yt-users

yt-users@python.org

9 participants
2736 discussions

by Vincenzo Antonuccio-Delogu

I would like to write a FITS file out of an off-axis projection along some given direction of a field ("i_nu") which I create as a derived field. However, the parameters I set in the main Python program (pl_inu.py) using set_field_parameter() are not passed down to the derived field i_nu. Here is the main macro I am using: """ pl_inu.py """ import numpy as np import yt from yt.utilities.cosmology import Cosmology from yt import derived_field import matplotlib.pyplot as plt from yt.fields.api import ValidateParameter from bckfl_fns import b_p,_e_dens, e_dens, _chi_nu,_kappa, f_kappa, _i_nu, f_chi_nu, los_unit_vector, proj_dist from yt import YTArray, YTQuantity float_formatter = "{:.3f}".format cosmo = Cosmology() LFLY = YTArray(1.0/cosmo.hubble_constant.value,"Mpc").in_cgs() TFLY = (2./3./cosmo.hubble_constant).in_cgs() MFLY = YTArray(5.23e12/cosmo.hubble_constant.value,"Msun").in_cgs() uo = {"length_unit":LFLY, "time_unit":TFLY, "mass_unit":MFLY} fname = 'virgoS12_str_hdf5_plt_cnt_0015' ds=yt.load(fname,units_override=uo) dd=ds.all_data() ds.add_field(("gas", "n_e"), function=_e_dens, units="cm**(-3)", sampling_type='cell', display_name="Electron density", force_override=True) ds.add_field(("gas", "kappa"), function=_kappa, units="kpc**(-1)", sampling_type='cell', display_name="N(E) norm coeff", force_override=True) ds.add_field(("gas", "chi_nu"), function=_chi_nu, units="kpc**(-1)", sampling_type='cell', display_name="synchr. abs. coeff.", force_override=True) ds.add_field(("gas", "i_nu"), function=_i_nu, units="W/(m**2)/Hz", sampling_type='cell', display_name="Synchr. emission", force_override=True, validators=[ValidateParameter(["lmin","l.o.s.","lmin origin","Background I_nu","Magnetic field","Electron p-law index","b(p)","nu (Ghz)"])]) # Output time (in Myr) # co = Cosmology() time = ds.parameters.get('time')*co.t_from_z(0.).in_units("Myr") p = 5./2. E_min = 1.5 E_max = 2.e1 bm4 = 0.01 nu = 1.5 dd.set_field_parameter("Magnetic field", bm4) dd.set_field_parameter("Electron p-law index",p) dd.set_field_parameter("1-p", (1-p)) dd.set_field_parameter("b(p)",b_p(p)) dd.set_field_parameter('E_min', E_min) dd.set_field_parameter('E_max', E_max) dd.set_field_parameter("nu (Ghz)", nu) eul_angles_deg=np.array([4.,22.]) n_dir = los_unit_vector(eul_angles_deg) pos_0 = YTArray([0.,0,-130],'kpc') grid_pos=YTArray([dd['gas','x'],dd['gas','y'],dd['gas','z']]).in_units('kpc') lmin = np.amin(proj_dist(n_dir,grid_pos,pos_0)) i_nu_lmin = YTQuantity(1.e-27,'W/(m**2)/Hz') dd.set_field_parameter('Background I_nu', i_nu_lmin) dd.set_field_parameter("lmin", lmin) dd.set_field_parameter("l.o.s.", n_dir) dd.set_field_parameter('lmin origin', pos_0) dd.set_field_parameter('grid pos', grid_pos) synchr_fits=yt.FITSOffAxisSlice(ds,n_dir,("gas", "i_nu"), width=((50,'kpc'))) fits_name = 'i_nu_r0000_15.fits' synchr_fits.writeto(fits_name, overwrite='True') ==== and this is the collection of functions I use to create the field "i_nu": """ bckfl_fns.py """ import sys import yt import numpy as np import global_vars from yt import derived_field from yt import YTArray, YTQuantity from yt.fields.api import ValidateParameter """ Derived fields in yt-FLASH """ def _kappa(field, data): import math from yt import YTQuantity if data.has_field_parameter("E_min"): E_min = data.get_field_parameter("E_min") else: E_min = 0. if data.has_field_parameter("E_max"): E_max = data.get_field_parameter("E_max") else: E_max = 0. ne_tot = data["gas", "n_e"].v if data.has_field_parameter("Electron p-law index"): p = data.get_field_parameter("Electron p-law index") else: p = 0. if data.has_field_parameter("E_min") and data.has_field_parameter("E_max") \ and data.has_field_parameter("Electron p-law index"): k=YTQuantity(1.0,"kpc**(-1)")*(1-p)*ne_tot/(pow(E_max,(1-p)) - pow(E_min,(1-p))) print("Inside kappa: p-law index is",p, E_min, E_max) else: k=YTQuantity(1.0,"kpc**(-1)") if np.any(k < 0): print("k negative!", k) return k def _chi_nu(field, data): if data.has_field_parameter("Electron p-law index") and \ data.has_field_parameter("b(p)") and \ data.has_field_parameter("Magnetic field") and \ data.has_field_parameter("nu (Ghz)"): p = data.get_field_parameter("Electron p-law index") bp = data.get_field_parameter("b(p)") bm4 = data.get_field_parameter("Magnetic field") nu = data.get_field_parameter("nu (Ghz)") ne_tot = data[("gas","n_e")].v kappa = data[("gas","kappa")] a = 6.445e-6 chi_nu=a*np.power(10,(p/2))*np.power(5.67,p)*kappa*bp*pow(bm4,(0.5*p+1))/np.power(nu,(0.5*p+2)) else: chi_nu=YTQuantity(0.0,"kpc**(-1)") return chi_nu def _i_nu(field, data): from unyt import kpc from yt import YTArray, YTQuantity from yt.units import mass_hydrogen # if data.has_field_parameter("lmin"): lmin = data.get_field_parameter("lmin") print("Inside _i_nu, lmin=",lmin) else: lmin = YTQuantity(0.0,"kpc") if data.has_field_parameter("l.o.s."): los = data.get_field_parameter("l.o.s.") print("Inside _i_nu, l.o.s.=",los) else: los = [0, 0, 0] if data.has_field_parameter("lmin origin"): pos_0 = data.get_field_parameter("lmin origin") print("Inside _i_nu, pos_0=",pos_0) else: pos_0 = data.ds.arr(np.zeros(3), 'kpc') if data.has_field_parameter("Background I_nu"): i_nulmin = data.get_field_parameter("Background I_nu") print("Inside _i_nu, i_nulmin=",i_nulmin) else: i_nu_lmin = 0. if data.has_field_parameter("Magnetic field"): bm4 = data.get_field_parameter("Magnetic field") print("Inside _i_nu, bm4=",bm4) else: bm4 = 1.e-20 ## i_nu_lmin=YTQuantity(i_nulmin,"W/(m**2)/Hz") # i_nu_lmin=YTQuantity(i_nulmin,"W/(m**2)/Hz").in_units("Jansky") if data.has_field_parameter("Electron p-law index"): p = data.get_field_parameter("Electron p-law index") print("Inside _i_nu, p=",p) fact_joc = np.power(10,-p) else: p=0. fact_joc = 0. if data.has_field_parameter("b(p)"): bp = data.get_field_parameter("b(p)") print("Inside _i_nu, b(p)=",bp) else: bp = 0. if data.has_field_parameter("nu (Ghz)"): nu = data.get_field_parameter("nu (Ghz)") print("Inside _i_nu, nu=",nu) else: nu = 0 ne_tot = data["gas","density"].v/mass_hydrogen.v kappa = data["kappa"] a = YTQuantity(4.97766e-17,'W/(m**2)/Hz') chi_nu = f_chi_nu(nu,bm4,p,bp,kappa) j_over_chi = a*fact_joc*(nu**2.5)/np.power(bm4,0.5) grid_pos=YTArray([data['gas','x'],data['gas','y'],data['gas','z']]).in_units('kpc') r = proj_dist(los,grid_pos,pos_0) ad = r-lmin print("Inside _i_nu", i_nulmin, j_over_chi, a) b = np.exp(-chi_nu*(r-lmin)) i_nu = i_nulmin*b + j_over_chi*(1-b) return i_nu """ General purpose functions """ def _e_dens(field, data): """ Computes electron density from gas density.""" from yt.units import mass_hydrogen return data[("gas","density")]/mass_hydrogen def e_dens(dens): """ Computes electron density from gas density.""" from yt.units import mass_hydrogen return dens.v/mass_hydrogen.v def f_kappa(ntot,emin,emax,p): import sys, math fk = (1-p)*ntot/(np.power(emax,(1-p))-np.power(emin,(1-p))) return fk def a_p(p): from scipy import interpolate as int_erp p=[1,1.5,2,2.5,3,3.5,4,4.5,5] bp=[2.056,0.909,0.529,0.359,0.269,0.217,0.186,0.167,0.157] f_interp=int_erp.interp1d(p,bp) return f_interp(p_inp) def b_p(p_inp): from scipy import interpolate as int_erp p=[1,1.5,2,2.5,3,3.5,4,4.5,5] bp=[0.397,0.314,0.269,0.244,0.233,0.230,0.236,0.248,0.268] f_interp=int_erp.interp1d(p,bp) return f_interp(p_inp) def f_chi_nu(nu,B,p,bp,kappa): import sys, math a1 = 5.67**p a2 = pow(10,p/2) c1 = 0.5*p + 1 c2 = 0.5*p + 2 abs_coeff = YTArray([6.445e-6],'kpc**(-1)') return abs_coeff def los_unit_vector(inp_angles): from numpy import radians from math import sin, cos eul_angles_rad=radians(inp_angles) v_dir = np.array([sin(eul_angles_rad[0])*cos(eul_angles_rad[1]),sin(eul_angles_rad[0])*sin(eul_angles_rad[1]),cos(eul_angles_rad[0])]) return v_dir def proj_dist(los,xyz,origin): import numpy as np d = ((xyz.T - origin)*los) dist = np.sqrt(np.sum(d*d, axis=1)) return dist ======= Fr some reasons I do not quite understand, the field parameters I define in the main program are not passed down to the "i_nu" field through the _i_nu function. Here the error message: > python3 pl_synchr_test.py yt : [WARNING ] 2021-10-16 17:45:34,946 Overriding code units: Use this option only if you know that the dataset doesn't define the units correctly or at all. yt : [INFO ] 2021-10-16 17:45:34,946 Overriding length_unit: 4.346024761918768e+24 cm. yt : [INFO ] 2021-10-16 17:45:34,947 Overriding time_unit: 2.897349841279178e+17 s. yt : [INFO ] 2021-10-16 17:45:34,947 Overriding mass_unit: 1.4647063306760563e+46 g. yt : [INFO ] 2021-10-16 17:45:35,024 Parameters: current_time = 0.0016112618581139734 yt : [INFO ] 2021-10-16 17:45:35,024 Parameters: domain_dimensions = [8 8 8] yt : [INFO ] 2021-10-16 17:45:35,024 Parameters: domain_left_edge = [-0.7 -0.7 -0.7] yt : [INFO ] 2021-10-16 17:45:35,024 Parameters: domain_right_edge = [0.7 0.7 0.7] yt : [INFO ] 2021-10-16 17:45:35,024 Parameters: cosmological_simulation = 0 Inside _i_nu, lmin= 0.0 Inside _i_nu, l.o.s.= 0.0 Inside _i_nu, pos_0= 0.0 Inside _i_nu, i_nulmin= 0.0 Inside _i_nu, bm4= 0.0 Inside _i_nu, p= 0.0 Inside _i_nu, b(p)= 0.0 Inside _i_nu, nu= 0.0 /g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/unyt/array.py:1778: RuntimeWarning: invalid value encountered in true_divide out_arr = func( Inside _i_nu 0.0 nan W/(Hz*m**2) 4.97766e-17 W/(Hz*m**2) yt : [INFO ] 2021-10-16 17:45:41,439 Making a fixed resolution buffer of (('gas', 'i_nu')) 512 by 512 Traceback (most recent call last): File "pl_synchr_test.py", line 64, in <module> synchr_fits=yt.FITSOffAxisSlice(ds,n_dir,("gas", "i_nu"), width=((50,'kpc'))) File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/visualization/fits_image.py", line 1275, in __init__ super().__init__(frb, fields=fields, length_unit=lunit, wcs=w) File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/visualization/fits_image.py", line 244, in __init__ this_img = img_data[field] File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/visualization/fixed_resolution.py", line 139, in __getitem__ buff = self.ds.coordinates.pixelize( File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/geometry/coordinates/cartesian_coordinates.py", line 221, in pixelize return self._oblique_pixelize(data_source, field, bounds, size, antialias) File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/geometry/coordinates/cartesian_coordinates.py", line 570, in _oblique_pixelize data_source[field], File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 258, in __getitem__ self.get_data(f) File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/data_objects/selection_objects/data_selection_objects.py", line 169, in get_data finfo.check_available(self) File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/fields/derived_field.py", line 244, in check_available validator(data) File "/g100/home/userexternal/vantonuc/.local/lib/python3.8/site-packages/yt/fields/derived_field.py", line 503, in __call__ raise NeedsParameter(doesnt_have) yt.fields.field_exceptions.NeedsParameter: (['lmin', 'l.o.s.', 'lmin origin', 'Background I_nu', 'Magnetic field', 'Electron p-law index', 'b(p)', 'nu (Ghz)']) ======== Many thanks in advance for any help/suggestions.

