pykdtree-0.2/0000755000767500076750000000000012153111634012623 5ustar esnesn00000000000000pykdtree-0.2/pykdtree/0000755000767500076750000000000012153111634014452 5ustar esnesn00000000000000pykdtree-0.2/pykdtree/__init__.py0000644000767500076750000000000012072551074016557 0ustar esnesn00000000000000pykdtree-0.2/pykdtree/_kdtree_core.c0000644000767500076750000012253312152037506017255 0ustar esnesn00000000000000/* pykdtree, Fast kd-tree implementation with OpenMP-enabled queries Copyright (C) 2013 Esben S. Nielsen This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ /* This kd-tree implementation is based on the scipy.spatial.cKDTree by Anne M. Archibald and libANN by David M. Mount and Sunil Arya. */ #include #include #include #include #define PA(i,d) (pa[no_dims * pidx[i] + d]) #define PASWAP(a,b) { uint32_t tmp = pidx[a]; pidx[a] = pidx[b]; pidx[b] = tmp; } typedef struct { float cut_val; int8_t cut_dim; uint32_t start_idx; uint32_t n; float cut_bounds_lv; float cut_bounds_hv; struct Node_float *left_child; struct Node_float *right_child; } Node_float; typedef struct { float *bbox; int8_t no_dims; uint32_t *pidx; struct Node_float *root; } Tree_float; typedef struct { double cut_val; int8_t cut_dim; uint32_t start_idx; uint32_t n; double cut_bounds_lv; double cut_bounds_hv; struct Node_double *left_child; struct Node_double *right_child; } Node_double; typedef struct { double *bbox; int8_t no_dims; uint32_t *pidx; struct Node_double *root; } Tree_double; void insert_point_float(uint32_t *closest_idx, float *closest_dist, uint32_t pidx, float cur_dist, uint32_t k); void get_bounding_box_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, float *bbox); int partition_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *bbox, int8_t *cut_dim, float *cut_val, uint32_t *n_lo); Tree_float* construct_tree_float(float *pa, int8_t no_dims, uint32_t n, uint32_t bsp); Node_float* construct_subtree_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, float *bbox); Node_float * create_node_float(uint32_t start_idx, uint32_t n, int is_leaf); void delete_subtree_float(Node_float *root); void delete_tree_float(Tree_float *tree); void print_tree_float(Node_float *root, int level); float calc_dist_float(float *point1_coord, float *point2_coord, int8_t no_dims); float get_cube_offset_float(int8_t dim, float *point_coord, float *bbox); float get_min_dist_float(float *point_coord, int8_t no_dims, float *bbox); void search_leaf_float(float *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *restrict point_coord, uint32_t k, uint32_t *restrict closest_idx, float *restrict closest_dist); void search_splitnode_float(Node_float *root, float *pa, uint32_t *pidx, int8_t no_dims, float *point_coord, float min_dist, uint32_t k, float distance_upper_bound, float eps_fac, uint32_t * closest_idx, float *closest_dist); void search_tree_float(Tree_float *tree, float *pa, float *point_coords, uint32_t num_points, uint32_t k, float distance_upper_bound, float eps, uint32_t *closest_idxs, float *closest_dists); void insert_point_double(uint32_t *closest_idx, double *closest_dist, uint32_t pidx, double cur_dist, uint32_t k); void get_bounding_box_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, double *bbox); int partition_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *bbox, int8_t *cut_dim, double *cut_val, uint32_t *n_lo); Tree_double* construct_tree_double(double *pa, int8_t no_dims, uint32_t n, uint32_t bsp); Node_double* construct_subtree_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, double *bbox); Node_double * create_node_double(uint32_t start_idx, uint32_t n, int is_leaf); void delete_subtree_double(Node_double *root); void delete_tree_double(Tree_double *tree); void print_tree_double(Node_double *root, int level); double calc_dist_double(double *point1_coord, double *point2_coord, int8_t no_dims); double get_cube_offset_double(int8_t dim, double *point_coord, double *bbox); double get_min_dist_double(double *point_coord, int8_t no_dims, double *bbox); void search_leaf_double(double *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *restrict point_coord, uint32_t k, uint32_t *restrict closest_idx, double *restrict closest_dist); void search_splitnode_double(Node_double *root, double *pa, uint32_t *pidx, int8_t no_dims, double *point_coord, double min_dist, uint32_t k, double distance_upper_bound, double eps_fac, uint32_t * closest_idx, double *closest_dist); void search_tree_double(Tree_double *tree, double *pa, double *point_coords, uint32_t num_points, uint32_t k, double distance_upper_bound, double eps, uint32_t *closest_idxs, double *closest_dists); /************************************************ Insert point into priority queue Params: closest_idx : index queue closest_dist : distance queue pidx : permutation index of data points cur_dist : distance to point inserted k : number of neighbours ************************************************/ void insert_point_float(uint32_t *closest_idx, float *closest_dist, uint32_t pidx, float cur_dist, uint32_t k) { int i; for (i = k - 1; i > 0; i--) { if (closest_dist[i - 1] > cur_dist) { closest_dist[i] = closest_dist[i - 1]; closest_idx[i] = closest_idx[i - 1]; } else { break; } } closest_idx[i] = pidx; closest_dist[i] = cur_dist; } /************************************************ Get the bounding box of a set of points Params: pa : data points pidx : permutation index of data points no_dims: number of dimensions n : number of points bbox : bounding box (return) ************************************************/ void get_bounding_box_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, float *bbox) { float cur; int8_t bbox_idx; /* Use first data point to initialize */ for (int8_t i = 0; i < no_dims; i++) { bbox[2 * i] = bbox[2 * i + 1] = PA(0, i); } /* Update using rest of data points */ for (uint32_t i = 1; i < n; i++) { for (int8_t j = 0; j < no_dims; j++) { bbox_idx = 2 * j; cur = PA(i, j); if (cur < bbox[bbox_idx]) { bbox[bbox_idx] = cur; } else if (cur > bbox[bbox_idx + 1]) { bbox[bbox_idx + 1] = cur; } } } } /************************************************ Partition a range of data points by manipulation the permutation index. The sliding midpoint rule is used for the partitioning. Params: pa : data points pidx : permutation index of data points no_dims: number of dimensions start_idx : index of first data point to use n : number of data points bbox : bounding box of data points cut_dim : dimension used for partition (return) cut_val : value of cutting point (return) n_lo : number of point below cutting plane (return) ************************************************/ int partition_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *bbox, int8_t *cut_dim, float *cut_val, uint32_t *n_lo) { int8_t dim = 0; uint32_t p, q; float size = 0, min_val, max_val, split, side_len, cur_val; uint32_t end_idx = start_idx + n - 1; /* Find largest bounding box side */ for (int8_t i = 0; i < no_dims; i++) { side_len = bbox[2 * i + 1] - bbox[2 * i]; if (side_len > size) { dim = i; size = side_len; } } min_val = bbox[2 * dim]; max_val = bbox[2 * dim + 1]; /* Check for zero length or inconsistent */ if (min_val >= max_val) return 1; /* Use middle for splitting */ split = (min_val + max_val) / 2; /* Partition all data points around middle */ p = start_idx; q = end_idx; while (p <= q) { if (PA(p, dim) < split) { p++; } else if (PA(q, dim) >= split) { /* Guard for underflow */ if (q > 0) { q--; } else { break; } } else { PASWAP(p, q); p++; q--; } } /* Check for empty splits */ if (p == start_idx) { /* No points less than split. Split at lowest point instead. Minimum 1 point will be in lower box. */ uint32_t j = start_idx; split = PA(j, dim); for (uint32_t i = start_idx + 1; i <= end_idx; i++) { /* Find lowest point */ cur_val = PA(i, dim); if (cur_val < split) { j = i; split = cur_val; } } PASWAP(j, start_idx); p = start_idx + 1; } else if (p == end_idx + 1) { /* No points greater than split. Split at highest point instead. Minimum 1 point will be in higher box. */ uint32_t j = end_idx; split = PA(j, dim); for (uint32_t i = start_idx; i < end_idx; i++) { /* Find highest point */ cur_val = PA(i, dim); if (cur_val > split) { j = i; split = cur_val; } } PASWAP(j, end_idx); p = end_idx; } /* Set return values */ *cut_dim = dim; *cut_val = split; *n_lo = p - start_idx; return 0; } /************************************************ Construct a sub tree over a range of data points. Params: pa : data points pidx : permutation index of data points no_dims: number of dimensions start_idx : index of first