Recent Releases of tensorflow-mri

tensorflow-mri - v0.23.1

Updated JOSS paper

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Published by jennifersteeden 9 months ago

tensorflow-mri -

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Published by jennifersteeden 10 months ago

tensorflow-mri - TensorFlow MRI 0.23.1

Release 0.23.0

This release bumps the supported TF version to v2.10.x. No other new features or bug fixes are included.

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Published by github-actions[bot] about 1 year ago

tensorflow-mri -

Tutorials added

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tensorflow-mri - TensorFlow MRI 0.22.0

Release 0.22.0

This release bumps the supported TF version to v2.10.x. No other new features or bug fixes are included.

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Published by github-actions[bot] over 3 years ago

tensorflow-mri - TensorFlow MRI 0.21.0

Release 0.21.0

This release contains new functionality for wavelet decomposition and reconstruction and optimized Gram matrices for some linear operators. It also redesigns the convex optimization module and contains some improvements to the documentation.

Breaking Changes

  • tfmri.convex:

    • Argument ndim has been removed from all functions.
    • All functions will now require the domain dimension to be specified. Therefore, domain_dimension is now the first positional argument in several functions including ConvexFunctionIndicatorBall, ConvexFunctionNorm and ConvexFunctionTotalVariation. However, while this parameter is no longer optional, it is now possible to pass dynamic or static information as opposed to static only (at least in the general case, but specific operators may have additional restrictions).
    • For consistency and accuracy, argument axis of ConvexFunctionTotalVariation has been renamed to axes.

Major Features and Improvements

  • tfmri.convex:

    • Added new class ConvexFunctionL1Wavelet, which enables image/signal reconstruction with L1-wavelet regularization.
    • Added new argument gram_operator to ConvexFunctionLeastSquares, which allows the user to specify a custom, potentially more efficient Gram matrix.
  • tfmri.linalg:

    • Added new classes LinearOperatorNUFFT and LinearOperatorGramNUFFT to enable the use of NUFFT as a linear operator.
    • Added new class LinearOperatorWavelet to enable the use of wavelets as a linear operator.
  • tfmri.sampling:

    • Added new ordering type sorted_half to radial_trajectory.
  • tfmri.signal:

    • Added new functions wavedec and waverec for wavelet decomposition and reconstruction, as well as utilities wavelet_coeffs_to_tensor, tensor_to_wavelet_coeffs, and max_wavelet_level.

Bug Fixes and Other Changes

  • tfmri.recon:

    • Improved error reporting for least_squares.

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tensorflow-mri - TensorFlow MRI 0.20.0

Release 0.20.0

Major Features and Improvements

  • tfmri.layers:

    • Added new layers MaxPooling1D, MaxPooling2D, MaxPooling3D, AveragePooling1D, AveragePooling2D and AveragePooling3D. These are drop-in replacements for the core Keras layers of the same name, but they also support complex values.
    • Added new layers DWT1D, DWT2D, DWT3D, IDWT1D, IDWT2D, and IDWT3D to compute 1D, 2D and 3D forward and inverse discrete wavelet transforms.
    • Layer ConvBlock is now deprecated in favor of the new endpoints in the tfmri.models submodule.
    • Layer UNet is now deprecated in favor of the new endpoints in the tfmri.models submodule.
  • tfmri.models:

    • Added new models ConvBlock1D, ConvBlock2D and ConvBlock3D. These replace the previous ConvBlock layer, which is now deprecated.
    • Added new models UNet1D, UNet2D and UNet3D. These replace the previous UNet layer, which is now deprecated.

Bug Fixes and Other Changes

  • tfmri.signal:

    • Improved static shape inference for dwt op.

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tensorflow-mri - TensorFlow MRI 0.19.0

Release 0.19.0

This release bumps the supported TensorFlow version to 2.9.

