[yt-svn] commit/yt: 4 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Aug 17 11:17:23 PDT 2016
4 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/9412c8580db7/
Changeset: 9412c8580db7
Branch: yt
User: ngoldbaum
Date: 2016-08-11 18:49:00+00:00
Summary: Apply unit overrides before setting the code unit attributes. Fixes #1259
Affected #: 2 files
diff -r a46f10f9e09c7cdca438f19057a9ddd6f4361c31 -r 9412c8580db795f4faed4c1abb40e0182f9165a2 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -889,10 +889,12 @@
return new_unit
def set_code_units(self):
- self._set_code_unit_attributes()
# here we override units, if overrides have been provided.
self._override_code_units()
+ # set attributes like ds.length_unit
+ self._set_code_unit_attributes()
+
self.unit_registry.modify("code_length", self.length_unit)
self.unit_registry.modify("code_mass", self.mass_unit)
self.unit_registry.modify("code_time", self.time_unit)
@@ -932,19 +934,22 @@
def _override_code_units(self):
if len(self.units_override) == 0:
return
- mylog.warning("Overriding code units. This is an experimental and potentially "+
- "dangerous option that may yield inconsistent results, and must be used "+
- "very carefully, and only if you know what you want from it.")
+ mylog.warning(
+ "Overriding code units. This is an experimental and potentially "
+ "dangerous option that may yield inconsistent results, and must be "
+ "used very carefully, and only if you know what you want from it.")
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g"),
- ("velocity","cm/s"), ("magnetic","gauss"), ("temperature","K")]:
+ ("velocity","cm/s"), ("magnetic","gauss"),
+ ("temperature","K")]:
val = self.units_override.get("%s_unit" % unit, None)
if val is not None:
if isinstance(val, YTQuantity):
val = (val.v, str(val.units))
elif not isinstance(val, tuple):
val = (val, cgs)
- u = getattr(self, "%s_unit" % unit)
- mylog.info("Overriding %s_unit: %g %s -> %g %s.", unit, u.v, u.units, val[0], val[1])
+ u = getattr(self, "%s_unit" % unit, None)
+ mylog.info("Overriding %s_unit: %g -> %g %s.",
+ unit, u, val[0], val[1])
setattr(self, "%s_unit" % unit, self.quan(val[0], val[1]))
_arr = None
diff -r a46f10f9e09c7cdca438f19057a9ddd6f4361c31 -r 9412c8580db795f4faed4c1abb40e0182f9165a2 yt/frontends/athena/data_structures.py
--- a/yt/frontends/athena/data_structures.py
+++ b/yt/frontends/athena/data_structures.py
@@ -471,12 +471,15 @@
def _set_code_unit_attributes(self):
"""
- Generates the conversion to various physical _units based on the parameter file
+ Generates the conversion to various physical _units based on the
+ parameter file
"""
if "length_unit" not in self.units_override:
self.no_cgs_equiv_length = True
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g")]:
- # We set these to cgs for now, but they may be overridden later.
+ # We set these to cgs for now, but they may have been overriden
+ if getattr(self, unit+'_unit', None) is not None:
+ continue
mylog.warning("Assuming 1.0 = 1.0 %s", cgs)
setattr(self, "%s_unit" % unit, self.quan(1.0, cgs))
self.magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
https://bitbucket.org/yt_analysis/yt/commits/b3cbcebe2168/
Changeset: b3cbcebe2168
Branch: yt
User: ngoldbaum
Date: 2016-08-11 20:23:32+00:00
Summary: Add test to verify magnetic unit is getting recalculated correctly
Affected #: 1 file
diff -r 9412c8580db795f4faed4c1abb40e0182f9165a2 -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 yt/frontends/athena/tests/test_outputs.py
--- a/yt/frontends/athena/tests/test_outputs.py
+++ b/yt/frontends/athena/tests/test_outputs.py
@@ -49,6 +49,20 @@
test_blast.__name__ = test.description
yield test
+uo_blast = {
+ 'length_unit': (1.0, 'pc'),
+ 'mass_unit': (2.38858753789e-24, 'g/cm**3*pc**3'),
+ 'time_unit': (1.0, 's*pc/km'),
+}
+
+ at requires_file(blast)
+def test_blast_override():
+ # verify that overriding units causes derived unit values to be updated.
+ # see issue #1259
+ ds = load(blast, units_override=uo_blast)
+ assert_equal(float(ds.magnetic_unit.in_units('gauss')),
+ 5.478674679698131e-07)
+
uo_stripping = {"time_unit":3.086e14,
"length_unit":8.0236e22,
"mass_unit":9.999e-30*8.0236e22**3}
https://bitbucket.org/yt_analysis/yt/commits/19206d2a44d7/
Changeset: 19206d2a44d7
Branch: yt
User: ngoldbaum
Date: 2016-08-11 21:00:18+00:00
Summary: Fix issues with all frontends that use units_override interface
Affected #: 18 files
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -25,7 +25,8 @@
from yt.data_objects.octree_subset import \
OctreeSubset
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.oct_container import \
ARTOctreeContainer
from yt.frontends.art.definitions import \
@@ -243,10 +244,10 @@
mass = aM0 * 1.98892e33
self.cosmological_simulation = True
- self.mass_unit = self.quan(mass, "g*%s" % ng**3)
- self.length_unit = self.quan(box_proper, "Mpc")
- self.velocity_unit = self.quan(velocity, "cm/s")
- self.time_unit = self.length_unit / self.velocity_unit
+ setdefaultattr(self, 'mass_unit', self.quan(mass, "g*%s" % ng**3))
+ setdefaultattr(self, 'length_unit', self.quan(box_proper, "Mpc"))
+ setdefaultattr(self, 'velocity_unit', self.quan(velocity, "cm/s"))
+ setdefaultattr(self, 'time_unit', self.length_unit / self.velocity_unit)
def _parse_parameter_file(self):
"""
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/artio/data_structures.py
--- a/yt/frontends/artio/data_structures.py
+++ b/yt/frontends/artio/data_structures.py
@@ -30,7 +30,8 @@
ARTIOFieldInfo
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.geometry_handler import \
Index, \
YTDataChunk
@@ -354,10 +355,13 @@
self.storage_filename = storage_filename
def _set_code_unit_attributes(self):
- self.mass_unit = self.quan(self.parameters["unit_m"], "g")
- self.length_unit = self.quan(self.parameters["unit_l"], "cm")
