[Yt-svn] yt-commit r750 - in trunk: tests/regression_scripts yt/lagos
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Thu Sep 4 08:34:24 PDT 2008
Author: mturk
Date: Thu Sep 4 08:34:22 2008
New Revision: 750
URL: http://yt.spacepope.org/changeset/750
Log:
* Added RTIntegrator module. Note that I am checking in both the Cython and the C modules, but the Cython-processed one is the one that will be compiled by distutils.
* Added some regression scripts for the RT Integrator, as an example of how to look at the output.
The Cython code has a lot of baggage, but it's fairly fast. Plus, it's much,
much easier to debug, and I suspect it'll be better in the long run to use
this. I don't see conversion of existing modules, however.
Added:
trunk/tests/regression_scripts/test_radtrans.py
trunk/tests/regression_scripts/test_radtrans1d.py
trunk/yt/lagos/RTIntegrator.c
trunk/yt/lagos/RTIntegrator.pyx
Modified:
trunk/yt/lagos/setup.py
Added: trunk/tests/regression_scripts/test_radtrans.py
==============================================================================
--- (empty file)
+++ trunk/tests/regression_scripts/test_radtrans.py Thu Sep 4 08:34:22 2008
@@ -0,0 +1,49 @@
+from yt.lagos import RTIntegrator as RT
+import numpy as na
+import pylab, time
+
+size = 16
+
+i_s = na.ones((size*2,size*2), dtype='float')
+o_s = na.zeros((size,size,size), dtype='float')
+e = na.ones((size,size,size), dtype='float') * 0
+e[:,:,size/2:] = 0.0
+a = na.ones((size,size,size), dtype='float')
+#a[:,:,:size/2] = 0.0
+
+def output_plots(image_field, axis):
+ arr = image_field.swapaxes(0, axis)
+ for i in range(arr.shape[axis]):
+ print i
+ pylab.clf()
+ pylab.imshow(arr[i,...], interpolation='nearest')
+ pylab.colorbar()
+ pylab.clim(image_field.min(), image_field.max())
+ pylab.savefig("RT/image_%s_%04i.png" % (axis,i))
+
+dx = 1.0/size
+t1 = time.time()
+RT.Transfer3D(i_s, o_s, e, a, 2,4, 2,4, 2, 8, 2, 2, dx)
+t2 = time.time()
+print "Took %0.3e seconds for a %s box" % (t2-t1, o_s.shape)
+
+pylab.clf()
+pylab.plot(range(size), o_s[:,0,0].ravel())
+pylab.savefig("RT/line_plot_0.png")
+
+pylab.clf()
+pylab.plot(range(size), o_s[0,:,0].ravel())
+pylab.savefig("RT/line_plot_1.png")
+
+pylab.clf()
+pylab.plot(range(size), o_s[0,0,:].ravel())
+pylab.savefig("RT/line_plot_2.png")
+
+pylab.clf()
+pylab.imshow(i_s, interpolation='nearest')
+pylab.colorbar()
+pylab.savefig("RT/resultant_image.png")
+
+output_plots(o_s, 0)
+output_plots(o_s, 1)
+output_plots(o_s, 2)
Added: trunk/tests/regression_scripts/test_radtrans1d.py
==============================================================================
--- (empty file)
+++ trunk/tests/regression_scripts/test_radtrans1d.py Thu Sep 4 08:34:22 2008
@@ -0,0 +1,22 @@
+from yt.lagos import RTIntegrator as RT
+import numpy as na
+import pylab, time
+
+size = 1024
+
+i_s = 1.0
+o_s = na.zeros(size, dtype='float')
+e = na.ones(size, dtype='float') * 0
+e[size/2:] = 0.0
+a = na.ones(size, dtype='float')
+#a[:,:,:size/2] = 0.0
+
+dx = na.ones(size, dtype='float') * 1.0/size
+t1 = time.time()
+RT.Transfer1D(i_s, o_s, e, a, dx, 0, size)
+t2 = time.time()
+print "Took %0.3e seconds for a %s box" % (t2-t1, o_s.shape)
+
+pylab.clf()
+pylab.plot(range(size), o_s)
+pylab.savefig("RT/line_plot_0.png")
Added: trunk/yt/lagos/RTIntegrator.c
==============================================================================
--- (empty file)
+++ trunk/yt/lagos/RTIntegrator.c Thu Sep 4 08:34:22 2008
@@ -0,0 +1,1813 @@
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+ if (__pyx_1) {
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+ __pyx_3 = PyNumber_Remainder(__pyx_kp_16, __pyx_2); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ PyTuple_SET_ITEM(__pyx_2, 0, __pyx_3);
