Units for camera.draw_line
Hi yt-users, Newb question: I’m trying to draw a line on my volume render of some FLASH data using camera.draw_line but I’m getting an error. My guess is that it is something to do with units, but I can’t figure out how to fix what I’m doing. I’m assuming that draw_line using code units, which for FLASH should be cgs. Here is my code snippet: cam = ds.camera(c, L, W, N, transfer_function=tf, ds=ds, no_ghost=True, fields=field, log_fields=[False]) im = cam.snapshot() cam.draw_coordinate_vectors(im) cam.draw_domain(im) cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.]) And here is the error I get when I run it: Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.]) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 415, in draw_lin\ e dx0 = ((x0-self.origin)*self.orienter.unit_vectors[1]).sum() File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 716, in __rsub__ lo = sanitize_units_add(self, left_object, "subtraction") File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) yt.utilities.exceptions.YTUnitOperationError: The subtraction operator for YTArrays with units (code_length) an\ d (1) is not well defined. Any help or guidance would be much appreciated! Thanks, Sean ----------------------------------------------------------- Sean M. Couch Theoretical Astrophysics Including Relativity California Institute of Technology Mail Code 350-17 Pasadena, CA 91125 (626) 395-4282 www.tapir.caltech.edu/~smc <http://www.tapir.caltech.edu/~smc> _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Sean, Can you try again with: cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit) It looks like this function was never properly updated for yt-3.0. What's happening is that the camera's origin vector is a YTArray, but the second and third argument of the draw_line function are specified in that function's docstrings as ndarrays. When the draw_line function tries to compute the difference between camera.origin and [2e8, 0, 0], it throws a unit error (as it should) since camera.origin has units of code_length (which is the same as centimeters for your FLASH simulation), but x0 is unitless. We should probably add some code to the draw_line function so that if a user passes in a list or ndarray rather than a YTArray, we cast x0 and x1 to be YTArrays in code_length units. This would be a super simple initial contribution to yt, if you're up for it. -Nathan On Mon, Dec 29, 2014 at 2:07 PM, Sean Couch <smc@tapir.caltech.edu> wrote:
Hi yt-users,
Newb question: I’m trying to draw a line on my volume render of some FLASH data using camera.draw_line but I’m getting an error. My guess is that it is something to do with units, but I can’t figure out how to fix what I’m doing. I’m assuming that draw_line using code units, which for FLASH should be cgs. Here is my code snippet:
cam = ds.camera(c, L, W, N, transfer_function=tf, ds=ds, no_ghost=True, fields=field, log_fields=[False]) im = cam.snapshot()
cam.draw_coordinate_vectors(im) cam.draw_domain(im) cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.])
And here is the error I get when I run it:
Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.]) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 415, in draw_lin\ e dx0 = ((x0-self.origin)*self.orienter.unit_vectors[1]).sum() File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 716, in __rsub__ lo = sanitize_units_add(self, left_object, "subtraction") File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) yt.utilities.exceptions.YTUnitOperationError: The subtraction operator for YTArrays with units (code_length) an\ d (1) is not well defined.
Any help or guidance would be much appreciated!
Thanks, Sean
----------------------------------------------------------- Sean M. Couch Theoretical Astrophysics Including Relativity California Institute of Technology Mail Code 350-17 Pasadena, CA 91125 (626) 395-4282 www.tapir.caltech.edu/~smc
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Hi Nathan, Thanks! That seems to have fixed the units problem, but another has cropped up. I’m guessing this is related to draw_lines not being fully updated to yt 3.0: Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 426, in draw_lin\ e lines(im, np.array([px0,px1]), np.array([py0,py1]), color=np.array([color,color]),flip=1) File "misc_utilities.pyx", line 215, in yt.utilities.lib.misc_utilities.lines (yt/utilities/lib/misc_utilitie\ s.c:4877) I’m looking into the source code now, but I thought you might have an idea straightaway. Sean
On Dec 29, 2014, at 2:22 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Sean,
Can you try again with:
cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit)
It looks like this function was never properly updated for yt-3.0. What's happening is that the camera's origin vector is a YTArray, but the second and third argument of the draw_line function are specified in that function's docstrings as ndarrays. When the draw_line function tries to compute the difference between camera.origin and [2e8, 0, 0], it throws a unit error (as it should) since camera.origin has units of code_length (which is the same as centimeters for your FLASH simulation), but x0 is unitless.
We should probably add some code to the draw_line function so that if a user passes in a list or ndarray rather than a YTArray, we cast x0 and x1 to be YTArrays in code_length units. This would be a super simple initial contribution to yt, if you're up for it.