1 day, 1 hour

Error when attempting to call surface object

by Sam Patrick

Hi all, I've been trying to do some preliminary experimentation with YT's surface object. I have the following snippet of code: sphere = ds.sphere(center, radius) surf = ds.surface(sphere, ('gas', 'density'), 1e-23) ratio = (surf.volume() / surf.surface_area).in_units('pc') However when trying to run the code I get the following error: File "my_analysis.py", line 107, in contours ratio = (surf.volume() / surf.surface_area).in_units('pc') File "/home/brs/stack/yt/yt/data_objects/selection_objects/data_selection_objects.py", line 1394, in volume return self.quantities.total_quantity(("index", "cell_volume")) File "/home/brs/stack/yt/yt/data_objects/derived_quantities.py", line 172, in __call__ rv = super().__call__(fields) File "/home/brs/stack/yt/yt/data_objects/derived_quantities.py", line 55, in __call__ for sto, ds in parallel_objects(chunks, -1, storage=storage): File "/home/brs/stack/yt/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 527, in parallel_objects for result_id, obj in oiter: File "/home/brs/stack/yt/yt/data_objects/selection_objects/data_selection_objects.py", line 94, in chunks for ci, chunk in enumerate(self.index._chunk(self, chunking_style, **kwargs)): File "/home/brs/stack/yt/yt/geometry/geometry_handler.py", line 233, in _chunk self._identify_base_chunk(dobj) File "/home/brs/stack/yt/yt/geometry/grid_geometry_handler.py", line 335, in _identify_base_chunk gi = dobj.selector.select_grids( File "/home/brs/stack/yt/yt/data_objects/selection_objects/data_selection_objects.py", line 73, in selector raise YTDataSelectorNotImplemented(self._type_name) P019 yt : [ERROR ] 2021-09-13 12:14:32,552 YTDataSelectorNotImplemented: Data selector 'surface' not implemented. I was hoping someone could help with this. My yt version is 4.1.dev0 and my Python version is 3.8.5 Many thanks, Sam Patrick

1 week, 6 days

Re: Yt will soon drop support for Python 3.6

by Clément Robert

This is a gentle reminder. Have a nice day Clément > On 28 Sep 2021, at 20:33, Clément Robert <clement.robert(a)protonmail.com> wrote: > > Dear yt users, > > As was previously mentionned in yt 4.0.0's release notes, we're planning to drop > support for Python 3.6 in our next feature release (4.1.0). The change is set to > happen on the dev branch of yt not earlier than October the 20th, this year. > This means that if you wish to use our most recent features and bugfixes past this date, you'll > need to make sure you're running Python 3.7 or newer. Note that the > 4.0.x series will retain compatibility with Python 3.6. > > The exact method to upgrade your Python runtime depends on what tool(s) you used to > install Python or to manage your environments. In general, please lookup the > method that applies to your tools. Here is the documentation for some common > methods: > > - using venv (see "--upgrade" flag) https://docs.python.org/3/library/venv.html > - using conda https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pyth… > > In general, yt is primarily tested with the latest Python versions available, so > we recommend upgrading Python to the latest version available to you. > > There will be a reminder in two weeks from now. > Note that we're also planning to officially support Python 3.10 as soon as possible, > but likely not earlier than mid-October. > > Have a great day, > Clément Robert, on behalf of the yt dev team

