[Yt-svn] yt: 2 new changesets
hg at spacepope.org
hg at spacepope.org
Fri Jun 25 10:48:57 PDT 2010
hg Repository: yt
details: yt/rev/f2d1856b34da
changeset: 1811:f2d1856b34da
user: J.S. Oishi <jsoishi at gmail.com>
date:
Fri Jun 25 10:46:32 2010 -0700
description:
corrected grid viewer for proper domain width scaling.
hg Repository: yt
details: yt/rev/de8e0404cac4
changeset: 1812:de8e0404cac4
user: J.S. Oishi <jsoishi at gmail.com>
date:
Fri Jun 25 10:48:46 2010 -0700
description:
merged
diffstat:
doc/install_script.sh | 8 +-
yt/amr_utils.c | 1227 ++++++++++++++-----------
yt/extensions/DualEPS.py | 409 +++++++-
yt/extensions/StarAnalysis.py | 138 ++-
yt/extensions/merger_tree.py | 125 ++
yt/extensions/opengl_image_viewer.py | 4 +-
yt/extensions/volume_rendering/TransferFunction.py | 110 ++-
yt/lagos/HaloFinding.py | 495 ++++++++-
yt/lagos/TwoPointFunctions.py | 160 ++-
yt/raven/plot_collection.py | 15 +-
yt/reason/tvtk_interface.py | 7 +-
11 files changed, 1916 insertions(+), 782 deletions(-)
diffs (truncated from 5685 to 300 lines):
diff -r 97fa3280f8bf -r de8e0404cac4 doc/install_script.sh
--- a/doc/install_script.sh Tue Jun 22 15:59:19 2010 -0700
+++ b/doc/install_script.sh Fri Jun 25 10:48:46 2010 -0700
@@ -233,8 +233,8 @@
[ $INST_PNG -eq 1 ] && get_enzotools libpng-1.2.43.tar.gz
[ $INST_WXPYTHON -eq 1 ] && get_enzotools wxPython-src-2.8.10.1.tar.bz2
get_enzotools Python-2.6.3.tgz
-get_enzotools numpy-1.3.0.tar.gz
-get_enzotools matplotlib-0.99.1.2.tar.gz
+get_enzotools numpy-1.4.1.tar.gz
+get_enzotools matplotlib-0.99.3.tar.gz
get_enzotools ipython-0.10.tar.gz
get_enzotools h5py-1.2.0.tar.gz
@@ -352,14 +352,14 @@
echo "Installing pip"
( ${DEST_DIR}/bin/easy_install-2.6 pip 2>&1 ) 1>> ${LOG_FILE} || do_exit
-do_setup_py numpy-1.3.0 ${NUMPY_ARGS}
+do_setup_py numpy-1.4.1 ${NUMPY_ARGS}
if [ -n "${MPL_SUPP_LDFLAGS}" ]
then
export LDFLAGS="${MPL_SUPP_LDFLAGS}"
echo "Setting LDFLAGS ${LDFLAGS}"
fi
-do_setup_py matplotlib-0.99.1.2
+do_setup_py matplotlib-0.99.3
unset LDFLAGS
do_setup_py ipython-0.10
do_setup_py h5py-1.2.0
diff -r 97fa3280f8bf -r de8e0404cac4 yt/amr_utils.c
--- a/yt/amr_utils.c Tue Jun 22 15:59:19 2010 -0700
+++ b/yt/amr_utils.c Fri Jun 25 10:48:46 2010 -0700
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.12.1 on Sun Jun 6 18:13:46 2010 */
+/* Generated by Cython 0.12.1 on Thu Jun 24 08:40:25 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -482,7 +482,7 @@
PyObject *grids;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":552
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":569
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -515,7 +515,7 @@
int refined_pos;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":520
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":537
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -574,13 +574,14 @@
int nv[2];
int vp_strides[3];
int im_strides[3];
+ int vd_strides[3];
PyObject *ax_vec;
PyObject *ay_vec;
__pyx_t_5numpy_float64_t *x_vec;
__pyx_t_5numpy_float64_t *y_vec;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":293
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":299
* tv[offset + k] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -606,7 +607,7 @@
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":520
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":537
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -634,7 +635,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_TransferFunctionProxy *__pyx_vtabptr_2yt_9amr_utils_TransferFunctionProxy;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":552
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":569
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -681,7 +682,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_VectorPlane *__pyx_vtabptr_2yt_9amr_utils_VectorPlane;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":293
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":299
* tv[offset + k] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -1462,6 +1463,7 @@
static char __pyx_k__root_nodes[] = "root_nodes";
static char __pyx_k__slab_start[] = "slab_start";
static char __pyx_k__suboffsets[] = "suboffsets";
+static char __pyx_k__vd_strides[] = "vd_strides";
static char __pyx_k__vp_strides[] = "vp_strides";
static char __pyx_k__weight_val[] = "weight_val";
static char __pyx_k__box_lengths[] = "box_lengths";
@@ -1711,6 +1713,7 @@
static PyObject *__pyx_n_s__v;
static PyObject *__pyx_n_s__val;
static PyObject *__pyx_n_s__values;
+static PyObject *__pyx_n_s__vd_strides;
static PyObject *__pyx_n_s__vp;
static PyObject *__pyx_n_s__vp_dir;
static PyObject *__pyx_n_s__vp_pos;
@@ -13667,12 +13670,12 @@
__Pyx_RefNannyFinishContext();
}
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":232
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":233
* cdef np.float64_t *x_vec, *y_vec
*
* def __cinit__(self, # <<<<<<<<<<<<<<
* np.ndarray[np.float64_t, ndim=3] vp_pos,
- * np.ndarray[np.float64_t, ndim=1] vp_dir,
+ * np.ndarray vp_dir,
*/
static int __pyx_pf_2yt_9amr_utils_11VectorPlane___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
@@ -13688,9 +13691,6 @@
Py_buffer __pyx_bstruct_center;
Py_ssize_t __pyx_bstride_0_center = 0;
Py_ssize_t __pyx_bshape_0_center = 0;
- Py_buffer __pyx_bstruct_vp_dir;
- Py_ssize_t __pyx_bstride_0_vp_dir = 0;
- Py_ssize_t __pyx_bshape_0_vp_dir = 0;
