Mailman 3 March 2014 - yt-dev

workshop hangout
by Matthew Turk 23 Mar '14

23 Mar '14

Hi all, Tomorrow if anybody wants to "hangout" in, feel free. We're going to be starting around 9AM pacific time, so just let me know and we'll figure something out. Also, we've been encouraging everyone to get on IRC. -Matt

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Issue #811: Pressure alias for the FLASH frontend doesn't work (yt_analysis/yt)
by John ZuHone 23 Mar '14

23 Mar '14

New issue 811: Pressure alias for the FLASH frontend doesn't work https://bitbucket.org/yt_analysis/yt/issue/811/pressure-alias-for-the-flash… John ZuHone: Attempting to use the `"pressure"` alias for the FLASH `"pres"` field results in the following error, demonstrated by the following script: ``` #!python from yt.mods import * ds = load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0100") sp = ds.sphere("c", (100,"kpc")) sp["pressure"] ``` ``` #!python ERROR: RuntimeError: Something has gone terribly wrong, _function is NullFunc [yt.fields.derived_field] astropy: [ERROR ] 2014-03-23 13:41:30,084 RuntimeError: Something has gone terribly wrong, _function is NullFunc --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-4-a43a895d2820> in <module>() ----> 1 sp["pressure"] /Users/jzuhone/Source/yt-3.x/yt/data_objects/data_containers.pyc in __getitem__(self, key) 210 return self.field_data[f] 211 else: --> 212 self.get_data(f) 213 # fi.units is the unit expression string. We depend on the registry 214 # hanging off the dataset to define this unit object. /Users/jzuhone/Source/yt-3.x/yt/data_objects/data_containers.pyc in get_data(self, fields) 619 620 fields_to_generate += gen_fluids + gen_particles --> 621 self._generate_fields(fields_to_generate) 622 623 def _generate_fields(self, fields_to_generate): /Users/jzuhone/Source/yt-3.x/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate) 636 fi = self.pf._get_field_info(*field) 637 try: --> 638 fd = self._generate_field(field) 639 if type(fd) == np.ndarray: 640 fd = self.pf.arr(fd, fi.units) /Users/jzuhone/Source/yt-3.x/yt/data_objects/data_containers.pyc in _generate_field(self, field) 247 tr = self._generate_particle_field(field) 248 else: --> 249 tr = self._generate_fluid_field(field) 250 if tr is None: 251 raise YTCouldNotGenerateField(field, self.pf) /Users/jzuhone/Source/yt-3.x/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field) 267 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 268 else: --> 269 rv = finfo(gen_obj) 270 return rv 271 /Users/jzuhone/Source/yt-3.x/yt/fields/derived_field.pyc in __call__(self, data) 177 if self._function is NullFunc: 178 raise RuntimeError( --> 179 "Something has gone terribly wrong, _function is NullFunc") 180 with self.unit_registry(data): 181 dd = self._function(self, data) RuntimeError: Something has gone terribly wrong, _function is NullFunc ``` Responsible: jzuhone

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Issue #810: Unexpected units behavior creating yt sphere with unit_refactor (yt_analysis/yt)
by Brian Crosby 23 Mar '14

23 Mar '14

New issue 810: Unexpected units behavior creating yt sphere with unit_refactor https://bitbucket.org/yt_analysis/yt/issue/810/unexpected-units-behavior-cr… Brian Crosby: Creating a sphere object using a YTQuantity for the radius creates an object that appears to have the value of the radius in cm, despite calling it code_length. Example: In [4]: my_sphere = pf.sphere(location, YTQuantity(10, 'kpc')) In [5]: my_sphere Out[5]: YTSphere (moving7_0010): center=[ 0.75073242 0.75024414 0.75024414] code_length, radius=3.08567758096e+22 code_length Creating the sphere with a tuple rather than a YTQuantity behaves normally. Example: In [6]: my_sphere = pf.sphere(location, (10, 'kpc')) In [7]: my_sphere Out[7]: YTSphere (moving7_0010): center=[ 0.75073242 0.75024414 0.75024414] code_length, radius=10.0 kpc Responsible: ngoldbaum

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Issue #809: Showing plots in the notebook broken for old versions of Ipython (yt_analysis/yt)
by Andrew Myers 23 Mar '14