- self.time_unit = self.quan(self.parameters["unit_t"], "s")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(
+ self, 'mass_unit', self.quan(self.parameters["unit_m"], "g"))
+ setdefaultattr(
+ self, 'length_unit', self.quan(self.parameters["unit_l"], "cm"))
+ setdefaultattr(
+ self, 'time_unit', self.quan(self.parameters["unit_t"], "s"))
+ setdefaultattr(self, 'velocity_unit', self.length_unit / self.time_unit)
def _parse_parameter_file(self):
# hard-coded -- not provided by headers
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -22,8 +22,9 @@
import numpy as np
from yt.funcs import \
+ ensure_tuple, \
mylog, \
- ensure_tuple
+ setdefaultattr
from yt.data_objects.grid_patch import AMRGridPatch
from yt.extern.six.moves import zip as izip
from yt.geometry.grid_geometry_handler import GridIndex
@@ -608,10 +609,10 @@
self._setup2d()
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
def _setup1d(self):
# self._index_class = BoxlibHierarchy1D
@@ -1016,10 +1017,11 @@
self.particle_types_raw = self.particle_types
def _set_code_unit_attributes(self):
- self.mass_unit = self.quan(1.0, "Msun")
- self.time_unit = self.quan(1.0 / 3.08568025e19, "s")
- self.length_unit = self.quan(1.0 / (1 + self.current_redshift), "Mpc")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "Msun"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0 / 3.08568025e19, "s"))
+ setdefaultattr(self, 'length_unit',
+ self.quan(1.0 / (1 + self.current_redshift), "Mpc"))
+ setdefaultattr(self, 'velocity_unit', self.length_unit / self.time_unit)
def _guess_pcast(vals):
# Now we guess some things about the parameter and its type
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -23,7 +23,9 @@
from stat import \
ST_CTIME
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.extern import six
@@ -275,14 +277,19 @@
self.parameters["EOSType"] = -1 # default
def _set_code_unit_attributes(self):
- mylog.warning("Setting code length to be 1.0 cm")
- mylog.warning("Setting code mass to be 1.0 g")
- mylog.warning("Setting code time to be 1.0 s")
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.magnetic_unit = self.quan(np.sqrt(4.*np.pi), "gauss")
- self.velocity_unit = self.length_unit / self.time_unit
+ if not hasattr(self, 'length_unit'):
+ mylog.warning("Setting code length unit to be 1.0 cm")
+ if not hasattr(self, 'mass_unit'):
+ mylog.warning("Setting code mass unit to be 1.0 g")
+ if not hasattr(self, 'time_unit'):
+ mylog.warning("Setting code time unit to be 1.0 s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'magnetic_unit',
+ self.quan(np.sqrt(4.*np.pi), "gauss"))
+ setdefaultattr(self, 'velocity_unit',
+ self.length_unit / self.time_unit)
def _localize(self, f, default):
if f is None:
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/enzo/data_structures.py
--- a/yt/frontends/enzo/data_structures.py
+++ b/yt/frontends/enzo/data_structures.py
@@ -28,7 +28,8 @@
from yt.funcs import \
ensure_list, \
ensure_tuple, \
- get_pbar
+ get_pbar, \
+ setdefaultattr
from yt.config import ytcfg
from yt.data_objects.grid_patch import \
AMRGridPatch
@@ -917,11 +918,12 @@
if box_size is None:
box_size = self.parameters["Physics"]["Cosmology"]\
["CosmologyComovingBoxSize"]
- self.length_unit = self.quan(box_size, "Mpccm/h")
- self.mass_unit = \
- self.quan(k['urho'], 'g/cm**3') * (self.length_unit.in_cgs())**3
- self.time_unit = self.quan(k['utim'], 's')
- self.velocity_unit = self.quan(k['uvel'], 'cm/s')
+ setdefaultattr(self, 'length_unit', self.quan(box_size, "Mpccm/h"))
+ setdefaultattr(
+ self, 'mass_unit',
+ self.quan(k['urho'], 'g/cm**3') * (self.length_unit.in_cgs())**3)
+ setdefaultattr(self, 'time_unit', self.quan(k['utim'], 's'))
+ setdefaultattr(self, 'velocity_unit', self.quan(k['uvel'], 'cm/s'))
else:
if "LengthUnits" in self.parameters:
length_unit = self.parameters["LengthUnits"]
@@ -937,15 +939,16 @@
mylog.warning("Setting 1.0 in code units to be 1.0 s")
length_unit = mass_unit = time_unit = 1.0
- self.length_unit = self.quan(length_unit, "cm")
- self.mass_unit = self.quan(mass_unit, "g")
- self.time_unit = self.quan(time_unit, "s")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(self, 'length_unit', self.quan(length_unit, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(time_unit, "s"))
+ setdefaultattr(
+ self, 'velocity_unit', self.length_unit / self.time_unit)
magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
(self.time_unit**2 * self.length_unit))
magnetic_unit = np.float64(magnetic_unit.in_cgs())
- self.magnetic_unit = self.quan(magnetic_unit, "gauss")
+ setdefaultattr(self, 'magnetic_unit', self.quan(magnetic_unit, "gauss"))
def cosmology_get_units(self):
"""
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/exodus_ii/data_structures.py
--- a/yt/frontends/exodus_ii/data_structures.py
+++ b/yt/frontends/exodus_ii/data_structures.py
@@ -14,6 +14,8 @@
#-----------------------------------------------------------------------------
import numpy as np
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.unstructured_mesh_handler import \
UnstructuredIndex
from yt.data_objects.unstructured_mesh import \
@@ -163,9 +165,9 @@
# should be set, along with examples of how to set them to standard
# values.
#
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
#
# These can also be set:
# self.velocity_unit = self.quan(1.0, "cm/s")
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/fits/data_structures.py
--- a/yt/frontends/fits/data_structures.py
+++ b/yt/frontends/fits/data_structures.py
@@ -25,8 +25,9 @@
from yt.config import ytcfg
from yt.funcs import \
+ ensure_list, \
mylog, \
- ensure_list
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -447,10 +448,10 @@
mylog.warning("No length conversion provided. Assuming 1 = 1 cm.")
