[Yt-svn] yt: 12 new changesets
hg at spacepope.org
hg at spacepope.org
Sun Jun 6 15:16:23 PDT 2010
hg Repository: yt
details: yt/rev/cf72cd0296b9
changeset: 1734:cf72cd0296b9
user: Matthew Turk <matthewturk at gmail.com>
date:
Fri Jun 04 20:02:06 2010 -0700
description:
Adding docstrings in NumPy format to the FixedResolutionBuffer object.
hg Repository: yt
details: yt/rev/c8794ff7e84c
changeset: 1735:c8794ff7e84c
user: mturk
date:
Tue Jun 01 09:55:13 2010 -0700
description:
[svn r1736] Adding initial import of coding standards and docstring examples and idioms.
hg Repository: yt
details: yt/rev/ec092fc90fe0
changeset: 1736:ec092fc90fe0
user: dcollins
date:
Wed Jun 02 15:40:28 2010 -0700
description:
[svn r1737] Added image scaling to green and alpha channels
hg Repository: yt
details: yt/rev/788da1687cb0
changeset: 1737:788da1687cb0
user: mturk
date:
Fri Jun 04 19:53:12 2010 -0700
description:
[svn r1738] This should fix the case where data_style == enzo_packed_3d *and* the paths in
the hierarchy are absolute.
hg Repository: yt
details: yt/rev/d2a7a9253995
changeset: 1738:d2a7a9253995
user: mturk
date:
Fri Jun 04 22:57:48 2010 -0700
description:
[svn r1739] Adding the long-overdue import of FRB-related machinery into mods.py.
hg Repository: yt
details: yt/rev/b35c5a27743c
changeset: 1739:b35c5a27743c
user: Matthew Turk <matthewturk at gmail.com>
date:
Fri Jun 04 23:16:55 2010 -0700
description:
Merging from trunk
hg Repository: yt
details: yt/rev/25e560e75758
changeset: 1740:25e560e75758
user: Matthew Turk <matthewturk at gmail.com>
date:
Sun Jun 06 00:32:09 2010 -0700
description:
Making progress on documenting the PlotCollection.
hg Repository: yt
details: yt/rev/2c90c3422bd6
changeset: 1741:2c90c3422bd6
user: Matthew Turk <matthewturk at gmail.com>
date:
Sun Jun 06 17:59:33 2010 -0400
description:
Adding a bunch of docstrings and removed the add_slice_interpolated.
hg Repository: yt
details: yt/rev/b61c678bc5ca
changeset: 1742:b61c678bc5ca
user: Matthew Turk <matthewturk at gmail.com>
date:
Sun Jun 06 18:14:04 2010 -0400
description:
Sam says this fixes non-equal width/height image saving
hg Repository: yt
details: yt/rev/e47760306070
changeset: 1743:e47760306070
user: Matthew Turk <matthewturk at gmail.com>
date:
Sun Jun 06 18:14:40 2010 -0400
description:
Re-cythonized
hg Repository: yt
details: yt/rev/0b03d9c92d1c
changeset: 1744:0b03d9c92d1c
user: Matthew Turk <matthewturk at gmail.com>
date:
Sun Jun 06 18:15:40 2010 -0400
description:
Fixed doc compilation failures
hg Repository: yt
details: yt/rev/810aa16f6441
changeset: 1745:810aa16f6441
user: Matthew Turk <matthewturk at gmail.com>
date:
Sun Jun 06 18:16:06 2010 -0400
description:
Merging
diffstat:
yt/_amr_utils/png_writer.pyx | 4 +-
yt/amr_utils.c | 1159 +++++++++++++++++-------------------
yt/extensions/MergerTree.py | 9 +-
yt/extensions/image_writer.py | 4 +
yt/extensions/kdtree/fKD.f90 | 173 +++++-
yt/extensions/kdtree/fKD.v | 42 +-
yt/extensions/kdtree/fKD_source.f90 | 10 +-
yt/lagos/HierarchyType.py | 2 +-
yt/lagos/OutputTypes.py | 19 +-
yt/lagos/StructureFunctionGenerator.py | 750 ------------------------
yt/lagos/TwoPointFunctions.py | 796 +++++++++++++++++++++++++
yt/lagos/__init__.py | 2 +-
yt/lagos/parallelHOP/parallelHOP.py | 9 +-
yt/mods.py | 6 +-
yt/raven/FixedResolution.py | 148 ++++-
yt/raven/PlotCollection.py | 464 +++++++++++---
yt/raven/PlotTypes.py | 6 +-
17 files changed, 2097 insertions(+), 1506 deletions(-)
diffs (truncated from 6358 to 300 lines):
diff -r d74f191d9663 -r 810aa16f6441 yt/_amr_utils/png_writer.pyx
--- a/yt/_amr_utils/png_writer.pyx Thu Jun 03 15:23:06 2010 -0700
+++ b/yt/_amr_utils/png_writer.pyx Sun Jun 06 18:16:06 2010 -0400
@@ -104,8 +104,8 @@
# This is something of a translation of the matplotlib _png module
cdef png_byte *pix_buffer = <png_byte *> buffer.data
- cdef int width = buffer.shape[0]
- cdef int height = buffer.shape[1]
+ cdef int width = buffer.shape[1]
+ cdef int height = buffer.shape[0]
cdef FILE* fileobj = fopen(filename, "wb")
cdef png_bytep *row_pointers
diff -r d74f191d9663 -r 810aa16f6441 yt/amr_utils.c
--- a/yt/amr_utils.c Thu Jun 03 15:23:06 2010 -0700
+++ b/yt/amr_utils.c Sun Jun 06 18:16:06 2010 -0400
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.12.1 on Wed May 26 14:57:59 2010 */
+/* Generated by Cython 0.12.1 on Sun Jun 6 18:13:46 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -482,7 +482,7 @@
PyObject *grids;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":549
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":552
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -515,7 +515,7 @@
