperator type

2.0.0

PyLops has undergone significant changes in this release, including new LinearOperators, more features, new examples and bugfixes. To aid users in navigating the breaking changes, we provide the following document MIGRATION_V1_V2.md.

New Features

• Multiplication of linear operators by N-dimensional arrays is now supported via the new dims/dimsd properties. Users do not need to use .ravel and .reshape as often anymore. See the migration guide for more information.
• Typing annotations for several submodules (avo, basicoperators, signalprocessing, utils, optimization, waveeqprocessing)
• New pylops.TorchOperator wraps a Pylops operator into a PyTorch function
• New pylops.signalprocessing.Patch3D applies a linear operator repeatedly to patches of the model vector
• Each of Sliding1D, Sliding2D, Sliding3D, Patch2D and Patch3D have an associated slidingXd_design or patchXd_design functions associated with them to aid the user in designing the windows
• FirstDerivative and SecondDerivative, and therefore other derivative operators which rely on the (e.g., Gradient) support higher order stencils
• pylops.waveeqprocessing.Kirchhoff substitutes pylops.waveeqprocessing.Demigration and incorporates a variety of new functionalities
• New pylops.waveeqprocessing.AcousticWave2D wraps the Devito acoutic wave propagator providing a wave-equation based Born modeling operator with a reverse-time migration adjoint
• Solvers can now be implemented via the pylops.optimization.basesolver.Solver class. They can now be used through a functional interface with lowercase name (e.g., splitbregman) or via class interface with CamelCase name (e.g., SplitBregman). Moreover, solvers now accept callbacks defined by the Callbacks interface (see e.g., MetricsCallback).
• Metrics such as mean absolute error (mae), mean squared error (mse) and others
• New pylops.utils.signalprocessing.dip_estimate estimates local dips in an image (measured in radians) in a stabler way than pylops.utils.signalprocessing.dip_estimate did for slopes.
• New pylops.utils.tapers.tapernd for N-dimensional tapers
• New wavelets Klauder and Ormsby

Documentation

• Installation has been revamped
• Revamped guide on how to implement a new LinearOperator from scratch
• New guide on how to implement a new solver from scratch
• New tutorials:
  • Solvers (Advanced)
  • Deblending
  • Automatic Differentiation
• New gallery examples:
  • Patching
  • Wavelets

1.18.3

• Fixed pylops.optimization.basic.lsqr, pylops.optimization.sparsity.ISTA, and pylops.optimization.sparsity.FISTA to work with cupy arrays. This change was required by how recent cupy versions handle scalars, which are not converted directly into float types, rather kept as cupy arrays.
• Fixed bug in pylops.waveeqprocessing.Deghosting introduced in commit 7e596d4

1.18.2

• Refractored pylops.utils.dottest, and added two new optional input parameters (atol and rtol)
• Added optional parameter densesolver to pylops.LinearOperator.div

1.18.1

• !DELETED! due to a mistake in the release process

1.18.0

• Added NMO example to gallery
• Extended pylops.basicoperators.Laplacian to N-dimensional arrays
• Added forward kind to pylops.basicoperators.SecondDerivative and pylops.basicoperators.Laplacian
• Added chirp-sliding kind to pylops.waveeqprocessing.seismicinterpolation.SeismicInterpolation
• Fixed bug due to the new internal structure of LinearOperator submodule introduced in scipy1.8.0

