[yt-svn] commit/yt: 6 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Mar 9 09:32:48 PST 2016
6 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/f493146895b9/
Changeset: f493146895b9
Branch: yt
User: MatthewTurk
Date: 2016-03-05 22:39:46+00:00
Summary: Add a method to compute the minimum level for smoothed covering grids.
Affected #: 1 file
diff -r 8bb44733b706b98bcab4d691ab4bc207e6424a12 -r f493146895b9f9beb05d691e5f2182657863ef49 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -860,6 +860,7 @@
"""
_type_name = "smoothed_covering_grid"
filename = None
+ _min_level = None
@wraps(YTCoveringGrid.__init__)
def __init__(self, *args, **kwargs):
ds = kwargs['ds']
@@ -886,12 +887,46 @@
self._pdata_source.min_level = level_state.current_level
self._pdata_source.max_level = level_state.current_level
+ def _compute_minimum_level(self):
+ # This attempts to determine the minimum level that we should be
+ # starting on for this box. It does this by identifying the minimum
+ # level that could contribute to the minimum bounding box at that
+ # level; that means that all cells from coarser levels will be replaced.
+ if self._min_level is not None:
+ return self._min_level
+ ils = LevelState()
+ min_level = 0
+ for l in range(self.level, 0, -1):
+ dx = self._base_dx / self.ds.relative_refinement(0, l)
+ start_index, end_index, dims = self._minimal_box(dx)
+ ils.left_edge = start_index * dx + self.ds.domain_left_edge
+ ils.right_edge = ils.left_edge + dx * dims
+ ils.current_dx = dx
+ ils.current_level = l
+ self._setup_data_source(ils)
+ # Reset the max_level
+ ils.data_source.min_level = 0
+ ils.data_source.max_level = self.level
+ ils.data_source.loose_selection = True
+ min_level = self.level
+ for chunk in ils.data_source.chunks([], "io"):
+ # With our odd selection methods, we can sometimes get no-sized ires.
+ if chunk.ires.size == 0: continue
+ min_level = min(chunk.ires.min(), min_level)
+ if min_level >= l:
+ break
+ self._min_level = min_level
+ return min_level
def _fill_fields(self, fields):
fields = [f for f in fields if f not in self.field_data]
if len(fields) == 0: return
ls = self._initialize_level_state(fields)
+ min_level = self._compute_minimum_level()
for level in range(self.level + 1):
+ if level < min_level:
+ self._update_level_state(ls)
+ continue
domain_dims = self.ds.domain_dimensions.astype("int64") \
* self.ds.relative_refinement(0, ls.current_level)
tot = ls.current_dims.prod()
https://bitbucket.org/yt_analysis/yt/commits/5127e9201253/
Changeset: 5127e9201253
Branch: yt
User: MatthewTurk
Date: 2016-03-05 23:47:42+00:00
Summary: This speeds things up a fair amount without breaking the tests.
Note a few things -- in case ires is not cached, we only access it one time.
Additionally, we make the assumption that any cells that would contribute to
the preceding levels *will* be selected via non-loose selection. This may be
dangerous, so may not stay in.
Affected #: 1 file
diff -r f493146895b9f9beb05d691e5f2182657863ef49 -r 5127e920125357e7fdcb1d9e1105388bed0bc101 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -906,13 +906,14 @@
self._setup_data_source(ils)
# Reset the max_level
ils.data_source.min_level = 0
- ils.data_source.max_level = self.level
- ils.data_source.loose_selection = True
+ ils.data_source.max_level = l
+ ils.data_source.loose_selection = False
min_level = self.level
for chunk in ils.data_source.chunks([], "io"):
# With our odd selection methods, we can sometimes get no-sized ires.
- if chunk.ires.size == 0: continue
- min_level = min(chunk.ires.min(), min_level)
+ ir = chunk.ires
+ if ir.size == 0: continue
+ min_level = min(ir.min(), min_level)
if min_level >= l:
break
self._min_level = min_level
https://bitbucket.org/yt_analysis/yt/commits/45cb166144db/
Changeset: 45cb166144db
Branch: yt
User: MatthewTurk
Date: 2016-03-06 05:35:41+00:00
Summary: Implement a special case fill_mask_selector for region selectors.
