Oh - this is for Castro. On Tue, Jul 2, 2013 at 1:53 PM, Noel Scudder wrote:

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 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@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

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi Noel, I've submitted a patch for this: https://bitbucket.org/yt_analysis/yt/pull-request/541/ensuring-that-castro-d... To test it out, navigate to the yt source directory and do: hg pull -r af95c72 https://bitbucket.org/ngoldbaum/yt hg up python setup.py build_ext -i And then run your test scripts one more time. Please comment on the PR if it fixes your problems. -Nathan On Tue, Jul 2, 2013 at 10:56 AM, Nathan Goldbaum wrote:

No, I mean which simulation code. I'll need to patch the frontend for that simulation code.

On Tue, Jul 2, 2013 at 10:53 AM, Noel Scudder

...

wrote:

...

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 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@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

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org