[yt-svn] commit/yt: 8 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sat Jul 18 06:51:40 PDT 2015
8 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/0d6ac4368c99/
Changeset: 0d6ac4368c99
Branch: yt
User: BW Keller
Date: 2015-07-14 21:26:16+00:00
Summary: Fixes Issue #1035. Problem was that code_length changes its meaning
between after it was applied.
Affected #: 1 file
diff -r b7b8cdbad2505dea1391bddbe3ab6e5d65f2e9b6 -r 0d6ac4368c991d9fd829d41fd4499c52971045e9 yt/frontends/tipsy/data_structures.py
--- a/yt/frontends/tipsy/data_structures.py
+++ b/yt/frontends/tipsy/data_structures.py
@@ -180,7 +180,7 @@
self.domain_left_edge = None
self.domain_right_edge = None
else:
- bbox = self.arr(self.bounding_box, 'code_length', dtype="float64")
+ bbox = self.arr(self.bounding_box, dtype="float64")
if bbox.shape == (2, 3):
bbox = bbox.transpose()
self.domain_left_edge = bbox[:,0]
https://bitbucket.org/yt_analysis/yt/commits/8720621b3491/
Changeset: 8720621b3491
Branch: yt
User: BW Keller
Date: 2015-07-15 00:12:23+00:00
Summary: Tipsy datasets were not being generated with smoothing lengths, and this led to some strange behaviour
(biases in calculations of cell-averaged quantities and plots).
Affected #: 1 file
diff -r 0d6ac4368c991d9fd829d41fd4499c52971045e9 -r 8720621b3491489baf0dfe6a235a928433590052 yt/frontends/tipsy/fields.py
--- a/yt/frontends/tipsy/fields.py
+++ b/yt/frontends/tipsy/fields.py
@@ -16,6 +16,8 @@
#-----------------------------------------------------------------------------
from yt.frontends.sph.fields import SPHFieldInfo
+from yt.fields.particle_fields import add_volume_weighted_smoothed_field, add_nearest_neighbor_field
+from yt.utilities.physical_constants import mp, kb
class TipsyFieldInfo(SPHFieldInfo):
aux_particle_fields = {
@@ -44,3 +46,29 @@
self.aux_particle_fields[field[1]] not in self.known_particle_fields:
self.known_particle_fields += (self.aux_particle_fields[field[1]],)
super(TipsyFieldInfo,self).__init__(ds, field_list, slice_info)
+
+ def setup_particle_fields(self, ptype, *args, **kwargs):
+
+ # setup some special fields that only make sense for SPH particles
+
+ if ptype in ("PartType0", "Gas"):
+ self.setup_gas_particle_fields(ptype)
+
+ super(TipsyFieldInfo, self).setup_particle_fields(
+ ptype, *args, **kwargs)
+
+
+ def setup_gas_particle_fields(self, ptype):
+
+ def _smoothing_length(field, data):
+ # For now, we hardcode num_neighbors. We should make this configurable
+ # in the future.
+ num_neighbors = 64
+ fn, = add_nearest_neighbor_field(ptype, "particle_position", self, num_neighbors)
+ return data[ptype, 'nearest_neighbor_distance_%d' % num_neighbors]
+
+ self.add_field(
+ (ptype, "smoothing_length"),
+ function=_smoothing_length,
+ particle_type=True,
+ units="code_length")
https://bitbucket.org/yt_analysis/yt/commits/a8ba56ca7f9b/
Changeset: a8ba56ca7f9b
Branch: bugfix-1035
User: BW Keller
Date: 2015-07-15 00:15:20+00:00
Summary: Bugfix for Issue #1035
Affected #: 0 files
https://bitbucket.org/yt_analysis/yt/commits/f1f968e3cd05/
Changeset: f1f968e3cd05
Branch: bugfix-1035
User: BW Keller
Date: 2015-07-17 15:55:42+00:00
Summary: Leave bbox as a Numpy array until it has units assigned.
Affected #: 1 file
diff -r a8ba56ca7f9ba525ced99ecc6b99dc6bd9ff184f -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd yt/frontends/tipsy/data_structures.py
--- a/yt/frontends/tipsy/data_structures.py
+++ b/yt/frontends/tipsy/data_structures.py
@@ -180,7 +180,7 @@
self.domain_left_edge = None
self.domain_right_edge = None
else:
- bbox = self.arr(self.bounding_box, dtype="float64")
+ bbox = np.array(self.bounding_box, dtype="float64")
if bbox.shape == (2, 3):
bbox = bbox.transpose()
self.domain_left_edge = bbox[:,0]
https://bitbucket.org/yt_analysis/yt/commits/fa91228a919d/
Changeset: fa91228a919d
Branch: yt
User: bwkeller
Date: 2015-07-17 17:20:44+00:00
Summary: Merged yt_analysis/yt into yt
Affected #: 41 files
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -11,6 +11,7 @@
yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c
yt/analysis_modules/ppv_cube/ppv_utils.c
yt/frontends/ramses/_ramses_reader.cpp
+yt/frontends/sph/smoothing_kernel.c
yt/geometry/fake_octree.c
yt/geometry/grid_container.c
yt/geometry/grid_visitors.c
@@ -40,6 +41,7 @@
yt/utilities/lib/mesh_utilities.c
yt/utilities/lib/misc_utilities.c
yt/utilities/lib/Octree.c
+yt/utilities/lib/GridTree.c
yt/utilities/lib/origami.c
yt/utilities/lib/pixelization_routines.c
yt/utilities/lib/png_writer.c
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a README
--- a/README
+++ b/README
@@ -20,4 +20,5 @@
For more information on installation, what to do if you run into problems, or
ways to help development, please visit our website.
-Enjoy!
\ No newline at end of file
+Enjoy!
+
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -641,7 +641,7 @@
TORNADO='tornado-4.0.2'
ZEROMQ='zeromq-4.0.5'
ZLIB='zlib-1.2.8'
-SETUPTOOLS='setuptools-16.0'
+SETUPTOOLS='setuptools-18.0.1'
# Now we dump all our SHA512 files out.
echo '856220fa579e272ac38dcef091760f527431ff3b98df9af6e68416fcf77d9659ac5abe5c7dee41331f359614637a4ff452033085335ee499830ed126ab584267 Cython-0.22.tar.gz' > Cython-0.22.tar.gz.sha512
@@ -669,7 +669,7 @@
echo '93591068dc63af8d50a7925d528bc0cccdd705232c529b6162619fe28dddaf115e8a460b1842877d35160bd7ed480c1bd0bdbec57d1f359085bd1814e0c1c242 tornado-4.0.2.tar.gz' > tornado-4.0.2.tar.gz.sha512
echo '0d928ed688ed940d460fa8f8d574a9819dccc4e030d735a8c7db71b59287ee50fa741a08249e356c78356b03c2174f2f2699f05aa7dc3d380ed47d8d7bab5408 zeromq-4.0.5.tar.gz' > zeromq-4.0.5.tar.gz.sha512
echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
-echo '38a89aad89dc9aa682dbfbca623e2f69511f5e20d4a3526c01aabbc7e93ae78f20aac566676b431e111540b41540a1c4f644ce4174e7ecf052318612075e02dc setuptools-16.0.tar.gz' > setuptools-16.0.tar.gz.sha512
+echo '9b318ce2ee2cf787929dcb886d76c492b433e71024fda9452d8b4927652a298d6bd1bdb7a4c73883a98e100024f89b46ea8aa14b250f896e549e6dd7e10a6b41 setuptools-18.0.1.tar.gz' > setuptools-18.0.1.tar.gz.sha512
# Individual processes
[ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
[ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/analyzing/analysis_modules/SZ_projections.ipynb
--- a/doc/source/analyzing/analysis_modules/SZ_projections.ipynb
+++ b/doc/source/analyzing/analysis_modules/SZ_projections.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:2cc168b2c1737c67647aa29892c0213e7a58233fa53c809f9cd975a4306e9bc8"
+ "signature": "sha256:487383ec23a092310522ec25bd02ad2eb16a3402c5ed3d2b103d33fe17697b3c"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -70,6 +70,13 @@
]
},
{
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "<font color='red'>**NOTE**</font>: Currently, use of the SZpack library to create S-Z projections in yt is limited to Python 2.x."
+ ]
+ },
+ {
"cell_type": "heading",
"level": 2,
"metadata": {},
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/analyzing/fields.rst
--- a/doc/source/analyzing/fields.rst
+++ b/doc/source/analyzing/fields.rst
@@ -174,7 +174,7 @@
Field plugins can be loaded dynamically, although at present this is not
particularly useful. Plans for extending field plugins to dynamically load, to
-enable simple definition of common types (gradient, divergence, etc), and to
+enable simple definition of common types (divergence, curl, etc), and to
more verbosely describe available fields, have been put in place for future
versions.
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/cookbook/fit_spectrum.py
--- a/doc/source/cookbook/fit_spectrum.py
+++ b/doc/source/cookbook/fit_spectrum.py
@@ -10,10 +10,10 @@
def _OVI_number_density(field, data):
return data['H_number_density']*2.0
-# Define a function that will accept a ds and add the new field
+# Define a function that will accept a ds and add the new field
# defined above. This will be given to the LightRay below.
def setup_ds(ds):
- ds.add_field("O_p5_number_density",
+ ds.add_field(("gas","O_p5_number_density"),
function=_OVI_number_density,
units="cm**-3")
@@ -62,7 +62,7 @@
# Get all fields that need to be added to the light ray
fields = ['temperature']
-for s, params in species_dicts.iteritems():
+for s, params in species_dicts.items():
fields.append(params['field'])
# Make a light ray, and set njobs to -1 to use one core
@@ -79,7 +79,7 @@
sp = AbsorptionSpectrum(900.0, 1400.0, 50000)
# Iterate over species
-for s, params in species_dicts.iteritems():
+for s, params in species_dicts.items():
# Iterate over transitions for a single species
for i in range(params['numLines']):
# Add the lines to the spectrum
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/cookbook/free_free_field.py
--- a/doc/source/cookbook/free_free_field.py
+++ /dev/null
@@ -1,105 +0,0 @@
-### THIS RECIPE IS CURRENTLY BROKEN IN YT-3.0
-### DO NOT TRUST THIS RECIPE UNTIL THIS LINE IS REMOVED
-
-import numpy as np
-import yt
-# Need to grab the proton mass from the constants database
-from yt.utilities.physical_constants import mp
-
-exit()
-# Define the emission field
-
-keVtoerg = 1.602e-9 # Convert energy in keV to energy in erg
-KtokeV = 8.617e-08 # Convert degrees Kelvin to degrees keV
-sqrt3 = np.sqrt(3.)
-expgamma = 1.78107241799 # Exponential of Euler's constant
-
-
-def _FreeFree_Emission(field, data):
-
- if data.has_field_parameter("Z"):
- Z = data.get_field_parameter("Z")
- else:
- Z = 1.077 # Primordial H/He plasma
-
- if data.has_field_parameter("mue"):
- mue = data.get_field_parameter("mue")
- else:
- mue = 1./0.875 # Primordial H/He plasma
-
- if data.has_field_parameter("mui"):
- mui = data.get_field_parameter("mui")
- else:
- mui = 1./0.8125 # Primordial H/He plasma
-
- if data.has_field_parameter("Ephoton"):
- Ephoton = data.get_field_parameter("Ephoton")
- else:
- Ephoton = 1.0 # in keV
-
- if data.has_field_parameter("photon_emission"):
- photon_emission = data.get_field_parameter("photon_emission")
- else:
- photon_emission = False # Flag for energy or photon emission
-
- n_e = data["density"]/(mue*mp)
- n_i = data["density"]/(mui*mp)
- kT = data["temperature"]*KtokeV
-
- # Compute the Gaunt factor
-
- g_ff = np.zeros(kT.shape)
- g_ff[Ephoton/kT > 1.] = np.sqrt((3./np.pi)*kT[Ephoton/kT > 1.]/Ephoton)
- g_ff[Ephoton/kT < 1.] = (sqrt3/np.pi)*np.log((4./expgamma) *
- kT[Ephoton/kT < 1.]/Ephoton)
-
- eps_E = 1.64e-20*Z*Z*n_e*n_i/np.sqrt(data["temperature"]) * \
- np.exp(-Ephoton/kT)*g_ff
-
- if photon_emission:
- eps_E /= (Ephoton*keVtoerg)
-
- return eps_E
-
-yt.add_field("FreeFree_Emission", function=_FreeFree_Emission)
-
-# Define the luminosity derived quantity
-def _FreeFreeLuminosity(data):
- return (data["FreeFree_Emission"]*data["cell_volume"]).sum()
-
-
-def _combFreeFreeLuminosity(data, luminosity):
- return luminosity.sum()
-
-yt.add_quantity("FreeFree_Luminosity", function=_FreeFreeLuminosity,
- combine_function=_combFreeFreeLuminosity, n_ret=1)
-
-ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
-
-sphere = ds.sphere(ds.domain_center, (100., "kpc"))
-
-# Print out the total luminosity at 1 keV for the sphere
-
-print("L_E (1 keV, primordial) = ", sphere.quantities["FreeFree_Luminosity"]())
-
-# The defaults for the field assume a H/He primordial plasma.
-# Let's set the appropriate parameters for a pure hydrogen plasma.
-
-sphere.set_field_parameter("mue", 1.0)
-sphere.set_field_parameter("mui", 1.0)
-sphere.set_field_parameter("Z", 1.0)
-
-print("L_E (1 keV, pure hydrogen) = ", sphere.quantities["FreeFree_Luminosity"]())
-
-# Now let's print the luminosity at an energy of E = 10 keV
-
-sphere.set_field_parameter("Ephoton", 10.0)
-
-print("L_E (10 keV, pure hydrogen) = ", sphere.quantities["FreeFree_Luminosity"]())
-
-# Finally, let's set the flag for photon emission, to get the total number
-# of photons emitted at this energy:
-
-sphere.set_field_parameter("photon_emission", True)
-
-print("L_ph (10 keV, pure hydrogen) = ", sphere.quantities["FreeFree_Luminosity"]())
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/cookbook/simulation_analysis.py
--- a/doc/source/cookbook/simulation_analysis.py
+++ b/doc/source/cookbook/simulation_analysis.py
@@ -2,11 +2,11 @@
yt.enable_parallelism()
import collections
-# Enable parallelism in the script (assuming it was called with
+# Enable parallelism in the script (assuming it was called with
# `mpirun -np <n_procs>` )
yt.enable_parallelism()
-# By using wildcards such as ? and * with the load command, we can load up a
+# By using wildcards such as ? and * with the load command, we can load up a
# Time Series containing all of these datasets simultaneously.
ts = yt.load('enzo_tiny_cosmology/DD????/DD????')
@@ -16,7 +16,7 @@
# Create an empty dictionary
data = {}
-# Iterate through each dataset in the Time Series (using piter allows it
+# Iterate through each dataset in the Time Series (using piter allows it
# to happen in parallel automatically across available processors)
for ds in ts.piter():
ad = ds.all_data()
@@ -31,6 +31,6 @@
# Print out all the values we calculated.
print("Dataset Redshift Density Min Density Max")
print("---------------------------------------------------------")
-for key, val in od.iteritems():
+for key, val in od.items():
print("%s %05.3f %5.3g g/cm^3 %5.3g g/cm^3" % \
(key, val[1], val[0][0], val[0][1]))
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/cookbook/time_series.py
--- a/doc/source/cookbook/time_series.py
+++ b/doc/source/cookbook/time_series.py
@@ -12,7 +12,7 @@
storage = {}
-# By using the piter() function, we can iterate on every dataset in
+# By using the piter() function, we can iterate on every dataset in
# the TimeSeries object. By using the storage keyword, we can populate
# a dictionary where the dataset is the key, and sto.result is the value
# for later use when the loop is complete.
@@ -25,13 +25,13 @@
sphere = ds.sphere("c", (100., "kpc"))
# Calculate the entropy within that sphere
entr = sphere["entropy"].sum()
- # Store the current time and sphere entropy for this dataset in our
+ # Store the current time and sphere entropy for this dataset in our
# storage dictionary as a tuple
store.result = (ds.current_time.in_units('Gyr'), entr)
# Convert the storage dictionary values to a Nx2 array, so the can be easily
# plotted
-arr = np.array(storage.values())
+arr = np.array(list(storage.values()))
# Plot up the results: time versus entropy
plt.semilogy(arr[:,0], arr[:,1], 'r-')
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/developing/intro.rst
--- a/doc/source/developing/intro.rst
+++ b/doc/source/developing/intro.rst
@@ -142,3 +142,77 @@
federated database for simulation outputs, and so on and so forth.
yt is an ambitious project. Let's be ambitious together.
+
+yt Community Code of Conduct
+----------------------------
+
+The community of participants in open source
+Scientific projects is made up of members from around the
+globe with a diverse set of skills, personalities, and
+experiences. It is through these differences that our
+community experiences success and continued growth. We
+expect everyone in our community to follow these guidelines
+when interacting with others both inside and outside of our
+community. Our goal is to keep ours a positive, inclusive,
+successful, and growing community.
+
+As members of the community,
+
+- We pledge to treat all people with respect and
+ provide a harassment- and bullying-free environment,
+ regardless of sex, sexual orientation and/or gender
+ identity, disability, physical appearance, body size,
+ race, nationality, ethnicity, and religion. In
+ particular, sexual language and imagery, sexist,
+ racist, or otherwise exclusionary jokes are not
+ appropriate.
