""" The :mod:`sklearn.feature_extraction.image` submodule gathers utilities to extract features from images. """ # Authors: Emmanuelle Gouillart # Gael Varoquaux # Olivier Grisel # Vlad Niculae # License: BSD 3 clause from itertools import product import numbers import numpy as np from scipy import sparse from numpy.lib.stride_tricks import as_strided from ..utils import check_array, check_random_state from ..utils.fixes import astype from ..base import BaseEstimator __all__ = ['PatchExtractor', 'extract_patches_2d', 'grid_to_graph', 'img_to_graph', 'reconstruct_from_patches_2d'] ############################################################################### # From an image to a graph def _make_edges_3d(n_x, n_y, n_z=1): """Returns a list of edges for a 3D image. Parameters =========== n_x: integer The size of the grid in the x direction. n_y: integer The size of the grid in the y direction. n_z: integer, optional The size of the grid in the z direction, defaults to 1 """ vertices = np.arange(n_x * n_y * n_z).reshape((n_x, n_y, n_z)) edges_deep = np.vstack((vertices[:, :, :-1].ravel(), vertices[:, :, 1:].ravel())) edges_right = np.vstack((vertices[:, :-1].ravel(), vertices[:, 1:].ravel())) edges_down = np.vstack((vertices[:-1].ravel(), vertices[1:].ravel())) edges = np.hstack((edges_deep, edges_right, edges_down)) return edges def _compute_gradient_3d(edges, img): n_x, n_y, n_z = img.shape gradient = np.abs(img[edges[0] // (n_y * n_z), (edges[0] % (n_y * n_z)) // n_z, (edges[0] % (n_y * n_z)) % n_z] - img[edges[1] // (n_y * n_z), (edges[1] % (n_y * n_z)) // n_z, (edges[1] % (n_y * n_z)) % n_z]) return gradient # XXX: Why mask the image after computing the weights? def _mask_edges_weights(mask, edges, weights=None): """Apply a mask to edges (weighted or not)""" inds = np.arange(mask.size) inds = inds[mask.ravel()] ind_mask = np.logical_and(np.in1d(edges[0], inds), np.in1d(edges[1], inds)) edges = edges[:, ind_mask] if weights is not None: weights = weights[ind_mask] if len(edges.ravel()): maxval = edges.max() else: maxval = 0 order = np.searchsorted(np.unique(edges.ravel()), np.arange(maxval + 1)) edges = order[edges] if weights is None: return edges else: return edges, weights def _to_graph(n_x, n_y, n_z, mask=None, img=None, return_as=sparse.coo_matrix, dtype=None): """Auxiliary function for img_to_graph and grid_to_graph """ edges = _make_edges_3d(n_x, n_y, n_z) if dtype is None: if img is None: dtype = np.int else: dtype = img.dtype if img is not None: img = np.atleast_3d(img) weights = _compute_gradient_3d(edges, img) if mask is not None: edges, weights = _mask_edges_weights(mask, edges, weights) diag = img.squeeze()[mask] else: diag = img.ravel() n_voxels = diag.size else: if mask is not None: mask = astype(mask, dtype=np.bool, copy=False) mask = np.asarray(mask, dtype=np.bool) edges = _mask_edges_weights(mask, edges) n_voxels = np.sum(mask) else: n_voxels = n_x * n_y * n_z weights = np.ones(edges.shape[1], dtype=dtype) diag = np.ones(n_voxels, dtype=dtype) diag_idx = np.arange(n_voxels) i_idx = np.hstack((edges[0], edges[1])) j_idx = np.hstack((edges[1], edges[0])) graph = sparse.coo_matrix((np.hstack((weights, weights, diag)), (np.hstack((i_idx, diag_idx)), np.hstack((j_idx, diag_idx)))), (n_voxels, n_voxels), dtype=dtype) if return_as is np.ndarray: return graph.toarray() return return_as(graph) def img_to_graph(img, mask=None, return_as=sparse.coo_matrix, dtype=None): """Graph of the pixel-to-pixel gradient connections Edges are weighted with the gradient values. Read more in the :ref:`User Guide `. Parameters ---------- img : ndarray, 2D or 3D 2D or 3D image mask : ndarray of booleans, optional An optional mask of the image, to consider only part of the pixels. return_as : np.ndarray or a sparse matrix class, optional The class to use to build the returned adjacency matrix. dtype : None or dtype, optional The data of the returned sparse matrix. By default it is the dtype of img Notes ----- For scikit-learn versions 0.14.1 and prior, return_as=np.ndarray was handled by returning a dense np.matrix instance. Going forward, np.ndarray returns an np.ndarray, as expected. For compatibility, user code relying on this method should wrap its calls in ``np.asarray`` to avoid type issues. """ img = np.atleast_3d(img) n_x, n_y, n_z = img.shape return _to_graph(n_x, n_y, n_z, mask, img, return_as, dtype) def grid_to_graph(n_x, n_y, n_z=1, mask=None, return_as=sparse.coo_matrix, dtype=np.int): """Graph of the pixel-to-pixel connections Edges exist if 2 voxels are connected. Parameters ---------- n_x : int Dimension in x axis n_y : int Dimension in y axis n_z : int, optional, default 1 Dimension in z axis mask : ndarray of booleans, optional An optional mask of the image, to consider only part of the pixels. return_as : np.ndarray or a sparse matrix class, optional The class to use to build the returned adjacency matrix. dtype : dtype, optional, default int The data of the returned sparse matrix. By default it is int Notes ----- For scikit-learn versions 0.14.1 and prior, return_as=np.ndarray was handled by returning a dense np.matrix instance. Going forward, np.ndarray returns an np.ndarray, as expected. For compatibility, user code relying on this method should wrap its calls in ``np.asarray`` to avoid type issues. """ return _to_graph(n_x, n_y, n_z, mask=mask, return_as=return_as, dtype=dtype) ############################################################################### # From an image to a set of small image patches def _compute_n_patches(i_h, i_w, p_h, p_w, max_patches=None): """Compute the number of patches that will be extracted in an image. Read more in the :ref:`User Guide `. Parameters ---------- i_h : int The image height i_w : int The image with p_h : int The height of a patch p_w : int The width of a patch max_patches : integer or float, optional default is None The maximum number of patches to extract. If max_patches is a float between 0 and 1, it is taken to be a proportion of the total number of patches. """ n_h = i_h - p_h + 1 n_w = i_w - p_w + 1 all_patches = n_h * n_w if max_patches: if (isinstance(max_patches, (numbers.Integral)) and max_patches < all_patches): return max_patches elif (isinstance(max_patches, (numbers.Real)) and 0 < max_patches < 1): return int(max_patches * all_patches) else: raise ValueError("Invalid value for max_patches: %r" % max_patches) else: return all_patches def extract_patches(arr, patch_shape=8, extraction_step=1): """Extracts patches of any n-dimensional array in place using strides. Given an n-dimensional array it will return a 2n-dimensional array with the first n dimensions indexing patch position and the last n indexing the patch content. This operation is immediate (O(1)). A reshape performed on the first n dimensions will cause numpy to copy data, leading to a list of extracted patches. Read more in the :ref:`User Guide `. Parameters ---------- arr : ndarray n-dimensional array of which patches are to be extracted patch_shape : integer or tuple of length arr.ndim Indicates the shape of the patches to be extracted. If an integer is given, the shape will be a hypercube of sidelength given by its value. extraction_step : integer or tuple of length arr.ndim Indicates step size at which extraction shall be performed. If integer is given, then the step is uniform in all dimensions. Returns ------- patches : strided ndarray 2n-dimensional array indexing patches on first n dimensions and containing patches on the last n dimensions. These dimensions are fake, but this way no data is copied. A simple reshape invokes a copying operation to obtain a list of patches: result.reshape([-1] + list(patch_shape)) """ arr_ndim = arr.ndim if isinstance(patch_shape, numbers.Number): patch_shape = tuple([patch_shape] * arr_ndim) if isinstance(extraction_step, numbers.Number): extraction_step = tuple([extraction_step] * arr_ndim) patch_strides = arr.strides slices = [slice(None, None, st) for st in extraction_step] indexing_strides = arr[slices].strides patch_indices_shape = ((np.array(arr.shape) - np.array(patch_shape)) // np.array(extraction_step)) + 1 shape = tuple(list(patch_indices_shape) + list(patch_shape)) strides = tuple(list(indexing_strides) + list(patch_strides)) patches = as_strided(arr, shape=shape, strides=strides) return patches def extract_patches_2d(image, patch_size, max_patches=None, random_state=None): """Reshape a 2D image into a collection of patches The resulting patches are allocated in a dedicated array. Read more in the :ref:`User Guide `. Parameters ---------- image : array, shape = (image_height, image_width) or (image_height, image_width, n_channels) The original image data. For color images, the last dimension specifies the channel: a RGB image would have `n_channels=3`. patch_size : tuple of ints (patch_height, patch_width) the dimensions of one patch max_patches : integer or float, optional default is None The maximum number of patches to extract. If max_patches is a float between 0 and 1, it is taken to be a proportion of the total number of patches. random_state : int or RandomState Pseudo number generator state used for random sampling to use if `max_patches` is not None. Returns ------- patches : array, shape = (n_patches, patch_height, patch_width) or (n_patches, patch_height, patch_width, n_channels) The collection of patches extracted from the image, where `n_patches` is either `max_patches` or the total number of patches that can be extracted. Examples -------- >>> from sklearn.feature_extraction import image >>> one_image = np.arange(16).reshape((4, 