Hi Sam, This is very strange. I believe that it's likely a conflict between our implementation of clip in yt 3.x and the numpy version, and my guess is that it has been fixed in unyt or in newer versions of yt. Which version of yt are you using? On Wed, Sep 16, 2020 at 5:26 AM Sam Patrick via yt-users < yt-users@python.org> wrote:

Hi all,

I'm trying to do a volume render of the temperature field inside a sphere with the following code:

val, loc = ds.find_max('density') sp = ds.sphere(loc, SP_DIST) source = VolumeSource(sp, 'temperature') scene = Scene() scene.add_source(source)

# v is calculated based on angular momentum camera = scene.add_camera(sp, lens_type= 'perspective') cam_position = loc + v * CAM_DIST camera.set_position(cam_position) camera.set_focus(loc)

source.set_field('temperature') source.set_log(True) bounds = (UPPER, LOWER) tf = yt.ColorTransferFunction(np.log10(bounds)) tf.add_layers(12, colormap='jet') source.tfh.tf = tf source.tfh.bounds = bounds source.tfh.plot('transfer_function.png', profile_field='temperature') scene.save("render_t={:.3f}".format(times[i]), sigma_clip= 1)

Upon saving though I encounter the error:

Traceback (most recent call last): File "plot_3d.py", line 51, in <module> scene.save("render_t={:.3f}".format(times[i]), sigma_clip= 1) #last sigma = 2 File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/visualization/volume_rendering/scene.py",

line 310, in save yt : [INFO ] 2020-09-15 10:34:02,783 Saving render render_t=0.000.png self._last_render.write_png(fname, sigma_clip=sigma_clip) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/data_objects/image_array.py",

line 289, in write_png scaled = self.rescale(inline=False) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/data_objects/image_array.py",

line 242, in rescale np.clip(out, 0.0, 1.0, out) File "<__array_function__ internals>", line 6, in clip File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/fromnumeric.py",

line 2084, in clip return _wrapfunc(a, 'clip', a_min, a_max, out=out, **kwargs) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/fromnumeric.py",

line 61, in _wrapfunc return bound(*args, **kwds) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/_methods.py",

line 132, in _clip um.clip, a, min, max, out=out, casting=casting, **kwargs) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/_methods.py",

line 85, in _clip_dep_invoke_with_casting return ufunc(*args, out=out, **kwargs) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/units/yt_array.py",

line 1401, in __array_ufunc__ "added to YTArray." % (str(ufunc), len(inputs))) RuntimeError: Support for the <ufunc 'clip'> ufunc with 3 inputs has not beenadded to YTArray.

I would also like to eventually add a colorbar to the side of the created image which represents the transfer function and annotate text as well. Does the render functionality allow me to do this? Any help on these topics would be much appreciated.

Many thanks, Sam Patrick _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: matthewturk@gmail.com