Hi, I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else? Thanks! Stella
Hi Stella, I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing: pf.h.camera and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself. Let me know if you run into any more problems! -Matt On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi,
I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else?
Thanks! Stella _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Matt, Thanks! That got me past the camera-specific error. However, I am running into an error in amr_kdtree, which has a call in the old form to pf['DomainLeftEdge']: KeyError Traceback (most recent call last) /n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 135 cam = pf.h.camera(c, L, W, (Nvec,Nvec), 136 transfer_function = tf, pf = pf, fields=["log_den"], --> 137 north_vector = north) 138 cam.zoom(1.0) 139 #take a picture /n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/ volume_rendering/camera.pyc in __init__(self, center, normal_vector, width, resolution, transfer_function, north_vector, steady_north, volume, fields, log_fields, sub_samples, pf, use_kd, l_max, no_ghost, tree_type) 193 if self.use_kd: 194 volume = AMRKDTree(self.pf, l_max=l_max, fields=self.fields, no_ghost=no_ghost, tree_type=tree_type, --> 195 log_fields = log_fields) 196 else: 197 volume = HomogenizedVolume(fields, pf = self.pf, /n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/ amr_kdtree.pyc in __init__(self, pf, l_max, le, re, fields, no_ghost, tree_type, log_fields) 271 272 if le is None: --> 273 self.domain_left_edge = pf['DomainLeftEdge'] 274 else: 275 self.domain_left_edge = le /n/home05/soffner/yt-x86_64/src/yt-hg/yt/data_objects/ static_output.pyc in __getitem__(self, key) 113 self.conversion_factors]: 114 if key in d: return d[key] --> 115 raise KeyError(key) 116 117 def keys(self): KeyError: 'DomainLeftEdge' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ ytwindmovie.py> On Nov 23, 2010, at 3:32 PM, Matthew Turk wrote:
Hi Stella,
I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing:
pf.h.camera
and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself.
Let me know if you run into any more problems!
-Matt
On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner <soffner@cfa.harvard.edu
wrote: Hi,
I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else?
Thanks! Stella _______________________________________________ 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 Stella, You're right, that code was not using the correct parameters. I have corrected it and pushed a new changeset. -Matt PS For what it's worth, this doesn't seem to be related to Mike's problem from the other thread, which I will defer to the author of the amr_kdtree module, Sam Skillman. :) On Tue, Nov 23, 2010 at 3:49 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi Matt,
Thanks! That got me past the camera-specific error. However, I am running into an error in amr_kdtree, which has a call in the old form to pf['DomainLeftEdge']:
KeyError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 135 cam = pf.h.camera(c, L, W, (Nvec,Nvec), 136 transfer_function = tf, pf = pf, fields=["log_den"], --> 137 north_vector = north) 138 cam.zoom(1.0) 139 #take a picture
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc in __init__(self, center, normal_vector, width, resolution, transfer_function, north_vector, steady_north, volume, fields, log_fields, sub_samples, pf, use_kd, l_max, no_ghost, tree_type) 193 if self.use_kd: 194 volume = AMRKDTree(self.pf, l_max=l_max, fields=self.fields, no_ghost=no_ghost, tree_type=tree_type, --> 195 log_fields = log_fields) 196 else: 197 volume = HomogenizedVolume(fields, pf = self.pf,
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc in __init__(self, pf, l_max, le, re, fields, no_ghost, tree_type, log_fields) 271 272 if le is None: --> 273 self.domain_left_edge = pf['DomainLeftEdge'] 274 else: 275 self.domain_left_edge = le
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in __getitem__(self, key) 113 self.conversion_factors]: 114 if key in d: return d[key] --> 115 raise KeyError(key) 116 117 def keys(self):
KeyError: 'DomainLeftEdge' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:32 PM, Matthew Turk wrote:
Hi Stella,
I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing:
pf.h.camera
and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself.
Let me know if you run into any more problems!
-Matt
On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi,
I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else?
