[yt-svn] commit/yt: 2 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Jun 14 14:14:46 PDT 2017
2 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/bbce7672522d/
Changeset: bbce7672522d
User: ngoldbaum
Date: 2017-05-29 16:30:11+00:00
Summary: remove unused kdtree and parallel components from grid_traversal.pyx
Affected #: 8 files
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd setup.py
--- a/setup.py
+++ b/setup.py
@@ -154,14 +154,10 @@
depends=["yt/utilities/lib/origami_tags.h"]),
Extension("yt.utilities.lib.grid_traversal",
["yt/utilities/lib/grid_traversal.pyx",
- "yt/utilities/lib/fixed_interpolator.c",
- "yt/utilities/lib/kdtree.c"],
+ "yt/utilities/lib/fixed_interpolator.c"],
include_dirs=["yt/utilities/lib/"],
libraries=std_libs,
- extra_compile_args=omp_args,
- extra_link_args=omp_args,
- depends=["yt/utilities/lib/kdtree.h",
- "yt/utilities/lib/fixed_interpolator.h"]),
+ depends=["yt/utilities/lib/fixed_interpolator.h"]),
Extension("yt.utilities.lib.image_samplers",
["yt/utilities/lib/image_samplers.pyx",
"yt/utilities/lib/fixed_interpolator.c"],
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/utilities/lib/grid_traversal.pyx
--- a/yt/utilities/lib/grid_traversal.pyx
+++ b/yt/utilities/lib/grid_traversal.pyx
@@ -26,8 +26,6 @@
FIT_eval_transfer_with_light
from fixed_interpolator cimport *
-from cython.parallel import prange, parallel, threadid
-
DEF Nch = 4
@cython.boundscheck(False)
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/utilities/lib/image_samplers.pxd
--- a/yt/utilities/lib/image_samplers.pxd
+++ b/yt/utilities/lib/image_samplers.pxd
@@ -17,7 +17,6 @@
import numpy as np
cimport numpy as np
cimport cython
-cimport kdtree_utils
from .volume_container cimport VolumeContainer
from .partitioned_grid cimport PartitionedGrid
@@ -85,7 +84,6 @@
cdef VolumeRenderAccumulator *vra
cdef public object tf_obj
cdef public object my_field_tables
- cdef kdtree_utils.kdtree **trees
cdef object tree_containers
cdef class LightSourceRenderSampler(ImageSampler):
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/utilities/lib/image_samplers.pyx
--- a/yt/utilities/lib/image_samplers.pyx
+++ b/yt/utilities/lib/image_samplers.pyx
@@ -51,7 +51,6 @@
np.float64_t star_coeff
np.float64_t star_er
np.float64_t star_sigma_num
- kdtree_utils.kdtree *star_list
np.float64_t *light_dir
np.float64_t *light_rgba
int grey_opacity
@@ -295,7 +294,7 @@
np.ndarray[np.float64_t, ndim=1] y_vec,
np.ndarray[np.float64_t, ndim=1] width,
tf_obj, n_samples = 10,
- star_list = None, **kwargs):
+ **kwargs):
ImageSampler.__init__(self, vp_pos, vp_dir, center, bounds, image,
x_vec, y_vec, width, **kwargs)
cdef int i
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/utilities/lib/kdtree.c
--- a/yt/utilities/lib/kdtree.c
+++ /dev/null
@@ -1,761 +0,0 @@
-/*
-This file is part of ``kdtree'', a library for working with kd-trees.
-Copyright (C) 2007-2011 John Tsiombikas <nuclear at siggraph.org>
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-3. The name of the author may not be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
-OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
-OF SUCH DAMAGE.
-*/
-/* single nearest neighbor search written by Tamas Nepusz <tamas at cs.rhul.ac.uk> */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include "kdtree.h"
-
-#ifdef MS_WIN32
-#include <malloc.h>
-#endif
-
-#ifdef USE_LIST_NODE_ALLOCATOR
-
-#ifndef NO_PTHREADS
-#include <pthread.h>
-#else
-
-#ifndef I_WANT_THREAD_BUGS
-#error "You are compiling with the fast list node allocator, with pthreads disabled! This WILL break if used from multiple threads."
-#endif /* I want thread bugs */
-
-#endif /* pthread support */
-#endif /* use list node allocator */
-
-struct kdhyperrect {
- int dim;
- npy_float64 *min, *max; /* minimum/maximum coords */
-};
-
-struct kdnode {
- npy_float64 *pos;
- int dir;
- void *data;
-
- struct kdnode *left, *right; /* negative/positive side */
-};
-
-struct res_node {
- struct kdnode *item;
- npy_float64 dist_sq;
- struct res_node *next;
-};
-
-struct kdtree {
- int dim;
- struct kdnode *root;
- struct kdhyperrect *rect;
- void (*destr)(void*);
-};
-
-struct kdres {
- struct kdtree *tree;
- struct res_node *rlist, *riter;
- int size;
-};
-
-#define SQ(x) ((x) * (x))
-
-
-static void clear_rec(struct kdnode *node, void (*destr)(void*));
-static int insert_rec(struct kdnode **node, const npy_float64 *pos, void *data, int dir, int dim);
-static int rlist_insert(struct res_node *list, struct kdnode *item, npy_float64 dist_sq);
-static void clear_results(struct kdres *set);
-
-static struct kdhyperrect* hyperrect_create(int dim, const npy_float64 *min, const npy_float64 *max);
-static void hyperrect_free(struct kdhyperrect *rect);
-static struct kdhyperrect* hyperrect_duplicate(const struct kdhyperrect *rect);
-static void hyperrect_extend(struct kdhyperrect *rect, const npy_float64 *pos);
-static npy_float64 hyperrect_dist_sq(struct kdhyperrect *rect, const npy_float64 *pos);
-
-#ifdef USE_LIST_NODE_ALLOCATOR
-static struct res_node *alloc_resnode(void);
-static void free_resnode(struct res_node*);
-#else
-#define alloc_resnode() malloc(sizeof(struct res_node))
-#define free_resnode(n) free(n)
-#endif
-
-
-
-struct kdtree *kd_create(int k)
-{
- struct kdtree *tree;
-
- if(!(tree = malloc(sizeof *tree))) {
- return 0;
- }
-
- tree->dim = k;
- tree->root = 0;
- tree->destr = 0;
- tree->rect = 0;
-
- return tree;
-}
-
-void kd_free(struct kdtree *tree)
-{
- if(tree) {
- kd_clear(tree);
- free(tree);
- }
-}
-
-static void clear_rec(struct kdnode *node, void (*destr)(void*))
-{
- if(!node) return;
-
- clear_rec(node->left, destr);
- clear_rec(node->right, destr);
-
- if(destr) {
- destr(node->data);
- }
- free(node->pos);
- free(node);
-}
-
-void kd_clear(struct kdtree *tree)
-{
- clear_rec(tree->root, tree->destr);
- tree->root = 0;
-
- if (tree->rect) {
- hyperrect_free(tree->rect);
- tree->rect = 0;
- }
-}
-
-void kd_data_destructor(struct kdtree *tree, void (*destr)(void*))
-{
- tree->destr = destr;
-}
-
-
-static int insert_rec(struct kdnode **nptr, const npy_float64 *pos, void *data, int dir, int dim)
-{
- int new_dir;
- struct kdnode *node;
-
- if(!*nptr) {
- if(!(node = malloc(sizeof *node))) {
- return -1;
- }
- if(!(node->pos = malloc(dim * sizeof *node->pos))) {
- free(node);
