Thanks, but I'm having issue with 3.4.1. The error however is different and an Assertion error: Traceback (most recent call last):
File "particles.py", line 21, in <module>
ds.add_particle_filter('stars')
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 657, in add_particle_filter
self.index
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 504, in index
self, dataset_type=self.dataset_type)
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 357, in __init__
super(RAMSESIndex, self).__init__(ds, dataset_type)
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 50, in __init__
self._setup_geometry()
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/geometry/oct_geometry_handler.py", line 25, in _setup_geometry
self._initialize_oct_handler()
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 361, in _initialize_oct_handler
for i in range(self.dataset['ncpu'])]
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 361, in <listcomp>
for i in range(self.dataset['ncpu'])]
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 67, in __init__
self._read_amr_header()
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 191, in _read_amr_header
hvals.update(fpu.read_attrs(f, header))
File "/Users/samhitha/Desktop/AUR/yt-conda/lib/python3.7/site-packages/yt/utilities/fortran_utils.py", line 86, in read_attrs
assert(s1 == s2)
AssertionError
Is it not possible to revert to 3.4.0 at all? I tried doing: conda install -c conda-forge yt=3.4.0 but have issue with pyembree: Traceback (most recent call last):
File "/home/samvad/yt-conda/bin/yt", line 4, in <module>
import yt.utilities.command_line
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/__init__.py", line 102, in <module>
from yt.visualization.api import \
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/api.py", line 22, in <module>
from .particle_plots import \
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/particle_plots.py", line 18, in <module>
from yt.visualization.fixed_resolution import \
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", line 23, in <module>
from .volume_rendering.api import off_axis_projection
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", line 23, in <module>
from .camera import Camera
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", line 21, in <module>
from .utils import data_source_or_all
File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", line 11, in <module>
from yt.utilities.lib import mesh_traversal
File "rtcore_scene.pxd", line 61, in init yt.utilities.lib.mesh_traversal
ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, try recompiling. Expected 32, got 24
On Fri, May 3, 2019 at 5:11 PM Corentin CADIOU <contact@cphyc.me> wrote:
Hey,
Indeed, the previous version was actually able to read these files — even if invalid. The code should have never worked in the first place if it wanted to be compliant with the binary format RAMSES uses. I think that the easiest fix is to use a version of yt prior to commit #016c7e04bdf443d16b0431369be364dbb152e4ed ( https://github.com/yt-project/yt/commit/016c7e04bdf443d16b0431369be364dbb152...). The latest release that do *not* include this commit is yt 3.4.1. If you installed yt using git, you can easily switch to yt 3.4.1 by running in the folder that contains yt
git checkout yt-3.4.1 pip install .
If installed via conda, simpy run conda install -c conda-forge yt=3.4.1.
Cheers,
Corentin
On 03/05/2019 15.33, Vadlamani Samhitha wrote:
I see. Thank you. But I’m pretty positive I didn’t face this issue with the version I had before ( 3.4.0 ) as I was able to get the required plots. It’s just that when I upgraded and trying to do the same plots that I face this issue and I am unable get back to the older version now. Is there a possibility that outputs could have been corrupted during the upgrade somehow?
On Fri, 3 May 2019 at 3:25 PM, Corentin CADIOU <contact@cphyc.me> wrote:
Hi,
The issue is that your amr file does not contain any value for the field ‘mass_sph’. In fact, yt should *not* haver never been able to read it because the structure is somehow broken.