Thanks! Stella _______________________________________________ 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
Hi Matt, Thanks, again! Now a new error: I called camera with a log_fields argument, but it seems that kd tree code does not recognize this. Sadly, if I bi-pass this by not using the log field, the code seg faults right after 'About to cast'. This last thing could just be my script. Anyway, I'm using the latest, rather than the stable version, which maybe I should use instead. AttributeError Traceback (most recent call last) /n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 140 cam.zoom(1.0) 141 #take a picture --> 142 vals = cam.snapshot() 143 max = vals.max() 144 print "Max= ", max, "Min= ", vals.min() /n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/ volume_rendering/camera.pyc in snapshot(self, fn) 324 tfp = TransferFunctionProxy(self.transfer_function) # Reset it every time 325 tfp.ns = self.sub_samples --> 326 self.volume.initialize_source() 327 if self.use_kd: 328 self.volume.reset_cast() /n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/ amr_kdtree.pyc in initialize_source(self) 773 def initialize_source(self): 774 if self.tree_type is 'domain': --> 775 self.get_bricks() 776 777 def kd_ray_cast(self,image, tfp, vector_plane, back_center, front_center): /n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/ amr_kdtree.pyc in get_bricks(self) 345 for i,field in enumerate(self.fields): 346 vcd = current_node ['grid '].get_vertex_centered_data (field,smoothed=True,no_ghost=self.no_ghost).astype('float64') --> 347 if self.log_field[i]: vcd = na.log10(vcd) 348 dds.append(vcd) 349 current_saved_grids.append(current_node['grid']) AttributeError: 'AMRKDTree' object has no attribute 'log_field' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ ytwindmovie.py> On Nov 23, 2010, at 3:51 PM, Matthew Turk wrote:
Hi Stella,
You're right, that code was not using the correct parameters. I have corrected it and pushed a new changeset.
-Matt
PS For what it's worth, this doesn't seem to be related to Mike's problem from the other thread, which I will defer to the author of the amr_kdtree module, Sam Skillman. :)
On Tue, Nov 23, 2010 at 3:49 PM, Stella Offner <soffner@cfa.harvard.edu
wrote: Hi Matt,
Thanks! That got me past the camera-specific error. However, I am running into an error in amr_kdtree, which has a call in the old form to pf['DomainLeftEdge']:
KeyError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 135 cam = pf.h.camera(c, L, W, (Nvec,Nvec), 136 transfer_function = tf, pf = pf, fields=["log_den"], --> 137 north_vector = north) 138 cam.zoom(1.0) 139 #take a picture
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/ volume_rendering/camera.pyc in __init__(self, center, normal_vector, width, resolution, transfer_function, north_vector, steady_north, volume, fields, log_fields, sub_samples, pf, use_kd, l_max, no_ghost, tree_type) 193 if self.use_kd: 194 volume = AMRKDTree(self.pf, l_max=l_max, fields=self.fields, no_ghost=no_ghost, tree_type=tree_type, --> 195 log_fields = log_fields) 196 else: 197 volume = HomogenizedVolume(fields, pf = self.pf,
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/ amr_kdtree.pyc in __init__(self, pf, l_max, le, re, fields, no_ghost, tree_type, log_fields) 271 272 if le is None: --> 273 self.domain_left_edge = pf['DomainLeftEdge'] 274 else: 275 self.domain_left_edge = le
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/data_objects/ static_output.pyc in __getitem__(self, key) 113 self.conversion_factors]: 114 if key in d: return d[key] --> 115 raise KeyError(key) 116 117 def keys(self):
KeyError: 'DomainLeftEdge' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:32 PM, Matthew Turk wrote:
Hi Stella,
I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing:
pf.h.camera
and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself.
Let me know if you run into any more problems!
-Matt
On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner <soffner@cfa.harvard.edu
wrote:
Hi,
I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else?
Thanks! Stella _______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Stella, It looks to me like the amr_kdtree did not, in fact, retain API compatibility with the old mechanism for grid homogenization. I took have seen segfaults from the casting segment, but I believed them to be a result of a poor choice in field tables, as I was actually projecting some odd derived quantities. Evidently this was not the case, and there is an underlying problem. To work around this, I suggest you use the old version. To do this, you can either supply a volume (using HomogenizedVolume, as in the past) or supply the keyword argument use_kd=False when creating the camera object. The latter is probably easier. Let me know if this *still* gives you problems. I'm sorry that this has been a hassle. -Matt On Tue, Nov 23, 2010 at 4:30 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi Matt,
Thanks, again! Now a new error: I called camera with a log_fields argument, but it seems that kd tree code does not recognize this. Sadly, if I bi-pass this by not using the log field, the code seg faults right after 'About to cast'. This last thing could just be my script. Anyway, I'm using the latest, rather than the stable version, which maybe I should use instead.
