Sorry for the delay in replying.
On Friday, February 21, 2014, <
hyschive@ntu.edu.tw> wrote:
Dear all,
I'm a new user of yt and is trying to use it for analyzing our octree AMR data, which is similar to FLASH. We are stilling testing yt version 2.x, and currently we are able to create a slice image together with the underlying AMR grid distribution WITHOUT providing any parent-children relation between each grid. However, after we further set up the parent-children relation, the plot (e.g., the SlicePlot command) failed with the following error messages:
===============Error Message================================================
ValueError Traceback (most recent call last)
<ipython-input-3-e98bfe3813b1> in <module>()
----> 1 p=SlicePlot(pf,2,"Density",center=(0.501,0.501,0.501))
/work1/ftd/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in __init__(self, pf, axis, fields, center, width, origin)
805 slc = pf.h.slice(axis, center[axis], fields=fields)
806 print slc,bounds,origin
--> 807 PWViewerMPL.__init__(self, slc, bounds, origin=origin)
808
809 class ProjectionPlot(PWViewerMPL):
/work1/ftd/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in __init__(self, *args, **kwargs)
446 self._field_transform[field] = linear_transform
447
--> 448 if setup: self._setup_plots()
449
450 @invalidate_plot
/work1/ftd/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in _setup_plots(self)
617 print self.plots[f].image,self.plots[f].cax
618 self.plots[f].cb = self.plots[f].figure.colorbar(
--> 619 self.plots[f].image, cax = self.plots[f].cax)
620
621 if self.oblique == False:
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.pyc in colorbar(self, mappable, cax, ax, **kw)
1194 cax, kw = cbar.make_axes(ax, **kw)
1195 cax.hold(True)
-> 1196 cb = cbar.Colorbar(cax, mappable, **kw)
1197
1198 def on_changed(m):
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.pyc in __init__(self, ax, mappable, **kw)
741 kw['alpha'] = mappable.get_alpha()
742
--> 743 ColorbarBase.__init__(self, ax, **kw)
744
745
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.pyc in __init__(self, ax, cmap, norm, alpha, values, boundaries, orientation, extend, spacing, ticks, format, drawedges, filled)
256 # The rest is in a method so we can recalculate when clim changes.
257 self.config_axis()
--> 258 self.draw_all()
259
260 def _patch_ax(self):
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.pyc in draw_all(self)
270 and do all the drawing.
271 '''
--> 272 self._process_values()
273 self._find_range()
274 X, Y = self._mesh()
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.pyc in _process_values(self, b)
568 self.norm.vmin = 0
569 self.norm.vmax = 1
--> 570 b = self.norm.inverse(self._uniform_y(self.cmap.N+1))
571 if self.extend in ('both', 'min'):
572 b[0] = b[0] - 1
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/matplotlib/colors.pyc in inverse(self, value)
946 if cbook.iterable(value):
947 val = ma.asarray(value)
--> 948 return vmin * ma.power((vmax/vmin), val)
949 else:
950 return vmin * pow((vmax/vmin), value)
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.pyc in __mul__(self, other)
3640 def __mul__(self, other):
3641 "Multiply other by self, and return a new masked array."
-> 3642 return multiply(self, other)
3643 #
3644 def __rmul__(self, other):
/work1/ftd/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.pyc in __call__(self, a, b, *args, **kwargs)
934 # Case 1. : scalar
935 if not result.ndim:
--> 936 if m:
937 return masked
938 return result
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
==========End of Error Message==================================================
So, my questions are as follows.
1. What is the necessary information for constructing the tree structure in yt?Currently the SlicePlot command failed only after we set up the "Parent" and "Children" variables for each grid in the function "_populate_grid_objects".
Typically the information is necessary just to check the masking of grid objects; Parent is considerably less important for this than Children.
There is a diagnostic that can be run to examine the volume:
vol = 0.0
dv = pf.domain_width.prod(dtype="float64")
for g in pf.h.grids:
vol += g.dds.prod(dtype="float64") * g.child_mask.sum()
print np.abs(vol - dv)/dv
What it looks like is happening, based on the error message, is that somehow the total values in a slice are being set to the same thing everywhere. This diagnostic -- which should produce a value of 0.0 -- should help track that down.
2. Does the SlicePlot command need to know the parent-children relation of each grid? If no, why it will fail after we set up the relation?
It only needs to know the children of a grid, so that it can mask out overlapping regions.
3. Will yt automatically construct the "neighbor" information for nearby grids at the same AMR refinement level? If no, how does it handle the operations requiring spatial derivative (e.g., curl and divergence)?
It will do so, yup.
Any suggestion will be welcome, and thanks for the help in advance :)
I suspect something might be going wrong with the way the children pointers are set up. Can you show how you're constructing them? It's possible that there is an off-by-one or something that is creeping in.
-Matt
Sincerely,
Hsi-Yu
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