profile plots combining different datasets
by ｔyuta
Dear yt-users,
Hi, I want to ask you about profile plot. I'm analyzing Enzo data, and I'm
trying to plot metallicity-cellmass of different 12 datasets into one
curve. I can plot 12 curves on one image, but that's not what I want. Does
anyone know some good way, or links to documentation?
I've attached the 12-curve plot. I want to sum up all the curves to get one
curve.
Thanks,
Y.T.[image: 埋め込み画像 2]
1 year, 2 months
Integration of a field along line of sight
by tazkera haque
Dear YT people,
I need to do integration of density field along line of sight. I know the
ProjectionPlot function plots the integration of a field along line of
sight.
yt.ProjectionPlot(ds, 'z', 'density, center= 'm')
However, I was wondering if it is possible to get the projection as an
array (or new field) , so that I can make a ProfilePlot of the integrated
field along line of sight and another field ('Mass')
In other words, I want to do the following:
sp = ds.sphere("max", (200, "kpc"))
proj = yt.ProfilePlot(sp, 'Integrated_Density_along_Line_Of_Sight', 'Mass)
Thanks
Tazkera
1 year, 2 months
Annotation on profileplots
by ｔyuta
Dear yt-users,
Hi, I want to annotate some lines on 1D profile plots, like on projection
plots or slice plots. I looked through the yt documentation, and I found:
Callbacks can be applied to plots created with SlicePlot
<http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html...>
, ProjectionPlot
<http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html...>
, OffAxisSlicePlot
<http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html...>,
or OffAxisProjectionPlot
<http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html...>
by
calling one of the annotate_ methods that hang off of the plot object.
on plot modification page, which means annotate_line method is not
effective for profile plots (I actually tried this on profile plots, and it
did not work). Is there any good way to annotate lines on 1D profile plots?
Also, I want to change the fontsize of numbers and labels on the axes of
profileplots. How can I do this?
For example, I want to annotate vertical line on density=1e-25, and change
the fontsize of "density", "10**-28", ..., "10**-21".
Thanks,
Y.T.
[image: 埋め込み画像 1]
1 year, 2 months
Plot Callbacks for OffAxis Plots
by Joseph Tomlinson
Hey yt-users,
I am trying to use OffAxis Slice and Projection plots using planes defined
by two light rays in Enzo data.
I have recently tried added callbacks for visualization of the clumps of
gas and star particles but whenever I use annotate_clumps and
annotate_particles with OffAxis plots I always get an error saying that
they do not have the method.
I assume that this is a consequence of how the OffAxis plots are made and
there is no easy way around this but I wanted to check to make sure before
I give up on OffAxis plots.
If you don't understand what I mean here is a short bit of pseudo code to
explain.
L=[1,1,0]
cut = SlicePlot(ds, L, 'Density')
cut.annotate_particles((300,'kpc'), ptype=2)
AttributeError: 'OffAxisSlicePlot' object has no attribute
'annotate_particles'
Thanks,
Joe Tomlinson
1 year, 3 months
Saving and loading Arbitrary grid data
by Li,Qi
Dear user group,
I am trying to smooth particle data output from GIZMO onto an arbitrary grid, then save the object as data set and reload in order to do volume rendering. However I can not handle the reloaded data set.
To clarify, I smooth yt sample data — FIRE_M12i_ref11 onto a 64**3 grid, the code is like this:
1 import yt
2
3 ytname='FIRE_M12i_ref11/snapshot_600.hdf5'
4 ds=yt.load(ytname)
5
6 # define the region
7 left = ds.domain_left_edge
8 right = ds.domain_right_edge
9
10 #now create an abitrary grid and save
11 arb = ds.arbitrary_grid(left, right,dims=[64, 64, 64])
12
13 fn = arb.save_as_dataset(fields=[('PartType0','density')])
14
15 arb_ds = yt.load('snapshot_600_arbitrary_grid.h5')
16 print arb_ds.field_list
And it returns an error:
Traceback (most recent call last):
File "arbgrid_clean.py", line 16, in <module>
print arb_ds.field_list
...
...
File "/Users/heavyfat/anaconda/lib/python2.7/site-packages/yt/frontends/ytdata/io.py", line 244, in _initialize_index
pos[:,0] = _get_position_array(ptype, f, "x")
ValueError: could not broadcast input array from shape (64,64,64) into shape (262144)
So, how I can save/load a usable arbitrary grid dataset?
Thanks and looking forward to your suggestions.
Best regards,
Qi
1 year, 3 months
Yt training workshops
by Nick Gnedin
Folk,
Do you plan any more training workshops/hackatons in the future? I work
with a couple of students who would benefit from such, self-learning
from the docs is kind of slow.
Thanks,
Nick Gnedin
1 year, 3 months
About ProfilePlot
by ｔyuta
Dear yt-users,
Hi, I have a question on ProfilePlot. I want to make profile plot of dark
matter density, taking gas density as a bin field, weighted by dark matter
mass in the cell.I could make the plot, but the plot looks strange (it
looks like chopped in small pieces). Also, I tried other plot changing
n_bins like 64,32,16,8,... but they still be "chopped", or sometimes there
were no line at all. For comparison, I made a plot weighted by cell_mass
(which I don't want), and this look OK. To my understanding, if and only if
there is at least 1 cell which fall into each bin, there should be some
nonzero value no matter what weight I use, so the range of density which
has nonzero dark matter density doesn't depend on the choice of weight
field. It seems there is a discrepancy between these two plots.
Could you tell me what's wrong with me?
I tried on yt example dataset, IsolatedGalaxy/galaxy0030/galaxy0030.