Major Features and Improvements

  • tfmri.image:

    • Added new arguments batch_dims and image_dims to image_gradients, gradient_magnitude, psnr, ssim and ssim_multiscale.
    • Argument rank of psnr, ssim and ssim_multiscale is now deprecated. To update, use image_dims instead.
    • image_gradients and gradient_magnitude now support complex inputs.
  • tfmri.losses:

    • Added new arguments batch_dims and image_dims to all image quality losses. Argument rank is now deprecated (use image_dims instead).
    • Added new arguments multichannel and complex_part to all image quality losses. These mirror the behaviour of the corresponding metrics and allows for single-channel inputs and extraction of parts from complex numbers, respectively.
    • The canonical API names StructuralSimilarityLoss and MultiscaleStructuralSimilarityLoss have been changed to SSIMLoss and SSIMMultiscaleLoss, respectively. The old names are still available, but may be removed in the future.
  • tfmri.metrics:

    • Image quality metrics can now accept complex inputs without also specifying complex_part, in which case the unmodified complex values will be passed to the downstream function. This may not be supported for all metrics.
    • Added new arguments batch_dims and image_dims to all image quality metrics. Argument rank is now deprecated (use image_dims instead).
    • The canonical API names PeakSignalToNoiseRatio, StructuralSimilarity and MultiscaleStructuralSimilarity have been changed to PSNR, SSIM and SSIMMultiscale, respectively. The old names are still available, but may be removed in the future.
  • tfmri.recon:

    • Added new argument preserve_phase to tfmri.recon.pf. This allows the user to recover the phase as well as the magnitude during partial Fourier reconstruction. Argument return_complex has the same behaviour and is now deprecated.
    • Added new aliases adjoint (for adj), least_squares (for lstsq) and partial_fourier (for pf). These are now the canonical aliases, but the old ones will still be supported.
  • tfmri.signal:

    • Added new ops dwt and idwt to compute the N-dimensional discrete wavelet transform and its inverse, respectively.
  • tfmri.plot:

    • Added new argument norm to image_sequence, tiled_image and tiled_image_sequence. This allows the user to specify the scaling to be applied before the colormap.

Bug Fixes and Other Changes

  • Fixed a bug with k-space weighting in homodyne detection method of tfmri.recon.partial_fourier.
  • Like core TensorFlow, we now compile with _GLIBCXX_USE_CXX11_ABI=1.
  • Like core TensorFlow, Python wheels now conform to manylinux2014, an upgrade from manylinux2010.

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tensorflow-mri - TensorFlow MRI 0.18.0

Release 0.18.0

Major Features and Improvements

  • tfmri.convex:

    • All references to ndim in ConvexFunction and its subclasses have been deprecated in favor of domain_dimension or domain_shape. This applies to constructor arguments, properties and methods.
    • Refactored static and dynamic shape properties and methods to single-source shape information on the _shape and _shape_tensor methods. domain_dimension, domain_dimension_tensor, batch_shape and batch_shape_tensor now just call shape and shape_tensor and should not be overriden.
  • tfmri.initializers:

    • New module with initializers VarianceScaling, GlorotNormal, GlorotUniform, HeNormal, HeUniform, LecunNormal and LecunUniform. All initializers are drop-in replacements for their Keras counterparts and support complex values.
  • tfmri.io:

    • New function parse_twix to parse TWIX RAID files (Siemens raw data).
  • tfmri.layers:

    • Added new layers Conv1D, Conv2D and Conv3D. All layers are drop-in replacements for their Keras counterparts and support complex values.

Bug Fixes and Other Changes

  • Using a new API import system, which should address some issues with the autocomplete features of some editors.

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Published by github-actions[bot] almost 4 years ago

tensorflow-mri - TensorFlow MRI 0.17.0

Release 0.17.0

Breaking Changes

  • tfmri.signal:

    • Renamed keyword argument traj of filter_kspace and crop_kspace to trajectory.

Major Features and Improvements

  • tfmri.plot:

    • New utility tiled_image.

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tensorflow-mri - TensorFlow MRI 0.16.0

Release 0.16.0

Breaking Changes

  • tfmri.convex:

    • Several of the inputs and outputs of admm_minimize have been renamed to improve clarity and to make the interface more consistent with the tfmri.optimize module.