4)) >>> one_image array([[ 0, 1, 2, 3], [ 4, 5, 6, 7], [ 8, 9, 10, 11], [12, 13, 14, 15]]) >>> patches = image.extract_patches_2d(one_image, (2, 2)) >>> print(patches.shape) (9, 2, 2) >>> patches[0] array([[0, 1], [4, 5]]) >>> patches[1] array([[1, 2], [5, 6]]) >>> patches[8] array([[10, 11], [14, 15]]) """ i_h, i_w = image.shape[:2] p_h, p_w = patch_size if p_h > i_h: raise ValueError("Height of the patch should be less than the height" " of the image.") if p_w > i_w: raise ValueError("Width of the patch should be less than the width" " of the image.") image = check_array(image, allow_nd=True) image = image.reshape((i_h, i_w, -1)) n_colors = image.shape[-1] extracted_patches = extract_patches(image, patch_shape=(p_h, p_w, n_colors), extraction_step=1) n_patches = _compute_n_patches(i_h, i_w, p_h, p_w, max_patches) if max_patches: rng = check_random_state(random_state) i_s = rng.randint(i_h - p_h + 1, size=n_patches) j_s = rng.randint(i_w - p_w + 1, size=n_patches) patches = extracted_patches[i_s, j_s, 0] else: patches = extracted_patches patches = patches.reshape(-1, p_h, p_w, n_colors) # remove the color dimension if useless if patches.shape[-1] == 1: return patches.reshape((n_patches, p_h, p_w)) else: return patches def reconstruct_from_patches_2d(patches, image_size): """Reconstruct the image from all of its patches. Patches are assumed to overlap and the image is constructed by filling in the patches from left to right, top to bottom, averaging the overlapping regions. Read more in the :ref:`User Guide `. Parameters ---------- patches : array, shape = (n_patches, patch_height, patch_width) or (n_patches, patch_height, patch_width, n_channels) The complete set of patches. If the patches contain colour information, channels are indexed along the last dimension: RGB patches would have `n_channels=3`. image_size : tuple of ints (image_height, image_width) or (image_height, image_width, n_channels) the size of the image that will be reconstructed Returns ------- image : array, shape = image_size the reconstructed image """ i_h, i_w = image_size[:2] p_h, p_w = patches.shape[1:3] img = np.zeros(image_size) # compute the dimensions of the patches array n_h = i_h - p_h + 1 n_w = i_w - p_w + 1 for p, (i, j) in zip(patches, product(range(n_h), range(n_w))): img[i:i + p_h, j:j + p_w] += p for i in range(i_h): for j in range(i_w): # divide by the amount of overlap # XXX: is this the most efficient way? memory-wise yes, cpu wise? img[i, j] /= float(min(i + 1, p_h, i_h - i) * min(j + 1, p_w, i_w - j)) return img class PatchExtractor(BaseEstimator): """Extracts patches from a collection of images Read more in the :ref:`User Guide `. Parameters ---------- patch_size : tuple of ints (patch_height, patch_width) the dimensions of one patch max_patches : integer or float, optional default is None The maximum number of patches per image to extract. If max_patches is a float in (0, 1), it is taken to mean a proportion of the total number of patches. random_state : int or RandomState Pseudo number generator state used for random sampling. """ def __init__(self, patch_size=None, max_patches=None, random_state=None): self.patch_size = patch_size self.max_patches = max_patches self.random_state = random_state def fit(self, X, y=None): """Do nothing and return the estimator unchanged This method is just there to implement the usual API and hence work in pipelines. """ return self def transform(self, X): """Transforms the image samples in X into a matrix of patch data. Parameters ---------- X : array, shape = (n_samples, image_height, image_width) or (n_samples, image_height, image_width, n_channels) Array of images from which to extract patches. For color images, the last dimension specifies the channel: a RGB image would have `n_channels=3`. Returns ------- patches: array, shape = (n_patches, patch_height, patch_width) or (n_patches, patch_height, patch_width, n_channels) The collection of patches extracted from the images, where `n_patches` is either `n_samples * max_patches` or the total number of patches that can be extracted. """ self.random_state = check_random_state(self.random_state) n_images, i_h, i_w = X.shape[:3] X = np.reshape(X, (n_images, i_h, i_w, -1)) n_channels = X.shape[-1] if self.patch_size is None: patch_size = i_h // 10, i_w // 10 else: patch_size = self.patch_size # compute the dimensions of the patches array p_h, p_w = patch_size n_patches = _compute_n_patches(i_h, i_w, p_h, p_w, self.max_patches) patches_shape = (n_images * n_patches,) + patch_size if n_channels > 1: patches_shape += (n_channels,) # extract the patches patches = np.empty(patches_shape) for ii, image in enumerate(X): patches[ii * n_patches:(ii + 1) * n_patches] = extract_patches_2d( image, patch_size, self.max_patches, self.random_state) return patches