[yt-svn] commit/yt: 3 new changesets
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commits-noreply at bitbucket.org
Sat Sep 24 14:00:34 PDT 2016
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/9380c2c09e07/
Changeset: 9380c2c09e07
Branch: yt
User: ngoldbaum
Date: 2016-09-05 15:57:03+00:00
Summary: Fix type issue in octree construction. Closes #1272
Affected #: 2 files
diff -r 068ad05bda58e31a1684d907398a61ce93fd595c -r 9380c2c09e078c7a706d068958d7df74ebdbe491 yt/frontends/stream/tests/test_stream_octree.py
--- /dev/null
+++ b/yt/frontends/stream/tests/test_stream_octree.py
@@ -0,0 +1,26 @@
+import yt
+import numpy as np
+
+OCT_MASK_LIST = [8, 0, 0, 0, 0, 8, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0,
+ 8, 0, 0, 0, 0, 0, 0, 0,
+ 0]
+
+
+def test_octree():
+ # See Issue #1272
+ octree_mask = np.array(OCT_MASK_LIST, dtype=np.uint8)
+
+ quantities = {}
+ quantities[('gas', 'density')] = np.ones((22, 1), dtype=float)
+
+ bbox = np.array([[-10., 10.], [-10., 10.], [-10., 10.]])
+
+ ds = yt.load_octree(octree_mask=octree_mask,
+ data=quantities,
+ bbox=bbox,
+ over_refine_factor=0,
+ partial_coverage=0)
+
+ proj = ds.proj('density', 'x')
+ proj['density']
diff -r 068ad05bda58e31a1684d907398a61ce93fd595c -r 9380c2c09e078c7a706d068958d7df74ebdbe491 yt/geometry/oct_visitors.pxd
--- a/yt/geometry/oct_visitors.pxd
+++ b/yt/geometry/oct_visitors.pxd
@@ -100,7 +100,7 @@
cdef class FillFileIndicesO(OctVisitor):
cdef np.uint8_t[:] levels
- cdef np.uint8_t[:] file_inds
+ cdef np.int64_t[:] file_inds
cdef np.uint8_t[:] cell_inds
cdef class FillFileIndicesR(OctVisitor):
https://bitbucket.org/yt_analysis/yt/commits/67d9c9260497/
Changeset: 67d9c9260497
Branch: yt
User: ngoldbaum
Date: 2016-09-23 17:51:20+00:00
Summary: update load_octree docstrings
Affected #: 1 file
diff -r 9380c2c09e078c7a706d068958d7df74ebdbe491 -r 67d9c9260497877eb4aa57f8d935eb4106cd85e4 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -1497,10 +1497,13 @@
Parameters
----------
octree_mask : np.ndarray[uint8_t]
- This is a depth-first refinement mask for an Octree. It should be of
- size n_octs * 8, where each item is 1 for an oct-cell being refined and
- 0 for it not being refined. Note that for over_refine_factors != 1,
- the children count will still be 8, so this is always 8.
+ This is a depth-first refinement mask for an Octree. It should be
+ of size n_octs * 8 (but see note about the root oct below), where
+ each item is 1 for an oct-cell being refined and 0 for it not being
+ refined. For over_refine_factors != 1, the children count will
+ still be 8, so there will stil be n_octs * 8 entries. Note that if
+ the root oct is not refined, there will be only one entry
+ for the root, so the size of the mask will be (n_octs - 1)*8 + 1.
data : dict
A dictionary of 1D arrays. Note that these must of the size of the
number of "False" values in the ``octree_mask``.
@@ -1522,8 +1525,29 @@
Determines whether the data will be treated as periodic along
each axis
partial_coverage : boolean
- Whether or not an oct can be refined cell-by-cell, or whether all 8 get
- refined.
+ Whether or not an oct can be refined cell-by-cell, or whether all
+ 8 get refined.
+
+ Example
+ -------
+
+ >>> import yt
+ >>> import numpy as np
+ >>> oct_mask = [8, 0, 0, 0, 0, 8, 0, 8,
+ ... 0, 0, 0, 0, 0, 0, 0, 0,
+ ... 8, 0, 0, 0, 0, 0, 0, 0,
+ ... 0]
+ >>>
+ >>> octree_mask = np.array(oct_mask, dtype=np.uint8)
+ >>> quantities = {}
+ >>> quantities['gas', 'density'] = np.random.random((22, 1), dtype='f8')
+ >>> bbox = np.array([[-10., 10.], [-10., 10.], [-10., 10.]])