Here’s what I get from your file (as read by yt)
ncpu [4, 30, 4] ndim [4, 3, 4] nx [12, 3, 3, 3, 12] nlevelmax [4, 11, 4] ngridmax [4, 2000000, 4] nboundary [4, 6, 4] ngrid_current [4, 8722, 4] boxlen [8, 2000.0, 8] nout [12, 1, 1, 2, 12] tout [8, 50000.0, 8] aout [8, 1.100000023841858, 8] t [8, 0.0, 8] dtold [88, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 88] dtnew [88, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 88] nstep [8, 0, 0, 8] stat [24, 0.0, 0.0, 0.0, 24] cosm [56, 1.0, 0.0, 0.0, 0.0, 1.0, 10.0, 0.0, 56] timing [40, 1.0, 0.0, 1.0, 0.0, 0.0, 40] mass_sph [0, 2.801034444074e-311, 0]
The first and last item of each list are the length of each record (in bytes). For example the first record that contains ncpu has a length of 4 bytes and contains the value 30 (ncpu=30). However, the last record (mass_sph) has a length of 0 even though one even though it is not empty. I am not sure how that could happen, but it’s definitely on RAMSES side. The last line should read mass_sph [8, 2.801034444074e-311, 8].
I have to think about how that could be fixed.
On 03/05/2019 14.56, Vadlamani Samhitha wrote:
Hi,
If it's only one of the air files, I'm attaching it below. Let me know if you would need the entire output folder too. Thank you.
On Fri, May 3, 2019 at 2:52 PM Corentin CADIOU <contact@cphyc.me> wrote:
Hey Vadlamani,
This looks like a bug to me. Could you share one of your file amr_xxxxx.out00001? It looks like yt has troubles reading the headers.
This can either be due to a backward incompatible change on yt side (which would be a bug) or maybe your file became corrupted at some point.
Cheers, Corentin
On 02/05/2019 18.03, Vadlamani Samhitha wrote:
Hi,
I was able to upgrade to the latest version and still have an issue with annotating particles on density map. I'm getting the following error:
Traceback (most recent call last):
File "density.py", line 47, in <module>
plot = yt.ProjectionPlot(ds, 'z', 'density', width=(800, "kpc"), center="c")
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/visualization/plot_window.py", line 1464, in __init__
validate_mesh_fields(test_data_source, fields)
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/visualization/plot_window.py", line 132, in validate_mesh_fields
canonical_fields = data_source._determine_fields(fields)
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/data_containers.py", line 1165, in _determine_fields
finfo = self.ds._get_field_info("unknown", fname)
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 756, in _get_field_info
self.index
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 509, in index
self, dataset_type=self.dataset_type)
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 236, in __init__
super(RAMSESIndex, self).__init__(ds, dataset_type)
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 50, in __init__
self._setup_geometry()
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/oct_geometry_handler.py", line 25, in _setup_geometry
self._initialize_oct_handler()
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 245, in _initialize_oct_handler
for i in cpu_list]
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 245, in <listcomp>
for i in cpu_list]
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 82, in __init__
self._read_amr_header()
File "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", line 141, in _read_amr_header
hvals.update(f.read_attrs(header))
File "yt/utilities/cython_fortran_utils.pyx", line 223, in yt.utilities.cython_fortran_utils.FortranFile.read_attrs
IndexError: index 0 is out of bounds for axis 0 with size 0
On Tue, Apr 30, 2019 at 4:39 AM Vadlamani Samhitha < vadlamani.samhitha@gmail.com> wrote:
Downgraded to initial version, but the 'Index error' still persists. Did a conda installation from scratch too. Reported it as a bug.
On Mon, Apr 29, 2019 at 6:00 PM Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hmm, I'm not sure, perhaps try uninstalling pyembree?
You can also try creating a new conda environment from scratch.
On Mon, Apr 29, 2019 at 10:56 AM Vadlamani Samhitha < vadlamani.samhitha@gmail.com> wrote:
Thanks again, sorry but looks like I've messed up the installation. The installation wasn't right and I don't get the issue.