Major Features and Improvements

  • tfmri.convex:

    • admm_minimize now supports batches of inputs.
    • admm_minimize has two new arguments f_prox_kwargs and g_prox_kwargs that allow passing additional arguments to the proximal operators of f and g.
    • admm_minimize has a new argument name that allows specifying the name of the operation.
    • Method _prox of ConvexFunctionQuadratic has a new argument solver_kwargs that allows passing additional arguments to the internal solver.
    • New properties shape and batch_shape for ConvexFunction and its subclasses. These allow retrieval of static shape information.
    • New methods ndim_tensor, shape_tensor and batch_shape_tensor for ConvexFunction and its subclasses. These allow retrieval of the dynamic shape information.
  • tfmri.linalg:

    • New argument bypass_gradient for conjugate_gradient.
  • tfmri.recon:

    • lstsq has a new argument return_optimizer_state which allows the user to retrieve the internal optimizer state.
  • tfmri.optimize:

    • New function gradient_descent implementing the gradient descent method for minimization of differentiable functions.
  • tfmri.plot:

    • New argument dpi for functions image_sequence and tiled_image_sequence.
    • New function close, alias of matplotlib.pyplot.close.

Bug Fixes and Other Changes

  • tfmri.convex:

    • Fixed a bug in method prox of ConvexFunctionNorm, ConvexFunctionL2Squared and ConvexFunctionQuadratic that caused errors when running in graph mode.
  • tfmri.linalg:

    • Fixed a bug in internal linear algebra framework that would cause errors when running in graph mode.
  • tfmri.plot:

    • Removed lazy import mechanism which was causing problems when using matplotlib outside TFMRI. For now we use regular imports.

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Published by github-actions[bot] almost 4 years ago

tensorflow-mri - TensorFlow MRI 0.15.0

Release 0.15.0

Major Features and Improvements

  • tfmri.plot:

    • image_sequence and tiled_image_sequence now support different layout mechanisms via the argument layout.
    • image_sequence and tiled_image_sequence now support display bounding boxes via the arguments bbox_inches and pad_inches.

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tensorflow-mri - TensorFlow MRI 0.14.0

Release 0.14.0

Major Features and Improvements

  • tfmri.convex:

    • Added new classes ConvexFunctionNorm, ConvexFunctionIndicatorBall, ConvexFunctionIndicatorL1Ball and ConvexFunctionIndicatorL2Ball.
    • Added new method conj to ConvexFunction and its subclasses to support computation of convex conjugates.
  • tfmri.math:

    • Added new indicator functions: indicator_box, indicator_simplex and indicator_ball.
    • Added new projection functions: project_onto_box, project_onto_simplex and project_onto_ball.
  • tfmri.plot:

    • image_sequence and tiled_image_sequence now support RGB(A) data.
    • image_sequence and tiled_image_sequence now support use of titles via the arguments fig_title and subplot_titles.

Bug Fixes and Other Changes

  • tfmri.convex:

    • ConvexFunction will no longer raise an error when passed a tf.Tensor in the scale parameter.
  • tfmri.sampling:

    • spiral_trajectory will now return a tensor with known static shape.

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tensorflow-mri - TensorFlow MRI 0.13.0

Release 0.13.0

Major Features and Improvements

  • Moved most API endpoints into submodules. Direct access to these operators from the tfmri namespace is still possible, but this use is deprecated and will be removed in Release 1.0.0.

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tensorflow-mri - TensorFlow MRI 0.12.0

Release 0.12.0

Major Features and Improvements

  • tfmri.linalg:

    • New module containing linear algebra operators.
    • New classes LinearOperator, LinearOperatorAddition, LinearOperatorAdjoint, LinearOperatorComposition, LinearOperatorDiag, LinearOperatorFiniteDifference, LinearOperatorGramMatrix, LinearOperatorMRI and LinearOperatorScaledIdentity and new function conjugate_gradient.
  • tfmri.plot:

    • New module containing plotting utilities.
    • New functions image_sequence, tiled_image_sequence and show.
  • tfmri.recon:

    • New module containing functionality for image reconstruction.
    • New functions adj, grappa, lstsq, pf and sense. These are now the canonical API for image reconstruction.

Bug Fixes and Other Changes

  • New API export system, currently enabled for namespaces tfmri.linalg, tfmri.plot, tfmri.recon and tfmri.summary. The remaining namespaces will be moved to this API system in future releases.
  • Improvements to documentation: reduced verbosity of TOC tree and added links for common types.

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tensorflow-mri - TensorFlow MRI 0.11.0

Release 0.11.0

This release includes a redesign of the API docs.