length_factor = 1.0
length_unit = "cm"
- self.length_unit = self.quan(length_factor,length_unit)
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
+ setdefaultattr(self, 'length_unit', self.quan(length_factor,length_unit))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
if "beam_size" in self.specified_parameters:
beam_size = self.specified_parameters["beam_size"]
beam_size = self.quan(beam_size[0], beam_size[1]).in_cgs().value
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -22,7 +22,9 @@
AMRGridPatch
from yt.data_objects.static_output import \
Dataset, ParticleFile
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.geometry.grid_geometry_handler import \
GridIndex
from yt.geometry.particle_geometry_handler import \
@@ -246,13 +248,14 @@
else:
length_factor = 1.0
temperature_factor = 1.0
- self.magnetic_unit = self.quan(b_factor, "gauss")
- self.length_unit = self.quan(length_factor, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
- self.temperature_unit = self.quan(temperature_factor, "K")
+ setdefaultattr(self, 'magnetic_unit', self.quan(b_factor, "gauss"))
+ setdefaultattr(self, 'length_unit', self.quan(length_factor, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
+ setdefaultattr(
+ self, 'temperature_unit', self.quan(temperature_factor, "K"))
def set_code_units(self):
super(FLASHDataset, self).set_code_units()
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/gadget_fof/data_structures.py
--- a/yt/frontends/gadget_fof/data_structures.py
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -33,7 +33,8 @@
GadgetFOFFieldInfo, \
GadgetFOFHaloFieldInfo
from yt.funcs import \
- only_on_root
+ only_on_root, \
+ setdefaultattr
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.utilities.cosmology import \
@@ -232,7 +233,8 @@
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
- self.length_unit = self.quan(length_unit[0], length_unit[1])
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
@@ -244,7 +246,8 @@
else:
velocity_unit = (1e5, "cmcm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
- self.velocity_unit = self.quan(velocity_unit[0], velocity_unit[1])
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(velocity_unit[0], velocity_unit[1]))
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
@@ -259,7 +262,7 @@
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
- self.mass_unit = self.quan(mass_unit[0], mass_unit[1])
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
@@ -267,7 +270,7 @@
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
time_unit = (1., "s")
- self.time_unit = self.quan(time_unit[0], time_unit[1])
+ setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1]))
def __repr__(self):
return self.basename.split(".", 1)[0]
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -18,7 +18,9 @@
import numpy as np
import weakref
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -205,7 +207,7 @@
"Use units_override to specify the units")
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g")]:
- setattr(self, "%s_unit"%unit, self.quan(1.0, cgs))
+ setdefaultattr(self, "%s_unit"%unit, self.quan(1.0, cgs))
if len(self.units_override) == 0:
mylog.warning("Assuming 1.0 = 1.0 %s", cgs)
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -19,7 +19,9 @@
import os
from yt.extern.six import string_types
from yt.funcs import \
- just_one, ensure_tuple
+ ensure_tuple, \
+ just_one, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -223,17 +225,17 @@
un = unit_name[:-5]
un = un.replace('magnetic', 'magnetic_field', 1)
unit = self.unit_system[un]
- setattr(self, unit_name, self.quan(value, unit))
- setattr(self, unit_name, self.quan(value, unit))
+ setdefaultattr(self, unit_name, self.quan(value, unit))
+ setdefaultattr(self, unit_name, self.quan(value, unit))
if unit_name in h5f["/field_types"]:
if unit_name in self.field_units:
mylog.warning("'field_units' was overridden by 'dataset_units/%s'"
% (unit_name))
self.field_units[unit_name] = str(unit)
else:
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
h5f.close()
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/halo_catalog/data_structures.py
--- a/yt/frontends/halo_catalog/data_structures.py
+++ b/yt/frontends/halo_catalog/data_structures.py
@@ -23,6 +23,8 @@
from .fields import \
HaloCatalogFieldInfo
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.data_objects.static_output import \
@@ -76,10 +78,10 @@
self.parameters.update(hvals)
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.velocity_unit = self.quan(1.0, "cm / s")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm / s"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/moab/data_structures.py
--- a/yt/frontends/moab/data_structures.py
+++ b/yt/frontends/moab/data_structures.py
@@ -19,6 +19,8 @@
import weakref
from yt.data_objects.unstructured_mesh import \
SemiStructuredMesh
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.unstructured_mesh_handler import \
UnstructuredIndex
from yt.data_objects.static_output import \
@@ -78,9 +80,9 @@
def _set_code_unit_attributes(self):
# Almost everything is regarded as dimensionless in MOAB, so these will
# not be used very much or at all.
- self.length_unit = self.quan(1.0, "cm")
- self.time_unit = self.quan(1.0, "s")
- self.mass_unit = self.quan(1.0, "g")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
def _parse_parameter_file(self):
self._handle = h5py.File(self.parameter_filename, "r")
@@ -161,9 +163,9 @@
def _set_code_unit_attributes(self):
