diff --git a/bin/parse_gmsh.py b/bin/parse_gmsh.py index ab93329..b0e011c 100755 --- a/bin/parse_gmsh.py +++ b/bin/parse_gmsh.py @@ -21,50 +21,15 @@ del os, atexit, readline, rlcompleter, save_history, historyPath import sys import pickle from itertools import combinations +from collections import defaultdict +from scipy.spatial import KDTree + +from grid.simplex import face import numpy as np THREE_NODE_TRIANGLE = 2 -class point(object): - def __init__(self, xyz): - self.index = index - - self.xyz = xyz - self.faces = [] - - def __getitem__(self, i): - if isinstance(i, int): - if i == 0: - return self.xyz[0] - elif i == 1: - return self.xyz[1] - elif i == 2: - return self.xyz[2] - else: - raise IndexError("there are only (x,y,z)") - else: - raise TypeError("only point.x and point[0] access allowed") - - def _getx(self): - return self.xyz[0] - x = property(_getx) - def _gety(self): - return self.xyz[1] - y = property(_gety) - def _getz(self): - return self.xyz[2] - z = property(_getz) - - def __str__(self): - return '%s' % self.xyz - __repr__ = __str__ - -class face(object): - def __init__(self): - self.neighbors = [] - self.points = [] - if __name__ == '__main__': if len(sys.argv) != 2: print >> sys.stderr, "usage: %s " % sys.argv[0] @@ -81,8 +46,7 @@ if __name__ == '__main__': node_count = int(gmsh_file.readline()) - points = [] - nppoints = np.zeros((node_count, 3)) + verts = np.zeros((node_count, 3)) for i in xrange(node_count): cur_line = gmsh_file.readline() (index, x,y,z) = cur_line.split() @@ -91,19 +55,20 @@ if __name__ == '__main__': y = float(y) z = float(z) - nppoints[i][0] = x - nppoints[i][1] = y - nppoints[i][2] = z - points.append(point(nppoints[i])) + verts[i][0] = x + verts[i][1] = y + verts[i][2] = z + tree = KDTree(verts) - gmsh_file.readline() # $EndNodes - gmsh_file.readline() # $Elements + gmsh_file.readline() # $E ndNodes + gmsh_file.readline() # $E lements element_count = int(gmsh_file.readline()) - faceobjs = {} - neighbors = {} + faces = {} + neighbors = {} + faces_for_vert = defaultdict(list) for i in xrange(element_count): cur_line = gmsh_file.readline() @@ -115,17 +80,17 @@ if __name__ == '__main__': if(node_type == THREE_NODE_TRIANGLE): points_for_cur_face = [i-1 for i in rest[rest[0]+1:]] - cur_face = face() + cur_face = face(cur_face_index) for cur_point in points_for_cur_face: - points[cur_point].faces.append(cur_face_index) + faces_for_vert[cur_point].append(cur_face_index) - cur_face.points = points_for_cur_face + cur_face.verts = points_for_cur_face - faceobjs[cur_face_index] = cur_face + faces[cur_face_index] = cur_face edges = [tuple(sorted(i)) for i in combinations(points_for_cur_face, 2)] - # edge is two points + # edge is two verts for edge in edges: if edge in neighbors: neighbors[edge].append(cur_face_index) @@ -134,8 +99,8 @@ if __name__ == '__main__': for k,v in neighbors.iteritems(): if len(v) > 1: - faceobjs[v[0]].neighbors.append(v[1]) - faceobjs[v[1]].neighbors.append(v[0]) + faces[v[0]].add_neighbor(faces[v[1]]) + faces[v[1]].add_neighbor(faces[v[0]]) - pickle.dump([(p[0], p[1], p[2]) for p in points], open('/tmp/points.p', 'w')) - pickle.dump([f.points for f in faceobjs.itervalues()], open('/tmp/faces.p', 'w')) + pickle.dump([(p[0], p[1], p[2]) for p in verts], open('/tmp/points.p', 'w')) + pickle.dump([f.verts for f in faces.itervalues()], open('/tmp/faces.p', 'w')) diff --git a/bin/test2d-connectivity.py b/bin/test2d-connectivity.py index 7e2b818..bc48453 100755 --- a/bin/test2d-connectivity.py +++ b/bin/test2d-connectivity.py @@ -67,4 +67,3 @@ if __name__ == '__main__': good.append(d[True]) draw_gb(bad = bad, good = good) - diff --git a/bin/test2d-qhull-specific.py b/bin/test2d-qhull-specific.py index 9d7a7b4..1e6360b 100755 --- a/bin/test2d-qhull-specific.py +++ b/bin/test2d-qhull-specific.py @@ -1,4 +1,4 @@ -#!