Affected #: 1 file
diff -r 5127e920125357e7fdcb1d9e1105388bed0bc101 -r 45cb166144db8c5737f00d881306e9f9054c3f74 yt/geometry/selection_routines.pyx
--- a/yt/geometry/selection_routines.pyx
+++ b/yt/geometry/selection_routines.pyx
@@ -18,7 +18,7 @@
cimport numpy as np
cimport cython
from libc.stdlib cimport malloc, free
-from yt.utilities.lib.fp_utils cimport fclip, iclip, fmax, fmin
+from yt.utilities.lib.fp_utils cimport fclip, iclip, fmax, fmin, imin, imax
from .oct_container cimport OctreeContainer, OctAllocationContainer, Oct
cimport oct_visitors
from .oct_visitors cimport cind
@@ -806,6 +806,7 @@
cdef np.float64_t right_edge[3]
cdef np.float64_t right_edge_shift[3]
cdef bint loose_selection
+ cdef bint check_period
@cython.boundscheck(False)
@cython.wraparound(False)
@@ -823,6 +824,7 @@
# This is for if we want to include zones that overlap and whose
# centers are not strictly included.
self.loose_selection = getattr(dobj, "loose_selection", False)
+ self.check_period = False
for i in range(3):
region_width[i] = RE[i] - LE[i]
@@ -838,9 +840,11 @@
if p[i]:
# shift so left_edge guaranteed in domain
if LE[i] < DLE[i]:
+ self.check_period = True
LE[i] += DW[i]
RE[i] += DW[i]
elif LE[i] > DRE[i]:
+ self.check_period = True
LE[i] -= DW[i]
RE[i] -= DW[i]
else:
@@ -902,6 +906,52 @@
return 0
return 1
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int fill_mask_selector(self, np.float64_t left_edge[3],
+ np.float64_t right_edge[3],
+ np.float64_t dds[3], int dim[3],
+ np.ndarray[np.uint8_t, ndim=3, cast=True] child_mask,
+ np.ndarray[np.uint8_t, ndim=3] mask,
+ int level):
+ cdef int i, j, k
+ cdef int total = 0, this_level = 0
+ cdef np.float64_t pos[3]
+ if level < self.min_level or level > self.max_level:
+ return 0
+ if level == self.max_level:
+ this_level = 1
+ cdef int si[3], ei[3]
+ #print self.left_edge[0], self.left_edge[1], self.left_edge[2],
+ #print self.right_edge[0], self.right_edge[1], self.right_edge[2],
+ #print self.right_edge_shift[0], self.right_edge_shift[1], self.right_edge_shift[2]
+ if not self.check_period:
+ for i in range(3):
+ si[i] = <int> ((self.left_edge[i] - left_edge[i])/dds[i])
+ ei[i] = <int> ((self.right_edge[i] - left_edge[i])/dds[i])
+ si[i] = iclip(si[i] - 1, 0, dim[i])
+ ei[i] = iclip(ei[i] + 1, 0, dim[i])
+ else:
+ for i in range(3):
+ si[i] = 0
+ ei[i] = dim[i]
+ with nogil:
+ pos[0] = left_edge[0] + (si[0] + 0.5) * dds[0]
+ for i in range(si[0], ei[0]):
+ pos[1] = left_edge[1] + (si[1] + 0.5) * dds[1]
+ for j in range(si[1], ei[1]):
+ pos[2] = left_edge[2] + (si[2] + 0.5) * dds[2]
+ for k in range(si[2], ei[2]):
+ if child_mask[i, j, k] == 1 or this_level == 1:
+ mask[i, j, k] = self.select_cell(pos, dds)
+ total += mask[i, j, k]
+ pos[2] += dds[2]
+ pos[1] += dds[1]
+ pos[0] += dds[0]
+ return total
+
+
def _hash_vals(self):
return (("left_edge[0]", self.left_edge[0]),
("left_edge[1]", self.left_edge[1]),
https://bitbucket.org/yt_analysis/yt/commits/ef83562fe788/
Changeset: ef83562fe788
Branch: yt
User: MatthewTurk
Date: 2016-03-06 16:05:53+00:00
Summary: Fix period checking code.