# Almost everything is regarded as dimensionless in MOAB, so these will
# not be used very much or at all.
- self.length_unit = self.quan(1.0, "cm")
- self.time_unit = self.quan(1.0, "s")
- self.mass_unit = self.quan(1.0, "g")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
def _parse_parameter_file(self):
# not sure if this import has side-effects so I'm not deleting it
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/owls_subfind/data_structures.py
--- a/yt/frontends/owls_subfind/data_structures.py
+++ b/yt/frontends/owls_subfind/data_structures.py
@@ -24,7 +24,9 @@
from .fields import \
OWLSSubfindFieldInfo
-from yt.funcs import only_on_root
+from yt.funcs import \
+ only_on_root, \
+ setdefaultattr
from yt.utilities.exceptions import \
YTException
from yt.utilities.logger import ytLogger as \
@@ -176,7 +178,8 @@
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
- self.length_unit = self.quan(length_unit[0], length_unit[1])
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
@@ -185,7 +188,8 @@
else:
velocity_unit = (1e5, "cm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
- self.velocity_unit = self.quan(velocity_unit[0], velocity_unit[1])
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(velocity_unit[0], velocity_unit[1]))
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
@@ -200,7 +204,7 @@
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
- self.mass_unit = self.quan(mass_unit[0], mass_unit[1])
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
@@ -208,7 +212,7 @@
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
time_unit = (1., "s")
- self.time_unit = self.quan(time_unit[0], time_unit[1])
+ setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1]))
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/ramses/data_structures.py
--- a/yt/frontends/ramses/data_structures.py
+++ b/yt/frontends/ramses/data_structures.py
@@ -23,7 +23,8 @@
from yt.extern.six import string_types
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.oct_geometry_handler import \
OctreeIndex
from yt.geometry.geometry_handler import \
@@ -565,17 +566,21 @@
# For now assume an atomic ideal gas with cosmic abundances (x_H = 0.76)
mean_molecular_weight_factor = _X**-1
- self.density_unit = self.quan(density_unit, 'g/cm**3')
- self.magnetic_unit = self.quan(magnetic_unit, "gauss")
- self.pressure_unit = self.quan(pressure_unit, 'dyne/cm**2')
- self.time_unit = self.quan(time_unit, "s")
- self.mass_unit = self.quan(mass_unit, "g")
- self.velocity_unit = self.quan(length_unit, 'cm') / self.time_unit
- self.temperature_unit = (self.velocity_unit**2*mp*
- mean_molecular_weight_factor/kb).in_units('K')
+ setdefaultattr(self, 'density_unit', self.quan(density_unit, 'g/cm**3'))
+ setdefaultattr(self, 'magnetic_unit', self.quan(magnetic_unit, "gauss"))
+ setdefaultattr(self, 'pressure_unit',
+ self.quan(pressure_unit, 'dyne/cm**2'))
+ setdefaultattr(self, 'time_unit', self.quan(time_unit, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit, "g"))
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(length_unit, 'cm') / self.time_unit)
+ temperature_unit = (
+ self.velocity_unit**2*mp*mean_molecular_weight_factor/kb)
+ setdefaultattr(self, 'temperature_unit', temperature_unit.in_units('K'))
# Only the length unit get scales by a factor of boxlen
- self.length_unit = self.quan(length_unit * boxlen, "cm")
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit * boxlen, "cm"))
def _parse_parameter_file(self):
# hardcoded for now
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/rockstar/data_structures.py
--- a/yt/frontends/rockstar/data_structures.py
+++ b/yt/frontends/rockstar/data_structures.py
@@ -22,12 +22,14 @@
from .fields import \
RockstarFieldInfo
-from yt.utilities.cosmology import Cosmology
-from yt.geometry.particle_geometry_handler import \
- ParticleIndex
from yt.data_objects.static_output import \
Dataset, \
ParticleFile
+from yt.funcs import \
+ setdefaultattr
+from yt.geometry.particle_geometry_handler import \
+ ParticleIndex
+from yt.utilities.cosmology import Cosmology
import yt.utilities.fortran_utils as fpu
from .definitions import \
@@ -92,10 +94,10 @@
def _set_code_unit_attributes(self):
z = self.current_redshift
- self.length_unit = self.quan(1.0 / (1.0+z), "Mpc / h")
- self.mass_unit = self.quan(1.0, "Msun / h")
- self.velocity_unit = self.quan(1.0, "km / s")
- self.time_unit = self.length_unit / self.velocity_unit
+ setdefaultattr(self, 'length_unit', self.quan(1.0 / (1.0+z), "Mpc / h"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "Msun / h"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "km / s"))
+ setdefaultattr(self, 'time_unit', self.length_unit / self.velocity_unit)
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -28,7 +28,8 @@
from yt.data_objects.static_output import \
Dataset, ParticleFile
from yt.funcs import \
- get_requests
+ get_requests, \
+ setdefaultattr
from .fields import \
SDFFieldInfo
from yt.utilities.sdf import \
@@ -177,16 +178,22 @@
return self._midx
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, self.parameters.get("length_unit", 'kpc'))
- self.velocity_unit = self.quan(1.0, self.parameters.get("velocity_unit", 'kpc/Gyr'))
- self.time_unit = self.quan(1.0, self.parameters.get("time_unit", 'Gyr'))
+ setdefaultattr(
+ self, 'length_unit',
+ self.quan(1.0, self.parameters.get("length_unit", 'kpc')))
+ setdefaultattr(
+ self, 'velocity_unit',
+ self.quan(1.0, self.parameters.get("velocity_unit", 'kpc/Gyr')))
+ setdefaultattr(
+ self, 'time_unit',
+ self.quan(1.0, self.parameters.get("time_unit", 'Gyr')))
mass_unit = self.parameters.get("mass_unit", '1e10 Msun')
if ' ' in mass_unit:
factor, unit = mass_unit.split(' ')
else:
factor = 1.0
unit = mass_unit
- self.mass_unit = self.quan(float(factor), unit)
+ setdefaultattr(self, 'mass_unit', self.quan(float(factor), unit))
@classmethod
def _is_valid(cls, *args, **kwargs):
diff -r b3cbcebe2168bc87c0b88dc17eb80639257991a8 -r 19206d2a44d760a42eb98f98db54776a1f10932f yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -1004,3 +1004,12 @@
def get_interactivity():
return interactivity
+
+def setdefaultattr(obj, name, value):
+ """Set attribute with *name* on *obj* with *value* if it doesn't exist yet
+
+ Analogous to dict.setdefault
+ """
+ if not hasattr(obj, name):
+ setattr(obj, name, value)
+ return getattr(obj, name)
https://bitbucket.org/yt_analysis/yt/commits/e01aafd56e01/
Changeset: e01aafd56e01
Branch: yt
User: jzuhone
Date: 2016-08-17 18:16:45+00:00
Summary: Merged in ngoldbaum/yt (pull request #2334)
Apply unit overrides before setting the code unit attributes. Fixes #1259
Affected #: 21 files
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -889,10 +889,12 @@
return new_unit
def set_code_units(self):
- self._set_code_unit_attributes()
# here we override units, if overrides have been provided.
self._override_code_units()
+ # set attributes like ds.length_unit
+ self._set_code_unit_attributes()
+
self.unit_registry.modify("code_length", self.length_unit)
self.unit_registry.modify("code_mass", self.mass_unit)
self.unit_registry.modify("code_time", self.time_unit)
@@ -932,19 +934,22 @@
def _override_code_units(self):
if len(self.units_override) == 0:
return
- mylog.warning("Overriding code units. This is an experimental and potentially "+
- "dangerous option that may yield inconsistent results, and must be used "+
- "very carefully, and only if you know what you want from it.")
