[Yt-svn] yt: Fixed channel linkages. Emission scale for ColorTransferFun...
hg at spacepope.org
hg at spacepope.org
Thu Apr 1 01:03:43 PDT 2010
hg Repository: yt
details: yt/rev/b02c9c1919db
changeset: 1511:b02c9c1919db
user: Matthew Turk <matthewturk at gmail.com>
date:
Thu Apr 01 01:03:30 2010 -0700
description:
Fixed channel linkages. Emission scale for ColorTransferFunction is still not
clear to me. The correct mechanism for identifying the emission and absorption
for false-color, non-continuous items is in general not clear to me either.
diffstat:
yt/_amr_utils/VolumeIntegrator.pyx | 6 +
yt/amr_utils.c | 934 +++++++++++++-------------
yt/extensions/volume_rendering/TransferFunction.py | 18 +-
3 files changed, 477 insertions(+), 481 deletions(-)
diffs (truncated from 3221 to 300 lines):
diff -r cdd9081a939a -r b02c9c1919db yt/_amr_utils/VolumeIntegrator.pyx
--- a/yt/_amr_utils/VolumeIntegrator.pyx Wed Mar 31 23:53:37 2010 -0700
+++ b/yt/_amr_utils/VolumeIntegrator.pyx Thu Apr 01 01:03:30 2010 -0700
@@ -195,9 +195,15 @@
# integration here:
# I_{i+1} = ds * C_i + (1.0 - ds*alpha_i) * I_i
for i in range(3):
+ # This is the new way: alpha corresponds to opacity of a given
+ # slice. Previously it was ill-defined, but represented some
+ # measure of emissivity.
ta = (1.0 - dt*trgba[i+3])
rgba[i ] = dt*trgba[i ] + ta * rgba[i ]
rgba[i+3] = dt*trgba[i+3] + ta * rgba[i+3]
+ # This is the old way:
+ #rgba[i ] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
+ #rgba[i+3] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
cdef class VectorPlane:
cdef public object avp_pos, avp_dir, acenter, aimage
diff -r cdd9081a939a -r b02c9c1919db yt/amr_utils.c
--- a/yt/amr_utils.c Wed Mar 31 23:53:37 2010 -0700
+++ b/yt/amr_utils.c Thu Apr 01 01:03:30 2010 -0700
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.12.1 on Wed Mar 31 20:44:53 2010 */
+/* Generated by Cython 0.12.1 on Thu Apr 1 00:44:35 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -460,7 +460,7 @@
PyObject *grids;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":519
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":521
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -493,7 +493,7 @@
int refined_pos;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":487
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":489
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -539,7 +539,7 @@
__pyx_t_5numpy_float64_t *y_vec;
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":266
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":268
* tv[(((k*self.nv[1])+j)*self.nv[0]+i)] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -565,7 +565,7 @@
};
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":519
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":521
* return 1
*
* cdef class ProtoPrism: # <<<<<<<<<<<<<<
@@ -579,8 +579,8 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_ProtoPrism *__pyx_vtabptr_2yt_9amr_utils_ProtoPrism;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":202
- * rgba[i+3] = dt*trgba[i+3] + ta * rgba[i+3]
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":204
+ * #rgba[i+3] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
*
* cdef class VectorPlane: # <<<<<<<<<<<<<<
* cdef public object avp_pos, avp_dir, acenter, aimage
@@ -595,7 +595,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_VectorPlane *__pyx_vtabptr_2yt_9amr_utils_VectorPlane;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":266
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":268
* tv[(((k*self.nv[1])+j)*self.nv[0]+i)] = fv[k]
*
* cdef class PartitionedGrid: # <<<<<<<<<<<<<<
@@ -611,7 +611,7 @@
static struct __pyx_vtabstruct_2yt_9amr_utils_PartitionedGrid *__pyx_vtabptr_2yt_9amr_utils_PartitionedGrid;
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":487
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":489
* tf.eval_transfer(dt, self.dvs, rgba, grad)
*
* cdef class GridFace: # <<<<<<<<<<<<<<
@@ -13452,7 +13452,7 @@
* ta = (1.0 - dt*trgba[i+3])
* rgba[i ] = dt*trgba[i ] + ta * rgba[i ] # <<<<<<<<<<<<<<
* rgba[i+3] = dt*trgba[i+3] + ta * rgba[i+3]
- *
+ * #rgba[i ] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
*/
(__pyx_v_rgba[__pyx_v_i]) = ((__pyx_v_dt * (__pyx_v_trgba[__pyx_v_i])) + (__pyx_v_ta * (__pyx_v_rgba[__pyx_v_i])));
@@ -13460,8 +13460,8 @@
* ta = (1.0 - dt*trgba[i+3])
* rgba[i ] = dt*trgba[i ] + ta * rgba[i ]
* rgba[i+3] = dt*trgba[i+3] + ta * rgba[i+3] # <<<<<<<<<<<<<<
- *
- * cdef class VectorPlane:
+ * #rgba[i ] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
+ * #rgba[i+3] += trgba[i] * (1.0 - rgba[i+3])*dt*trgba[i+3]
*/
(__pyx_v_rgba[(__pyx_v_i + 3)]) = ((__pyx_v_dt * (__pyx_v_trgba[(__pyx_v_i + 3)])) + (__pyx_v_ta * (__pyx_v_rgba[(__pyx_v_i + 3)])));
}
@@ -13470,7 +13470,7 @@
__Pyx_RefNannyFinishContext();
}
