Mailman 3 May 2013 - yt-dev

Issue #570: Healpix volume rendering produces garbled, artifacted images (yt_analysis/yt)
by Nathan Goldbaum May 17, 2013

May 17, 2013

New issue 570: Healpix volume rendering produces garbled, artifacted images https://bitbucket.org/yt_analysis/yt/issue/570/healpix-volume-rendering-pro… Nathan Goldbaum: Using the sample script from the docs: ``` #!python from yt.mods import * import yt.visualization.volume_rendering.camera as camera pf = load("IsolatedGalaxy/galaxy0030/galaxy0030") image = camera.allsky_projection(pf, [0.5,0.5,0.5], 100.0/pf['kpc'], 64, "Density") camera.plot_allsky_healpix(image, 64, "allsky.png", "… [View More]

3 3

reorganizing YTEPs
by Britton Smith May 17, 2013

May 17, 2013

Hi all, One of the things that came out of the yt strategy meeting last week was a discussion of reorganizing how the YTEPs are listed. Currently, it looks like this: http://ytep.readthedocs.org/en/latest/ There are essentially two problems with this. First, once a YTEP is accepted, it is difficult to tell the status of the actual enhancement that was proposed. Is it being implemented? Is it done? Second, because we are doing revisions in PRs, there is no listing of unaccepted YTEPs. … [View More]

3 4

Issue #569: healpix rendering error (yt_analysis/yt)
by Anonymous May 17, 2013

May 17, 2013

New issue 569: healpix rendering error https://bitbucket.org/yt_analysis/yt/issue/569/healpix-rendering-error Anonymous: Running the example script from the documentation for healpix rendering gave me: Traceback (most recent call last): File "healpix.py", line 18, in <module> camera.snapshot() File "/Users/gso/Documents/dev-yt/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 1282, in snapshot tfp = TransferFunctionProxy(self.transfer_function) NameError: global … [View More]

1 0

Consolidating Boxlib frontends
by Matthew Turk May 17, 2013

May 17, 2013

Hi all, I'm spending a bit of time today looking over the Boxlib frontends and identifying commonalities and differences. I wanted to write with some of my initial findings as well as some specific questions. Casey, Andrew, and Jeff I would particularly like your feedback, but I also intend to submit this for detailed review and collaboration. My general plan is to consolidate the data_structures, IO and definitions into a single Boxlib frontend, with subclasses that cover each of the … [View More]

6 20

Issue #568: Slicing with cylindrical coordinates (yt_analysis/yt)
by rth May 17, 2013

May 17, 2013

New issue 568: Slicing with cylindrical coordinates https://bitbucket.org/yt_analysis/yt/issue/568/slicing-with-cylindrical-coo… rth: # Slicing with cylindrical coordinates # Currenly slicing a 2d cylindrical FLASH simulation along the θ axis with yt-3.0 gives wrong results. ``` #!python from yt.mods import * # file included in the attachement pf = load('./test_hdf5_plt_cnt_0013') fig = SlicePlot(pf, 2, ['r', 'z', 'theta', 'dens'], fontsize=10, origin="domain") fig.save(mpl_kwargs={'… [View More]bbox_inches':'tight', 'dpi': 500}) ``` the produced figures are attached. 1. Slice_z_theta.png: this projection is supposed to be a constant as there is just one cell in θ direction. On the figure though, there are also some additional cells (ghost cells?) in between blocks with diffferent levels of refinement, that seem to have completely arbitrary values. 2. Slice_z_r.png: same issue as in 1. 3. Slice_z_z.png: the plot should be linearly increasing along the z axis, and it is not the case. 4. Slice_z_dens.png: Density slice. Same issue as 1. the labels are actually misleading: all the plots were done in (r‚ z) plane. Actually, using yt-2.4 and replacing (r, z, θ) -> (x, y, z) still presents the same issue of arbitrary cells between blocks of different levels of refinement in a density slice. Up to now I was using Antony Sopatz's [flash.output.slice](http://flash.uchicago.edu/site/flashcode/user_support/t…, altought based on pf.h.slice, did not show the same behaviour. Unless I seriously misunderstand something, or I messed up my yt installation. Can someone please try to reproduce the attached plots? # Spatial derivatives in cyllindrical # Compuring a spatial derivative of a field fails in yt-3.0. ``` #!python from yt.mods import * # closely based on add_grad and replacing 'x' by 'r' def _gradr(field, data): grad = data['dens'][2:,1:-1,1:-1] - data['dens'][:-2,1:-1,1:-1] grad /= 2.0*data["dr"].flat[0] g = np.zeros(data['dens'].shape, dtype='float64') g[1:-1,1:-1,1:-1] = np.abs(grad) return g add_field("Grad_dens_r", function=_gradr, take_log=False, validators=[ValidateSpatial(1,['dens', 'dr'])], ) pf = load('./test_hdf5_plt_cnt_0013') fig = SlicePlot(pf, 2, 'Grad_dens_r', fontsize=10, origin="domain") #fig.annotate_grids() fig.save(mpl_kwargs={'bbox_inches':'tight', 'dpi': 500}) ``` ``` #!python S1 = 2303214662 ; S2 = 0 ; jname 1 256s = 264 Traceback (most recent call last): File "test_case.py", line 18, in <module> fig = SlicePlot(pf, 2, 'Grad_dens_r', fontsize=10, origin="domain") File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/visualization/plot_window.py", line 1226, in __init__ slc.get_data(fields) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/data_containers.py", line 500, in get_data self._generate_fields(fields_to_generate) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/data_containers.py", line 510, in _generate_fields self.field_data[field] = self._generate_field(field) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/data_containers.py", line 226, in _generate_field return self._generate_fluid_field(field) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/data_containers.py", line 239, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/data_containers.py", line 263, in _generate_spatial_fluid data = gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz][mask] File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/data_containers.py", line 200, in __getitem__ self.get_data(f) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/construction_data_containers.py", line 437, in get_data if len(fill) > 0: self._fill_fields(fill) File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/construction_data_containers.py", line 555, in _fill_fields chunk.ires) File "misc_utilities.pyx", line 551, in yt.utilities.lib.misc_utilities.fill_region (yt/utilities/lib/misc_utilities.c:10025) ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float' ``` temporarily fixing the dtype problem in ```data_objects/construction_data_containers.py```, produces a plot that is definitely not d/dr (see Slice_dens_r.png attached). I don't know if the fact that line 510 of ```data_objects/data_containers.py``` there is ``` #!python try: self.field_data[field] = self._generate_field(field) except GenerationInProgress as gip: for f in gip.fields: if f not in fields_to_generate: fields_to_generate.append(f) #else: # raise ``` that is silenly ignoring ```NeedsGridType``` exceptions, for this plot, could have something to do with it. ``` #!python File "/mnt/netapp2/yurchak.r/src/yt-3.0/yt/data_objects/field_info_container.py", line 558, in __call__ raise NeedsGridType(self.ghost_zones,self.fields) yt.data_objects.field_info_container.NeedsGridType: (1, ['dens', 'dr']) ``` Thank you. [View Less]