Affected #: 1 file
diff -r 45cb166144db8c5737f00d881306e9f9054c3f74 -r ef83562fe788decbbeed7cd8524ad88e5f27dd3b yt/geometry/selection_routines.pyx
--- a/yt/geometry/selection_routines.pyx
+++ b/yt/geometry/selection_routines.pyx
@@ -838,13 +838,16 @@
for i in range(3):
if p[i]:
+ # First, we check if any criteria requires a period check,
+ # without any adjustments. This is for short-circuiting the
+ # short-circuit of the loop down below in mask filling.
+ if LE[i] < DLE[i] or LE[i] > DRE[i] or RE[i] > DRE[i]:
+ self.check_period = True
# shift so left_edge guaranteed in domain
if LE[i] < DLE[i]:
- self.check_period = True
LE[i] += DW[i]
RE[i] += DW[i]
elif LE[i] > DRE[i]:
- self.check_period = True
LE[i] -= DW[i]
RE[i] -= DW[i]
else:
https://bitbucket.org/yt_analysis/yt/commits/a74c12c0cbbc/
Changeset: a74c12c0cbbc
Branch: yt
User: MatthewTurk
Date: 2016-03-06 16:06:07+00:00
Summary: Switch to memoryviews for arrays we know are in code units.
Affected #: 1 file
diff -r ef83562fe788decbbeed7cd8524ad88e5f27dd3b -r a74c12c0cbbcf5510e94a087cafd0f1226341195 yt/geometry/selection_routines.pyx
--- a/yt/geometry/selection_routines.pyx
+++ b/yt/geometry/selection_routines.pyx
@@ -814,11 +814,11 @@
cdef int i
# We are modifying dobj.left_edge and dobj.right_edge , so here we will
# do an in-place conversion of those arrays.
- cdef np.ndarray[np.float64_t, ndim=1] RE = _ensure_code(dobj.right_edge)
- cdef np.ndarray[np.float64_t, ndim=1] LE = _ensure_code(dobj.left_edge)
- cdef np.ndarray[np.float64_t, ndim=1] DW = _ensure_code(dobj.ds.domain_width)
- cdef np.ndarray[np.float64_t, ndim=1] DLE = _ensure_code(dobj.ds.domain_left_edge)
- cdef np.ndarray[np.float64_t, ndim=1] DRE = _ensure_code(dobj.ds.domain_right_edge)
+ cdef np.float64_t[:] RE = _ensure_code(dobj.right_edge)
+ cdef np.float64_t[:] LE = _ensure_code(dobj.left_edge)
+ cdef np.float64_t[:] DW = _ensure_code(dobj.ds.domain_width)
+ cdef np.float64_t[:] DLE = _ensure_code(dobj.ds.domain_left_edge)
+ cdef np.float64_t[:] DRE = _ensure_code(dobj.ds.domain_right_edge)
cdef np.float64_t region_width[3]
cdef bint p[3]
# This is for if we want to include zones that overlap and whose
https://bitbucket.org/yt_analysis/yt/commits/14b7d1b6b906/
Changeset: 14b7d1b6b906
Branch: yt
User: atmyers
Date: 2016-03-09 17:32:34+00:00
Summary: Merged in MatthewTurk/yt (pull request #2025)
Ghost zone optimization and experimentation
Affected #: 2 files
diff -r 7bc62a2db2deb15cade23e01644d40baff873d96 -r 14b7d1b6b9060f8364cff88cc0f006a8c1a7e9e6 yt/data_objects/construction_data_containers.py
--- a/yt/data_objects/construction_data_containers.py
+++ b/yt/data_objects/construction_data_containers.py
@@ -860,6 +860,7 @@
"""
_type_name = "smoothed_covering_grid"
filename = None
+ _min_level = None
@wraps(YTCoveringGrid.__init__)
def __init__(self, *args, **kwargs):
ds = kwargs['ds']
@@ -886,12 +887,47 @@
self._pdata_source.min_level = level_state.current_level
self._pdata_source.max_level = level_state.current_level
+ def _compute_minimum_level(self):
+ # This attempts to determine the minimum level that we should be
+ # starting on for this box. It does this by identifying the minimum
+ # level that could contribute to the minimum bounding box at that
+ # level; that means that all cells from coarser levels will be replaced.