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+ __pyx_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_2), NULL); if (unlikely(!__pyx_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(((PyObject *)__pyx_2)); __pyx_2 = 0;
+ __Pyx_Raise(__pyx_3, 0, 0);
+ Py_DECREF(__pyx_3); __pyx_3 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L6;
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+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":74
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+}
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+ {"Transfer1D", (PyCFunction)__pyx_pf_2yt_5lagos_12RTIntegrator_Transfer1D, METH_VARARGS|METH_KEYWORDS, 0},
+ {0, 0, 0, 0}
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+
+static void __pyx_init_filenames(void); /*proto*/
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+static struct PyModuleDef __pyx_moduledef = {
+ PyModuleDef_HEAD_INIT,
+ "RTIntegrator",
+ 0, /* m_doc */
+ -1, /* m_size */
+ __pyx_methods /* m_methods */,
+ NULL, /* m_reload */
+ NULL, /* m_traverse */
+ NULL, /* m_clear */
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+ {&__pyx_kp_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 1, 1, 1},
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+ {&__pyx_kp_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 0},
+ {&__pyx_kp_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 0},
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+ __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_kp_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ return 0;
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+}
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+ __pyx_L1_error:;
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+}
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+PyMODINIT_FUNC initRTIntegrator(void); /*proto*/
+PyMODINIT_FUNC initRTIntegrator(void)
+#else
+PyMODINIT_FUNC PyInit_RTIntegrator(void); /*proto*/
+PyMODINIT_FUNC PyInit_RTIntegrator(void)
+#endif
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+ __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Libary function declarations ---*/
+ __pyx_init_filenames();
+ /*--- Initialize various global constants etc. ---*/
+ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Module creation code ---*/
+ #if PY_MAJOR_VERSION < 3
+ __pyx_m = Py_InitModule4("RTIntegrator", __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ #else
+ __pyx_m = PyModule_Create(&__pyx_moduledef);
+ #endif
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME);
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+ if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ /*--- Builtin init code ---*/
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+ __pyx_skip_dispatch = 0;
+ /*--- Global init code ---*/
+ /*--- Function export code ---*/
+ /*--- Type init code ---*/
+ /*--- Type import code ---*/
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject)); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Function import code ---*/
+ /*--- Execution code ---*/
+
+ /* "/Users/matthewturk/Development/yt/trunk/yt/lagos/RTIntegrator.pyx":1
+ * import numpy as np # <<<<<<<<<<<<<<
+ * cimport numpy as np
+ * cimport cython
+ */
+ __pyx_1 = __Pyx_Import(__pyx_kp_numpy, 0); if (unlikely(!__pyx_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_kp_np, __pyx_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ Py_DECREF(__pyx_1); __pyx_1 = 0;
+
+ /* "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Cython-0.9.8.1.1-py2.5-macosx-10.3-fat.egg/Cython/Includes/numpy.pxd":36
+ * # experimental exception made for __getbuffer__ and __releasebuffer__
+ * # -- the details of this may change.
+ * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
+ * # This implementation of getbuffer is geared towards Cython
+ * # requirements, and does not yet fullfill the PEP (specifically,
+ */
+ #if PY_MAJOR_VERSION < 3
+ return;
+ #else
+ return __pyx_m;
+ #endif
+ __pyx_L1_error:;
+ Py_XDECREF(__pyx_1);
+ __Pyx_AddTraceback("yt.lagos.RTIntegrator");
+ #if PY_MAJOR_VERSION >= 3
+ return NULL;
+ #endif
+}
+
+static const char *__pyx_filenames[] = {
+ "RTIntegrator.pyx",
+ "numpy.pxd",
+};
+
+/* Runtime support code */
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+ __pyx_f = __pyx_filenames;
+}
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+static INLINE void __Pyx_SafeReleaseBuffer(PyObject* obj, Py_buffer* info) {
+ if (info->buf == NULL) return;
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+ __Pyx_ReleaseBuffer(obj, info);
+}
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+static INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
+ buf->buf = NULL;
+ buf->strides = __Pyx_zeros;
+ buf->shape = __Pyx_zeros;
+ buf->suboffsets = __Pyx_minusones;
+}
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+ while (1) {
+ switch (*ts) {
+ case 10:
+ case 13:
+ case ' ':
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+ default:
+ return ts;
+ }
+ }
+}
+
+static INLINE const char* __Pyx_BufferTypestringCheckEndian(const char* ts) {
+ int num = 1;
+ int little_endian = ((char*)&num)[0];
+ int ok = 1;
+ switch (*ts) {
+ case '@':
+ case '=':
+ ++ts; break;
+ case '<':
+ if (little_endian) ++ts;
+ else ok = 0;
+ break;
+ case '>':
+ case '!':
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+ else ok = 0;
+ break;
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+ if (!ok) {
+ PyErr_Format(PyExc_ValueError, "Buffer has wrong endianness (rejecting on '%s')", ts);
+ return NULL;
+ }
+ return ts;
+}
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+static void __Pyx_BufferNdimError(Py_buffer* buffer, int expected_ndim) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer has wrong number of dimensions (expected %d, got %d)",
+ expected_ndim, buffer->ndim);
+}
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+static const char* __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_float_t(const char* ts) {
+ int ok;
+ if (*ts == '1') ++ts;
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+ case 'd': ok = (sizeof(__pyx_t_5numpy_float_t) == sizeof(double) && (__pyx_t_5numpy_float_t)-1 < 0); break;
+ case 'g': ok = (sizeof(__pyx_t_5numpy_float_t) == sizeof(long double) && (__pyx_t_5numpy_float_t)-1 < 0); break; default: ok = 0;
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+ PyErr_Format(PyExc_ValueError, "Buffer datatype mismatch (rejecting on '%s')", ts);
+ return NULL;
+ } else return ts + 1;
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+}
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+static int __Pyx_GetBuffer_nn___pyx_t_5numpy_float_t(PyObject* obj, Py_buffer* buf, int flags, int nd) {
+ const char* ts;
+ if (obj == Py_None) {
+ __Pyx_ZeroBuffer(buf);
+ return 0;
+ }
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+ if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
+ if (buf->ndim != nd) {
+ __Pyx_BufferNdimError(buf, nd);
+ goto fail;
+ }
+ ts = buf->format;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheckEndian(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ ts = __Pyx_BufferTypestringCheck_item_nn___pyx_t_5numpy_float_t(ts);
+ if (!ts) goto fail;
+ ts = __Pyx_ConsumeWhitespace(ts);
+ if (*ts != 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected non-struct buffer data type (expected end, got '%s')", ts);
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
+static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, 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 INLINE void __Pyx_RaiseArgtupleTooLong(
+ Py_ssize_t num_expected,
+ Py_ssize_t num_found)
+{
+ const char* error_message =
+ #if PY_VERSION_HEX < 0x02050000
+ "function takes at most %d positional arguments (%d given)";
+ #else
+ "function takes at most %zd positional arguments (%zd given)";
+ #endif
+ PyErr_Format(PyExc_TypeError, error_message, num_expected, num_found);
+}
+
+#if (PY_MAJOR_VERSION < 3) && !(Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_NEWBUFFER)
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pf_5numpy_7ndarray___getbuffer__(obj, view, flags);
+ else {
+ PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+ return -1;
+ }
+}
+
+static void __Pyx_ReleaseBuffer(PyObject *obj, Py_buffer *view) {
+
+}
+
+#endif
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
+ PyObject *__import__ = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ __import__ = PyObject_GetAttrString(__pyx_b, "__import__");
+ if (!__import__)
+ goto bad;
+ 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;
