[yt-svn] commit/yt: 2 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Aug 26 07:50:30 PDT 2014
2 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/91feae9d7a79/
Changeset: 91feae9d7a79
Branch: yt
User: mzingale
Date: 2014-08-26 16:14:38
Summary: add some caveats to the BoxLib frontend docs
Affected #: 1 file
diff -r 2401a32b4fbf9e1ab76d3f3327832e056dcce71f -r 91feae9d7a79cb056c96c8500cc3a933e3a779a5 doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -178,6 +178,14 @@
For Maestro and Castro, you would not need the ``inputs`` file, and you
would have a ``job_info`` file in the plotfile directory.
+.. rubric:: Caveats
+
+* yt does not read the Maestro base state (although you can have Maestro
+ map it to a full Cartesian state variable before writing the plotfile
+ to get around this).
+* yt does not know about particles in Maestro.
+
+
.. _loading-enzo-data:
Enzo Data
https://bitbucket.org/yt_analysis/yt/commits/ba24b263607d/
Changeset: ba24b263607d
Branch: yt
User: mzingale
Date: 2014-08-26 16:15:16
Summary: merge
Affected #: 5 files
diff -r 91feae9d7a79cb056c96c8500cc3a933e3a779a5 -r ba24b263607d3dcf750cdc974f99151480325bfa yt/fields/cosmology_fields.py
--- a/yt/fields/cosmology_fields.py
+++ b/yt/fields/cosmology_fields.py
@@ -82,9 +82,9 @@
raise NeedsParameter("omega_baryon")
co = data.ds.cosmology
# critical_density(z) ~ omega_lambda + omega_matter * (1 + z)^3
- # mean density(z) ~ omega_matter * (1 + z)^3
+ # mean matter density(z) ~ omega_matter * (1 + z)^3
return data[ftype, "density"] / omega_baryon / co.critical_density(0.0) / \
- (1.0 + data.ds.hubble_constant)**3
+ (1.0 + data.ds.current_redshift)**3
registry.add_field((ftype, "baryon_overdensity"),
function=_baryon_overdensity,
@@ -99,9 +99,9 @@
co = data.ds.cosmology
# critical_density(z) ~ omega_lambda + omega_matter * (1 + z)^3
# mean density(z) ~ omega_matter * (1 + z)^3
- return data[ftype, "density"] / data.ds.omega_matter / \
+ return data[ftype, "matter_density"] / data.ds.omega_matter / \
co.critical_density(0.0) / \
- (1.0 + data.ds.hubble_constant)**3
+ (1.0 + data.ds.current_redshift)**3
registry.add_field((ftype, "matter_overdensity"),
function=_matter_overdensity,
diff -r 91feae9d7a79cb056c96c8500cc3a933e3a779a5 -r ba24b263607d3dcf750cdc974f99151480325bfa yt/frontends/enzo/fields.py
--- a/yt/frontends/enzo/fields.py
+++ b/yt/frontends/enzo/fields.py
@@ -219,6 +219,7 @@
self.add_output_field(
("enzo", te_name),
units = "code_velocity**2")
+ self.alias(("gas", "total_energy"), ("enzo", te_name))
def _tot_minus_kin(field, data):
return data[te_name] - 0.5*(
data["x-velocity"]**2.0
@@ -226,6 +227,7 @@
+ data["z-velocity"]**2.0 )
self.add_field(
("gas", "thermal_energy"),
+ function = _tot_minus_kin,
units = "erg/g")
def setup_particle_fields(self, ptype):
diff -r 91feae9d7a79cb056c96c8500cc3a933e3a779a5 -r ba24b263607d3dcf750cdc974f99151480325bfa yt/frontends/enzo/io.py
--- a/yt/frontends/enzo/io.py
+++ b/yt/frontends/enzo/io.py
@@ -44,7 +44,10 @@
if not hasattr(v, "shape") or v.dtype == "O":
continue
elif len(v.dims) == 1:
- if add_io: fields.append( ("io", str(name)) )
+ if grid.ds.dimensionality == 1:
+ fields.append( ("enzo", str(name)) )
+ elif add_io:
+ fields.append( ("io", str(name)) )
else:
fields.append( ("enzo", str(name)) )
f.close()
@@ -238,12 +241,14 @@
fields = []
add_io = "io" in grid.ds.particle_types
for name, v in self.grids_in_memory[grid.id].items():
-
# NOTE: This won't work with 1D datasets or references.
if not hasattr(v, "shape") or v.dtype == "O":
continue
elif v.ndim == 1:
- if add_io: fields.append( ("io", str(name)) )
+ if grid.ds.dimensionality == 1:
+ fields.append( ("enzo", str(name)) )
+ elif add_io:
+ fields.append( ("io", str(name)) )
else:
fields.append( ("enzo", str(name)) )
return fields
diff -r 91feae9d7a79cb056c96c8500cc3a933e3a779a5 -r ba24b263607d3dcf750cdc974f99151480325bfa yt/geometry/selection_routines.pyx
--- a/yt/geometry/selection_routines.pyx
+++ b/yt/geometry/selection_routines.pyx
@@ -442,7 +442,7 @@
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[1]
+ pos[2] += dds[2]
pos[1] += dds[1]
pos[0] += dds[0]
if total == 0: return None
diff -r 91feae9d7a79cb056c96c8500cc3a933e3a779a5 -r ba24b263607d3dcf750cdc974f99151480325bfa yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -369,32 +369,34 @@
class GridBoundaryCallback(PlotCallback):
"""
- annotate_grids(alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None, cmap='B-W LINEAR_r', edgecolors=None,
- linewidth=1.0):
+ annotate_grids(alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False,
+ periodic=True, min_level=None, max_level=None,
+ cmap='B-W LINEAR_r', edgecolors=None, linewidth=1.0):
- Draws grids on an existing PlotWindow object.