- return -1;
- }
- memcpy(node->pos, pos, dim * sizeof *node->pos);
- node->data = data;
- node->dir = dir;
- node->left = node->right = 0;
- *nptr = node;
- return 0;
- }
-
- node = *nptr;
- new_dir = (node->dir + 1) % dim;
- if(pos[node->dir] < node->pos[node->dir]) {
- return insert_rec(&(*nptr)->left, pos, data, new_dir, dim);
- }
- return insert_rec(&(*nptr)->right, pos, data, new_dir, dim);
-}
-
-int kd_insert(struct kdtree *tree, const npy_float64 *pos, void *data)
-{
- if (insert_rec(&tree->root, pos, data, 0, tree->dim)) {
- return -1;
- }
-
- if (tree->rect == 0) {
- tree->rect = hyperrect_create(tree->dim, pos, pos);
- } else {
- hyperrect_extend(tree->rect, pos);
- }
-
- return 0;
-}
-
-int kd_insertf(struct kdtree *tree, const float *pos, void *data)
-{
- static npy_float64 sbuf[16];
- npy_float64 *bptr, *buf = 0;
- int res, dim = tree->dim;
-
- if(dim > 16) {
-#ifndef NO_ALLOCA
- if(dim <= 256)
- bptr = buf = alloca(dim * sizeof *bptr);
- else
-#endif
- if(!(bptr = buf = malloc(dim * sizeof *bptr))) {
- return -1;
- }
- } else {
- bptr = sbuf;
- }
-
- while(dim-- > 0) {
- *bptr++ = *pos++;
- }
-
- res = kd_insert(tree, buf, data);
-#ifndef NO_ALLOCA
- if(tree->dim > 256)
-#else
- if(tree->dim > 16)
-#endif
- free(buf);
- return res;
-}
-
-int kd_insert3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, void *data)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_insert(tree, buf, data);
-}
-
-int kd_insert3f(struct kdtree *tree, float x, float y, float z, void *data)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_insert(tree, buf, data);
-}
-
-static int find_nearest(struct kdnode *node, const npy_float64 *pos, npy_float64 range, struct res_node *list, int ordered, int dim)
-{
- npy_float64 dist_sq, dx;
- int i, ret, added_res = 0;
-
- if(!node) return 0;
-
- dist_sq = 0;
- for(i=0; i<dim; i++) {
- dist_sq += SQ(node->pos[i] - pos[i]);
- }
- if(dist_sq <= SQ(range)) {
- if(rlist_insert(list, node, ordered ? dist_sq : -1.0) == -1) {
- return -1;
- }
- added_res = 1;
- }
-
- dx = pos[node->dir] - node->pos[node->dir];
-
- ret = find_nearest(dx <= 0.0 ? node->left : node->right, pos, range, list, ordered, dim);
- if(ret >= 0 && fabs(dx) < range) {
- added_res += ret;
- ret = find_nearest(dx <= 0.0 ? node->right : node->left, pos, range, list, ordered, dim);
- }
- if(ret == -1) {
- return -1;
- }
- added_res += ret;
-
- return added_res;
-}
-
-static void kd_nearest_i(struct kdnode *node, const npy_float64 *pos, struct kdnode **result, npy_float64 *result_dist_sq, struct kdhyperrect* rect)
-{
- int dir = node->dir;
- int i, side;
- npy_float64 dummy, dist_sq;
- struct kdnode *nearer_subtree, *farther_subtree;
- npy_float64 *nearer_hyperrect_coord, *farther_hyperrect_coord;
-
- /* Decide whether to go left or right in the tree */
- dummy = pos[dir] - node->pos[dir];
- if (dummy <= 0) {
- nearer_subtree = node->left;
- farther_subtree = node->right;
- nearer_hyperrect_coord = rect->max + dir;
- farther_hyperrect_coord = rect->min + dir;
- side = 0;
- } else {
- nearer_subtree = node->right;
- farther_subtree = node->left;
- nearer_hyperrect_coord = rect->min + dir;
- farther_hyperrect_coord = rect->max + dir;
- side = 1;
- }
-
- if (nearer_subtree) {
- /* Slice the hyperrect to get the hyperrect of the nearer subtree */
- dummy = *nearer_hyperrect_coord;
- *nearer_hyperrect_coord = node->pos[dir];
- /* Recurse down into nearer subtree */
- kd_nearest_i(nearer_subtree, pos, result, result_dist_sq, rect);
- /* Undo the slice */
- *nearer_hyperrect_coord = dummy;
- }
-
- /* Check the distance of the point at the current node, compare it
- * with our best so far */
- dist_sq = 0;
- for(i=0; i < rect->dim; i++) {
- dist_sq += SQ(node->pos[i] - pos[i]);
- }
- if (dist_sq < *result_dist_sq) {
- *result = node;
- *result_dist_sq = dist_sq;
- }
-
- if (farther_subtree) {
- /* Get the hyperrect of the farther subtree */
- dummy = *farther_hyperrect_coord;
- *farther_hyperrect_coord = node->pos[dir];
- /* Check if we have to recurse down by calculating the closest
- * point of the hyperrect and see if it's closer than our
- * minimum distance in result_dist_sq. */
- if (hyperrect_dist_sq(rect, pos) < *result_dist_sq) {
- /* Recurse down into farther subtree */
- kd_nearest_i(farther_subtree, pos, result, result_dist_sq, rect);
- }
- /* Undo the slice on the hyperrect */
- *farther_hyperrect_coord = dummy;
- }
-}
-
-struct kdres *kd_nearest(struct kdtree *kd, const npy_float64 *pos)
-{
- struct kdhyperrect *rect;
- struct kdnode *result;
- struct kdres *rset;
- npy_float64 dist_sq;
- int i;
-
- if (!kd) return 0;
- if (!kd->rect) return 0;
-
- /* Allocate result set */
- if(!(rset = malloc(sizeof *rset))) {
- return 0;
- }
- if(!(rset->rlist = alloc_resnode())) {
- free(rset);
- return 0;
- }
- rset->rlist->next = 0;
- rset->tree = kd;
-
- /* Duplicate the bounding hyperrectangle, we will work on the copy */
- if (!(rect = hyperrect_duplicate(kd->rect))) {
- kd_res_free(rset);
- return 0;
- }
-
- /* Our first guesstimate is the root node */
- result = kd->root;
- dist_sq = 0;
- for (i = 0; i < kd->dim; i++)
- dist_sq += SQ(result->pos[i] - pos[i]);
-
- /* Search for the nearest neighbour recursively */
- kd_nearest_i(kd->root, pos, &result, &dist_sq, rect);
-
- /* Free the copy of the hyperrect */
- hyperrect_free(rect);
-
- /* Store the result */
- if (result) {
- if (rlist_insert(rset->rlist, result, -1.0) == -1) {
- kd_res_free(rset);
- return 0;
- }
- rset->size = 1;
- kd_res_rewind(rset);
- return rset;
- } else {
- kd_res_free(rset);
- return 0;
- }
-}
-
-struct kdres *kd_nearestf(struct kdtree *tree, const float *pos)
-{
- static npy_float64 sbuf[16];
- npy_float64 *bptr, *buf = 0;
- int dim = tree->dim;
- struct kdres *res;
-
- if(dim > 16) {
-#ifndef NO_ALLOCA
- if(dim <= 256)
- bptr = buf = alloca(dim * sizeof *bptr);
- else
-#endif
- if(!(bptr = buf = malloc(dim * sizeof *bptr))) {
- return 0;
- }
- } else {
- bptr = sbuf;
- }
-
- while(dim-- > 0) {
- *bptr++ = *pos++;
- }
-
- res = kd_nearest(tree, buf);
-#ifndef NO_ALLOCA
- if(tree->dim > 256)
-#else
- if(tree->dim > 16)
-#endif
- free(buf);
- return res;
-}
-
-struct kdres *kd_nearest3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z)
-{
- npy_float64 pos[3];
- pos[0] = x;
- pos[1] = y;
- pos[2] = z;
- return kd_nearest(tree, pos);