AttributeError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 140 cam.zoom(1.0) 141 #take a picture --> 142 vals = cam.snapshot() 143 max = vals.max() 144 print "Max= ", max, "Min= ", vals.min()
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc in snapshot(self, fn) 324 tfp = TransferFunctionProxy(self.transfer_function) # Reset it every time 325 tfp.ns = self.sub_samples --> 326 self.volume.initialize_source() 327 if self.use_kd: 328 self.volume.reset_cast()
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc in initialize_source(self) 773 def initialize_source(self): 774 if self.tree_type is 'domain': --> 775 self.get_bricks() 776 777 def kd_ray_cast(self,image, tfp, vector_plane, back_center, front_center):
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc in get_bricks(self) 345 for i,field in enumerate(self.fields): 346 vcd = current_node['grid'].get_vertex_centered_data(field,smoothed=True,no_ghost=self.no_ghost).astype('float64') --> 347 if self.log_field[i]: vcd = na.log10(vcd) 348 dds.append(vcd) 349 current_saved_grids.append(current_node['grid'])
AttributeError: 'AMRKDTree' object has no attribute 'log_field' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:51 PM, Matthew Turk wrote:
Hi Stella,
You're right, that code was not using the correct parameters. I have corrected it and pushed a new changeset.
-Matt
PS For what it's worth, this doesn't seem to be related to Mike's problem from the other thread, which I will defer to the author of the amr_kdtree module, Sam Skillman. :)
On Tue, Nov 23, 2010 at 3:49 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi Matt,
Thanks! That got me past the camera-specific error. However, I am running into an error in amr_kdtree, which has a call in the old form to pf['DomainLeftEdge']:
KeyError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 135 cam = pf.h.camera(c, L, W, (Nvec,Nvec), 136 transfer_function = tf, pf = pf, fields=["log_den"], --> 137 north_vector = north) 138 cam.zoom(1.0) 139 #take a picture
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc in __init__(self, center, normal_vector, width, resolution, transfer_function, north_vector, steady_north, volume, fields, log_fields, sub_samples, pf, use_kd, l_max, no_ghost, tree_type) 193 if self.use_kd: 194 volume = AMRKDTree(self.pf, l_max=l_max, fields=self.fields, no_ghost=no_ghost, tree_type=tree_type, --> 195 log_fields = log_fields) 196 else: 197 volume = HomogenizedVolume(fields, pf = self.pf,
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc in __init__(self, pf, l_max, le, re, fields, no_ghost, tree_type, log_fields) 271 272 if le is None: --> 273 self.domain_left_edge = pf['DomainLeftEdge'] 274 else: 275 self.domain_left_edge = le
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in __getitem__(self, key) 113 self.conversion_factors]: 114 if key in d: return d[key] --> 115 raise KeyError(key) 116 117 def keys(self):
KeyError: 'DomainLeftEdge' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:32 PM, Matthew Turk wrote:
Hi Stella,
I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing:
pf.h.camera
and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself.
Let me know if you run into any more problems!
-Matt
On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi,
I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else?
Thanks! Stella _______________________________________________ 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
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Hi guys, I was recently trying to render some derived fields that can have some zero values in them, and this was giving me seg faults as well in seemingly the same place. I went into the definition of the field and put in nonzero, but quite small, floor value and this went away. Britton On Tue, Nov 23, 2010 at 5:30 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Stella,
It looks to me like the amr_kdtree did not, in fact, retain API compatibility with the old mechanism for grid homogenization. I took have seen segfaults from the casting segment, but I believed them to be a result of a poor choice in field tables, as I was actually projecting some odd derived quantities. Evidently this was not the case, and there is an underlying problem.
To work around this, I suggest you use the old version. To do this, you can either supply a volume (using HomogenizedVolume, as in the past) or supply the keyword argument use_kd=False when creating the camera object. The latter is probably easier.
Let me know if this *still* gives you problems. I'm sorry that this has been a hassle.
-Matt
On Tue, Nov 23, 2010 at 4:30 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi Matt,
Thanks, again! Now a new error: I called camera with a log_fields argument, but it seems that kd tree code does not recognize this. Sadly, if I bi-pass this by not using the log field, the code seg faults right after 'About to cast'. This last thing could just be my script. Anyway, I'm using the latest, rather than the stable version, which maybe I should use instead.