Upon doing yt --help I get:
Traceback (most recent call last): > > File "/home/samvad/yt-conda/bin/yt", line 4, in <module> > > import yt.utilities.command_line > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/__init__.py", line > 102, in <module> > > from yt.visualization.api import \ > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/api.py", > line 22, in <module> > > from .particle_plots import \ > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/particle_plots.py", > line 18, in <module> > > from yt.visualization.fixed_resolution import \ > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", > line 23, in <module> > > from .volume_rendering.api import off_axis_projection > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", > line 23, in <module> > > from .camera import Camera > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", > line 21, in <module> > > from .utils import data_source_or_all > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", > line 11, in <module> > > from yt.utilities.lib import mesh_traversal > > File "rtcore_scene.pxd", line 61, in init > yt.utilities.lib.mesh_traversal > > ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, > try recompiling. Expected 32, got 24 > > -bash-4.2$ yt version > > Traceback (most recent call last): > > File "/home/samvad/yt-conda/bin/yt", line 4, in <module> > > import yt.utilities.command_line > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/__init__.py", line > 102, in <module> > > from yt.visualization.api import \ > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/api.py", > line 22, in <module> > > from .particle_plots import \ > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/particle_plots.py", > line 18, in <module> > > from yt.visualization.fixed_resolution import \ > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", > line 23, in <module> > > from .volume_rendering.api import off_axis_projection > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", > line 23, in <module> > > from .camera import Camera > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", > line 21, in <module> > > from .utils import data_source_or_all > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", > line 11, in <module> > > from yt.utilities.lib import mesh_traversal > > File "rtcore_scene.pxd", line 61, in init > yt.utilities.lib.mesh_traversal > > ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, > try recompiling. Expected 32, got 24 > > -bash-4.20.9169398134926968nbsp; > > On Mon, Apr 29, 2019 at 5:30 PM Nathan Goldbaum < nathan12343@gmail.com> wrote:
> Sure, you can use conda to install any version of any package. Just > specify the version when you install: > > conda install -c conda-forge yt=3.4.1 > > On Mon, Apr 29, 2019 at 10:27 AM Vadlamani Samhitha < > vadlamani.samhitha@gmail.com> wrote: > >> Will do, but is it possible to revert to the old version for now >> since none of my scripts are working with the latest version? A fresh >> installation of 3.4.0? >> >> On Mon, Apr 29, 2019 at 3:25 PM Nathan Goldbaum < >> nathan12343@gmail.com> wrote: >> >>> Hmm, not sure what’s happening there, you might need to report >>> this as a bug on yt’s github, if you can please include a data file and >>> script that triggers this error. >>> >>> On Mon, Apr 29, 2019 at 8:00 AM Vadlamani Samhitha < >>> vadlamani.samhitha@gmail.com> wrote: >>> >>>> Thank you, have done the upgrade but the following error is >>>> popping up: >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> File "density.py", line 43, in <module> >>>>> >>>>> ds.add_field(name=("gas", "density_threshold"), >>>>> function=density_threshold, units="H/cm**3") >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", >>>>> line 1227, in add_field >>>>> >>>>> self.index >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", >>>>> line 509, in index >>>>> >>>>> self, dataset_type=self.dataset_type) >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>>>> line 236, in __init__ >>>>> >>>>> super(RAMSESIndex, self).