+ mylog.warning(
+ "Overriding code units. This is an experimental and potentially "
+ "dangerous option that may yield inconsistent results, and must be "
+ "used very carefully, and only if you know what you want from it.")
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g"),
- ("velocity","cm/s"), ("magnetic","gauss"), ("temperature","K")]:
+ ("velocity","cm/s"), ("magnetic","gauss"),
+ ("temperature","K")]:
val = self.units_override.get("%s_unit" % unit, None)
if val is not None:
if isinstance(val, YTQuantity):
val = (val.v, str(val.units))
elif not isinstance(val, tuple):
val = (val, cgs)
- u = getattr(self, "%s_unit" % unit)
- mylog.info("Overriding %s_unit: %g %s -> %g %s.", unit, u.v, u.units, val[0], val[1])
+ u = getattr(self, "%s_unit" % unit, None)
+ mylog.info("Overriding %s_unit: %g -> %g %s.",
+ unit, u, val[0], val[1])
setattr(self, "%s_unit" % unit, self.quan(val[0], val[1]))
_arr = None
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -25,7 +25,8 @@
from yt.data_objects.octree_subset import \
OctreeSubset
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.oct_container import \
ARTOctreeContainer
from yt.frontends.art.definitions import \
@@ -243,10 +244,10 @@
mass = aM0 * 1.98892e33
self.cosmological_simulation = True
- self.mass_unit = self.quan(mass, "g*%s" % ng**3)
- self.length_unit = self.quan(box_proper, "Mpc")
- self.velocity_unit = self.quan(velocity, "cm/s")
- self.time_unit = self.length_unit / self.velocity_unit
+ setdefaultattr(self, 'mass_unit', self.quan(mass, "g*%s" % ng**3))
+ setdefaultattr(self, 'length_unit', self.quan(box_proper, "Mpc"))
+ setdefaultattr(self, 'velocity_unit', self.quan(velocity, "cm/s"))
+ setdefaultattr(self, 'time_unit', self.length_unit / self.velocity_unit)
def _parse_parameter_file(self):
"""
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/artio/data_structures.py
--- a/yt/frontends/artio/data_structures.py
+++ b/yt/frontends/artio/data_structures.py
@@ -30,7 +30,8 @@
ARTIOFieldInfo
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.geometry_handler import \
Index, \
YTDataChunk
@@ -354,10 +355,13 @@
self.storage_filename = storage_filename
def _set_code_unit_attributes(self):
- self.mass_unit = self.quan(self.parameters["unit_m"], "g")
- self.length_unit = self.quan(self.parameters["unit_l"], "cm")
- self.time_unit = self.quan(self.parameters["unit_t"], "s")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(
+ self, 'mass_unit', self.quan(self.parameters["unit_m"], "g"))
+ setdefaultattr(
+ self, 'length_unit', self.quan(self.parameters["unit_l"], "cm"))
+ setdefaultattr(
+ self, 'time_unit', self.quan(self.parameters["unit_t"], "s"))
+ setdefaultattr(self, 'velocity_unit', self.length_unit / self.time_unit)
def _parse_parameter_file(self):
# hard-coded -- not provided by headers
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/athena/data_structures.py
--- a/yt/frontends/athena/data_structures.py
+++ b/yt/frontends/athena/data_structures.py
@@ -471,12 +471,15 @@
def _set_code_unit_attributes(self):
"""
- Generates the conversion to various physical _units based on the parameter file
+ Generates the conversion to various physical _units based on the
+ parameter file
"""
if "length_unit" not in self.units_override:
self.no_cgs_equiv_length = True
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g")]:
- # We set these to cgs for now, but they may be overridden later.
+ # We set these to cgs for now, but they may have been overriden
+ if getattr(self, unit+'_unit', None) is not None:
+ continue
mylog.warning("Assuming 1.0 = 1.0 %s", cgs)
setattr(self, "%s_unit" % unit, self.quan(1.0, cgs))
self.magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/athena/tests/test_outputs.py
--- a/yt/frontends/athena/tests/test_outputs.py
+++ b/yt/frontends/athena/tests/test_outputs.py
@@ -49,6 +49,20 @@
test_blast.__name__ = test.description
yield test
+uo_blast = {
+ 'length_unit': (1.0, 'pc'),
+ 'mass_unit': (2.38858753789e-24, 'g/cm**3*pc**3'),
+ 'time_unit': (1.0, 's*pc/km'),
+}
+
+ at requires_file(blast)
+def test_blast_override():
+ # verify that overriding units causes derived unit values to be updated.
