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

[Nathan Goldbaum]

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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