Breaking Changes

  • tfmri:

    • LinearOperatorMRI: Argument sens_norm now defaults to True.
    • conjugate_gradient: Argument max_iter is now called max_iterations.
    • SVDCoilCompressor renamed to CoilCompressorSVD for consistency with the rest of the API.
    • filter_kspace: Argument filter_type has been renamed to filter_fn and can accept a callable in addition to a string.

Major Features and Improvements

  • tfmri:

    • Added new ops expand_trajectory and expand_density, which complement the existing flatten_trajectory and flatten_density.

Bug Fixes and Other Changes

  • tfmri:

    • hann and hamming now return 0 outside their domain, as expected.
    • atanfilt now returns the correct values for the negative part of the domain.
    • Improved error reporting for filter_kspace.

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tensorflow-mri - TensorFlow MRI 0.10.0

Release 0.10.0

This release focuses on MRI reconstruction, with new functionality and major refactoring of image reconstruction module as well as the associated linear algebra and convex optimization modules.

This release also bumps the supported TensorFlow version to 2.8.

Breaking Changes

  • tfmri:

    • compress_coils no longer accepts a matrix argument. Use SVDCoilCompressor instead.
    • compress_coils no longer accepts a tol argument.
    • coil_compression_matrix has been removed. Use SVDCoilCompressor instead.
    • Keyword argument num_output_coils of compress_coils has been renamed to out_coils.
    • Removed LinearOperatorFFT, LinearOperatorNUFFT, LinearOperatorParallelMRI, LinearOperatorSensitivityModulation, LinearOperatorInterp, LinearOperatorRealWeighting. Use LinearOperatorMRI instead.
    • Removed LinearOperatorDifference. Use LinearOperatorFiniteDifference instead.
    • ConvexOperator abstract base class and all its subclasses have been removed. Use ConvexFunction and/or one of its subclasses instead.
    • Removed reconstruct op. Use one of the new reconstruction ops instead (see below).
    • Removed reconstruct_partial_kspace op. Use reconstruct_pf instead.

Major Features and Improvements

  • tfmri:

    • Added new ops broadcast_dynamic_shapes and broadcast_static_shapes to broadcast multiple shapes.
    • estimate_coil_sensitivities with method='espirit' can now be called with a statically unknown number of coils (graph mode).
    • estimate_coil_sensitivities with method='espirit' will now set the static number of maps, if possible (graph mode).
    • Added new class SVDCoilCompressor for flexible coil compression functionality.
    • Added new ops ConvexFunction, ConvexFunctionAffineMappingComposition, ConvexFunctionLinearOperatorComposition, ConvexFunctionL1Norm, ConvexFunctionL2Norm, ConvexFunctionL2NormSquared, ConvexFunctionTikhonov, ConvexFunctionTotalVariation, ConvexFunctionQuadratic and ConvexFunctionLeastSquares.
    • Added new image ops image_gradients and gradient_magnitude.
    • Added new image ops gmsd, gmsd2d and gmsd3d.
    • Added new image op extract_and_scale_complex_part.
    • Added new ops LinearOperatorMRI and LinearOperatorFiniteDifference.
    • conjugate_gradient now has seamless support for linear operators with the imaging mixin.
    • Added new math op normalize_no_nan.
    • Added new math ops block_soft_threshold, shrinkage and soft_threshold.
    • Added new op admm_minimize implementing the ADMM algorithm.
    • Added new reconstruction ops reconstruct_adj, reconstruct_lstsq, reconstruct_grappa, reconstruct_sense and reconstruct_pf.
    • Added new signal ops hann and atanfilt.
    • filter_kspace now supports Cartesian inputs and additional keyword arguments for filtering function via filter_kwargs.
    • Added new ops density_grid and random_sampling_mask for generation of Cartesian masks.
    • radial_density: added new parameter tiny_number, mirroring the one in radial_trajectory.
  • tfmri.callbacks:

    • TensorBoardImages: added new parameters display_fn, concat_axis, feature_keys, label_keys, prediction_keys and complex_part. These enable different levels of customization of the display function.
  • tfmri.metrics:

    • Added new argument multichannel to PeakSignalToNoiseRatio, StructuralSimilarity and MultiscaleStructuralSimilarity. This enables these metrics to accept inputs that do not have a channel axis, by setting multichannel=False.
    • Added new argument complex_part to PeakSignalToNoiseRatio, StructuralSimilarity and MultiscaleStructuralSimilarity. This enables these metrics to accept complex inputs and calculate the metric from the specified part.

