using yt for non-spatial data
Hello yt-users, I saw a yt presentation at the Python Astronomy Meeting and am interested to see if yt could be used for non-spatial data. My specific problem is MCMC chains in 19 (or up to 23) dimensional parameter space in which none of the parameters are nuisance parameters. I thought yt could be used to visualize and analyze such data. I tried to load the chain as particles and managed to do so, but am having problems plotting. I pasted the code below. Has anyone used yt for non-spatial data? Cheers, Carolin ----------- In [81]: mcchain.keys() ## a dictionary containing dimensions of the chain Out[81]: ['particle_position_z', 'particle_mass', 'particle_position_x', 'particle_position_y', 'qso'] In [82]: mcyt = yt.load_particles(mcchain) yt : [INFO ] 2015-04-23 09:47:39,235 Parameters: current_time = 0.0 yt : [INFO ] 2015-04-23 09:47:39,235 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2015-04-23 09:47:39,237 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2015-04-23 09:47:39,237 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2015-04-23 09:47:39,238 Parameters: cosmological_simulation = 0.0 In [83]: circle = mcyt.sphere([0.5, 0.5, 0.5], 0.25) yt : [INFO ] 2015-04-23 09:47:45,741 Allocating for 1.000e+04 particles yt : [INFO ] 2015-04-23 09:47:45,763 Identified 7.130e+02 octs yt : [INFO ] 2015-04-23 09:47:45,897 Loading field plugins. yt : [INFO ] 2015-04-23 09:47:45,898 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-04-23 09:47:45,898 Loaded astro (15 new fields) yt : [INFO ] 2015-04-23 09:47:45,898 Loaded cosmology (22 new fields) yt : [INFO ] 2015-04-23 09:47:45,899 Loaded fluid (64 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded geometric (112 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded local (112 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded my_plugins (120 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded species (122 new fields) In [84]: pl=yt.ProjectionPlot(circle, 'x', 'y') --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-84-685c784708ec> in <module>() ----> 1 pl=yt.ProjectionPlot(circle, 'x', 'y') /Users/cvillforth/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in __init__(self, ds, axis, fields, center, width, axes_unit, weight_field, max_level, origin, fontsize, field_parameters, data_source, method, proj_style, window_size, aspect) 1212 self.ts = ts 1213 ds = self.ds = ts[0] -> 1214 axis = fix_axis(axis, ds) 1215 # proj_style is deprecated, but if someone specifies then it trumps 1216 # method. /Users/cvillforth/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/yt/funcs.pyc in fix_axis(axis, ds) 649 650 def fix_axis(axis, ds): --> 651 return ds.coordinates.axis_id.get(axis, axis) 652 653 def get_image_suffix(name): AttributeError: 'YTSphere' object has no attribute 'coordinates' -------------------------------------------------------------------------------- Dr Carolin Villforth SUPA Advanced Fellow University of St Andrews (SUPA) School of Physics & Astronomy North Haugh, St Andrews, Fife KY16 9SS UK cv21@st-andrews.ac.uk Office: 272 phone +44 (0) 1334 46 1612 http://www-star.st-and.ac.uk/~cv21/cv21/Home.html -------------------------------------------------------------------------------- _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Carolin,
The first argument to ProjectionPlot should be a dataset object and not a
data container. Can you try this instead:
pl=yt.ProjectionPlot(*mcyt*, 'x', 'y')
Additionally, if you want to project just the values in the sphere, you can
try this:
pl=yt.ProjectionPlot(*mcyt*, 'x', 'y', data_source=circle)
You're a pioneer in unexplored territory here, so please let us know how it
goes!
Britton
On Thu, Apr 23, 2015 at 10:56 AM, Carolin Villforth
Hello yt-users,
I saw a yt presentation at the Python Astronomy Meeting and am interested to see if yt could be used for non-spatial data. My specific problem is MCMC chains in 19 (or up to 23) dimensional parameter space in which none of the parameters are nuisance parameters. I thought yt could be used to visualize and analyze such data. I tried to load the chain as particles and managed to do so, but am having problems plotting. I pasted the code below.
Has anyone used yt for non-spatial data?
Cheers,
Carolin
-----------
In [81]: mcchain.keys() ## a dictionary containing dimensions of the chain Out[81]: ['particle_position_z', 'particle_mass', 'particle_position_x', 'particle_position_y', 'qso']
In [82]: mcyt = yt.load_particles(mcchain) yt : [INFO ] 2015-04-23 09:47:39,235 Parameters: current_time = 0.0 yt : [INFO ] 2015-04-23 09:47:39,235 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2015-04-23 09:47:39,237 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2015-04-23 09:47:39,237 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2015-04-23 09:47:39,238 Parameters: cosmological_simulation = 0.0
In [83]: circle = mcyt.sphere([0.5, 0.5, 0.5], 0.25) yt : [INFO ] 2015-04-23 09:47:45,741 Allocating for 1.000e+04 particles yt : [INFO ] 2015-04-23 09:47:45,763 Identified 7.130e+02 octs yt : [INFO ] 2015-04-23 09:47:45,897 Loading field plugins. yt : [INFO ] 2015-04-23 09:47:45,898 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-04-23 09:47:45,898 Loaded astro (15 new fields) yt : [INFO ] 2015-04-23 09:47:45,898 Loaded cosmology (22 new fields) yt : [INFO ] 2015-04-23 09:47:45,899 Loaded fluid (64 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded geometric (112 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded local (112 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded my_plugins (120 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded species (122 new fields)
In [84]: pl=yt.ProjectionPlot(circle, 'x', 'y') --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-84-685c784708ec> in <module>() ----> 1 pl=yt.ProjectionPlot(circle, 'x', 'y')
/Users/cvillforth/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in __init__(self, ds, axis, fields, center, width, axes_unit, weight_field, max_level, origin, fontsize, field_parameters, data_source, method, proj_style, window_size, aspect) 1212 self.ts = ts 1213 ds = self.ds = ts[0] -> 1214 axis = fix_axis(axis, ds) 1215 # proj_style is deprecated, but if someone specifies then it trumps 1216 # method.
/Users/cvillforth/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/yt/funcs.pyc in fix_axis(axis, ds) 649 650 def fix_axis(axis, ds): --> 651 return ds.coordinates.axis_id.get(axis, axis) 652 653 def get_image_suffix(name):
AttributeError: 'YTSphere' object has no attribute 'coordinates'
-------------------------------------------------------------------------------- Dr Carolin Villforth SUPA Advanced Fellow University of St Andrews (SUPA) School of Physics & Astronomy North Haugh, St Andrews, Fife KY16 9SS UK cv21@st-andrews.ac.uk Office: 272 phone +44 (0) 1334 46 1612 http://www-star.st-and.ac.uk/~cv21/cv21/Home.html
--------------------------------------------------------------------------------
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participants (2)
-
Britton Smith -
Carolin Villforth