/usr/bin/python2.6 +#!/usr/bin/env python import sys from grid.DD import grid @@ -24,6 +24,8 @@ g = grid(verts,q) exact = exact_func(X) +d = {True:0, False:0} + try: answer = g.run_baker(X) d[improved_answer(answer, exact)] += 1 diff --git a/distribute_setup.py b/distribute_setup.py deleted file mode 100644 index 0021336..0000000 --- a/distribute_setup.py +++ /dev/null @@ -1,477 +0,0 @@ -#!python -"""Bootstrap distribute installation - -If you want to use setuptools in your package's setup.py, just include this -file in the same directory with it, and add this to the top of your setup.py:: - - from distribute_setup import use_setuptools - use_setuptools() - -If you want to require a specific version of setuptools, set a download -mirror, or use an alternate download directory, you can do so by supplying -the appropriate options to ``use_setuptools()``. - -This file can also be run as a script to install or upgrade setuptools. -""" -import os -import sys -import time -import fnmatch -import tempfile -import tarfile -from distutils import log - -try: - from site import USER_SITE -except ImportError: - USER_SITE = None - -try: - import subprocess - - def _python_cmd(*args): - args = (sys.executable,) + args - return subprocess.call(args) == 0 - -except ImportError: - # will be used for python 2.3 - def _python_cmd(*args): - args = (sys.executable,) + args - # quoting arguments if windows - if sys.platform == 'win32': - def quote(arg): - if ' ' in arg: - return '"%s"' % arg - return arg - args = [quote(arg) for arg in args] - return os.spawnl(os.P_WAIT, sys.executable, *args) == 0 - -DEFAULT_VERSION = "0.6.10" -DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/" -SETUPTOOLS_FAKED_VERSION = "0.6c11" - -SETUPTOOLS_PKG_INFO = """\ -Metadata-Version: 1.0 -Name: setuptools -Version: %s -Summary: xxxx -Home-page: xxx -Author: xxx -Author-email: xxx -License: xxx -Description: xxx -""" % SETUPTOOLS_FAKED_VERSION - - -def _install(tarball): - # extracting the tarball - tmpdir = tempfile.mkdtemp() - log.warn('Extracting in %s', tmpdir) - old_wd = os.getcwd() - try: - os.chdir(tmpdir) - tar = tarfile.open(tarball) - _extractall(tar) - tar.close() - - # going in the directory - subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) - os.chdir(subdir) - log.warn('Now working in %s', subdir) - - # installing - log.warn('Installing Distribute') - if not _python_cmd('setup.py', 'install'): - log.warn('Something went wrong during the installation.') - log.warn('See the error message above.') - finally: - os.chdir(old_wd) - - -def _build_egg(egg, tarball, to_dir): - # extracting the tarball - tmpdir = tempfile.mkdtemp() - log.warn('Extracting in %s', tmpdir) - old_wd = os.getcwd() - try: - os.chdir(tmpdir) - tar = tarfile.open(tarball) - _extractall(tar) - tar.close() - - # going in the directory - subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) - os.chdir(subdir) - log.warn('Now working in %s', subdir) - - # building an egg - log.warn('Building a Distribute egg in %s', to_dir) - _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir) - - finally: - os.chdir(old_wd) - # returning the result - log.warn(egg) - if not os.path.exists(egg): - raise IOError('Could not build the egg.') - - -def _do_download(version, download_base, to_dir, download_delay): - egg = os.path.join(to_dir, 'distribute-%s-py%d.