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"ipykernel", "ipython", "jupyter-client", "matplotlib", "nbsphinx", "nc-time-axis", "netCDF4", "numbagg", "pooch", "pydap", "rasterio", "scanpydoc", "scipy", "seaborn", "sphinx-autosummary-accessors", "sphinx-rtd-theme", "zarr"] -io = ["cfgrib", "cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "rasterio", "scipy", "zarr"] +accel = ["bottleneck", "flox", "numbagg", "opt-einsum", "scipy"] +complete = ["xarray[accel,io,parallel,viz]"] +io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"] parallel = ["dask[complete]"] viz = ["matplotlib", "nc-time-axis", "seaborn"] [metadata] lock-version = "2.0" python-versions = ">=3.11,<3.13" -content-hash = "5c4e0bfd29d204b600e87f8a89ce33722f09be7135dbf7b79feda74c373a333f" +content-hash = "2d02b803c08a292a83b0cc27ebc461fdf06c38b22be6430128658ebb34be7d16" diff --git a/pyproject.toml b/pyproject.toml index b8c7194..d85628e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,13 +7,12 @@ license = "MIT" [tool.poetry.dependencies] python = ">=3.11,<3.13" -numpy = "^1.24" +numpy = "^1.26" tensorly = "^0.8.1" matplotlib = "^3.5.0" tqdm = "^4.65" -seaborn = "^0.11.2" -svgutils = "^0.3.4" -xarray = "^2022.6.0" +seaborn = "^0.13" +xarray = "^2023" ipykernel = "^6.16.0" tensorpack = "^0.11" scikit-learn = "^1.1.3" @@ -22,7 +21,7 @@ openpyxl = "^3.1.2" setuptools = "^69.5.1" [tool.poetry.dev-dependencies] -pytest = "^6.2" +pytest = "^8.3" pytest-cov = "^3.0.0" tensordata = {git = "https://github.com/meyer-lab/tensordata.git", branch = "main"} diff --git a/timpute/common.py b/timpute/common.py index ae879ce..a393a25 100644 --- a/timpute/common.py +++ b/timpute/common.py @@ -5,7 +5,6 @@ from string import ascii_lowercase import matplotlib from matplotlib import gridspec, pyplot as plt -import svgutils.transform as st from matplotlib.lines import Line2D @@ -56,16 +55,3 @@ def subplotLabel(axs): """ Place subplot labels on figure. """ for ii, ax in enumerate(axs): ax.text(-0.2, 1.2, ascii_lowercase[ii], transform=ax.transAxes, fontsize=16, fontweight="bold", va="top") - - -def overlayCartoon(figFile, cartoonFile, x, y, scalee=1, scale_x=1, scale_y=1): - """ Add cartoon to a figure file. """ - - # Overlay Figure cartoons - template = st.fromfile(figFile) - cartoon = st.fromfile(cartoonFile).getroot() - - cartoon.moveto(x, y, scale_x=scalee * scale_x, scale_y=scalee * scale_y) - - template.append(cartoon) - template.save(figFile) \ No newline at end of file diff --git a/timpute/method_ALS.py b/timpute/method_ALS.py index fa1eec0..466eddf 100644 --- a/timpute/method_ALS.py +++ b/timpute/method_ALS.py @@ -1,136 +1,23 @@ import numpy as np -import warnings import tensorly as tl from tensorly.cp_tensor import ( cp_to_tensor, CPTensor, - cp_norm, - cp_normalize, - validate_cp_rank, ) from tensorly.tenalg.core_tenalg.mttkrp import unfolding_dot_khatri_rao from .initialization import initialize_fac -# Authors: Jean Kossaifi -# Chris Swierczewski -# Sam Schneider -# Aaron Meurer - -# License: BSD 3 clause - - -def sparsify_tensor(tensor, card): - """Zeros out all elements in the `tensor` except `card` elements with maximum absolute values. - - Parameters - ---------- - tensor : ndarray - card : int - Desired number of non-zero elements in the `tensor` - - Returns - ------- - ndarray of shape tensor.shape - """ - if card >= np.prod(tensor.shape): - return tensor - bound = tl.sort(tl.abs(tensor), axis=None)[-card] - - return tl.where( - tl.abs(tensor) < bound, tl.zeros(tensor.shape, **tl.context(tensor)), tensor - ) - - -def error_calc(tensor, norm_tensor, weights, factors, sparsity, mask, mttkrp=None): - r"""Perform the error calculation. Different forms are used here depending upon - the available information. If `mttkrp=None` or masking is being performed, then