int refined_pos;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":517
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":520
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -580,7 +580,7 @@
__pyx_t_5numpy_float64_t *y_vec;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":294
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":293
* tv[offset + k] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -606,7 +606,7 @@
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":517
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":520
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -634,7 +634,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_TransferFunctionProxy *__pyx_vtabptr_2yt_9amr_utils_TransferFunctionProxy;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":549
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":552
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -665,7 +665,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_QuadTree *__pyx_vtabptr_2yt_9amr_utils_QuadTree;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":223
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":222
* #rgba[i+3] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
*
* cdef class VectorPlane: # <<<<<<<<<<<<<<
@@ -681,7 +681,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_VectorPlane *__pyx_vtabptr_2yt_9amr_utils_VectorPlane;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":294
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":293
* tv[offset + k] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -13550,106 +13550,27 @@
static void __pyx_f_2yt_9amr_utils_21TransferFunctionProxy_eval_transfer(struct __pyx_obj_2yt_9amr_utils_TransferFunctionProxy *__pyx_v_self, __pyx_t_5numpy_float64_t __pyx_v_dt, __pyx_t_5numpy_float64_t *__pyx_v_dvs, __pyx_t_5numpy_float64_t *__pyx_v_rgba, __pyx_t_5numpy_float64_t *__pyx_v_grad) {
int __pyx_v_i;
int __pyx_v_fid;
- int __pyx_v_use;
__pyx_t_5numpy_float64_t __pyx_v_ta;
__pyx_t_5numpy_float64_t __pyx_v_trgba[6];
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_t_5;
__Pyx_RefNannySetupContext("eval_transfer");
__Pyx_INCREF((PyObject *)__pyx_v_self);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":188
- * # early-cutoff. We check all the field tables, because we want to be
- * # able to attenuate even in the presence of no emissivity.
- * use = 0 # <<<<<<<<<<<<<<
- * for i in range(self.n_field_tables):
- * fid = self.field_tables[i].field_id
- */
- __pyx_v_use = 0;
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":189
- * # able to attenuate even in the presence of no emissivity.
- * use = 0
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":194
+ * # use = 1
+ * # break
* for i in range(self.n_field_tables): # <<<<<<<<<<<<<<
- * fid = self.field_tables[i].field_id
- * if (dvs[fid] >= self.field_tables[i].bounds[0]) and \
+ * self.istorage[i] = FIT_get_value(&self.field_tables[i], dvs)
+ * # We have to do this after the interpolation
*/
__pyx_t_1 = __pyx_v_self->n_field_tables;
for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
__pyx_v_i = __pyx_t_2;
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":190
- * use = 0
- * for i in range(self.n_field_tables):
- * fid = self.field_tables[i].field_id # <<<<<<<<<<<<<<
- * if (dvs[fid] >= self.field_tables[i].bounds[0]) and \
- * (dvs[fid] <= self.field_tables[i].bounds[1]):
- */
- __pyx_v_fid = (__pyx_v_self->field_tables[__pyx_v_i]).field_id;
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":191
- * for i in range(self.n_field_tables):
- * fid = self.field_tables[i].field_id
- * if (dvs[fid] >= self.field_tables[i].bounds[0]) and \ # <<<<<<<<<<<<<<
- * (dvs[fid] <= self.field_tables[i].bounds[1]):
- * use = 1
- */
- __pyx_t_3 = ((__pyx_v_dvs[__pyx_v_fid]) >= ((__pyx_v_self->field_tables[__pyx_v_i]).bounds[0]));
- if (__pyx_t_3) {
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":192
- * fid = self.field_tables[i].field_id
- * if (dvs[fid] >= self.field_tables[i].bounds[0]) and \
- * (dvs[fid] <= self.field_tables[i].bounds[1]): # <<<<<<<<<<<<<<
- * use = 1
- * break
- */
- __pyx_t_4 = ((__pyx_v_dvs[__pyx_v_fid]) <= ((__pyx_v_self->field_tables[__pyx_v_i]).bounds[1]));
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_3;
- }
- if (__pyx_t_5) {
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":193
- * if (dvs[fid] >= self.field_tables[i].bounds[0]) and \
- * (dvs[fid] <= self.field_tables[i].bounds[1]):
- * use = 1 # <<<<<<<<<<<<<<
- * break
- * for i in range(self.n_field_tables):
- */
- __pyx_v_use = 1;
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":194
- * (dvs[fid] <= self.field_tables[i].bounds[1]):
