Mailman 3 January 2014 - yt-dev

Orientation, coordinate systems
by Matthew Turk April 15, 2014

April 15, 2014

Hi all, I'd like to open up the discussion of "fixing" the yt coordinate systems, as we move nearer and nearer on 3.0. Jeff, Nathan and Britton have brought this up a couple times, that the x/y/z ordering is not consistent with what they expect, and I'd like to figure out if we can fix that now -- it's as good a time as any for bandaid ripping. It may just be a matter of the transposition of buffers and the x_dict and y_dict, or it might be more complex, although I suspect it won't be much more than fixing those two items. -Matt

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Issue #769: In-place operators of arrays/floats and YTArrays/YTQuantities don't result in unitified structures (yt_analysis/yt)
by John ZuHone Jan. 31, 2014

Jan. 31, 2014

New issue 769: In-place operators of arrays/floats and YTArrays/YTQuantities don't result in unitified structures https://bitbucket.org/yt_analysis/yt/issue/769/in-place-operators-of-arrays… John ZuHone: For example, this: ``` #!python x = np.arange(10) y = YTQuantity(1.0, "cm") x *= y ``` Doesn't return a `YTArray`. Should it? Responsible: MatthewTurk

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Issue #768: Units and exponents (yt_analysis/yt)
by Matthew Turk Jan. 31, 2014

Jan. 31, 2014

New issue 768: Units and exponents https://bitbucket.org/yt_analysis/yt/issue/768/units-and-exponents Matthew Turk: Exponents don't seem to change the units of a YTArray. ``` #!python from yt.units import cm import numpy as np cm_arr = np.array([1.0,1.0]) * cm print cm**3 print cm_arr * cm_arr print cm_arr**3 ``` Responsible: ngoldbaum

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Issue #767: Unitrefactor: Stream datasets are always setting code_length == cm (yt_analysis/yt)
by John ZuHone Jan. 31, 2014

Jan. 31, 2014

New issue 767: Unitrefactor: Stream datasets are always setting code_length == cm https://bitbucket.org/yt_analysis/yt/issue/767/unitrefactor-stream-datasets… John ZuHone: I can't get any length units to be returned in anything other than code units: ``` #!python pf = load_uniform_grid(data, ddims, length_unit=2*R*cm_per_kpc) pf.domain_right_edge pf.domain_right_edge.in_units("cm") pf.domain_right_edge.in_units("kpc") ``` gives: ``` #!python YTArray([ 1., 1., 1.]) code_length YTArray([ 1., 1., 1.]) cm YTArray([ 3.24077929e-22, 3.24077929e-22, 3.24077929e-22]) kpc ``` which is what happens regardless of what goes in for `length_unit`. Responsible: MatthewTurk

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Field parameters and covering grids in 3.0
by Nathan Goldbaum Jan. 31, 2014

Jan. 31, 2014

Hi all (particularly Matt, I suspect), I'm having an issue doing isocontour flux extraction on a disk in yt-3.0. I'm using this script: from yt.mods import * pf = load('HiResIsolatedgalaxy/DD0044/DD0044') dd = pf.h.disk('c', [0,0,1], (20, 'kpc'), (3, 'kpc')) radii = (np.arange(100)+1)/100.*20 fluxes = [] for r in radii: iso = pf.h.surface(dd, 'Radiuskpc', r) print iso['Density'] This produces the following traceback: http://paste.yt-project.org/show/4263/ The issue seems to be that the "center" field parameter isn't being passed down to the grid object that is generating the covering grid. Right now it looks as if the `retrieve_ghost_zones` method attached to the grid object expects to find entries in the grid patch object's field_parameters dict. It seems as if I could update the grid patch with the field parameters from the disk object before the call to `_extract_isocontours_from_grid`. This makes me think that there might be a reason why it's not already set up like that. Has the way we handle field parameters changed much in the 3.0 codebase? Thanks for your help, Nathan

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Cannot build yt-2.7dev
by Nathan Goldbaum Jan. 31, 2014

Jan. 31, 2014

Hi all, I've suddenly started having issues with cython trying to process grid_traversal.pyx in the yt branch. See: http://paste.yt-project.org/show/4262/ This might be related to Cython 0.20, as I had that installed initially. That said, I've tried with 0.19 and 0.18, and both fail in the same way. This is strange, since I'm pretty sure I build 2.7dev sometime last week and I don't think anything has changed. Is anyone else seeing the same thing? Thanks! -Nathan

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gdf frontend and standards in tension?
by j s oishi Jan. 30, 2014

