yt volume render/AMRKDtree help
by Renyue Cen
Hi,
I did some simple volume rendering with the following script:
volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"],
no_ghost=False, tree_type="domain",
le=c-0.5*WW, re=c+0.5*WW)
cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False,
north_vector=L, steady_north=True)
cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j))
I got rather strange results in that the pictures look symmetric, which I am pretty
sure can not be true.
I attach the obtained plot.
Note that I am using KD tree and using 32 cores.
Your help at your earliest convenience is appreciated.
Best,
Renyue
5 years, 7 months
Re: [yt-users] slice plot
by stefano bovino
Hi Kacper,
my minimal resolution is less than 1 AU, the problem seems more related to
the Matt's issue.
The script is the same as in the yt website, here the link:
http://yt-project.org/doc/cookbook/multi_plot_slice_and_proj.py
the output of pf.h.find_max("Density") :
(1.139355201341093e-11, array([ 0.49722083, 0.50645245, 0.49492896]))
Thanks
Stefano
---------- Forwarded message ----------
From: Kacper Kowalik <xarthisius.kk(a)gmail.com>
Date: Mon, Apr 29, 2013 at 1:35 PM
Subject: Re: [yt-users] slice plot
To: yt-users(a)lists.spacepope.org
On 04/29/2013 01:22 PM, stefano bovino wrote:
> Hi all,
> when using the following script fromt the yt.project website
> multi_plot_slice_and_proj.py<
http://yt-project.org/doc/cookbook/multi_plot_slice_and_proj.py>I
> have problems if I change the resolution from mpc to pc.
>
> slc_frb = slc.to_frb((1.0, "mpc"), 512) --> slc_frb = slc.to_frb((1.0,
> "pc"), 512)
>
> I even tried other ways (or scripts) to plot a slice of the density
> changing the resolution, but the problem is still there. Do you have any
> solution?
>
> I just would like to create a 9 panels plot with slice of density, H2, and
> Temperature with three different width (on the pc scale).
Hi Stefano,
what is the size of your computational domain or size of the smallest
cell you have? You can obtain that information using:
yt stats output_filename
Cheers,
Kacper
5 years, 11 months
slice plot
by stefano bovino
Hi all,
when using the following script fromt the yt.project website
multi_plot_slice_and_proj.py<http://yt-project.org/doc/cookbook/multi_plot_slice_and_proj.py>I
have problems if I change the resolution from mpc to pc.
slc_frb = slc.to_frb((1.0, "mpc"), 512) --> slc_frb = slc.to_frb((1.0,
"pc"), 512)
I even tried other ways (or scripts) to plot a slice of the density
changing the resolution, but the problem is still there. Do you have any
solution?
I just would like to create a 9 panels plot with slice of density, H2, and
Temperature with three different width (on the pc scale).
Thank you in advance.
5 years, 11 months
phase objects in the modern era
by David Collins
Hi, all--
I'm running into problems making phase objects. It looks like the error is
in the color bar, and is similar to other errors I get when trying to use
PlotCollections. The hash I'm on is 34b95297062b. I'm trying:
pf = load(fname)
pc = PlotCollection(pf,'c')
phase=pc.add_phase_object(pf.h.all_data(),['CellMass',
'x-velocity','CellVolume'],weight=None)
min/max are as follows:
CellMass: [4.1e-12,1.5e-03] (30631133,)
x-velocity: [-7.2e+01,5.5e+01]
CellVolume: [1.45e-11,6.0e-08]
Is there a more up-to-date manner to do this that doesn't use
PlotCollection? Or is there something obvious that I'm missing?
It seems to be choking in plot_types.py/__init_colorbar
def __init_colorbar(self):
temparray = np.ones((self.x_bins.size, self.y_bins.size))
self.norm = matplotlib.colors.Normalize()
self.image = self._axes.pcolormesh(self.x_bins, self.y_bins,
temparray, shading='flat',
norm=self.norm, cmap=self.cmap,
rasterized=True)
self.colorbar = self._figure.colorbar(self.image,
extend='neither', shrink=0.95,
format="%0.2e" )
It looks like what's happening is figure.colorbar chokes on the fact that
temparray is "ones", so the spacing between elements is zero. This is
outside of my yt knowledge, though.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "p14_phase_test.py", line 4, in <module>
phase=pc.add_phase_object(pf.h.all_data(),['CellMass','x-velocity','CellVolume'])
File
"/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py",
line 1184, in add_phase_object
figure=figure, axes=axes))
File
"/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py",
line 815, in __init__
self.__init_colorbar()
File
"/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py",
line 834, in __init_colorbar
format="%0.2e" )
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py",
line 1387, in colorbar
cb = cbar.colorbar_factory(cax, mappable, **kw)
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 1173, in colorbar_factory
cb = Colorbar(cax, mappable, **kwargs)
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 854, in __init__
ColorbarBase.__init__(self, ax, **kw)
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 298, in __init__
self.draw_all()
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 323, in draw_all
self._config_axes(X, Y)
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 409, in _config_axes
self.update_ticks()
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 345, in update_ticks
ticks, ticklabels, offset_string = self._ticker()
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 560, in _ticker
ticks = self._locate(b)
File
"/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 808, in _locate
z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db
FloatingPointError: invalid value encountered in divide
5 years, 11 months
problem with zoom slice plot
by Latif
Hi all,
I am trying to create a simple slice plot for the central 1 pc of a
simulation box of size 1 mpc using the following simplest script.