I'm working with yt-3.4.0.
this is my code:
import yt
from yt.data_objects.particle_filters import add_particle_filter
def stars(pfilter, data):
filter = data[(pfilter.filtered_type, "particle_type")] == 2
return filter
def DMparticles(pfilter, data):
filter = data[(pfilter.filtered_type, "particle_type")] == 1
return filter
add_particle_filter("stars", function=stars, filtered_type='io',
requires=["particle_type"])
add_particle_filter("DMparticles", function=DMparticles, filtered_type='io',
requires=["particle_type"])
def only_DM(field, data):
return data['deposit','DMparticles_density']
def DM_in_cell_mass(field, data):
return (data['only_DM_Density']*data['cell_volume'])
ds_all=yt.load("~/IsolatedGalaxy/galaxy0030/galaxy0030")
ds_all.add_particle_filter('stars')
ds_all.add_particle_filter('DMparticles')
ds_all.add_field(("gas", "only_DM_Density"), units="g/cm**3",
function=only_DM)
ds_all.add_field(("gas", "DM_cell_mass"), units="g",
function=DM_in_cell_mass)
sp = ds_all.sphere([0.5, 0.5, 0.5], (10, "kpc"))
lineplot_gas_DM_density_128 = yt.ProfilePlot(sp, "density", [
"only_DM_Density"], weight_field="DM_cell_mass", n_bins=128)
lineplot_gas_DM_density_gasweighted_128 = yt.ProfilePlot(sp, "density", [
"only_DM_Density"], weight_field="cell_mass", n_bins=128)
lineplot_gas_DM_density_gasweighted_128.save("128_gasweighted")
lineplot_gas_DM_density_128.save("128_DMweighted")
Sincerely,
Y.T.
1 year, 3 months
Question on derived field
by ｔyuta
Dear yt users,
Hi, I have a question on derived field. I want to define "Dark Matter cell
mass", which can be defined by (Dark matter density) * (cell_volume). To
check that "Dark Matter cell mass" defined well, I also tried to define
"my_cell_mass", which should give the same value as the default
'cell_mass', but it gave me an error, and I don't have any idea what the
problem is. Could you help me with the problem?
I'm working on Enzo data.
Here is my python code (I'm sorry that it's lengthy):
import yt
from yt.data_objects.particle_filters import add_particle_filter
def stars(pfilter, data):
filter = data[(pfilter.filtered_type, "particle_type")] == 2
return filter
def DMparticles(pfilter, data):
filter = data[(pfilter.filtered_type, "particle_type")] == 1
return filter
add_particle_filter("stars", function=stars, filtered_type='io',
requires=["particle_type"])
add_particle_filter("DMparticles", function=DMparticles,
filtered_type='io', requires=["particle_type"])
def only_DM(field, data):
return data['deposit','DMparticles_density']
def DM_in_cell_mass(field, data):
return (data['only_DM_Density']*data['cell_volume'])
def my_cell_mass(field, data):
return (data['density']*data['cell_volume'])
ds_all=yt.load("/.../redshift00??")
ds_all.add_particle_filter('stars')
ds_all.add_particle_filter('DMparticles')
ds_all.add_field(("gas", "only_DM_Density"), units="g/cm**3",
function=only_DM)
ds_all.add_field(("gas", "DM_in_cell_mass"), units="g",
function=DM_in_cell_mass)
ds_all.add_field(("gas", "my_cell_mass"), units="g", function=my_cell_mass)
sp = ds_all.sphere([centerx, centery, centerz], ((somevalue), "kpc"))
sp['cell_volume']
YTArray([ 4.44089210e-16, 4.44089210e-16, 4.44089210e-16, ...,
6.93889390e-18, 6.93889390e-18, 6.93889390e-18]) code_length**3
sp[('gas', 'my_cell_mass')]
YTFieldNotFound: Could not find field '('gas', 'my_cell_mass')' in redshift00??.
Best,
Y.T.
1 year, 3 months
particle filters
by ｔyuta
Dear yt users,
Hi, I want to know about particle filters. I learned that I can specify
some particle type by doing like this:
def stars(pfilter, data):
filter = data[(pfilter.filtered_type, "particle_type")] == 2
return filter
I learned that the filter for star is No.2 from this example. What about
other particles like gas or dark matter ? (Nathan kindly told me that dark
matter is 0, but fragmentary information I got from google search suggest
that it's 1, so I'm confused...) Is there any good documentation for this?
I'm working with Enzo data.
Best,
Y.T.
1 year, 3 months
Problem while installing YT with Rockstar
by Prateek Gupta
Hello everybody,
I am trying to install yt with enabling ROCKSTAR with the attached
install_script.sh. I got some OS related error of FIlename is too long:
Building Rockstar
********************************************
FAILURE REPORT:
********************************************
config=config)
File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/
lib/python3.6/site-packages/conda_build/build.py", line 1030, in build
create_env(config.build_prefix, specs, config=config)
File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/
lib/python3.6/site-packages/conda_build/build.py", line 736, in create_env
os.makedirs(join(prefix, 'conda-meta'))
File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/lib/python3.6/os.py",
line 210, in makedirs
makedirs(head, mode, exist_ok)
File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/lib/python3.6/os.py",
line 220, in makedirs
mkdir(name, mode)
OSError: [Errno 36] File name too long: '/home/dumbo/Documents/PhD_
Simulation/YT_Halo/yt-conda/conda-bld/rockstar_1508075330148/_b_env_
placehold_placehold_placehold_placehold_placehold_placehold_
placehold_placehold_placehold_placehold_placehold_placehold_
placehold_placehold_placehold_placehold_p'
********************************************
********************************************
Failure. Check
/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/yt_install.log.
The last 10 lines are above.
Please provide me some solution so that I can successfully enable ROCKSTAR.
Thanks
With best regards,
-Prateek
1 year, 3 months