__init__(ds, dataset_type) >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", >>>>> line 50, in __init__ >>>>> >>>>> self._setup_geometry() >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/oct_geometry_handler.py", >>>>> line 25, in _setup_geometry >>>>> >>>>> self._initialize_oct_handler() >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>>>> line 245, in _initialize_oct_handler >>>>> >>>>> for i in cpu_list] >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>>>> line 245, in <listcomp> >>>>> >>>>> for i in cpu_list] >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>>>> line 82, in __init__ >>>>> >>>>> self._read_amr_header() >>>>> >>>>> File >>>>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>>>> line 141, in _read_amr_header >>>>> >>>>> hvals.update(f.read_attrs(header)) >>>>> >>>>> File "yt/utilities/cython_fortran_utils.pyx", line 223, in >>>>> yt.utilities.cython_fortran_utils.FortranFile.read_attrs >>>>> >>>>> IndexError: index 0 is out of bounds for axis 0 with size 0 >>>>> >>>> >>>> On Mon, Apr 29, 2019 at 1:51 PM Nathan Goldbaum < >>>> nathan12343@gmail.com> wrote: >>>> >>>>> Yes, use conda-forge: >>>>> >>>>> conda update -c conda-forge yt >>>>> >>>>> On Mon, Apr 29, 2019 at 6:32 AM Vadlamani Samhitha < >>>>> vadlamani.samhitha@gmail.com> wrote: >>>>> >>>>>> I installed yt from conda so, yt update is only being done to >>>>>> 3.4.1 version with 'yt conda update' and with this my scripts are throwing >>>>>> assertion errors. Is there a way I could do a conda update to the latest >>>>>> version specifically? >>>>>> >>>>>> On Mon, Apr 29, 2019 at 1:05 PM Nathan Goldbaum < >>>>>> nathan12343@gmail.com> wrote: >>>>>> >>>>>>> The latest stable release is 3.5.1, please try updating your >>>>>>> yt installation. >>>>>>> >>>>>>> On Mon, Apr 29, 2019 at 5:58 AM Vadlamani Samhitha < >>>>>>> vadlamani.samhitha@gmail.com> wrote: >>>>>>> >>>>>>>> 3.4.0 >>>>>>>> >>>>>>>> On Mon, Apr 29, 2019 at 12:52 PM Nathan Goldbaum < >>>>>>>> nathan12343@gmail.com> wrote: >>>>>>>> >>>>>>>>> What yt version are you using? >>>>>>>>> >>>>>>>>> On Mon, Apr 29, 2019 at 5:34 AM Vadlamani Samhitha < >>>>>>>>> vadlamani.samhitha@gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, I did try that as well, but doing so gives 'unexpected >>>>>>>>>> keyword' error. >>>>>>>>>> >>>>>>>>>> Traceback (most recent call last): >>>>>>>>>>> >>>>>>>>>>> File "density.py", line 57, in <module> >>>>>>>>>>> >>>>>>>>>>> plot.save(fil) >>>>>>>>>>> >>>>>>>>>>> File >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_container.py", >>>>>>>>>>> line 94, in newfunc >>>>>>>>>>> >>>>>>>>>>> args[0]._setup_plots() >>>>>>>>>>> >>>>>>>>>>> File >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>>>>>>>>>> line 948, in _setup_plots >>>>>>>>>>> >>>>>>>>>>> self.run_callbacks() >>>>>>>>>>> >>>>>>>>>>> File >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>>>>>>>>>> line 997, in run_callbacks >>>>>>>>>>> >>>>>>>>>>> callback = CallbackMaker(*args[1:], **kwargs) >>>>>>>>>>> >>>>>>>>>>> TypeError: __init__() got an unexpected keyword argument >>>>>>>>>>> 'data_source' >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mon, Apr 29, 2019 at 12:18 PM