+ if self._min_level is not None:
+ return self._min_level
+ ils = LevelState()
+ min_level = 0
+ for l in range(self.level, 0, -1):
+ dx = self._base_dx / self.ds.relative_refinement(0, l)
+ start_index, end_index, dims = self._minimal_box(dx)
+ ils.left_edge = start_index * dx + self.ds.domain_left_edge
+ ils.right_edge = ils.left_edge + dx * dims
+ ils.current_dx = dx
+ ils.current_level = l
+ self._setup_data_source(ils)
+ # Reset the max_level
+ ils.data_source.min_level = 0
+ ils.data_source.max_level = l
+ ils.data_source.loose_selection = False
+ min_level = self.level
+ for chunk in ils.data_source.chunks([], "io"):
+ # With our odd selection methods, we can sometimes get no-sized ires.
+ ir = chunk.ires
+ if ir.size == 0: continue
+ min_level = min(ir.min(), min_level)
+ if min_level >= l:
+ break
+ self._min_level = min_level
+ return min_level
def _fill_fields(self, fields):
fields = [f for f in fields if f not in self.field_data]
if len(fields) == 0: return
ls = self._initialize_level_state(fields)
+ min_level = self._compute_minimum_level()
for level in range(self.level + 1):
+ if level < min_level:
+ self._update_level_state(ls)
+ continue
domain_dims = self.ds.domain_dimensions.astype("int64") \
* self.ds.relative_refinement(0, ls.current_level)
tot = ls.current_dims.prod()
diff -r 7bc62a2db2deb15cade23e01644d40baff873d96 -r 14b7d1b6b9060f8364cff88cc0f006a8c1a7e9e6 yt/geometry/selection_routines.pyx
--- a/yt/geometry/selection_routines.pyx
+++ b/yt/geometry/selection_routines.pyx
@@ -18,7 +18,7 @@
cimport numpy as np
cimport cython
from libc.stdlib cimport malloc, free
-from yt.utilities.lib.fp_utils cimport fclip, iclip, fmax, fmin
+from yt.utilities.lib.fp_utils cimport fclip, iclip, fmax, fmin, imin, imax
from .oct_container cimport OctreeContainer, OctAllocationContainer, Oct
cimport oct_visitors
from .oct_visitors cimport cind
@@ -806,6 +806,7 @@
cdef np.float64_t right_edge[3]
cdef np.float64_t right_edge_shift[3]
cdef bint loose_selection
+ cdef bint check_period
@cython.boundscheck(False)
@cython.wraparound(False)
