Dear yt:
I am plotting streamlines using yt and I want to make it look "nicer". Something like the outward moving wave has different color scheme. I am not sure how to play around with color scheme.
Any suggestions? Link to the movie and script is below
Thanks in advance
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Dear yt:
I am plotting streamlines using yt and I want to make it look "nicer".
Something like the outward moving wave has different color scheme. I am not
sure how to play around with color scheme.
Any suggestions? Link to the movie and script is below
Thanks in advance
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
--
*SK2*
*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
Einstein.**"*
Dear YT users,
I ran into a problem with hdf5 on lustre file systems after a recent
update (check file system with df -Tvh). The binaries h5ls, h5dump etc
were not able to load files, neither yt/python via the python interface.
I found out that hdf5 version 1.10 has problems with (at leat our)
lustre file system
downgrading hdf to version 1.8.18
$> conda install hdf5=1.8.18
solved the hdf5 problem and brought up the recursion problem that Travis
Thieme reported earlier.
$> conda install numpy=1.13.3
did the job for me!
Cheers,
Philipp
Hello everyone,
I’m a new user of yt and I’ve been encountering a problem when trying to make a SlicePlot of some ALMA data I have been working with. I’m also not sure what the best way to format these emails are, but I’ll include as mush detail as I can.
Basically, when using SlicePlot, I get this error —> RecursionError: maximum recursion depth exceeded
Here’s some info about what I’m using:
- Python version: 3.6.4
- yt version: 3.3.5
- jupyter version: 4.4.0
My four lines of code are:
import yt
ds = yt.load(‘data.fits', nan_mask=0.0, z_axis_decomp=True)
slc = yt.SlicePlot(ds, "z", ["Intensity"], origin="native")
slc.show()
And I get the following error:
---------------------------------------------------------------------------
RecursionError Traceback (most recent call last)
<ipython-input-9-46c5ac6a89f9> in <module>()
----> 1 slc = yt.SlicePlot(ds, "z", ["Intensity"], origin="native")
2 slc.show()
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in SlicePlot(ds, normal, fields, axis, *args, **kwargs)
1911 del kwargs['north_vector']
1912
-> 1913 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in __init__(self, ds, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters, window_size, aspect, data_source)
1265 PWViewerMPL.__init__(self, slc, bounds, origin=origin,
1266 fontsize=fontsize, fields=fields,
-> 1267 window_size=window_size, aspect=aspect)
1268 if axes_unit is None:
1269 axes_unit = get_axes_unit(width, ds)
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in __init__(self, *args, **kwargs)
636 self._plot_type = kwargs.pop("plot_type")
637 self._splat_color = kwargs.pop("splat_color", None)
--> 638 PlotWindow.__init__(self, *args, **kwargs)
639
640 def _setup_origin(self):
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in __init__(self, data_source, bounds, buff_size, antialias, periodic, origin, oblique, window_size, fields, fontsize, aspect, setup)
215 self._field_transform[field] = linear_transform
216 self.setup_callbacks()
--> 217 self._setup_plots()
218
219 def _initialize_dataset(self, ts):
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in _setup_plots(self)
705 return
706 if not self._data_valid:
--> 707 self._recreate_frb()
708 self._data_valid = True
709 self._colorbar_valid = True
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in _recreate_frb(self)
276 # At this point the frb has the valid bounds, size, aliasing, etc.
277 if old_fields is None:
--> 278 self._frb._get_data_source_fields()
279 else:
280 # Restore the old fields
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in _get_data_source_fields(self)
160 for f in fields:
161 if f not in exclude and f[0] not in self.data_source.ds.particle_types:
--> 162 self[f]
163
164 def _is_ion( self, fname ):
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in __getitem__(self, item)
147 # self._period, int(self.periodic)
148 ia = ImageArray(buff, input_units=self.data_source[item].units,
--> 149 info=self._get_info(item))
150 self.data[item] = ia
151 return self.data[item]
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in _get_info(self, item)
198 ftype, fname = field = self.data_source._determine_fields(item)[0]
199 finfo = self.data_source.ds._get_field_info(*field)
--> 200 info['data_source'] = self.data_source.__str__()
201 info['axis'] = self.data_source.axis
202 info['field'] = str(item)
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/data_objects/data_containers.py in __repr__(self)
943 for i in self._con_args:
944 try:
--> 945 s += ", %s=%s" % (i, getattr(self, i).in_base(unit_system=self.ds.unit_system))
946 except AttributeError:
947 s += ", %s=%s" % (i, getattr(self, i))
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/units/yt_array.py in __str__(self)
453
454 """
--> 455 return super(YTArray, self).__str__()+' '+self.units.__str__()
456
457 #
~/miniconda3/envs/astro36/lib/python3.6/site-packages/numpy/core/arrayprint.py in array_str(a, max_line_width, precision, suppress_small)
1398 # in quotes. So we return the str of the scalar value.