1 0

Issue #567: Setup script should test for openmp support (yt_analysis/yt)
by Nathan Goldbaum May 14, 2013

May 14, 2013

New issue 567: Setup script should test for openmp support https://bitbucket.org/yt_analysis/yt/issue/567/setup-script-should-test-for… Nathan Goldbaum: I think this wil just require compiling a small test program and then checking for errors. This should remove the necessity to manually set compilers on OS X and improve the compatibility of the setup script in general. Something like this should work (although we don't care about the version): http://stackoverflow.com/a/13612520 Responsible: ngoldbaum

1 0

Issue #566: Spatial fields double-read data (yt_analysis/yt)
by Matthew Turk May 13, 2013

May 13, 2013

New issue 566: Spatial fields double-read data https://bitbucket.org/yt_analysis/yt/issue/566/spatial-fields-double-read-d… Matthew Turk: Because of where the spatial field validation occurs, it is possible for spatial fields to double-read data with the new 3.0 chunking system. The check for validators occurs after the call to `_read_fluid_fields`. Responsible: MatthewTurk

1 0

Issue #565: Athena Answer Testing (yt_analysis/yt)
by Sam Skillman May 11, 2013

May 11, 2013

New issue 565: Athena Answer Testing https://bitbucket.org/yt_analysis/yt/issue/565/athena-answer-testing Sam Skillman: Add Athena answer testing that covers the various permutations of {unigrid, SMR} and {serial, parallel}. Responsible: samskillman

1 0

Units PR
by Nathan Goldbaum May 10, 2013

May 10, 2013

Hi all, The units refactor is proceeding apace - hopefully we'll ready for more widespread testing sometime this Summer. Over the past week, Casey and I went over the work we did at the yt workshop and tried to condense it into an expanded YTEP. The PR is here: https://bitbucket.org/caseywstark/ytep/src/56395e05b77c/source/YTEPs/YTEP-0… This touches on a lot of user-facing functionality (for the better, I think, but I'm certainly biased ;), so if you have any comments on things we've … [View More]

2 2

Removing the max_level keyword argument from ProjectionPlot
by Nathan Goldbaum May 10, 2013

May 10, 2013

Hi all, As part of the eternal journey that is making yt's plotting code as awesome as possible, we've endeavored to make the plotting code as flexible as it needs to be for quick use but simple enough that a use isn't overloaded by unnecessary or barely-used keyword arguments. Right now there is a pending PR to rework some of the plotting routines, adding a couple of new features, and, per the subject of this e-mail, removing the max_level keyword from ProjectionPlot. I could see how having … [View More]

4 6