Jan. 30, 2014

Hi all, I've adapted yt's gdf_writer.py into a standalone class called pygdf ( https://bitbucket.org/jsoishi/pygdf). I've done this so that any python code can now save data in the gdf format. While doing this, I came across something in the yt gdf frontend that I'm not quite sure I understand. In the grid metadata, yt expects /grid_particle_count to be a 2-D array, but the gdf standard clearly states this should be a 1-D (int64, N) array, where N is the number of grids. Further complicating the issue is the fact that if I create a 1-D array for /grid_particle_count, the failure point in the following script from yt.mods import * pf = load("/tmp/blah.gdf") sp = SlicePlot(pf, 2, "Density") is actually in data_objects/grid_patch.py, not in the gdf frontend itself. The file /tmp/blah.gdf can be generated by running the test.py script in pygdf. The obvious workaround is to simply make /grid_particle_count a 2D array (this is especially so since I'm not actually using particles at the moment), but I'm not sure why this should be so. The total count of particles in N grids seems to be better fit in a 1-D array to me. However, I'd like to understand better what's going on. Any pointers or clarification would be very helpful. Also, any feedback on pygdf would be most welcome! thanks, j

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Mailing list issues
by Matthew Turk Jan. 29, 2014

Jan. 29, 2014

Hi all, We were having some mailing list issues earlier in the day, but I have been assured they are now fixed. So if you're seeing this, and got a bounce earlier, the clog seems to have been resolved. Sorry about that. -Matt

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Unitrefactor versus old-school units
by Nathan Goldbaum Jan. 28, 2014

Jan. 28, 2014

Hi all, I've spent a bit of time today comparing the current tip of 3.0 to the current unitrefactor, in an attempt to see whether field accesses on data objects will return answers that are consistent with what we were returning before. The specific comparison I'm doing is based on the IsolatedGalaxy dataset. This dataset has a large number of on-disk fields and is a good exercise of yt's field detection and derived fields machinery. I'm looking at whether field accesses on data objects return results that are identical to the results we get in the current 3.0 tip. The full testing script has been pasted here: http://paste.yt-project.org/show/4250 The results (just what the script printed to my terminal) are pasted here: http://paste.yt-project.org/show/4251 There appear to be three things that happened in this test: 1. The field access returned bitwise identical results 2. The field access returned results that are slightly different (~1e-6 level). 3. The field access returned results that are order-unity different. Obviously the first case isn't an issue. I believe all instances of the third case are due to comparing quantities that have different units (for example, particle_position_[x,y,z] used to return data in code units, but now does so in CGS). Case 2 is a little bit more involved and I'm not sure what to do about it in general -- thus this message ;) I'll take the density field as an example to illustrate what is happening. In the parameter file for this dataset, I see the following: MassUnits = 8.11471e+43 DensityUnits = 2.76112e-30 TimeUnits = 2.32946e+18 LengthUnits = 3.086e+24 Right now, unitrefactor is using the values of MassUnits and LengthUnits to construct the YTArray that contains the field data for the ('enzo', 'Density') field since this field has units of `code_mass/code_length**3`. The conversion factors from `code_mass` and `code_length` to CGS are exactly the MassUnits and LengthUnits variables from the dataset parameter file. So, the CGS conversion factor for the array is: MassUnits / LengthUnits**3 = 2.761197257954595e-30 g / cm**3 A careful reader will note that this is only equal to the DensityUnits in the parameter file up to rounding in the fifth decimal place. This difference, it turns out, is the source of the differences I saw in the comparison. I haven't gone through the rest of the fields in detail, but i suspect the all the remaining fields showing small differences to all have issues of this sort. My guess is the fields that compare exactly will either have a CGS conversion factor of unity, or the conversion factor was derived directly from MassUnits, LengthUnits, and TimeUnits in the data file. I'm not sure what the proper way to handle this is. Right now unitrefactor is ignoring the on-disk CGS conversion factor for Density. I don't think this choice should matter in principle, since mass and density units should be algebraically related via the LengthUnits. Unfortunately, rounding errors in the parameter file mean there will likely be a small amount of disagreement. Should we attempt to be more fastidious about adopting the proper conversion factors in the enzo frontend, if a conversion factor is available on disk? Should we not worry about these minor differences in field accesses that unitrefactor is introducing? Should we have units like `code_density` for all on-disk fields with available CGS conversion factors? If so, how do we deal with the fact that the conversion from code_density to code_mass/code_length**3 is not straightforward? Thanks for any help or advice anyone who has gotten this far can provide :) Cheers, Nathan

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Weekly Hangout
by Matthew Turk Jan. 27, 2014

Jan. 27, 2014

Hi all, In the interest of promoting more discussion, easier forums for chatting and raising of issues and so on, I'm going to start experimenting with holding low-intensity, no-frills hangouts on Friday mornings at 11AM Eastern time. I'll set up the hangout and if anyone shows up, we can talk about where things are, or specific issues. No pressure to attend, and if you do, no pressure to bring any issues. The idea is to keep it more true to the name "hangout" than "meeting." :) I'm not sure if I can schedule this in advance on G+, but I'm going to try to, so keep an eye on the plus page at http://plus.google.com/+ytprojectorg to see if the event shows up there. We'll start out this Friday, and see how it goes for a few weeks. -Matt

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