yt-dev June 2013

yt-dev@python.org

8 participants
26 discussions

Issue #594: Add a cookbook recipe that shows off draw_coordinate_vectors (yt_analysis/yt)
by Nathan Goldbaum 14 Jun '13

14 Jun '13

New issue 594: Add a cookbook recipe that shows off draw_coordinate_vectors https://bitbucket.org/yt_analysis/yt/issue/594/add-a-cookbook-recipe-that-s… Nathan Goldbaum: Probably can modify one of the extant recipes to use it.

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New software installer from STScI
by Nathan Goldbaum 14 Jun '13

14 Jun '13

Hi all, I'd like to bring everyone's attention to ureka (http://ssb.stsci.edu/ureka/) a new binary distribution centered around python, IRAF, and commonly used astronomical image viewing and visualization software (e.g. DS9). They include a large number of python modules, in fact most of yt's source dependencies: http://ssb.stsci.edu/ureka/1.0beta5/docs/python_modules.html#sec-python-mod… All this software is available for OS X and linux and because it's a binary download it should run significantly quicker than yt's install script. I'll admit that I haven't tried installing it yet but it might be worthwhile to experiment a bit. If it's a good fit, we could add instructions to the website or the docs or even try to get them to include yt out of the box. -Nathan

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Issue #593: RADMC-3D converter does not work on FLASH data (yt_analysis/yt)
by Thomas Peters 13 Jun '13

13 Jun '13

New issue 593: RADMC-3D converter does not work on FLASH data https://bitbucket.org/yt_analysis/yt/issue/593/radmc-3d-converter-does-not-… Thomas Peters: The layer-style AMR input files for RADMC-3D generated from FLASH input data are corrupted. A typical error message from RADMC-3D looks as follows: Reading grid file and prepare grid tree... ERROR in layers: layer out of bounds layer number = 19 layer parent = 0 nnxyz parent = 8 8 32 ixyz = -2 5 1 nxyz = 4 4 4 Has anyone successfully used the converter for a FLASH dataset?

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Issue #592: Fields that combine deposited particle quantities with gas do not work (yt_analysis/yt)
by Nathan Goldbaum 13 Jun '13

13 Jun '13

New issue 592: Fields that combine deposited particle quantities with gas do not work https://bitbucket.org/yt_analysis/yt/issue/592/fields-that-combine-deposite… Nathan Goldbaum: This was exposed on an enzo-3.0 dataset, but I've reproduced it using IsolatedGalaxy. One minor note: the yt-3.0 `TotalMass` field still depends on `Dark_Matter_Density`. I can't remember if we merged from yt-2.6dev before that was patched so this might not be a merge error, but I suspect it is. In any case, the `Matter_Density` correctly uses `particle_density`, so I've used it below: ``` #!python $ yt plot -a 2 -w 25 -u kpc -f Matter_Density IsolatedGalaxy/galaxy0030/galaxy0030 yt : [INFO ] 2013-06-12 18:42:33,994 Parameters: current_time = 0.00600002000283 yt : [INFO ] 2013-06-12 18:42:33,994 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2013-06-12 18:42:33,995 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-06-12 18:42:33,995 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-06-12 18:42:33,996 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2013-06-12 18:42:33,996 Adding plot for axis 2 Parsing Hierarchy100% |||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt : [INFO ] 2013-06-12 18:42:34,018 Gathering a field list (this may take a moment.) yt : [INFO ] 2013-06-12 18:42:34,031 Adding unknown field SFR_Density to list of fields yt : [INFO ] 2013-06-12 18:42:34,031 Adding unknown field Forming_Stellar_Mass_Density to list of fields yt : [INFO ] 2013-06-12 18:42:34,031 Adding unknown field Galaxy1Colour to list of fields yt : [INFO ] 2013-06-12 18:42:34,031 Adding unknown field kphHeI to list of fields yt : [INFO ] 2013-06-12 18:42:34,031 Adding unknown field MBHColour to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field Phi_pField to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field Galaxy2Colour to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field Average_creation_time to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field gammaHI to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field kphHI to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field kphHeII to list of fields yt : [INFO ] 2013-06-12 18:42:34,032 Adding unknown field Star_Particle_Density to list of fields yt : [INFO ] 2013-06-12 18:42:34,036 Adding unknown field PhiField to list of fields Traceback (most recent call last): File "/usr/local/share/python/yt", line 9, in <module> load_entry_point('yt==3.0dev', 'console_scripts', 'yt')() File "/Users/goldbaum/Documents/yt-3.0/yt/utilities/command_line.py", line 1691, in run_main args.func(args) File "/Users/goldbaum/Documents/yt-3.0/yt/utilities/command_line.py", line 97, in run self(args) File "/Users/goldbaum/Documents/yt-3.0/yt/utilities/command_line.py", line 1319, in __call__ width=width) File "/Users/goldbaum/Documents/yt-3.0/yt/visualization/plot_window.py", line 1246, in __init__ slc.get_data(fields) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 521, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 537, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 226, in _generate_field return self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 242, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/field_info_container.py", line 482, in __call__ dd = self._function(self, data) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/universal_fields.py", line 411, in _Matter_Density return (data['Density'] + data['particle_density']) TypeError: unsupported operand type(s) for +: 'NoneType' and 'float' ``` I put a breakpoint inside `_Matter_Density` and It looks like an exception is raised when yt attempts to retrieve `particle_density` during field detection. This exception is never raised to the user level (see #589) so execution proceeds normally. When the field is finally called by the script, 'Density' is returned as `None`, I guess since the field detection didn't finish properly. Responsible: MatthewTurk