+ # see issue #1259
+ ds = load(blast, units_override=uo_blast)
+ assert_equal(float(ds.magnetic_unit.in_units('gauss')),
+ 5.478674679698131e-07)
+
uo_stripping = {"time_unit":3.086e14,
"length_unit":8.0236e22,
"mass_unit":9.999e-30*8.0236e22**3}
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -22,8 +22,9 @@
import numpy as np
from yt.funcs import \
+ ensure_tuple, \
mylog, \
- ensure_tuple
+ setdefaultattr
from yt.data_objects.grid_patch import AMRGridPatch
from yt.extern.six.moves import zip as izip
from yt.geometry.grid_geometry_handler import GridIndex
@@ -608,10 +609,10 @@
self._setup2d()
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
def _setup1d(self):
# self._index_class = BoxlibHierarchy1D
@@ -1016,10 +1017,11 @@
self.particle_types_raw = self.particle_types
def _set_code_unit_attributes(self):
- self.mass_unit = self.quan(1.0, "Msun")
- self.time_unit = self.quan(1.0 / 3.08568025e19, "s")
- self.length_unit = self.quan(1.0 / (1 + self.current_redshift), "Mpc")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "Msun"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0 / 3.08568025e19, "s"))
+ setdefaultattr(self, 'length_unit',
+ self.quan(1.0 / (1 + self.current_redshift), "Mpc"))
+ setdefaultattr(self, 'velocity_unit', self.length_unit / self.time_unit)
def _guess_pcast(vals):
# Now we guess some things about the parameter and its type
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/chombo/data_structures.py
--- a/yt/frontends/chombo/data_structures.py
+++ b/yt/frontends/chombo/data_structures.py
@@ -23,7 +23,9 @@
from stat import \
ST_CTIME
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.extern import six
@@ -275,14 +277,19 @@
self.parameters["EOSType"] = -1 # default
def _set_code_unit_attributes(self):
- mylog.warning("Setting code length to be 1.0 cm")
- mylog.warning("Setting code mass to be 1.0 g")
- mylog.warning("Setting code time to be 1.0 s")
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.magnetic_unit = self.quan(np.sqrt(4.*np.pi), "gauss")
- self.velocity_unit = self.length_unit / self.time_unit
+ if not hasattr(self, 'length_unit'):
+ mylog.warning("Setting code length unit to be 1.0 cm")
+ if not hasattr(self, 'mass_unit'):
+ mylog.warning("Setting code mass unit to be 1.0 g")
+ if not hasattr(self, 'time_unit'):
+ mylog.warning("Setting code time unit to be 1.0 s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'magnetic_unit',
+ self.quan(np.sqrt(4.*np.pi), "gauss"))
+ setdefaultattr(self, 'velocity_unit',
+ self.length_unit / self.time_unit)
def _localize(self, f, default):
if f is None:
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/enzo/data_structures.py
--- a/yt/frontends/enzo/data_structures.py
+++ b/yt/frontends/enzo/data_structures.py
@@ -28,7 +28,8 @@
from yt.funcs import \
ensure_list, \
ensure_tuple, \
- get_pbar
+ get_pbar, \
+ setdefaultattr
from yt.config import ytcfg
from yt.data_objects.grid_patch import \
AMRGridPatch
@@ -917,11 +918,12 @@
if box_size is None:
box_size = self.parameters["Physics"]["Cosmology"]\
["CosmologyComovingBoxSize"]
- self.length_unit = self.quan(box_size, "Mpccm/h")
- self.mass_unit = \
- self.quan(k['urho'], 'g/cm**3') * (self.length_unit.in_cgs())**3
- self.time_unit = self.quan(k['utim'], 's')
- self.velocity_unit = self.quan(k['uvel'], 'cm/s')
+ setdefaultattr(self, 'length_unit', self.quan(box_size, "Mpccm/h"))
+ setdefaultattr(
+ self, 'mass_unit',
+ self.quan(k['urho'], 'g/cm**3') * (self.length_unit.in_cgs())**3)
+ setdefaultattr(self, 'time_unit', self.quan(k['utim'], 's'))
+ setdefaultattr(self, 'velocity_unit', self.quan(k['uvel'], 'cm/s'))
else:
if "LengthUnits" in self.parameters:
length_unit = self.parameters["LengthUnits"]
@@ -937,15 +939,16 @@
mylog.warning("Setting 1.0 in code units to be 1.0 s")
length_unit = mass_unit = time_unit = 1.0
- self.length_unit = self.quan(length_unit, "cm")
- self.mass_unit = self.quan(mass_unit, "g")
- self.time_unit = self.quan(time_unit, "s")
- self.velocity_unit = self.length_unit / self.time_unit
+ setdefaultattr(self, 'length_unit', self.quan(length_unit, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(time_unit, "s"))
+ setdefaultattr(
+ self, 'velocity_unit', self.length_unit / self.time_unit)
magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
(self.time_unit**2 * self.length_unit))
magnetic_unit = np.float64(magnetic_unit.in_cgs())
- self.magnetic_unit = self.quan(magnetic_unit, "gauss")
+ setdefaultattr(self, 'magnetic_unit', self.quan(magnetic_unit, "gauss"))
def cosmology_get_units(self):
"""
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/exodus_ii/data_structures.py
--- a/yt/frontends/exodus_ii/data_structures.py
+++ b/yt/frontends/exodus_ii/data_structures.py
@@ -14,6 +14,8 @@
#-----------------------------------------------------------------------------
import numpy as np
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.unstructured_mesh_handler import \
UnstructuredIndex
from yt.data_objects.unstructured_mesh import \
@@ -163,9 +165,9 @@
# should be set, along with examples of how to set them to standard
# values.
#
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
#
# These can also be set:
# self.velocity_unit = self.quan(1.0, "cm/s")
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/fits/data_structures.py
--- a/yt/frontends/fits/data_structures.py
+++ b/yt/frontends/fits/data_structures.py
@@ -25,8 +25,9 @@
from yt.config import ytcfg
from yt.funcs import \
+ ensure_list, \
mylog, \
- ensure_list
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -447,10 +448,10 @@
mylog.warning("No length conversion provided. Assuming 1 = 1 cm.")