2 weeks, 2 days

Error when attempting plot derived_fields quantities

by 贺一峰

Hi all, I have been trying to plot derived field of vorticity and the computation domain is set to be periodic. It always does not work though I tried to adjust different plotting domains. Meanwhile it can plot field figures of primitive quantities. Here is part of error info: ---------ERROR INFO----------------------------------------------------------------------------------------- P001 yt : [INFO ] 2021-10-06 19:50:59,037 Parameters: current_time = 3e-06 P001 yt : [INFO ] 2021-10-06 19:50:59,037 Parameters: domain_dimensions = [1024 128 1] P001 yt : [INFO ] 2021-10-06 19:50:59,037 Parameters: domain_left_edge = [0. 0. 0.] P001 yt : [INFO ] 2021-10-06 19:50:59,038 Parameters: domain_right_edge = [0.032 0.004 1. ] command in line argument loading data File "vorfield.py", line 76, in <module> slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((0.016,'cm'),(0.002,'cm')),center=([0.016,0.002,0.],'cm')) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1986, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1282, in __init__ slc.get_data(fields) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1583, in get_data self._generate_fields(fields_to_generate) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1603, in _generate_fields fd = self._generate_field(field) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 293, in _generate_field tr = self._generate_fluid_field(field) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 311, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 341, in _generate_spatial_fluid gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz], File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 256, in __getitem__ self.get_data(f) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 691, in get_data if len(fill) > 0: self._fill_fields(fill) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 1053, in _fill_fields for chunk in ls.data_source.chunks(fields, "io"): File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1464, in chunks self.get_data() # Ensure we have built ourselves File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1507, in get_data self.index._identify_base_chunk(self) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/geometry/grid_geometry_handler.py", line 290, in _identify_base_chunk gi = dobj.selector.select_grids(self.grid_left_edge, File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1459, in selector self._selector = sclass(self) File "yt/geometry/selection_routines.pyx", line 860, in yt.geometry.selection_routines.RegionSelector.__init__ RuntimeError: Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 2. Region left edge = -1.25 code_length, Region right edge = 2.25 code_length Dataset left edge = 0.0 code_length, Dataset right edge = 1.0 code_length This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to load a smaller region that does not border the edge or override the periodicity for this dataset. ---------ERROR INFO---------------------------------------------------------------------------------------- Here is part of python code ----------PYCODE--------------------------- ### u,v means velocity(primitive quantities) in X,Y direction ### vort_z means vorticity(derived quantity) in Z direnction def vort_z_func(field, data): return ( + data['boxlib', 'v_gradient_x'] - data['boxlib', 'u_gradient_y'] ) u_gradient = ds.add_gradient_fields(("boxlib","u")) v_gradient = ds.add_gradient_fields(("boxlib","v")) derived_fields = [ # field name, units, displayname ('vort_z', '1 / cm', 'Vorticity in z direction'), ] for name, unitstr, dispname in derived_fields: ds.add_field( ('boxlib', name), units = unitstr, function = eval(name + '_func'), sampling_type = 'cell', display_name = dispname ) slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((0.016,'cm'),(0.002,'cm')),center=([0.016,0.002,0.],'cm')) ----------PYCODE--------------------------- Thanks a lot! Best Wishes, He Yifeng College of Engineering, Peking University

3 weeks, 1 day

Error when attempting plot derived_fields quantities

by 贺一峰

3 weeks, 1 day

ImportError when importing HaloCatalog: cannot import name 'ensure_list' from 'yt.funcs'