the - full tensor must be constructed. Otherwise, the mttkrp is used to reduce the calculation cost. - - Parameters - ---------- - tensor : tensor - norm_tensor : float - The l2 norm of tensor. - weights : tensor - The current CP weights - factors : tensor - The current CP factors - sparsity : float or int - Whether we allow for a sparse component - mask : bool - Whether masking is being performed. - mttkrp : tensor or None - The mttkrp product, if available. - - Returns - ------- - unnorml_rec_error : float - The unnormalized reconstruction error. - tensor : tensor - The tensor, in case it has been updated by masking. - norm_tensor: float - The tensor norm, in case it has been updated by masking. - """ - - # If we have to update the mask we already have to build the full tensor - if (mask is not None) or (mttkrp is None): - low_rank_component = cp_to_tensor((weights, factors)) - - # Update the tensor based on the mask - if mask is not None: - tensor = tensor * mask + low_rank_component * (1 - mask) - norm_tensor = tl.norm(tensor, 2) - - if sparsity: - sparse_component = sparsify_tensor(tensor - low_rank_component, sparsity) - else: - sparse_component = 0.0 - - unnorml_rec_error = tl.norm(tensor - low_rank_component - sparse_component, 2) - else: - if sparsity: - low_rank_component = cp_to_tensor((weights, factors)) - sparse_component = sparsify_tensor(tensor - low_rank_component, sparsity) - - unnorml_rec_error = tl.norm( - tensor - low_rank_component - sparse_component, 2 - ) - else: - # ||tensor - rec||^2 = ||tensor||^2 + ||rec||^2 - 2* - factors_norm = cp_norm((weights, factors)) - - # mttkrp and factor for the last mode. This is equivalent to the - # inner product - iprod = tl.sum(tl.sum(mttkrp * tl.conj(factors[-1]), axis=0)) - unnorml_rec_error = tl.sqrt( - tl.abs(norm_tensor**2 + factors_norm**2 - 2 * iprod) - ) - - return unnorml_rec_error, tensor, norm_tensor - def perform_ALS( tensor, rank, n_iter_max=100, init=None, - svd="svd", - normalize_factors=False, - orthogonalise=False, tol=1e-6, - random_state=None, - verbose=0, - return_errors=False, - sparsity=None, - l2_reg=0, mask=None, - cvg_criterion="abs_rec_error", - fixed_modes=None, - svd_mask_repeats=5, - linesearch=False, callback=None, -) -> tl.cp_tensor.CPTensor: +) -> tl.cp_tensor.CPTensor: """CANDECOMP/PARAFAC decomposition via alternating least squares (ALS) Computes a rank-`rank` decomposition of `tensor` [1]_ such that: @@ -147,38 +34,15 @@ def perform_ALS( Type of factor matrix initialization. If a CPTensor is passed, this is directly used for initalization. See `initialize_factors`. - svd : str, default is 'truncated_svd' - function to use to compute the SVD, acceptable values in tensorly.SVD_FUNS - normalize_factors : if True, aggregate the weights of each factor in a 1D-tensor - of shape (rank, ), which will contain the norms of the factors tol : float, optional (Default: 1e-6) Relative reconstruction error tolerance. The algorithm is considered to have found the global minimum when the reconstruction error is less than `tol`. - random_state : {None, int, np.random.RandomState} - verbose : int, optional - Level of verbosity - return_errors : bool, optional - Activate return of iteration errors mask : ndarray array of booleans with the same shape as ``tensor`` should be 0 where the values are missing and 1 everywhere else. Note: if tensor is sparse, then mask should also be sparse with a fill value of 1 (or True). Allows for missing values [2]_ - cvg_criterion : {'abs_rec_error', 'rec_error'}, optional - Stopping criterion for ALS, works if `tol` is not None. - If 'rec_error', ALS stops at current iteration if ``(previous rec_error - current rec_error) < tol``. - If 'abs_rec_error', ALS terminates when `|previous rec_error - current rec_error| < tol`. - sparsity : float or int - If `sparsity` is not None, we approximate tensor as a sum of low_rank_component and sparse_component, where low_rank_component = cp_to_tensor((weights, factors)). `sparsity` denotes desired fraction or number of non-zero elements in the sparse_component of the `tensor`. - fixed_modes : list, default is None - A list of modes for which the initial value is not modified. - The last mode cannot be fixed due to error computation. - svd_mask_repeats: int - If using a tensor with masked values, this initializes using SVD multiple times to - remove the effect of these missing values on the initialization. - linesearch : bool, default is False - Whether to perform line search as proposed by Bro [3]. Returns ------- @@ -189,7 +53,6 @@ def perform_ALS( * weights of the (normalized) factors otherwise * factors : List of factors of the CP decomposition element `i` is of shape ``(tensor.shape[i], rank)`` - * sparse_component : nD array of shape tensor.shape. Returns only if `sparsity` is not None. errors : list A list of reconstruction errors at each iteration of the algorithms. @@ -203,204 +66,57 @@ def perform_ALS( .. [3] R. Bro, "Multi-Way Analysis in the Food Industry: Models, Algorithms, and Applications", PhD., University of Amsterdam, 1998 """ - tensor = np.nan_to_num(tensor) - rank = validate_cp_rank(tl.shape(tensor), rank=rank) - - if return_errors: - DeprecationWarning( - "return_errors argument will be removed in the next version of TensorLy. Please use a callback function instead." - ) - - if orthogonalise and not isinstance(orthogonalise, int): - orthogonalise = n_iter_max - - if linesearch: - acc_pow = 2.0 # Extrapolate to the iteration^(1/acc_pow) ahead - acc_fail = 0 # How many times acceleration have failed - max_fail = 4 # Increase acc_pow with one after max_fail failure + if init is None: + init = initialize_fac(tensor, rank, method="random") - - if init is None: init = initialize_fac(tensor,rank,method='random') - - weights, factors = init rec_errors = [] norm_tensor = tl.norm(tensor, 2) - if l2_reg: - Id = tl.eye(rank, **tl.context(tensor)) * l2_reg - else: - Id = 0 - - if fixed_modes is None: - fixed_modes = [] - - if fixed_modes == list(range(tl.ndim(tensor))): # Check If all modes are fixed - cp_tensor = CPTensor( - (weights, factors) - ) # No need to run optimization algorithm, just return the initialization - return cp_tensor - - if tl.ndim(tensor) - 1 in fixed_modes: - warnings.warn( - "You asked for fixing the last mode, which is not supported.\n The last mode will not be fixed. Consider using tl.moveaxis()" - ) - fixed_modes.remove(tl.ndim(tensor) - 1) - modes_list = [mode for mode in range(tl.ndim(tensor)) if mode not in fixed_modes] - - if sparsity: - sparse_component = tl.zeros_like(tensor) - if isinstance(sparsity, float): - sparsity = int(sparsity * np.prod(tensor.shape)) - else: - sparsity = int(sparsity) for iteration in range(n_iter_max): - if orthogonalise and iteration <= orthogonalise: - factors = [ - tl.qr(f)[0] if min(tl.shape(f)) >= rank else f - for i, f in enumerate(factors) - ] - - if linesearch and iteration % 2 == 0: - factors_last = [tl.copy(f) for f in factors] - weights_last = tl.copy(weights) - - if verbose > 1: - print("Starting iteration", iteration + 1) - for mode in modes_list: - if verbose > 1: - print("Mode", mode, "of", tl.ndim(tensor)) - - pseudo_inverse = tl.tensor(np.ones((rank, rank)), **tl.context(tensor)) + for mode in range(np.ndim(tensor)): + pseudo_inverse = np.ones((rank, rank)) for i, factor in enumerate(factors): if i != mode: - pseudo_inverse = pseudo_inverse * tl.dot( - tl.conj(tl.transpose(factor)), factor - ) - pseudo_inverse += Id + pseudo_inverse = pseudo_inverse * np.dot(factor.T, factor) pseudo_inverse = ( - tl.reshape(weights, (-1, 