length_factor = 1.0
length_unit = "cm"
- self.length_unit = self.quan(length_factor,length_unit)
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
+ setdefaultattr(self, 'length_unit', self.quan(length_factor,length_unit))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
if "beam_size" in self.specified_parameters:
beam_size = self.specified_parameters["beam_size"]
beam_size = self.quan(beam_size[0], beam_size[1]).in_cgs().value
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/flash/data_structures.py
--- a/yt/frontends/flash/data_structures.py
+++ b/yt/frontends/flash/data_structures.py
@@ -22,7 +22,9 @@
AMRGridPatch
from yt.data_objects.static_output import \
Dataset, ParticleFile
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.geometry.grid_geometry_handler import \
GridIndex
from yt.geometry.particle_geometry_handler import \
@@ -246,13 +248,14 @@
else:
length_factor = 1.0
temperature_factor = 1.0
- self.magnetic_unit = self.quan(b_factor, "gauss")
- self.length_unit = self.quan(length_factor, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
- self.velocity_unit = self.quan(1.0, "cm/s")
- self.temperature_unit = self.quan(temperature_factor, "K")
+ setdefaultattr(self, 'magnetic_unit', self.quan(b_factor, "gauss"))
+ setdefaultattr(self, 'length_unit', self.quan(length_factor, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm/s"))
+ setdefaultattr(
+ self, 'temperature_unit', self.quan(temperature_factor, "K"))
def set_code_units(self):
super(FLASHDataset, self).set_code_units()
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/gadget_fof/data_structures.py
--- a/yt/frontends/gadget_fof/data_structures.py
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -33,7 +33,8 @@
GadgetFOFFieldInfo, \
GadgetFOFHaloFieldInfo
from yt.funcs import \
- only_on_root
+ only_on_root, \
+ setdefaultattr
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.utilities.cosmology import \
@@ -232,7 +233,8 @@
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
- self.length_unit = self.quan(length_unit[0], length_unit[1])
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
@@ -244,7 +246,8 @@
else:
velocity_unit = (1e5, "cmcm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
- self.velocity_unit = self.quan(velocity_unit[0], velocity_unit[1])
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(velocity_unit[0], velocity_unit[1]))
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
@@ -259,7 +262,7 @@
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
- self.mass_unit = self.quan(mass_unit[0], mass_unit[1])
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
@@ -267,7 +270,7 @@
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
time_unit = (1., "s")
- self.time_unit = self.quan(time_unit[0], time_unit[1])
+ setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1]))
def __repr__(self):
return self.basename.split(".", 1)[0]
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -18,7 +18,9 @@
import numpy as np
import weakref
-from yt.funcs import mylog
+from yt.funcs import \
+ mylog, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -205,7 +207,7 @@
"Use units_override to specify the units")
for unit, cgs in [("length", "cm"), ("time", "s"), ("mass", "g")]:
- setattr(self, "%s_unit"%unit, self.quan(1.0, cgs))
+ setdefaultattr(self, "%s_unit"%unit, self.quan(1.0, cgs))
if len(self.units_override) == 0:
mylog.warning("Assuming 1.0 = 1.0 %s", cgs)
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -19,7 +19,9 @@
import os
from yt.extern.six import string_types
from yt.funcs import \
- just_one, ensure_tuple
+ ensure_tuple, \
+ just_one, \
+ setdefaultattr
from yt.data_objects.grid_patch import \
AMRGridPatch
from yt.geometry.grid_geometry_handler import \
@@ -223,17 +225,17 @@
un = unit_name[:-5]
un = un.replace('magnetic', 'magnetic_field', 1)
unit = self.unit_system[un]
- setattr(self, unit_name, self.quan(value, unit))
- setattr(self, unit_name, self.quan(value, unit))
+ setdefaultattr(self, unit_name, self.quan(value, unit))
+ setdefaultattr(self, unit_name, self.quan(value, unit))
if unit_name in h5f["/field_types"]:
if unit_name in self.field_units:
mylog.warning("'field_units' was overridden by 'dataset_units/%s'"
% (unit_name))
self.field_units[unit_name] = str(unit)
else:
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
h5f.close()
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/halo_catalog/data_structures.py
--- a/yt/frontends/halo_catalog/data_structures.py
+++ b/yt/frontends/halo_catalog/data_structures.py
@@ -23,6 +23,8 @@
from .fields import \
HaloCatalogFieldInfo
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.data_objects.static_output import \
@@ -76,10 +78,10 @@
self.parameters.update(hvals)
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, "cm")
- self.mass_unit = self.quan(1.0, "g")
- self.velocity_unit = self.quan(1.0, "cm / s")
- self.time_unit = self.quan(1.0, "s")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "cm / s"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/moab/data_structures.py
--- a/yt/frontends/moab/data_structures.py
+++ b/yt/frontends/moab/data_structures.py
@@ -19,6 +19,8 @@
import weakref
from yt.data_objects.unstructured_mesh import \
SemiStructuredMesh
+from yt.funcs import \
+ setdefaultattr
from yt.geometry.unstructured_mesh_handler import \
UnstructuredIndex
from yt.data_objects.static_output import \
@@ -78,9 +80,9 @@
def _set_code_unit_attributes(self):
# Almost everything is regarded as dimensionless in MOAB, so these will
# not be used very much or at all.
- self.length_unit = self.quan(1.0, "cm")
- self.time_unit = self.quan(1.0, "s")
- self.mass_unit = self.quan(1.0, "g")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
def _parse_parameter_file(self):
self._handle = h5py.File(self.parameter_filename, "r")
@@ -161,9 +163,9 @@
def _set_code_unit_attributes(self):