Problem occurs when I set plot width as can be seen in attached plot. I
tried stable version of yt as well development fork but did not get any
success. Slice works well without any problem if I use pc.add_slice
method. Any ideas what is going wrong here.
thanks in advance,
Cheers
Latif
SlicePlot(pf, 'x', "Density", width = (800.0, 'kpc')).save()
5 years, 11 months
Setting zlim
by david collins
Hi, all--
I'm trying to set the color map and extents for some plots, but it doesn't
seem to be taking: If I do
field= 'Density'
proj = pf.h.proj(ax,field,source=cut_region)
pw = proj.to_pw()
pw.set_cmap('Density','gray')
pw.set_zlim = [0.1,50]
pw.save('wtfc.png')
pp = ProjectionPlot(pf,0,'Density')
pp.set_cmap('Density','gray')
pp.set_zlim = [0.1,50]
pp.save('wtfd.png')
the two plots should have the same range on the color map, but they don't.
I tried calls to "refresh" n both pp and pw, but that didn't help. What
am I missing?
d.
--
Sent from my computer.
5 years, 11 months
cut region vs. projection?
by David Collins
Hi, all--
Can I hand a cut_region to a projection?
I want to make a bunch of projections based on parameters, and don't want
to have to instantiate 47 different fields. I'm hoping something like
region = pf.h.all_data().cut_region('grid["Density"] > 0.1 and
grid["Density"] < 0.2')
proj = pf.h.proj(0,"Density",region=cut_region)
or something like that. Is that possible? I'm poking around the help and
source, but no method immediately popped out at me.
Thanks,
d.
5 years, 11 months
cannot find some particle fields
by Jean-Claude Passy
Hi all,
sorry, I have a pretty dumb question.
I have a non-cosmological simulation with only 1 particle. I can get the particle_mass field, but yt throws the following error when I try to grab particle_index:
---------------------------------------------------------------------------------------------------------------------------------
In [1]: pf = load('CE0001')
yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: current_time = 0.00149998503444
yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: domain_dimensions = [32 32 32]
yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: domain_left_edge = [ 0. 0. 0.]
yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: domain_right_edge = [ 1. 1. 1.]
yt : [INFO ] 2013-04-24 00:32:02,191 Parameters: cosmological_simulation = 0.0
In [2]: region = pf.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
yt : [INFO ] 2013-04-24 00:32:05,802 Getting the binary hierarchy
yt : [INFO ] 2013-04-24 00:32:05,805 Finished with binary hierarchy reading
In [3]: region['particle_mass']
yt : [INFO ] 2013-04-24 00:32:12,685 Getting particle_mass using ParticleIO
Out[3]: array([ 6585896.1408])
In [4]: region['particle_index']
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/scripts/iyt in <module>()
----> 1 region['particle_index']
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)
328 if key not in self.fields:
329 self.fields.append(key)
--> 330 self.get_data(key)
331 return self.field_data[key]
332
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids, force_particle_read)
2614 pass
2615 if field not in self.hierarchy.field_list and not in_grids:
-> 2616 if self._generate_field(field):
2617 continue # True means we already assigned it
2618 mylog.info("Getting field %s from %s", field, len(self._grids))
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field)
361 return True
362 else: # Can't find the field, try as it might
--> 363 raise KeyError(field)
364
365 def _generate_field_in_grids(self, field, num_ghost_zones=0):
KeyError: 'particle_index'
---------------------------------------------------------------------------------------------------------------------------------
However, the field is there:
---------------------------------------------------------------------------------------------------------------------------------
[ 0:30:13] Obiwan:$ h5ls CE0001.cpu0000/Grid00000004
Dark_Matter_Density Dataset {52, 52, 52}
Density Dataset {52, 52, 52}
TotalEnergy Dataset {52, 52, 52}
particle_index Dataset {1}
particle_mass Dataset {1}
particle_position_x Dataset {1}
particle_position_y Dataset {1}
particle_position_z Dataset {1}
particle_type Dataset {1}
particle_velocity_x Dataset {1}
particle_velocity_y Dataset {1}
particle_velocity_z Dataset {1}
x-velocity Dataset {52, 52, 52}
y-velocity Dataset {52, 52, 52}
z-velocity Dataset {52, 52, 52}
[ 0:30:13] Obiwan:$ h5ls -d CE0001.cpu0000/Grid00000004/particle_index
particle_index Dataset {1}
Data:
(0) 0
---------------------------------------------------------------------------------------------------------------------------------
Am I missing something obvious?
Thanks a lot for you help,
JC
5 years, 11 months
SlicePlot y-axis problem
by Caroline Van Borm
Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any
data, for any field. yt just hangs and no plot is created. For the x-
and z-axes everything works fine, and a ProjectionPlot along the y-axis
is also not a problem.
I have tried updating yt and installing the current development version,
but to no avail.
Any help is much appreciated!
Best regards,
Caroline
5 years, 11 months