-}
-
-struct kdres *kd_nearest3f(struct kdtree *tree, float x, float y, float z)
-{
- npy_float64 pos[3];
- pos[0] = x;
- pos[1] = y;
- pos[2] = z;
- return kd_nearest(tree, pos);
-}
-
-struct kdres *kd_nearest_range(struct kdtree *kd, const npy_float64 *pos, npy_float64 range)
-{
- int ret;
- struct kdres *rset;
-
- if(!(rset = malloc(sizeof *rset))) {
- return 0;
- }
- if(!(rset->rlist = alloc_resnode())) {
- free(rset);
- return 0;
- }
- rset->rlist->next = 0;
- rset->tree = kd;
-
- if((ret = find_nearest(kd->root, pos, range, rset->rlist, 0, kd->dim)) == -1) {
- kd_res_free(rset);
- return 0;
- }
- rset->size = ret;
- kd_res_rewind(rset);
- return rset;
-}
-
-struct kdres *kd_nearest_rangef(struct kdtree *kd, const float *pos, float range)
-{
- static npy_float64 sbuf[16];
- npy_float64 *bptr, *buf = 0;
- int dim = kd->dim;
- struct kdres *res;
-
- if(dim > 16) {
-#ifndef NO_ALLOCA
- if(dim <= 256)
- bptr = buf = alloca(dim * sizeof *bptr);
- else
-#endif
- if(!(bptr = buf = malloc(dim * sizeof *bptr))) {
- return 0;
- }
- } else {
- bptr = sbuf;
- }
-
- while(dim-- > 0) {
- *bptr++ = *pos++;
- }
-
- res = kd_nearest_range(kd, buf, range);
-#ifndef NO_ALLOCA
- if(kd->dim > 256)
-#else
- if(kd->dim > 16)
-#endif
- free(buf);
- return res;
-}
-
-struct kdres *kd_nearest_range3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, npy_float64 range)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_nearest_range(tree, buf, range);
-}
-
-struct kdres *kd_nearest_range3f(struct kdtree *tree, float x, float y, float z, float range)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_nearest_range(tree, buf, range);
-}
-
-void kd_res_free(struct kdres *rset)
-{
- clear_results(rset);
- free_resnode(rset->rlist);
- free(rset);
-}
-
-int kd_res_size(struct kdres *set)
-{
- return (set->size);
-}
-
-void kd_res_rewind(struct kdres *rset)
-{
- rset->riter = rset->rlist->next;
-}
-
-int kd_res_end(struct kdres *rset)
-{
- return rset->riter == 0;
-}
-
-int kd_res_next(struct kdres *rset)
-{
- rset->riter = rset->riter->next;
- return rset->riter != 0;
-}
-
-void *kd_res_item(struct kdres *rset, npy_float64 *pos)
-{
- if(rset->riter) {
- if(pos) {
- memcpy(pos, rset->riter->item->pos, rset->tree->dim * sizeof *pos);
- }
- return rset->riter->item->data;
- }
- return 0;
-}
-
-void *kd_res_itemf(struct kdres *rset, float *pos)
-{
- if(rset->riter) {
- if(pos) {
- int i;
- for(i=0; i<rset->tree->dim; i++) {
- pos[i] = rset->riter->item->pos[i];
- }
- }
- return rset->riter->item->data;
- }
- return 0;
-}
-
-void *kd_res_item3(struct kdres *rset, npy_float64 *x, npy_float64 *y, npy_float64 *z)
-{
- if(rset->riter) {
- if(*x) *x = rset->riter->item->pos[0];
- if(*y) *y = rset->riter->item->pos[1];
- if(*z) *z = rset->riter->item->pos[2];
- }
- return 0;
-}
-
-void *kd_res_item3f(struct kdres *rset, float *x, float *y, float *z)
-{
- if(rset->riter) {
- if(*x) *x = rset->riter->item->pos[0];
- if(*y) *y = rset->riter->item->pos[1];
- if(*z) *z = rset->riter->item->pos[2];
- }
- return 0;
-}
-
-void *kd_res_item_data(struct kdres *set)
-{
- return kd_res_item(set, 0);
-}
-
-/* ---- hyperrectangle helpers ---- */
-static struct kdhyperrect* hyperrect_create(int dim, const npy_float64 *min, const npy_float64 *max)
-{
- size_t size = dim * sizeof(npy_float64);
- struct kdhyperrect* rect = 0;
-
- if (!(rect = malloc(sizeof(struct kdhyperrect)))) {
- return 0;
- }
-
- rect->dim = dim;
- if (!(rect->min = malloc(size))) {
- free(rect);
- return 0;
- }
- if (!(rect->max = malloc(size))) {
- free(rect->min);
- free(rect);
- return 0;
- }
- memcpy(rect->min, min, size);
- memcpy(rect->max, max, size);
-
- return rect;
-}
-
-static void hyperrect_free(struct kdhyperrect *rect)
-{
- free(rect->min);
- free(rect->max);
- free(rect);
-}
-
-static struct kdhyperrect* hyperrect_duplicate(const struct kdhyperrect *rect)
-{
- return hyperrect_create(rect->dim, rect->min, rect->max);
-}
-
-static void hyperrect_extend(struct kdhyperrect *rect, const npy_float64 *pos)
-{
- int i;
-
- for (i=0; i < rect->dim; i++) {
- if (pos[i] < rect->min[i]) {
- rect->min[i] = pos[i];
- }
- if (pos[i] > rect->max[i]) {
- rect->max[i] = pos[i];
- }
- }
-}
-
-static npy_float64 hyperrect_dist_sq(struct kdhyperrect *rect, const npy_float64 *pos)
-{
- int i;
- npy_float64 result = 0;
-
- for (i=0; i < rect->dim; i++) {
- if (pos[i] < rect->min[i]) {
- result += SQ(rect->min[i] - pos[i]);
- } else if (pos[i] > rect->max[i]) {
- result += SQ(rect->max[i] - pos[i]);
- }
- }
-
- return result;
-}
-
-/* ---- static helpers ---- */
-
-#ifdef USE_LIST_NODE_ALLOCATOR
-/* special list node allocators. */
-static struct res_node *free_nodes;
-
-#ifndef NO_PTHREADS
-static pthread_mutex_t alloc_mutex = PTHREAD_MUTEX_INITIALIZER;
-#endif
-
-static struct res_node *alloc_resnode(void)
-{
- struct res_node *node;
-
-#ifndef NO_PTHREADS
- pthread_mutex_lock(&alloc_mutex);
-#endif
-
- if(!free_nodes) {
- node = malloc(sizeof *node);
- } else {
- node = free_nodes;
- free_nodes = free_nodes->next;
- node->next = 0;
- }
-
-#ifndef NO_PTHREADS
- pthread_mutex_unlock(&alloc_mutex);
-#endif
-
- return node;
-}
-
-static void free_resnode(struct res_node *node)
-{
-#ifndef NO_PTHREADS
- pthread_mutex_lock(&alloc_mutex);
-#endif
-
- node->next = free_nodes;
- free_nodes = node;
-
-#ifndef NO_PTHREADS
- pthread_mutex_unlock(&alloc_mutex);
-#endif
-}
-#endif /* list node allocator or not */
-
-
-/* inserts the item. if dist_sq is >= 0, then do an ordered insert */
-static int rlist_insert(struct res_node *list, struct kdnode *item, npy_float64 dist_sq)
-{
- struct res_node *rnode;
-
- if(!(rnode = alloc_resnode())) {
- return -1;
- }
- rnode->item = item;
- rnode->dist_sq = dist_sq;
-
- if(dist_sq >= 0.0) {
- while(list->next && list->next->dist_sq < dist_sq) {
- list = list->next;
- }
- }
- rnode->next = list->next;
- list->next = rnode;
- return 0;
-}
-
-static void clear_results(struct kdres *rset)
-{
- struct res_node *tmp, *node = rset->rlist->next;
-
- while(node) {
- tmp = node;
- node = node->next;
- free_resnode(tmp);
- }
-
- rset->rlist->next = 0;
-}
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/utilities/lib/kdtree.h
--- a/yt/utilities/lib/kdtree.h
+++ /dev/null
@@ -1,116 +0,0 @@
-/*
-This file is part of ``kdtree'', a library for working with kd-trees.