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Issue #591: HI Density for RAMSES? (yt_analysis/yt)
by Kyle Stewart 10 Jun '13

10 Jun '13

New issue 591: HI Density for RAMSES? https://bitbucket.org/yt_analysis/yt/issue/591/hi-density-for-ramses Kyle Stewart: I will probably be doing a lot of testing of RAMSES functionality in the near future, with the added Ramses support features available in 3.0. One of the first things I've noticed is that there is no HI_Density field for RAMSES files. I'm not sure how much work is required to set one up, but this would be a great thing to have.

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Issue #590: Orientation arrows for volume rendering (yt_analysis/yt)
by Erik Rosolowsky 10 Jun '13

10 Jun '13

New issue 590: Orientation arrows for volume rendering https://bitbucket.org/yt_analysis/yt/issue/590/orientation-arrows-for-volum… Erik Rosolowsky: In my recent experience using yt, it was difficult to construct a sample set of axes that orient the volume render with respect to the original coordinate axes of the data set in question. This feature is particularly useful for rendering observational data. I tried implementing this through a series of draw_box, but it wasn't of the quality that the rest of the yt was producing. ``` #!python x0 = np.array([0.4,0.7,0.5]) dx = np.array([0.05,0.0,0.0]) camera.draw_box(image,x0,x0+dx,color=np.array([1.,1.,1.,1.0])) ``` Requests from my collaborators included both clearer lines, with arrow heads and the ability to render text along the arrows. Responsible: samskillman

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Issue #589: Field detection catches all exceptions raised by broken fields (yt_analysis/yt)
by Nathan Goldbaum 07 Jun '13

07 Jun '13

New issue 589: Field detection catches all exceptions raised by broken fields https://bitbucket.org/yt_analysis/yt/issue/589/field-detection-catches-all-… Nathan Goldbaum: Right now yt-3.0 field detection catches all exception raised during field discovery. This happens on line 190 of `geometry_handler.py` in the 3.0a2 release. We should only catch exceptions that indicate that a field isn't available for the dataset (e.g. `YTFieldNotFound`) and let all other exceptions, indicating that a field is broken somehow, continue to be elevated. Once this is fixed, a user will immediately know that a newly created field that contains a bug is broken, since an exception will be raised during field detection.

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Issue #588: annotate_contour on only half the image (yt_analysis/yt)
by Kyle Stewart 07 Jun '13

07 Jun '13

New issue 588: annotate_contour on only half the image https://bitbucket.org/yt_analysis/yt/issue/588/annotate_contour-on-only-hal… Kyle Stewart: I came across a curious bug where I was looking at a SlicePlot and using annotate_contour to add density contours on top of the plot. When zoomed pretty far out, everything works fine, but when I began to zoom in on the galaxy in my simulation, the contours stopped displaying correctly, and began to only display on *exactly* half the image (the left half). Code: ``` #!python p=SlicePlot(pf, 2, ["Density", "HI_Density", "Temperature"], center=center, width=(500,'kpc')) p.annotate_contour("Density") p.save("test1") p.set_width(140,'kpc') p.save("test2") ``` I thought maybe it would help to call p.annotate_contour("Density") again after re-setting the width, but that doesn't accomplish anything. I've included the resulting images.