by Ian Woodward

I'm running yt 4.0.1 and yt_astro_analysis 1.0.0. I'm trying to import HaloCatalog. I use: from yt_astro_analysis.halo_analysis.api import HaloCatalog but get the error below. On checking funcs.py, it appears that the function 'ensure_list' doesn't exist. Are yt 4.0.1 and yt_astro_analysis 1.0.0 out of sync? I'd be grateful for any suggestions about how to fix this. Cheers Ian ImportError Traceback (most recent call last) /tmp/ipykernel_9530/3924969598.py in <module> 3 import yt 4 import yt_astro_analysis ----> 5 from yt_astro_analysis.halo_analysis.api import HaloCatalog ~/miniconda3/envs/enzo/lib/python3.7/site-packages/yt_astro_analysis/halo_analysis/api.py in <module> 15 16 ---> 17 from yt_astro_analysis.halo_analysis.halo_catalog import \ 18 HaloCatalog 19 ~/miniconda3/envs/enzo/lib/python3.7/site-packages/yt_astro_analysis/halo_analysis/halo_catalog.py in <module> 30 from yt_astro_analysis.halo_analysis.halo_object import \ 31 Halo ---> 32 from yt_astro_analysis.halo_analysis.halo_callbacks import \ 33 callback_registry 34 from yt_astro_analysis.halo_analysis.halo_filters import \ ~/miniconda3/envs/enzo/lib/python3.7/site-packages/yt_astro_analysis/halo_analysis/halo_callbacks.py in <module> 27 from yt.utilities.exceptions import \ 28 YTSphereTooSmall ---> 29 from yt.funcs import \ 30 ensure_list 31 from yt.utilities.logger import ytLogger as mylog ImportError: cannot import name 'ensure_list' from 'yt.funcs' (/home/ian/miniconda3/envs/enzo/lib/python3.7/site-packages/yt/funcs.py)

3 weeks, 2 days

Yt will soon drop support for Python 3.6

by Clément Robert

Dear yt users, As was previously mentionned in yt 4.0.0's release notes, we're planning to drop support for Python 3.6 in our next feature release (4.1.0). The change is set to happen on the dev branch of yt not earlier than October the 20th, this year. This means that if you wish to use our most recent features and bugfixes past this date, you'll need to make sure you're running Python 3.7 or newer. Note that the 4.0.x series will retain compatibility with Python 3.6. The exact method to upgrade your Python runtime depends on what tool(s) you used to install Python or to manage your environments. In general, please lookup the method that applies to your tools. Here is the documentation for some common methods: - using venv (see "--upgrade" flag) https://docs.python.org/3/library/venv.html - using conda https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pyth… In general, yt is primarily tested with the latest Python versions available, so we recommend upgrading Python to the latest version available to you. There will be a reminder in two weeks from now. Note that we're also planning to officially support Python 3.10 as soon as possible, but likely not earlier than mid-October. Have a great day, Clément Robert, on behalf of the yt dev team

1 month

Yt-colormaps in matplotlib

by adrian.jost＠mail.de

Hi, I found some cool colormaps in the yt package and I was wondering how to use them for normal plots created via matplotlib (the colormap I'm looking for is not available in matplotlib, at least it is not listed on the matplotlib website). Can anybody help me please?

1 month

LTP in python

by jackyhuynh30＠gmail.com

Dear sir, I see in scikitimage have LBP in package feature in texture.pyx and texture.py . With LBP is the center pixel's value is greater than the neighbor's value, write "0". Otherwise, write "1". With code as : # signed / thresholded texture for i in range(P): if texture[i] - image[r, c] >= 0: signed_texture[i] = 1 else: signed_texture[i] = 0 Local ternary patterns (LTP) are an extension of Local binary patterns (LBP), Unlike LBP, it does not threshold the pixels into 0 and 1, rather it uses a threshold constant to threshold pixels into three values. Considering k as the threshold constant, c as the value of the center pixel, a neighboring pixel p, the result of threshold is: 1 if p >c+k 0 if p > c-k && p <c+k 1 if p < c-k with my code as : # signed / thresholded texture for i in range(P): if texture[i] - (image[r, c]+T) > 0: signed_texture[i] = 1 elif texture[i] - (image[r, c]-T) < 0: signed_texture[i] = -1 elif texture[i] - (image[r, c]+T) <= 0 && texture[i] - (image[r, c]-T) >= 0: signed_texture[i] = 0 but i not sure this is correct with python , Pls help me In C++ i see code : unsigned short lut[8][3]; int radius; float thresholdPos; float thresholdNeg; FeatureLTP() : radius(1) , thresholdPos( 0.1f) , thresholdNeg(-0.1f) { unsigned short cnt = 0; for (int i = 0; i < 8; i++) { for (int j = 0; j < 3; j++) lut[i][j] = cnt++; cnt++; //we skip the 4th number (only three patterns) } } int operator() (const Mat &I, Mat &fI) const { CV_Assert(I.isContinuous() && (I.channels() == 1)); Mat_<float> m(I); Mat_<ushort> n(m.size()); n = 0; const float *p = (const float*)m.ptr(); for (int r=radius; r<m.rows-radius; r++) { for (int c=radius; c<m.cols-radius; c++) { const float cval = p[r * m.cols + c]; static const int off[8][2] = {-1,-1, -1,0, -1,1, 0,1, 1,1, 1,0, 1,-1, 0,-1}; for (int li=0; li<8; li++) { // walk neighbours: int y = r + off[li][0] * radius; int x = c + off[li][1] * radius; float diff = p[y * m.cols + x] - cval; n(r,c) += (diff > thresholdPos) ? lut[li][0] : (diff < thresholdNeg) ? lut[li][1] : lut[li][2]; } } } fI = n; return 256; } this is difference with python ? Pls help me , I new python and c++ thankyou so much