-Copyright (C) 2007-2011 John Tsiombikas <nuclear at siggraph.org>
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-3. The name of the author may not be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
-OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
-OF SUCH DAMAGE.
-*/
-#ifndef _KDTREE_H_
-#define _KDTREE_H_
-#include "Python.h"
-#include "numpy/ndarrayobject.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-struct kdtree;
-struct kdres;
-
-
-/* create a kd-tree for "k"-dimensional data */
-struct kdtree *kd_create(int k);
-
-/* free the struct kdtree */
-void kd_free(struct kdtree *tree);
-
-/* remove all the elements from the tree */
-void kd_clear(struct kdtree *tree);
-
-/* if called with non-null 2nd argument, the function provided
- * will be called on data pointers (see kd_insert) when nodes
- * are to be removed from the tree.
- */
-void kd_data_destructor(struct kdtree *tree, void (*destr)(void*));
-
-/* insert a node, specifying its position, and optional data */
-int kd_insert(struct kdtree *tree, const npy_float64 *pos, void *data);
-int kd_insertf(struct kdtree *tree, const float *pos, void *data);
-int kd_insert3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, void *data);
-int kd_insert3f(struct kdtree *tree, float x, float y, float z, void *data);
-
-/* Find one of the nearest nodes from the specified point.
- *
- * This function returns a pointer to a result set with at most one element.
- */
-struct kdres *kd_nearest(struct kdtree *tree, const npy_float64 *pos);
-struct kdres *kd_nearestf(struct kdtree *tree, const float *pos);
-struct kdres *kd_nearest3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z);
-struct kdres *kd_nearest3f(struct kdtree *tree, float x, float y, float z);
-
-/* Find any nearest nodes from the specified point within a range.
- *
- * This function returns a pointer to a result set, which can be manipulated
- * by the kd_res_* functions.
- * The returned pointer can be null as an indication of an error. Otherwise
- * a valid result set is always returned which may contain 0 or more elements.
- * The result set must be deallocated with kd_res_free, after use.
- */
-struct kdres *kd_nearest_range(struct kdtree *tree, const npy_float64 *pos, npy_float64 range);
-struct kdres *kd_nearest_rangef(struct kdtree *tree, const float *pos, float range);
-struct kdres *kd_nearest_range3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, npy_float64 range);
-struct kdres *kd_nearest_range3f(struct kdtree *tree, float x, float y, float z, float range);
-
-/* frees a result set returned by kd_nearest_range() */
-void kd_res_free(struct kdres *set);
-
-/* returns the size of the result set (in elements) */
-int kd_res_size(struct kdres *set);
-
-/* rewinds the result set iterator */
-void kd_res_rewind(struct kdres *set);
-
-/* returns non-zero if the set iterator reached the end after the last element */
-int kd_res_end(struct kdres *set);
-
-/* advances the result set iterator, returns non-zero on success, zero if
- * there are no more elements in the result set.
- */
-int kd_res_next(struct kdres *set);
-
-/* returns the data pointer (can be null) of the current result set item
- * and optionally sets its position to the pointers(s) if not null.
- */
-void *kd_res_item(struct kdres *set, npy_float64 *pos);
-void *kd_res_itemf(struct kdres *set, float *pos);
-void *kd_res_item3(struct kdres *set, npy_float64 *x, npy_float64 *y, npy_float64 *z);
-void *kd_res_item3f(struct kdres *set, float *x, float *y, float *z);
-
-/* equivalent to kd_res_item(set, 0) */
-void *kd_res_item_data(struct kdres *set);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _KDTREE_H_ */
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/utilities/lib/kdtree_utils.pxd
--- a/yt/utilities/lib/kdtree_utils.pxd
+++ /dev/null
@@ -1,43 +0,0 @@
-"""
-A light interface to kdtree, from http://code.google.com/p/kdtree/
-
-
-
-"""
-
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
-
-import numpy as np
-cimport numpy as np
-cimport cython
-
-cdef extern from "kdtree.h":
- struct kdtree
- struct kdres
-
- kdtree *kd_create(int k)
- void kd_free(kdtree *tree)
-
- int kd_insert3(kdtree *tree, np.float64_t x, np.float64_t y, np.float64_t z, void *data)
- kdres *kd_nearest3(kdtree *tree, np.float64_t x, np.float64_t y,
- np.float64_t z) nogil
-
- kdres *kd_nearest_range3(kdtree *tree, np.float64_t x, np.float64_t y, np.float64_t z,
- np.float64_t range) nogil
-
- void kd_res_free(kdres *set) nogil
- int kd_res_size(kdres *set) nogil
- int kd_res_next(kdres *set) nogil
- void kd_res_rewind(kdres *set) nogil
-
- void kd_res_item3(kdres *set, np.float64_t *x, np.float64_t *y,
- np.float64_t *z) nogil
- void *kd_res_item_data(kdres *set) nogil
-
- void kd_data_destructor(kdtree *tree, void (*destr)(void*))
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r bbce7672522d2153664ba3032223ace97f5c66cd yt/visualization/volume_rendering/old_camera.py
--- a/yt/visualization/volume_rendering/old_camera.py
+++ b/yt/visualization/volume_rendering/old_camera.py
@@ -617,10 +617,7 @@
np.array(self.width, dtype='float64'), self.transfer_function, self.sub_samples)
return args, {'lens_type': 'plane-parallel'}
- star_trees = None
def get_sampler(self, args, kwargs):
- if self.star_trees is not None:
- kwargs = {'star_list': self.star_trees}
if self.use_light:
if self.light_dir is None:
self.set_default_light_dir()
https://bitbucket.org/yt_analysis/yt/commits/dd6dc6a11c26/
Changeset: dd6dc6a11c26
User: jzuhone
Date: 2017-06-14 21:14:35+00:00
Summary: Merge pull request #1430 from ngoldbaum/cython-setup
Remove unused kdtree and parallel components from grid_traversal.pyx
Affected #: 8 files
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 setup.py
--- a/setup.py
+++ b/setup.py
@@ -154,14 +154,10 @@
depends=["yt/utilities/lib/origami_tags.h"]),
Extension("yt.utilities.lib.grid_traversal",
["yt/utilities/lib/grid_traversal.pyx",
- "yt/utilities/lib/fixed_interpolator.c",
- "yt/utilities/lib/kdtree.c"],
+ "yt/utilities/lib/fixed_interpolator.c"],