data point to use n : number of data points bsp : number of points per leaf bbox : bounding box of set of data points ************************************************/ Node_float* construct_subtree_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, float *bbox) { /* Create new node */ int is_leaf = (n <= bsp); Node_float *root = create_node_float(start_idx, n, is_leaf); if (is_leaf) { /* Make leaf node */ root->cut_dim = -1; } else { /* Make split node */ int rval; int8_t cut_dim; uint32_t n_lo; float cut_val; /* Partition data set and set node info */ rval = partition_float(pa, pidx, no_dims, start_idx, n, bbox, &cut_dim, &cut_val, &n_lo); if (rval == 1) { root->cut_dim = -1; return root; } root->cut_val = cut_val; root->cut_dim = cut_dim; /* Recurse on both subsets */ float lv = bbox[2 * cut_dim]; float hv = bbox[2 * cut_dim + 1]; /* Set bounds for cut dimension */ root->cut_bounds_lv = lv; root->cut_bounds_hv = hv; /* Update bounding box before call to lower subset and restore after */ bbox[2 * cut_dim + 1] = cut_val; root->left_child = (struct Node_float *)construct_subtree_float(pa, pidx, no_dims, start_idx, n_lo, bsp, bbox); bbox[2 * cut_dim + 1] = hv; /* Update bounding box before call to higher subset and restore after */ bbox[2 * cut_dim] = cut_val; root->right_child = (struct Node_float *)construct_subtree_float(pa, pidx, no_dims, start_idx + n_lo, n - n_lo, bsp, bbox); bbox[2 * cut_dim] = lv; } return root; } /************************************************ Construct a tree over data points. Params: pa : data points no_dims: number of dimensions n : number of data points bsp : number of points per leaf ************************************************/ Tree_float* construct_tree_float(float *pa, int8_t no_dims, uint32_t n, uint32_t bsp) { Tree_float *tree = (Tree_float *)malloc(sizeof(Tree_float)); tree->no_dims = no_dims; /* Initialize permutation array */ uint32_t *pidx = (uint32_t *)malloc(sizeof(uint32_t) * n); for (uint32_t i = 0; i < n; i++) { pidx[i] = i; } float *bbox = (float *)malloc(2 * sizeof(float) * no_dims); get_bounding_box_float(pa, pidx, no_dims, n, bbox); tree->bbox = bbox; /* Construct subtree on full dataset */ tree->root = (struct Node_float *)construct_subtree_float(pa, pidx, no_dims, 0, n, bsp, bbox); tree->pidx = pidx; return tree; } /************************************************ Create a tree node. Params: start_idx : index of first data point to use n : number of data points ************************************************/ Node_float* create_node_float(uint32_t start_idx, uint32_t n, int is_leaf) { Node_float *new_node; if (is_leaf) { /* Allocate only the part of the struct that will be used in a leaf node. This relies on the C99 specification of struct layout conservation and padding and that dereferencing is never attempted for the node pointers in a leaf. */ new_node = (Node_float *)malloc(sizeof(Node_float) - 2 * sizeof(Node_float *)); } else { new_node = (Node_float *)malloc(sizeof(Node_float)); } new_node->n = n; new_node->start_idx = start_idx; return new_node; } /************************************************ Delete subtree Params: root : root node of subtree to delete ************************************************/ void delete_subtree_float(Node_float *root) { if (root->cut_dim != -1) { delete_subtree_float((Node_float *)root->left_child); delete_subtree_float((Node_float *)root->right_child); } free(root); } /************************************************ Delete tree Params: tree : Tree struct of kd tree ************************************************/ void delete_tree_float(Tree_float *tree) { delete_subtree_float((Node_float *)tree->root); free(tree->bbox); free(tree->pidx); free(tree); } /************************************************ Print ************************************************/ void print_tree_float(Node_float *root, int level) { for (int i = 0; i < level; i++) { printf(" "); } printf("(cut_val: %f, cut_dim: %i)\n", root->cut_val, root->cut_dim); if (root->cut_dim != -1) print_tree_float((Node_float *)root->left_child, level + 1); if (root->cut_dim != -1) print_tree_float((Node_float *)root->right_child, level + 1); } /************************************************ Calculate squared cartesian distance between points Params: point1_coord : point 1 point2_coord : point 2 ************************************************/ float calc_dist_float(float *point1_coord, float *point2_coord, int8_t no_dims) { /* Calculate squared distance */ float dist = 0, dim_dist; for (int8_t i = 0; i < no_dims; i++) { dim_dist = point2_coord[i] - point1_coord[i]; dist += dim_dist * dim_dist; } return dist; } /************************************************ Get squared distance from point to cube in specified dimension Params: dim : dimension point_coord : cartesian coordinates of point bbox : cube ************************************************/ float get_cube_offset_float(int8_t dim, float *point_coord, float *bbox) { float dim_coord = point_coord[dim]; if (dim_coord < bbox[2 * dim]) { /* Left of cube in dimension */ return dim_coord - bbox[2 * dim]; } else if (dim_coord > bbox[2 * dim + 1]) { /* Right of cube in dimension */ return dim_coord - bbox[2 * dim + 1]; } else { /* Inside cube in dimension */ return 0.; } } /************************************************ Get minimum squared distance between point and cube. Params: point_coord : cartesian coordinates of point no_dims : number of dimensions bbox : cube ************************************************/ float get_min_dist_float(float *point_coord, int8_t no_dims, float *bbox) { float cube_offset = 0, cube_offset_dim; for (int8_t i = 0; i < no_dims; i++) { cube_offset_dim = get_cube_offset_float(i, point_coord, bbox); cube_offset += cube_offset_dim * cube_offset_dim; } return cube_offset; } /************************************************ Search a leaf node for closest point Params: pa : data points pidx : permutation index of data points no_dims : number of dimensions start_idx : index of first data point to use size : number of data points point_coord : query point closest_idx : index of closest data point found (return) closest_dist : distance to closest point (return) ************************************************/ void search_leaf_float(float *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *restrict point_coord, uint32_t k, uint32_t *restrict closest_idx, float *restrict closest_dist) { float cur_dist; /* Loop through all points in leaf */ for (uint32_t i = 0; i < n; i++) { /* Get distance to query point */ cur_dist = calc_dist_float(&PA(start_idx + i, 0), point_coord, no_dims); /* Update closest info if new point is closest so far*/ if (cur_dist < closest_dist[k - 1]) { insert_point_float(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k); } } } /************************************************ Search subtree for nearest to query point Params: root : root node of subtree pa : data points pidx : permutation index of data points no_dims : number of dimensions point_coord : query point min_dist : minumum distance to nearest neighbour closest_idx : index of closest data point found (return) closest_dist : distance to closest point (return) ************************************************/ void search_splitnode_float(Node_float *root, float *pa, uint32_t *pidx, int8_t no_dims, float *point_coord, float min_dist, uint32_t k, float distance_upper_bound, float eps_fac, uint32_t *closest_idx, float *closest_dist) { int8_t dim; float dist_left, dist_right; float new_offset; float box_diff; /* Skip if distance bound exeeded */ if (min_dist > distance_upper_bound) { return; } dim = root->cut_dim; /* Handle leaf node */ if (dim == -1) { search_leaf_float(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, closest_idx, closest_dist); return; } /* Get distance to cutting plane */ new_offset = point_coord[dim] - root->cut_val; if (new_offset < 0) { /* Left of cutting plane */ dist_left = min_dist; if (dist_left < closest_dist[k - 1] * eps_fac) { /* Search left subtree if minimum distance is below limit */ search_splitnode_float((Node_float *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } /* Right of cutting plane. Update minimum distance. See Algorithms for Fast Vector Quantization Sunil Arya and David M. Mount. */ box_diff = root->cut_bounds_lv - point_coord[dim]; if (box_diff < 0) { box_diff = 0; } dist_right = min_dist - box_diff * box_diff + new_offset * new_offset; if (dist_right < closest_dist[k - 1] * eps_fac) { /* Search right subtree if minimum distance is below limit*/ search_splitnode_float((Node_float *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } } else { /* Right of cutting plane */ dist_right = min_dist; if (dist_right < closest_dist[k - 1] * eps_fac) { /* Search right subtree if minimum distance is below limit*/ search_splitnode_float((Node_float *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } /* Left of cutting plane. Update minimum distance. See Algorithms for Fast Vector Quantization Sunil Arya and David M. Mount. */ box_diff = point_coord[dim] - root->cut_bounds_hv; if (box_diff < 0) { box_diff = 0; } dist_left = min_dist - box_diff * box_diff + new_offset * new_offset; if (dist_left < closest_dist[k - 1] * eps_fac) { /* Search left subtree if minimum distance is below limit*/ search_splitnode_float((Node_float *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } } } /************************************************ Search for nearest neighbour for a set of query points Params: tree : Tree struct of kd tree pa : data points pidx : permutation index of data points point_coords : query points num_points : number of query points closest_idx : index of closest data point found (return) closest_dist : distance to closest point (return) ************************************************/ void search_tree_float(Tree_float *tree, float *pa, float *point_coords, uint32_t num_points, uint32_t k, float distance_upper_bound, float eps, uint32_t *closest_idxs, float *closest_dists) { float min_dist; float eps_fac = 1 / ((1 + eps) * (1 + eps)); int8_t no_dims = tree->no_dims; float *bbox = tree->bbox; uint32_t *pidx = tree->pidx; Node_float *root = (Node_float *)tree->root; /* Queries are OpenMP enabled */ #pragma omp parallel { /* The low chunk size is important to avoid L2 cache trashing for spatial coherent query datasets */ #pragma omp for schedule(static, 100) nowait for (uint32_t i = 0; i < num_points; i++) { for (uint32_t j = 0; j < k; j++) { closest_idxs[i * k + j] = UINT32_MAX; closest_dists[i * k + j] = DBL_MAX; } min_dist = get_min_dist_float(point_coords + no_dims * i, no_dims, bbox); search_splitnode_float(root, pa, pidx, no_dims, point_coords + no_dims * i, min_dist, k, distance_upper_bound, eps_fac, &closest_idxs[i * k], &closest_dists[i * k]); } } } /************************************************ Insert point into priority queue Params: closest_idx : index queue closest_dist : distance queue pidx : permutation index of data points cur_dist : distance to point inserted k : number of neighbours ************************************************/ void insert_point_double(uint32_t *closest_idx, double *closest_dist, uint32_t pidx, double cur_dist, uint32_t k) { int i; for (i = k - 1; i > 0; i--) { if (closest_dist[i - 1] > cur_dist) { closest_dist[i] = closest_dist[i - 1]; closest_idx[i] = closest_idx[i - 1]; } else { break; } } closest_idx[i] = pidx; closest_dist[i] = cur_dist; } /************************************************ Get the bounding box of a set of points Params: pa : data points pidx : permutation index of data points no_dims: number of dimensions n : number of points bbox : bounding box (return) ************************************************/ void get_bounding_box_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, double *bbox) { double cur; int8_t bbox_idx; /* Use first data point to initialize */ for (int8_t i = 0; i < no_dims; i++) { bbox[2 * i] = bbox[2 * i + 1] = PA(0, i); } /* Update using rest of data points */ for (uint32_t i = 1; i < n; i++) { for (int8_t j = 0; j < no_dims; j++) { bbox_idx = 2 * j; cur = PA(i, j); if (cur < bbox[bbox_idx]) { bbox[bbox_idx] = cur; } else if (cur > bbox[bbox_idx + 1]) { bbox[bbox_idx + 1] = cur; } } } } /************************************************ Partition a range of data points by manipulation the permutation index. The sliding midpoint rule is used for the partitioning. Params: pa : data points pidx : permutation index of data points no_dims: number of dimensions start_idx : index of first data point to use n : number of data points bbox : bounding box of data points cut_dim : dimension used for partition (return) cut_val : value of cutting point (return) n_lo : number of point below cutting plane (return) ************************************************/ int partition_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *bbox, int8_t *cut_dim, double *cut_val, uint32_t *n_lo) { int8_t dim = 0; uint32_t p, q; double size = 0, min_val, max_val, split, side_len, cur_val; uint32_t end_idx = start_idx + n - 1; /* Find largest bounding box side */ for (int8_t i = 0; i < no_dims; i++) { side_len = bbox[2 * i + 1] - bbox[2 * i]; if (side_len > size) { dim = i; size = side_len; } } min_val = bbox[2 * dim]; max_val = bbox[2 * dim + 1]; /* Check for zero length or inconsistent */ if (min_val >= max_val) return 1; /* Use middle for splitting */ split = (min_val + max_val) / 2; /* Partition all data points around middle */ p = start_idx; q = end_idx; while (p <= q) { if (PA(p, dim) < split) { p++; } else if (PA(q, dim) >= split) { /* Guard for underflow */ if (q > 0) { q--; } else { break; } } else { PASWAP(p, q); p++; q--; } } /* Check for empty splits */ if (p == start_idx) { /* No points less than split. Split at lowest point instead. Minimum 1 point will be in lower box. */ uint32_t j = start_idx; split = PA(j, dim); for (uint32_t i = start_idx + 1; i <= end_idx; i++) { /* Find lowest point */ cur_val = PA(i, dim); if (cur_val < split) { j = i; split = cur_val; } } PASWAP(j, start_idx); p = start_idx + 1; } else if (p == end_idx + 1) { /* No points greater than split. Split at highest point instead. Minimum 1 point will be in higher box. */ uint32_t j = end_idx; split = PA(j, dim); for (uint32_t i = start_idx; i < end_idx; i++) { /* Find highest point */ cur_val = PA(i, dim); if (cur_val > split) { j = i; split = cur_val; } } PASWAP(j, end_idx); p = end_idx; } /* Set return values */ *cut_dim = dim; *cut_val = split; *n_lo = p - start_idx; return 0; } /************************************************ Construct a sub tree over a range of data points. Params: pa : data points pidx : permutation index of data points no_dims: number of dimensions start_idx : index of first data point to use n : number of data points bsp : number of points per leaf bbox : bounding box of set of data points ************************************************/ Node_double* construct_subtree_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, double *bbox) { /* Create new node */ int is_leaf = (n <= bsp); Node_double *root = create_node_double(start_idx, n, is_leaf); if (is_leaf) { /* Make leaf node */ root->cut_dim = -1; } else { /* Make split node */ int rval; int8_t cut_dim; uint32_t n_lo; double cut_val; /* Partition data set and set node info */ rval = partition_double(pa, pidx, no_dims, start_idx, n, bbox, &cut_dim, &cut_val, &n_lo); if (rval == 1) { root->cut_dim = -1; return root; } root->cut_val = cut_val; root->cut_dim = cut_dim; /* Recurse on both subsets */ double lv = bbox[2 * cut_dim]; double hv = bbox[2 * cut_dim + 1]; /* Set bounds for cut dimension */ root->cut_bounds_lv = lv; root->cut_bounds_hv = hv; /* Update bounding box before call to lower subset and restore after */ bbox[2 * cut_dim + 1] = cut_val; root->left_child = (struct Node_double *)construct_subtree_double(pa, pidx, no_dims, start_idx, n_lo, bsp, bbox); bbox[2 * cut_dim + 1] = hv; /* Update bounding box before call to higher subset and restore after */ bbox[2 * cut_dim] = cut_val; root->right_child = (struct Node_double *)construct_subtree_double(pa, pidx, no_dims, start_idx + n_lo, n - n_lo, bsp, bbox); bbox[2 * cut_dim] = lv; } return root; } /************************************************ Construct a tree over data points. Params: pa : data points no_dims: number of dimensions n : number of data points bsp : number of points per leaf ************************************************/ Tree_double* construct_tree_double(double *pa, int8_t no_dims, uint32_t n, uint32_t bsp) { Tree_double *tree = (Tree_double *)malloc(sizeof(Tree_double)); tree->no_dims = no_dims; /* Initialize permutation array */ uint32_t *pidx = (uint32_t *)malloc(sizeof(uint32_t) * n); for (uint32_t i = 0; i < n; i++) { pidx[i] = i; } double *bbox = (double *)malloc(2 * sizeof(double) * no_dims); get_bounding_box_double(pa, pidx, no_dims, n, bbox); tree->bbox = bbox; /* Construct subtree on full dataset */ tree->root = (struct Node_double *)construct_subtree_double(pa, pidx, no_dims, 0, n, bsp, bbox); tree->pidx = pidx; return tree; } /************************************************ Create a tree node. Params: start_idx : index of first data point to use n : number of data points ************************************************/ Node_double* create_node_double(uint32_t start_idx, uint32_t n, int is_leaf) { Node_double *new_node; if (is_leaf) { /* Allocate only the part of the struct that will be used in a leaf node. This relies on the C99 specification of struct layout conservation and padding and that dereferencing is never attempted for the node pointers in a leaf. */ new_node = (Node_double *)malloc(sizeof(Node_double) - 2 * sizeof(Node_double *)); } else { new_node = (Node_double *)malloc(sizeof(Node_double)); } new_node->n = n; new_node->start_idx = start_idx; return new_node; } /************************************************ Delete subtree Params: root : root node of subtree to delete ************************************************/ void delete_subtree_double(Node_double *root) { if (root->cut_dim != -1) { delete_subtree_double((Node_double *)root->left_child); delete_subtree_double((Node_double *)root->right_child); } free(root); } /************************************************ Delete tree Params: tree : Tree struct of kd tree ************************************************/ void delete_tree_double(Tree_double *tree) { delete_subtree_double((Node_double *)tree->root); free(tree->bbox); free(tree->pidx); free(tree); } /************************************************ Print ************************************************/ void print_tree_double(Node_double *root, int level) { for (int i = 0; i < level; i++) { printf(" "); } printf("(cut_val: %f, cut_dim: %i)\n", root->cut_val, root->cut_dim); if (root->cut_dim != -1) print_tree_double((Node_double *)root->left_child, level + 1); if (root->cut_dim != -1) print_tree_double((Node_double *)root->right_child, level + 1); } /************************************************ Calculate squared cartesian distance between points Params: point1_coord : point 1 point2_coord : point 2 ************************************************/ double calc_dist_double(double *point1_coord, double *point2_coord, int8_t no_dims) { /* Calculate squared distance */ double dist = 0, dim_dist; for (int8_t i = 0; i < no_dims; i++) { dim_dist = point2_coord[i] - point1_coord[i]; dist += dim_dist * dim_dist; } return dist; } /************************************************ Get squared distance from point to cube in specified dimension Params: dim : dimension point_coord : cartesian coordinates of point bbox : cube ************************************************/ double get_cube_offset_double(int8_t dim, double *point_coord, double *bbox) { double dim_coord = point_coord[dim]; if (dim_coord < bbox[2 * dim]) { /* Left of cube in dimension */ return dim_coord - bbox[2 * dim]; } else if (dim_coord > bbox[2 * dim + 1]) { /* Right of cube in dimension */ return dim_coord - bbox[2 * dim + 1]; } else { /* Inside cube in dimension */ return 0.; } } /************************************************ Get minimum squared distance between point and cube. Params: point_coord : cartesian coordinates of point no_dims : number of dimensions bbox : cube ************************************************/ double get_min_dist_double(double *point_coord, int8_t no_dims, double *bbox) { double cube_offset = 0, cube_offset_dim; for (int8_t i = 0; i < no_dims; i++) { cube_offset_dim = get_cube_offset_double(i, point_coord, bbox); cube_offset += cube_offset_dim * cube_offset_dim; } return cube_offset; } /************************************************ Search a leaf node for closest point Params: pa : data points pidx : permutation index of data points no_dims : number of dimensions start_idx : index of first data point to use size : number of data points point_coord : query point closest_idx : index of closest data point found (return) closest_dist : distance to closest point (return) ************************************************/ void search_leaf_double(double *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *restrict point_coord, uint32_t k, uint32_t *restrict closest_idx, double *restrict closest_dist) { double cur_dist; /* Loop through all points in leaf */ for (uint32_t i = 0; i < n; i++) { /* Get distance to query point */ cur_dist = calc_dist_double(&PA(start_idx + i, 0), point_coord, no_dims); /* Update closest info if new point is closest so far*/ if (cur_dist < closest_dist[k - 1]) { insert_point_double(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k); } } } /************************************************ Search subtree for nearest to query point Params: root : root node of subtree pa : data points pidx : permutation index of data points no_dims : number of dimensions point_coord : query point min_dist : minumum distance to nearest neighbour closest_idx : index of closest data point found (return) closest_dist : distance to closest point (return) ************************************************/ void search_splitnode_double(Node_double *root, double *pa, uint32_t *pidx, int8_t no_dims, double *point_coord, double min_dist, uint32_t k, double distance_upper_bound, double eps_fac, uint32_t *closest_idx, double *closest_dist) { int8_t dim; double dist_left, dist_right; double new_offset; double box_diff; /* Skip if distance bound exeeded */ if (min_dist > distance_upper_bound) { return; } dim = root->cut_dim; /* Handle leaf node */ if (dim == -1) { search_leaf_double(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, closest_idx, closest_dist); return; } /* Get distance to cutting plane */ new_offset = point_coord[dim] - root->cut_val; if (new_offset < 0) { /* Left of cutting plane */ dist_left = min_dist; if (dist_left < closest_dist[k - 1] * eps_fac) { /* Search left subtree if minimum distance is below limit */ search_splitnode_double((Node_double *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } /* Right of cutting plane. Update minimum distance. See Algorithms for Fast Vector Quantization Sunil Arya and David M. Mount. */ box_diff = root->cut_bounds_lv - point_coord[dim]; if (box_diff < 0) { box_diff = 0; } dist_right = min_dist - box_diff * box_diff + new_offset * new_offset; if (dist_right < closest_dist[k - 1] * eps_fac) { /* Search right subtree if minimum distance is below limit*/ search_splitnode_double((Node_double *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } } else { /* Right of cutting plane */ dist_right = min_dist; if (dist_right < closest_dist[k - 1] * eps_fac) { /* Search right subtree if minimum distance is below limit*/ search_splitnode_double((Node_double *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } /* Left of cutting plane. Update minimum distance. See Algorithms for Fast Vector Quantization Sunil Arya and David M. Mount. */ box_diff = point_coord[dim] - root->cut_bounds_hv; if (box_diff < 0) { box_diff = 0; } dist_left = min_dist - box_diff * box_diff + new_offset * new_offset; if (dist_left < closest_dist[k - 1] * eps_fac) { /* Search left subtree if minimum distance is below limit*/ search_splitnode_double((Node_double *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, closest_idx, closest_dist); } } } /************************************************ Search for nearest neighbour for a set of query points Params: tree : Tree struct of kd tree pa : data points pidx : permutation index of data points point_coords : query points num_points : number of query points closest_idx : index of closest data point found (return) closest_dist : distance to closest point (return) ************************************************/ void search_tree_double(Tree_double *tree, double *pa, double *point_coords, uint32_t num_points, uint32_t k, double distance_upper_bound, double eps, uint32_t *closest_idxs, double *closest_dists) { double min_dist; double eps_fac = 1 / ((1 + eps) * (1 + eps)); int8_t no_dims = tree->no_dims; double *bbox = tree->bbox; uint32_t *pidx = tree->pidx; Node_double *root = (Node_double *)tree->root; /* Queries are OpenMP enabled */ #pragma omp parallel { /* The low chunk size is important to avoid L2 cache trashing for spatial coherent query datasets */ #pragma omp for schedule(static, 100) nowait for (uint32_t i = 0; i < num_points; i++) { for (uint32_t j = 0; j < k; j++) { closest_idxs[i * k + j] = UINT32_MAX; closest_dists[i * k + j] = DBL_MAX; } min_dist = get_min_dist_double(point_coords + no_dims * i, no_dims, bbox); search_splitnode_double(root, pa, pidx, no_dims, point_coords + no_dims * i, min_dist, k, distance_upper_bound, eps_fac, &closest_idxs[i * k], &closest_dists[i * k]); } } } pykdtree-0.2/pykdtree/kdtree.c0000644000767500076750000125356712152037506016123 0ustar esnesn00000000000000/* Generated by Cython 0.18 on Tue May 28 10:49:15 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? 