1)) + np.reshape(weights, (-1, 1)) * pseudo_inverse - * tl.reshape(weights, (1, -1)) + * np.reshape(weights, (1, -1)) ) mttkrp = unfolding_dot_khatri_rao(tensor, (weights, factors), mode) - factor = tl.transpose( - tl.solve(tl.conj(tl.transpose(pseudo_inverse)), tl.transpose(mttkrp)) - ) + factor = np.linalg.solve(pseudo_inverse.T, mttkrp.T).T factors[mode] = factor - if normalize_factors and mode != modes_list[-1]: - weights, factors = cp_normalize((weights, factors)) - - # Will we be performing a line search iteration - if linesearch and iteration % 2 == 0 and iteration > 5: - line_iter = True - else: - line_iter = False - - # Calculate the current unnormalized error if we need it - if (tol or return_errors) and not line_iter: - unnorml_rec_error, tensor, norm_tensor = error_calc( - tensor, norm_tensor, weights, factors, sparsity, mask, mttkrp - ) - else: - if mask is not None: - tensor = tensor * mask + tl.cp_to_tensor( - (weights, factors), mask=1 - mask - ) - # Start line search if requested. - if line_iter: - jump = iteration ** (1.0 / acc_pow) - - new_weights = weights_last + (weights - weights_last) * jump - new_factors = [ - factors_last[ii] + (factors[ii] - factors_last[ii]) * jump - for ii in range(tl.ndim(tensor)) - ] - - new_rec_error, new_tensor, new_norm_tensor = error_calc( - tensor, norm_tensor, new_weights, new_factors, sparsity, mask - ) - - if (new_rec_error / new_norm_tensor) < rec_errors[-1]: - factors, weights = new_factors, new_weights - tensor, norm_tensor = new_tensor, new_norm_tensor - unnorml_rec_error = new_rec_error - acc_fail = 0 - - if verbose: - print(f"Accepted line search jump of {jump}.") - else: - unnorml_rec_error, tensor, norm_tensor = error_calc( - tensor, norm_tensor, weights, factors, sparsity, mask, mttkrp - ) - acc_fail += 1 - - if verbose: - print(f"Line search failed for jump of {jump}.") + # Calculate the current unnormalized error + low_rank_component = cp_to_tensor((weights, factors)) - if acc_fail == max_fail: - acc_pow += 1.0 - acc_fail = 0 + # Update the tensor based on the mask + if mask is not None: + tensor = tensor * mask + low_rank_component * (1 - mask) + norm_tensor = tl.norm(tensor, 2) - if verbose: - print("Reducing acceleration.") + unnorml_rec_error = tl.norm(tensor - low_rank_component, 2) - if (tol or return_errors) and not line_iter: + if tol: rec_error = unnorml_rec_error / norm_tensor rec_errors.append(rec_error) if callback is not None: cp_tensor = CPTensor((weights, factors)) - - if sparsity: - sparse_component = sparsify_tensor( - tensor - cp_to_tensor((weights, factors)), sparsity - ) - retVal = callback((cp_tensor, sparse_component), rec_error) - else: - retVal = callback(cp_tensor) + callback(cp_tensor) if tol is not None: if iteration >= 1: rec_error_decrease = rec_errors[-2] - rec_errors[-1] - if verbose: - print( - f"iteration {iteration}, reconstruction error: {rec_error}, decrease = {rec_error_decrease}, unnormalized = {unnorml_rec_error}" - ) - - if cvg_criterion == "abs_rec_error": - stop_flag = abs(rec_error_decrease) < tol - elif cvg_criterion == "rec_error": - stop_flag = rec_error_decrease < tol - else: - raise TypeError("Unknown convergence criterion") - - if stop_flag: - if verbose: - print(f"PARAFAC converged after {iteration} iterations") + if abs(rec_error_decrease) < tol: break - else: - if verbose: - print(f"reconstruction error={rec_errors[-1]}") - if normalize_factors: - weights, factors = cp_normalize((weights, factors)) - cp_tensor = CPTensor((weights, factors)) - if sparsity: - sparse_component = sparsify_tensor( - tensor - cp_to_tensor((weights, factors)), sparsity - ) - cp_tensor = (cp_tensor, sparse_component) - - if return_errors: - return cp_tensor, rec_errors - else: - return cp_tensor \ No newline at end of file + return cp_tensor