include_dirs=["yt/utilities/lib/"],
libraries=std_libs,
- extra_compile_args=omp_args,
- extra_link_args=omp_args,
- depends=["yt/utilities/lib/kdtree.h",
- "yt/utilities/lib/fixed_interpolator.h"]),
+ depends=["yt/utilities/lib/fixed_interpolator.h"]),
Extension("yt.utilities.lib.image_samplers",
["yt/utilities/lib/image_samplers.pyx",
"yt/utilities/lib/fixed_interpolator.c"],
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/utilities/lib/grid_traversal.pyx
--- a/yt/utilities/lib/grid_traversal.pyx
+++ b/yt/utilities/lib/grid_traversal.pyx
@@ -26,8 +26,6 @@
FIT_eval_transfer_with_light
from fixed_interpolator cimport *
-from cython.parallel import prange, parallel, threadid
-
DEF Nch = 4
@cython.boundscheck(False)
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/utilities/lib/image_samplers.pxd
--- a/yt/utilities/lib/image_samplers.pxd
+++ b/yt/utilities/lib/image_samplers.pxd
@@ -17,7 +17,6 @@
import numpy as np
cimport numpy as np
cimport cython
-cimport kdtree_utils
from .volume_container cimport VolumeContainer
from .partitioned_grid cimport PartitionedGrid
@@ -85,7 +84,6 @@
cdef VolumeRenderAccumulator *vra
cdef public object tf_obj
cdef public object my_field_tables
- cdef kdtree_utils.kdtree **trees
cdef object tree_containers
cdef class LightSourceRenderSampler(ImageSampler):
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/utilities/lib/image_samplers.pyx
--- a/yt/utilities/lib/image_samplers.pyx
+++ b/yt/utilities/lib/image_samplers.pyx
@@ -51,7 +51,6 @@
np.float64_t star_coeff
np.float64_t star_er
np.float64_t star_sigma_num
- kdtree_utils.kdtree *star_list
np.float64_t *light_dir
np.float64_t *light_rgba
int grey_opacity
@@ -295,7 +294,7 @@
np.ndarray[np.float64_t, ndim=1] y_vec,
np.ndarray[np.float64_t, ndim=1] width,
tf_obj, n_samples = 10,
- star_list = None, **kwargs):
+ **kwargs):
ImageSampler.__init__(self, vp_pos, vp_dir, center, bounds, image,
x_vec, y_vec, width, **kwargs)
cdef int i
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/utilities/lib/kdtree.c
--- a/yt/utilities/lib/kdtree.c
+++ /dev/null
@@ -1,761 +0,0 @@
-/*
-This file is part of ``kdtree'', a library for working with kd-trees.
-Copyright (C) 2007-2011 John Tsiombikas <nuclear at siggraph.org>
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-3. The name of the author may not be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
-OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
-OF SUCH DAMAGE.
-*/
-/* single nearest neighbor search written by Tamas Nepusz <tamas at cs.rhul.ac.uk> */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include "kdtree.h"
-
-#ifdef MS_WIN32
-#include <malloc.h>
-#endif
-
-#ifdef USE_LIST_NODE_ALLOCATOR
-
-#ifndef NO_PTHREADS
-#include <pthread.h>
-#else
-
-#ifndef I_WANT_THREAD_BUGS
-#error "You are compiling with the fast list node allocator, with pthreads disabled! This WILL break if used from multiple threads."
-#endif /* I want thread bugs */
-
-#endif /* pthread support */
-#endif /* use list node allocator */
-
-struct kdhyperrect {
- int dim;
- npy_float64 *min, *max; /* minimum/maximum coords */
-};
-
-struct kdnode {
- npy_float64 *pos;
- int dir;
- void *data;
-
- struct kdnode *left, *right; /* negative/positive side */
-};
-
-struct res_node {
- struct kdnode *item;
- npy_float64 dist_sq;
- struct res_node *next;
-};
-
-struct kdtree {
- int dim;
- struct kdnode *root;
- struct kdhyperrect *rect;
- void (*destr)(void*);
-};
-
-struct kdres {
- struct kdtree *tree;
- struct res_node *rlist, *riter;
- int size;
-};
-
-#define SQ(x) ((x) * (x))
-
-
-static void clear_rec(struct kdnode *node, void (*destr)(void*));
-static int insert_rec(struct kdnode **node, const npy_float64 *pos, void *data, int dir, int dim);
-static int rlist_insert(struct res_node *list, struct kdnode *item, npy_float64 dist_sq);
-static void clear_results(struct kdres *set);
-
-static struct kdhyperrect* hyperrect_create(int dim, const npy_float64 *min, const npy_float64 *max);
-static void hyperrect_free(struct kdhyperrect *rect);
-static struct kdhyperrect* hyperrect_duplicate(const struct kdhyperrect *rect);
-static void hyperrect_extend(struct kdhyperrect *rect, const npy_float64 *pos);
-static npy_float64 hyperrect_dist_sq(struct kdhyperrect *rect, const npy_float64 *pos);
-
-#ifdef USE_LIST_NODE_ALLOCATOR
-static struct res_node *alloc_resnode(void);
-static void free_resnode(struct res_node*);
-#else
-#define alloc_resnode() malloc(sizeof(struct res_node))
-#define free_resnode(n) free(n)
-#endif
-
-
-
-struct kdtree *kd_create(int k)
-{
- struct kdtree *tree;
-
- if(!(tree = malloc(sizeof *tree))) {
- return 0;
- }
-
- tree->dim = k;
- tree->root = 0;
- tree->destr = 0;
- tree->rect = 0;
-
- return tree;
-}
-
-void kd_free(struct kdtree *tree)
-{
- if(tree) {
- kd_clear(tree);
- free(tree);
- }
-}
-
-static void clear_rec(struct kdnode *node, void (*destr)(void*))
-{
- if(!node) return;
-
- clear_rec(node->left, destr);
- clear_rec(node->right, destr);
-
- if(destr) {
- destr(node->data);
- }
- free(node->pos);
- free(node);
-}
-
-void kd_clear(struct kdtree *tree)
-{
- clear_rec(tree->root, tree->destr);
- tree->root = 0;
-
- if (tree->rect) {
- hyperrect_free(tree->rect);
- tree->rect = 0;
- }
-}
-
-void kd_data_destructor(struct kdtree *tree, void (*destr)(void*))
-{
- tree->destr = destr;
-}
-
-
-static int insert_rec(struct kdnode **nptr, const npy_float64 *pos, void *data, int dir, int dim)
-{
- int new_dir;
- struct kdnode *node;
-
- if(!*nptr) {
- if(!(node = malloc(sizeof *node))) {
- return -1;
- }
- if(!(node->pos = malloc(dim * sizeof *node->pos))) {
- free(node);
- return -1;
- }
- memcpy(node->pos, pos, dim * sizeof *node->pos);
- node->data = data;
- node->dir = dir;
- node->left = node->right = 0;
- *nptr = node;
- return 0;
- }
-
- node = *nptr;
- new_dir = (node->dir + 1) % dim;
- if(pos[node->dir] < node->pos[node->dir]) {
- return insert_rec(&(*nptr)->left, pos, data, new_dir, dim);
- }
- return insert_rec(&(*nptr)->right, pos, data, new_dir, dim);
-}
-
-int kd_insert(struct kdtree *tree, const npy_float64 *pos, void *data)
-{