-Nathan
On Mon, Dec 29, 2014 at 2:07 PM, Sean Couch <smc@tapir.caltech.edu <mailto:smc@tapir.caltech.edu>> wrote: Hi yt-users,
Newb question: I’m trying to draw a line on my volume render of some FLASH data using camera.draw_line but I’m getting an error. My guess is that it is something to do with units, but I can’t figure out how to fix what I’m doing. I’m assuming that draw_line using code units, which for FLASH should be cgs. Here is my code snippet:
cam = ds.camera(c, L, W, N, transfer_function=tf, ds=ds, no_ghost=True, fields=field, log_fields=[False]) im = cam.snapshot()
cam.draw_coordinate_vectors(im) cam.draw_domain(im) cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.])
And here is the error I get when I run it:
Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.]) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 415, in draw_lin\ e dx0 = ((x0-self.origin)*self.orienter.unit_vectors[1]).sum() File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 716, in __rsub__ lo = sanitize_units_add(self, left_object, "subtraction") File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) yt.utilities.exceptions.YTUnitOperationError: The subtraction operator for YTArrays with units (code_length) an\ d (1) is not well defined.
Any help or guidance would be much appreciated!
Thanks, Sean
----------------------------------------------------------- Sean M. Couch Theoretical Astrophysics Including Relativity California Institute of Technology Mail Code 350-17 Pasadena, CA 91125 (626) 395-4282 <tel:%28626%29%20395-4282> www.tapir.caltech.edu/~smc <http://www.tapir.caltech.edu/~smc>
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On Mon, Dec 29, 2014 at 3:27 PM, Sean Couch <smc@tapir.caltech.edu> wrote:
Hi Nathan,
Thanks! That seems to have fixed the units problem, but another has cropped up. I’m guessing this is related to draw_lines not being fully updated to yt 3.0:
Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 426, in draw_lin\ e lines(im, np.array([px0,px1]), np.array([py0,py1]), color=np.array([color,color]),flip=1) File "misc_utilities.pyx", line 215, in yt.utilities.lib.misc_utilities.lines (yt/utilities/lib/misc_utilitie\ s.c:4877)
Yeah, it looks like it's not calling the lines() function correctly. I was able to reproduce this on my laptop and have issued a pull request to fix it, along with the issue you originally noticed with the draw_line function. The reason why this was never updated is that there aren't any tests for this function. To head off breakage in the future, I've also added a quick test for these functions. https://bitbucket.org/yt_analysis/yt/pull-request/1380/fixing-issues-with-th... You can test that locally by pulling in the changes to your local copy of the yt mercurial repository: $ hg pull -r 2596e9f https://bitbucket.org/ngoldbaum/yt $ hg update 2596e9f $ python setup.py develop You might see an error on the hg update step if you've made local changes. You can save any local changes you've made with "hg shelve" or just delete them with "hg update -C 2596e9f". If you could leave a comment saying whether or not this fixes your issue on the pull request, that would be great. -Nathan
I’m looking into the source code now, but I thought you might have an idea straightaway.
Sean
On Dec 29, 2014, at 2:22 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Sean,
Can you try again with:
cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit)
It looks like this function was never properly updated for yt-3.0. What's happening is that the camera's origin vector is a YTArray, but the second and third argument of the draw_line function are specified in that function's docstrings as ndarrays. When the draw_line function tries to compute the difference between camera.origin and [2e8, 0, 0], it throws a unit error (as it should) since camera.origin has units of code_length (which is the same as centimeters for your FLASH simulation), but x0 is unitless.
We should probably add some code to the draw_line function so that if a user passes in a list or ndarray rather than a YTArray, we cast x0 and x1 to be YTArrays in code_length units. This would be a super simple initial contribution to yt, if you're up for it.
-Nathan
On Mon, Dec 29, 2014 at 2:07 PM, Sean Couch <smc@tapir.caltech.edu> wrote:
Hi yt-users,
Newb question: I’m trying to draw a line on my volume render of some FLASH data using camera.draw_line but I’m getting an error. My guess is that it is something to do with units, but I can’t figure out how to fix what I’m doing. I’m assuming that draw_line using code units, which for FLASH should be cgs. Here is my code snippet:
cam = ds.camera(c, L, W, N, transfer_function=tf, ds=ds, no_ghost=True, fields=field, log_fields=[False]) im = cam.snapshot()
cam.draw_coordinate_vectors(im) cam.draw_domain(im) cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.])
And here is the error I get when I run it:
Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.]) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 415, in draw_lin\ e dx0 = ((x0-self.origin)*self.orienter.unit_vectors[1]).sum() File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 716, in __rsub__ lo = sanitize_units_add(self, left_object, "subtraction") File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) yt.utilities.exceptions.YTUnitOperationError: The subtraction operator for YTArrays with units (code_length) an\ d (1) is not well defined.
Any help or guidance would be much appreciated!