+
+- We pledge to respect the work of others by
+ recognizing acknowledgment/citation requests of
+ original authors. As authors, we pledge to be explicit
+ about how we want our own work to be cited or
+ acknowledged.
+
+- We pledge to welcome those interested in joining the
+ community, and realize that including people with a
+ variety of opinions and backgrounds will only serve to
+ enrich our community. In particular, discussions
+ relating to pros/cons of various technologies,
+ programming languages, and so on are welcome, but
+ these should be done with respect, taking proactive
+ measure to ensure that all participants are heard and
+ feel confident that they can freely express their
+ opinions.
+
+- We pledge to welcome questions and answer them
+ respectfully, paying particular attention to those new
+ to the community. We pledge to provide respectful
+ criticisms and feedback in forums, especially in
+ discussion threads resulting from code
+ contributions.
+
+- We pledge to be conscientious of the perceptions of
+ the wider community and to respond to criticism
+ respectfully. We will strive to model behaviors that
+ encourage productive debate and disagreement, both
+ within our community and where we are criticized. We
+ will treat those outside our community with the same
+ respect as people within our community.
+
+- We pledge to help the entire community follow the
+ code of conduct, and to not remain silent when we see
+ violations of the code of conduct. We will take action
+ when members of our community violate this code such as
+ contacting confidential at yt-project.org (all emails sent to
+ this address will be treated with the strictest
+ confidence) or talking privately with the person.
+
+This code of conduct applies to all
+community situations online and offline, including mailing
+lists, forums, social media, conferences, meetings,
+associated social events, and one-to-one interactions.
+
+The yt Community Code of Conduct was adapted from the
+`Astropy Community Code of Conduct
+<http://www.astropy.org/about.html#codeofconduct>`_,
+which was partially inspired by the PSF code of conduct.
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -1079,6 +1079,76 @@
.. _loading-pyne-data:
+Halo Catalog Data
+-----------------
+
+yt has support for reading halo catalogs produced by Rockstar and the inline
+FOF/SUBFIND halo finders of Gadget and OWLS. The halo catalogs are treated as
+particle datasets where each particle represents a single halo. At this time,
+yt does not have the ability to load the member particles for a given halo.
+However, once loaded, further halo analysis can be performed using
+:ref:`halo_catalog`.
+
+In the case where halo catalogs are written to multiple files, one must only
+give the path to one of them.
+
+Gadget FOF/SUBFIND
+^^^^^^^^^^^^^^^^^^
+
+The two field types for GadgetFOF data are "Group" (FOF) and "Subhalo" (SUBFIND).
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("gadget_fof_halos/groups_042/fof_subhalo_tab_042.0.hdf5")
+ ad = ds.all_data()
+ # The halo mass
+ print ad["Group", "particle_mass"]
+ print ad["Subhalo", "particle_mass"]
+ # Halo ID
+ print ad["Group", "particle_identifier"]
+ print ad["Subhalo", "particle_identifier"]
+ # positions
+ print ad["Group", "particle_position_x"]
+ # velocities
+ print ad["Group", "particle_velocity_x"]
+
+Multidimensional fields can be accessed through the field name followed by an
+underscore and the index.
+
+.. code-block:: python
+
+ # x component of the spin
+ print ad["Subhalo", "SubhaloSpin_0"]
+
+OWLS FOF/SUBFIND
+^^^^^^^^^^^^^^^^
+
+OWLS halo catalogs have a very similar structure to regular Gadget halo catalogs.
+The two field types are "FOF" and "SUBFIND".
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("owls_fof_halos/groups_008/group_008.0.hdf5")
+ ad = ds.all_data()
+ # The halo mass
+ print ad["FOF", "particle_mass"]
+
+Rockstar
+^^^^^^^^
+
+Rockstar halo catalogs are loaded by providing the path to one of the .bin files.
+The single field type available is "halos".
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("rockstar_halos/halos_0.0.bin")
+ ad = ds.all_data()
+ # The halo mass
+ print ad["halos", "particle_mass"]
+
PyNE Data
---------
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -1011,7 +1011,7 @@
"""
f = h5py.File(file_name, 'w')
- for ion, params in lineDic.iteritems():
+ for ion, params in lineDic.items():
f.create_dataset("{0}/N".format(ion),data=params['N'])
f.create_dataset("{0}/b".format(ion),data=params['b'])
f.create_dataset("{0}/z".format(ion),data=params['z'])
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
@@ -343,7 +343,7 @@
del output["object"]
# Combine results from each slice.
- all_slices = all_storage.keys()
+ all_slices = list(all_storage.keys())
all_slices.sort()
for my_slice in all_slices:
if save_slice_images:
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -22,6 +22,7 @@
import glob
import os
import os.path as path
+from functools import cmp_to_key
from collections import defaultdict
from yt.extern.six import add_metaclass
from yt.extern.six.moves import zip as izip
@@ -39,7 +40,7 @@
TINY
from yt.utilities.physical_ratios import \
rho_crit_g_cm3_h2
-
+
from .hop.EnzoHop import RunHOP
from .fof.EnzoFOF import RunFOF
@@ -138,9 +139,9 @@
c[2] = self["particle_position_z"] - self.ds.domain_left_edge[2]
com = []
for i in range(3):
- # A halo is likely periodic around a boundary if the distance
+ # A halo is likely periodic around a boundary if the distance
# between the max and min particle
- # positions are larger than half the box.
+ # positions are larger than half the box.
# So skip the rest if the converse is true.
# Note we might make a change here when periodicity-handling is
# fully implemented.
@@ -444,7 +445,7 @@
Msun2g = mass_sun_cgs
rho_crit = rho_crit * ((1.0 + z) ** 3.0)
# Get some pertinent information about the halo.
- self.mass_bins = self.ds.arr(np.zeros(self.bin_count + 1,
+ self.mass_bins = self.ds.arr(np.zeros(self.bin_count + 1,
dtype='float64'),'Msun')
dist = np.empty(thissize, dtype='float64')
cen = self.center_of_mass()
@@ -475,7 +476,7 @@
self.overdensity = self.mass_bins * Msun2g / \
(4./3. * math.pi * rho_crit * \
(self.radial_bins )**3.0)
-
+
def _get_ellipsoid_parameters_basic(self):
np.seterr(all='ignore')
# check if there are 4 particles to form an ellipsoid
@@ -501,7 +502,7 @@
for axis in range(np.size(DW)):
cases = np.array([position[axis],
position[axis] + DW[axis],
- position[axis] - DW[axis]])
+ position[axis] - DW[axis]])
# pick out the smallest absolute distance from com
position[axis] = np.choose(np.abs(cases).argmin(axis=0), cases)
# find the furthest particle's index
@@ -571,7 +572,7 @@
_name = "RockstarHalo"
# See particle_mask
_radjust = 4.
-
+
def maximum_density(self):
r"""Not implemented."""
return -1
@@ -635,11 +636,11 @@
def get_ellipsoid_parameters(self):
r"""Calculate the parameters that describe the ellipsoid of
the particles that constitute the halo.
-
+
Parameters
----------
None
-
+
Returns
-------
tuple : (cm, mag_A, mag_B, mag_C, e0_vector, tilt)
@@ -650,7 +651,7 @@
#. mag_C as a float.
#. e0_vector as an array.
#. tilt as a float.
-
+
Examples
--------
>>> params = halos[0].get_ellipsoid_parameters()
@@ -662,22 +663,22 @@
basic_parameters[4], basic_parameters[5]]), basic_parameters[6]]
toreturn.extend(updated)
return tuple(toreturn)
-
+
def get_ellipsoid(self):
r"""Returns an ellipsoidal data object.
-
+
This will generate a new, empty ellipsoidal data object for this
halo.
-
+
Parameters
----------
None.
-
+
Returns
-------
ellipsoid : `yt.data_objects.data_containers.YTEllipsoidBase`
The ellipsoidal data object.
-
+
Examples
--------
>>> ell = halos[0].get_ellipsoid()
@@ -686,7 +687,7 @@
ell = self.data.ds.ellipsoid(ep[0], ep[1], ep[2], ep[3],
ep[4], ep[5])
return ell
-
+
class HOPHalo(Halo):
_name = "HOPHalo"
pass
@@ -763,14 +764,14 @@
self.size, key)
if field_data is not None:
if key == 'particle_index':
- #this is an index for turning data sorted by particle index
+ #this is an index for turning data sorted by particle index
#into the same order as the fields on disk
self._pid_sort = field_data.argsort().argsort()
#convert to YTArray using the data from disk
if key == 'particle_mass':
field_data = self.ds.arr(field_data, 'Msun')
else:
- field_data = self.ds.arr(field_data,
+ field_data = self.ds.arr(field_data,
self.ds._get_field_info('unknown',key).units)
self._saved_fields[key] = field_data
return self._saved_fields[key]
@@ -856,21 +857,21 @@
basic_parameters[4], basic_parameters[5]]), basic_parameters[6]]
toreturn.extend(updated)
return tuple(toreturn)
-
+
def get_ellipsoid(self):
- r"""Returns an ellipsoidal data object.
+ r"""Returns an ellipsoidal data object.
This will generate a new, empty ellipsoidal data object for this
halo.
-
+
Parameters
----------
None.
-
+
Returns
-------
ellipsoid : `yt.data_objects.data_containers.YTEllipsoidBase`
The ellipsoidal data object.
-
+
Examples
--------
>>> ell = halos[0].get_ellipsoid()
@@ -947,11 +948,11 @@
def maximum_density(self):
r"""Undefined for text halos."""
return -1
-
+
def maximum_density_location(self):
r"""Undefined, default to CoM"""
return self.center_of_mass()
-
+
def get_size(self):
# Have to just get it from the sphere.
return self["particle_position_x"].size
@@ -964,8 +965,8 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is True (default), only run it on the dark matter particles,
- otherwise on all particles. Returns an iterable collection of
+ *dm_only* is True (default), only run it on the dark matter particles,
+ otherwise on all particles. Returns an iterable collection of
*HopGroup* items.
"""
self._data_source = data_source
@@ -1051,7 +1052,7 @@
ellipsoid_data : bool.
Whether to print the ellipsoidal information to the file.
Default = False.
-
+
Examples
--------
>>> halos.write_out("HopAnalysis.out")
@@ -1144,10 +1145,10 @@
_halo_dt = np.dtype([('id', np.int64), ('pos', (np.float32, 6)),
('corevel', (np.float32, 3)), ('bulkvel', (np.float32, 3)),
('m', np.float32), ('r', np.float32), ('child_r', np.float32),
- ('vmax_r', np.float32),
+ ('vmax_r', np.float32),
('mgrav', np.float32), ('vmax', np.float32),
('rvmax', np.float32), ('rs', np.float32),
- ('klypin_rs', np.float32),
+ ('klypin_rs', np.float32),
('vrms', np.float32), ('J', (np.float32, 3)),
('energy', np.float32), ('spin', np.float32),
('alt_m', (np.float32, 4)), ('Xoff', np.float32),
@@ -1221,9 +1222,9 @@
"""
Read the out_*.list text file produced
by Rockstar into memory."""
-
+
ds = self.ds
- # In order to read the binary data, we need to figure out which
+ # In order to read the binary data, we need to figure out which
# binary files belong to this output.
basedir = os.path.dirname(self.out_list)
s = self.out_list.split('_')[-1]
@@ -1523,12 +1524,14 @@
id += 1
def haloCmp(h1, h2):
+ def cmp(a, b):
+ return (a > b) - (a < b)
c = cmp(h1.total_mass(), h2.total_mass())
if c != 0:
return -1 * c
if c == 0:
return cmp(h1.center_of_mass()[0], h2.center_of_mass()[0])
- self._groups.sort(haloCmp)
+ self._groups.sort(key=cmp_to_key(haloCmp))
sorted_max_dens = {}
for i, halo in enumerate(self._groups):
if halo.id in self._max_dens:
@@ -1873,7 +1876,7 @@
class LoadTextHaloes(GenericHaloFinder, TextHaloList):
r"""Load a text file of halos.
-
+
Like LoadHaloes, but when all that is available is a plain
text file. This assumes the text file has the 3-positions of halos
along with a radius. The halo objects created are spheres.
@@ -1882,7 +1885,7 @@
----------
fname : String
The name of the text file to read in.
-
+
columns : dict
A dict listing the column name : column number pairs for data
in the text file. It is zero-based (like Python).
@@ -1890,7 +1893,7 @@
Any column name outside of ['x', 'y', 'z', 'r'] will be attached
to each halo object in the supplementary dict 'supp'. See
example.
-
+
comment : String
If the first character of a line is equal to this, the line is
skipped. Default = "#".
@@ -1915,7 +1918,7 @@
Parameters
----------
fname : String
- The name of the Rockstar file to read in. Default =
+ The name of the Rockstar file to read in. Default =
"rockstar_halos/out_0.list'.
Examples
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/analysis_modules/level_sets/clump_handling.py
--- a/yt/analysis_modules/level_sets/clump_handling.py
+++ b/yt/analysis_modules/level_sets/clump_handling.py
@@ -20,7 +20,8 @@
from yt.fields.derived_field import \
ValidateSpatial
from yt.funcs import mylog
-
+from yt.extern.six import string_types
+
from .clump_info_items import \
clump_info_registry
from .clump_validators import \
@@ -268,7 +269,7 @@
def write_clump_index(clump, level, fh):
top = False
- if not isinstance(fh, file):
+ if isinstance(fh, string_types):
fh = open(fh, "w")
top = True
for q in range(level):
@@ -285,7 +286,7 @@
def write_clumps(clump, level, fh):
top = False
- if not isinstance(fh, file):
+ if isinstance(fh, string_types):
fh = open(fh, "w")
top = True
if ((clump.children is None) or (len(clump.children) == 0)):
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/data_objects/time_series.py
--- a/yt/data_objects/time_series.py
+++ b/yt/data_objects/time_series.py
@@ -130,7 +130,7 @@
def __new__(cls, outputs, *args, **kwargs):
if isinstance(outputs, string_types):
outputs = get_filenames_from_glob_pattern(outputs)
- ret = super(DatasetSeries, cls).__new__(cls, *args, **kwargs)
+ ret = super(DatasetSeries, cls).__new__(cls)
try:
ret._pre_outputs = outputs[:]
except TypeError:
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/api.py
--- a/yt/frontends/api.py
+++ b/yt/frontends/api.py
@@ -27,6 +27,7 @@
'fits',
'flash',
'gadget',
+ 'gadget_fof',
'gdf',
'halo_catalog',
'http_stream',
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -76,7 +76,7 @@
for key, val in self._handle.attrs.items():
if key.startswith('component_'):
comp_number = int(re.match('component_(\d+)', key).groups()[0])
- field_dict[val] = comp_number
+ field_dict[val.decode('utf-8')] = comp_number
self._field_dict = field_dict
return self._field_dict
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/fits/io.py
--- a/yt/frontends/fits/io.py
+++ b/yt/frontends/fits/io.py
@@ -32,7 +32,7 @@
def _read_particle_coords(self, chunks, ptf):
pdata = self.ds._handle[self.ds.first_image].data
assert(len(ptf) == 1)
- ptype = ptf.keys()[0]
+ ptype = list(ptf.keys())[0]
x = np.asarray(pdata.field("X"), dtype="=f8")
y = np.asarray(pdata.field("Y"), dtype="=f8")
z = np.ones(x.shape)
@@ -43,7 +43,7 @@
def _read_particle_fields(self, chunks, ptf, selector):
pdata = self.ds._handle[self.ds.first_image].data
assert(len(ptf) == 1)
- ptype = ptf.keys()[0]
+ ptype = list(ptf.keys())[0]
field_list = ptf[ptype]
x = np.asarray(pdata.field("X"), dtype="=f8")
y = np.asarray(pdata.field("Y"), dtype="=f8")
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/fits/misc.py
--- a/yt/frontends/fits/misc.py
+++ b/yt/frontends/fits/misc.py
@@ -12,14 +12,18 @@
import numpy as np
import base64
-from yt.extern.six.moves import StringIO
+from yt.extern.six import PY3
from yt.fields.derived_field import ValidateSpatial
from yt.utilities.on_demand_imports import _astropy
from yt.funcs import mylog, get_image_suffix
from yt.visualization._mpl_imports import FigureCanvasAgg
from yt.units.yt_array import YTQuantity, YTArray
from yt.utilities.fits_image import FITSImageData
-
+if PY3:
+ from io import BytesIO as IO
+else:
+ from yt.extern.six.moves import StringIO as IO
+
import os
def _make_counts(emin, emax):
@@ -255,12 +259,12 @@
def _repr_html_(self):
ret = ''
- for k, v in self.plots.iteritems():
+ for k, v in self.plots.items():
canvas = FigureCanvasAgg(v)
- f = StringIO()
+ f = IO()
canvas.print_figure(f)
f.seek(0)
- img = base64.b64encode(f.read())
+ img = base64.b64encode(f.read()).decode()
ret += r'<img style="max-width:100%%;max-height:100%%;" ' \
r'src="data:image/png;base64,%s"><br>' % img
return ret
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget/data_structures.py
--- a/yt/frontends/gadget/data_structures.py
+++ b/yt/frontends/gadget/data_structures.py
@@ -387,7 +387,7 @@
@classmethod
def _is_valid(self, *args, **kwargs):
need_groups = ['Header']
- veto_groups = ['FOF']
+ veto_groups = ['FOF', 'Group', 'Subhalo']
valid = True
try:
fh = h5py.File(args[0], mode='r')
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/__init__.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/__init__.py
@@ -0,0 +1,15 @@
+"""
+API for HaloCatalog frontend.