AttributeError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 140 cam.zoom(1.0) 141 #take a picture --> 142 vals = cam.snapshot() 143 max = vals.max() 144 print "Max= ", max, "Min= ", vals.min()
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc
in snapshot(self, fn) 324 tfp = TransferFunctionProxy(self.transfer_function) # Reset it every time 325 tfp.ns = self.sub_samples --> 326 self.volume.initialize_source() 327 if self.use_kd: 328 self.volume.reset_cast()
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc
in initialize_source(self) 773 def initialize_source(self): 774 if self.tree_type is 'domain': --> 775 self.get_bricks() 776 777 def kd_ray_cast(self,image, tfp, vector_plane, back_center, front_center):
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc
in get_bricks(self) 345 for i,field in enumerate(self.fields): 346 vcd =
current_node['grid'].get_vertex_centered_data(field,smoothed=True,no_ghost=self.no_ghost).astype('float64')
--> 347 if self.log_field[i]: vcd = na.log10(vcd) 348 dds.append(vcd) 349 current_saved_grids.append(current_node['grid'])
AttributeError: 'AMRKDTree' object has no attribute 'log_field' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:51 PM, Matthew Turk wrote:
Hi Stella,
You're right, that code was not using the correct parameters. I have corrected it and pushed a new changeset.
-Matt
PS For what it's worth, this doesn't seem to be related to Mike's problem from the other thread, which I will defer to the author of the amr_kdtree module, Sam Skillman. :)
On Tue, Nov 23, 2010 at 3:49 PM, Stella Offner <soffner@cfa.harvard.edu
wrote:
Hi Matt,
Thanks! That got me past the camera-specific error. However, I am
running
into an error in amr_kdtree, which has a call in the old form to pf['DomainLeftEdge']:
KeyError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 135 cam = pf.h.camera(c, L, W, (Nvec,Nvec), 136 transfer_function = tf, pf = pf, fields=["log_den"], --> 137 north_vector = north) 138 cam.zoom(1.0) 139 #take a picture
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc
in __init__(self, center, normal_vector, width, resolution, transfer_function, north_vector, steady_north, volume, fields, log_fields, sub_samples, pf, use_kd, l_max, no_ghost, tree_type) 193 if self.use_kd: 194 volume = AMRKDTree(self.pf, l_max=l_max, fields=self.fields, no_ghost=no_ghost, tree_type=tree_type, --> 195 log_fields = log_fields) 196 else: 197 volume = HomogenizedVolume(fields, pf = self.pf,
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc
in __init__(self, pf, l_max, le, re, fields, no_ghost, tree_type, log_fields) 271 272 if le is None: --> 273 self.domain_left_edge = pf['DomainLeftEdge'] 274 else: 275 self.domain_left_edge = le
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in __getitem__(self, key) 113 self.conversion_factors]: 114 if key in d: return d[key] --> 115 raise KeyError(key) 116 117 def keys(self):
KeyError: 'DomainLeftEdge' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:32 PM, Matthew Turk wrote:
Hi Stella,
I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing:
pf.h.camera
and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself.
Let me know if you run into any more problems!
-Matt
On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner < soffner@cfa.harvard.edu> wrote:
Hi,
I updated yt to the new release, and now I'm getting 'NameError:
name
'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else?
Thanks! Stella _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi All, I've pushed a change (c8a955052039) that _should_ fix this issue. If it doesn't work, could one of you send me a full example script off list that seems to get the right answer (and runs) with the older homogenized volume? Best, Sam On Tue, Nov 23, 2010 at 3:43 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi guys,
I was recently trying to render some derived fields that can have some zero values in them, and this was giving me seg faults as well in seemingly the same place. I went into the definition of the field and put in nonzero, but quite small, floor value and this went away.
Britton
On Tue, Nov 23, 2010 at 5:30 PM, Matthew Turk <matthewturk@gmail.com>wrote:
Hi Stella,
It looks to me like the amr_kdtree did not, in fact, retain API compatibility with the old mechanism for grid homogenization. I took have seen segfaults from the casting segment, but I believed them to be a result of a poor choice in field tables, as I was actually projecting some odd derived quantities. Evidently this was not the case, and there is an underlying problem.
To work around this, I suggest you use the old version. To do this, you can either supply a volume (using HomogenizedVolume, as in the past) or supply the keyword argument use_kd=False when creating the camera object. The latter is probably easier.
Let me know if this *still* gives you problems. I'm sorry that this has been a hassle.
-Matt
On Tue, Nov 23, 2010 at 4:30 PM, Stella Offner <soffner@cfa.harvard.edu> wrote:
Hi Matt,
Thanks, again! Now a new error: I called camera with a log_fields argument, but it seems that kd tree code does not recognize this. Sadly, if I bi-pass this by not using the log field, the code seg faults right after 'About to cast'. This last thing could just be my script. Anyway, I'm using the latest, rather than the stable version, which maybe I should use instead.
