Hi all: I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as: @derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"])) Then I add the gradient field: pf.add_gradient_fields(("gas","logP")) which seems to work and I can find it in pf.derived_field_list. But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects. Is this because logP does not have a unit? Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset? Thanks! Yuan
On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all:
I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as:
@derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"]))
Then I add the gradient field:
pf.add_gradient_fields(("gas","logP"))
which seems to work and I can find it in pf.derived_field_list.
But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
Can you pastebin the full traceback?
Is this because logP does not have a unit?
Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset?
Not right now, no.
Thanks! Yuan
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Traceback (most recent call last): File "logP.py", line 11, in <module> a=dd["gas","logP_gradient_y"] File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 253, in __getitem__ self.get_data(f) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 751, in get_data self._generate_fields(fields_to_generate) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 771, in _generate_fields fd = self._generate_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 290, in _generate_field tr = self._generate_fluid_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 308, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 318, in _generate_spatial_fluid rv = self.ds.arr(np.empty(self.ires.size, dtype="float64"), units) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 332, in __new__ units = Unit(input_units, registry=registry) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 204, in __new__ unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 496, in _get_unit_data_from_expr unit_data = _get_unit_data_from_expr(expr, unit_symbol_lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 504, in _get_unit_data_from_expr "objects." % str(unit_expr)) yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects. On Thu, Aug 13, 2015 at 3:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all:
I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as:
@derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"]))
Then I add the gradient field:
pf.add_gradient_fields(("gas","logP"))
which seems to work and I can find it in pf.derived_field_list.
But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
Can you pastebin the full traceback?
Is this because logP does not have a unit?
Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset?
Not right now, no.
Thanks! Yuan
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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So I *think* the parenthesis in the units are coming from this line: https://bitbucket.org/yt_analysis/yt/src/603eab147248f1a165778c76208906201eb... And I think this is happening because no one has tried to create a gradient field for a unitless field. This is something we should be able to do, but it's definitely a corner case. I don't have a script to run to test out any possible fixes, is there any chance you could make a script that uses one of the public test datasets on yt-project.org/data so I can reproduce your issue locally? Please also feel free to try fixing this yourself in your local copy of yt so you can make a PR. I think all we need to do is modify the line I linked to so if "field_units" is an empty string, we drop the parenthesis and just make the gradient field units "1/cm". On Thu, Aug 13, 2015 at 2:30 PM, Yuan Li <bear0980@gmail.com> wrote:
Traceback (most recent call last): File "logP.py", line 11, in <module> a=dd["gas","logP_gradient_y"] File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 253, in __getitem__ self.get_data(f) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 751, in get_data self._generate_fields(fields_to_generate) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 771, in _generate_fields fd = self._generate_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 290, in _generate_field tr = self._generate_fluid_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 308, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 318, in _generate_spatial_fluid rv = self.ds.arr(np.empty(self.ires.size, dtype="float64"), units) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 332, in __new__ units = Unit(input_units, registry=registry) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 204, in __new__ unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 496, in _get_unit_data_from_expr unit_data = _get_unit_data_from_expr(expr, unit_symbol_lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 504, in _get_unit_data_from_expr "objects." % str(unit_expr)) yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
On Thu, Aug 13, 2015 at 3:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all:
I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as:
@derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"]))
Then I add the gradient field:
pf.add_gradient_fields(("gas","logP"))
which seems to work and I can find it in pf.derived_field_list.
But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
Can you pastebin the full traceback?
Is this because logP does not have a unit?
Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset?
Not right now, no.
Thanks! Yuan
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Nathan, I think you are probably right! The script is super short: import yt import numpy as numpy from yt import derived_field @derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"])) pf=yt.load("DD0060/data0060") #load your data pf.add_gradient_fields(("gas","logP")) print pf.derived_field_list dd=pf.all_data() a=dd["gas","logP_gradient_y"] I forgot how to make a PR...It has been a while. I should relearn it, but it might be easier for you to do this one :). Thank you!! Yuan On Thu, Aug 13, 2015 at 3:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
So I *think* the parenthesis in the units are coming from this line:
https://bitbucket.org/yt_analysis/yt/src/603eab147248f1a165778c76208906201eb...
And I think this is happening because no one has tried to create a gradient field for a unitless field. This is something we should be able to do, but it's definitely a corner case.