+ module = PyObject_CallFunction(__import__, "OOOO",
+ name, global_dict, empty_dict, list);
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(__import__);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result)
+ PyErr_SetObject(PyExc_NameError, name);
+ return result;
+}
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
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+ }
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+ }
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+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
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+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
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+ 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
+ }
+ PyErr_Restore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(char *module_name, char *class_name,
+ long size)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(module_name);
+ #else
+ py_name = PyUnicode_FromString(module_name);
+ #endif
+ if (!py_name)
+ goto bad;
+
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ result = PyObject_GetAttrString(py_module, class_name);
+ 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;
+ }
+ if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s does not appear to be the correct type object",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_name);
+ Py_XDECREF(result);
+ return 0;
+}
+#endif
+
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ 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
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyObject *empty_string = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(__pyx_filename);
+ #else
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (__pyx_clineno) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #endif
+ }
+ else {
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+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
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+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ #if PY_MAJOR_VERSION < 3
+ empty_string = PyString_FromStringAndSize("", 0);
+ #else
+ empty_string = PyBytes_FromStringAndSize("", 0);
+ #endif
+ if (!empty_string) goto bad;
+ py_code = PyCode_New(
+ 0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*int kwonlyargcount,*/
+ #endif
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ empty_string, /*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,*/
+ __pyx_lineno, /*int firstlineno,*/
+ empty_string /*PyObject *lnotab*/
+ );
+ if (!py_code) 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 = __pyx_lineno;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ Py_XDECREF(empty_string);
+ 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->is_identifier)) {
+ *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_identifier || (t->is_unicode && t->intern)) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->is_unicode) {
+ *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;
+}
+
+/* Type Conversion Functions */
+
+static 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 INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ if (x == Py_True) return 1;
+ else if (x == Py_False) return 0;
+ else return PyObject_IsTrue(x);
+}
+
+static INLINE PY_LONG_LONG __pyx_PyInt_AsLongLong(PyObject* x) {
+ if (PyInt_CheckExact(x)) {
+ return PyInt_AS_LONG(x);
+ }
+ else if (PyLong_CheckExact(x)) {
+ return PyLong_AsLongLong(x);
+ }
+ else {
+ PY_LONG_LONG val;
+ PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1;
+ val = __pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static INLINE unsigned PY_LONG_LONG __pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ if (PyInt_CheckExact(x)) {
+ long val = PyInt_AS_LONG(x);
+ if (unlikely(val < 0)) {
+ PyErr_SetString(PyExc_TypeError, "Negative assignment to unsigned type.");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return val;
+ }
+ else if (PyLong_CheckExact(x)) {
+ return PyLong_AsUnsignedLongLong(x);
+ }
+ else {
+ PY_LONG_LONG val;
+ PyObject* tmp = PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1;
+ val = __pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+
+static INLINE unsigned char __pyx_PyInt_unsigned_char(PyObject* x) {
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ unsigned char val = (unsigned char)long_val;
+ if (unlikely((val != long_val) || (long_val < 0))) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned char");
+ return (unsigned char)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE unsigned short __pyx_PyInt_unsigned_short(PyObject* x) {
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ unsigned short val = (unsigned short)long_val;
+ if (unlikely((val != long_val) || (long_val < 0))) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to unsigned short");
+ return (unsigned short)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE char __pyx_PyInt_char(PyObject* x) {
