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August 2019

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12 discussions

Problem running volume rendering example
by Christoph Schaefer 05 Aug '19

05 Aug '19

Hi yt-users, I’ve wanted to have a look into the volume rendering examples. However, when I run the following code from the examples (https://yt-project.org/doc/quickstart/volume_rendering.html) import yt ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030") sc = yt.create_scene(ds) sc.camera.set_width(ds.quan(20, 'kpc')) source = sc.sources['source_00'] tf = yt.ColorTransferFunction((-28, -24)) tf.add_layers(4, w=0.01) source.set_transfer_function(tf) sc.show() I get the following (error) output: (full output, see below) : Support for the <ufunc 'clip'> ufunc with 3 inputs has not beenadded to YTArray. Am I missing something? installation is yt 3.5.1 numpy 1.17. matplotlib 3.1.1 Thanks for any help Christoph --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) ~/src/python_virtual_env/lib/python3.7/site-packages/IPython/core/formatters.py in __call__(self, obj) 343 method = get_real_method(obj, self.print_method) 344 if method is not None: --> 345 return method() 346 return None 347 else: ~/src/python_virtual_env/lib/python3.7/site-packages/yt/visualization/volume_rendering/scene.py in _repr_png_(self) 926 png = self._last_render.write_png(filename=None, 927 sigma_clip=self._sigma_clip, --> 928 background='black') 929 self._sigma_clip = None 930 return png ~/src/python_virtual_env/lib/python3.7/site-packages/yt/data_objects/image_array.py in write_png(self, filename, sigma_clip, background, rescale, clip_ratio) 287 """ 288 if rescale: --> 289 scaled = self.rescale(inline=False) 290 else: 291 scaled = self ~/src/python_virtual_env/lib/python3.7/site-packages/yt/data_objects/image_array.py in rescale(self, cmax, amax, inline) 240 np.multiply(self[:, :, 3], 1.0/amax, out[:, :, 3]) 241 --> 242 np.clip(out, 0.0, 1.0, out) 243 return out 244 <__array_function__ internals> in clip(*args, **kwargs) ~/src/python_virtual_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py in clip(a, a_min, a_max, out, **kwargs) 2035 2036 """ -> 2037 return _wrapfunc(a, 'clip', a_min, a_max, out=out, **kwargs) 2038 2039 ~/src/python_virtual_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py in _wrapfunc(obj, method, *args, **kwds) 59 60 try: ---> 61 return bound(*args, **kwds) 62 except TypeError: 63 # A TypeError occurs if the object does have such a method in its ~/src/python_virtual_env/lib/python3.7/site-packages/numpy/core/_methods.py in _clip(a, min, max, out, casting, **kwargs) 130 else: 131 return _clip_dep_invoke_with_casting( --> 132 um.clip, a, min, max, out=out, casting=casting, **kwargs) 133 134 def _mean(a, axis=None, dtype=None, out=None, keepdims=False): ~/src/python_virtual_env/lib/python3.7/site-packages/numpy/core/_methods.py in _clip_dep_invoke_with_casting(ufunc, out, casting, *args, **kwargs) 83 # try to deal with broken casting rules 84 try: ---> 85 return ufunc(*args, out=out, **kwargs) 86 except _exceptions._UFuncOutputCastingError as e: 87 # Numpy 1.17.0, 2019-02-24 ~/src/python_virtual_env/lib/python3.7/site-packages/yt/units/yt_array.py in __array_ufunc__(self, ufunc, method, *inputs, **kwargs) 1399 raise RuntimeError( 1400 "Support for the %s ufunc with %i inputs has not been" -> 1401 "added to YTArray." % (str(ufunc), len(inputs))) 1402 if unit is None: 1403 out_arr = np.array(out_arr, copy=False) RuntimeError : Support for the <ufunc 'clip'> ufunc with 3 inputs has not beenadded to YTArray. <Scene Object>: Sources: source_00: <Volume Source>:YTRegion (galaxy0030): , center=[1.543e+24 1.543e+24 1.543e+24] cm, left_edge=[0. 0. 0.] cm, right_edge=[3.086e+24 3.086e+24 3.086e+24] cm transfer_function:<Color Transfer Function Object>: x_bounds:[-28, -24] nbins:256 features: ('gaussian', 'location(x):-28', 'width(x):0.01', 'height(y):(0.43, 0.024, 0.047, 0.001)') ('gaussian', 'location(x):-27', 'width(x):0.01', 'height(y):(0.34, 0.34, 0.68, 0.01)') ('gaussian', 'location(x):-25', 'width(x):0.01', 'height(y):(0.66, 0.66, 0.32, 0.1)') ('gaussian', 'location(x):-24', 'width(x):0.01', 'height(y):(0.98, 0.98, 0.91, 1)') Camera: <Camera Object>: position:[1. 1. 1.] code_length focus:[0.5 0.5 0.5] code_length north_vector:[ 0.81649658 -0.40824829 -0.40824829] dimensionless width:[0.01999791 0.01999791 0.01999791] unitary light:None resolution:(512, 512) Lens: <Lens Object>: lens_type:plane-parallel viewpoint:[-11545.30474893 -11545.30474893 -11545.30474893] code_length

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axis & labels in volume rendereing
by Maximilian Fabricius 05 Aug '19

05 Aug '19

All, I wondered if there is a way to do this: I have been creating volume renderings of spectroscopic datacubes for a while now. What I miss yet is coordinate axis *with labels*. Like here https://doc.qt.io/qt-5.9/qtdatavisualization-volumetric-example.html Any ideas on how to achieve this? Many thanks, Max

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