ZeroDivisionError accessing field from ray in spherical 1D FLASH data
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division --------------------------------------------------------------------------- ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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 Luke,
Nah, not a bad influence. Try putting it at the cell center instead of the cell edge. :) (0.0, 0.0) will be the very corner of the domain, so it's skimming along the surface of a cell.
On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer
ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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
Thanks for working with me on this Matt, but I got a new one for you:
In [164]: print pf.domain_width [ 4.00000000e+11 3.14159265e+00 1.74532925e-02]
In [165]: ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5)) yt : [INFO ] 2014-06-23 14:22:26,386 Getting field x from 0 ERROR: ValueError: need at least one array to concatenate [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:22:26,386 ValueError: need at least one array to concatenate --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-165-9633905f901e> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
ValueError: need at least one array to concatenate
could this be something about the data being 1D?
Actually, I have no idea if this means anything, but when I ask for the dimensionality:
In [172]: pf.dimensionality Out[172]: 2
In [171]: pf.domain_dimensions Out[171]: array([ 8, 16, 1])
But my FLASH log confirms the dimensionality is 1...
On Jun 23, 2014, at 2:19 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Nah, not a bad influence. Try putting it at the cell center instead of the cell edge. :) (0.0, 0.0) will be the very corner of the domain, so it's skimming along the surface of a cell.
On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer
ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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Hi Luke,
Not sure if the dimensionality is a problem or not. But it's saying it doesn't find any grids intersecting with the ray, which is confusing. What's the output of "pf.domain_left_edge" and "pf.domain_right_edge"?
On Mon, Jun 23, 2014 at 1:27 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks for working with me on this Matt, but I got a new one for you:
In [164]: print pf.domain_width [ 4.00000000e+11 3.14159265e+00 1.74532925e-02]
In [165]: ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5)) yt : [INFO ] 2014-06-23 14:22:26,386 Getting field x from 0 ERROR: ValueError: need at least one array to concatenate [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:22:26,386 ValueError: need at least one array to concatenate
ValueError Traceback (most recent call last) <ipython-input-165-9633905f901e> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
ValueError: need at least one array to concatenate
could this be something about the data being 1D?
Actually, I have no idea if this means anything, but when I ask for the dimensionality:
In [172]: pf.dimensionality Out[172]: 2
In [171]: pf.domain_dimensions Out[171]: array([ 8, 16, 1])
But my FLASH log confirms the dimensionality is 1...
On Jun 23, 2014, at 2:19 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Nah, not a bad influence. Try putting it at the cell center instead of the cell edge. :) (0.0, 0.0) will be the very corner of the domain, so it's skimming along the surface of a cell.
On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer
ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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In [173]: pf.domain_left_edge Out[173]: array([ 0., 0., 0.])
In [174]: pf.domain_right_edge Out[174]: array([ 4.00000000e+11, 3.14159265e+00, 1.74532925e-02])
On Jun 23, 2014, at 2:35 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Not sure if the dimensionality is a problem or not. But it's saying it doesn't find any grids intersecting with the ray, which is confusing. What's the output of "pf.domain_left_edge" and "pf.domain_right_edge"?
On Mon, Jun 23, 2014 at 1:27 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks for working with me on this Matt, but I got a new one for you:
In [164]: print pf.domain_width [ 4.00000000e+11 3.14159265e+00 1.74532925e-02]
In [165]: ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5)) yt : [INFO ] 2014-06-23 14:22:26,386 Getting field x from 0 ERROR: ValueError: need at least one array to concatenate [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:22:26,386 ValueError: need at least one array to concatenate
ValueError Traceback (most recent call last) <ipython-input-165-9633905f901e> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
ValueError: need at least one array to concatenate
could this be something about the data being 1D?
Actually, I have no idea if this means anything, but when I ask for the dimensionality:
In [172]: pf.dimensionality Out[172]: 2
In [171]: pf.domain_dimensions Out[171]: array([ 8, 16, 1])
But my FLASH log confirms the dimensionality is 1...
On Jun 23, 2014, at 2:19 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Nah, not a bad influence. Try putting it at the cell center instead of the cell edge. :) (0.0, 0.0) will be the very corner of the domain, so it's skimming along the surface of a cell.
On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer
ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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Well, that's weird! It might be related to it being in 1D. Can you try doing a similar operation with a yt-3.0 "bleeding edge" install? 3.0 will have much better support for spherical data.
On Mon, Jun 23, 2014 at 1:38 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
In [173]: pf.domain_left_edge Out[173]: array([ 0., 0., 0.])
In [174]: pf.domain_right_edge Out[174]: array([ 4.00000000e+11, 3.14159265e+00, 1.74532925e-02])
On Jun 23, 2014, at 2:35 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Not sure if the dimensionality is a problem or not. But it's saying it doesn't find any grids intersecting with the ray, which is confusing. What's the output of "pf.domain_left_edge" and "pf.domain_right_edge"?