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/api.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/api.py
@@ -0,0 +1,26 @@
+"""
+API for GadgetFOF frontend
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2015, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from .data_structures import \
+ GadgetFOFDataset
+
+from .io import \
+ IOHandlerGadgetFOFHDF5
+
+from .fields import \
+ GadgetFOFFieldInfo
+
+from . import tests
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/data_structures.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -0,0 +1,246 @@
+"""
+Data structures for GadgetFOF frontend.
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from collections import defaultdict
+import h5py
+import numpy as np
+import stat
+import weakref
+import struct
+import glob
+import time
+import os
+
+from .fields import \
+ GadgetFOFFieldInfo
+
+from yt.utilities.cosmology import \
+ Cosmology
+from yt.utilities.definitions import \
+ mpc_conversion, sec_conversion
+from yt.utilities.exceptions import \
+ YTException
+from yt.utilities.logger import ytLogger as \
+ mylog
+from yt.geometry.particle_geometry_handler import \
+ ParticleIndex
+from yt.data_objects.static_output import \
+ Dataset, \
+ ParticleFile
+from yt.frontends.gadget.data_structures import \
+ _fix_unit_ordering
+import yt.utilities.fortran_utils as fpu
+from yt.units.yt_array import \
+ YTArray, \
+ YTQuantity
+
+class GadgetFOFParticleIndex(ParticleIndex):
+ def __init__(self, ds, dataset_type):
+ super(GadgetFOFParticleIndex, self).__init__(ds, dataset_type)
+
+ def _calculate_particle_index_starts(self):
+ # Halo indices are not saved in the file, so we must count by hand.
+ # File 0 has halos 0 to N_0 - 1, file 1 has halos N_0 to N_0 + N_1 - 1, etc.
+ particle_count = defaultdict(int)
+ offset_count = 0
+ for data_file in self.data_files:
+ data_file.index_start = dict([(ptype, particle_count[ptype]) for
+ ptype in data_file.total_particles])
+ data_file.offset_start = offset_count
+ for ptype in data_file.total_particles:
+ particle_count[ptype] += data_file.total_particles[ptype]
+ offset_count += data_file.total_offset
+
+ def _calculate_file_offset_map(self):
+ # After the FOF is performed, a load-balancing step redistributes halos
+ # and then writes more fields. Here, for each file, we create a list of
+ # files which contain the rest of the redistributed particles.
+ ifof = np.array([data_file.total_particles["Group"]
+ for data_file in self.data_files])
+ isub = np.array([data_file.total_offset
+ for data_file in self.data_files])
+ subend = isub.cumsum()
+ fofend = ifof.cumsum()
+ istart = np.digitize(fofend - ifof, subend - isub) - 1
+ iend = np.clip(np.digitize(fofend, subend), 0, ifof.size - 2)
+ for i, data_file in enumerate(self.data_files):
+ data_file.offset_files = self.data_files[istart[i]: iend[i] + 1]
+
+ def _detect_output_fields(self):
+ # TODO: Add additional fields
+ dsl = []
+ units = {}
+ for dom in self.data_files:
+ fl, _units = self.io._identify_fields(dom)
+ units.update(_units)
+ dom._calculate_offsets(fl)
+ for f in fl:
+ if f not in dsl: dsl.append(f)
+ self.field_list = dsl
+ ds = self.dataset
+ ds.particle_types = tuple(set(pt for pt, ds in dsl))
+ # This is an attribute that means these particle types *actually*
+ # exist. As in, they are real, in the dataset.
+ ds.field_units.update(units)
+ ds.particle_types_raw = ds.particle_types
+
+ def _setup_geometry(self):
+ super(GadgetFOFParticleIndex, self)._setup_geometry()
+ self._calculate_particle_index_starts()
+ self._calculate_file_offset_map()
+
+class GadgetFOFHDF5File(ParticleFile):
+ def __init__(self, ds, io, filename, file_id):
+ super(GadgetFOFHDF5File, self).__init__(ds, io, filename, file_id)
+ with h5py.File(filename, "r") as f:
+ self.header = dict((field, f.attrs[field]) \
+ for field in f.attrs.keys())
+
+class GadgetFOFDataset(Dataset):
+ _index_class = GadgetFOFParticleIndex
+ _file_class = GadgetFOFHDF5File
+ _field_info_class = GadgetFOFFieldInfo
+ _suffix = ".hdf5"
+
+ def __init__(self, filename, dataset_type="gadget_fof_hdf5",
+ n_ref=16, over_refine_factor=1,
+ unit_base=None, units_override=None):
+ self.n_ref = n_ref
+ self.over_refine_factor = over_refine_factor
+ if unit_base is not None and "UnitLength_in_cm" in unit_base:
+ # We assume this is comoving, because in the absence of comoving
+ # integration the redshift will be zero.
+ unit_base['cmcm'] = 1.0 / unit_base["UnitLength_in_cm"]
+ self._unit_base = unit_base
+ if units_override is not None:
+ raise RuntimeError("units_override is not supported for GadgetFOFDataset. "+
+ "Use unit_base instead.")
+ super(GadgetFOFDataset, self).__init__(filename, dataset_type,
+ units_override=units_override)
+
+ def _parse_parameter_file(self):
+ handle = h5py.File(self.parameter_filename, mode="r")
+ hvals = {}
+ hvals.update((str(k), v) for k, v in handle["/Header"].attrs.items())
+ hvals["NumFiles"] = hvals["NumFiles"]
+
+ self.dimensionality = 3
+ self.refine_by = 2
+ self.unique_identifier = \
+ int(os.stat(self.parameter_filename)[stat.ST_CTIME])
+
+ # Set standard values
+ self.domain_left_edge = np.zeros(3, "float64")
+ self.domain_right_edge = np.ones(3, "float64") * hvals["BoxSize"]
+ nz = 1 << self.over_refine_factor
+ self.domain_dimensions = np.ones(3, "int32") * nz
+ self.cosmological_simulation = 1
+ self.periodicity = (True, True, True)
+ self.current_redshift = hvals["Redshift"]
+ self.omega_lambda = hvals["OmegaLambda"]
+ self.omega_matter = hvals["Omega0"]
+ self.hubble_constant = hvals["HubbleParam"]
+
+ cosmology = Cosmology(hubble_constant=self.hubble_constant,
+ omega_matter=self.omega_matter,
+ omega_lambda=self.omega_lambda)
+ self.current_time = cosmology.t_from_z(self.current_redshift)
+
+ self.parameters = hvals
+ prefix = os.path.abspath(
+ os.path.join(os.path.dirname(self.parameter_filename),
+ os.path.basename(self.parameter_filename).split(".", 1)[0]))
+
+ suffix = self.parameter_filename.rsplit(".", 1)[-1]
+ self.filename_template = "%s.%%(num)i.%s" % (prefix, suffix)
+ self.file_count = len(glob.glob(prefix + "*" + self._suffix))
+ if self.file_count == 0:
+ raise YTException(message="No data files found.", ds=self)
+ self.particle_types = ("Group", "Subhalo")
+ self.particle_types_raw = ("Group", "Subhalo")
+
+ handle.close()
+
+ def _set_code_unit_attributes(self):
+ # Set a sane default for cosmological simulations.
+ if self._unit_base is None and self.cosmological_simulation == 1:
+ mylog.info("Assuming length units are in Mpc/h (comoving)")
+ self._unit_base = dict(length = (1.0, "Mpccm/h"))
+ # The other same defaults we will use from the standard Gadget
+ # defaults.
+ unit_base = self._unit_base or {}
+
+ if "length" in unit_base:
+ length_unit = unit_base["length"]
+ elif "UnitLength_in_cm" in unit_base:
+ if self.cosmological_simulation == 0:
+ length_unit = (unit_base["UnitLength_in_cm"], "cm")
+ else:
+ length_unit = (unit_base["UnitLength_in_cm"], "cmcm/h")
+ else:
+ raise RuntimeError
+ length_unit = _fix_unit_ordering(length_unit)
+ self.length_unit = self.quan(length_unit[0], length_unit[1])
+
+ if "velocity" in unit_base:
+ velocity_unit = unit_base["velocity"]
+ elif "UnitVelocity_in_cm_per_s" in unit_base:
+ velocity_unit = (unit_base["UnitVelocity_in_cm_per_s"], "cm/s")
+ else:
+ if self.cosmological_simulation == 0:
+ velocity_unit = (1e5, "cm/s")
+ else:
+ velocity_unit = (1e5, "cmcm/s")
+ velocity_unit = _fix_unit_ordering(velocity_unit)
+ 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.
+ if "mass" in unit_base:
+ mass_unit = unit_base["mass"]
+ elif "UnitMass_in_g" in unit_base:
+ if self.cosmological_simulation == 0:
+ mass_unit = (unit_base["UnitMass_in_g"], "g")
+ else:
+ mass_unit = (unit_base["UnitMass_in_g"], "g/h")
+ else:
+ # 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])
+
+ if "time" in unit_base:
+ time_unit = unit_base["time"]
+ elif "UnitTime_in_s" in unit_base:
+ time_unit = (unit_base["UnitTime_in_s"], "s")
+ else:
+ time_unit = (1., "s")
+ self.time_unit = self.quan(time_unit[0], time_unit[1])
+
+ @classmethod
+ def _is_valid(self, *args, **kwargs):
+ need_groups = ['Group', 'Header', 'Subhalo']
+ veto_groups = ['FOF']
+ valid = True
+ try:
+ fh = h5py.File(args[0], mode='r')
+ valid = all(ng in fh["/"] for ng in need_groups) and \
+ not any(vg in fh["/"] for vg in veto_groups)
+ fh.close()
+ except:
+ valid = False
+ pass
+ return valid
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/fields.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/fields.py
@@ -0,0 +1,48 @@
+"""
+GadgetFOF-specific fields
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2015, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.funcs import mylog
+from yt.fields.field_info_container import \
+ FieldInfoContainer
+from yt.units.yt_array import \
+ YTArray
+
+m_units = "code_mass"
+p_units = "code_length"
+v_units = "code_velocity"
+
+class GadgetFOFFieldInfo(FieldInfoContainer):
+ known_other_fields = (
+ )
+
+ known_particle_fields = (
+ ("GroupPos_0", (p_units, ["Group", "particle_position_x"], None)),
+ ("GroupPos_1", (p_units, ["Group", "particle_position_y"], None)),
+ ("GroupPos_2", (p_units, ["Group", "particle_position_z"], None)),
+ ("GroupVel_0", (v_units, ["Group", "particle_velocity_x"], None)),
+ ("GroupVel_1", (v_units, ["Group", "particle_velocity_y"], None)),
+ ("GroupVel_2", (v_units, ["Group", "particle_velocity_z"], None)),
+ ("GroupMass", (m_units, ["Group", "particle_mass"], None)),
+ ("GroupLen", ("", ["Group", "particle_number"], None)),
+ ("SubhaloPos_0", (p_units, ["Subhalo", "particle_position_x"], None)),
+ ("SubhaloPos_1", (p_units, ["Subhalo", "particle_position_y"], None)),
+ ("SubhaloPos_2", (p_units, ["Subhalo", "particle_position_z"], None)),
+ ("SubhaloVel_0", (v_units, ["Subhalo", "particle_velocity_x"], None)),
+ ("SubhaloVel_1", (v_units, ["Subhalo", "particle_velocity_y"], None)),
+ ("SubhaloVel_2", (v_units, ["Subhalo", "particle_velocity_z"], None)),
+ ("SubhaloMass", (m_units, ["Subhalo", "particle_mass"], None)),
+ ("SubhaloLen", ("", ["Subhalo", "particle_number"], None)),
+)
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/io.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/io.py
@@ -0,0 +1,207 @@
+"""
+GadgetFOF data-file handling function
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+import h5py
+import numpy as np
+
+from yt.utilities.exceptions import *
+from yt.funcs import mylog
+
+from yt.utilities.io_handler import \
+ BaseIOHandler
+
+from yt.utilities.lib.geometry_utils import compute_morton
+
+class IOHandlerGadgetFOFHDF5(BaseIOHandler):
+ _dataset_type = "gadget_fof_hdf5"
+
+ def __init__(self, ds):
+ super(IOHandlerGadgetFOFHDF5, self).__init__(ds)
+ self.offset_fields = set([])
+
+ def _read_fluid_selection(self, chunks, selector, fields, size):
+ raise NotImplementedError
+
+ def _read_particle_coords(self, chunks, ptf):
+ # This will read chunks and yield the results.
+ chunks = list(chunks)
+ data_files = set([])
+ for chunk in chunks:
+ for obj in chunk.objs:
+ data_files.update(obj.data_files)
+ for data_file in sorted(data_files):
+ with h5py.File(data_file.filename, "r") as f:
+ for ptype, field_list in sorted(ptf.items()):
+ pcount = data_file.total_particles[ptype]
+ coords = f[ptype]["%sPos" % ptype].value.astype("float64")
+ coords = np.resize(coords, (pcount, 3))
+ x = coords[:, 0]
+ y = coords[:, 1]
+ z = coords[:, 2]
+ yield ptype, (x, y, z)
+
+ def _read_offset_particle_field(self, field, data_file, fh):
+ field_data = np.empty(data_file.total_particles["Group"], dtype="float64")
+ fofindex = np.arange(data_file.total_particles["Group"]) + data_file.index_start["Group"]
+ for offset_file in data_file.offset_files:
+ if fh.filename == offset_file.filename:
+ ofh = fh
+ else:
+ ofh = h5py.File(offset_file.filename, "r")
+ subindex = np.arange(offset_file.total_offset) + offset_file.offset_start
+ substart = max(fofindex[0] - subindex[0], 0)
+ subend = min(fofindex[-1] - subindex[0], subindex.size - 1)
+ fofstart = substart + subindex[0] - fofindex[0]
+ fofend = subend + subindex[0] - fofindex[0]
+ field_data[fofstart:fofend + 1] = ofh["Subhalo"][field][substart:subend + 1]
+ return field_data
+
+ def _read_particle_fields(self, chunks, ptf, selector):
+ # Now we have all the sizes, and we can allocate
+ chunks = list(chunks)
+ data_files = set([])
+ for chunk in chunks:
+ for obj in chunk.objs:
+ data_files.update(obj.data_files)
+ for data_file in sorted(data_files):
+ with h5py.File(data_file.filename, "r") as f:
+ for ptype, field_list in sorted(ptf.items()):
+ pcount = data_file.total_particles[ptype]
+ if pcount == 0: continue
+ coords = f[ptype]["%sPos" % ptype].value.astype("float64")
+ coords = np.resize(coords, (pcount, 3))
+ x = coords[:, 0]
+ y = coords[:, 1]
+ z = coords[:, 2]
+ mask = selector.select_points(x, y, z, 0.0)
+ del x, y, z
+ if mask is None: continue
+ for field in field_list:
+ if field in self.offset_fields:
+ field_data = \
+ self._read_offset_particle_field(field, data_file, f)
+ else:
+ if field == "particle_identifier":
+ field_data = \
+ np.arange(data_file.total_particles[ptype]) + \
+ data_file.index_start[ptype]
+ elif field in f[ptype]:
+ field_data = f[ptype][field].value.astype("float64")
+ else:
+ fname = field[:field.rfind("_")]
+ field_data = f[ptype][fname].value.astype("float64")
+ my_div = field_data.size / pcount
+ if my_div > 1:
+ field_data = np.resize(field_data, (pcount, my_div))
+ findex = int(field[field.rfind("_") + 1:])
+ field_data = field_data[:, findex]
+ data = field_data[mask]
+ yield (ptype, field), data
+
+ def _initialize_index(self, data_file, regions):
+ pcount = sum(data_file.total_particles.values())
+ morton = np.empty(pcount, dtype='uint64')
+ if pcount == 0: return morton
+ mylog.debug("Initializing index % 5i (% 7i particles)",
+ data_file.file_id, pcount)
+ ind = 0
+ with h5py.File(data_file.filename, "r") as f:
+ if not f.keys(): return None
+ dx = np.finfo(f["Group"]["GroupPos"].dtype).eps
+ dx = 2.0*self.ds.quan(dx, "code_length")
+
+ for ptype in data_file.ds.particle_types_raw:
+ if data_file.total_particles[ptype] == 0: continue
+ pos = f[ptype]["%sPos" % ptype].value.astype("float64")
+ pos = np.resize(pos, (data_file.total_particles[ptype], 3))
+ pos = data_file.ds.arr(pos, "code_length")
+
+ # These are 32 bit numbers, so we give a little lee-way.
+ # Otherwise, for big sets of particles, we often will bump into the
+ # domain edges. This helps alleviate that.