Py_buffer __pyx_bstruct_x_vec;
Py_ssize_t __pyx_bstride_0_x_vec = 0;
Py_ssize_t __pyx_bshape_0_x_vec = 0;
@@ -13715,6 +13715,7 @@
int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
__pyx_t_5numpy_float64_t __pyx_t_3;
+ int __pyx_t_4;
static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vp_pos,&__pyx_n_s__vp_dir,&__pyx_n_s__center,&__pyx_n_s__bounds,&__pyx_n_s__image,&__pyx_n_s__x_vec,&__pyx_n_s__y_vec,0};
__Pyx_RefNannySetupContext("__cinit__");
if (unlikely(__pyx_kwds)) {
@@ -13740,41 +13741,41 @@
values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vp_dir);
if (likely(values[1])) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__center);
if (likely(values[2])) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 2); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 2); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__bounds);
if (likely(values[3])) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 3); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 3); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__image);
if (likely(values[4])) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 4); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 4); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x_vec);
if (likely(values[5])) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 5); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 5); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 6:
values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y_vec);
if (likely(values[6])) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 6); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 6); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
__pyx_v_vp_pos = ((PyArrayObject *)values[0]);
__pyx_v_vp_dir = ((PyArrayObject *)values[1]);
@@ -13796,7 +13797,7 @@
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("yt.amr_utils.VectorPlane.__cinit__");
return -1;
@@ -13810,55 +13811,48 @@
__Pyx_INCREF((PyObject *)__pyx_v_x_vec);
__Pyx_INCREF((PyObject *)__pyx_v_y_vec);
__pyx_bstruct_vp_pos.buf = NULL;
- __pyx_bstruct_vp_dir.buf = NULL;
__pyx_bstruct_center.buf = NULL;
__pyx_bstruct_image.buf = NULL;
__pyx_bstruct_x_vec.buf = NULL;
__pyx_bstruct_y_vec.buf = NULL;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vp_pos), __pyx_ptype_5numpy_ndarray, 1, "vp_pos", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vp_dir), __pyx_ptype_5numpy_ndarray, 1, "vp_dir", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_center), __pyx_ptype_5numpy_ndarray, 1, "center", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_image), __pyx_ptype_5numpy_ndarray, 1, "image", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_bshape_0_vp_pos = __pyx_bstruct_vp_pos.shape[0]; __pyx_bshape_1_vp_pos = __pyx_bstruct_vp_pos.shape[1]; __pyx_bshape_2_vp_pos = __pyx_bstruct_vp_pos.shape[2];
{
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- __pyx_bshape_0_vp_dir = __pyx_bstruct_vp_dir.shape[0];
- {
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+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_bstruct_center, (PyObject*)__pyx_v_center, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_bstride_0_center = __pyx_bstruct_center.strides[0];
__pyx_bshape_0_center = __pyx_bstruct_center.shape[0];
{
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+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_bstruct_image, (PyObject*)__pyx_v_image, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_bshape_0_image = __pyx_bstruct_image.shape[0]; __pyx_bshape_1_image = __pyx_bstruct_image.shape[1]; __pyx_bshape_2_image = __pyx_bstruct_image.shape[2];
{
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+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_bstruct_x_vec, (PyObject*)__pyx_v_x_vec, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_bstride_0_x_vec = __pyx_bstruct_x_vec.strides[0];
__pyx_bshape_0_x_vec = __pyx_bstruct_x_vec.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_bstruct_y_vec, (PyObject*)__pyx_v_y_vec, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_bstruct_y_vec, (PyObject*)__pyx_v_y_vec, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_bstride_0_y_vec = __pyx_bstruct_y_vec.strides[0];
__pyx_bshape_0_y_vec = __pyx_bstruct_y_vec.shape[0];
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":241
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":242
* np.ndarray[np.float64_t, ndim=1] y_vec):
* cdef int i, j
* self.avp_pos = vp_pos # <<<<<<<<<<<<<<
@@ -13871,7 +13865,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->avp_pos);
((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->avp_pos = ((PyObject *)__pyx_v_vp_pos);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":242
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":243
* cdef int i, j
* self.avp_pos = vp_pos
* self.avp_dir = vp_dir # <<<<<<<<<<<<<<
@@ -13884,7 +13878,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->avp_dir);
((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->avp_dir = ((PyObject *)__pyx_v_vp_dir);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":243
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":244
* self.avp_pos = vp_pos
* self.avp_dir = vp_dir
* self.acenter = center # <<<<<<<<<<<<<<
@@ -13897,7 +13891,7 @@
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