1399 if a.shape == ():
-> 1400 return str(a[()])
1401
1402 return array2string(a, max_line_width, precision, suppress_small, ' ', "")
... last 2 frames repeated, from the frame below ...
~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/units/yt_array.py in __str__(self)
453
454 """
--> 455 return super(YTArray, self).__str__()+' '+self.units.__str__()
456
457 #
RecursionError: maximum recursion depth exceeded
I’m following the tutorial on the yt website called FITS Radio Cubes in yt (http://yt-project.org/doc/cookbook/fits_radio_cubes.html <http://yt-project.org/doc/cookbook/fits_radio_cubes.html>). I’ve tried uninstalling yt and reinstalling. I should add that I was able to make the plot before with no problems, it was only after I updated my python packages I started to receive this error. Any help is appreciated. Thank you.
Best Regards,
Travis Thieme
Graduate Student
Institute of Astronomy
National Tsing Hua University
Hi all,
I am concerned about the velocity unit when yt reads EAGLE simulation.
To convert the on-disk peculiar velocity (call this raw_velocity) to a physical velocity [cm/s]:
physical velocity [cm/s] = raw_velocity * sqrt(a) * 1e5
When I specify: ad['PartType0','Velocity'].in_units('km/s')
The output says it is in km/s, so I would expect this is the physical velocity.
However, the output actually does not multiply the raw_velocity by sqrt(a)
Looking at the source code (and its comments), I am not sure if this is intentional, or is this sqrt(a) accidentally missed out.
https://github.com/yt-project/yt/blob/master/yt/frontends/gadget/data_str...
Line 490-499
A possibly relevant discussion (several years ago) with Gadget using yt (this is now fixed):
https://bitbucket.org/yt_analysis/yt/pull-requests/1710/gadget-cosmology-...
So, does yt intentionally not to multiply the velocity unit by sqrt(a) factor, or is the factor accidentally missed out?
This could be confusing for relative new users like myself. Apologize if this is well known for experts.
Thanks,
Stephanie
Hi,
I am working on data from ramses and I have the following output files from
my simulations:
amr
grav
hydro
part and
info.txt
However, when I try to make projection plots, I am obtaining the error:
FutureWarning: Conversion of the second argument of issubdtype from `float`
> to `np.floating` is deprecated. In future, it will be treated as
> `np.float64 == np.dtype(float).type`.
>
> from ._conv import register_converters as _register_converters
>
> yt : [INFO ] 2018-01-19 16:31:46,982 Parameters: current_time
> = 0.254337758876396
>
> yt : [INFO ] 2018-01-19 16:31:46,982 Parameters: domain_dimensions
> = [32 32 32]
>
> yt : [INFO ] 2018-01-19 16:31:46,983 Parameters: domain_left_edge
> = [0. 0. 0.]
>
> yt : [INFO ] 2018-01-19 16:31:46,983 Parameters: domain_right_edge
> = [1. 1. 1.]
>
> yt : [INFO ] 2018-01-19 16:31:46,983 Parameters:
> cosmological_simulation = 0
>
> Traceback (most recent call last):
>
> File "pyt.py", line 11, in <module>
>
> p = yt.ProjectionPlot(ds, "x", "density")
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py",
> line 1441, in __init__
>
> validate_mesh_fields(test_data_source, fields)
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py",
> line 132, in validate_mesh_fields
>
> canonical_fields = data_source._determine_fields(fields)
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/data_objects/data_containers.py",
> line 1127, in _determine_fields
>
> finfo = self.ds._get_field_info("unknown", fname)
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/data_objects/static_output.py",
> line 711, in _get_field_info
>
> self.index
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/data_objects/static_output.py",
> line 504, in index
>
> self, dataset_type=self.dataset_type)
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py",
> line 357, in __init__
>
> super(RAMSESIndex, self).__init__(ds, dataset_type)
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/geometry/geometry_handler.py",
> line 50, in __init__
>
> self._setup_geometry()
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/geometry/oct_geometry_handler.py",
> line 25, in _setup_geometry
>
> self._initialize_oct_handler()
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py",
> line 361, in _initialize_oct_handler
>
> for i in range(self.dataset['ncpu'])]
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py",
> line 361, in <listcomp>
>
> for i in range(self.dataset['ncpu'])]
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py",
> line 67, in __init__
>
> self._read_amr_header()
>
> File
> "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py",
> line 191, in _read_amr_header
>
> hvals.update(fpu.read_attrs(f, header))
>
> File
> "/Users/samhitha/Documents/yt-conda/lib/python3.6/site-packages/yt/utilities/fortran_utils.py",
> line 86, in read_attrs
>
> assert(s1 == s2)
>
> AssertionError
>
I tried specifying the fields externally using:
ds =
> yt.load("/Users/xxxx/SIM001/output_00002/info_00002.txt",fields=["density",
> "velocity_x", "velocity_y", "velocity_z", "thermal_pressure", "var6",
> "var7"])
>
p = yt.ProjectionPlot(ds, "x", "density")
PS: Rebooting the system didn't work in my case. Any help is greatly
appreciated.