- if (insert_rec(&tree->root, pos, data, 0, tree->dim)) {
- return -1;
- }
-
- if (tree->rect == 0) {
- tree->rect = hyperrect_create(tree->dim, pos, pos);
- } else {
- hyperrect_extend(tree->rect, pos);
- }
-
- return 0;
-}
-
-int kd_insertf(struct kdtree *tree, const float *pos, void *data)
-{
- static npy_float64 sbuf[16];
- npy_float64 *bptr, *buf = 0;
- int res, dim = tree->dim;
-
- if(dim > 16) {
-#ifndef NO_ALLOCA
- if(dim <= 256)
- bptr = buf = alloca(dim * sizeof *bptr);
- else
-#endif
- if(!(bptr = buf = malloc(dim * sizeof *bptr))) {
- return -1;
- }
- } else {
- bptr = sbuf;
- }
-
- while(dim-- > 0) {
- *bptr++ = *pos++;
- }
-
- res = kd_insert(tree, buf, data);
-#ifndef NO_ALLOCA
- if(tree->dim > 256)
-#else
- if(tree->dim > 16)
-#endif
- free(buf);
- return res;
-}
-
-int kd_insert3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, void *data)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_insert(tree, buf, data);
-}
-
-int kd_insert3f(struct kdtree *tree, float x, float y, float z, void *data)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_insert(tree, buf, data);
-}
-
-static int find_nearest(struct kdnode *node, const npy_float64 *pos, npy_float64 range, struct res_node *list, int ordered, int dim)
-{
- npy_float64 dist_sq, dx;
- int i, ret, added_res = 0;
-
- if(!node) return 0;
-
- dist_sq = 0;
- for(i=0; i<dim; i++) {
- dist_sq += SQ(node->pos[i] - pos[i]);
- }
- if(dist_sq <= SQ(range)) {
- if(rlist_insert(list, node, ordered ? dist_sq : -1.0) == -1) {
- return -1;
- }
- added_res = 1;
- }
-
- dx = pos[node->dir] - node->pos[node->dir];
-
- ret = find_nearest(dx <= 0.0 ? node->left : node->right, pos, range, list, ordered, dim);
- if(ret >= 0 && fabs(dx) < range) {
- added_res += ret;
- ret = find_nearest(dx <= 0.0 ? node->right : node->left, pos, range, list, ordered, dim);
- }
- if(ret == -1) {
- return -1;
- }
- added_res += ret;
-
- return added_res;
-}
-
-static void kd_nearest_i(struct kdnode *node, const npy_float64 *pos, struct kdnode **result, npy_float64 *result_dist_sq, struct kdhyperrect* rect)
-{
- int dir = node->dir;
- int i, side;
- npy_float64 dummy, dist_sq;
- struct kdnode *nearer_subtree, *farther_subtree;
- npy_float64 *nearer_hyperrect_coord, *farther_hyperrect_coord;
-
- /* Decide whether to go left or right in the tree */
- dummy = pos[dir] - node->pos[dir];
- if (dummy <= 0) {
- nearer_subtree = node->left;
- farther_subtree = node->right;
- nearer_hyperrect_coord = rect->max + dir;
- farther_hyperrect_coord = rect->min + dir;
- side = 0;
- } else {
- nearer_subtree = node->right;
- farther_subtree = node->left;
- nearer_hyperrect_coord = rect->min + dir;
- farther_hyperrect_coord = rect->max + dir;
- side = 1;
- }
-
- if (nearer_subtree) {
- /* Slice the hyperrect to get the hyperrect of the nearer subtree */
- dummy = *nearer_hyperrect_coord;
- *nearer_hyperrect_coord = node->pos[dir];
- /* Recurse down into nearer subtree */
- kd_nearest_i(nearer_subtree, pos, result, result_dist_sq, rect);
- /* Undo the slice */
- *nearer_hyperrect_coord = dummy;
- }
-
- /* Check the distance of the point at the current node, compare it
- * with our best so far */
- dist_sq = 0;
- for(i=0; i < rect->dim; i++) {
- dist_sq += SQ(node->pos[i] - pos[i]);
- }
- if (dist_sq < *result_dist_sq) {
- *result = node;
- *result_dist_sq = dist_sq;
- }
-
- if (farther_subtree) {
- /* Get the hyperrect of the farther subtree */
- dummy = *farther_hyperrect_coord;
- *farther_hyperrect_coord = node->pos[dir];
- /* Check if we have to recurse down by calculating the closest
- * point of the hyperrect and see if it's closer than our
- * minimum distance in result_dist_sq. */
- if (hyperrect_dist_sq(rect, pos) < *result_dist_sq) {
- /* Recurse down into farther subtree */
- kd_nearest_i(farther_subtree, pos, result, result_dist_sq, rect);
- }
- /* Undo the slice on the hyperrect */
- *farther_hyperrect_coord = dummy;
- }
-}
-
-struct kdres *kd_nearest(struct kdtree *kd, const npy_float64 *pos)
-{
- struct kdhyperrect *rect;
- struct kdnode *result;
- struct kdres *rset;
- npy_float64 dist_sq;
- int i;
-
- if (!kd) return 0;
- if (!kd->rect) return 0;
-
- /* Allocate result set */
- if(!(rset = malloc(sizeof *rset))) {
- return 0;
- }
- if(!(rset->rlist = alloc_resnode())) {
- free(rset);
- return 0;
- }
- rset->rlist->next = 0;
- rset->tree = kd;
-
- /* Duplicate the bounding hyperrectangle, we will work on the copy */
- if (!(rect = hyperrect_duplicate(kd->rect))) {
- kd_res_free(rset);
- return 0;
- }
-
- /* Our first guesstimate is the root node */
- result = kd->root;
- dist_sq = 0;
- for (i = 0; i < kd->dim; i++)
- dist_sq += SQ(result->pos[i] - pos[i]);
-
- /* Search for the nearest neighbour recursively */
- kd_nearest_i(kd->root, pos, &result, &dist_sq, rect);
-
- /* Free the copy of the hyperrect */
- hyperrect_free(rect);
-
- /* Store the result */
- if (result) {
- if (rlist_insert(rset->rlist, result, -1.0) == -1) {
- kd_res_free(rset);
- return 0;
- }
- rset->size = 1;
- kd_res_rewind(rset);
- return rset;
- } else {
- kd_res_free(rset);
- return 0;
- }
-}
-
-struct kdres *kd_nearestf(struct kdtree *tree, const float *pos)
-{
- static npy_float64 sbuf[16];
- npy_float64 *bptr, *buf = 0;
- int dim = tree->dim;
- struct kdres *res;
-
- if(dim > 16) {
-#ifndef NO_ALLOCA
- if(dim <= 256)
- bptr = buf = alloca(dim * sizeof *bptr);
- else
-#endif
- if(!(bptr = buf = malloc(dim * sizeof *bptr))) {
- return 0;
- }
- } else {
- bptr = sbuf;
- }
-
- while(dim-- > 0) {
- *bptr++ = *pos++;
- }
-
- res = kd_nearest(tree, buf);
-#ifndef NO_ALLOCA
- if(tree->dim > 256)
-#else
- if(tree->dim > 16)
-#endif
- free(buf);
- return res;
-}
-
-struct kdres *kd_nearest3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z)
-{
- npy_float64 pos[3];
- pos[0] = x;
- pos[1] = y;
- pos[2] = z;
- return kd_nearest(tree, pos);
-}
-
-struct kdres *kd_nearest3f(struct kdtree *tree, float x, float y, float z)
-{
- npy_float64 pos[3];
- pos[0] = x;
- pos[1] = y;
- pos[2] = z;
- return kd_nearest(tree, pos);
-}
-
-struct kdres *kd_nearest_range(struct kdtree *kd, const npy_float64 *pos, npy_float64 range)