1.17.0

• Added pylops.utils.describe.describe method
• Added fftengine to pylops.waveeqprocessing.Marchenko
• Added ifftshift_before and fftshift_after optional input parameters in pylops.signalprocessing.FFT
• Added norm optional input parameter to pylops.signalprocessing.FFT2D and pylops.signalprocessing.FFTND
• Added scipy backend to pylops.signalprocessing.FFT and pylops.signalprocessing.FFT2D and pylops.signalprocessing.FFTND
• Added eps optional input parameter in pylops.utils.signalprocessing.slope_estimate
• Added pre-commit hooks
• Improved pre-commit hooks
• Vectorized pylops.utils.signalprocessing.slope_estimate
• Handlexd nfft<nt case in pylops.signalprocessing.FFT and pylops.signalprocessing.FFT2D and pylops.signalprocessing.FFTND
• Introduced automatic casting of dtype in `pylops.MatrixMult
• Improved documentation and definition of optinal parameters of pylops.Spread
• Major clean up of documentation and mathematical formulas
• Major refractoring of the inner structure of pylops.signalprocessing.FFT and pylops.signalprocessing.FFT2D and pylops.signalprocessing.FFTND
• Reduced warnings in test suite
• Reduced computational time of test_wavedecomposition in the test suite
• Fixed bug in pylops.signalprocessing.Sliding1D, pylops.signalprocessing.Sliding2D and pylops.signalprocessing.Sliding3D where the dtype of the Restriction operator is inffered from Op
• Fixed bug in pylops.signalprocessing.Radon2D and pylops.signalprocessing.Radon3D when using centered spatial axes
• Fixed scaling in pylops.signalprocessing.FFT with real=True to pass the dot-test

1.16.0

• Added pylops.utils.estimators module for trace estimation
• Added x0 in pylops.optimization.sparsity.ISTA and pylops.optimization.sparsity.FISTA to handle non-zero initial guess
• Modified pylops.optimization.sparsity.ISTA and pylops.optimization.sparsity.FISTA to handle multiple right hand sides
• Modified creation of haxis in pylops.signalprocessing.Radon2D and pylops.signalprocessing.Radon3D to allow for uncentered spatial axes
• Fixed _rmatvec for explicit in pylops.LinearOperator._ColumnLinearOperator

1.15.0

• Added pylops.signalprocessing.Shift operator.
• Added option to choose derivative kind in pylops.avo.poststack.PoststackInversion and pylops.avo.prestack.PrestackInversion
• Improved efficiency of adjoint of pylops.signalprocessing.Fredholm1 by applying complex conjugation to the vectors.
• Added vsvp to pylops.avo.prestack.PrestackInversion allowing to use user defined VS/VP ratio.
• Added kind to pylops.basicoperators.CausalIntegration allowing full, half, or trapezoidal integration
• Fixed _hardthreshold_percentile in pylops.optimization.sparsity - Issue #249.
• Fixed r2norm in pylops.optimization.solver.cgls

1.14.0

• Added pylops.optimization.solver.lsqr solver
• Added utility routine pylops.utils.scalability_test for scalability tests when using multiprocessing
• Added pylops.avo.avo.ps AVO modelling option and restructured pylops.avo.prestack.PrestackLinearModelling to allow passing any function handle that can perform AVO modelling apart from those directly available
• Added R-linear operators (when setting the property clinear=False of a linear operator). pylops.basicoperators.Real, pylops.basicoperators.Imag, and pylops.basicoperators.Conj
• Added possibility to run operators pylops.basicoperators.HStack, pylops.basicoperators.VStack, pylops.basicoperators.Block pylops.basicoperators.BlockDiag, and pylops.signalprocessing.Sliding3D using multiprocessing
• Added dtype to vector X when using scipy.sparse.linalg.lobpcg in eigs method of pylops.LinearOperator
• Use kind=forward fot FirstDerivative in pylops.avo.poststack.PoststackInversion inversion when dealing with L1 regularized inversion as it makes the inverse problem more stable (no ringing in solution)
• Changed cost in pylops.optimization.solver.cg and pylops.optimization.solver.cgls to be L2 norms of residuals
• Fixed pylops.utils.dottest.dottest for imaginary vectors and to ensure u and v vectors are of same dtype of the operator

1.13.0

• Added pylops.signalprocessing.Sliding1D and pylops.signalprocessing.Patch2D operators
• Added pylops.basicoperators.MemoizeOperator operator
• Added decay and analysis option in pylops.optimization.sparsity.ISTA and pylops.optimization.sparsity.FISTA solvers
• Added toreal and toimag methods to pylops.LinearOperator
• Make nr and nc optional in pylops.utils.dottest.dottest
• Fixed complex check in pylops.basicoperators.MatrixMult when working with complex-valued cupy arrays
• Fixed bug in data reshaping in check in pylops.avo.prestack.PrestackInversion
• Fixed loading error when using old cupy and/or cusignal

1.12.0

• Modified all operators and solvers to work with cupy arrays
• Added eigs and solver submodules to optimization
• Added deps and backend submodules to utils
• Fixed bug in pylops.signalprocessing.Convolve2D and pylops.signalprocessing.ConvolveND when dealing with filters that have less dimensions than the input vector.

