[yt-users] No 'astype' attribute error - clump finding, volume rendering

Tue Jul 2 10:53:03 PDT 2013

Hi Nathan,

Well, I just updated to the latest version of yt, 2.5.4, and I've been
using that - is that what you mean?

-Noel

On Tue, Jul 2, 2013 at 1:16 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> Hi Noel,
>
> I believe pf.domain_dimensions should be a numpy array while in your case
> it's actually a list. It looks like this is due to a bug in the frontend
> you're using.  Which code is this for?  This should be an easy fix.
>
> -Nathan
>
>
> On Tue, Jul 2, 2013 at 10:12 AM, Noel Scudder <noel.scudder at stonybrook.edu
> > wrote:
>
>> Hi yt users,
>>
>> I have a (hopefully) simple question I'm hoping to get cleared up.
>> I've run into the same error both in clump finding and volume rendering:
>> AttributeError: 'list' object has no attribute 'astype'.
>>
>> My volume rendering script:
>> ----------------------
>> from yt.mods import *
>> pf = load("plt_derr_perr_grav_00020")
>> field = "pressure"
>> pf.h
>>
>> #color transfer function/layer creation I'll leave out for clarity
>>
>> c = [5.0e9, 5.0e9, 5.0e9]
>> L = [0.15, 1.0, 0.20]
>> W = (pf.domain_right_edge - pf.domain_left_edge)*0.5
>> Nvec = 768
>>
>> cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = tf,
>> fields=[field], pf=pf, no_ghost=False)
>>
>> im = cam.snapshot(clip_ratio=6.0)
>>
>> ...
>> ----------------------
>>
>> Without "no_ghost=False", the script runs as it's supposed to. If it's
>> included, I get the following message:
>>
>>   File "<stdin>", line 1, in <module>
>>   File "volume.py", line 17, in <module>
>>     cam.snapshot("v1.png")
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py",
>> line 684, in snapshot
>>     self.initialize_source()
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py",
>> line 636, in initialize_source
>>     return self.volume.initialize_source()
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py",
>> line 200, in initialize_source
>>     for b in self.traverse():
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py",
>> line 210, in traverse
>>     yield self.get_brick_data(node)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py",
>> line 284, in get_brick_data
>>     vcd =
>> grid.get_vertex_centered_data(field,smoothed=True,no_ghost=self.no_ghost).astype('float64')
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line
>> 510, in get_vertex_centered_data
>>     cg = self.retrieve_ghost_zones(1, field, smoothed=smoothed)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line
>> 477, in retrieve_ghost_zones
>>     level, new_left_edge, **kwargs)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 3867, in __init__
>>     self.pf.domain_dimensions.astype("float64"))
>> AttributeError: 'list' object has no attribute 'astype'
>>
>>
>> My clump-finding script closely follows the "Identifying Clumps" recipe
>> in the cookbook:
>> ----------------------
>> from yt.mods import *
>> from yt.analysis_modules.level_sets.api import *
>>
>> field = "density"
>> step = 2.0
>>
>> pf = load("plt_derr_perr_grav_00020")
>> pf.h
>>
>> data_source = pf.h.all_data()
>> c_min = 10**na.floor(na.log10(data_source[field]).min()  )
>> c_max = 10**na.floor(na.log10(data_source[field]).max()+1)
>>
>> function = 'self.data[\'%s\'].size > 8' %field
>>
>> master_clump = Clump(data_source, None, field, function=function)
>> find_clumps(master_clump, c_min, c_max, step)
>>
>> ...
>> ----------------------
>> An error will occur occur at find_clumps:
>>
>> Finding clumps: min: 1.500000e-04, max: 1.500000e+07, step: 2.000000
>> First pass100%
>> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>> Time: 00:00:00
>> Traceback (most recent call last):
>>    | ETA:  --:--:--
>>   File "<stdin>", line 1, in <module>
>>   File "clumps.py", line 30, in <module>
>>     find_clumps(master_clump, c_min, c_max, step)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 179, in find_clumps
>>     clump.find_children(min_val)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 120, in find_children
>>     self.cached_fields)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/contour_finder.py",
>> line 107, in identify_contours
>>     cg = grid.retrieve_ghost_zones(1, "tempContours", smoothed=False)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line
>> 479, in retrieve_ghost_zones
>>     cube = self.hierarchy.covering_grid(level, new_left_edge, **kwargs)
>>   File
>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 3706, in __init__
>>     self.dds = self.pf.domain_width/rdx.astype("float64")
>> AttributeError: 'list' object has no attribute 'astype'
>>
>>
>> Can anyone tell me why I am getting this error in both cases? I've been
>> doing my utmost, but I'm not familiar enough with python nor yt yet.Thanks
>> for your help!
>>
>> Cheers,
>>
>> Noel Scudder
>>
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>>
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