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/* "numpy.pxd":732 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< * ctypedef npy_uint64 uint64_t * #ctypedef npy_uint96 uint96_t */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; /* "numpy.pxd":733 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< * #ctypedef npy_uint96 uint96_t * #ctypedef npy_uint128 uint128_t */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; /* "numpy.pxd":737 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t * #ctypedef npy_float80 float80_t */ typedef npy_float32 __pyx_t_5numpy_float32_t; /* "numpy.pxd":738 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< * #ctypedef npy_float80 float80_t * #ctypedef npy_float128 float128_t */ typedef npy_float64 __pyx_t_5numpy_float64_t; /* "numpy.pxd":747 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t */ typedef npy_long __pyx_t_5numpy_int_t; 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/*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; 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/*proto*/ __PYX_EXTERN_C DL_IMPORT(void) delete_tree_float(struct __pyx_t_8pykdtree_6kdtree_tree_float *); /*proto*/ __PYX_EXTERN_C DL_IMPORT(struct __pyx_t_8pykdtree_6kdtree_tree_double) *construct_tree_double(double *, int8_t, uint32_t, uint32_t); /*proto*/ __PYX_EXTERN_C DL_IMPORT(void) search_tree_double(struct __pyx_t_8pykdtree_6kdtree_tree_double *, double *, double *, uint32_t, uint32_t, double, double, uint32_t *, double *); /*proto*/ __PYX_EXTERN_C DL_IMPORT(void) delete_tree_double(struct __pyx_t_8pykdtree_6kdtree_tree_double *); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 }; static __Pyx_TypeInfo __Pyx_TypeInfo_nn_uint32_t = { "uint32_t", NULL, sizeof(uint32_t), { 0 }, 0, IS_UNSIGNED(uint32_t) ? 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/* proto */ static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_8data_pts___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_1n___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_4ndim___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_8leafsize___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static char __pyx_k_1[] = "leafsize must be greater than zero"; static char __pyx_k_3[] = "distance_upper_bound"; static char __pyx_k_5[] = "Number of neighbours must be greater than zero"; 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static PyObject *__pyx_k_tuple_16; static PyObject *__pyx_k_tuple_18; static PyObject *__pyx_k_tuple_20; static PyObject *__pyx_k_tuple_23; static PyObject *__pyx_k_tuple_24; static PyObject *__pyx_k_tuple_26; /* Python wrapper */ static int __pyx_pw_8pykdtree_6kdtree_6KDTree_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_8pykdtree_6kdtree_6KDTree_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;} if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1; __pyx_r = __pyx_pf_8pykdtree_6kdtree_6KDTree___cinit__(((struct __pyx_obj_8pykdtree_6kdtree_KDTree *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "pykdtree/kdtree.pyx":86 * cdef readonly uint32_t leafsize * * def __cinit__(KDTree self): # <<<<<<<<<<<<<< * self._kdtree_float = NULL * self._kdtree_double = NULL */ static int __pyx_pf_8pykdtree_6kdtree_6KDTree___cinit__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__", 0); /* "pykdtree/kdtree.pyx":87 * * def __cinit__(KDTree self): * self._kdtree_float = NULL # <<<<<<<<<<<<<< * self._kdtree_double = NULL * */ __pyx_v_self->_kdtree_float = NULL; /* "pykdtree/kdtree.pyx":88 * def __cinit__(KDTree self): * self._kdtree_float = NULL * self._kdtree_double = NULL # <<<<<<<<<<<<<< * * def __init__(KDTree self, np.ndarray data_pts not None, int leafsize=16): */ __pyx_v_self->_kdtree_double = NULL; __pyx_r = 0; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_8pykdtree_6kdtree_6KDTree_3__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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} else { __pyx_t_2 = __pyx_t_3; } if (__pyx_t_2) { /* "numpy.pxd":219 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_18), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; /* "numpy.pxd":221 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< * info.ndim = ndim * if copy_shape: */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); /* "numpy.pxd":222 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< * if copy_shape: * # Allocate new buffer for strides and shape info. */ __pyx_v_info->ndim = __pyx_v_ndim; 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#else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); value = Py_None; } #endif PyErr_NormalizeException(&type, &value, &tb); } else { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (PyExceptionClass_Check(type)) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyEval_CallObject(type, args); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, __Pyx_TypeInfo* type) { stack[0].field = &ctx->root; stack[0].parent_offset = 0; ctx->root.type = type; ctx->root.name = "buffer dtype"; ctx->root.offset = 0; ctx->head = stack; ctx->head->field = &ctx->root; ctx->fmt_offset = 0; ctx->head->parent_offset = 0; ctx->new_packmode = '@'; ctx->enc_packmode = '@'; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->is_complex = 0; ctx->is_valid_array = 0; ctx->struct_alignment = 0; while (type->typegroup == 'S') { ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = 0; type = type->fields->type; } } static int __Pyx_BufFmt_ParseNumber(const char** ts) { int count; const char* t = *ts; if (*t < '0' || *t > '9') { return -1; } else { count = *t++ - '0'; while (*t >= '0' && *t < '9') { count *= 10; count += *t++ - '0'; } } *ts = t; return count; } static int __Pyx_BufFmt_ExpectNumber(const char **ts) { int number = __Pyx_BufFmt_ParseNumber(ts); if (number == -1) /* First char was not a digit */ PyErr_Format(PyExc_ValueError,\ "Does not understand character buffer dtype format string ('%c')", **ts); return number; } static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%c'", ch); } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; case 'h': return "'short'"; case 'H': return "'unsigned short'"; case 'i': return "'int'"; case 'I': return "'unsigned int'"; case 'l': return "'long'"; case 'L': return "'unsigned long'"; case 'q': return "'long long'"; case 'Q': return "'unsigned long long'"; case 'f': return (is_complex ? "'complex float'" : "'float'"); case 'd': return (is_complex ? "'complex double'" : "'double'"); case 'g': return (is_complex ? "'complex long double'" : "'long double'"); case 'T': return "a struct"; case 'O': return "Python object"; case 'P': return "a pointer"; case 's': case 'p': return "a string"; case 0: return "end"; default: return "unparseable format string"; } } static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return 2; case 'i': case 'I': case 'l': case 'L': return 4; case 'q': case 'Q': return 8; case 'f': return (is_complex ? 8 : 4); case 'd': return (is_complex ? 16 : 8); case 'g': { PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); return 0; } case 'O': case 'P': return sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(float) * (is_complex ? 2 : 1); case 'd': return sizeof(double) * (is_complex ? 2 : 1); case 'g': return sizeof(long double) * (is_complex ? 