Wise, John H < >>>>>>>>>> jwise@physics.gatech.edu> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Because there are many optional arguments to >>>>>>>>>>> annotate_particles, you >>>>>>>>>>> have to specify that dd is the data_source. Try >>>>>>>>>>> >>>>>>>>>>> plot.annotate_particles(1.0, data_source=dd) >>>>>>>>>>> >>>>>>>>>>> John >>>>>>>>>>> >>>>>>>>>>> On 4/27/2019 15:46, Vadlamani Samhitha wrote: >>>>>>>>>>> > Hi, >>>>>>>>>>> > >>>>>>>>>>> > I am trying to overlap two different projection plots >>>>>>>>>>> (particles and >>>>>>>>>>> > density) with two different color bars. However, I >>>>>>>>>>> couldn't figure out a >>>>>>>>>>> > way to do that but found over plotting particles over >>>>>>>>>>> fluids. >>>>>>>>>>> > >>>>>>>>>>> > So, I have RAMSES data which can't distinguish between >>>>>>>>>>> dark matter and >>>>>>>>>>> > stars through particle types but only with mass cut_off. >>>>>>>>>>> So I create a >>>>>>>>>>> > filter for the particles accordingly and supply it as >>>>>>>>>>> the 'data_source' >>>>>>>>>>> > argument in 'annotate_particles'. So, I do the following: >>>>>>>>>>> > >>>>>>>>>>> > defstars(pfilter, data): >>>>>>>>>>> > >>>>>>>>>>> > # age = (data.ds.current_time - >>>>>>>>>>> data[pfilter.filtered_type, >>>>>>>>>>> > "particle_birth_time"]).in_units('Myr') >>>>>>>>>>> > >>>>>>>>>>> > stars_only = data[pfilter.filtered_type, >>>>>>>>>>> > "particle_mass"].in_units('Msun') >>>>>>>>>>> > >>>>>>>>>>> > filter= (stars_only<4e6) >>>>>>>>>>> > >>>>>>>>>>> > returnfilter >>>>>>>>>>> > >>>>>>>>>>> > yt.add_particle_filter("stars", function=stars, >>>>>>>>>>> filtered_type='io', >>>>>>>>>>> > requires=["particle_mass"]) >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > ini=1 >>>>>>>>>>> > >>>>>>>>>>> > fin=2 >>>>>>>>>>> > >>>>>>>>>>> > forx inrange(ini, fin): >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> filename="/lunarc/nobackup/users/samvad/SQ-8-5/output/output_%0*d/info_%0*d.txt" >>>>>>>>>>> >>>>>>>>>>> > % (5,x,5,x) >>>>>>>>>>> > >>>>>>>>>>> > ds = yt.load(filename) >>>>>>>>>>> > >>>>>>>>>>> > ds.define_unit("H", (1.674*10**(-24), "g")) >>>>>>>>>>> > >>>>>>>>>>> > defdensity_threshold(field, data): >>>>>>>>>>> > >>>>>>>>>>> > dens=data["gas", >>>>>>>>>>> "density"].in_units('H/cm**3') >>>>>>>>>>> > >>>>>>>>>>> > dens[dens < 0] = 0 >>>>>>>>>>> > >>>>>>>>>>> > returndens >>>>>>>>>>> > >>>>>>>>>>> > ds.add_field(name=("gas", >>>>>>>>>>> "density_threshold"), >>>>>>>>>>> > function=density_threshold, units="H/cm**3") >>>>>>>>>>> > >>>>>>>>>>> > ad=ds.all_data() >>>>>>>>>>> > >>>>>>>>>>> > denst=ad["gas", >>>>>>>>>>> "density_threshold"].in_units('H/cm**3') >>>>>>>>>>> > >>>>>>>>>>> > #plot = yt.SlicePlot(ds, 'z', 'density_threshold', >>>>>>>>>>> width=(400, "kpc")) >>>>>>>>>>> > >>>>>>>>>>> > plot = yt.ProjectionPlot(ds, 'z', 'density', >>>>>>>>>>> > weight_field='density', width=(800, "kpc"), >>>>>>>>>>> center="c") >>>>>>>>>>> > >>>>>>>>>>> > ds.add_particle_filter('stars') >>>>>>>>>>> > >>>>>>>>>>> > dd=ds.all_data() >>>>>>>>>>> > >>>>>>>>>>> > plot.annotate_particles(1.0, dd) >>>>>>>>>>> > >>>>>>>>>>> > plot.set_cmap(field='density', cmap='Blues') >>>>>>>>>>> > >>>>>>>>>>> > plot.set_unit(("gas", "density"), "H/cm**3") >>>>>>>>>>> > >>>>>>>>>>> > plot.set_zlim(("gas", "density"), 1e-4, >>>>>>>>>>> 1e-1) >>>>>>>>>>> > >>>>>>>>>>> > plot.annotate_timestamp() >>>>>>>>>>> > >>>>>>>>>>> > fil="density_%0*d.png" % (5,x) >>>>>>>>>>> > >>>>>>>>>>> > plot.save(fil) >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > But ending up with the error: >>>>>>>>>>> > >>>>>>>>>>> > Traceback (most recent call