%d.egg' - % (version, sys.version_info[0], sys.version_info[1])) - if not os.path.exists(egg): - tarball = download_setuptools(version, download_base, - to_dir, download_delay) - _build_egg(egg, tarball, to_dir) - sys.path.insert(0, egg) - import setuptools - setuptools.bootstrap_install_from = egg - - -def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, - to_dir=os.curdir, download_delay=15, no_fake=True): - # making sure we use the absolute path - to_dir = os.path.abspath(to_dir) - was_imported = 'pkg_resources' in sys.modules or \ - 'setuptools' in sys.modules - try: - try: - import pkg_resources - if not hasattr(pkg_resources, '_distribute'): - if not no_fake: - _fake_setuptools() - raise ImportError - except ImportError: - return _do_download(version, download_base, to_dir, download_delay) - try: - pkg_resources.require("distribute>="+version) - return - except pkg_resources.VersionConflict: - e = sys.exc_info()[1] - if was_imported: - sys.stderr.write( - "The required version of distribute (>=%s) is not available,\n" - "and can't be installed while this script is running. Please\n" - "install a more recent version first, using\n" - "'easy_install -U distribute'." - "\n\n(Currently using %r)\n" % (version, e.args[0])) - sys.exit(2) - else: - del pkg_resources, sys.modules['pkg_resources'] # reload ok - return _do_download(version, download_base, to_dir, - download_delay) - except pkg_resources.DistributionNotFound: - return _do_download(version, download_base, to_dir, - download_delay) - finally: - if not no_fake: - _create_fake_setuptools_pkg_info(to_dir) - -def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, - to_dir=os.curdir, delay=15): - """Download distribute from a specified location and return its filename - - `version` should be a valid distribute version number that is available - as an egg for download under the `download_base` URL (which should end - with a '/'). `to_dir` is the directory where the egg will be downloaded. - `delay` is the number of seconds to pause before an actual download - attempt. - """ - # making sure we use the absolute path - to_dir = os.path.abspath(to_dir) - try: - from urllib.request import urlopen - except ImportError: - from urllib2 import urlopen - tgz_name = "distribute-%s.tar.gz" % version - url = download_base + tgz_name - saveto = os.path.join(to_dir, tgz_name) - src = dst = None - if not os.path.exists(saveto): # Avoid repeated downloads - try: - log.warn("Downloading %s", url) - src = urlopen(url) - # Read/write all in one block, so we don't create a corrupt file - # if the download is interrupted. - data = src.read() - dst = open(saveto, "wb") - dst.write(data) - finally: - if src: - src.close() - if dst: - dst.close() - return os.path.realpath(saveto) - - -def _patch_file(path, content): - """Will backup the file then patch it""" - existing_content = open(path).read() - if existing_content == content: - # already patched - log.warn('Already patched.') - return False - log.warn('Patching...') - _rename_path(path) - f = open(path, 'w') - try: - f.write(content) - finally: - f.close() - return True - - -def _same_content(path, content): - return open(path).read() == content - -def _no_sandbox(function): - def __no_sandbox(*args, **kw): - try: - from setuptools.sandbox import DirectorySandbox - def violation(*args): - pass - DirectorySandbox._old = DirectorySandbox._violation - DirectorySandbox._violation = violation - patched = True - except ImportError: - patched = False - - try: - return function(*args, **kw) - finally: - if patched: - DirectorySandbox._violation = DirectorySandbox._old - del DirectorySandbox._old - - return __no_sandbox - -@_no_sandbox -def _rename_path(path): - new_name = path + '.OLD.