2 : 1); case 'O': case 'P': return sizeof(void*); default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } typedef struct { char c; short x; } __Pyx_st_short; typedef struct { char c; int x; } __Pyx_st_int; typedef struct { char c; long x; } __Pyx_st_long; typedef struct { char c; float x; } __Pyx_st_float; typedef struct { char c; double x; } __Pyx_st_double; typedef struct { char c; long double x; } __Pyx_st_longdouble; typedef struct { char c; void *x; } __Pyx_st_void_p; #ifdef HAVE_LONG_LONG typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_st_float) - sizeof(float); case 'd': return sizeof(__Pyx_st_double) - sizeof(double); case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } /* These are for computing the padding at the end of the struct to align on the first member of the struct. This will probably the same as above, but we don't have any guarantees. */ typedef struct { short x; char c; } __Pyx_pad_short; typedef struct { int x; char c; } __Pyx_pad_int; typedef struct { long x; char c; } __Pyx_pad_long; typedef struct { float x; char c; } __Pyx_pad_float; typedef struct { double x; char c; } __Pyx_pad_double; typedef struct { long double x; char c; } __Pyx_pad_longdouble; typedef struct { void *x; char c; } __Pyx_pad_void_p; #ifdef HAVE_LONG_LONG typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { switch (ch) { case 'c': return 'H'; case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); case 'O': return 'O'; case 'P': return 'P'; default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { if (ctx->head == NULL || ctx->head->field == &ctx->root) { const char* expected; const char* quote; if (ctx->head == NULL) { expected = "end"; quote = ""; } else { expected = ctx->head->field->type->name; quote = "'"; } PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected %s%s%s but got %s", quote, expected, quote, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); } else { __Pyx_StructField* field = ctx->head->field; __Pyx_StructField* parent = (ctx->head - 1)->field; PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), parent->type->name, field->name); } } static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { char group; size_t size, offset, arraysize = 1; if (ctx->enc_type == 0) return 0; if (ctx->head->field->type->arraysize[0]) { int i, ndim = 0; if (ctx->enc_type == 's' || ctx->enc_type == 'p') { ctx->is_valid_array = ctx->head->field->type->ndim == 1; ndim = 1; if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %zu", ctx->head->field->type->arraysize[0], ctx->enc_count); return -1; } } if (!ctx->is_valid_array) { PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", ctx->head->field->type->ndim, ndim); return -1; } for (i = 0; i < ctx->head->field->type->ndim; i++) { arraysize *= ctx->head->field->type->arraysize[i]; } ctx->is_valid_array = 0; ctx->enc_count = 1; } group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); do { __Pyx_StructField* field = ctx->head->field; __Pyx_TypeInfo* type = field->type; if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); } else { size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); } if (ctx->enc_packmode == '@') { size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); size_t align_mod_offset; if (align_at == 0) return -1; align_mod_offset = ctx->fmt_offset % align_at; if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; if (ctx->struct_alignment == 0) ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, ctx->is_complex); } if (type->size != size || type->typegroup != group) { if (type->typegroup == 'C' && type->fields != NULL) { size_t parent_offset = ctx->head->parent_offset + field->offset; ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = parent_offset; continue; } if ((type->typegroup == 'H' || group == 'H') && type->size == size) { } else { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } } offset = ctx->head->parent_offset + field->offset; if (ctx->fmt_offset != offset) { PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); return -1; } ctx->fmt_offset += size; if (arraysize) ctx->fmt_offset += (arraysize - 1) * size; --ctx->enc_count; /* Consume from buffer string */ while (1) { if (field == &ctx->root) { ctx->head = NULL; if (ctx->enc_count != 0) { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } break; /* breaks both loops as ctx->enc_count == 0 */ } ctx->head->field = ++field; if (field->type == NULL) { --ctx->head; field = ctx->head->field; continue; } else if (field->type->typegroup == 'S') { size_t parent_offset = ctx->head->parent_offset + field->offset; if (field->type->fields->type == NULL) continue; /* empty struct */ field = field->type->fields; ++ctx->head; ctx->head->field = field; ctx->head->parent_offset = parent_offset; break; } else { break; } } } while (ctx->enc_count); ctx->enc_type = 0; ctx->is_complex = 0; return 0; } static CYTHON_INLINE PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; int i = 0, number; int ndim = ctx->head->field->type->ndim; ; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, "Cannot handle repeated arrays in format string"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; while (*ts && *ts != ')') { if (isspace(*ts)) continue; number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) return PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %d", ctx->head->field->type->arraysize[i], number); if (*ts != ',' && *ts != ')') return PyErr_Format(PyExc_ValueError, "Expected a comma in format string, got '%c'", *ts); if (*ts == ',') ts++; i++; } if (i != ndim) return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", ctx->head->field->type->ndim, i); if (!*ts) { PyErr_SetString(PyExc_ValueError, "Unexpected end of format string, expected ')'"); return NULL; } ctx->is_valid_array = 1; ctx->new_count = 1; *tsp = ++ts; return Py_None; } static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { int got_Z = 0; while (1) { switch(*ts) { case 0: if (ctx->enc_type != 0 && ctx->head == NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; if (ctx->head != NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } return ts; case ' ': case 10: case 13: ++ts; break; case '<': if (!__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '>': case '!': if (__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '=': case '@': case '^': ctx->new_packmode = *ts++; break; case 'T': /* substruct */ { const char* ts_after_sub; size_t i, struct_count = ctx->new_count; size_t struct_alignment = ctx->struct_alignment; ctx->new_count = 1; ++ts; if (*ts != '{') { PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ ctx->enc_count = 0; ctx->struct_alignment = 0; ++ts; ts_after_sub = ts; for (i = 0; i != struct_count; ++i) { ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); if (!ts_after_sub) return NULL; } ts = ts_after_sub; if (struct_alignment) ctx->struct_alignment = struct_alignment; } break; case '}': /* end of substruct; either repeat or move on */ { size_t alignment = ctx->struct_alignment; ++ts; if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ if (alignment && ctx->fmt_offset % alignment) { ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); } } return ts; case 'x': if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->fmt_offset += ctx->new_count; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->enc_packmode = ctx->new_packmode; ++ts; break; case 'Z': got_Z = 1; ++ts; if (*ts != 'f' && *ts != 'd' && *ts != 'g') { __Pyx_BufFmt_RaiseUnexpectedChar('Z'); return NULL; } /* fall through */ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 's': case 'p': if (ctx->enc_type == *ts && got_Z == ctx->is_complex && ctx->enc_packmode == ctx->new_packmode) { ctx->enc_count += ctx->new_count; } else { if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_count = ctx->new_count; ctx->enc_packmode = ctx->new_packmode; ctx->enc_type = *ts; ctx->is_complex = got_Z; } ++ts; ctx->new_count = 1; got_Z = 0; break; case ':': ++ts; while(*ts != ':') ++ts; ++ts; break; case '(': if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; break; default: { int number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; ctx->new_count = (size_t)number; } } } } static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { buf->buf = NULL; buf->obj = NULL; buf->strides = __Pyx_zeros; buf->shape = __Pyx_zeros; buf->suboffsets = __Pyx_minusones; } static CYTHON_INLINE int __Pyx_GetBufferAndValidate( Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) { if (obj == Py_None || obj == NULL) { __Pyx_ZeroBuffer(buf); return 0; } buf->buf = NULL; if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; if (buf->ndim != nd) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", nd, buf->ndim); goto fail; } if (!cast) { __Pyx_BufFmt_Context ctx; __Pyx_BufFmt_Init(&ctx, stack, dtype); if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; } if ((unsigned)buf->itemsize != dtype->size) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", buf->itemsize, (buf->itemsize > 1) ? "s" : "", dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); goto fail; } if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; return 0; fail:; __Pyx_ZeroBuffer(buf); return -1; } static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { if (info->buf == NULL) return; if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; __Pyx_ReleaseBuffer(info); } static void __Pyx_RaiseBufferFallbackError(void) { PyErr_Format(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint32_t) == sizeof(char)) || (sizeof(uint32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint32_t) == sizeof(int)) || (sizeof(uint32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t val) { const int8_t neg_one = (int8_t)-1, const_zero = (int8_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int8_t) == sizeof(char)) || (sizeof(int8_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int8_t) == sizeof(int)) || (sizeof(int8_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int8_t), little, !is_unsigned); } } #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { CYTHON_UNUSED PyObject *getbuffer_cobj; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, "__pyx_getbuffer"))) { getbufferproc func; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)"); #else func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj); #endif Py_DECREF(getbuffer_cobj); if (!func) goto fail; return func(obj, view, flags); } else { PyErr_Clear(); } #endif PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name); #if PY_VERSION_HEX < 0x02060000 fail: #endif return -1; } static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyObject *obj = view->obj; CYTHON_UNUSED PyObject *releasebuffer_cobj; if (!obj) return; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) { PyBuffer_Release(view); return; } #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, "__pyx_releasebuffer"))) { releasebufferproc func; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)"); #else func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj); #endif Py_DECREF(releasebuffer_cobj); if (!func) goto fail; func(obj, view); return; } else { PyErr_Clear(); } #endif goto nofail; #if PY_VERSION_HEX < 0x02060000 fail: #endif PyErr_WriteUnraisable(obj); nofail: Py_DECREF(obj); view->obj = NULL; } #endif /* PY_MAJOR_VERSION < 3 */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint32_t) == sizeof(char)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint32_t) == sizeof(short)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint32_t) == sizeof(int)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint32_t) == sizeof(long)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else uint32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (uint32_t)-1; } } #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); } #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return x + y*(__pyx_t_float_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { __pyx_t_float_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrtf(z.real*z.real + z.imag*z.imag); #else return hypotf(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { float denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(a, a); case 3: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, a); case 4: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_absf(a); theta = atan2f(a.imag, a.real); } lnr = logf(r); z_r = expf(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cosf(z_theta); z.imag = z_r * sinf(z_theta); return z; } #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); } #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return x + y*(__pyx_t_double_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { __pyx_t_double_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrt(z.real*z.real + z.imag*z.imag); #else return hypot(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { double denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(a, a); case 3: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, a); case 4: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_abs(a); theta = atan2(a.imag, a.real); } lnr = log(r); z_r = exp(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cos(z_theta); z.imag = z_r * sin(z_theta); return z; } #endif #endif static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; Py_ssize_t basicsize; #ifdef Py_LIMITED_API PyObject *py_basicsize; #endif py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ pykdtree-0.2/pykdtree/test_tree.py0000644000767500076750000003023012151640733017025 0ustar esnesn00000000000000import numpy as np from pykdtree.kdtree import KDTree data_pts_real = np.array([[ 790535.062, -369324.656, 6310963.5 ], [ 790024.312, -365155.688, 6311270. ], [ 789515.75 , -361009.469, 6311572. ], [ 789011. , -356886.562, 6311869.5 ], [ 788508.438, -352785.969, 6312163. ], [ 788007.25 , -348707.219, 6312452. ], [ 787509.188, -344650.875, 6312737. ], [ 787014.438, -340616.906, 6313018. ], [ 786520.312, -336604.156, 6313294.5 ], [ 786030.312, -332613.844, 6313567. ], [ 785541.562, -328644.375, 6313835.5 ], [ 785054.75 , -324696.031, 6314100.5 ], [ 784571.188, -320769.5 , 6314361.5 ], [ 784089.312, -316863.562, 6314618.5 ], [ 783610.562, -312978.719, 6314871.5 ], [ 783133. , -309114.312, 6315121. ], [ 782658.25 , -305270.531, 6315367. ], [ 782184.312, -301446.719, 6315609. ], [ 781715.062, -297643.844, 6315847.5 ], [ 781246.188, -293860.281, 6316083. ], [ 780780.125, -290096.938, 6316314.5 ], [ 780316.312, -286353.469, 6316542.5 ], [ 779855.625, -282629.75 , 6316767.5 ], [ 779394.75 , -278924.781, 6316988.5 ], [ 778937.312, -275239.625, 6317206.5 ], [ 778489.812, -271638.094, 6317418. ], [ 778044.688, -268050.562, 6317626. ], [ 777599.688, -264476.75 , 6317831.5 ], [ 777157.625, -260916.859, 6318034. ], [ 776716.688, -257371.125, 6318233.5 ], [ 776276.812, -253838.891, 6318430.5 ], [ 775838.125, -250320.266, 6318624.5 ], [ 775400.75 , -246815.516, 6318816.5 ], [ 774965.312, -243324.953, 6319005. ], [ 774532.062, -239848.25 , 6319191. ], [ 774100.25 , -236385.516, 6319374.5 ], [ 773667.875, -232936.016, 6319555.5 ], [ 773238.562, -229500.812, 6319734. ], [ 772810.938, -226079.562, 6319909.5 ], [ 772385.25 , -222672.219, 6320082.5 ], [ 771960. , -219278.5 , 6320253. ], [ 771535.938, -215898.609, 6320421. ], [ 771114. , -212532.625, 6320587. ], [ 770695. , -209180.859, 6320749.5 ], [ 770275.25 , -205842.562, 6320910.5 ], [ 769857.188, -202518.125, 6321068.5 ], [ 769442.312, -199207.844, 6321224.5 ], [ 769027.812, -195911.203, 6321378. ], [ 768615.938, -192628.859, 6321529. ], [ 768204.688, -189359.969, 6321677.5 ], [ 767794.062, -186104.844, 6321824. ], [ 767386.25 , -182864.016, 6321968.5 ], [ 766980.062, -179636.969, 6322110. ], [ 766575.625, -176423.75 , 6322249.5 ], [ 766170.688, -173224.172, 6322387. ], [ 765769.812, -170038.984, 6322522.5 ], [ 765369.5 , -166867.312, 6322655. ], [ 764970.562, -163709.594, 6322786. ], [ 764573. , -160565.781, 6322914.5 ], [ 764177.75 , -157435.938, 6323041. ], [ 763784.188, -154320.062, 6323165.5 ], [ 763392.375, -151218.047, 6323288. ], [ 763000.938, -148129.734, 6323408. ], [ 762610.812, -145055.344, 6323526.5 ], [ 762224.188, -141995.141, 6323642.5 ], [ 761847.188, -139025.734, 6323754. ], [ 761472.375, -136066.312, 6323863.5 ], [ 761098.125, -133116.859, 6323971.5 ], [ 760725.25 , -130177.484, 6324077.5 ], [ 760354. , -127247.984, 6324181.5 ], [ 759982.812, -124328.336, 6324284.5 ], [ 759614. , -121418.844, 6324385. ], [ 759244.688, -118519.102, 6324484.5 ], [ 758877.125, -115629.305, 6324582. ], [ 758511.562, -112749.648, 6324677.5 ], [ 758145.625, -109879.82 , 6324772.5 ], [ 757781.688, -107019.953, 6324865. ], [ 757418.438, -104170.047, 6324956. ], [ 757056.562, -101330.125, 6325045.5 ], [ 756697. , -98500.266, 6325133.5 ], [ 756337.375, -95680.289, 6325219.5 ], [ 755978.062, -92870.148, 6325304.5 ], [ 755621.188, -90070.109, 6325387.5 ], [ 755264.625, -87280.008, 6325469. ], [ 754909.188, -84499.828, 6325549. ], [ 754555.062, -81729.609, 6325628. ], [ 754202.938, -78969.43 , 6325705. ], [ 753850.688, -76219.133, 6325781. ], [ 753499.875, -73478.836, 6325855. ], [ 753151.375, -70748.578, 6325927.5 ], [ 752802.312, -68028.188, 6325999. ], [ 752455.75 , -65317.871, 6326068.5 ], [ 752108.625, -62617.344, 6326137.5 ], [ 751764.125, -59926.969, 6326204.5 ], [ 751420.125, -57246.434, 6326270. ], [ 751077.438, -54575.902, 6326334.5 ], [ 750735.312, -51915.363, 6326397.5 ], [ 750396.188, -49264.852, 6326458.5 ], [ 750056.375, -46624.227, 6326519. ], [ 749718.875, -43993.633, 6326578. ]]) def test1d(): data_pts = np.arange(1000) kdtree = KDTree(data_pts, leafsize=15) query_pts = np.arange(400, 300, -10) dist, idx = kdtree.query(query_pts) assert idx[0] == 400 assert dist[0] == 0 assert idx[1] == 390 def test3d(): #7, 93, 45 query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]]) kdtree = KDTree(data_pts_real) dist, idx = kdtree.query(query_pts, sqr_dists=True) epsilon = 1e-5 assert idx[0] == 7 assert idx[1] == 93 assert idx[2] == 45 assert dist[0] == 0 assert abs(dist[1] - 3.) < epsilon * dist[1] assert abs(dist[2] - 20001.) < epsilon * dist[2] def test3d_float32(): #7, 93, 45 query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]], dtype=np.float32) kdtree = KDTree(data_pts_real.astype(np.float32)) dist, idx = kdtree.query(query_pts, sqr_dists=True) epsilon = 1e-5 assert idx[0] == 7 assert idx[1] == 93 assert idx[2] == 45 assert dist[0] == 0 assert abs(dist[1] - 3.) < epsilon * dist[1] assert abs(dist[2] - 20001.) < epsilon * dist[2] assert kdtree.data_pts.dtype == np.float32 def test3d_float32_mismatch(): #7, 93, 45 query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]], dtype=np.float32) kdtree = KDTree(data_pts_real) dist, idx = kdtree.query(query_pts, sqr_dists=True) def test3d_float32_mismatch2(): #7, 93, 45 query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]]) kdtree = KDTree(data_pts_real.astype(np.float32)) try: dist, idx = kdtree.query(query_pts, sqr_dists=True) assert False except TypeError: assert True def test3d_8n(): query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]]) kdtree = KDTree(data_pts_real) dist, idx = kdtree.query(query_pts, k=8) exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, 8.17063009e+03, 1.20904577e+04, 1.22902057e+04, 1.60775136e+04], [ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, 5.43793210e+03, 8.07855631e+03, 8.17119970e+03, 1.07513693e+04], [ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, 6.81038455e+03, 9.89140135e+03, 1.01918659e+04, 1.31892516e+04]]) exp_idx = np.array([[ 7, 8, 6, 9, 5, 10, 4, 11], [93, 94, 92, 95, 91, 96, 90, 97], [45, 46, 44, 47, 43, 48, 42, 49]]) assert np.array_equal(idx, exp_idx) assert np.allclose(dist, exp_dist) def test3d_8n_ub(): query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]]) kdtree = KDTree(data_pts_real) dist, idx = kdtree.query(query_pts, k=8, distance_upper_bound=10e3, sqr_dists=False) exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, 8.17063009e+03, np.Inf, np.Inf, np.Inf], [ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, 5.43793210e+03, 8.07855631e+03, 8.17119970e+03, np.Inf], [ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, 6.81038455e+03, 9.89140135e+03, np.Inf, np.Inf]]) n = 100 exp_idx = np.array([[ 7, 8, 6, 9, 5, n, n, n], [93, 94, 92, 95, 91, 96, 90, n], [45, 46, 44, 47, 43, 48, n, n]]) assert np.array_equal(idx, exp_idx) assert np.allclose(dist, exp_dist) def test3d_8n_ub_leaf20(): query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]]) kdtree = KDTree(data_pts_real, leafsize=20) dist, idx = kdtree.query(query_pts, k=8, distance_upper_bound=10e3, sqr_dists=False) exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, 8.17063009e+03, np.Inf, np.Inf, np.Inf], [ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, 5.43793210e+03, 8.07855631e+03, 8.17119970e+03, np.Inf], [ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, 6.81038455e+03, 9.89140135e+03, np.Inf, np.Inf]]) n = 100 exp_idx = np.array([[ 7, 8, 6, 9, 5, n, n, n], [93, 94, 92, 95, 91, 96, 90, n], [45, 46, 44, 47, 43, 48, n, n]]) assert np.array_equal(idx, exp_idx) assert np.allclose(dist, exp_dist) def test3d_8n_ub_eps(): query_pts = np.array([[ 787014.438, -340616.906, 6313018.], [751763.125, -59925.969, 6326205.5], [769957.188, -202418.125, 6321069.5]]) kdtree = KDTree(data_pts_real) dist, idx = kdtree.query(query_pts, k=8, eps=0.1, distance_upper_bound=10e3, sqr_dists=False) exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, 8.17063009e+03, np.Inf, np.Inf, np.Inf], [ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, 5.43793210e+03, 8.07855631e+03, 8.17119970e+03, np.Inf], [ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, 6.81038455e+03, 9.89140135e+03, np.Inf, np.Inf]]) n = 100 exp_idx = np.array([[ 7, 8, 6, 9, 5, n, n, n], [93, 94, 92, 95, 91, 96, 90, n], [45, 46, 44, 47, 43, 48, n, n]]) assert np.array_equal(idx, exp_idx) assert np.allclose(dist, exp_dist) pykdtree-0.2/MANIFEST.in0000644000767500076750000000004412151640733014364 0ustar esnesn00000000000000exclude pykdtree/render_template.py pykdtree-0.2/setup.py0000644000767500076750000000525112153111375014342 0ustar esnesn00000000000000#pykdtree, Fast kd-tree implementation with OpenMP-enabled queries # #Copyright (C) 2013 Esben S. Nielsen # #This program is free software: you can redistribute it and/or modify #it under the terms of the GNU General Public License as published by #the Free Software Foundation, either version 3 of the License, or #(at your option) any later version. # #This program is distributed in the hope that it will be useful, #but WITHOUT ANY WARRANTY; without even the implied warranty of #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #GNU General Public License for more details. # #You should have received a copy of the GNU General Public License #along with this program. If not, see . import os from setuptools import setup, Extension from setuptools.command.build_ext import build_ext import numpy # Get OpenMP setting from environment try: use_omp = int(os.environ['USE_OMP']) except KeyError: use_omp = True # Custom builder to handler compiler flags. Edit if needed. class build_ext_subclass(build_ext): def build_extensions(self): comp = self.compiler.compiler_type if comp in ('unix', 'cygwin', 'mingw32'): # Check if build is with OpenMP if use_omp: extra_compile_args = ['-std=c99', '-O3', '-fopenmp'] extra_link_args=['-lgomp'] else: extra_compile_args = ['-std=c99', '-O3'] extra_link_args = [] else: # Add support for more compilers here raise ValueError(('Compiler flags undefined for %s.', 'Please modify setup.py and add compiler flags') % comp) self.extensions[0].extra_compile_args = extra_compile_args self.extensions[0].extra_link_args = extra_link_args build_ext.build_extensions(self) setup( name='pykdtree', version=0.2, description='Fast kd-tree implementation with OpenMP-enabled queries', author='Esben S. Nielsen', author_email='esn@dmi.dk', packages = ['pykdtree'], install_requires=['numpy'], ext_modules = [Extension('pykdtree.kdtree', ['pykdtree/kdtree.c', 'pykdtree/_kdtree_core.c'], include_dirs=[numpy.get_include()])], cmdclass = {'build_ext': build_ext_subclass }, classifiers=[ 'Development Status :: 4 - Beta', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Programming Language :: Python', 'Operating System :: OS Independent', 'Intended Audience :: Science/Research', 'Topic :: Scientific/Engineering' ] ) pykdtree-0.2/PKG-INFO0000644000767500076750000000104012153111634013713 0ustar esnesn00000000000000Metadata-Version: 1.1 Name: pykdtree Version: 0.2 Summary: Fast kd-tree implementation with OpenMP-enabled queries Home-page: UNKNOWN Author: Esben S. Nielsen Author-email: esn@dmi.dk License: UNKNOWN Description: UNKNOWN Platform: UNKNOWN Classifier: Development Status :: 4 - Beta Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) Classifier: Programming Language :: Python Classifier: Operating System :: OS Independent Classifier: Intended Audience :: Science/Research Classifier: Topic :: Scientific/Engineering pykdtree-0.2/pykdtree.egg-info/0000755000767500076750000000000012153111634016144 5ustar esnesn00000000000000pykdtree-0.2/pykdtree.egg-info/requires.txt0000644000767500076750000000000512153111633020536 0ustar esnesn00000000000000numpypykdtree-0.2/pykdtree.egg-info/PKG-INFO0000644000767500076750000000104012153111633017233 0ustar esnesn00000000000000Metadata-Version: 1.1 Name: pykdtree Version: 0.2 Summary: Fast kd-tree implementation with OpenMP-enabled queries Home-page: UNKNOWN Author: Esben S. Nielsen Author-email: esn@dmi.dk License: UNKNOWN Description: UNKNOWN Platform: UNKNOWN Classifier: Development Status :: 4 - Beta Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) Classifier: Programming Language :: Python Classifier: Operating System :: OS Independent Classifier: Intended Audience :: Science/Research Classifier: Topic :: Scientific/Engineering pykdtree-0.2/pykdtree.egg-info/top_level.txt0000644000767500076750000000001112153111633020665 0ustar esnesn00000000000000pykdtree pykdtree-0.2/pykdtree.egg-info/dependency_links.txt0000644000767500076750000000000112153111633022211 0ustar esnesn00000000000000 pykdtree-0.2/pykdtree.egg-info/SOURCES.txt0000644000767500076750000000043112153111634020026 0ustar esnesn00000000000000MANIFEST.in README setup.cfg setup.py pykdtree/__init__.py pykdtree/_kdtree_core.c pykdtree/kdtree.c pykdtree/test_tree.py pykdtree.egg-info/PKG-INFO pykdtree.egg-info/SOURCES.txt pykdtree.egg-info/dependency_links.txt pykdtree.egg-info/requires.txt pykdtree.egg-info/top_level.txtpykdtree-0.2/setup.cfg0000644000767500076750000000012612153111634014443 0ustar esnesn00000000000000[nosetests] nocapture = 1 [egg_info] tag_build = tag_date = 0 tag_svn_revision = 0 pykdtree-0.2/README0000777000767500076750000000000012104654020015164 2README.rstustar esnesn00000000000000