- Adds grid boundaries to a plot, optionally with alpha-blending. By default,
- colors different levels of grids with different colors going from white to
- black, but you can change to any arbitrary colormap with cmap keyword, to all black
- grid edges for all levels with cmap=None and edgecolors=None, or to an arbitrary single
- color for grid edges with edgecolors='YourChosenColor' defined in any of the standard ways
- (e.g., edgecolors='white', edgecolors='r', edgecolors='#00FFFF', or edgecolor='0.3', where
- the last is a float in 0-1 scale indicating gray).
- Note that setting edgecolors overrides cmap if you have both set to non-None values.
- Cutoff for display is at min_pix wide. draw_ids puts the grid id in the corner of the grid.
- (Not so great in projections...). One can set min and maximum level of
- grids to display, and can change the linewidth of the displayed grids.
+ Draws grids on an existing PlotWindow object. Adds grid boundaries to a
+ plot, optionally with alpha-blending. By default, colors different levels of
+ grids with different colors going from white to black, but you can change to
+ any arbitrary colormap with cmap keyword, to all black grid edges for all
+ levels with cmap=None and edgecolors=None, or to an arbitrary single color
+ for grid edges with edgecolors='YourChosenColor' defined in any of the
+ standard ways (e.g., edgecolors='white', edgecolors='r',
+ edgecolors='#00FFFF', or edgecolor='0.3', where the last is a float in 0-1
+ scale indicating gray). Note that setting edgecolors overrides cmap if you
+ have both set to non-None values. Cutoff for display is at min_pix
+ wide. draw_ids puts the grid id in the corner of the grid. (Not so great in
+ projections...). One can set min and maximum level of grids to display, and
+ can change the linewidth of the displayed grids.
"""
_type_name = "grids"
- def __init__(self, alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None, cmap='B-W LINEAR_r', edgecolors=None,
- linewidth=1.0):
+
+ def __init__(self, alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False,
+ periodic=True, min_level=None, max_level=None,
+ cmap='B-W LINEAR_r', edgecolors=None, linewidth=1.0):
PlotCallback.__init__(self)
self.alpha = alpha
self.min_pix = min_pix
self.min_pix_ids = min_pix_ids
- self.draw_ids = draw_ids # put grid numbers in the corner.
+ self.draw_ids = draw_ids # put grid numbers in the corner.
self.periodic = periodic
self.min_level = min_level
self.max_level = max_level
@@ -437,20 +439,22 @@
left_edge_y = np.array((GLE[:,py_index]+pyo-y0)*dy) + yy0
right_edge_x = np.array((GRE[:,px_index]+pxo-x0)*dx) + xx0
right_edge_y = np.array((GRE[:,py_index]+pyo-y0)*dy) + yy0
- visible = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
- ( levels >= min_level) & \
- ( levels <= max_level)
+ xwidth = xpix * (right_edge_x - left_edge_x) / (xx1 - xx0)
+ ywidth = ypix * (right_edge_y - left_edge_y) / (yy1 - yy0)
+ visible = np.logical_and(
+ np.logical_and(xwidth > self.min_pix, ywidth > self.min_pix),
+ np.logical_and(levels >= min_level, levels <= max_level))
# Grids can either be set by edgecolors OR a colormap.
if self.edgecolors is not None:
- edgecolors = colorConverter.to_rgba(self.edgecolors, alpha=self.alpha)
+ edgecolors = colorConverter.to_rgba(
+ self.edgecolors, alpha=self.alpha)
else: # use colormap if not explicity overridden by edgecolors
if self.cmap is not None:
- sample_levels = levels[(levels <= max_level) & (levels >= min_level)]
- color_bounds = [0,plot.data.pf.h.max_level]
- edgecolors = apply_colormap(sample_levels*1.0, color_bounds=color_bounds,
- cmap_name=self.cmap)[0,:,:]*1.0/255.
+ color_bounds = [0,plot.data.ds.index.max_level]
+ edgecolors = apply_colormap(
+ levels[visible]*1.0, color_bounds=color_bounds,
+ cmap_name=self.cmap)[0,:,:]*1.0/255.
edgecolors[:,3] = self.alpha
else:
edgecolors = (0.0,0.0,0.0,self.alpha)
@@ -461,13 +465,16 @@
(left_edge_y, right_edge_y, right_edge_y, left_edge_y)])
verts=verts.transpose()[visible,:,:]
grid_collection = matplotlib.collections.PolyCollection(
- verts, facecolors="none", edgecolors=edgecolors, linewidth=self.linewidth)
+ verts, facecolors="none", edgecolors=edgecolors,
+ linewidth=self.linewidth)
plot._axes.hold(True)
plot._axes.add_collection(grid_collection)
if self.draw_ids:
- visible_ids = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix_ids ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
+ visible_ids = np.logical_and(
+ np.logical_and(xwidth > self.min_pix_ids,
+ ywidth > self.min_pix_ids),
+ np.logical_and(levels >= min_level, levels <= max_level))
active_ids = np.unique(plot.data['grid_indices'])
for i in np.where(visible_ids)[0]:
plot._axes.text(
Repository URL: https://bitbucket.org/yt_analysis/yt/
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