Mailman 3 September 2014 - yt-dev

Issue #903: Plot.set_xlim Error using ProfilePlot.from_profiles (yt_analysis/yt)
by Alan Kap Sept. 17, 2014

Sept. 17, 2014

New issue 903: Plot.set_xlim Error using ProfilePlot.from_profiles https://bitbucket.org/yt_analysis/yt/issue/903/plotset_xlim-error-using Alan Kap: import yt from yt import derived_field from yt.units import kpc from matplotlib import pylab as plt # Lists to hold profiles, labels, and plot specifications. profiles = [] labels = [] center = [0.5,0.5,0.5] @derived_field(name = "code_r", units = "") def _code_r(field, data): return data["spherical_r"]/kpc/10 ran = [1,2,4,15] for i in ran: … [View More]

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Issue #902: dataset volume() function is broken (yt_analysis/yt)
by Cameron Hummels Sept. 16, 2014

Sept. 16, 2014

New issue 902: dataset volume() function is broken https://bitbucket.org/yt_analysis/yt/issue/902/dataset-volume-function-is-b… Cameron Hummels: Demo script: import yt ds = yt.load('DD0046/DD0046') ad = ds.all_data() print ad.volume() Traceback: http://paste.yt-project.org/show/5120/ Responsible: chummels

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Issue #901: Derived quantity total_mass fails on DM-only datasets (yt_analysis/yt)
by Cameron Hummels Sept. 16, 2014

Sept. 16, 2014

New issue 901: Derived quantity total_mass fails on DM-only datasets https://bitbucket.org/yt_analysis/yt/issue/901/derived-quantity-total_mass-… Cameron Hummels: In trying to calculate the mass of objects in an enzo dark matter only dataset, yt fails. It expects a ('gas', 'particle_mass') field to exist for this dataset, because that is what the field_info object thinks exists for this dataset. I think this may be indicative of more significant problems for particle-only datasets (at least … [View More]

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units for Eagle sph frontend I/O in current_time
by Gabriel Altay Sept. 16, 2014

Sept. 16, 2014

Hi all, I'm working on adding an EagleDataset to complement Hillary's recent addition of the EagleNetworkDataset. I've been testing what I have using the recently uploaded OWLS and Eagle snapshots on the yt data site and am having trouble with the time units. As is, the code won't read non-zoom Eagle runs. However, the problem with the time units exists in the OWLS frontend too. The following example reads the OWLS snapshot on the yt data website and prints the current time in cgs units. … [View More]

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what units should be used when setting self.current_time for sph frontends?
by Gabriel Altay Sept. 15, 2014

Sept. 15, 2014

Hi all, I'm working on adding an EagleDataset to complement Hillary's recent addition of the EagleNetworkDataset. I've been testing what I have using the recently uploaded OWLS and Eagle snapshots on the yt data site and am having trouble with the time units. As is, the code won't read non-zoom Eagle runs. However, the problem with the time units exists in the OWLS frontend too. The following example reads the OWLS snapshot on the yt data website and prints the current time in cgs units. … [View More]

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Notes for the first yt team coordinator meeting
by Nathan Goldbaum Sept. 15, 2014

Sept. 15, 2014

Hi all, We just finished up our first monthly scheduled meeting. For more details about our governance and management plan going forward, YTEP-1776 [0], which was hashed out as a community discussion last month. The notes for the meeting are available in a google doc [1]. If you have any questions, comments, or suggestions please feel free to reply to this thread. We've preliminarily scheduled the next meeting to happen during the yt development workshop at NCSA next month. -Nathan [0] … [View More]

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Issue #900: yt modifies logger, which clashes with astropy's logging system (yt_analysis/yt)
by Adam Ginsburg Sept. 15, 2014

Sept. 15, 2014

New issue 900: yt modifies logger, which clashes with astropy's logging system https://bitbucket.org/yt_analysis/yt/issue/900/yt-modifies-logger-which-cla… Adam Ginsburg: I'd like to be able to disable yt's modifications to logger. An example: ``` In [1]: from astropy import log In [2]: log.info('blah') INFO: blah [unknown] In [3]: import yt In [4]: log.info('blah') INFO: blah [unknown] astropy: [INFO ] 2014-09-15 20:22:46,643 blah ``` After importing yt, the logger message is … [View More]

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Issue #899: my_plugins.py file tries to find fields on initialization and fails if not found (yt_analysis/yt)
by Devin Silvia Sept. 15, 2014

Sept. 15, 2014

New issue 899: my_plugins.py file tries to find fields on initialization and fails if not found https://bitbucket.org/yt_analysis/yt/issue/899/my_pluginspy-file-tries-to-f… Devin Silvia: my_plugins.py used to be able to contain user-defined fields that would only actually be created if specifically requested. Now, it would appear that yt tries to load all of the fields in my_plugins.py upon initialization. Since some fields only can be defined if certain fields are in the data, this does … [View More]