1.11.1

• Fixed import of pyfttw when not available in pylops.signalprocessing.ChirpRadon3D

1.11.0

• Added pylops.signalprocessing.ChirpRadon2D and pylops.signalprocessing.ChirpRadon3D operators.
• Fixed bug in the inferred dimensions for regularization data creation in pylops.optimization.leastsquares.NormalEquationsInversion, pylops.optimization.leastsquares.RegularizedInversion, and pylops.optimization.sparsity.SplitBregman.
• Changed dtype of pylops.HStack to allow automatic inference from dtypes of input operator.
• Modified dtype of pylops.waveeqprocessing.Marchenko operator to ensure that outputs of forward and adjoint are real arrays.
• Reverted to previous complex-friendly implementation of pylops.optimization.sparsity._softthreshold to avoid division by 0.

1.10.0

• Added tosparse method to pylops.LinearOperator.
• Added kind=linear in pylops.signalprocessing.Seislet operator.
• Added kind to pylops.basicoperators.FirstDerivative. operator to perform forward and backward (as well as centered) derivatives.
• Added kind to pylops.optimization.sparsity.IRLS solver to choose between data or model sparsity.
• Added possibility to use scipy.sparse.linalg.lobpcg in pylops.LinearOperator.eigs and pylops.LinearOperator.cond.
• Added possibility to use scipy.signal.oaconvolve in pylops.signalprocessing.Convolve1D.
• Added NRegs to pylops.optimization.leastsquares.NormalEquationsInversion to allow providing regularization terms directly in the form of H^T H.

1.9.1

• Changed internal behaviour of pylops.sparsity.OMP when niter_inner=0. Automatically reverts to Matching Pursuit algorithm.
• Changed handling of dtype in pylops.signalprocessing.FFT and pylops.signalprocessing.FFT2D to ensure that the type of the input vector is retained when applying forward and adjoint.
• Added dtype parameter to the FFT calls in the definition of the pylops.waveeqprocessing.MDD operation. This ensure that the type of the real part of G input is enforced to the output vectors of the forward and adjoint operations.

1.9.0

• Added pylops.waveeqprocessing.Deghosting and pylops.signalprocessing.Seislet operators
• Added hard and half thresholds in pylops.optimization.sparsity.ISTA and pylops.optimization.sparsity.FISTA solvers
• Added prescaled input parameter to pylops.waveeqprocessing.MDC and pylops.waveeqprocessing.Marchenko
• Added sinc interpolation to pylops.signalprocessing.Interp (kind == 'sinc')
• Modified pylops.waveeqprocessing.marchenko.directwave to to model analytical responses from both sources of volume injection (derivative=False) and source of volume injection rate (derivative=True)
• Added pylops.LinearOperator.asoperator method to pylops.LinearOperator
• Added pylops.utils.signalprocessing.slope_estimate function
• Fixed bug in pylops.signalprocessing.Radon2D and pylops.signalprocessing.Radon3D when onthefly=True returning the same result as when onthefly=False

1.8.0

• Added todense method to pylops.LinearOperator
• Added pylops.signalprocessing.Bilinear, pylops.signalprocessing.DWT, and pylops.signalprocessing.DWT2 operators
• Added pylops.waveeqprocessing.PressureToVelocity, pylops.waveeqprocessing.UpDownComposition3Doperator, and pylops.waveeqprocessing.PhaseShift operators
• Fixed bug in pylops.basicoperators.Kronecker (see Issue #125)