+ if (sizeof(char) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ char val = (char)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to char");
+ return (char)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE short __pyx_PyInt_short(PyObject* x) {
+ if (sizeof(short) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ short val = (short)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to short");
+ return (short)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE int __pyx_PyInt_int(PyObject* x) {
+ if (sizeof(int) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ int val = (int)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to int");
+ return (int)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE long __pyx_PyInt_long(PyObject* x) {
+ if (sizeof(long) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ long val = (long)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to long");
+ return (long)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE signed char __pyx_PyInt_signed_char(PyObject* x) {
+ if (sizeof(signed char) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ signed char val = (signed char)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed char");
+ return (signed char)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE signed short __pyx_PyInt_signed_short(PyObject* x) {
+ if (sizeof(signed short) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ signed short val = (signed short)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed short");
+ return (signed short)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE signed int __pyx_PyInt_signed_int(PyObject* x) {
+ if (sizeof(signed int) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ signed int val = (signed int)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed int");
+ return (signed int)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE signed long __pyx_PyInt_signed_long(PyObject* x) {
+ if (sizeof(signed long) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ signed long val = (signed long)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to signed long");
+ return (signed long)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
+static INLINE long double __pyx_PyInt_long_double(PyObject* x) {
+ if (sizeof(long double) < sizeof(long)) {
+ long long_val = __pyx_PyInt_AsLong(x);
+ long double val = (long double)long_val;
+ if (unlikely((val != long_val) )) {
+ PyErr_SetString(PyExc_OverflowError, "value too large to convert to long double");
+ return (long double)-1;
+ }
+ return val;
+ }
+ else {
+ return __pyx_PyInt_AsLong(x);
+ }
+}
+
Added: trunk/yt/lagos/RTIntegrator.pyx
==============================================================================
--- (empty file)
+++ trunk/yt/lagos/RTIntegrator.pyx Thu Sep 4 08:34:22 2008
@@ -0,0 +1,46 @@
+import numpy as np
+cimport numpy as np
+cimport cython
+
+ at cython.boundscheck(False)
+def Transfer3D(np.ndarray[np.float_t, ndim=2] i_s,
+ np.ndarray[np.float_t, ndim=3] o_s,
+ np.ndarray[np.float_t, ndim=3] e,
+ np.ndarray[np.float_t, ndim=3] a,
+ int imin, int imax, int jmin, int jmax,
+ int kmin, int kmax, int istride, int jstride,
+ float dx):
+ """
+ This function accepts an incoming slab (*i_s*), a buffer
+ for an outgoing set of values at every point in the grid (*o_s*),
+ an emission array (*e*), an absorption array (*a*), and dimensions of
+ the grid (*imin*, *imax*, *jmin*, *jmax*, *kmin*, *kmax*) as well
+ as strides in the *i* and *j* directions, and a *dx* of the grid being
+ integrated.
+ """
+ cdef int i, ii
+ cdef int j, jj
+ cdef int k, kk
+ cdef float temp
+ for i in range((imax-imin)*istride):
+ ii = i + imin*istride
+ for j in range((jmax-jmin)*jstride):
+ jj = j + jmin*jstride
+ temp = i_s[ii,jj]
+ for k in range(kmax-kmin):
+ o_s[i,j,k] = temp + dx*(e[i,j,k] - temp*a[i,j,k])
+ temp = o_s[i,j,k]
+ i_s[ii,jj] = temp
+
+ at cython.boundscheck(False)
+def Transfer1D(float i_s,
+ np.ndarray[np.float_t, ndim=1] o_s,
+ np.ndarray[np.float_t, ndim=1] e,
+ np.ndarray[np.float_t, ndim=1] a,
+ np.ndarray[np.float_t, ndim=1] dx,
+ int imin, int imax):
+ cdef int i
+ for i in range(imin, imax):
+ o_s[i] = i_s + dx[i]*(e[i] - i_s*a[i])
+ i_s = o_s[i]
+ return i_s
Modified: trunk/yt/lagos/setup.py
==============================================================================
--- trunk/yt/lagos/setup.py (original)
+++ trunk/yt/lagos/setup.py Thu Sep 4 08:34:22 2008
@@ -19,6 +19,7 @@
config = Configuration('lagos',parent_package,top_path)
config.make_config_py() # installs __config__.py
config.add_extension("PointCombine", "yt/lagos/PointCombine.c", libraries=["m"])
+ config.add_extension("RTIntegrator", "yt/lagos/RTIntegrator.c")
config.add_subpackage("hop")
H5dir = check_for_hdf5()
if H5dir is not None:
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