Hi Suoqing and all,
I tried following the examples for projection generation that are shown in
the yt manual but my plots are still not coming out as desired. The first
three plots I have plotted are indicated below. Plots for checkpoints 1 and
2 are fine but checkpoint 3 and others that follow are coming out as either
extreme zoomed in or distorted. Any ideas how I might correct this?
Thank you,
Kezman
1st checkpoint 2nd checkpoint
3rd checkpoint
[image: Inline image 4] [image: Inline image 2] [image: Inline
image 1]
Kezman Saboi
Barrett Honors College|Arizona State University
Astrophysics
Phone|480-819-5031
On Thu, Jan 4, 2018 at 12:39 AM, <yt-users-request(a)lists.spacepope.org>
wrote:
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> Today's Topics:
>
> 1. Re: Tracking a blob (Suoqing Ji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Jan 2018 13:49:45 -0800
> From: Suoqing Ji <suoqing(a)physics.ucsb.edu>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Tracking a blob
> Message-ID: <4D51786E-22B3-4F62-938E-A6CE8B2387F9(a)physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Kezman,
>
> ?origin? specifies the axis and your plot domain, and what you?re looking
> for is the ?center? parameter, and provide the coordinates of the blob to
> the parameter ?center?. You can find some similar SlicePlot examples with a
> specified plot center here: http://yt-project.org/docs/
> dev/visualizing/plots.html#slice-plots <http://yt-project.org/docs/
> dev/visualizing/plots.html#slice-plots>
>
> Best wishes,
> ?
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://physics.ucsb.edu/~suoqing
>
> > On Jan 3, 2018, at 12:30 PM, Kezman Saboi <ksaboi(a)asu.edu> wrote:
> >
> > Hi,
> >
> > I am trying to create projections of a blob (a gas cloud) that is in
> motion but I keep on having problems with plotting it such that it is at
> the center of the plot. I have tried using origin = 'native' but it does
> not seem to be helping. Could anyone please offer guidance?
> >
> >
> > Thank you,
> >
> >
> > Kezman Saboi
> > Barrett Honors College|Arizona State University
> > Astrophysics
> > Phone|480-819-5031
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi All,
I'm trying to get YT to read a vector which is stored as part of particle
structure in Enzo (a vector in the active particle structure). The data
looks OK when I view the raw HDF5 data using hdfview. I find that in some
snapshots YT can read the data but not in others. If there is more than one
particle things get worse for sure.
It could be that when writing to the HDF5 file I haven't put the data in a
format that is compatible with YT.
I've attached a simple script that will fall over when trying to read the
data and a link to the enzo output (size = 12 GBs). The active particles
are in files DD0120.cpu0022 (Grid 3072), DD0120.cpu0023 (Grid 3076) and
DD0014 (Grid 3080). YT falls over in the io_handler but it's not obvious to
me whether I need to modify that code or the format that I write the data
to the HDF5 file in.
Any help/pointers would be much appreciated.
Cheers,
John
Link to dataset:
https://www.dropbox.com/sh/o6acuvia1sqyp7y/AAC0lEI5lZ6bGa0tP2-G1jLea?dl=0
Hello,
I previously have not had any issues using yt, but today was forced to do a clean install of yt using the install script (same as I had done two months ago). However, this time I get a RecursionError when trying to use SlicePlot.
The installer installed Python 3.6.4 and yt version 3.4.0.
Perhaps of note is an additional FutureWarning message that I previously had not seen saying that the “Conversion of the second argument of issubdtype from ‘float’ to ‘np.floating’ is deprecated. In the future, it will be treated as ‘np.float64 == np.dtype(float).type’.” This warning originated from “yt-conda/lib/python3.6/site-packages/h5py/__init__.py:36”
I would greatly appreciate any assistance in fixing this issue with SlicePlot.
Thank you very much,
Nick