- * use = 1
- * break # <<<<<<<<<<<<<<
- * for i in range(self.n_field_tables):
- * self.istorage[i] = FIT_get_value(&self.field_tables[i], dvs)
- */
- goto __pyx_L4_break;
- goto __pyx_L5;
- }
- __pyx_L5:;
- }
- __pyx_L4_break:;
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":195
- * use = 1
- * break
- * for i in range(self.n_field_tables): # <<<<<<<<<<<<<<
- * self.istorage[i] = FIT_get_value(&self.field_tables[i], dvs)
- * # We have to do this after the interpolation
- */
- __pyx_t_1 = __pyx_v_self->n_field_tables;
- for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
- __pyx_v_i = __pyx_t_2;
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":196
- * break
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":195
+ * # break
* for i in range(self.n_field_tables):
* self.istorage[i] = FIT_get_value(&self.field_tables[i], dvs) # <<<<<<<<<<<<<<
* # We have to do this after the interpolation
@@ -13658,7 +13579,7 @@
(__pyx_v_self->istorage[__pyx_v_i]) = __pyx_f_2yt_9amr_utils_FIT_get_value((&(__pyx_v_self->field_tables[__pyx_v_i])), __pyx_v_dvs);
}
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":198
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":197
* self.istorage[i] = FIT_get_value(&self.field_tables[i], dvs)
* # We have to do this after the interpolation
* for i in range(self.n_field_tables): # <<<<<<<<<<<<<<
@@ -13669,7 +13590,7 @@
for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
__pyx_v_i = __pyx_t_2;
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":199
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":198
* # We have to do this after the interpolation
* for i in range(self.n_field_tables):
* fid = self.field_tables[i].weight_table_id # <<<<<<<<<<<<<<
@@ -13678,22 +13599,22 @@
*/
__pyx_v_fid = (__pyx_v_self->field_tables[__pyx_v_i]).weight_table_id;
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":200
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":199
* for i in range(self.n_field_tables):
* fid = self.field_tables[i].weight_table_id
* if fid != -1: self.istorage[i] *= self.istorage[fid] # <<<<<<<<<<<<<<
* for i in range(6):
* trgba[i] = self.istorage[self.field_table_ids[i]]
*/
- __pyx_t_5 = (__pyx_v_fid != -1);
- if (__pyx_t_5) {
+ __pyx_t_3 = (__pyx_v_fid != -1);
+ if (__pyx_t_3) {
(__pyx_v_self->istorage[__pyx_v_i]) *= (__pyx_v_self->istorage[__pyx_v_fid]);
- goto __pyx_L10;
- }
- __pyx_L10:;
- }
-
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":201
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
+ }
+
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":200
* fid = self.field_tables[i].weight_table_id
* if fid != -1: self.istorage[i] *= self.istorage[fid]
* for i in range(6): # <<<<<<<<<<<<<<
@@ -13703,7 +13624,7 @@
for (__pyx_t_1 = 0; __pyx_t_1 < 6; __pyx_t_1+=1) {
__pyx_v_i = __pyx_t_1;
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":202
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":201
* if fid != -1: self.istorage[i] *= self.istorage[fid]
* for i in range(6):
* trgba[i] = self.istorage[self.field_table_ids[i]] # <<<<<<<<<<<<<<
@@ -13713,7 +13634,7 @@
(__pyx_v_trgba[__pyx_v_i]) = (__pyx_v_self->istorage[(__pyx_v_self->field_table_ids[__pyx_v_i])]);
}
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":212
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":211
* # integration here:
* # I_{i+1} = ds * C_i + (1.0 - ds*alpha_i) * I_i
* for i in range(3): # <<<<<<<<<<<<<<
@@ -13723,7 +13644,7 @@
for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) {
__pyx_v_i = __pyx_t_1;
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":216
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":215
* # slice. Previously it was ill-defined, but represented some
* # measure of emissivity.
* ta = fmax((1.0 - dt*trgba[i+3]), 0.0) # <<<<<<<<<<<<<<
@@ -13732,7 +13653,7 @@
*/
__pyx_v_ta = __pyx_f_2yt_9amr_utils_fmax((1.0 - (__pyx_v_dt * (__pyx_v_trgba[(__pyx_v_i + 3)]))), 0.0);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":217
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":216
* # measure of emissivity.
* ta = fmax((1.0 - dt*trgba[i+3]), 0.0)
* rgba[i ] = dt*trgba[i ] + ta * rgba[i ] # <<<<<<<<<<<<<<
@@ -13746,7 +13667,7 @@
__Pyx_RefNannyFinishContext();
}
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":233
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":232
* cdef np.float64_t *x_vec, *y_vec
*
* def __cinit__(self, # <<<<<<<<<<<<<<
@@ -13819,41 +13740,41 @@
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 = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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