[yt-users] pf.h.region error

Elizabeth Tasker tasker at astro1.sci.hokudai.ac.jp
Wed Feb 22 11:51:59 PST 2012


And that's fixed it -- thanks Matt.

(Thank you for your suggestion Hannes -- I also thought processing
that calculation might be an error and tried with numbers. This time
though, no luck).



On 22 February 2012 14:36, Matthew Turk <matthewturk at gmail.com> wrote:
> The problem lies with incorrect harrays files, which get parsed on hierarchy
> instantiation. Wipe them out and you will be fine.
>
> Adding validation to hierarchy serialization sounds like a good introductory
> project for any keen new developers. :-)
>
> On Feb 22, 2012 2:22 PM, "Elizabeth Tasker"
> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>
>> (As an amendment, it throws the same error when trying to create a
>> projection of the whole data set:
>>
>> p = pc.add_projection("Density", 0) )
>>
>> Elizabeth
>>
>>
>>
>> On 22 February 2012 14:10, Elizabeth Tasker
>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>> > Occasionally, when I try and create a region, I get this error;
>> >
>> >
>> >
>> > ValueError                                Traceback (most recent call
>> > last)
>> >
>> > /work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in <module>()
>> >     20 pc = PlotCollection(pf, center=center)
>> >     21
>> > ---> 22 reg = pf.h.region(center, [center[0]-0.5*width,
>> > center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width,
>> > center[1]+0.5*width, center[2]+0.5*dept
>> > h])
>> >     23
>> >     24 p = pc.add_projection('Density', 2, data_source=reg)
>> >
>> > /work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc
>> > in hierarchy(self)
>> >    167                 raise RuntimeError("You should not instantiate
>> > StaticOutput.")
>> >    168             self._instantiated_hierarchy =
>> > self._hierarchy_class(
>> > --> 169                 self, data_style=self.data_style)
>> >    170         return self._instantiated_hierarchy
>> >    171     h = hierarchy  # alias
>> >
>> >
>> > /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc
>> > in __init__(self, pf, data_style)
>> >    160             self.float_type = 'float64'
>> >    161
>> > --> 162         AMRHierarchy.__init__(self, pf, data_style)
>> >    163         # sync it back
>> >    164         self.parameter_file.data_style = self.data_style
>> >
>> > /work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc
>> > in __init__(self, pf, data_style)
>> >     68
>> >     69         mylog.debug("Parsing hierarchy.")
>> > ---> 70         self._parse_hierarchy()
>> >     71
>> >     72         mylog.debug("Constructing grid objects.")
>> >
>> >
>> > /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc
>> > in _parse_hierarchy(self)
>> >    226             return line.split()[2:]
>> >    227         if os.path.exists(self.hierarchy_filename[:-9] +
>> > "harrays"):
>> > --> 228             if self._parse_binary_hierarchy(): return
>> >    229         t1 = time.time()
>> >    230         pattern = r"Pointer:
>> > Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$"
>> >
>> >
>> > /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc
>> > in _parse_binary_hierarchy(self)
>> >    300         except h5py.h5.H5Error:
>> >    301             return False
>> > --> 302         self.grid_dimensions[:] = f["/ActiveDimensions"][:]
>> >    303         self.grid_left_edge[:] = f["/LeftEdges"][:]
>> >    304         self.grid_right_edge[:] = f["/RightEdges"][:]
>> >
>> > ValueError: shape mismatch: objects cannot be broadcast to a single
>> > shape
>> > WARNING: Failure executing file: <image_object.py>
>> >
>> >
>> > What I don't understand is that it'll happen on one data set, but then
>> > the next one (or the one before) in the simulation will be totally
>> > fine. My dtdump steps are small too, so I'm confused as to why this
>> > would occur. Both "width" and "depth" are neither very small or very
>> > large compared to "centre". (In kpc, centre = 16, 22, 16 and width =
>> > 4 and depth = 1.)
>> >
>> > Elizabeth
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