+ >>>
+ >>> ds = yt.load_octree(octree_mask=octree_mask,
+ ... data=quantities,
+ ... bbox=bbox,
+ ... over_refine_factor=0,
+ ... partial_coverage=0)
"""
https://bitbucket.org/yt_analysis/yt/commits/af34b428166a/
Changeset: af34b428166a
Branch: yt
User: xarthisius
Date: 2016-09-24 21:00:06+00:00
Summary: Merged in ngoldbaum/yt (pull request #2362)
Fix type issue in octree construction. Closes #1272
Affected #: 3 files
diff -r 71960f84ae9d3e12d70759e342b2bc581581674c -r af34b428166a02df3f069fa33f5df3ca8cf58545 yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -1497,10 +1497,13 @@
Parameters
----------
octree_mask : np.ndarray[uint8_t]
- This is a depth-first refinement mask for an Octree. It should be of
- size n_octs * 8, where each item is 1 for an oct-cell being refined and
- 0 for it not being refined. Note that for over_refine_factors != 1,
- the children count will still be 8, so this is always 8.
+ This is a depth-first refinement mask for an Octree. It should be
+ of size n_octs * 8 (but see note about the root oct below), where
+ each item is 1 for an oct-cell being refined and 0 for it not being
+ refined. For over_refine_factors != 1, the children count will
+ still be 8, so there will stil be n_octs * 8 entries. Note that if
+ the root oct is not refined, there will be only one entry
+ for the root, so the size of the mask will be (n_octs - 1)*8 + 1.
data : dict
A dictionary of 1D arrays. Note that these must of the size of the
number of "False" values in the ``octree_mask``.
@@ -1522,8 +1525,29 @@
Determines whether the data will be treated as periodic along
each axis
partial_coverage : boolean
- Whether or not an oct can be refined cell-by-cell, or whether all 8 get
- refined.
+ Whether or not an oct can be refined cell-by-cell, or whether all
+ 8 get refined.
+
+ Example
+ -------
+
+ >>> import yt
+ >>> import numpy as np
+ >>> oct_mask = [8, 0, 0, 0, 0, 8, 0, 8,
+ ... 0, 0, 0, 0, 0, 0, 0, 0,
+ ... 8, 0, 0, 0, 0, 0, 0, 0,
+ ... 0]
+ >>>
+ >>> octree_mask = np.array(oct_mask, dtype=np.uint8)
+ >>> quantities = {}
+ >>> quantities['gas', 'density'] = np.random.random((22, 1), dtype='f8')
+ >>> bbox = np.array([[-10., 10.], [-10., 10.], [-10., 10.]])
+ >>>
+ >>> ds = yt.load_octree(octree_mask=octree_mask,
+ ... data=quantities,
+ ... bbox=bbox,
+ ... over_refine_factor=0,
+ ... partial_coverage=0)
"""
diff -r 71960f84ae9d3e12d70759e342b2bc581581674c -r af34b428166a02df3f069fa33f5df3ca8cf58545 yt/frontends/stream/tests/test_stream_octree.py
--- /dev/null
+++ b/yt/frontends/stream/tests/test_stream_octree.py
@@ -0,0 +1,26 @@
+import yt
+import numpy as np
+
+OCT_MASK_LIST = [8, 0, 0, 0, 0, 8, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0,
+ 8, 0, 0, 0, 0, 0, 0, 0,
+ 0]
+
+
+def test_octree():
+ # See Issue #1272
+ octree_mask = np.array(OCT_MASK_LIST, dtype=np.uint8)
+
+ quantities = {}
+ quantities[('gas', 'density')] = np.ones((22, 1), dtype=float)
+
+ bbox = np.array([[-10., 10.], [-10., 10.], [-10., 10.]])
+
+ ds = yt.load_octree(octree_mask=octree_mask,
+ data=quantities,
+ bbox=bbox,
+ over_refine_factor=0,
+ partial_coverage=0)
+
+ proj = ds.proj('density', 'x')
+ proj['density']
diff -r 71960f84ae9d3e12d70759e342b2bc581581674c -r af34b428166a02df3f069fa33f5df3ca8cf58545 yt/geometry/oct_visitors.pxd
--- a/yt/geometry/oct_visitors.pxd
+++ b/yt/geometry/oct_visitors.pxd
@@ -100,7 +100,7 @@
cdef class FillFileIndicesO(OctVisitor):
cdef np.uint8_t[:] levels
- cdef np.uint8_t[:] file_inds
+ cdef np.int64_t[:] file_inds
cdef np.uint8_t[:] cell_inds
cdef class FillFileIndicesR(OctVisitor):
Repository URL: https://bitbucket.org/yt_analysis/yt/
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