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tensorflow-mri - TensorFlow MRI 0.9.0

Release 0.9.0

Major Features and Improvements

  • tfmr:

    • Added new parameter tiny_number to radial_trajectory and spiral_trajectory. This parameter can be used to control which tiny golden angle is used for tiny golden angle trajectories. Previously it was only possible to use the 7th tiny golden angle (which is now the default).
    • radial_trajectory and spiral_trajectory will now warn the user when a non-optimal number of views is specified for golden angle ordering.
  • tfmr.layers:

    • Added new functionality to ConvBlock:
    • A different activation for the last layer can now be specified with out_activation.
    • Bias vectors for convolutional layers can now be disabled with use_bias=False.
    • Block can now be made residual with use_residual=True.
    • Dropout layers may now be added with use_dropout=True. Additionally, the parameters dropout_rate and dropout_type can be used to specify the dropout rate and type (standard or spatial), respectively.
    • Added optional dropout layers to UNet. Dropout can be configured with the parameters use_dropout, dropout_rate and dropout_type.

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tensorflow-mri - TensorFlow MRI 0.8.0

Release 0.8.0

This release bumps the supported TensorFlow version to 2.7.

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tensorflow-mri - TensorFlow MRI 0.7.0

Release 0.7.0

Breaking Changes

  • tfmr:

    • The scaling of the densities returned by estimate_density, radial_density and estimate_radial_density has changed. This harmonizes the values returned by all three functions and enables correct NUFFT normalization. Any application relying on exact density values should be checked. Applications that only rely on the relative scaling between points should not be affected.
    • estimate_radial_density no longer accepts the input base_resolution. However, it will now accept the optional input readout_os.

Major Features and Improvements

  • tfmr:

    • Added new ops flatten_trajectory and flatten_density.
    • central_crop and resize_with_crop_or_pad now accept shape arguments whose length is less than the rank of tensor.
    • Added new argument norm to LinearOperatorFFT, LinearOperatorNUFFT and LinearOperatorParallelMRI. This argument controls FFT normalization.
    • Added new argument mask to LinearOperatorParallelMRI.
    • Added new argument padding_mode to op resize_with_crop_or_pad.
    • Added new method 'pics' to reconstruct.
    • Added new parameter ndim to TotalVariationRegularizer.
  • tfmr.callbacks:

    • Added module.
    • Added new callback TensorBoardImages.
  • tfmr.io:

    • Added module.
    • Added new function encode_gif.
  • tfmr.layers:

    • Added module.
    • Added new convolutional layers ConvBlock and UNet.
    • Added new preprocessing layers AddChannelDimension, Cast, ExpandDims, KSpaceResampling, RepeatTensor, ResizeWithCropOrPad, ScaleByMinMax and Transpose.
  • tfmr.losses:

    • Added module.
    • Added new losses StructuralSimilarityLoss, MultiscaleStructuralSimilarityLoss, ssim_loss and ssim_multiscale_loss.
  • tfmr.metrics:

    • Added new metrics DiceIndex and JaccardIndex (aliases of F1Score and IoU, respectively).
  • tfmr.summary:

    • Added module.
    • Added new function gif.

Bug Fixes and Other Changes

  • tfmr:

    • Fixed a bug in static shape inference for ops central_crop and resize_with_crop_or_pad.
    • Fixed a bug in view_as_complex that would result in incorrect results for multidimensional arrays.
    • Fixed a bug in LinearOperatorNUFFT that would result in incorrect batch shape processing when the rank of domain_shape was equal to the number of spatial dimensions.
    • Fixed a bug in TotalVariationRegularizer that would sometimes cause it to return an array instead of a scalar.

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tensorflow-mri - TensorFlow MRI 0.6.2

Release 0.6.2

Bug Fixes and Other Changes

  • tfmr:

    • Fixed a bug that would cause radial_density to fail when in graph mode.