+ np.clip(pos, self.ds.domain_left_edge + dx,
+ self.ds.domain_right_edge - dx, pos)
+ if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
+ np.any(pos.max(axis=0) > self.ds.domain_right_edge):
+ raise YTDomainOverflow(pos.min(axis=0),
+ pos.max(axis=0),
+ self.ds.domain_left_edge,
+ self.ds.domain_right_edge)
+ regions.add_data_file(pos, data_file.file_id)
+ morton[ind:ind+pos.shape[0]] = compute_morton(
+ pos[:,0], pos[:,1], pos[:,2],
+ data_file.ds.domain_left_edge,
+ data_file.ds.domain_right_edge)
+ ind += pos.shape[0]
+ return morton
+
+ def _count_particles(self, data_file):
+ with h5py.File(data_file.filename, "r") as f:
+ pcount = {"Group": f["Header"].attrs["Ngroups_ThisFile"],
+ "Subhalo": f["Header"].attrs["Nsubgroups_ThisFile"]}
+ data_file.total_offset = 0 # need to figure out how subfind works here
+ return pcount
+
+ def _identify_fields(self, data_file):
+ fields = []
+ pcount = data_file.total_particles
+ if sum(pcount.values()) == 0: return fields, {}
+ with h5py.File(data_file.filename, "r") as f:
+ for ptype in self.ds.particle_types_raw:
+ if data_file.total_particles[ptype] == 0: continue
+ fields.append((ptype, "particle_identifier"))
+ my_fields, my_offset_fields = \
+ subfind_field_list(f[ptype], ptype, data_file.total_particles)
+ fields.extend(my_fields)
+ self.offset_fields = self.offset_fields.union(set(my_offset_fields))
+ return fields, {}
+
+def subfind_field_list(fh, ptype, pcount):
+ fields = []
+ offset_fields = []
+ for field in fh.keys():
+ if isinstance(fh[field], h5py.Group):
+ my_fields, my_offset_fields = \
+ subfind_field_list(fh[field], ptype, pcount)
+ fields.extend(my_fields)
+ my_offset_fields.extend(offset_fields)
+ else:
+ if not fh[field].size % pcount[ptype]:
+ my_div = fh[field].size / pcount[ptype]
+ fname = fh[field].name[fh[field].name.find(ptype) + len(ptype) + 1:]
+ if my_div > 1:
+ for i in range(my_div):
+ fields.append((ptype, "%s_%d" % (fname, i)))
+ else:
+ fields.append((ptype, fname))
+ elif ptype == "Subfind" and \
+ not fh[field].size % fh["/Subfind"].attrs["Number_of_groups"]:
+ # These are actually Group fields, but they were written after
+ # a load balancing step moved halos around and thus they do not
+ # correspond to the halos stored in the Group group.
+ my_div = fh[field].size / fh["/Subfind"].attrs["Number_of_groups"]
+ fname = fh[field].name[fh[field].name.find(ptype) + len(ptype) + 1:]
+ if my_div > 1:
+ for i in range(my_div):
+ fields.append(("Group", "%s_%d" % (fname, i)))
+ else:
+ fields.append(("Group", fname))
+ offset_fields.append(fname)
+ else:
+ mylog.warn("Cannot add field (%s, %s) with size %d." % \
+ (ptype, fh[field].name, fh[field].size))
+ continue
+ return fields, offset_fields
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/setup.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/setup.py
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('gadget_fof', parent_package, top_path)
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/gadget_fof/tests/test_outputs.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/tests/test_outputs.py
@@ -0,0 +1,56 @@
+"""
+GadgetFOF frontend tests using gadget_fof datasets
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+import os.path
+from yt.testing import \
+ assert_equal
+from yt.utilities.answer_testing.framework import \
+ FieldValuesTest, \
+ requires_ds, \
+ requires_file, \
+ data_dir_load
+from yt.frontends.gadget_fof.api import GadgetFOFDataset
+
+p_types = ("Group", "Subhalo")
+p_fields = ("particle_position_x", "particle_position_y",
+ "particle_position_z", "particle_velocity_x",
+ "particle_velocity_y", "particle_velocity_z",
+ "particle_mass", "particle_identifier")
+_fields = tuple([(p_type, p_field) for p_type in p_types
+ for p_field in p_fields])
+
+# a dataset with empty files
+g5 = "gadget_fof_halos/groups_005/fof_subhalo_tab_005.0.hdf5"
+g42 = "gadget_fof_halos/groups_042/fof_subhalo_tab_042.0.hdf5"
+
+
+ at requires_ds(g5)
+def test_fields_g5():
+ ds = data_dir_load(g5)
+ yield assert_equal, str(ds), os.path.basename(g5)
+ for field in _fields:
+ yield FieldValuesTest(g5, field, particle_type=True)
+
+
+ at requires_ds(g42)
+def test_fields_g42():
+ ds = data_dir_load(g42)
+ yield assert_equal, str(ds), os.path.basename(g42)
+ for field in _fields:
+ yield FieldValuesTest(g42, field, particle_type=True)
+
+ at requires_file(g42)
+def test_GadgetFOFDataset():
+ assert isinstance(data_dir_load(g42), GadgetFOFDataset)
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/halo_catalog/io.py
--- a/yt/frontends/halo_catalog/io.py
+++ b/yt/frontends/halo_catalog/io.py
@@ -39,7 +39,7 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
@@ -57,7 +57,7 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/owls/io.py
--- a/yt/frontends/owls/io.py
+++ b/yt/frontends/owls/io.py
@@ -70,7 +70,7 @@
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files, key=lambda x: x.filename):
f = _get_h5_handle(data_file.filename)
# This double-reads
for ptype, field_list in sorted(ptf.items()):
@@ -88,7 +88,7 @@
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files, key=lambda x: x.filename):
f = _get_h5_handle(data_file.filename)
for ptype, field_list in sorted(ptf.items()):
if data_file.total_particles[ptype] == 0:
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/owls_subfind/data_structures.py
--- a/yt/frontends/owls_subfind/data_structures.py
+++ b/yt/frontends/owls_subfind/data_structures.py
@@ -27,11 +27,14 @@
from .fields import \
OWLSSubfindFieldInfo
-from yt.utilities.cosmology import Cosmology
+from yt.utilities.cosmology import \
+ Cosmology
from yt.utilities.definitions import \
mpc_conversion, sec_conversion
from yt.utilities.exceptions import \
- YTException
+ YTException
+from yt.utilities.logger import ytLogger as \
+ mylog
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.data_objects.static_output import \
@@ -170,6 +173,7 @@
# The other same defaults we will use from the standard Gadget
# defaults.
unit_base = self._unit_base or {}
+
if "length" in unit_base:
length_unit = unit_base["length"]
elif "UnitLength_in_cm" in unit_base:
@@ -182,7 +186,6 @@
length_unit = _fix_unit_ordering(length_unit)
self.length_unit = self.quan(length_unit[0], length_unit[1])
- unit_base = self._unit_base or {}
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
elif "UnitVelocity_in_cm_per_s" in unit_base:
@@ -191,6 +194,7 @@
velocity_unit = (1e5, "cm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
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.
if "mass" in unit_base:
@@ -205,7 +209,14 @@
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])
- self.time_unit = self.quan(unit_base["UnitTime_in_s"], "s")
+
+ if "time" in unit_base:
+ time_unit = unit_base["time"]
+ elif "UnitTime_in_s" in unit_base:
+ time_unit = (unit_base["UnitTime_in_s"], "s")
+ else:
+ time_unit = (1., "s")
+ self.time_unit = self.quan(time_unit[0], time_unit[1])
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/ramses/data_structures.py
--- a/yt/frontends/ramses/data_structures.py
+++ b/yt/frontends/ramses/data_structures.py
@@ -491,13 +491,22 @@
"""
Generates the conversion to various physical _units based on the parameter file
"""
- # Note that unit_l *already* converts to proper!
- # Also note that unit_l must be multiplied by the boxlen parameter to
- # ensure we are correctly set up for the current domain.
- length_unit = self.parameters['unit_l']
- boxlen = self.parameters['boxlen']
- density_unit = self.parameters['unit_d']
- mass_unit = density_unit * (length_unit * boxlen)**3
+ #Please note that for all units given in the info file, the boxlen
+ #still needs to be folded in, as shown below!
+
+ boxlen=self.parameters['boxlen']
+ length_unit = self.parameters['unit_l'] * boxlen
+ density_unit = self.parameters['unit_d']/ boxlen**3
+
+ # In the mass unit, the factors of boxlen cancel back out, so this
+ #is equivalent to unit_d*unit_l**3
+
+ mass_unit = density_unit * length_unit**3
+
+ # Cosmological runs are done in lookback conformal time.
+ # To convert to proper time, the time unit is calculated from
+ # the expansion factor. This is not yet done here!
+
time_unit = self.parameters['unit_t']
magnetic_unit = np.sqrt(4*np.pi * mass_unit /
(time_unit**2 * length_unit))
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/ramses/io.py
--- a/yt/frontends/ramses/io.py
+++ b/yt/frontends/ramses/io.py
@@ -20,7 +20,12 @@
BaseIOHandler
from yt.utilities.logger import ytLogger as mylog
import yt.utilities.fortran_utils as fpu
-from yt.extern.six.moves import cStringIO
+from yt.extern.six import PY3
+
+if PY3:
+ from io import BytesIO as IO
+else:
+ from cStringIO import StringIO as IO
class IOHandlerRAMSES(BaseIOHandler):
_dataset_type = "ramses"
@@ -37,7 +42,7 @@
f = open(subset.domain.hydro_fn, "rb")
# This contains the boundary information, so we skim through
# and pick off the right vectors
- content = cStringIO(f.read())
+ content = IO(f.read())
rv = subset.fill(content, fields, selector)
for ft, f in fields:
d = rv.pop(f)
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/rockstar/io.py
--- a/yt/frontends/rockstar/io.py
+++ b/yt/frontends/rockstar/io.py
@@ -28,6 +28,7 @@
from yt.utilities.lib.geometry_utils import compute_morton
from yt.geometry.oct_container import _ORDER_MAX
+from operator import attrgetter
class IOHandlerRockstarBinary(BaseIOHandler):
_dataset_type = "rockstar_binary"
@@ -45,12 +46,11 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
-
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files,key=attrgetter("filename")):
pcount = data_file.header['num_halos']
with open(data_file.filename, "rb") as f:
f.seek(data_file._position_offset, os.SEEK_SET)
@@ -66,11 +66,11 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files,key=attrgetter("filename")):
pcount = data_file.header['num_halos']
with open(data_file.filename, "rb") as f:
for ptype, field_list in sorted(ptf.items()):
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/frontends/setup.py
--- a/yt/frontends/setup.py
+++ b/yt/frontends/setup.py
@@ -17,6 +17,7 @@
config.add_subpackage("fits")
config.add_subpackage("flash")
config.add_subpackage("gadget")
+ config.add_subpackage("gadget_fof")
config.add_subpackage("gdf")
config.add_subpackage("halo_catalog")
config.add_subpackage("http_stream")
@@ -34,11 +35,12 @@
config.add_subpackage("athena/tests")
config.add_subpackage("boxlib/tests")
config.add_subpackage("chombo/tests")
+ config.add_subpackage("eagle/tests")
config.add_subpackage("enzo/tests")
- config.add_subpackage("eagle/tests")
config.add_subpackage("fits/tests")
config.add_subpackage("flash/tests")
config.add_subpackage("gadget/tests")
+ config.add_subpackage("gadget_fof/tests")
config.add_subpackage("moab/tests")
config.add_subpackage("owls/tests")
config.add_subpackage("owls_subfind/tests")
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/utilities/fits_image.py
--- a/yt/utilities/fits_image.py
+++ b/yt/utilities/fits_image.py
@@ -122,7 +122,7 @@
for key in fields:
if key not in exclude_fields:
if hasattr(img_data[key], "units"):
- self.field_units[key] = str(img_data[key].units)
+ self.field_units[key] = img_data[key].units
else:
self.field_units[key] = "dimensionless"
mylog.info("Making a FITS image of field %s" % key)
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/visualization/color_maps.py
--- a/yt/visualization/color_maps.py
+++ b/yt/visualization/color_maps.py
@@ -11,7 +11,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
import numpy as np
-from yt.extern.six.moves import zip as izip
import matplotlib
import matplotlib.colors as cc
@@ -86,9 +85,9 @@
194.5*_vs**2.88+99.72*np.exp(-77.24*(_vs-0.742)**2.0)
+ 45.40*_vs**0.089+10.0)/255.0
-cdict = {'red':zip(_vs,_kamae_red,_kamae_red),
- 'green':zip(_vs,_kamae_grn,_kamae_grn),
- 'blue':zip(_vs,_kamae_blu,_kamae_blu)}
+cdict = {'red':np.transpose([_vs,_kamae_red,_kamae_red]),
+ 'green':np.transpose([_vs,_kamae_grn,_kamae_grn]),
+ 'blue':np.transpose([_vs,_kamae_blu,_kamae_blu])}
add_cmap('kamae', cdict)
# This one is a simple black & green map
@@ -151,9 +150,9 @@
_vs = np.linspace(0,1,256)
for k,v in list(_cm.color_map_luts.items()):
if k not in yt_colormaps and k not in mcm.cmap_d:
- cdict = { 'red': zip(_vs,v[0],v[0]),
- 'green': zip(_vs,v[1],v[1]),
- 'blue': zip(_vs,v[2],v[2]) }
+ cdict = { 'red': np.transpose([_vs,v[0],v[0]]),
+ 'green': np.transpose([_vs,v[1],v[1]]),
+ 'blue': np.transpose([_vs,v[2],v[2]]) }
add_cmap(k, cdict)
def _extract_lookup_table(cmap_name):
@@ -393,9 +392,9 @@
# Second number is the (0..1) number to interpolate to when coming *from below*
# Third number is the (0..1) number to interpolate to when coming *from above*
_vs = np.linspace(0,1,256)
- cdict = {'red': zip(_vs, cmap[:,0], cmap[:,0]),
- 'green': zip(_vs, cmap[:,1], cmap[:,1]),
- 'blue': zip(_vs, cmap[:,2], cmap[:,2])}
+ cdict = {'red': np.transpose([_vs, cmap[:,0], cmap[:,0]]),
+ 'green': np.transpose([_vs, cmap[:,1], cmap[:,1]]),
+ 'blue': np.transpose([_vs, cmap[:,2], cmap[:,2]])}
if name is not None:
add_cmap(name, cdict)
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -27,7 +27,6 @@
import numpy as np
import weakref
import re
-import string
class FixedResolutionBuffer(object):
r"""
@@ -178,13 +177,13 @@
pstr = m.string[m.start()+1:m.end()-1]
segments = fname.split("_")
for i,s in enumerate(segments):
- segments[i] = string.capitalize(s)
+ segments[i] = s.capitalize()
if s == pstr:
ipstr = i
element = segments[ipstr-1]
roman = pnum2rom[pstr[1:]]
label = element + '\ ' + roman + '\ ' + \
- string.join(segments[ipstr+1:], '\ ')
+ '\ '.join(segments[ipstr+1:])
else:
label = fname
return label
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -170,7 +170,7 @@
bitmap_array = np.concatenate([bitmap_array.astype('uint8'),
alpha_channel], axis=-1)
if transpose:
- bitmap_array = bitmap_array.swapaxes(0,1)
+ bitmap_array = bitmap_array.swapaxes(0,1).copy(order="C")
if filename is not None:
pw.write_png(bitmap_array, filename)
else:
diff -r 8720621b3491489baf0dfe6a235a928433590052 -r fa91228a919dda447788e79a9a51ca9728bbfb9a yt/visualization/profile_plotter.py
--- a/yt/visualization/profile_plotter.py
+++ b/yt/visualization/profile_plotter.py
@@ -222,7 +222,7 @@
plot_spec = [plot_spec.copy() for p in profiles]
ProfilePlot._initialize_instance(self, profiles, label, plot_spec, y_log)
-
+
@validate_plot
def save(self, name=None, suffix=None):
r"""
@@ -530,15 +530,20 @@
xma = xmax
extrema = {p.x_field: ((xmi, str(p.x.units)), (xma, str(p.x.units)))}
units = {p.x_field: str(p.x.units)}
+ if self.x_log is None:
+ logs = None
+ else:
+ logs = {p.x_field: self.x_log}
for field in p.field_map.values():
units[field] = str(p.field_data[field].units)
self.profiles[i] = \
create_profile(p.data_source, p.x_field,
n_bins=len(p.x_bins)-1,
- fields=p.field_map.values(),
+ fields=list(p.field_map.values()),
weight_field=p.weight_field,
accumulation=p.accumulation,
fractional=p.fractional,
+ logs=logs,
extrema=extrema, units=units)
return self
@@ -1146,6 +1151,14 @@
extrema = {p.x_field: ((xmin, str(p.x.units)), (xmax, str(p.x.units))),
p.y_field: ((p.y_bins.min(), str(p.y.units)),
(p.y_bins.max(), str(p.y.units)))}
+ if self.x_log is not None or self.y_log is not None:
+ logs = {}
+ else:
+ logs = None
+ if self.x_log is not None:
+ logs[p.x_field] = self.x_log
+ if self.y_log is not None:
+ logs[p.y_field] = self.y_log
deposition = getattr(self.profile, "deposition", None)
if deposition is None:
additional_kwargs = {'accumulation': p.accumulation,
@@ -1155,11 +1168,12 @@
self.profile = create_profile(
p.data_source,
[p.x_field, p.y_field],
- p.field_map.values(),
+ list(p.field_map.values()),
n_bins=[len(p.x_bins)-1, len(p.y_bins)-1],
weight_field=p.weight_field,
units=units,
extrema=extrema,
+ logs=logs,
**additional_kwargs)
for field in zunits:
self.profile.set_field_unit(field, zunits[field])
@@ -1201,6 +1215,14 @@
extrema = {p.x_field: ((p.x_bins.min(), str(p.x.units)),
(p.x_bins.max(), str(p.x.units))),
p.y_field: ((ymin, str(p.y.units)), (ymax, str(p.y.units)))}
+ if self.x_log is not None or self.y_log is not None:
+ logs = {}
+ else:
+ logs = None
+ if self.x_log is not None:
+ logs[p.x_field] = self.x_log
+ if self.y_log is not None:
+ logs[p.y_field] = self.y_log
deposition = getattr(self.profile, "deposition", None)
if deposition is None:
additional_kwargs = {'accumulation': p.accumulation,
@@ -1210,11 +1232,12 @@
self.profile = create_profile(
p.data_source,
[p.x_field, p.y_field],
- p.field_map.values(),
+ list(p.field_map.values()),
n_bins=[len(p.x_bins)-1, len(p.y_bins)-1],
weight_field=p.weight_field,
units=units,
extrema=extrema,
+ logs=logs,
**additional_kwargs)
for field in zunits:
self.profile.set_field_unit(field, zunits[field])
https://bitbucket.org/yt_analysis/yt/commits/a4f19a0f6144/
Changeset: a4f19a0f6144
Branch: bugfix-1035
User: bwkeller
Date: 2015-07-17 17:21:24+00:00
Summary: Merged yt into bugfix-1035
Affected #: 42 files
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -11,6 +11,7 @@
yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c
yt/analysis_modules/ppv_cube/ppv_utils.c
yt/frontends/ramses/_ramses_reader.cpp
+yt/frontends/sph/smoothing_kernel.c
yt/geometry/fake_octree.c
yt/geometry/grid_container.c
yt/geometry/grid_visitors.c
@@ -40,6 +41,7 @@
yt/utilities/lib/mesh_utilities.c
yt/utilities/lib/misc_utilities.c
yt/utilities/lib/Octree.c
+yt/utilities/lib/GridTree.c
yt/utilities/lib/origami.c
yt/utilities/lib/pixelization_routines.c
yt/utilities/lib/png_writer.c
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 README
--- a/README
+++ b/README
@@ -20,4 +20,5 @@
For more information on installation, what to do if you run into problems, or
ways to help development, please visit our website.
