OVERPLOTTING PARTICLE PROJECTION MAP ON DENSITY PROJECTION MAP
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:
def stars(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)
return filter
yt.add_particle_filter("stars", function=stars, filtered_type='io', requires=["particle_mass"])
ini=1
fin=2
for x in range(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"))
def density_threshold(field, data):
dens=data["gas", "density"].in_units('H/cm**3')
dens[dens < 0] = 0
return dens
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround to get > particle plot over density plot in a simpler way? Thank you. > > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org >
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround > to get > > particle plot over density plot in a simpler way? Thank you. > > > > _______________________________________________ > > yt-users mailing list -- yt-users@python.org > > To unsubscribe send an email to yt-users-leave@python.org > > > > -- > John Wise > Associate Professor of Physics > Center for Relativistic Astrophysics, Georgia Tech > http://cosmo.gatech.edu > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround >> to get >> > particle plot over density plot in a simpler way? Thank you. >> > >> > _______________________________________________ >> > yt-users mailing list -- yt-users@python.org >> > To unsubscribe send an email to yt-users-leave@python.org >> > >> >> -- >> John Wise >> Associate Professor of Physics >> Center for Relativistic Astrophysics, Georgia Tech >> http://cosmo.gatech.edu >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a workaround >>> to get >>> > particle plot over density plot in a simpler way? Thank you. >>> > >>> > _______________________________________________ >>> > yt-users mailing list -- yt-users@python.org >>> > To unsubscribe send an email to yt-users-leave@python.org >>> > >>> >>> -- >>> John Wise >>> Associate Professor of Physics >>> Center for Relativistic Astrophysics, Georgia Tech >>> http://cosmo.gatech.edu >>> _______________________________________________ >>> yt-users mailing list -- yt-users@python.org >>> To unsubscribe send an email to yt-users-leave@python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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 understand the issue here. Is there a >>>> workaround to get >>>> > particle plot over density plot in a simpler way? Thank you. >>>> > >>>> > _______________________________________________ >>>> > yt-users mailing list -- yt-users@python.org >>>> > To unsubscribe send an email to yt-users-leave@python.org >>>> > >>>> >>>> -- >>>> John Wise >>>> Associate Professor of Physics >>>> Center for Relativistic Astrophysics, Georgia Tech >>>> http://cosmo.gatech.edu >>>> _______________________________________________ >>>> yt-users mailing list -- yt-users@python.org >>>> To unsubscribe send an email to yt-users-leave@python.org >>>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users@python.org >>> To unsubscribe send an email to yt-users-leave@python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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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-4.2$
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 understand the issue here. Is there a >>>>> workaround to get >>>>> > particle plot over density plot in a simpler way? Thank you. >>>>> > >>>>> > _______________________________________________ >>>>> > yt-users mailing list -- yt-users@python.org >>>>> > To unsubscribe send an email to yt-users-leave@python.org >>>>> > >>>>> >>>>> -- >>>>> John Wise >>>>> Associate Professor of Physics >>>>> Center for Relativistic Astrophysics, Georgia Tech >>>>> http://cosmo.gatech.edu >>>>> _______________________________________________ >>>>> yt-users mailing list -- yt-users@python.org >>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>> >>>> _______________________________________________ >>>> yt-users mailing list -- yt-users@python.org >>>> To unsubscribe send an email to yt-users-leave@python.org >>>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users@python.org >>> To unsubscribe send an email to yt-users-leave@python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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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-4.2$
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 understand the issue here. Is there a >>>>>> workaround to get >>>>>> > particle plot over density plot in a simpler way? Thank you. >>>>>> > >>>>>> > _______________________________________________ >>>>>> > yt-users mailing list -- yt-users@python.org >>>>>> > To unsubscribe send an email to yt-users-leave@python.org >>>>>> > >>>>>> >>>>>> -- >>>>>> John Wise >>>>>> Associate Professor of Physics >>>>>> Center for Relativistic Astrophysics, Georgia Tech >>>>>> http://cosmo.gatech.edu >>>>>> _______________________________________________ >>>>>> yt-users mailing list -- yt-users@python.org >>>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list -- yt-users@python.org >>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>> >>>> _______________________________________________ >>>> yt-users mailing list -- yt-users@python.org >>>> To unsubscribe send an email to yt-users-leave@python.org >>>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users@python.org >>> To unsubscribe send an email to yt-users-leave@python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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-4.2$
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 understand the issue here. Is there a >>>>>>> workaround to get >>>>>>> > particle plot over density plot in a simpler way? Thank you. >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > yt-users mailing list -- yt-users@python.org >>>>>>> > To unsubscribe send an email to yt-users-leave@python.org >>>>>>> > >>>>>>> >>>>>>> -- >>>>>>> John Wise >>>>>>> Associate Professor of Physics >>>>>>> Center for Relativistic Astrophysics, Georgia Tech >>>>>>> http://cosmo.gatech.edu >>>>>>> _______________________________________________ >>>>>>> yt-users mailing list -- yt-users@python.org >>>>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>>>> >>>>>> _______________________________________________ >>>>>> yt-users mailing list -- yt-users@python.org >>>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list -- yt-users@python.org >>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>> >>>> _______________________________________________ >>>> yt-users mailing list -- yt-users@python.org >>>> To unsubscribe send an email to yt-users-leave@python.org >>>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users@python.org >>> To unsubscribe send an email to yt-users-leave@python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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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-4.2$
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 understand the issue here. Is there a >>>>>>>> workaround to get >>>>>>>> > particle plot over density plot in a simpler way? Thank you. >>>>>>>> > >>>>>>>> > _______________________________________________ >>>>>>>> > yt-users mailing list -- yt-users@python.org >>>>>>>> > To unsubscribe send an email to yt-users-leave@python.org >>>>>>>> > >>>>>>>> >>>>>>>> -- >>>>>>>> John Wise >>>>>>>> Associate Professor of Physics >>>>>>>> Center for Relativistic Astrophysics, Georgia Tech >>>>>>>> http://cosmo.gatech.edu >>>>>>>> _______________________________________________ >>>>>>>> yt-users mailing list -- yt-users@python.org >>>>>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> yt-users mailing list -- yt-users@python.org >>>>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>>>> >>>>>> _______________________________________________ >>>>>> yt-users mailing list -- yt-users@python.org >>>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list -- yt-users@python.org >>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>> >>>> _______________________________________________ >>>> yt-users mailing list -- yt-users@python.org >>>> To unsubscribe send an email to yt-users-leave@python.org >>>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users@python.org >>> To unsubscribe send an email to yt-users-leave@python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
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participants (3)
-
Nathan Goldbaum -
Vadlamani Samhitha -
Wise, John H