Thanks, Sean
----------------------------------------------------------- Sean M. Couch Theoretical Astrophysics Including Relativity California Institute of Technology Mail Code 350-17 Pasadena, CA 91125 (626) 395-4282 www.tapir.caltech.edu/~smc
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Thanks, Nathan! This fixed it. Comment left also on pull request. Sean
On Dec 29, 2014, at 4:24 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Mon, Dec 29, 2014 at 3:27 PM, Sean Couch <smc@tapir.caltech.edu <mailto:smc@tapir.caltech.edu>> wrote: Hi Nathan,
Thanks! That seems to have fixed the units problem, but another has cropped up. I’m guessing this is related to draw_lines not being fully updated to yt 3.0:
Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 426, in draw_lin\ e lines(im, np.array([px0,px1]), np.array([py0,py1]), color=np.array([color,color]),flip=1) File "misc_utilities.pyx", line 215, in yt.utilities.lib.misc_utilities.lines (yt/utilities/lib/misc_utilitie\ s.c:4877)
Yeah, it looks like it's not calling the lines() function correctly. I was able to reproduce this on my laptop and have issued a pull request to fix it, along with the issue you originally noticed with the draw_line function. The reason why this was never updated is that there aren't any tests for this function. To head off breakage in the future, I've also added a quick test for these functions.
https://bitbucket.org/yt_analysis/yt/pull-request/1380/fixing-issues-with-th... <https://bitbucket.org/yt_analysis/yt/pull-request/1380/fixing-issues-with-the-draw_line-function/diff>
You can test that locally by pulling in the changes to your local copy of the yt mercurial repository:
$ hg pull -r 2596e9f https://bitbucket.org/ngoldbaum/yt <https://bitbucket.org/ngoldbaum/yt> $ hg update 2596e9f $ python setup.py develop
You might see an error on the hg update step if you've made local changes. You can save any local changes you've made with "hg shelve" or just delete them with "hg update -C 2596e9f".
If you could leave a comment saying whether or not this fixes your issue on the pull request, that would be great.
-Nathan
I’m looking into the source code now, but I thought you might have an idea straightaway.
Sean
On Dec 29, 2014, at 2:22 PM, Nathan Goldbaum <nathan12343@gmail.com <mailto:nathan12343@gmail.com>> wrote:
Hi Sean,
Can you try again with:
cam.draw_line(im, [2e8,0.,0.]*ds.length_unit, [0.,2e8,0.]*ds.length_unit)
It looks like this function was never properly updated for yt-3.0. What's happening is that the camera's origin vector is a YTArray, but the second and third argument of the draw_line function are specified in that function's docstrings as ndarrays. When the draw_line function tries to compute the difference between camera.origin and [2e8, 0, 0], it throws a unit error (as it should) since camera.origin has units of code_length (which is the same as centimeters for your FLASH simulation), but x0 is unitless.
We should probably add some code to the draw_line function so that if a user passes in a list or ndarray rather than a YTArray, we cast x0 and x1 to be YTArrays in code_length units. This would be a super simple initial contribution to yt, if you're up for it.
-Nathan
On Mon, Dec 29, 2014 at 2:07 PM, Sean Couch <smc@tapir.caltech.edu <mailto:smc@tapir.caltech.edu>> wrote: Hi yt-users,
Newb question: I’m trying to draw a line on my volume render of some FLASH data using camera.draw_line but I’m getting an error. My guess is that it is something to do with units, but I can’t figure out how to fix what I’m doing. I’m assuming that draw_line using code units, which for FLASH should be cgs. Here is my code snippet:
cam = ds.camera(c, L, W, N, transfer_function=tf, ds=ds, no_ghost=True, fields=field, log_fields=[False]) im = cam.snapshot()
cam.draw_coordinate_vectors(im) cam.draw_domain(im) cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.])
And here is the error I get when I run it:
Traceback (most recent call last): File "render_radv.py", line 53, in <module> cam.draw_line(im, [2e8,0.,0.], [0.,2e8,0.]) File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 415, in draw_lin\ e dx0 = ((x0-self.origin)*self.orienter.unit_vectors[1]).sum() File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 716, in __rsub__ lo = sanitize_units_add(self, left_object, "subtraction") File "/work/00863/smc/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) yt.utilities.exceptions.YTUnitOperationError: The subtraction operator for YTArrays with units (code_length) an\ d (1) is not well defined.
Any help or guidance would be much appreciated!
Thanks, Sean
----------------------------------------------------------- Sean M. Couch Theoretical Astrophysics Including Relativity California Institute of Technology Mail Code 350-17 Pasadena, CA 91125 (626) 395-4282 <tel:%28626%29%20395-4282> www.tapir.caltech.edu/~smc <http://www.tapir.caltech.edu/~smc>
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participants (2)
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Nathan Goldbaum -
Sean Couch