-Enjoy!
\ No newline at end of file
+Enjoy!
+
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -641,7 +641,7 @@
TORNADO='tornado-4.0.2'
ZEROMQ='zeromq-4.0.5'
ZLIB='zlib-1.2.8'
-SETUPTOOLS='setuptools-16.0'
+SETUPTOOLS='setuptools-18.0.1'
# Now we dump all our SHA512 files out.
echo '856220fa579e272ac38dcef091760f527431ff3b98df9af6e68416fcf77d9659ac5abe5c7dee41331f359614637a4ff452033085335ee499830ed126ab584267 Cython-0.22.tar.gz' > Cython-0.22.tar.gz.sha512
@@ -669,7 +669,7 @@
echo '93591068dc63af8d50a7925d528bc0cccdd705232c529b6162619fe28dddaf115e8a460b1842877d35160bd7ed480c1bd0bdbec57d1f359085bd1814e0c1c242 tornado-4.0.2.tar.gz' > tornado-4.0.2.tar.gz.sha512
echo '0d928ed688ed940d460fa8f8d574a9819dccc4e030d735a8c7db71b59287ee50fa741a08249e356c78356b03c2174f2f2699f05aa7dc3d380ed47d8d7bab5408 zeromq-4.0.5.tar.gz' > zeromq-4.0.5.tar.gz.sha512
echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
-echo '38a89aad89dc9aa682dbfbca623e2f69511f5e20d4a3526c01aabbc7e93ae78f20aac566676b431e111540b41540a1c4f644ce4174e7ecf052318612075e02dc setuptools-16.0.tar.gz' > setuptools-16.0.tar.gz.sha512
+echo '9b318ce2ee2cf787929dcb886d76c492b433e71024fda9452d8b4927652a298d6bd1bdb7a4c73883a98e100024f89b46ea8aa14b250f896e549e6dd7e10a6b41 setuptools-18.0.1.tar.gz' > setuptools-18.0.1.tar.gz.sha512
# Individual processes
[ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
[ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/analyzing/analysis_modules/SZ_projections.ipynb
--- a/doc/source/analyzing/analysis_modules/SZ_projections.ipynb
+++ b/doc/source/analyzing/analysis_modules/SZ_projections.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:2cc168b2c1737c67647aa29892c0213e7a58233fa53c809f9cd975a4306e9bc8"
+ "signature": "sha256:487383ec23a092310522ec25bd02ad2eb16a3402c5ed3d2b103d33fe17697b3c"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -70,6 +70,13 @@
]
},
{
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "<font color='red'>**NOTE**</font>: Currently, use of the SZpack library to create S-Z projections in yt is limited to Python 2.x."
+ ]
+ },
+ {
"cell_type": "heading",
"level": 2,
"metadata": {},
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/analyzing/fields.rst
--- a/doc/source/analyzing/fields.rst
+++ b/doc/source/analyzing/fields.rst
@@ -174,7 +174,7 @@
Field plugins can be loaded dynamically, although at present this is not
particularly useful. Plans for extending field plugins to dynamically load, to
-enable simple definition of common types (gradient, divergence, etc), and to
+enable simple definition of common types (divergence, curl, etc), and to
more verbosely describe available fields, have been put in place for future
versions.
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/cookbook/fit_spectrum.py
--- a/doc/source/cookbook/fit_spectrum.py
+++ b/doc/source/cookbook/fit_spectrum.py
@@ -10,10 +10,10 @@
def _OVI_number_density(field, data):
return data['H_number_density']*2.0
-# Define a function that will accept a ds and add the new field
+# Define a function that will accept a ds and add the new field
# defined above. This will be given to the LightRay below.
def setup_ds(ds):
- ds.add_field("O_p5_number_density",
+ ds.add_field(("gas","O_p5_number_density"),
function=_OVI_number_density,
units="cm**-3")
@@ -62,7 +62,7 @@
# Get all fields that need to be added to the light ray
fields = ['temperature']
-for s, params in species_dicts.iteritems():
+for s, params in species_dicts.items():
fields.append(params['field'])
# Make a light ray, and set njobs to -1 to use one core
@@ -79,7 +79,7 @@
sp = AbsorptionSpectrum(900.0, 1400.0, 50000)
# Iterate over species
-for s, params in species_dicts.iteritems():
+for s, params in species_dicts.items():
# Iterate over transitions for a single species
for i in range(params['numLines']):
# Add the lines to the spectrum
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/cookbook/free_free_field.py
--- a/doc/source/cookbook/free_free_field.py
+++ /dev/null
@@ -1,105 +0,0 @@
-### THIS RECIPE IS CURRENTLY BROKEN IN YT-3.0
-### DO NOT TRUST THIS RECIPE UNTIL THIS LINE IS REMOVED
-
-import numpy as np
-import yt
-# Need to grab the proton mass from the constants database
-from yt.utilities.physical_constants import mp
-
-exit()
-# Define the emission field
-
-keVtoerg = 1.602e-9 # Convert energy in keV to energy in erg
-KtokeV = 8.617e-08 # Convert degrees Kelvin to degrees keV
-sqrt3 = np.sqrt(3.)
-expgamma = 1.78107241799 # Exponential of Euler's constant
-
-
-def _FreeFree_Emission(field, data):
-
- if data.has_field_parameter("Z"):
- Z = data.get_field_parameter("Z")
- else:
- Z = 1.077 # Primordial H/He plasma
-
- if data.has_field_parameter("mue"):
- mue = data.get_field_parameter("mue")
- else:
- mue = 1./0.875 # Primordial H/He plasma
-
- if data.has_field_parameter("mui"):
- mui = data.get_field_parameter("mui")
- else:
- mui = 1./0.8125 # Primordial H/He plasma
-
- if data.has_field_parameter("Ephoton"):
- Ephoton = data.get_field_parameter("Ephoton")
- else:
- Ephoton = 1.0 # in keV
-
- if data.has_field_parameter("photon_emission"):
- photon_emission = data.get_field_parameter("photon_emission")
- else:
- photon_emission = False # Flag for energy or photon emission
-
- n_e = data["density"]/(mue*mp)
- n_i = data["density"]/(mui*mp)
- kT = data["temperature"]*KtokeV
-
- # Compute the Gaunt factor
-
- g_ff = np.zeros(kT.shape)
- g_ff[Ephoton/kT > 1.] = np.sqrt((3./np.pi)*kT[Ephoton/kT > 1.]/Ephoton)
- g_ff[Ephoton/kT < 1.] = (sqrt3/np.pi)*np.log((4./expgamma) *
- kT[Ephoton/kT < 1.]/Ephoton)
-
- eps_E = 1.64e-20*Z*Z*n_e*n_i/np.sqrt(data["temperature"]) * \
- np.exp(-Ephoton/kT)*g_ff
-
- if photon_emission:
- eps_E /= (Ephoton*keVtoerg)
-
- return eps_E
-
-yt.add_field("FreeFree_Emission", function=_FreeFree_Emission)
-
-# Define the luminosity derived quantity
-def _FreeFreeLuminosity(data):
- return (data["FreeFree_Emission"]*data["cell_volume"]).sum()
-
-
-def _combFreeFreeLuminosity(data, luminosity):
- return luminosity.sum()
-
-yt.add_quantity("FreeFree_Luminosity", function=_FreeFreeLuminosity,
- combine_function=_combFreeFreeLuminosity, n_ret=1)
-
-ds = yt.load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
-
-sphere = ds.sphere(ds.domain_center, (100., "kpc"))
-
-# Print out the total luminosity at 1 keV for the sphere
-
-print("L_E (1 keV, primordial) = ", sphere.quantities["FreeFree_Luminosity"]())
-
-# The defaults for the field assume a H/He primordial plasma.
-# Let's set the appropriate parameters for a pure hydrogen plasma.
-
-sphere.set_field_parameter("mue", 1.0)
-sphere.set_field_parameter("mui", 1.0)
-sphere.set_field_parameter("Z", 1.0)
-
-print("L_E (1 keV, pure hydrogen) = ", sphere.quantities["FreeFree_Luminosity"]())
-
-# Now let's print the luminosity at an energy of E = 10 keV
-
-sphere.set_field_parameter("Ephoton", 10.0)
-
-print("L_E (10 keV, pure hydrogen) = ", sphere.quantities["FreeFree_Luminosity"]())
-
-# Finally, let's set the flag for photon emission, to get the total number
-# of photons emitted at this energy:
-
-sphere.set_field_parameter("photon_emission", True)
-
-print("L_ph (10 keV, pure hydrogen) = ", sphere.quantities["FreeFree_Luminosity"]())
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/cookbook/simulation_analysis.py
--- a/doc/source/cookbook/simulation_analysis.py
+++ b/doc/source/cookbook/simulation_analysis.py
@@ -2,11 +2,11 @@
yt.enable_parallelism()
import collections
-# Enable parallelism in the script (assuming it was called with
+# Enable parallelism in the script (assuming it was called with
# `mpirun -np <n_procs>` )
yt.enable_parallelism()
-# By using wildcards such as ? and * with the load command, we can load up a
+# By using wildcards such as ? and * with the load command, we can load up a
# Time Series containing all of these datasets simultaneously.
ts = yt.load('enzo_tiny_cosmology/DD????/DD????')
@@ -16,7 +16,7 @@
# Create an empty dictionary
data = {}
-# Iterate through each dataset in the Time Series (using piter allows it
+# Iterate through each dataset in the Time Series (using piter allows it
# to happen in parallel automatically across available processors)
for ds in ts.piter():
ad = ds.all_data()
@@ -31,6 +31,6 @@
# Print out all the values we calculated.
print("Dataset Redshift Density Min Density Max")
print("---------------------------------------------------------")
-for key, val in od.iteritems():
+for key, val in od.items():
print("%s %05.3f %5.3g g/cm^3 %5.3g g/cm^3" % \
(key, val[1], val[0][0], val[0][1]))
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/cookbook/time_series.py
--- a/doc/source/cookbook/time_series.py
+++ b/doc/source/cookbook/time_series.py
@@ -12,7 +12,7 @@
storage = {}
-# By using the piter() function, we can iterate on every dataset in
+# By using the piter() function, we can iterate on every dataset in
# the TimeSeries object. By using the storage keyword, we can populate
# a dictionary where the dataset is the key, and sto.result is the value
# for later use when the loop is complete.
@@ -25,13 +25,13 @@
sphere = ds.sphere("c", (100., "kpc"))
# Calculate the entropy within that sphere
entr = sphere["entropy"].sum()
- # Store the current time and sphere entropy for this dataset in our
+ # Store the current time and sphere entropy for this dataset in our
# storage dictionary as a tuple
store.result = (ds.current_time.in_units('Gyr'), entr)
# Convert the storage dictionary values to a Nx2 array, so the can be easily
# plotted
-arr = np.array(storage.values())
+arr = np.array(list(storage.values()))
# Plot up the results: time versus entropy
plt.semilogy(arr[:,0], arr[:,1], 'r-')
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/developing/intro.rst
--- a/doc/source/developing/intro.rst
+++ b/doc/source/developing/intro.rst
@@ -142,3 +142,77 @@
federated database for simulation outputs, and so on and so forth.
yt is an ambitious project. Let's be ambitious together.
+
+yt Community Code of Conduct
+----------------------------
+
+The community of participants in open source
+Scientific projects is made up of members from around the
+globe with a diverse set of skills, personalities, and
+experiences. It is through these differences that our
+community experiences success and continued growth. We
+expect everyone in our community to follow these guidelines
+when interacting with others both inside and outside of our
+community. Our goal is to keep ours a positive, inclusive,
+successful, and growing community.
+
+As members of the community,
+
+- We pledge to treat all people with respect and
+ provide a harassment- and bullying-free environment,
+ regardless of sex, sexual orientation and/or gender
+ identity, disability, physical appearance, body size,
+ race, nationality, ethnicity, and religion. In
+ particular, sexual language and imagery, sexist,
+ racist, or otherwise exclusionary jokes are not
+ appropriate.
+
+- We pledge to respect the work of others by
+ recognizing acknowledgment/citation requests of
+ original authors. As authors, we pledge to be explicit
+ about how we want our own work to be cited or
+ acknowledged.
+
+- We pledge to welcome those interested in joining the
+ community, and realize that including people with a
+ variety of opinions and backgrounds will only serve to
+ enrich our community. In particular, discussions
+ relating to pros/cons of various technologies,
+ programming languages, and so on are welcome, but
+ these should be done with respect, taking proactive
+ measure to ensure that all participants are heard and
+ feel confident that they can freely express their
+ opinions.
+
+- We pledge to welcome questions and answer them
+ respectfully, paying particular attention to those new
+ to the community. We pledge to provide respectful
+ criticisms and feedback in forums, especially in
+ discussion threads resulting from code
+ contributions.
+
+- We pledge to be conscientious of the perceptions of
+ the wider community and to respond to criticism
+ respectfully. We will strive to model behaviors that
+ encourage productive debate and disagreement, both
+ within our community and where we are criticized. We
+ will treat those outside our community with the same
+ respect as people within our community.
+
+- We pledge to help the entire community follow the
+ code of conduct, and to not remain silent when we see
+ violations of the code of conduct. We will take action
+ when members of our community violate this code such as
+ contacting confidential at yt-project.org (all emails sent to
+ this address will be treated with the strictest
+ confidence) or talking privately with the person.
+
+This code of conduct applies to all
+community situations online and offline, including mailing
+lists, forums, social media, conferences, meetings,
+associated social events, and one-to-one interactions.
+
+The yt Community Code of Conduct was adapted from the
+`Astropy Community Code of Conduct
+<http://www.astropy.org/about.html#codeofconduct>`_,
+which was partially inspired by the PSF code of conduct.
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -1079,6 +1079,76 @@
.. _loading-pyne-data:
+Halo Catalog Data
+-----------------
+
+yt has support for reading halo catalogs produced by Rockstar and the inline
+FOF/SUBFIND halo finders of Gadget and OWLS. The halo catalogs are treated as
+particle datasets where each particle represents a single halo. At this time,
+yt does not have the ability to load the member particles for a given halo.
+However, once loaded, further halo analysis can be performed using
+:ref:`halo_catalog`.
+
+In the case where halo catalogs are written to multiple files, one must only
+give the path to one of them.
+
+Gadget FOF/SUBFIND
+^^^^^^^^^^^^^^^^^^
+
+The two field types for GadgetFOF data are "Group" (FOF) and "Subhalo" (SUBFIND).
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("gadget_fof_halos/groups_042/fof_subhalo_tab_042.0.hdf5")
+ ad = ds.all_data()
+ # The halo mass
+ print ad["Group", "particle_mass"]
+ print ad["Subhalo", "particle_mass"]
+ # Halo ID
+ print ad["Group", "particle_identifier"]
+ print ad["Subhalo", "particle_identifier"]
+ # positions
+ print ad["Group", "particle_position_x"]
+ # velocities
+ print ad["Group", "particle_velocity_x"]
+
+Multidimensional fields can be accessed through the field name followed by an
+underscore and the index.