# Almost everything is regarded as dimensionless in MOAB, so these will
# not be used very much or at all.
- self.length_unit = self.quan(1.0, "cm")
- self.time_unit = self.quan(1.0, "s")
- self.mass_unit = self.quan(1.0, "g")
+ setdefaultattr(self, 'length_unit', self.quan(1.0, "cm"))
+ setdefaultattr(self, 'time_unit', self.quan(1.0, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "g"))
def _parse_parameter_file(self):
# not sure if this import has side-effects so I'm not deleting it
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/owls_subfind/data_structures.py
--- a/yt/frontends/owls_subfind/data_structures.py
+++ b/yt/frontends/owls_subfind/data_structures.py
@@ -24,7 +24,9 @@
from .fields import \
OWLSSubfindFieldInfo
-from yt.funcs import only_on_root
+from yt.funcs import \
+ only_on_root, \
+ setdefaultattr
from yt.utilities.exceptions import \
YTException
from yt.utilities.logger import ytLogger as \
@@ -176,7 +178,8 @@
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
- self.length_unit = self.quan(length_unit[0], length_unit[1])
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
@@ -185,7 +188,8 @@
else:
velocity_unit = (1e5, "cm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
- self.velocity_unit = self.quan(velocity_unit[0], velocity_unit[1])
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(velocity_unit[0], velocity_unit[1]))
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
@@ -200,7 +204,7 @@
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
- self.mass_unit = self.quan(mass_unit[0], mass_unit[1])
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
@@ -208,7 +212,7 @@
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
time_unit = (1., "s")
- self.time_unit = self.quan(time_unit[0], time_unit[1])
+ setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1]))
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/ramses/data_structures.py
--- a/yt/frontends/ramses/data_structures.py
+++ b/yt/frontends/ramses/data_structures.py
@@ -23,7 +23,8 @@
from yt.extern.six import string_types
from yt.funcs import \
- mylog
+ mylog, \
+ setdefaultattr
from yt.geometry.oct_geometry_handler import \
OctreeIndex
from yt.geometry.geometry_handler import \
@@ -565,17 +566,21 @@
# For now assume an atomic ideal gas with cosmic abundances (x_H = 0.76)
mean_molecular_weight_factor = _X**-1
- self.density_unit = self.quan(density_unit, 'g/cm**3')
- self.magnetic_unit = self.quan(magnetic_unit, "gauss")
- self.pressure_unit = self.quan(pressure_unit, 'dyne/cm**2')
- self.time_unit = self.quan(time_unit, "s")
- self.mass_unit = self.quan(mass_unit, "g")
- self.velocity_unit = self.quan(length_unit, 'cm') / self.time_unit
- self.temperature_unit = (self.velocity_unit**2*mp*
- mean_molecular_weight_factor/kb).in_units('K')
+ setdefaultattr(self, 'density_unit', self.quan(density_unit, 'g/cm**3'))
+ setdefaultattr(self, 'magnetic_unit', self.quan(magnetic_unit, "gauss"))
+ setdefaultattr(self, 'pressure_unit',
+ self.quan(pressure_unit, 'dyne/cm**2'))
+ setdefaultattr(self, 'time_unit', self.quan(time_unit, "s"))
+ setdefaultattr(self, 'mass_unit', self.quan(mass_unit, "g"))
+ setdefaultattr(self, 'velocity_unit',
+ self.quan(length_unit, 'cm') / self.time_unit)
+ temperature_unit = (
+ self.velocity_unit**2*mp*mean_molecular_weight_factor/kb)
+ setdefaultattr(self, 'temperature_unit', temperature_unit.in_units('K'))
# Only the length unit get scales by a factor of boxlen
- self.length_unit = self.quan(length_unit * boxlen, "cm")
+ setdefaultattr(self, 'length_unit',
+ self.quan(length_unit * boxlen, "cm"))
def _parse_parameter_file(self):
# hardcoded for now
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/rockstar/data_structures.py
--- a/yt/frontends/rockstar/data_structures.py
+++ b/yt/frontends/rockstar/data_structures.py
@@ -22,12 +22,14 @@
from .fields import \
RockstarFieldInfo
-from yt.utilities.cosmology import Cosmology
-from yt.geometry.particle_geometry_handler import \
- ParticleIndex
from yt.data_objects.static_output import \
Dataset, \
ParticleFile
+from yt.funcs import \
+ setdefaultattr
+from yt.geometry.particle_geometry_handler import \
+ ParticleIndex
+from yt.utilities.cosmology import Cosmology
import yt.utilities.fortran_utils as fpu
from .definitions import \
@@ -92,10 +94,10 @@
def _set_code_unit_attributes(self):
z = self.current_redshift
- self.length_unit = self.quan(1.0 / (1.0+z), "Mpc / h")
- self.mass_unit = self.quan(1.0, "Msun / h")
- self.velocity_unit = self.quan(1.0, "km / s")
- self.time_unit = self.length_unit / self.velocity_unit
+ setdefaultattr(self, 'length_unit', self.quan(1.0 / (1.0+z), "Mpc / h"))
+ setdefaultattr(self, 'mass_unit', self.quan(1.0, "Msun / h"))
+ setdefaultattr(self, 'velocity_unit', self.quan(1.0, "km / s"))
+ setdefaultattr(self, 'time_unit', self.length_unit / self.velocity_unit)
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/frontends/sdf/data_structures.py
--- a/yt/frontends/sdf/data_structures.py
+++ b/yt/frontends/sdf/data_structures.py
@@ -28,7 +28,8 @@
from yt.data_objects.static_output import \
Dataset, ParticleFile
from yt.funcs import \
- get_requests
+ get_requests, \
+ setdefaultattr
from .fields import \
SDFFieldInfo
from yt.utilities.sdf import \
@@ -177,16 +178,22 @@
return self._midx
def _set_code_unit_attributes(self):
- self.length_unit = self.quan(1.0, self.parameters.get("length_unit", 'kpc'))
- self.velocity_unit = self.quan(1.0, self.parameters.get("velocity_unit", 'kpc/Gyr'))
- self.time_unit = self.quan(1.0, self.parameters.get("time_unit", 'Gyr'))
+ setdefaultattr(
+ self, 'length_unit',
+ self.quan(1.0, self.parameters.get("length_unit", 'kpc')))
+ setdefaultattr(
+ self, 'velocity_unit',
+ self.quan(1.0, self.parameters.get("velocity_unit", 'kpc/Gyr')))
+ setdefaultattr(
+ self, 'time_unit',
+ self.quan(1.0, self.parameters.get("time_unit", 'Gyr')))
mass_unit = self.parameters.get("mass_unit", '1e10 Msun')
if ' ' in mass_unit:
factor, unit = mass_unit.split(' ')
else:
factor = 1.0
unit = mass_unit
- self.mass_unit = self.quan(float(factor), unit)
+ setdefaultattr(self, 'mass_unit', self.quan(float(factor), unit))
@classmethod
def _is_valid(cls, *args, **kwargs):
diff -r 56c0b53b459c4cb6c6a3bdf67634e142ec4c0f52 -r e01aafd56e018aae048126104705318316daee70 yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -1004,3 +1004,12 @@
def get_interactivity():
return interactivity
+
+def setdefaultattr(obj, name, value):
+ """Set attribute with *name* on *obj* with *value* if it doesn't exist yet
+
+ Analogous to dict.setdefault
+ """
+ if not hasattr(obj, name):
+ setattr(obj, name, value)
+ return getattr(obj, name)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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