-{
- int ret;
- struct kdres *rset;
-
- if(!(rset = malloc(sizeof *rset))) {
- return 0;
- }
- if(!(rset->rlist = alloc_resnode())) {
- free(rset);
- return 0;
- }
- rset->rlist->next = 0;
- rset->tree = kd;
-
- if((ret = find_nearest(kd->root, pos, range, rset->rlist, 0, kd->dim)) == -1) {
- kd_res_free(rset);
- return 0;
- }
- rset->size = ret;
- kd_res_rewind(rset);
- return rset;
-}
-
-struct kdres *kd_nearest_rangef(struct kdtree *kd, const float *pos, float range)
-{
- static npy_float64 sbuf[16];
- npy_float64 *bptr, *buf = 0;
- int dim = kd->dim;
- struct kdres *res;
-
- if(dim > 16) {
-#ifndef NO_ALLOCA
- if(dim <= 256)
- bptr = buf = alloca(dim * sizeof *bptr);
- else
-#endif
- if(!(bptr = buf = malloc(dim * sizeof *bptr))) {
- return 0;
- }
- } else {
- bptr = sbuf;
- }
-
- while(dim-- > 0) {
- *bptr++ = *pos++;
- }
-
- res = kd_nearest_range(kd, buf, range);
-#ifndef NO_ALLOCA
- if(kd->dim > 256)
-#else
- if(kd->dim > 16)
-#endif
- free(buf);
- return res;
-}
-
-struct kdres *kd_nearest_range3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, npy_float64 range)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_nearest_range(tree, buf, range);
-}
-
-struct kdres *kd_nearest_range3f(struct kdtree *tree, float x, float y, float z, float range)
-{
- npy_float64 buf[3];
- buf[0] = x;
- buf[1] = y;
- buf[2] = z;
- return kd_nearest_range(tree, buf, range);
-}
-
-void kd_res_free(struct kdres *rset)
-{
- clear_results(rset);
- free_resnode(rset->rlist);
- free(rset);
-}
-
-int kd_res_size(struct kdres *set)
-{
- return (set->size);
-}
-
-void kd_res_rewind(struct kdres *rset)
-{
- rset->riter = rset->rlist->next;
-}
-
-int kd_res_end(struct kdres *rset)
-{
- return rset->riter == 0;
-}
-
-int kd_res_next(struct kdres *rset)
-{
- rset->riter = rset->riter->next;
- return rset->riter != 0;
-}
-
-void *kd_res_item(struct kdres *rset, npy_float64 *pos)
-{
- if(rset->riter) {
- if(pos) {
- memcpy(pos, rset->riter->item->pos, rset->tree->dim * sizeof *pos);
- }
- return rset->riter->item->data;
- }
- return 0;
-}
-
-void *kd_res_itemf(struct kdres *rset, float *pos)
-{
- if(rset->riter) {
- if(pos) {
- int i;
- for(i=0; i<rset->tree->dim; i++) {
- pos[i] = rset->riter->item->pos[i];
- }
- }
- return rset->riter->item->data;
- }
- return 0;
-}
-
-void *kd_res_item3(struct kdres *rset, npy_float64 *x, npy_float64 *y, npy_float64 *z)
-{
- if(rset->riter) {
- if(*x) *x = rset->riter->item->pos[0];
- if(*y) *y = rset->riter->item->pos[1];
- if(*z) *z = rset->riter->item->pos[2];
- }
- return 0;
-}
-
-void *kd_res_item3f(struct kdres *rset, float *x, float *y, float *z)
-{
- if(rset->riter) {
- if(*x) *x = rset->riter->item->pos[0];
- if(*y) *y = rset->riter->item->pos[1];
- if(*z) *z = rset->riter->item->pos[2];
- }
- return 0;
-}
-
-void *kd_res_item_data(struct kdres *set)
-{
- return kd_res_item(set, 0);
-}
-
-/* ---- hyperrectangle helpers ---- */
-static struct kdhyperrect* hyperrect_create(int dim, const npy_float64 *min, const npy_float64 *max)
-{
- size_t size = dim * sizeof(npy_float64);
- struct kdhyperrect* rect = 0;
-
- if (!(rect = malloc(sizeof(struct kdhyperrect)))) {
- return 0;
- }
-
- rect->dim = dim;
- if (!(rect->min = malloc(size))) {
- free(rect);
- return 0;
- }
- if (!(rect->max = malloc(size))) {
- free(rect->min);
- free(rect);
- return 0;
- }
- memcpy(rect->min, min, size);
- memcpy(rect->max, max, size);
-
- return rect;
-}
-
-static void hyperrect_free(struct kdhyperrect *rect)
-{
- free(rect->min);
- free(rect->max);
- free(rect);
-}
-
-static struct kdhyperrect* hyperrect_duplicate(const struct kdhyperrect *rect)
-{
- return hyperrect_create(rect->dim, rect->min, rect->max);
-}
-
-static void hyperrect_extend(struct kdhyperrect *rect, const npy_float64 *pos)
-{
- int i;
-
- for (i=0; i < rect->dim; i++) {
- if (pos[i] < rect->min[i]) {
- rect->min[i] = pos[i];
- }
- if (pos[i] > rect->max[i]) {
- rect->max[i] = pos[i];
- }
- }
-}
-
-static npy_float64 hyperrect_dist_sq(struct kdhyperrect *rect, const npy_float64 *pos)
-{
- int i;
- npy_float64 result = 0;
-
- for (i=0; i < rect->dim; i++) {
- if (pos[i] < rect->min[i]) {
- result += SQ(rect->min[i] - pos[i]);
- } else if (pos[i] > rect->max[i]) {
- result += SQ(rect->max[i] - pos[i]);
- }
- }
-
- return result;
-}
-
-/* ---- static helpers ---- */
-
-#ifdef USE_LIST_NODE_ALLOCATOR
-/* special list node allocators. */
-static struct res_node *free_nodes;
-
-#ifndef NO_PTHREADS
-static pthread_mutex_t alloc_mutex = PTHREAD_MUTEX_INITIALIZER;
-#endif
-
-static struct res_node *alloc_resnode(void)
-{
- struct res_node *node;
-
-#ifndef NO_PTHREADS
- pthread_mutex_lock(&alloc_mutex);
-#endif
-
- if(!free_nodes) {
- node = malloc(sizeof *node);
- } else {
- node = free_nodes;
- free_nodes = free_nodes->next;
- node->next = 0;
- }
-
-#ifndef NO_PTHREADS
- pthread_mutex_unlock(&alloc_mutex);
-#endif
-
- return node;
-}
-
-static void free_resnode(struct res_node *node)
-{
-#ifndef NO_PTHREADS
- pthread_mutex_lock(&alloc_mutex);
-#endif
-
- node->next = free_nodes;
- free_nodes = node;
-
-#ifndef NO_PTHREADS
- pthread_mutex_unlock(&alloc_mutex);
-#endif
-}
-#endif /* list node allocator or not */
-
-
-/* inserts the item. if dist_sq is >= 0, then do an ordered insert */
-static int rlist_insert(struct res_node *list, struct kdnode *item, npy_float64 dist_sq)
-{
- struct res_node *rnode;
-
- if(!(rnode = alloc_resnode())) {
- return -1;
- }
- rnode->item = item;
- rnode->dist_sq = dist_sq;
-
- if(dist_sq >= 0.0) {
- while(list->next && list->next->dist_sq < dist_sq) {
- list = list->next;
- }
- }
- rnode->next = list->next;
- list->next = rnode;
- return 0;
-}
-
-static void clear_results(struct kdres *rset)
-{
- struct res_node *tmp, *node = rset->rlist->next;
-
- while(node) {
- tmp = node;
- node = node->next;
- free_resnode(tmp);
- }
-
- rset->rlist->next = 0;
-}
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/utilities/lib/kdtree.h
--- a/yt/utilities/lib/kdtree.h
+++ /dev/null
@@ -1,116 +0,0 @@
-/*
-This file is part of ``kdtree'', a library for working with kd-trees.