@@ -813,16 +814,17 @@
cdef int i
# We are modifying dobj.left_edge and dobj.right_edge , so here we will
# do an in-place conversion of those arrays.
- cdef np.ndarray[np.float64_t, ndim=1] RE = _ensure_code(dobj.right_edge)
- cdef np.ndarray[np.float64_t, ndim=1] LE = _ensure_code(dobj.left_edge)
- cdef np.ndarray[np.float64_t, ndim=1] DW = _ensure_code(dobj.ds.domain_width)
- cdef np.ndarray[np.float64_t, ndim=1] DLE = _ensure_code(dobj.ds.domain_left_edge)
- cdef np.ndarray[np.float64_t, ndim=1] DRE = _ensure_code(dobj.ds.domain_right_edge)
+ cdef np.float64_t[:] RE = _ensure_code(dobj.right_edge)
+ cdef np.float64_t[:] LE = _ensure_code(dobj.left_edge)
+ cdef np.float64_t[:] DW = _ensure_code(dobj.ds.domain_width)
+ cdef np.float64_t[:] DLE = _ensure_code(dobj.ds.domain_left_edge)
+ cdef np.float64_t[:] DRE = _ensure_code(dobj.ds.domain_right_edge)
cdef np.float64_t region_width[3]
cdef bint p[3]
# This is for if we want to include zones that overlap and whose
# centers are not strictly included.
self.loose_selection = getattr(dobj, "loose_selection", False)
+ self.check_period = False
for i in range(3):
region_width[i] = RE[i] - LE[i]
@@ -836,6 +838,11 @@
for i in range(3):
if p[i]:
+ # First, we check if any criteria requires a period check,
+ # without any adjustments. This is for short-circuiting the
+ # short-circuit of the loop down below in mask filling.
+ if LE[i] < DLE[i] or LE[i] > DRE[i] or RE[i] > DRE[i]:
+ self.check_period = True
# shift so left_edge guaranteed in domain
if LE[i] < DLE[i]:
LE[i] += DW[i]
@@ -902,6 +909,52 @@
return 0
return 1
+ @cython.boundscheck(False)
+ @cython.wraparound(False)
+ @cython.cdivision(True)
+ cdef int fill_mask_selector(self, np.float64_t left_edge[3],
+ np.float64_t right_edge[3],
+ np.float64_t dds[3], int dim[3],
+ np.ndarray[np.uint8_t, ndim=3, cast=True] child_mask,
+ np.ndarray[np.uint8_t, ndim=3] mask,
+ int level):
+ cdef int i, j, k
+ cdef int total = 0, this_level = 0
+ cdef np.float64_t pos[3]
+ if level < self.min_level or level > self.max_level:
+ return 0
+ if level == self.max_level:
+ this_level = 1
+ cdef int si[3], ei[3]
+ #print self.left_edge[0], self.left_edge[1], self.left_edge[2],
+ #print self.right_edge[0], self.right_edge[1], self.right_edge[2],
+ #print self.right_edge_shift[0], self.right_edge_shift[1], self.right_edge_shift[2]
+ if not self.check_period:
+ for i in range(3):
+ si[i] = <int> ((self.left_edge[i] - left_edge[i])/dds[i])
+ ei[i] = <int> ((self.right_edge[i] - left_edge[i])/dds[i])
+ si[i] = iclip(si[i] - 1, 0, dim[i])
+ ei[i] = iclip(ei[i] + 1, 0, dim[i])
+ else:
+ for i in range(3):
+ si[i] = 0
+ ei[i] = dim[i]
+ with nogil:
+ pos[0] = left_edge[0] + (si[0] + 0.5) * dds[0]
+ for i in range(si[0], ei[0]):
+ pos[1] = left_edge[1] + (si[1] + 0.5) * dds[1]
+ for j in range(si[1], ei[1]):
+ pos[2] = left_edge[2] + (si[2] + 0.5) * dds[2]
+ for k in range(si[2], ei[2]):
+ if child_mask[i, j, k] == 1 or this_level == 1:
+ mask[i, j, k] = self.select_cell(pos, dds)
+ total += mask[i, j, k]
+ pos[2] += dds[2]
+ pos[1] += dds[1]
+ pos[0] += dds[0]
+ return total
+
+
def _hash_vals(self):
return (("left_edge[0]", self.left_edge[0]),
("left_edge[1]", self.left_edge[1]),
Repository URL: https://bitbucket.org/yt_analysis/yt/
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