1.7.0

• Added pylops.basicoperators.Gradient, pylops.basicoperators.Sum, pylops.basicoperators.FirstDirectionalDerivative, and pylops.basicoperators.SecondDirectionalDerivative operators
• Added pylops._ColumnLinearOperator private operator
• Added possibility to directly mix Linear operators and numpy/scipy 2d arrays in pylops.basicoperators.VStack and pylops.basicoperators.HStack and pylops.basicoperators.BlockDiagonal operators
• Added pylops.optimization.sparsity.OMP solver

1.6.0

• Added pylops.signalprocessing.ConvolveND operator
• Added pylops.utils.signalprocessing.nonstationary_convmtx to create matrix for non-stationary convolution
• Added possibility to perform seismic modelling (and inversion) with non-stationary wavelet in pylops.avo.poststack.PoststackLinearModelling
• Create private methods for pylops.basicoperators.Block, pylops.avo.poststack.PoststackLinearModelling, pylops.waveeqprocessing.MDC to allow calling different operators (e.g., from pylops-distributed or pylops-gpu) within the method

1.5.0

• Added conj method to pylops.LinearOperator
• Added pylops.basicoperators.Kronecker, pylops.basicoperators.Roll, and pylops.basicoperators.Transpose operators
• Added pylops.signalprocessing.Fredholm1 operator
• Added pylops.optimization.sparsity.SPGL1 and pylops.optimization.sparsity.SplitBregman solvers
• Sped up pylops.signalprocessing.Convolve1D using scipy.signal.fftconvolve for multi-dimensional signals
• Changes in implementation of pylops.waveeqprocessing.MDC and pylops.waveeqprocessing.Marchenko to take advantage of primitives operators
• Added epsRL1 option to pylops.avo.poststack.PoststackInversion and pylops.avo.prestack.PrestackInversion to include TV-regularization terms by means of pylops.optimization.sparsity.SplitBregman solver

1.4.0

• Added numba engine to pylops.basicoperators.Spread and pylops.basicoperators.Radon2D operators
• Added pylops.signalprocessing.Radon3D operator
• Added pylops.signalprocessing.Sliding2D and pylops.signalprocessing.Sliding3D operators
• Added pylops.signalprocessing.FFTND operator
• Added pylops.signalprocessing.Radon3D operator
• Added niter option to ``pylops.LinearOperator.eigs` method
• Added show option to pylops.optimization.sparsity.ISTA and pylops.optimization.sparsity.FISTA solvers
• Added pylops.waveeqprocessing.seismicinterpolation, pylops.waveequprocessing.waveeqdecomposition` and pylops.waveequprocessing.lsm`` submodules
• Added tests for engine in various operators
• Added documentation regarding usage of pylops Docker container

1.3.0

• Added fftw engine to FFT operator
• Added ISTA and FISTA sparse solvers
• Added possibility to broadcast (handle multi-dimensional arrays) to Diagonal and Restriction operators
• Added Interp operator
• Added Spread operator
• Added Radon2D operator

1.2.0

• Added eigs and cond methods to LinearOperator to estimate eigenvalues and conditioning number using scipy wrapping of ARPACK
• Modified default dtype for all operators to be float64 (or complex128) to be consistent with default dtypes used by numpy (and scipy) for real and complex floating point numbers.
• Added Flip operator
• Added Symmetrize operator
• Added Block operator
• Added Regression operator performing polynomial regression and modified LinearRegression to be a simple wrapper of the former when order=1
• Modified pylops.basicoperators.MatrixMult operator to work with both numpy ndarrays and scipy sparse matrices
• Added pylops.avo.prestack.PrestackInversion routine
• Added data weight optional input to NormalEquationsInversion and RegularizedInversion solvers
• Added IRLS solver

1.1.0

• Added CausalIntegration operator.

1.0.1

• Changed module from lops to pylops for consistency with library name (and pip install).
• Removed quickplots from utilities and matplotlib from requirements of PyLops.

1.0.0

• First official release.