-/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":210
+/* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":212
* cdef np.float64_t *x_vec, *y_vec
*
* def __cinit__(self, # <<<<<<<<<<<<<<
@@ -13543,41 +13543,41 @@
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 = 210; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __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 = 210; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 2); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __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 = 210; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 3); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __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 = 210; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 4); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __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 = 210; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 7, 7, 5); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __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 = 210; __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 = 212; __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 = 212; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
__pyx_v_vp_pos = ((PyArrayObject *)values[0]);
__pyx_v_vp_dir = ((PyArrayObject *)values[1]);
@@ -13599,7 +13599,7 @@
}
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 = 210; __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 = 212; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("yt.amr_utils.VectorPlane.__cinit__");
return -1;
@@ -13618,50 +13618,50 @@
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- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vp_dir), __pyx_ptype_5numpy_ndarray, 1, "vp_dir", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_x_vec), __pyx_ptype_5numpy_ndarray, 1, "x_vec", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_y_vec), __pyx_ptype_5numpy_ndarray, 1, "y_vec", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{
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{
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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 = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{
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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 = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{
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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 = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ 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 = 212; __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":219
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":221
* np.ndarray[np.float64_t, ndim=1] y_vec):
* cdef int i, j
* self.avp_pos = vp_pos # <<<<<<<<<<<<<<
@@ -13674,7 +13674,7 @@
__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":220
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":222
* cdef int i, j
* self.avp_pos = vp_pos
* self.avp_dir = vp_dir # <<<<<<<<<<<<<<
@@ -13687,7 +13687,7 @@
__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":221
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":223
* self.avp_pos = vp_pos
* self.avp_dir = vp_dir
* self.acenter = center # <<<<<<<<<<<<<<
@@ -13700,7 +13700,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->acenter);
((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->acenter = ((PyObject *)__pyx_v_center);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":222
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":224
* self.avp_dir = vp_dir
* self.acenter = center
* self.aimage = image # <<<<<<<<<<<<<<
@@ -13713,7 +13713,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->aimage);
((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->aimage = ((PyObject *)__pyx_v_image);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":223
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":225
* self.acenter = center
* self.aimage = image
* self.ax_vec = x_vec # <<<<<<<<<<<<<<
@@ -13726,7 +13726,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->ax_vec);
((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->ax_vec = ((PyObject *)__pyx_v_x_vec);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":224
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":226
* self.aimage = image
* self.ax_vec = x_vec
* self.ay_vec = y_vec # <<<<<<<<<<<<<<
@@ -13739,7 +13739,7 @@
__Pyx_DECREF(((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->ay_vec);
((struct __pyx_obj_2yt_9amr_utils_VectorPlane *)__pyx_v_self)->ay_vec = ((PyObject *)__pyx_v_y_vec);
- /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":225
+ /* "/Users/matthewturk/yt/yt/yt/_amr_utils/VolumeIntegrator.pyx":227
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