last): >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>>>>>>>>>> >>>>>>>>>>> > line 999, in run_callbacks >>>>>>>>>>> > >>>>>>>>>>> > callback(cbw) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>>>>>>>>>> >>>>>>>>>>> > line 53, in _check_geometry >>>>>>>>>>> > >>>>>>>>>>> > return func(self, plot) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>>>>>>>>>> >>>>>>>>>>> > line 1563, in __call__ >>>>>>>>>>> > >>>>>>>>>>> > s=self.p_size, c=self.color,alpha=self.alpha) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", >>>>>>>>>>> > line 1717, in inner >>>>>>>>>>> > >>>>>>>>>>> > return func(ax, *args, **kwargs) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", >>>>>>>>>>> >>>>>>>>>>> > line 4032, in scatter >>>>>>>>>>> > >>>>>>>>>>> > alpha=alpha >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>>>>>>>>>> >>>>>>>>>>> > line 880, in __init__ >>>>>>>>>>> > >>>>>>>>>>> > self.set_sizes(sizes) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>>>>>>>>>> >>>>>>>>>>> > line 853, in set_sizes >>>>>>>>>>> > >>>>>>>>>>> > scale = np.sqrt(self._sizes) * dpi / 72.0 * >>>>>>>>>>> self._factor >>>>>>>>>>> > >>>>>>>>>>> > AttributeError: 'YTRegion' object has no attribute 'sqrt' >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > During handling of the above exception, another >>>>>>>>>>> exception occurred: >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > Traceback (most recent call last): >>>>>>>>>>> > >>>>>>>>>>> > File "density.py", line 57, in <module> >>>>>>>>>>> > >>>>>>>>>>> > plot.save(fil) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_container.py", >>>>>>>>>>> >>>>>>>>>>> > line 94, in newfunc >>>>>>>>>>> > >>>>>>>>>>> > args[0]._setup_plots() >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>>>>>>>>>> >>>>>>>>>>> > line 948, in _setup_plots >>>>>>>>>>> > >>>>>>>>>>> > self.run_callbacks() >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>>>>>>>>>> >>>>>>>>>>> > line 1005, in run_callbacks >>>>>>>>>>> > >>>>>>>>>>> > sys.exc_info()[2]) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/six.py", line >>>>>>>>>>> > 692, in reraise >>>>>>>>>>> > >>>>>>>>>>> > raise value.with_traceback(tb) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>>>>>>>>>> >>>>>>>>>>> > line 999, in run_callbacks >>>>>>>>>>> > >>>>>>>>>>> > callback(cbw) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>>>>>>>>>> >>>>>>>>>>> > line 53, in _check_geometry >>>>>>>>>>> > >>>>>>>>>>> > return func(self, plot) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>>>>>>>>>> >>>>>>>>>>> > line 1563, in __call__ >>>>>>>>>>> > >>>>>>>>>>> > s=self.p_size, c=self.color,alpha=self.alpha) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", >>>>>>>>>>> > line 1717, in inner >>>>>>>>>>> > >>>>>>>>>>> > return func(ax, *args, **kwargs) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", >>>>>>>>>>> >>>>>>>>>>> > line 4032, in scatter >>>>>>>>>>> > >>>>>>>>>>> > alpha=alpha >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>>>>>>>>>> >>>>>>>>>>> > line 880, in __init__ >>>>>>>>>>> > >>>>>>>>>>> > self.set_sizes(sizes) >>>>>>>>>>> > >>>>>>>>>>> > File >>>>>>>>>>> > >>>>>>>>>>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>>>>>>>>>> >>>>>>>>>>> > line 853, in set_sizes >>>>>>>>>>> > >>>>>>>>>>> > scale = np.sqrt(self._sizes) * dpi / 72.0 * >>>>>>>>>>> self._factor >>>>>>>>>>> > >>>>>>>>>>> > yt.utilities.exceptions.YTPlotCallbackError: >>>>>>>>>>> annotate_particles >>>>>>>>>>> > callback failed with the following error: 'YTRegion' >>>>>>>>>>> object has no >>>>>>>>>>> > attribute 'sqrt' >>>>>>>>>>> > >>>>>>>>>>> > I don't seem to >>>>>>>>>> >>>>>>>>>>