AttributeError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 140 cam.zoom(1.0) 141 #take a picture --> 142 vals = cam.snapshot() 143 max = vals.max() 144 print "Max= ", max, "Min= ", vals.min()
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc
in snapshot(self, fn) 324 tfp = TransferFunctionProxy(self.transfer_function) # Reset it every time 325 tfp.ns = self.sub_samples --> 326 self.volume.initialize_source() 327 if self.use_kd: 328 self.volume.reset_cast()
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc
in initialize_source(self) 773 def initialize_source(self): 774 if self.tree_type is 'domain': --> 775 self.get_bricks() 776 777 def kd_ray_cast(self,image, tfp, vector_plane, back_center, front_center):
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc
in get_bricks(self) 345 for i,field in enumerate(self.fields): 346 vcd =
current_node['grid'].get_vertex_centered_data(field,smoothed=True,no_ghost=self.no_ghost).astype('float64')
--> 347 if self.log_field[i]: vcd = na.log10(vcd) 348 dds.append(vcd) 349 current_saved_grids.append(current_node['grid'])
AttributeError: 'AMRKDTree' object has no attribute 'log_field' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:51 PM, Matthew Turk wrote:
Hi Stella,
You're right, that code was not using the correct parameters. I have corrected it and pushed a new changeset.
-Matt
PS For what it's worth, this doesn't seem to be related to Mike's problem from the other thread, which I will defer to the author of the amr_kdtree module, Sam Skillman. :)
On Tue, Nov 23, 2010 at 3:49 PM, Stella Offner < soffner@cfa.harvard.edu> wrote:
Hi Matt,
Thanks! That got me past the camera-specific error. However, I am
running
into an error in amr_kdtree, which has a call in the old form to pf['DomainLeftEdge']:
KeyError Traceback (most recent call last)
/n/home05/soffner/yt-x86_64/src/yt-hg/scripts/iyt in <module>() 135 cam = pf.h.camera(c, L, W, (Nvec,Nvec), 136 transfer_function = tf, pf = pf, fields=["log_den"], --> 137 north_vector = north) 138 cam.zoom(1.0) 139 #take a picture
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.pyc
in __init__(self, center, normal_vector, width, resolution, transfer_function, north_vector, steady_north, volume, fields, log_fields, sub_samples, pf, use_kd, l_max, no_ghost, tree_type) 193 if self.use_kd: 194 volume = AMRKDTree(self.pf, l_max=l_max, fields=self.fields, no_ghost=no_ghost, tree_type=tree_type, --> 195 log_fields = log_fields) 196 else: 197 volume = HomogenizedVolume(fields, pf = self.pf ,
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc
in __init__(self, pf, l_max, le, re, fields, no_ghost, tree_type, log_fields) 271 272 if le is None: --> 273 self.domain_left_edge = pf['DomainLeftEdge'] 274 else: 275 self.domain_left_edge = le
/n/home05/soffner/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc
in __getitem__(self, key) 113 self.conversion_factors]: 114 if key in d: return d[key] --> 115 raise KeyError(key) 116 117 def keys(self):
KeyError: 'DomainLeftEdge' WARNING: Failure executing file: </n/home05/soffner/ytorionlib/ytwindmovie.py>
On Nov 23, 2010, at 3:32 PM, Matthew Turk wrote:
Hi Stella,
I've just pushed a change to include Camera and HomogenizedVolume in the yt.mods import. I also wanted to note that you can get a camera by doing:
pf.h.camera
and that I think unless you're doing something clever, you may no longer need to generate a HomogenizedVolume by hand. I think by default Camera will use the kD-tree, now, so you should be set just specifying the parameters for the rendering to pf.h.camera, and not the volume itself.
Let me know if you run into any more problems!
-Matt
On Tue, Nov 23, 2010 at 3:28 PM, Stella Offner < soffner@cfa.harvard.edu> wrote: > > Hi, > > I updated yt to the new release, and now I'm getting 'NameError: name > 'Camera' is not defined' for Camera and HomogenizedVolume (these were > both > part of the volume_rendering extension previously). Did these get > renamed > or > do I need to import something else? > > Thanks! > Stella > _______________________________________________ > 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
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participants (4)
-
Britton Smith -
Matthew Turk -
Sam Skillman -
Stella Offner