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tensorflow-mri - TensorFlow MRI 0.6.1

Release 0.6.1

This release contains some improvements to the documentation.

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tensorflow-mri - TensorFlow MRI 0.6.0

Release 0.6.0

Breaking Changes

  • The keyword arguments spacing and domain of the ops tfmr.radial_trajectory and tfmr.spiral_trajectory have been renamed to ordering and angle_range, respectively.
  • The range of the angles in 2D "full" radial/spiral trajectories will now be [0, 2 * pi] instead of [0, pi].
  • The range of the angles in 2D "half" radial trajectories will now be [0, pi] instead of [-pi/2, pi/2].
  • Multi-phase linear trajectories will now be interleaved.
  • The density calculated by radial_density will now be scaled differently.
  • Arguments domain_shape and points of LinearOperatorNUFFT have changed order.

Major Features and Improvements

  • tfmr:

    • Added new image ops total_variation and phantom.
    • Addew new array ops cartesian_product, meshgrid, ravel_multi_index and unravel_index.
    • Added new geometry module with ops rotate_2d and rotate_3d.
    • Added new optimizers module with op lbfgs_minimize.
    • Added new convex operators module with ops ConvexOperator, ConvexOperatorL1Norm, Regularizer and TotalVariationRegularizer.
    • Added new signal processing module with ops crop_kspace, filter_kspace and hamming.
    • Added new linear algebra ops LinearOperatorFFT and LinearOperatorInterp.
    • Added new math ops make_val_and_grad_fn, view_as_complex and view_as_real.
    • Added new k-space trajectory op estimate_radial_density.
    • Added new ordering methods "golden_half", "tiny_half" and "sphere_archimedean" to function radial_trajectory.
    • Added new method "inufft" to reconstruct.
    • Added new method "pipe" to estimate_density.
    • Added keyword argument rank to function radial_waveform.

Bug Fixes and Other Changes

  • tfmr:

    • Fixed a bug in radial_density that resulted in the DC component being underweighted.
    • Fixed a few bugs that would cause some ops to fail in graph mode.
    • Added graph mode tests.
    • Refactored testing modules.
    • Refactored linear algebra module.
    • Refactored utilities modules.
    • Added new utilities module plot_util.

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tensorflow-mri - TensorFlow MRI 0.5.0

Release 0.5.0

This release focuses on the new metrics module and implements several Keras metrics. It also adds some image reconstruction functionality.

Major Features and Improvements

  • tfmr:

    • Added new method "grappa" to reconstruct operation, implementing generalized autocalibrating partially parallel acquisitions (GRAPPA).
    • Added new operation reconstruct_partial_kspace for partial Fourier (PF) reconstruction. Supported PF methods are zero-filling, homodyne detection and projection onto convex sets.
    • Added new operation ravel_multi_index to convert arrays of multi-dimensionalindices to arrays of flat indices.
    • Added new operation extract_glimpses to extract patches or windows at the specified locations from N-dimensional images.
  • tfmr.metrics:

    • Added new confusion metrics module with multiple binary, multiclass and multilabel metrics: Accuracy, TruePositiveRate, TrueNegativeRate, PositivePredictiveValue, NegativePredictiveValue, Precision, Recall, Sensitivity, Specificity, Selectivity, TverskyIndex, FBetaScore, F1Score and IoU. This module also exposes the abstract base class ConfusionMetric.
    • Added new image quality assessment metrics module with 2D/3D PeakSignalToNoiseRatio, StructuralSimilarity and MultiscaleStructuralSimilarity.

Bug Fixes and Other Changes

  • tfmr:

    • Added new keyword argument coil_axis to coil_compression_matrix operation.

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tensorflow-mri - TensorFlow MRI 0.4.0

Release 0.4.0

Major Features and Improvements

  • Added coil compression functions tfmr.compress_coils and tfmr.coil_compression_matrix. Currently they implement the SVD coil compression method, but the API is prepared to support other methods which will be added in the future.

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tensorflow-mri - TensorFlow MRI 0.3.0

Release 0.3.0

Initial release of TensorFlow MRI.

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tensorflow-mri - TensorFlow MRI 0.2.0a1

Release 0.2.0

Initial release of TensorFlow MRI.

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