+
+.. code-block:: python
+
+ # x component of the spin
+ print ad["Subhalo", "SubhaloSpin_0"]
+
+OWLS FOF/SUBFIND
+^^^^^^^^^^^^^^^^
+
+OWLS halo catalogs have a very similar structure to regular Gadget halo catalogs.
+The two field types are "FOF" and "SUBFIND".
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("owls_fof_halos/groups_008/group_008.0.hdf5")
+ ad = ds.all_data()
+ # The halo mass
+ print ad["FOF", "particle_mass"]
+
+Rockstar
+^^^^^^^^
+
+Rockstar halo catalogs are loaded by providing the path to one of the .bin files.
+The single field type available is "halos".
+
+.. code-block:: python
+
+ import yt
+ ds = yt.load("rockstar_halos/halos_0.0.bin")
+ ad = ds.all_data()
+ # The halo mass
+ print ad["halos", "particle_mass"]
+
PyNE Data
---------
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -1011,7 +1011,7 @@
"""
f = h5py.File(file_name, 'w')
- for ion, params in lineDic.iteritems():
+ for ion, params in lineDic.items():
f.create_dataset("{0}/N".format(ion),data=params['N'])
f.create_dataset("{0}/b".format(ion),data=params['b'])
f.create_dataset("{0}/z".format(ion),data=params['z'])
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
@@ -343,7 +343,7 @@
del output["object"]
# Combine results from each slice.
- all_slices = all_storage.keys()
+ all_slices = list(all_storage.keys())
all_slices.sort()
for my_slice in all_slices:
if save_slice_images:
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -22,6 +22,7 @@
import glob
import os
import os.path as path
+from functools import cmp_to_key
from collections import defaultdict
from yt.extern.six import add_metaclass
from yt.extern.six.moves import zip as izip
@@ -39,7 +40,7 @@
TINY
from yt.utilities.physical_ratios import \
rho_crit_g_cm3_h2
-
+
from .hop.EnzoHop import RunHOP
from .fof.EnzoFOF import RunFOF
@@ -138,9 +139,9 @@
c[2] = self["particle_position_z"] - self.ds.domain_left_edge[2]
com = []
for i in range(3):
- # A halo is likely periodic around a boundary if the distance
+ # A halo is likely periodic around a boundary if the distance
# between the max and min particle
- # positions are larger than half the box.
+ # positions are larger than half the box.
# So skip the rest if the converse is true.
# Note we might make a change here when periodicity-handling is
# fully implemented.
@@ -444,7 +445,7 @@
Msun2g = mass_sun_cgs
rho_crit = rho_crit * ((1.0 + z) ** 3.0)
# Get some pertinent information about the halo.
- self.mass_bins = self.ds.arr(np.zeros(self.bin_count + 1,
+ self.mass_bins = self.ds.arr(np.zeros(self.bin_count + 1,
dtype='float64'),'Msun')
dist = np.empty(thissize, dtype='float64')
cen = self.center_of_mass()
@@ -475,7 +476,7 @@
self.overdensity = self.mass_bins * Msun2g / \
(4./3. * math.pi * rho_crit * \
(self.radial_bins )**3.0)
-
+
def _get_ellipsoid_parameters_basic(self):
np.seterr(all='ignore')
# check if there are 4 particles to form an ellipsoid
@@ -501,7 +502,7 @@
for axis in range(np.size(DW)):
cases = np.array([position[axis],
position[axis] + DW[axis],
- position[axis] - DW[axis]])
+ position[axis] - DW[axis]])
# pick out the smallest absolute distance from com
position[axis] = np.choose(np.abs(cases).argmin(axis=0), cases)
# find the furthest particle's index
@@ -571,7 +572,7 @@
_name = "RockstarHalo"
# See particle_mask
_radjust = 4.
-
+
def maximum_density(self):
r"""Not implemented."""
return -1
@@ -635,11 +636,11 @@
def get_ellipsoid_parameters(self):
r"""Calculate the parameters that describe the ellipsoid of
the particles that constitute the halo.
-
+
Parameters
----------
None
-
+
Returns
-------
tuple : (cm, mag_A, mag_B, mag_C, e0_vector, tilt)
@@ -650,7 +651,7 @@
#. mag_C as a float.
#. e0_vector as an array.
#. tilt as a float.
-
+
Examples
--------
>>> params = halos[0].get_ellipsoid_parameters()
@@ -662,22 +663,22 @@
basic_parameters[4], basic_parameters[5]]), basic_parameters[6]]
toreturn.extend(updated)
return tuple(toreturn)
-
+
def get_ellipsoid(self):
r"""Returns an ellipsoidal data object.
-
+
This will generate a new, empty ellipsoidal data object for this
halo.
-
+
Parameters
----------
None.
-
+
Returns
-------
ellipsoid : `yt.data_objects.data_containers.YTEllipsoidBase`
The ellipsoidal data object.
-
+
Examples
--------
>>> ell = halos[0].get_ellipsoid()
@@ -686,7 +687,7 @@
ell = self.data.ds.ellipsoid(ep[0], ep[1], ep[2], ep[3],
ep[4], ep[5])
return ell
-
+
class HOPHalo(Halo):
_name = "HOPHalo"
pass
@@ -763,14 +764,14 @@
self.size, key)
if field_data is not None:
if key == 'particle_index':
- #this is an index for turning data sorted by particle index
+ #this is an index for turning data sorted by particle index
#into the same order as the fields on disk
self._pid_sort = field_data.argsort().argsort()
#convert to YTArray using the data from disk
if key == 'particle_mass':
field_data = self.ds.arr(field_data, 'Msun')
else:
- field_data = self.ds.arr(field_data,
+ field_data = self.ds.arr(field_data,
self.ds._get_field_info('unknown',key).units)
self._saved_fields[key] = field_data
return self._saved_fields[key]
@@ -856,21 +857,21 @@
basic_parameters[4], basic_parameters[5]]), basic_parameters[6]]
toreturn.extend(updated)
return tuple(toreturn)
-
+
def get_ellipsoid(self):
- r"""Returns an ellipsoidal data object.
+ r"""Returns an ellipsoidal data object.
This will generate a new, empty ellipsoidal data object for this
halo.
-
+
Parameters
----------
None.
-
+
Returns
-------
ellipsoid : `yt.data_objects.data_containers.YTEllipsoidBase`
The ellipsoidal data object.
-
+
Examples
--------
>>> ell = halos[0].get_ellipsoid()
@@ -947,11 +948,11 @@
def maximum_density(self):
r"""Undefined for text halos."""
return -1
-
+
def maximum_density_location(self):
r"""Undefined, default to CoM"""
return self.center_of_mass()
-
+
def get_size(self):
# Have to just get it from the sphere.
return self["particle_position_x"].size
@@ -964,8 +965,8 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is True (default), only run it on the dark matter particles,
- otherwise on all particles. Returns an iterable collection of
+ *dm_only* is True (default), only run it on the dark matter particles,
+ otherwise on all particles. Returns an iterable collection of
*HopGroup* items.
"""
self._data_source = data_source
@@ -1051,7 +1052,7 @@
ellipsoid_data : bool.
Whether to print the ellipsoidal information to the file.
Default = False.
-
+
Examples
--------
>>> halos.write_out("HopAnalysis.out")
@@ -1144,10 +1145,10 @@
_halo_dt = np.dtype([('id', np.int64), ('pos', (np.float32, 6)),
('corevel', (np.float32, 3)), ('bulkvel', (np.float32, 3)),
('m', np.float32), ('r', np.float32), ('child_r', np.float32),
- ('vmax_r', np.float32),
+ ('vmax_r', np.float32),
('mgrav', np.float32), ('vmax', np.float32),
('rvmax', np.float32), ('rs', np.float32),
- ('klypin_rs', np.float32),
+ ('klypin_rs', np.float32),
('vrms', np.float32), ('J', (np.float32, 3)),
('energy', np.float32), ('spin', np.float32),
('alt_m', (np.float32, 4)), ('Xoff', np.float32),
@@ -1221,9 +1222,9 @@
"""
Read the out_*.list text file produced
by Rockstar into memory."""
-
+
ds = self.ds
- # In order to read the binary data, we need to figure out which
+ # In order to read the binary data, we need to figure out which
# binary files belong to this output.
basedir = os.path.dirname(self.out_list)
s = self.out_list.split('_')[-1]
@@ -1523,12 +1524,14 @@
id += 1
def haloCmp(h1, h2):
+ def cmp(a, b):
+ return (a > b) - (a < b)
c = cmp(h1.total_mass(), h2.total_mass())
if c != 0:
return -1 * c
if c == 0:
return cmp(h1.center_of_mass()[0], h2.center_of_mass()[0])
- self._groups.sort(haloCmp)
+ self._groups.sort(key=cmp_to_key(haloCmp))
sorted_max_dens = {}
for i, halo in enumerate(self._groups):
if halo.id in self._max_dens:
@@ -1873,7 +1876,7 @@
class LoadTextHaloes(GenericHaloFinder, TextHaloList):
r"""Load a text file of halos.
-
+
Like LoadHaloes, but when all that is available is a plain
text file. This assumes the text file has the 3-positions of halos
along with a radius. The halo objects created are spheres.
@@ -1882,7 +1885,7 @@
----------
fname : String
The name of the text file to read in.
-
+
columns : dict
A dict listing the column name : column number pairs for data
in the text file. It is zero-based (like Python).
@@ -1890,7 +1893,7 @@
Any column name outside of ['x', 'y', 'z', 'r'] will be attached
to each halo object in the supplementary dict 'supp'. See
example.
-
+
comment : String
If the first character of a line is equal to this, the line is
skipped. Default = "#".
@@ -1915,7 +1918,7 @@
Parameters
----------
fname : String
- The name of the Rockstar file to read in. Default =
+ The name of the Rockstar file to read in. Default =
"rockstar_halos/out_0.list'.
Examples
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/analysis_modules/level_sets/clump_handling.py
--- a/yt/analysis_modules/level_sets/clump_handling.py
+++ b/yt/analysis_modules/level_sets/clump_handling.py
@@ -20,7 +20,8 @@
from yt.fields.derived_field import \
ValidateSpatial
from yt.funcs import mylog
-
+from yt.extern.six import string_types
+
from .clump_info_items import \
clump_info_registry
from .clump_validators import \
@@ -268,7 +269,7 @@
def write_clump_index(clump, level, fh):
top = False
- if not isinstance(fh, file):
+ if isinstance(fh, string_types):
fh = open(fh, "w")
top = True
for q in range(level):
@@ -285,7 +286,7 @@
def write_clumps(clump, level, fh):
top = False
- if not isinstance(fh, file):
+ if isinstance(fh, string_types):
fh = open(fh, "w")
top = True
if ((clump.children is None) or (len(clump.children) == 0)):
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/data_objects/time_series.py
--- a/yt/data_objects/time_series.py
+++ b/yt/data_objects/time_series.py
@@ -130,7 +130,7 @@
def __new__(cls, outputs, *args, **kwargs):
if isinstance(outputs, string_types):
outputs = get_filenames_from_glob_pattern(outputs)
- ret = super(DatasetSeries, cls).__new__(cls, *args, **kwargs)
+ ret = super(DatasetSeries, cls).__new__(cls)
try:
ret._pre_outputs = outputs[:]
except TypeError:
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/api.py
--- a/yt/frontends/api.py
+++ b/yt/frontends/api.py
@@ -27,6 +27,7 @@
'fits',
'flash',
'gadget',
+ 'gadget_fof',
'gdf',
'halo_catalog',
'http_stream',
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -76,7 +76,7 @@
for key, val in self._handle.attrs.items():
if key.startswith('component_'):
comp_number = int(re.match('component_(\d+)', key).groups()[0])
- field_dict[val] = comp_number
+ field_dict[val.decode('utf-8')] = comp_number
self._field_dict = field_dict
return self._field_dict
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/fits/io.py
--- a/yt/frontends/fits/io.py
+++ b/yt/frontends/fits/io.py
@@ -32,7 +32,7 @@
def _read_particle_coords(self, chunks, ptf):
pdata = self.ds._handle[self.ds.first_image].data
assert(len(ptf) == 1)
- ptype = ptf.keys()[0]
+ ptype = list(ptf.keys())[0]
x = np.asarray(pdata.field("X"), dtype="=f8")
y = np.asarray(pdata.field("Y"), dtype="=f8")
z = np.ones(x.shape)
@@ -43,7 +43,7 @@
def _read_particle_fields(self, chunks, ptf, selector):
pdata = self.ds._handle[self.ds.first_image].data
assert(len(ptf) == 1)
- ptype = ptf.keys()[0]
+ ptype = list(ptf.keys())[0]
field_list = ptf[ptype]
x = np.asarray(pdata.field("X"), dtype="=f8")
y = np.asarray(pdata.field("Y"), dtype="=f8")
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/fits/misc.py
--- a/yt/frontends/fits/misc.py
+++ b/yt/frontends/fits/misc.py
@@ -12,14 +12,18 @@
import numpy as np
import base64
-from yt.extern.six.moves import StringIO
+from yt.extern.six import PY3
from yt.fields.derived_field import ValidateSpatial
from yt.utilities.on_demand_imports import _astropy
from yt.funcs import mylog, get_image_suffix
from yt.visualization._mpl_imports import FigureCanvasAgg
from yt.units.yt_array import YTQuantity, YTArray
from yt.utilities.fits_image import FITSImageData
-
+if PY3:
+ from io import BytesIO as IO
+else:
+ from yt.extern.six.moves import StringIO as IO
+
import os
def _make_counts(emin, emax):
@@ -255,12 +259,12 @@
def _repr_html_(self):
ret = ''
- for k, v in self.plots.iteritems():
+ for k, v in self.plots.items():
canvas = FigureCanvasAgg(v)
- f = StringIO()
+ f = IO()
canvas.print_figure(f)
f.seek(0)
- img = base64.b64encode(f.read())
+ img = base64.b64encode(f.read()).decode()
ret += r'<img style="max-width:100%%;max-height:100%%;" ' \
r'src="data:image/png;base64,%s"><br>' % img
return ret
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget/data_structures.py
--- a/yt/frontends/gadget/data_structures.py
+++ b/yt/frontends/gadget/data_structures.py
@@ -387,7 +387,7 @@
@classmethod
def _is_valid(self, *args, **kwargs):
need_groups = ['Header']
- veto_groups = ['FOF']
+ veto_groups = ['FOF', 'Group', 'Subhalo']
valid = True
try:
fh = h5py.File(args[0], mode='r')
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/__init__.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/__init__.py
@@ -0,0 +1,15 @@
+"""
+API for HaloCatalog frontend.
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/api.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/api.py
@@ -0,0 +1,26 @@
+"""
+API for GadgetFOF frontend
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2015, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from .data_structures import \
+ GadgetFOFDataset
+
+from .io import \
+ IOHandlerGadgetFOFHDF5
+
+from .fields import \
+ GadgetFOFFieldInfo
+
+from . import tests
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/data_structures.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -0,0 +1,246 @@
+"""
+Data structures for GadgetFOF frontend.
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from collections import defaultdict
+import h5py
+import numpy as np
+import stat
+import weakref
+import struct
+import glob
+import time
+import os
+
+from .fields import \
+ GadgetFOFFieldInfo
+
+from yt.utilities.cosmology import \
+ Cosmology
+from yt.utilities.definitions import \
+ mpc_conversion, sec_conversion
+from yt.utilities.exceptions import \
+ YTException
+from yt.utilities.logger import ytLogger as \
+ mylog
+from yt.geometry.particle_geometry_handler import \
+ ParticleIndex
+from yt.data_objects.static_output import \
+ Dataset, \
+ ParticleFile
+from yt.frontends.gadget.data_structures import \
+ _fix_unit_ordering
+import yt.utilities.fortran_utils as fpu
+from yt.units.yt_array import \
+ YTArray, \
+ YTQuantity
+
+class GadgetFOFParticleIndex(ParticleIndex):
+ def __init__(self, ds, dataset_type):
+ super(GadgetFOFParticleIndex, self).__init__(ds, dataset_type)
+
+ def _calculate_particle_index_starts(self):
+ # Halo indices are not saved in the file, so we must count by hand.
+ # File 0 has halos 0 to N_0 - 1, file 1 has halos N_0 to N_0 + N_1 - 1, etc.
+ particle_count = defaultdict(int)
+ offset_count = 0
+ for data_file in self.data_files:
+ data_file.index_start = dict([(ptype, particle_count[ptype]) for
+ ptype in data_file.total_particles])
+ data_file.offset_start = offset_count
+ for ptype in data_file.total_particles:
+ particle_count[ptype] += data_file.total_particles[ptype]
+ offset_count += data_file.total_offset
+
+ def _calculate_file_offset_map(self):
+ # After the FOF is performed, a load-balancing step redistributes halos
+ # and then writes more fields. Here, for each file, we create a list of
+ # files which contain the rest of the redistributed particles.
+ ifof = np.array([data_file.total_particles["Group"]
+ for data_file in self.data_files])
+ isub = np.array([data_file.total_offset
+ for data_file in self.data_files])
+ subend = isub.cumsum()
+ fofend = ifof.cumsum()
+ istart = np.digitize(fofend - ifof, subend - isub) - 1
+ iend = np.clip(np.digitize(fofend, subend), 0, ifof.size - 2)
+ for i, data_file in enumerate(self.data_files):
+ data_file.offset_files = self.data_files[istart[i]: iend[i] + 1]
+
+ def _detect_output_fields(self):
+ # TODO: Add additional fields
+ dsl = []
+ units = {}
+ for dom in self.data_files:
+ fl, _units = self.io._identify_fields(dom)
+ units.update(_units)
+ dom._calculate_offsets(fl)
+ for f in fl:
+ if f not in dsl: dsl.append(f)
+ self.field_list = dsl
+ ds = self.dataset
+ ds.particle_types = tuple(set(pt for pt, ds in dsl))
+ # This is an attribute that means these particle types *actually*
+ # exist. As in, they are real, in the dataset.