1 month

Re: Rockstar is not working

by Nick Gnedin

Britton, I tried your methods 1 and 2 and RS (Rockstar-Galaxies Version: 0.99.9-RC3-newA) runs with both to the end. However, I discovered a weird thing - the actual value for the particle mass has no effect. I ran it both with the default value and with the changed value, both values are correctly listed in corresponding out_0.list files: #Particle mass: 4.22991e+06 Msun/h [default value] #Particle mass: 5.02229e+06 Msun/h [assigned correct value] However, the produced mass functions are the same in both runs, and they differ by the OmegaM/OmegaDM factor (the ratio of 5.02229e+06/4.22991e+06) from the mass function that I consider correct (obtained with the old RS (Rockstar Version: 0.99.9-RC3) as implemented in yt '3.7.dev0' in yt.analysis_modules.halo_finding.rockstar.api, which also agrees with the analytical fit from hmf.py). Perhaps yt sets the RS particle mass correctly but feeds the actual particle data with the default mass? Nick On 9/10/2021 4:51 AM, Britton Smith wrote: > Hi Nick, > > Thanks for sending the script; I can see why my solution didn't work. > The time series object does not have a unit registry like a loaded > dataset. I issued a pull request to yt_astro_analysis which should fix > this by allowing you to do what you should have been able to all along. > https://github.com/yt-project/yt_astro_analysis/pull/84 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_yt-2Dprojec…> > > With this PR, you can now give the particle mass in three ways: > 1. as a regular float. This will assume units of Msun/h. This was the > original way that was broken and should now be fixed again. > 2. as a tuple of (value, unit) for example (5.02229e+06,"Msun/h"). > 3. as a unyt_quantity > > To make the 3rd option work, you would do > ts[0].quan(5.02229e+06,"Msun/h"), since ts[0] will be the first dataset. > The first two should work as is. > > Let me know if this works and I'll get the PR merged. > > Britton > > On Thu, Sep 9, 2021 at 4:25 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > Britton, > > Actually, your suggestion does not work: > > File "rs-hfc.py", line 19, in <module> > ts.unit_registry.add("h", 0.6814, dimensionless) > P010 yt : [ERROR ] 2021-09-09 10:23:11,397 AttributeError: > 'DatasetSeries' object has no attribute 'unit_registry' > > > Here is my script (based on your suggestion from a couple of years > back): > > sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") > sets.sort() > ts = yt.DatasetSeries(sets) > ts.unit_registry.add("h", 0.6814, dimensionless) > rh = HaloCatalog(data_ds=ts, finder_method='rockstar', > finder_kwargs={"num_readers":n, "num_writers":4, > "outbase":root+"/"+dir+"/rstest1", "particle_type":"N-BODY_0", > "particle_mass":yt.YTQuantity(5.02229e+06,"Msun/h")}) > rh.create() > del rh > del ts > > > > > > On 9/9/2021 9:01 AM, Britton Smith wrote: > > Hi Nick, > > > > Rockstar wants particle masses in units of Msun/h, so it's trying > to do > > that conversion. If your dataset doesn't have h defined, you can do > > something like this: > > > > from unyt.dimensions import dimensionless > > > > ds = yt.load(...) > > ds.unit_registry.add("h", VALUE, dimensionless) > > > > Hopefully, that does the trick. > > > > Britton > > > > > > On Tue, Sep 7, 2021 at 8:57 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote: > > > > > > Britton, > > > > You were right, when I updated yt and yt_astro_analysis to > the latest > > versions (and downgraded matplotlib to circumvent the > matplotlib._png > > bug), Rockstar now runs, but I encounter a unit error: > > > > File "rs-hfc.py", line 21, in <module> > > rh.create() > > File "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis > > ... > > File > > > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_object.py", > > > > line 972, in _get_unit_data_from_expr > > return _lookup_unit_symbol(unit_expr.name > <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF…> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF… <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF…>>, > > unit_symbol_lut) > > File > > > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_registry.py", > > > > line 330, in _lookup_unit_symbol > > raise UnitParseError( > > P011 yt : [ERROR ] 2021-09-07 14:39:16,965 UnitParseError: > Could not > > find unit symbol 'h' in the provided symbols. > > > > I removed any reference to h in my script, so I am > flabbergasted by > > that > > error. Here is my script: > > > > import yt, yt.funcs > > import glob, sys, os.path > > yt.enable_parallelism() > > from yt.extensions.astro_analysis.halo_analysis import > HaloCatalog > > > > root = > > > "/data/gnedin/REI/D/Cai.B20.N128L2.sf=1_uv=0.15_bw=10_res=100.WC1" > > n = 16 > > dirs = ( "A", ) > > for dir in dirs: > > sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") > > sets.sort() > > ts = yt.DatasetSeries(sets) > > rh = HaloCatalog(data_ds=ts, finder_method='rockstar', > > finder_kwargs={"num_readers":n, > "num_writers":4, > > "outbase":root+"/"+dir+"/rscor", "particle_type":"N-BODY_0", > > "particle_mass":yt.YTQuantity(5.02229e+06/0.6814,"Msun")}) > > rh.create() > > del rh > > del ts > > ## > > > > > > Nick > > > > > > On 9/6/2021 10:00 AM, Britton Smith wrote: > > > Hi Nick, > > > > > > I was not able to reproduce this error using the latest > dev yt and > > > yt_astro_analysis installed. The call to ytcfg.get looks > > correct to me. > > > The error looks to me like the older yt config parser > syntax, so > > the yt > > > installation may be out of date. > > > > > > Britton > > > > > > On Thu, Sep 2, 2021 at 1:40 AM Nick Gnedin > <gnedin(a)fnal.gov <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>> > > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>>> wrote: > > > > > > > > > Folks, > > > > > > I am trying to run rockstar using your instructions on > > > > > > > > > https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html#rockst… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>> > > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>>> > > > > > > and I am getting the following error almost immediately: > > > > > > Traceback (most recent call last): > > > File "rs-hfc.py", line 24, in <module> > > > hc.create() > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > > > line 333, in create > > > self._run(save_halos, save_output, > > > File > > > > > > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > > > > > line 301, in barrierize > > > return func(*args, **kwargs) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > > > line 224, in _run > > > self.finder_method(self) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py", > > > > > > line 39, in __call__ > > > return self.function(hc, *self.args, **self.kwargs) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py", > > > > > > line 87, in _rockstar_method > > > rh = RockstarHaloFinder(ds, **finder_kwargs) > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > > > > > line 214, in __init__ > > > self.runner = InlineRunner() > > > File > > > > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > > > > > line 44, in __init__ > > > psize = ytcfg.get("yt", "internals", > > "global_parallel_size") > > > File > > > > > > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/config.py", > > > line 137, in get > > > val = super(YTConfigParser, self).get(section, > option, > > *args, > > > **kwargs) > > > TypeError: get() takes 3 positional arguments but 4 > were given > > > > > > Nick Gnedin > > > > > > > > > -- > > > This email has been checked for viruses by AVG. > > > https://www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…>> > > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…>>> > > > > > > _______________________________________________ > > > yt-users mailing list -- yt-users(a)python.org > 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