I don't have a script to run to test out any possible fixes, is there any chance you could make a script that uses one of the public test datasets on yt-project.org/data so I can reproduce your issue locally?
Please also feel free to try fixing this yourself in your local copy of yt so you can make a PR. I think all we need to do is modify the line I linked to so if "field_units" is an empty string, we drop the parenthesis and just make the gradient field units "1/cm".
On Thu, Aug 13, 2015 at 2:30 PM, Yuan Li <bear0980@gmail.com> wrote:
Traceback (most recent call last): File "logP.py", line 11, in <module> a=dd["gas","logP_gradient_y"] File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 253, in __getitem__ self.get_data(f) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 751, in get_data self._generate_fields(fields_to_generate) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 771, in _generate_fields fd = self._generate_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 290, in _generate_field tr = self._generate_fluid_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 308, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 318, in _generate_spatial_fluid rv = self.ds.arr(np.empty(self.ires.size, dtype="float64"), units) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 332, in __new__ units = Unit(input_units, registry=registry) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 204, in __new__ unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 496, in _get_unit_data_from_expr unit_data = _get_unit_data_from_expr(expr, unit_symbol_lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 504, in _get_unit_data_from_expr "objects." % str(unit_expr)) yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
On Thu, Aug 13, 2015 at 3:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all:
I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as:
@derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"]))
Then I add the gradient field:
pf.add_gradient_fields(("gas","logP"))
which seems to work and I can find it in pf.derived_field_list.
But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
Can you pastebin the full traceback?
Is this because logP does not have a unit?
Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset?
Not right now, no.
Thanks! Yuan
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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See: https://bitbucket.org/yt_analysis/yt/pull-requests/1699/fix-issue-with-gradi... On Thu, Aug 13, 2015 at 2:52 PM, Yuan Li <bear0980@gmail.com> wrote:
Hi Nathan,
I think you are probably right!
The script is super short:
import yt import numpy as numpy from yt import derived_field @derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"])) pf=yt.load("DD0060/data0060") #load your data pf.add_gradient_fields(("gas","logP")) print pf.derived_field_list dd=pf.all_data() a=dd["gas","logP_gradient_y"]
I forgot how to make a PR...It has been a while. I should relearn it, but it might be easier for you to do this one :). Thank you!!
Yuan
On Thu, Aug 13, 2015 at 3:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
So I *think* the parenthesis in the units are coming from this line:
https://bitbucket.org/yt_analysis/yt/src/603eab147248f1a165778c76208906201eb...
And I think this is happening because no one has tried to create a gradient field for a unitless field. This is something we should be able to do, but it's definitely a corner case.
I don't have a script to run to test out any possible fixes, is there any chance you could make a script that uses one of the public test datasets on yt-project.org/data so I can reproduce your issue locally?
Please also feel free to try fixing this yourself in your local copy of yt so you can make a PR. I think all we need to do is modify the line I linked to so if "field_units" is an empty string, we drop the parenthesis and just make the gradient field units "1/cm".
On Thu, Aug 13, 2015 at 2:30 PM, Yuan Li <bear0980@gmail.com> wrote:
Traceback (most recent call last): File "logP.py", line 11, in <module> a=dd["gas","logP_gradient_y"] File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 253, in __getitem__ self.get_data(f) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 751, in get_data self._generate_fields(fields_to_generate) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 771, in _generate_fields fd = self._generate_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 290, in _generate_field tr = self._generate_fluid_field(field) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 308, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 318, in _generate_spatial_fluid rv = self.ds.arr(np.empty(self.ires.size, dtype="float64"), units) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line 332, in __new__ units = Unit(input_units, registry=registry) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 204, in __new__ unit_data = _get_unit_data_from_expr(unit_expr, registry.lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 496, in _get_unit_data_from_expr unit_data = _get_unit_data_from_expr(expr, unit_symbol_lut) File "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py", line 504, in _get_unit_data_from_expr "objects." % str(unit_expr)) yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
On Thu, Aug 13, 2015 at 3:28 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all:
I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as:
@derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"]))
Then I add the gradient field:
pf.add_gradient_fields(("gas","logP"))
which seems to work and I can find it in pf.derived_field_list.
But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
Can you pastebin the full traceback?
Is this because logP does not have a unit?
Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset?
Not right now, no.
Thanks! Yuan
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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participants (3)
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Nathan Goldbaum -
Yuan Li -
Yuan Li