%s' % time.time() - log.warn('Renaming %s into %s', path, new_name) - os.rename(path, new_name) - return new_name - -def _remove_flat_installation(placeholder): - if not os.path.isdir(placeholder): - log.warn('Unkown installation at %s', placeholder) - return False - found = False - for file in os.listdir(placeholder): - if fnmatch.fnmatch(file, 'setuptools*.egg-info'): - found = True - break - if not found: - log.warn('Could not locate setuptools*.egg-info') - return - - log.warn('Removing elements out of the way...') - pkg_info = os.path.join(placeholder, file) - if os.path.isdir(pkg_info): - patched = _patch_egg_dir(pkg_info) - else: - patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO) - - if not patched: - log.warn('%s already patched.', pkg_info) - return False - # now let's move the files out of the way - for element in ('setuptools', 'pkg_resources.py', 'site.py'): - element = os.path.join(placeholder, element) - if os.path.exists(element): - _rename_path(element) - else: - log.warn('Could not find the %s element of the ' - 'Setuptools distribution', element) - return True - - -def _after_install(dist): - log.warn('After install bootstrap.') - placeholder = dist.get_command_obj('install').install_purelib - _create_fake_setuptools_pkg_info(placeholder) - -@_no_sandbox -def _create_fake_setuptools_pkg_info(placeholder): - if not placeholder or not os.path.exists(placeholder): - log.warn('Could not find the install location') - return - pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1]) - setuptools_file = 'setuptools-%s-py%s.egg-info' % \ - (SETUPTOOLS_FAKED_VERSION, pyver) - pkg_info = os.path.join(placeholder, setuptools_file) - if os.path.exists(pkg_info): - log.warn('%s already exists', pkg_info) - return - - log.warn('Creating %s', pkg_info) - f = open(pkg_info, 'w') - try: - f.write(SETUPTOOLS_PKG_INFO) - finally: - f.close() - - pth_file = os.path.join(placeholder, 'setuptools.pth') - log.warn('Creating %s', pth_file) - f = open(pth_file, 'w') - try: - f.write(os.path.join(os.curdir, setuptools_file)) - finally: - f.close() - -def _patch_egg_dir(path): - # let's check if it's already patched - pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO') - if os.path.exists(pkg_info): - if _same_content(pkg_info, SETUPTOOLS_PKG_INFO): - log.warn('%s already patched.', pkg_info) - return False - _rename_path(path) - os.mkdir(path) - os.mkdir(os.path.join(path, 'EGG-INFO')) - pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO') - f = open(pkg_info, 'w') - try: - f.write(SETUPTOOLS_PKG_INFO) - finally: - f.close() - return True - - -def _before_install(): - log.warn('Before install bootstrap.') - _fake_setuptools() - - -def _under_prefix(location): - if 'install' not in sys.argv: - return True - args = sys.argv[sys.argv.index('install')+1:] - for index, arg in enumerate(args): - for option in ('--root', '--prefix'): - if arg.startswith('%s=' % option): - top_dir = arg.split('root=')[-1] - return location.startswith(top_dir) - elif arg == option: - if len(args) > index: - top_dir = args[index+1] - return location.startswith(top_dir) - elif option == '--user' and USER_SITE is not None: - return location.startswith(USER_SITE) - return True - - -def _fake_setuptools(): - log.warn('Scanning installed packages') - try: - import pkg_resources - except ImportError: - # we're cool - log.warn('Setuptools or Distribute does not seem to be installed.') - return - ws = pkg_resources.working_set - try: - setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools', - replacement=False)) - except TypeError: - # old distribute API - setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools')) - - if setuptools_dist is None: - log.warn('No setuptools distribution found') - return - # detecting if it was already faked - setuptools_location = setuptools_dist.location - log.warn('Setuptools installation detected at %s', setuptools_location) - - # if --root or --preix was provided, and if - # setuptools is not located in them, we don't patch it - if not _under_prefix(setuptools_location): - log.warn('Not patching, --root or --prefix is installing Distribute' - ' in another location') - return - - # let's see if its an egg - if not setuptools_location.endswith('.egg'): - log.warn('Non-egg installation') - res = _remove_flat_installation(setuptools_location) - if not res: - return - else: - log.warn('Egg installation') - pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO') - if (os.path.exists(pkg_info) and - _same_content(pkg_info, SETUPTOOLS_PKG_INFO)): - log.warn('Already patched.') - return - log.warn('Patching...') - # let's create a fake egg replacing setuptools one - res = _patch_egg_dir(setuptools_location) - if not res: - return - log.warn('Patched done.') - _relaunch() - - -def _relaunch(): - log.warn('Relaunching...') - # we have to relaunch the process - args = [sys.executable] + sys.argv - sys.exit(subprocess.call(args)) - - -def _extractall(self, path=".", members=None): - """Extract all members from the archive to the current working - directory and set owner, modification time and permissions on - directories afterwards. `path' specifies a different directory - to extract to. `members' is optional and must be a subset of the - list returned by getmembers(). - """ - import copy - import operator - from tarfile import ExtractError - directories = [] - - if members is None: - members = self - - for tarinfo in members: - if tarinfo.isdir(): - # Extract directories with a safe mode. - directories.append(tarinfo) - tarinfo = copy.copy(tarinfo) - tarinfo.mode = 448 # decimal for oct 0700 - self.extract(tarinfo, path) - - # Reverse sort directories. - if sys.version_info < (2, 4): - def sorter(dir1, dir2): - return cmp(dir1.name, dir2.name) - directories.sort(sorter) - directories.reverse() - else: - directories.sort(key=operator.attrgetter('name'), reverse=True) - - # Set correct owner, mtime and filemode on directories. - for tarinfo in directories: - dirpath = os.path.join(path, tarinfo.name) - try: - self.chown(tarinfo, dirpath) - self.utime(tarinfo, dirpath) - self.chmod(tarinfo, dirpath) - except ExtractError: - e = sys.exc_info()[1] - if self.errorlevel > 1: - raise - else: - self._dbg(1, "tarfile: %s" % e) - - -def main(argv, version=DEFAULT_VERSION): - """Install or upgrade setuptools and EasyInstall""" - tarball = download_setuptools() - _install(tarball) - - -if __name__ == '__main__': - main(sys.argv[1:]) diff --git a/lib/baker/__init__.py b/interp/baker/__init__.py similarity index 100% rename from lib/baker/__init__.py rename to interp/baker/__init__.py diff --git a/lib/grid/DD.py b/interp/grid/DD.py similarity index 100% rename from lib/grid/DD.py rename to interp/grid/DD.py diff --git a/lib/grid/DDD.py b/interp/grid/DDD.py similarity index 100% rename from lib/grid/DDD.py rename to interp/grid/DDD.py diff --git a/lib/grid/__init__.py b/interp/grid/__init__.py similarity index 95% rename from lib/grid/__init__.py rename to interp/grid/__init__.py index ebbb249..4374a9b 100644 --- a/lib/grid/__init__.py +++ b/interp/grid/__init__.py @@ -12,8 +12,22 @@ from simplex import face, contains from smcqdelaunay import * - class grid(object): + def __init__(self, points, q): + """ + this thing eats two pre-constructed arrays of floats: + points = array of arrays (i will convert to numpy.array) + [[x0,y0], [x1,y1], ...] + q = array (1D) of important values + """ + + self.points = np.array(points) + self.q = np.array(q) + self.tree = scipy.spatial.KDTree(self.points) + self.faces = {} + self.faces_for_vert = defaultdict(list) + +class delaunay_grid(grid): facet_re = re.compile(r''' -\s+(?Pf\d+).