+ ds.field_units.update(units)
+ ds.particle_types_raw = ds.particle_types
+
+ def _setup_geometry(self):
+ super(GadgetFOFParticleIndex, self)._setup_geometry()
+ self._calculate_particle_index_starts()
+ self._calculate_file_offset_map()
+
+class GadgetFOFHDF5File(ParticleFile):
+ def __init__(self, ds, io, filename, file_id):
+ super(GadgetFOFHDF5File, self).__init__(ds, io, filename, file_id)
+ with h5py.File(filename, "r") as f:
+ self.header = dict((field, f.attrs[field]) \
+ for field in f.attrs.keys())
+
+class GadgetFOFDataset(Dataset):
+ _index_class = GadgetFOFParticleIndex
+ _file_class = GadgetFOFHDF5File
+ _field_info_class = GadgetFOFFieldInfo
+ _suffix = ".hdf5"
+
+ def __init__(self, filename, dataset_type="gadget_fof_hdf5",
+ n_ref=16, over_refine_factor=1,
+ unit_base=None, units_override=None):
+ self.n_ref = n_ref
+ self.over_refine_factor = over_refine_factor
+ if unit_base is not None and "UnitLength_in_cm" in unit_base:
+ # We assume this is comoving, because in the absence of comoving
+ # integration the redshift will be zero.
+ unit_base['cmcm'] = 1.0 / unit_base["UnitLength_in_cm"]
+ self._unit_base = unit_base
+ if units_override is not None:
+ raise RuntimeError("units_override is not supported for GadgetFOFDataset. "+
+ "Use unit_base instead.")
+ super(GadgetFOFDataset, self).__init__(filename, dataset_type,
+ units_override=units_override)
+
+ def _parse_parameter_file(self):
+ handle = h5py.File(self.parameter_filename, mode="r")
+ hvals = {}
+ hvals.update((str(k), v) for k, v in handle["/Header"].attrs.items())
+ hvals["NumFiles"] = hvals["NumFiles"]
+
+ self.dimensionality = 3
+ self.refine_by = 2
+ self.unique_identifier = \
+ int(os.stat(self.parameter_filename)[stat.ST_CTIME])
+
+ # Set standard values
+ self.domain_left_edge = np.zeros(3, "float64")
+ self.domain_right_edge = np.ones(3, "float64") * hvals["BoxSize"]
+ nz = 1 << self.over_refine_factor
+ self.domain_dimensions = np.ones(3, "int32") * nz
+ self.cosmological_simulation = 1
+ self.periodicity = (True, True, True)
+ self.current_redshift = hvals["Redshift"]
+ self.omega_lambda = hvals["OmegaLambda"]
+ self.omega_matter = hvals["Omega0"]
+ self.hubble_constant = hvals["HubbleParam"]
+
+ cosmology = Cosmology(hubble_constant=self.hubble_constant,
+ omega_matter=self.omega_matter,
+ omega_lambda=self.omega_lambda)
+ self.current_time = cosmology.t_from_z(self.current_redshift)
+
+ self.parameters = hvals
+ prefix = os.path.abspath(
+ os.path.join(os.path.dirname(self.parameter_filename),
+ os.path.basename(self.parameter_filename).split(".", 1)[0]))
+
+ suffix = self.parameter_filename.rsplit(".", 1)[-1]
+ self.filename_template = "%s.%%(num)i.%s" % (prefix, suffix)
+ self.file_count = len(glob.glob(prefix + "*" + self._suffix))
+ if self.file_count == 0:
+ raise YTException(message="No data files found.", ds=self)
+ self.particle_types = ("Group", "Subhalo")
+ self.particle_types_raw = ("Group", "Subhalo")
+
+ handle.close()
+
+ def _set_code_unit_attributes(self):
+ # Set a sane default for cosmological simulations.
+ if self._unit_base is None and self.cosmological_simulation == 1:
+ mylog.info("Assuming length units are in Mpc/h (comoving)")
+ self._unit_base = dict(length = (1.0, "Mpccm/h"))
+ # The other same defaults we will use from the standard Gadget
+ # defaults.
+ unit_base = self._unit_base or {}
+
+ if "length" in unit_base:
+ length_unit = unit_base["length"]
+ elif "UnitLength_in_cm" in unit_base:
+ if self.cosmological_simulation == 0:
+ length_unit = (unit_base["UnitLength_in_cm"], "cm")
+ else:
+ length_unit = (unit_base["UnitLength_in_cm"], "cmcm/h")
+ else:
+ raise RuntimeError
+ length_unit = _fix_unit_ordering(length_unit)
+ self.length_unit = self.quan(length_unit[0], length_unit[1])
+
+ if "velocity" in unit_base:
+ velocity_unit = unit_base["velocity"]
+ elif "UnitVelocity_in_cm_per_s" in unit_base:
+ velocity_unit = (unit_base["UnitVelocity_in_cm_per_s"], "cm/s")
+ else:
+ if self.cosmological_simulation == 0:
+ velocity_unit = (1e5, "cm/s")
+ else:
+ velocity_unit = (1e5, "cmcm/s")
+ velocity_unit = _fix_unit_ordering(velocity_unit)
+ 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.
+ if "mass" in unit_base:
+ mass_unit = unit_base["mass"]
+ elif "UnitMass_in_g" in unit_base:
+ if self.cosmological_simulation == 0:
+ mass_unit = (unit_base["UnitMass_in_g"], "g")
+ else:
+ mass_unit = (unit_base["UnitMass_in_g"], "g/h")
+ else:
+ # 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])
+
+ if "time" in unit_base:
+ time_unit = unit_base["time"]
+ elif "UnitTime_in_s" in unit_base:
+ time_unit = (unit_base["UnitTime_in_s"], "s")
+ else:
+ time_unit = (1., "s")
+ self.time_unit = self.quan(time_unit[0], time_unit[1])
+
+ @classmethod
+ def _is_valid(self, *args, **kwargs):
+ need_groups = ['Group', 'Header', 'Subhalo']
+ veto_groups = ['FOF']
+ valid = True
+ try:
+ fh = h5py.File(args[0], mode='r')
+ valid = all(ng in fh["/"] for ng in need_groups) and \
+ not any(vg in fh["/"] for vg in veto_groups)
+ fh.close()
+ except:
+ valid = False
+ pass
+ return valid
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/fields.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/fields.py
@@ -0,0 +1,48 @@
+"""
+GadgetFOF-specific fields
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2015, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.funcs import mylog
+from yt.fields.field_info_container import \
+ FieldInfoContainer
+from yt.units.yt_array import \
+ YTArray
+
+m_units = "code_mass"
+p_units = "code_length"
+v_units = "code_velocity"
+
+class GadgetFOFFieldInfo(FieldInfoContainer):
+ known_other_fields = (
+ )
+
+ known_particle_fields = (
+ ("GroupPos_0", (p_units, ["Group", "particle_position_x"], None)),
+ ("GroupPos_1", (p_units, ["Group", "particle_position_y"], None)),
+ ("GroupPos_2", (p_units, ["Group", "particle_position_z"], None)),
+ ("GroupVel_0", (v_units, ["Group", "particle_velocity_x"], None)),
+ ("GroupVel_1", (v_units, ["Group", "particle_velocity_y"], None)),
+ ("GroupVel_2", (v_units, ["Group", "particle_velocity_z"], None)),
+ ("GroupMass", (m_units, ["Group", "particle_mass"], None)),
+ ("GroupLen", ("", ["Group", "particle_number"], None)),
+ ("SubhaloPos_0", (p_units, ["Subhalo", "particle_position_x"], None)),
+ ("SubhaloPos_1", (p_units, ["Subhalo", "particle_position_y"], None)),
+ ("SubhaloPos_2", (p_units, ["Subhalo", "particle_position_z"], None)),
+ ("SubhaloVel_0", (v_units, ["Subhalo", "particle_velocity_x"], None)),
+ ("SubhaloVel_1", (v_units, ["Subhalo", "particle_velocity_y"], None)),
+ ("SubhaloVel_2", (v_units, ["Subhalo", "particle_velocity_z"], None)),
+ ("SubhaloMass", (m_units, ["Subhalo", "particle_mass"], None)),
+ ("SubhaloLen", ("", ["Subhalo", "particle_number"], None)),
+)
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/io.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/io.py
@@ -0,0 +1,207 @@
+"""
+GadgetFOF data-file handling function
+
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+import h5py
+import numpy as np
+
+from yt.utilities.exceptions import *
+from yt.funcs import mylog
+
+from yt.utilities.io_handler import \
+ BaseIOHandler
+
+from yt.utilities.lib.geometry_utils import compute_morton
+
+class IOHandlerGadgetFOFHDF5(BaseIOHandler):
+ _dataset_type = "gadget_fof_hdf5"
+
+ def __init__(self, ds):
+ super(IOHandlerGadgetFOFHDF5, self).__init__(ds)
+ self.offset_fields = set([])
+
+ def _read_fluid_selection(self, chunks, selector, fields, size):
+ raise NotImplementedError
+
+ def _read_particle_coords(self, chunks, ptf):
+ # This will read chunks and yield the results.
+ chunks = list(chunks)
+ data_files = set([])
+ for chunk in chunks:
+ for obj in chunk.objs:
+ data_files.update(obj.data_files)
+ for data_file in sorted(data_files):
+ with h5py.File(data_file.filename, "r") as f:
+ for ptype, field_list in sorted(ptf.items()):
+ pcount = data_file.total_particles[ptype]
+ coords = f[ptype]["%sPos" % ptype].value.astype("float64")
+ coords = np.resize(coords, (pcount, 3))
+ x = coords[:, 0]
+ y = coords[:, 1]
+ z = coords[:, 2]
+ yield ptype, (x, y, z)
+
+ def _read_offset_particle_field(self, field, data_file, fh):
+ field_data = np.empty(data_file.total_particles["Group"], dtype="float64")
+ fofindex = np.arange(data_file.total_particles["Group"]) + data_file.index_start["Group"]
+ for offset_file in data_file.offset_files:
+ if fh.filename == offset_file.filename:
+ ofh = fh
+ else:
+ ofh = h5py.File(offset_file.filename, "r")
+ subindex = np.arange(offset_file.total_offset) + offset_file.offset_start
+ substart = max(fofindex[0] - subindex[0], 0)
+ subend = min(fofindex[-1] - subindex[0], subindex.size - 1)
+ fofstart = substart + subindex[0] - fofindex[0]
+ fofend = subend + subindex[0] - fofindex[0]
+ field_data[fofstart:fofend + 1] = ofh["Subhalo"][field][substart:subend + 1]
+ return field_data
+
+ def _read_particle_fields(self, chunks, ptf, selector):
+ # Now we have all the sizes, and we can allocate
+ chunks = list(chunks)
+ data_files = set([])
+ for chunk in chunks:
+ for obj in chunk.objs:
+ data_files.update(obj.data_files)
+ for data_file in sorted(data_files):
+ with h5py.File(data_file.filename, "r") as f:
+ for ptype, field_list in sorted(ptf.items()):
+ pcount = data_file.total_particles[ptype]
+ if pcount == 0: continue
+ coords = f[ptype]["%sPos" % ptype].value.astype("float64")
+ coords = np.resize(coords, (pcount, 3))
+ x = coords[:, 0]
+ y = coords[:, 1]
+ z = coords[:, 2]
+ mask = selector.select_points(x, y, z, 0.0)
+ del x, y, z
+ if mask is None: continue
+ for field in field_list:
+ if field in self.offset_fields:
+ field_data = \
+ self._read_offset_particle_field(field, data_file, f)
+ else:
+ if field == "particle_identifier":
+ field_data = \
+ np.arange(data_file.total_particles[ptype]) + \
+ data_file.index_start[ptype]
+ elif field in f[ptype]:
+ field_data = f[ptype][field].value.astype("float64")
+ else:
+ fname = field[:field.rfind("_")]
+ field_data = f[ptype][fname].value.astype("float64")
+ my_div = field_data.size / pcount
+ if my_div > 1:
+ field_data = np.resize(field_data, (pcount, my_div))
+ findex = int(field[field.rfind("_") + 1:])
+ field_data = field_data[:, findex]
+ data = field_data[mask]
+ yield (ptype, field), data
+
+ def _initialize_index(self, data_file, regions):
+ pcount = sum(data_file.total_particles.values())
+ morton = np.empty(pcount, dtype='uint64')
+ if pcount == 0: return morton
+ mylog.debug("Initializing index % 5i (% 7i particles)",
+ data_file.file_id, pcount)
+ ind = 0
+ with h5py.File(data_file.filename, "r") as f:
+ if not f.keys(): return None
+ dx = np.finfo(f["Group"]["GroupPos"].dtype).eps
+ dx = 2.0*self.ds.quan(dx, "code_length")
+
+ for ptype in data_file.ds.particle_types_raw:
+ if data_file.total_particles[ptype] == 0: continue
+ pos = f[ptype]["%sPos" % ptype].value.astype("float64")
+ pos = np.resize(pos, (data_file.total_particles[ptype], 3))
+ pos = data_file.ds.arr(pos, "code_length")
+
+ # These are 32 bit numbers, so we give a little lee-way.
+ # Otherwise, for big sets of particles, we often will bump into the
+ # domain edges. This helps alleviate that.
+ np.clip(pos, self.ds.domain_left_edge + dx,
+ self.ds.domain_right_edge - dx, pos)
+ if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
+ np.any(pos.max(axis=0) > self.ds.domain_right_edge):
+ raise YTDomainOverflow(pos.min(axis=0),
+ pos.max(axis=0),
+ self.ds.domain_left_edge,
+ self.ds.domain_right_edge)
+ regions.add_data_file(pos, data_file.file_id)
+ morton[ind:ind+pos.shape[0]] = compute_morton(
+ pos[:,0], pos[:,1], pos[:,2],
+ data_file.ds.domain_left_edge,
+ data_file.ds.domain_right_edge)
+ ind += pos.shape[0]
+ return morton
+
+ def _count_particles(self, data_file):
+ with h5py.File(data_file.filename, "r") as f:
+ pcount = {"Group": f["Header"].attrs["Ngroups_ThisFile"],
+ "Subhalo": f["Header"].attrs["Nsubgroups_ThisFile"]}
+ data_file.total_offset = 0 # need to figure out how subfind works here
+ return pcount
+
+ def _identify_fields(self, data_file):
+ fields = []
+ pcount = data_file.total_particles
+ if sum(pcount.values()) == 0: return fields, {}
+ with h5py.File(data_file.filename, "r") as f:
+ for ptype in self.ds.particle_types_raw:
+ if data_file.total_particles[ptype] == 0: continue
+ fields.append((ptype, "particle_identifier"))
+ my_fields, my_offset_fields = \
+ subfind_field_list(f[ptype], ptype, data_file.total_particles)
+ fields.extend(my_fields)
+ self.offset_fields = self.offset_fields.union(set(my_offset_fields))
+ return fields, {}
+
+def subfind_field_list(fh, ptype, pcount):
+ fields = []
+ offset_fields = []
+ for field in fh.keys():
+ if isinstance(fh[field], h5py.Group):
+ my_fields, my_offset_fields = \
+ subfind_field_list(fh[field], ptype, pcount)
+ fields.extend(my_fields)
+ my_offset_fields.extend(offset_fields)
+ else:
+ if not fh[field].size % pcount[ptype]:
+ my_div = fh[field].size / pcount[ptype]
+ fname = fh[field].name[fh[field].name.find(ptype) + len(ptype) + 1:]
+ if my_div > 1:
+ for i in range(my_div):
+ fields.append((ptype, "%s_%d" % (fname, i)))
+ else:
+ fields.append((ptype, fname))
+ elif ptype == "Subfind" and \
+ not fh[field].size % fh["/Subfind"].attrs["Number_of_groups"]:
+ # These are actually Group fields, but they were written after
+ # a load balancing step moved halos around and thus they do not
+ # correspond to the halos stored in the Group group.