23 Mar '14

New issue 809: Showing plots in the notebook broken for old versions of Ipython https://bitbucket.org/yt_analysis/yt/issue/809/showing-plots-in-the-noteboo… Andrew Myers: I noticed this when I updated an old yt installation that had Ipython version 0.11. Creating, say, a SlicePlot in the notebook and then calling show() produces the following error: ``` #!python --------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-4-bdbc9c77dc7a> in <module>() ----> 1 sl.show() /Users/atmyers/yt/src/yt-hg/yt/visualization/plot_container.pyc in show(self) 452 api_version = get_ipython_api_version() 453 if api_version in ('0.10', '0.11'): --> 454 self._send_zmq() 455 else: 456 from IPython.display import display /Users/atmyers/yt/src/yt-hg/yt/visualization/plot_container.pyc in _send_zmq(self) 427 # Due to a quirk in the matplotlib API, we need to create 428 # a dummy canvas variable here that is never used. --> 429 canvas = FigureCanvasAgg(v.figure) # NOQA 430 display(v.figure) 431 NameError: global name 'FigureCanvasAgg' is not defined ``` The fix is simply to add this import right before line 429. This likely eluded detection since this only affects users with rather old versions of Ipython... PR incoming shortly. Responsible: atmyers

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Issue #808: derived_field decorator in 3.0 experimental is finicky (yt_analysis/yt)
by Nathan Goldbaum 20 Mar '14

20 Mar '14

New issue 808: derived_field decorator in 3.0 experimental is finicky https://bitbucket.org/yt_analysis/yt/issue/808/derived_field-decorator-in-3… Nathan Goldbaum: Take as an example the following snippet: ``` #!python from yt.mods import * from yt.utilities.physical_constants import mh from IPython.display import display @derived_field(name='number_density', units='cm**-3') def number_density(field, data): return data['density']/(data.pf.parameters['mu']*mh) fields = ['number_density', 'temperature', 'grid_level'] ds = load('IsolatedGalaxy/galaxy0030/galaxy0030') slc = SlicePlot(ds, 2, fields, width=(20, 'kpc')) slc.save() ``` This currently fails with the following traceback: http://paste.yt-project.org/show/4409/ This actually should fail, since the parameter I'm really looking for is `'Mu'`, not `'mu'`. However, I'd hope I'd get traceback in the dictionary access. I guess that error is swallowed by the field detection machinery. Could we allow exceptions to be raised by user-supplied fields? Correcting the error (replacing `'mu'` with `'Mu'`) leads to the following traceback: http://paste.yt-project.org/show/4410/ So it looks like `number_density` is being mapped to the `index` field type rather than `gas`. Replacing `name='number_density'` with `name = ('gas', 'number_density')` allows the script to run without issues. Is there a way to _detect_ the correct field type purely from the field dependency chain or is that already happening but is broken somehow?

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Issue #807: Fix docs for transpose in write_bitmap (yt_analysis/yt)
by Sam Skillman 20 Mar '14

20 Mar '14

New issue 807: Fix docs for transpose in write_bitmap https://bitbucket.org/yt_analysis/yt/issue/807/fix-docs-for-transpose-in-wr… Sam Skillman: We should really add docs to write_bitmap on what we assume for the origin of the incoming array. Responsible: samskillman

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VR Scene Object
by Sam Skillman 19 Mar '14

19 Mar '14

Hi all, In preparation for the workshop next week, I'd like to start pushing a bit on the volume rendering scene object. I'd like to start from the work that was done at the last workshop since I know a large amount of work was done on it back then. Could someone please point me to a place where I can pull in those changes? Cheers, Sam

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field line tracing problems
by j s oishi 19 Mar '14

19 Mar '14

Hi All (especially Sam), I'm trying to understand some behavior in the streamlines that I don't completely understand. I've documented the problem in a notebook here: https://hub.yt-project.org/nb/2tmwor The notebook has a full statement of the problem. In essense, I'm not sure I understand why streams that I believe should terminate instantly upon launch (because they should walk directly out of the box) have thousands of elements in them (instead of one). I assume there are one or more misconceptions in my understanding, and I'd really welcome any suggestions. thanks, Jeff

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Graphviz installation -- reg
by Reju Sam John 18 Mar '14

18 Mar '14

Dear yt developers, Is there any plan to include Graphviz in the basic yt installation just like SQLite3 an other packages. It will be very useful for beginners like me if Graphviz got installed by installing yt. Looking forward to hearing from you all. Thank You, -- Reju Sam John

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Graphviz installation -- reg
by Reju Sam John 18 Mar '14

18 Mar '14

Dear yt developers, Is there any plan to include Graphviz in the basic yt installation just like SQLite3 an other packages. It will be very useful for beginners like me if Graphviz got installed by installing yt. Looking forward to hearing from you all. Thank You, -- Reju Sam John

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