*? vertices:\s(?P.*?)\n.*? @@ -29,20 +43,9 @@ class grid(object): (p\d+) ''', re.S|re.X) - def __init__(self, points, q): - """ - this thing eats two pre-constructed arrays of floats: - points = array of arrays (i will convert to numpy.array) - [[x0,y0], [x1,y1], ...] - q = array (1D) of important values - """ + grid.__init__(self, points,q) - self.points = np.array(points) - self.q = np.array(q) - self.tree = scipy.spatial.KDTree(self.points) - self.faces = {} - self.facets_for_point = defaultdict(list) def create_mesh(self, indicies): """ @@ -70,7 +73,7 @@ class grid(object): simplex = None checked_facets = [] - facets_to_check = self.facets_for_point[closest_point] + facets_to_check = self.faces_for_vert[closest_point] attempts = 0 while not simplex and facets_to_check: @@ -158,7 +161,7 @@ class grid(object): (dist, indicies) = self.tree.query(X, 2) simplex = None - for facet in self.facets_for_point[indicies[0]]: + for facet in self.faces_for_vert[indicies[0]]: if facet.contains(X, self): simplex = facet break @@ -215,7 +218,7 @@ class grid(object): for v in grid.vert_re.findall(verticies): vertex_index = int(v[1:]) cur_face.add_vert(vertex_index) - self.facets_for_point[vertex_index].append(cur_face) + self.faces_for_vert[vertex_index].append(cur_face) nghbrs = [(facet_name, i) for i in neighboring_facets.split()] facet_to_facets.extend(nghbrs) @@ -232,7 +235,7 @@ class grid(object): assert( len(self.points) == len(self.q) ) for c, i in enumerate(zip(self.points, self.q)): r += "%d %r: %0.4f" % (c,i[0], i[1]) - facet_str = ", ".join([f.name for f in self.facets_for_point[c]]) + facet_str = ", ".join([f.name for f in self.faces_for_vert[c]]) r += " faces: [%s]" % facet_str r += "\n" if self.faces: diff --git a/lib/grid/qhull.py b/interp/grid/qhull.py similarity index 100% rename from lib/grid/qhull.py rename to interp/grid/qhull.py diff --git a/lib/grid/simplex.py b/interp/grid/simplex.py similarity index 91% rename from lib/grid/simplex.py rename to interp/grid/simplex.py index d91fea8..5da423c 100644 --- a/lib/grid/simplex.py +++ b/interp/grid/simplex.py @@ -53,10 +53,12 @@ class face(object): return contains(X, [G.points[i] for i in self.verts]) def __str__(self): - neighbors = [i.name for i in self.neighbors] - return '%s: verts: %s neighbors: [%s]' %\ + neighbors = [str(i.name) for i in self.neighbors] + return '' %\ ( self.name, self.verts, ", ".join(neighbors) ) + + __repr__ = __str__ diff --git a/lib/grid/smcqdelaunay.py b/interp/grid/smcqdelaunay.py similarity index 100% rename from lib/grid/smcqdelaunay.py rename to interp/grid/smcqdelaunay.py diff --git a/lib/baker/tools.py b/interp/tools.py similarity index 100% rename from lib/baker/tools.py rename to interp/tools.py diff --git a/setup.py b/setup.py index 86a87d6..eb09743 100644 --- a/setup.py +++ b/setup.py @@ -1,17 +1,14 @@ -from distribute_setup import use_setuptools -use_setuptools() - from setuptools import setup, find_packages setup( - name = 'interpolosion', + name = 'interplosion', version = '0.01', - package_dir = {'':'lib'}, - packages = find_packages('lib'), + package_dir = {'':'interp'}, + packages = find_packages('interp'), install_requires = [ 'numpy', 'scipy', ], - entry_points = {'console_scripts': ['booze = baker.booze:main',]}, + # entry_points = {'console_scripts': ['booze = baker.booze:main',]}, ) diff --git a/test/baker.test.py b/test/baker.test.py index 583c723..bf62ce2 100755 --- a/test/baker.test.py +++ b/test/baker.test.py @@ -1,8 +1,8 @@ #!/usr/bin/env python import unittest -import baker -import grid +from interplosion import baker +from interplosion import grid import numpy as np import scipy.spatial