+ my_div = fh[field].size / fh["/Subfind"].attrs["Number_of_groups"]
+ fname = fh[field].name[fh[field].name.find(ptype) + len(ptype) + 1:]
+ if my_div > 1:
+ for i in range(my_div):
+ fields.append(("Group", "%s_%d" % (fname, i)))
+ else:
+ fields.append(("Group", fname))
+ offset_fields.append(fname)
+ else:
+ mylog.warn("Cannot add field (%s, %s) with size %d." % \
+ (ptype, fh[field].name, fh[field].size))
+ continue
+ return fields, offset_fields
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/setup.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/setup.py
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('gadget_fof', parent_package, top_path)
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/gadget_fof/tests/test_outputs.py
--- /dev/null
+++ b/yt/frontends/gadget_fof/tests/test_outputs.py
@@ -0,0 +1,56 @@
+"""
+GadgetFOF frontend tests using gadget_fof datasets
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+import os.path
+from yt.testing import \
+ assert_equal
+from yt.utilities.answer_testing.framework import \
+ FieldValuesTest, \
+ requires_ds, \
+ requires_file, \
+ data_dir_load
+from yt.frontends.gadget_fof.api import GadgetFOFDataset
+
+p_types = ("Group", "Subhalo")
+p_fields = ("particle_position_x", "particle_position_y",
+ "particle_position_z", "particle_velocity_x",
+ "particle_velocity_y", "particle_velocity_z",
+ "particle_mass", "particle_identifier")
+_fields = tuple([(p_type, p_field) for p_type in p_types
+ for p_field in p_fields])
+
+# a dataset with empty files
+g5 = "gadget_fof_halos/groups_005/fof_subhalo_tab_005.0.hdf5"
+g42 = "gadget_fof_halos/groups_042/fof_subhalo_tab_042.0.hdf5"
+
+
+ at requires_ds(g5)
+def test_fields_g5():
+ ds = data_dir_load(g5)
+ yield assert_equal, str(ds), os.path.basename(g5)
+ for field in _fields:
+ yield FieldValuesTest(g5, field, particle_type=True)
+
+
+ at requires_ds(g42)
+def test_fields_g42():
+ ds = data_dir_load(g42)
+ yield assert_equal, str(ds), os.path.basename(g42)
+ for field in _fields:
+ yield FieldValuesTest(g42, field, particle_type=True)
+
+ at requires_file(g42)
+def test_GadgetFOFDataset():
+ assert isinstance(data_dir_load(g42), GadgetFOFDataset)
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/halo_catalog/io.py
--- a/yt/frontends/halo_catalog/io.py
+++ b/yt/frontends/halo_catalog/io.py
@@ -39,7 +39,7 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
@@ -57,7 +57,7 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/owls/io.py
--- a/yt/frontends/owls/io.py
+++ b/yt/frontends/owls/io.py
@@ -70,7 +70,7 @@
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files, key=lambda x: x.filename):
f = _get_h5_handle(data_file.filename)
# This double-reads
for ptype, field_list in sorted(ptf.items()):
@@ -88,7 +88,7 @@
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files, key=lambda x: x.filename):
f = _get_h5_handle(data_file.filename)
for ptype, field_list in sorted(ptf.items()):
if data_file.total_particles[ptype] == 0:
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/owls_subfind/data_structures.py
--- a/yt/frontends/owls_subfind/data_structures.py
+++ b/yt/frontends/owls_subfind/data_structures.py
@@ -27,11 +27,14 @@
from .fields import \
OWLSSubfindFieldInfo
-from yt.utilities.cosmology import Cosmology
+from yt.utilities.cosmology import \
+ Cosmology
from yt.utilities.definitions import \
mpc_conversion, sec_conversion
from yt.utilities.exceptions import \
- YTException
+ YTException
+from yt.utilities.logger import ytLogger as \
+ mylog
from yt.geometry.particle_geometry_handler import \
ParticleIndex
from yt.data_objects.static_output import \
@@ -170,6 +173,7 @@
# The other same defaults we will use from the standard Gadget
# defaults.
unit_base = self._unit_base or {}
+
if "length" in unit_base:
length_unit = unit_base["length"]
elif "UnitLength_in_cm" in unit_base:
@@ -182,7 +186,6 @@
length_unit = _fix_unit_ordering(length_unit)
self.length_unit = self.quan(length_unit[0], length_unit[1])
- unit_base = self._unit_base or {}
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
elif "UnitVelocity_in_cm_per_s" in unit_base:
@@ -191,6 +194,7 @@
velocity_unit = (1e5, "cm/s")
velocity_unit = _fix_unit_ordering(velocity_unit)
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.
if "mass" in unit_base:
@@ -205,7 +209,14 @@
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])
- self.time_unit = self.quan(unit_base["UnitTime_in_s"], "s")
+
+ if "time" in unit_base:
+ time_unit = unit_base["time"]
+ elif "UnitTime_in_s" in unit_base:
+ time_unit = (unit_base["UnitTime_in_s"], "s")
+ else:
+ time_unit = (1., "s")
+ self.time_unit = self.quan(time_unit[0], time_unit[1])
@classmethod
def _is_valid(self, *args, **kwargs):
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/ramses/data_structures.py
--- a/yt/frontends/ramses/data_structures.py
+++ b/yt/frontends/ramses/data_structures.py
@@ -491,13 +491,22 @@
"""
Generates the conversion to various physical _units based on the parameter file
"""
- # Note that unit_l *already* converts to proper!
- # Also note that unit_l must be multiplied by the boxlen parameter to
- # ensure we are correctly set up for the current domain.
- length_unit = self.parameters['unit_l']
- boxlen = self.parameters['boxlen']
- density_unit = self.parameters['unit_d']
- mass_unit = density_unit * (length_unit * boxlen)**3
+ #Please note that for all units given in the info file, the boxlen
+ #still needs to be folded in, as shown below!
+
+ boxlen=self.parameters['boxlen']
+ length_unit = self.parameters['unit_l'] * boxlen
+ density_unit = self.parameters['unit_d']/ boxlen**3
+
+ # In the mass unit, the factors of boxlen cancel back out, so this
+ #is equivalent to unit_d*unit_l**3
+
+ mass_unit = density_unit * length_unit**3
+
+ # Cosmological runs are done in lookback conformal time.
+ # To convert to proper time, the time unit is calculated from
+ # the expansion factor. This is not yet done here!
+
time_unit = self.parameters['unit_t']
magnetic_unit = np.sqrt(4*np.pi * mass_unit /
(time_unit**2 * length_unit))
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/ramses/io.py
--- a/yt/frontends/ramses/io.py
+++ b/yt/frontends/ramses/io.py
@@ -20,7 +20,12 @@
BaseIOHandler
from yt.utilities.logger import ytLogger as mylog
import yt.utilities.fortran_utils as fpu
-from yt.extern.six.moves import cStringIO
+from yt.extern.six import PY3
+
+if PY3:
+ from io import BytesIO as IO
+else:
+ from cStringIO import StringIO as IO
class IOHandlerRAMSES(BaseIOHandler):
_dataset_type = "ramses"
@@ -37,7 +42,7 @@
f = open(subset.domain.hydro_fn, "rb")
# This contains the boundary information, so we skim through
# and pick off the right vectors
- content = cStringIO(f.read())
+ content = IO(f.read())
rv = subset.fill(content, fields, selector)
for ft, f in fields:
d = rv.pop(f)
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/rockstar/io.py
--- a/yt/frontends/rockstar/io.py
+++ b/yt/frontends/rockstar/io.py
@@ -28,6 +28,7 @@
from yt.utilities.lib.geometry_utils import compute_morton
from yt.geometry.oct_container import _ORDER_MAX
+from operator import attrgetter
class IOHandlerRockstarBinary(BaseIOHandler):
_dataset_type = "rockstar_binary"
@@ -45,12 +46,11 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
-
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files,key=attrgetter("filename")):
pcount = data_file.header['num_halos']
with open(data_file.filename, "rb") as f:
f.seek(data_file._position_offset, os.SEEK_SET)
@@ -66,11 +66,11 @@
data_files = set([])
# Only support halo reading for now.
assert(len(ptf) == 1)
- assert(ptf.keys()[0] == "halos")
+ assert(list(ptf.keys())[0] == "halos")
for chunk in chunks:
for obj in chunk.objs:
data_files.update(obj.data_files)
- for data_file in sorted(data_files):
+ for data_file in sorted(data_files,key=attrgetter("filename")):
pcount = data_file.header['num_halos']
with open(data_file.filename, "rb") as f:
for ptype, field_list in sorted(ptf.items()):
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/setup.py
--- a/yt/frontends/setup.py
+++ b/yt/frontends/setup.py
@@ -17,6 +17,7 @@
config.add_subpackage("fits")
config.add_subpackage("flash")
config.add_subpackage("gadget")
+ config.add_subpackage("gadget_fof")
config.add_subpackage("gdf")
config.add_subpackage("halo_catalog")
config.add_subpackage("http_stream")
@@ -34,11 +35,12 @@
config.add_subpackage("athena/tests")
config.add_subpackage("boxlib/tests")
config.add_subpackage("chombo/tests")
+ config.add_subpackage("eagle/tests")
config.add_subpackage("enzo/tests")
- config.add_subpackage("eagle/tests")
config.add_subpackage("fits/tests")
config.add_subpackage("flash/tests")
config.add_subpackage("gadget/tests")
+ config.add_subpackage("gadget_fof/tests")
config.add_subpackage("moab/tests")
config.add_subpackage("owls/tests")
config.add_subpackage("owls_subfind/tests")
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/frontends/tipsy/fields.py
--- a/yt/frontends/tipsy/fields.py
+++ b/yt/frontends/tipsy/fields.py
@@ -16,6 +16,8 @@
#-----------------------------------------------------------------------------
from yt.frontends.sph.fields import SPHFieldInfo
+from yt.fields.particle_fields import add_volume_weighted_smoothed_field, add_nearest_neighbor_field
+from yt.utilities.physical_constants import mp, kb
class TipsyFieldInfo(SPHFieldInfo):
aux_particle_fields = {
@@ -44,3 +46,29 @@
self.aux_particle_fields[field[1]] not in self.known_particle_fields:
self.known_particle_fields += (self.aux_particle_fields[field[1]],)
super(TipsyFieldInfo,self).__init__(ds, field_list, slice_info)
+
+ def setup_particle_fields(self, ptype, *args, **kwargs):
+
+ # setup some special fields that only make sense for SPH particles
+
+ if ptype in ("PartType0", "Gas"):
+ self.setup_gas_particle_fields(ptype)
+
+ super(TipsyFieldInfo, self).setup_particle_fields(
+ ptype, *args, **kwargs)
+
+
+ def setup_gas_particle_fields(self, ptype):
+
+ def _smoothing_length(field, data):
+ # For now, we hardcode num_neighbors. We should make this configurable
+ # in the future.
+ num_neighbors = 64
+ fn, = add_nearest_neighbor_field(ptype, "particle_position", self, num_neighbors)
+ return data[ptype, 'nearest_neighbor_distance_%d' % num_neighbors]
+
+ self.add_field(
+ (ptype, "smoothing_length"),
+ function=_smoothing_length,
+ particle_type=True,
+ units="code_length")
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/utilities/fits_image.py
--- a/yt/utilities/fits_image.py
+++ b/yt/utilities/fits_image.py
@@ -122,7 +122,7 @@
for key in fields:
if key not in exclude_fields:
if hasattr(img_data[key], "units"):
- self.field_units[key] = str(img_data[key].units)
+ self.field_units[key] = img_data[key].units
else:
self.field_units[key] = "dimensionless"
mylog.info("Making a FITS image of field %s" % key)
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/visualization/color_maps.py
--- a/yt/visualization/color_maps.py
+++ b/yt/visualization/color_maps.py
@@ -11,7 +11,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
import numpy as np
-from yt.extern.six.moves import zip as izip
import matplotlib
import matplotlib.colors as cc
@@ -86,9 +85,9 @@
194.5*_vs**2.88+99.72*np.exp(-77.24*(_vs-0.742)**2.0)
+ 45.40*_vs**0.089+10.0)/255.0
-cdict = {'red':zip(_vs,_kamae_red,_kamae_red),
- 'green':zip(_vs,_kamae_grn,_kamae_grn),
- 'blue':zip(_vs,_kamae_blu,_kamae_blu)}
+cdict = {'red':np.transpose([_vs,_kamae_red,_kamae_red]),
+ 'green':np.transpose([_vs,_kamae_grn,_kamae_grn]),
+ 'blue':np.transpose([_vs,_kamae_blu,_kamae_blu])}
add_cmap('kamae', cdict)
# This one is a simple black & green map
@@ -151,9 +150,9 @@
_vs = np.linspace(0,1,256)
for k,v in list(_cm.color_map_luts.items()):
if k not in yt_colormaps and k not in mcm.cmap_d:
- cdict = { 'red': zip(_vs,v[0],v[0]),
- 'green': zip(_vs,v[1],v[1]),
- 'blue': zip(_vs,v[2],v[2]) }
+ cdict = { 'red': np.transpose([_vs,v[0],v[0]]),
+ 'green': np.transpose([_vs,v[1],v[1]]),
+ 'blue': np.transpose([_vs,v[2],v[2]]) }
add_cmap(k, cdict)
def _extract_lookup_table(cmap_name):
@@ -393,9 +392,9 @@
# Second number is the (0..1) number to interpolate to when coming *from below*
# Third number is the (0..1) number to interpolate to when coming *from above*
_vs = np.linspace(0,1,256)
- cdict = {'red': zip(_vs, cmap[:,0], cmap[:,0]),
- 'green': zip(_vs, cmap[:,1], cmap[:,1]),
- 'blue': zip(_vs, cmap[:,2], cmap[:,2])}
+ cdict = {'red': np.transpose([_vs, cmap[:,0], cmap[:,0]]),
+ 'green': np.transpose([_vs, cmap[:,1], cmap[:,1]]),
+ 'blue': np.transpose([_vs, cmap[:,2], cmap[:,2]])}
if name is not None:
add_cmap(name, cdict)
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -27,7 +27,6 @@
import numpy as np
import weakref
import re
-import string
class FixedResolutionBuffer(object):
r"""
@@ -178,13 +177,13 @@
pstr = m.string[m.start()+1:m.end()-1]
segments = fname.split("_")
for i,s in enumerate(segments):
- segments[i] = string.capitalize(s)
+ segments[i] = s.capitalize()
if s == pstr:
ipstr = i
element = segments[ipstr-1]
roman = pnum2rom[pstr[1:]]
label = element + '\ ' + roman + '\ ' + \
- string.join(segments[ipstr+1:], '\ ')
+ '\ '.join(segments[ipstr+1:])
else:
label = fname
return label
diff -r f1f968e3cd056f51c5d2703ca33829ebb0b62acd -r a4f19a0f6144c12944b0cbfd351e887309d185a0 yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -170,7 +170,7 @@
bitmap_array = np.concatenate([bitmap_array.astype('uint8'),
alpha_channel], axis=-1)
if transpose:
- bitmap_array = bitmap_array.swapaxes(0,1)
+ bitmap_array = bitmap_array.swapaxes(0,1).copy(order="C")
if filename is not None:
pw.write_png(bitmap_array, filename)
else:
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/bc88878b5537/
Changeset: bc88878b5537
Branch: bugfix-1035
User: BW Keller
Date: 2015-07-17 17:23:36+00:00
Summary: Leave those changes for another PR
Affected #: 1 file
diff -r a4f19a0f6144c12944b0cbfd351e887309d185a0 -r bc88878b553718fc1a40772a913408871379e680 yt/frontends/tipsy/fields.py
--- a/yt/frontends/tipsy/fields.py
+++ b/yt/frontends/tipsy/fields.py
@@ -16,8 +16,6 @@
#-----------------------------------------------------------------------------
from yt.frontends.sph.fields import SPHFieldInfo
-from yt.fields.particle_fields import add_volume_weighted_smoothed_field, add_nearest_neighbor_field
-from yt.utilities.physical_constants import mp, kb
class TipsyFieldInfo(SPHFieldInfo):
aux_particle_fields = {
@@ -46,29 +44,3 @@
self.aux_particle_fields[field[1]] not in self.known_particle_fields:
self.known_particle_fields += (self.aux_particle_fields[field[1]],)
super(TipsyFieldInfo,self).__init__(ds, field_list, slice_info)
-
- def setup_particle_fields(self, ptype, *args, **kwargs):
-
- # setup some special fields that only make sense for SPH particles
-
- if ptype in ("PartType0", "Gas"):
- self.setup_gas_particle_fields(ptype)
-
- super(TipsyFieldInfo, self).setup_particle_fields(
- ptype, *args, **kwargs)
-
-
- def setup_gas_particle_fields(self, ptype):
-
- def _smoothing_length(field, data):
- # For now, we hardcode num_neighbors. We should make this configurable
- # in the future.
- num_neighbors = 64
- fn, = add_nearest_neighbor_field(ptype, "particle_position", self, num_neighbors)
- return data[ptype, 'nearest_neighbor_distance_%d' % num_neighbors]
-
- self.add_field(
- (ptype, "smoothing_length"),
- function=_smoothing_length,
- particle_type=True,
- units="code_length")
https://bitbucket.org/yt_analysis/yt/commits/7427f58f1825/
Changeset: 7427f58f1825
Branch: yt
User: jzuhone
Date: 2015-07-18 13:51:32+00:00
Summary: Merged in bwkeller/yt/bugfix-1035 (pull request #1641)
Bugfix for 1035
Affected #: 2 files
diff -r eef682fe125dc8f36c86c89453fc7ab6481c994d -r 7427f58f1825c352d68365489c615c7a25c59c5f yt/frontends/tipsy/data_structures.py
--- a/yt/frontends/tipsy/data_structures.py
+++ b/yt/frontends/tipsy/data_structures.py
@@ -180,7 +180,7 @@
self.domain_left_edge = None
self.domain_right_edge = None
else:
- bbox = self.arr(self.bounding_box, 'code_length', dtype="float64")
+ bbox = np.array(self.bounding_box, dtype="float64")
if bbox.shape == (2, 3):
bbox = bbox.transpose()
self.domain_left_edge = bbox[:,0]
Repository URL: https://bitbucket.org/yt_analysis/yt/
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