On Mon, Jun 23, 2014 at 1:27 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks for working with me on this Matt, but I got a new one for you:
In [164]: print pf.domain_width [ 4.00000000e+11 3.14159265e+00 1.74532925e-02]
In [165]: ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5)) yt : [INFO ] 2014-06-23 14:22:26,386 Getting field x from 0 ERROR: ValueError: need at least one array to concatenate [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:22:26,386 ValueError: need at least one array to concatenate
ValueError Traceback (most recent call last) <ipython-input-165-9633905f901e> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
ValueError: need at least one array to concatenate
could this be something about the data being 1D?
Actually, I have no idea if this means anything, but when I ask for the dimensionality:
In [172]: pf.dimensionality Out[172]: 2
In [171]: pf.domain_dimensions Out[171]: array([ 8, 16, 1])
But my FLASH log confirms the dimensionality is 1...
On Jun 23, 2014, at 2:19 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Nah, not a bad influence. Try putting it at the cell center instead of the cell edge. :) (0.0, 0.0) will be the very corner of the domain, so it's skimming along the surface of a cell.
On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer
ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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That worked! Thanks!
On Jun 23, 2014, at 3:14 PM, Matthew Turk matthewturk@gmail.com wrote:
Well, that's weird! It might be related to it being in 1D. Can you try doing a similar operation with a yt-3.0 "bleeding edge" install? 3.0 will have much better support for spherical data.
On Mon, Jun 23, 2014 at 1:38 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
In [173]: pf.domain_left_edge Out[173]: array([ 0., 0., 0.])
In [174]: pf.domain_right_edge Out[174]: array([ 4.00000000e+11, 3.14159265e+00, 1.74532925e-02])
On Jun 23, 2014, at 2:35 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Not sure if the dimensionality is a problem or not. But it's saying it doesn't find any grids intersecting with the ray, which is confusing. What's the output of "pf.domain_left_edge" and "pf.domain_right_edge"?
On Mon, Jun 23, 2014 at 1:27 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks for working with me on this Matt, but I got a new one for you:
In [164]: print pf.domain_width [ 4.00000000e+11 3.14159265e+00 1.74532925e-02]
In [165]: ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5)) yt : [INFO ] 2014-06-23 14:22:26,386 Getting field x from 0 ERROR: ValueError: need at least one array to concatenate [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:22:26,386 ValueError: need at least one array to concatenate
ValueError Traceback (most recent call last) <ipython-input-165-9633905f901e> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (3.14*0.5, 1.75e-2*0.5))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
ValueError: need at least one array to concatenate
could this be something about the data being 1D?
Actually, I have no idea if this means anything, but when I ask for the dimensionality:
In [172]: pf.dimensionality Out[172]: 2
In [171]: pf.domain_dimensions Out[171]: array([ 8, 16, 1])
But my FLASH log confirms the dimensionality is 1...
On Jun 23, 2014, at 2:19 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
Nah, not a bad influence. Try putting it at the cell center instead of the cell edge. :) (0.0, 0.0) will be the very corner of the domain, so it's skimming along the surface of a cell.
On Mon, Jun 23, 2014 at 1:16 PM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Thanks Matt, but now I'm having new problems with 'ortho_ray', following (http://yt-project.org/doc/visualizing/manual_plotting.html), I tried
> ray = pf.h.ortho_ray(0, (0.0,0.0))
which then gave me
yt : [INFO ] 2014-06-23 14:15:52,664 Getting field x from 8 ERROR: ValueError: cannot convert float NaN to integer [yt.data_objects.data_containers] astropy: [ERROR ] 2014-06-23 14:15:52,664 ValueError: cannot convert float NaN to integer
ValueError Traceback (most recent call last) <ipython-input-157-318ebcfbdb94> in <module>() ----> 1 ray = pf.h.ortho_ray(0, (0.0,0.0))
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, coords, fields, pf, **kwargs) 578 self.px, self.py = coords 579 self.sort_by = axis_names[self.axis] --> 580 self._refresh_data() 581 582 @property
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 304 """ 305 self.clear_data() --> 306 self.get_data() 307 308 def keys(self):
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 599 gdx = just_one(grid[self.px_dx]) 600 gdy = just_one(grid[self.py_dx]) --> 601 x_coord = int((self.px - grid.LeftEdge[self.px_ax])/gdx) 602 y_coord = int((self.py - grid.LeftEdge[self.py_ax])/gdy) 603 sl = [None,None,None]
ValueError: cannot convert float NaN to integer
Without doing anything wrong, perhaps I'm just a bad influence.
Luke
On Jun 23, 2014, at 2:05 PM, Matthew Turk matthewturk@gmail.com wrote:
Hi Luke,
You didn't do anything wrong. :) yt should be able to accept rays through "ray" that are orthogonal to the axes, but it can't because of some sloppiness. You have two options -- either use "ortho_ray" instead of "ray", which will make it orthogonal (and probably be a bit faster) or add jitter to the tune of 1e-12 to your 0.0 entries.
-Matt
On Mon, Jun 23, 2014 at 11:44 AM, Luke Zoltan Kelley lkelley@cfa.harvard.edu wrote:
Hello yt-users,
Just starting using YT, please forgive simple problems.
I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error:
from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density']
yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division
ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density']
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id]
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts)
/Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)()
ZeroDivisionError: float division
yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef
Any ideas what I'm doing wrong? Thanks! Luke
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participants (2)
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Luke Zoltan Kelley -
Matthew Turk