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Issue #587: OffAxisSlicePlot annote_velocity (yt_analysis/yt)
by Kyle Stewart 07 Jun '13

07 Jun '13

New issue 587: OffAxisSlicePlot annote_velocity https://bitbucket.org/yt_analysis/yt/issue/587/offaxissliceplot-annote_velo… Kyle Stewart: When I try to use annotate_velocity on the SlicePlot command it works fine, as before, but I get an error when I try to use it with the OffAxisSlicePlot command: The code I'm using is: ``` #!python gal=pf.h.sphere(center, 10.0/pf['kpc']) Lgal = gal.quantities["AngularMomentumVector"]() p=SlicePlot(pf, 2, ["Density", "HI_Density", "Temperature"], center=center, width=(140,'kpc')) p.annotate_velocity(factor=32) p.save("test") p=OffAxisSlicePlot(pf, Lgal, ["Density", "HI_Density", "Temperature"], center=center, width=(140,'kpc')) p.annotate_velocity(factor=32) p.save("test") ``` The SlicePlot part works fine. The error I get for the OffAxisSlicePlot is: ``` #!python In [347]: p.annotate_velocity(factor=32) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/scripts/iyt in <module>() ----> 1 p.annotate_velocity(factor=32) /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.py in newfunc(*args, **kwargs) 97 rv = f(*args, **kwargs) 98 args[0]._plot_valid = False ---> 99 args[0]._setup_plots() 100 return rv 101 return newfunc /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.py in _setup_plots(self) 956 label.set_fontproperties(fp) 957 --> 958 self.run_callbacks(f) 959 960 self._plot_valid = True /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_window.py in run_callbacks(self, f) 966 CallbackMaker = callback_registry[name] 967 callback = CallbackMaker(*args[1:], **kwargs) --> 968 callback(cbw) 969 for key in self._frb.keys(): 970 if key not in keys: /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_modifications.py in __call__(self, plot) 132 yv = "%s-velocity" % (y_names[plot.data.axis]) 133 qcb = QuiverCallback(xv, yv, self.factor, scale=self.scale, scale_units=self.scale_units, normalize=self.normalize) --> 134 return qcb(plot) 135 136 class MagFieldCallback(PlotCallback): /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/visualization/plot_modifications.py in __call__(self, plot) 629 plot.data['pdx'], plot.data['pdy'], plot.data['pdz'], 630 plot.data.center, plot.data._inv_mat, indices, --> 631 plot.data[self.field_x], 632 int(nx), int(ny), 633 (x0, x1, y0, y1),).transpose() /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/data_containers.py in __getitem__(self, key) 198 return self.field_data[f] 199 else: --> 200 self.get_data(f) 201 return self.field_data[f] 202 /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/data_containers.py in get_data(self, fields) 505 self.field_data.update(read_particles) 506 fields_to_generate = gen_fluids + gen_particles --> 507 self._generate_fields(fields_to_generate) 508 509 def _generate_fields(self, fields_to_generate): /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/data_containers.py in _generate_fields(self, fields_to_generate) 515 if field in self.field_data: continue 516 try: --> 517 self.field_data[field] = self._generate_field(field) 518 except GenerationInProgress as gip: 519 for f in gip.fields: /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/data_containers.py in _generate_field(self, field) 224 return self._generate_particle_field(field) 225 else: --> 226 return self._generate_fluid_field(field) 227 228 def _generate_fluid_field(self, field): /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/data_containers.py in _generate_fluid_field(self, field) 240 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 241 else: --> 242 rv = finfo(gen_obj) 243 return rv 244 /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/field_info_container.py in __call__(self, data) 478 ii = self.check_available(data) 479 original_fields = data.keys() # Copy --> 480 dd = self._function(self, data) 481 if dd is not None: 482 dd *= self._convert_function(data) /Users/kstewart/code/yt-3.0/yt-x86_64/src/yt-3.0-hg/yt/data_objects/universal_fields.py in _CuttingPlaneVelocityX(field, data) 886 bulk_velocity = np.zeros(3) 887 v_vec = np.array([data["%s-velocity" % ax] for ax in 'xyz']) \ --> 888 - bulk_velocity[...,np.newaxis] 889 return np.dot(x_vec, v_vec) 890 add_field("CuttingPlaneVelocityX", TypeError: unsupported operand type(s) for -: 'NoneType' and 'float' ```

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Issue #586: YT Dynamic Linking Error on SUSE (yt_analysis/yt)
by john_regan 06 Jun '13

06 Jun '13

New issue 586: YT Dynamic Linking Error on SUSE https://bitbucket.org/yt_analysis/yt/issue/586/yt-dynamic-linking-error-on-… john_regan: YT fails to link against it's own local copy of the libpng16.so.16 library successfully at runtime. The initial error is ImportError: libpng16.so.16: cannot open shared object file: No such file or directory Adding the YT path to LD_LIBRARY_PATH fixes this error but shows another error subsequently Instead YT links against the system png library causing a runtime error. ImportError: .../yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so: undefined symbol: png_set_longjmp_fn This is because of a dynamic linking error. ldd shows that _png.so is dynamically linking again the system png library libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007fffbfb56000) Setting LD_PRELOAD to point to YT's copy of the libpng.so.16.so fixes the issue. A fix in the install script for SUSE may be needed to avoid this workaround.

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yt-dev June 2013