-Copyright (C) 2007-2011 John Tsiombikas <nuclear at siggraph.org>
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-3. The name of the author may not be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
-WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
-OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
-OF SUCH DAMAGE.
-*/
-#ifndef _KDTREE_H_
-#define _KDTREE_H_
-#include "Python.h"
-#include "numpy/ndarrayobject.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-struct kdtree;
-struct kdres;
-
-
-/* create a kd-tree for "k"-dimensional data */
-struct kdtree *kd_create(int k);
-
-/* free the struct kdtree */
-void kd_free(struct kdtree *tree);
-
-/* remove all the elements from the tree */
-void kd_clear(struct kdtree *tree);
-
-/* if called with non-null 2nd argument, the function provided
- * will be called on data pointers (see kd_insert) when nodes
- * are to be removed from the tree.
- */
-void kd_data_destructor(struct kdtree *tree, void (*destr)(void*));
-
-/* insert a node, specifying its position, and optional data */
-int kd_insert(struct kdtree *tree, const npy_float64 *pos, void *data);
-int kd_insertf(struct kdtree *tree, const float *pos, void *data);
-int kd_insert3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, void *data);
-int kd_insert3f(struct kdtree *tree, float x, float y, float z, void *data);
-
-/* Find one of the nearest nodes from the specified point.
- *
- * This function returns a pointer to a result set with at most one element.
- */
-struct kdres *kd_nearest(struct kdtree *tree, const npy_float64 *pos);
-struct kdres *kd_nearestf(struct kdtree *tree, const float *pos);
-struct kdres *kd_nearest3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z);
-struct kdres *kd_nearest3f(struct kdtree *tree, float x, float y, float z);
-
-/* Find any nearest nodes from the specified point within a range.
- *
- * This function returns a pointer to a result set, which can be manipulated
- * by the kd_res_* functions.
- * The returned pointer can be null as an indication of an error. Otherwise
- * a valid result set is always returned which may contain 0 or more elements.
- * The result set must be deallocated with kd_res_free, after use.
- */
-struct kdres *kd_nearest_range(struct kdtree *tree, const npy_float64 *pos, npy_float64 range);
-struct kdres *kd_nearest_rangef(struct kdtree *tree, const float *pos, float range);
-struct kdres *kd_nearest_range3(struct kdtree *tree, npy_float64 x, npy_float64 y, npy_float64 z, npy_float64 range);
-struct kdres *kd_nearest_range3f(struct kdtree *tree, float x, float y, float z, float range);
-
-/* frees a result set returned by kd_nearest_range() */
-void kd_res_free(struct kdres *set);
-
-/* returns the size of the result set (in elements) */
-int kd_res_size(struct kdres *set);
-
-/* rewinds the result set iterator */
-void kd_res_rewind(struct kdres *set);
-
-/* returns non-zero if the set iterator reached the end after the last element */
-int kd_res_end(struct kdres *set);
-
-/* advances the result set iterator, returns non-zero on success, zero if
- * there are no more elements in the result set.
- */
-int kd_res_next(struct kdres *set);
-
-/* returns the data pointer (can be null) of the current result set item
- * and optionally sets its position to the pointers(s) if not null.
- */
-void *kd_res_item(struct kdres *set, npy_float64 *pos);
-void *kd_res_itemf(struct kdres *set, float *pos);
-void *kd_res_item3(struct kdres *set, npy_float64 *x, npy_float64 *y, npy_float64 *z);
-void *kd_res_item3f(struct kdres *set, float *x, float *y, float *z);
-
-/* equivalent to kd_res_item(set, 0) */
-void *kd_res_item_data(struct kdres *set);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _KDTREE_H_ */
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/utilities/lib/kdtree_utils.pxd
--- a/yt/utilities/lib/kdtree_utils.pxd
+++ /dev/null
@@ -1,43 +0,0 @@
-"""
-A light interface to kdtree, from http://code.google.com/p/kdtree/
-
-
-
-"""
-
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
-
-import numpy as np
-cimport numpy as np
-cimport cython
-
-cdef extern from "kdtree.h":
- struct kdtree
- struct kdres
-
- kdtree *kd_create(int k)
- void kd_free(kdtree *tree)
-
- int kd_insert3(kdtree *tree, np.float64_t x, np.float64_t y, np.float64_t z, void *data)
- kdres *kd_nearest3(kdtree *tree, np.float64_t x, np.float64_t y,
- np.float64_t z) nogil
-
- kdres *kd_nearest_range3(kdtree *tree, np.float64_t x, np.float64_t y, np.float64_t z,
- np.float64_t range) nogil
-
- void kd_res_free(kdres *set) nogil
- int kd_res_size(kdres *set) nogil
- int kd_res_next(kdres *set) nogil
- void kd_res_rewind(kdres *set) nogil
-
- void kd_res_item3(kdres *set, np.float64_t *x, np.float64_t *y,
- np.float64_t *z) nogil
- void *kd_res_item_data(kdres *set) nogil
-
- void kd_data_destructor(kdtree *tree, void (*destr)(void*))
diff -r fc8b883d884e901840c0eb707db889c4ac8bddc7 -r dd6dc6a11c26c2aa7bb30bbe22893518cbc65713 yt/visualization/volume_rendering/old_camera.py
--- a/yt/visualization/volume_rendering/old_camera.py
+++ b/yt/visualization/volume_rendering/old_camera.py
@@ -617,10 +617,7 @@
np.array(self.width, dtype='float64'), self.transfer_function, self.sub_samples)
return args, {'lens_type': 'plane-parallel'}
- star_trees = None
def get_sampler(self, args, kwargs):
- if self.star_trees is not None:
- kwargs = {'star_list': self.star_trees}
if self.use_light:
if self.light_dir is None:
self.set_default_light_dir()
Repository URL: https://bitbucket.org/yt_analysis/yt/
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