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Issue #898: PPV: Could not find field '('gas', 'v_los')' caused by PR #1176 (yt_analysis/yt)
by Kacper Kowalik Sept. 14, 2014

Sept. 14, 2014

New issue 898: PPV: Could not find field '('gas', 'v_los')' caused by PR #1176 https://bitbucket.org/yt_analysis/yt/issue/898/ppv-could-not-find-field-gas… Kacper Kowalik: Following script: ``` #!python import yt import numpy as np from yt.analysis_modules.ppv_cube.api import PPVCube nx, ny, nz = (64, 64, 64) R = 10. r_0 = 3. beta = 1.4 alpha = -1. x, y = np.mgrid[-R:R:nx * 1j, -R:R:ny * 1j] r = np.sqrt(x * x + y * y) theta = np.arctan2(y, x) dens = np.zeros((nx, ny, nz)) dens[:, :, nz /… [View More] 2 - 3:nz / 2 + 3] = (r ** alpha).reshape(nx, ny, 1) vel_theta = r / (1. + (r / r_0) ** beta) velx = np.zeros((nx, ny, nz)) vely = np.zeros((nx, ny, nz)) velx[:, :, nz / 2 - 3:nz / 2 + 3] = \ (-vel_theta * np.sin(theta)).reshape(nx, ny, 1) vely[:, :, nz / 2 - 3:nz / 2 + 3] = \ (vel_theta * np.cos(theta)).reshape(nx, ny, 1) dens[r > R] = 0.0 velx[r > R] = 0.0 vely[r > R] = 0.0 data = {"density": (dens, "g/cm**3"), "velocity_x": (velx, "km/s"), "velocity_y": (vely, "km/s"), "velocity_z": (np.zeros((nx, ny, nz)), "km/s")} bbox = np.array([[-0.5, 0.5], [-0.5, 0.5], [-0.5, 0.5]]) ds = yt.load_uniform_grid(data, (nx, ny, nz), length_unit=(2 * R, "kpc"), nprocs=1, bbox=bbox) i = 60. * np.pi / 180. L = [0.0, np.sin(i), np.sin(i)] cube = PPVCube(ds, L, "density", dims=( 100, 50, 25), velocity_bounds=(-1.5, 1.5, "km/s")) ``` yields: ``` #!text Traceback (most recent call last): File "ala.py", line 38, in <module> 100, 50, 25), velocity_bounds=(-1.5, 1.5, "km/s")) File "yt/analysis_modules/ppv_cube/ppv_cube.py", line 100, in __init__ (self.nx, self.ny), "intensity") File "yt/visualization/volume_rendering/camera.py", line 2376, in off_axis_projection image = projcam.snapshot() File "yt/visualization/volume_rendering/camera.py", line 2301, in snapshot image, sampler), File "yt/visualization/volume_rendering/camera.py", line 2258, in _render data = [(grid[field] * mask).astype("float64") for field in fields] File "yt/data_objects/grid_patch.py", line 90, in __getitem__ tr = super(AMRGridPatch, self).__getitem__(key) File "yt/data_objects/data_containers.py", line 240, in __getitem__ self.get_data(f) File "yt/data_objects/data_containers.py", line 673, in get_data self._generate_fields(fields_to_generate) File "yt/data_objects/data_containers.py", line 693, in _generate_fields fd = self._generate_field(field) File "yt/data_objects/data_containers.py", line 277, in _generate_field tr = self._generate_fluid_field(field) File "yt/data_objects/data_containers.py", line 297, in _generate_fluid_field rv = finfo(gen_obj) File "yt/fields/derived_field.py", line 184, in __call__ dd = self._function(self, data) File "yt/analysis_modules/ppv_cube/ppv_cube.py", line 159, in _intensity vlos = data["v_los"] File "yt/data_objects/grid_patch.py", line 90, in __getitem__ tr = super(AMRGridPatch, self).__getitem__(key) File "yt/data_objects/data_containers.py", line 233, in __getitem__ f = self._determine_fields([key])[0] File "yt/data_objects/data_containers.py", line 505, in _determine_fields raise YTFieldNotFound((ftype,fname),self.ds) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('gas', 'v_los')' in UniformGridData. ``` with current tip. Regression was introduced in changeset a9aa29ba3512 Responsible: drudd [View Less]

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Issue #897: my_plugins.py no longer appears to be supported in yt 3.0 (yt_analysis/yt)
by Anonymous Sept. 12, 2014

Sept. 12, 2014

New issue 897: my_plugins.py no longer appears to be supported in yt 3.0 https://bitbucket.org/yt_analysis/yt/issue/897/my_pluginspy-no-longer-appea… Anonymous: Specifically, add_field is "not defined" when yt tries to grab my_plugins.py This example for a my_plugins.py file fails: http://paste.yt-project.org/show/5115/

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