Trying to change axis on phaseplot
Hi all,
I am making a phaseplot where the x-axis is the distance along the z-axis and the y-axis is the velocity in the z direction. I am really, however, plotting distance above the disk, which is at [0.5,0.5,0.5] or [80,80,80] in kpc. Instead of my x-axis going from 70 to 120 where 80 is the disk position, I would like it to go from -10 to 40 where 0 is the disk position.
So, I thought I would define a new variable, zdisk, and use that, but have run into some problems. Since this plot works beautifully when I am not messing with the z-values, I am guessing that I have done something wrong defining my variable. Any help is much appreciated!!
Thanks, Stephanie
yt version: --- Version = 3.5.dev0 Changeset = f7ac18f5bf99 ---
Okay, so the code:
import sys import numpy as np import yt from yt.units import kpc
def _zdisk(field,data): return data['index','z'].in_units('kpc')-(80.,'kpc')
ds = yt.load("/mnt/ceph/users/stonnesen/data1/BPr16vs30arcfo/DD"+loop[i]+"/BPr16vs30arcfo"+loop[i])
yt.add_field(("gas","zdisk"), function=_zdisk,units="kpc") ad = ds.all_data() diska = ad.cut_region(["obj['Metal_Density']/obj['density'] > 0.25"]) profile = yt.create_profile(diska, ['zdisk','velocity_z'], 'cell_mass',n_bins=80,weight_field=None) histogram = profile.field_data['gas','cell_mass'] histogram[histogram < 1e37] = 0 plot2 = yt.PhasePlot.from_profile(profile) plot2.set_unit('zdisk','kpc') plot2.set_log('zdisk',False) plot2.set_unit('velocity_z','km/s') plot2.set_log('velocity_z',False) plot2.set_xlim(-10,40) plot2.set_ylim(-6e2,1.5e3) plot2.set_zlim('cell_mass',1e37,1e42) plot2.save('BPr16vs30arcfo'+loop[i]+'_tp25_alls_mcut_nbin80_zdisk')
______________________________ ______________________________
and now the error: yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: current_time = 3119.9999022826 yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2019-01-19 15:55:25,745 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2019-01-19 15:55:25,746 Parameters: cosmological_simulation = 0.0 /mnt/home/stonnesen/yt-conda/yt/yt/fields/local_fields.py:46: UserWarning: Because 'sampling_type' not specified, yt will assume a cell 'sampling_type' warnings.warn("Because 'sampling_type' not specified, yt will "
Parsing Hierarchy : 0%| | 0/4284 [00:00<?, ?it/s] Parsing Hierarchy : 23%|██▎ | 968/4284 [00:00<00:00, 9672.70it/s] Parsing Hierarchy : 40%|███▉ | 1702/4284 [00:00<00:00, 8971.55it/s] Parsing Hierarchy : 62%|██████▏ | 2643/4284 [00:00<00:00, 9101.75it/s] Parsing Hierarchy : 77%|███████▋ | 3298/4284 [00:00<00:00, 8334.29it/s] Parsing Hierarchy : 99%|█████████▉| 4241/4284 [00:00<00:00, 8660.50it/s] Parsing Hierarchy : 100%|██████████| 4284/4284 [00:00<00:00, 8466.80it/s] yt : [INFO ] 2019-01-19 15:55:26,407 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "yt_allphaseplot_newz.py", line 40, in <module> profile = yt.create_profile(diska, ['zdisk','velocity_z'], 'cell_mass',n_bins=80,weight_field=None) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/profiles.py", line 1042, in create_profile bin_fields = data_source._determine_fields(bin_fields) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/data_containers.py", line 1165, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 756, in _get_field_info self.index File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 514, in index self.create_field_info() File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 571, in create_field_info self.field_info.load_all_plugins(self.default_fluid_type) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 276, in load_all_plugins self.find_dependencies(loaded) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 289, in find_dependencies deps, unavailable = self.check_derived_fields(loaded) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 362, in check_derived_fields fd = fi.get_dependencies(ds = self.ds) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/derived_field.py", line 216, in get_dependencies e[self.name] File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_detector.py", line 108, in __missing__ vv = finfo(self) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/derived_field.py", line 256, in __call__ dd = self._function(self, data) File "yt_allphaseplot_newz.py", line 21, in _zdisk return data['index','z'].in_units('kpc')-(80.,'kpc') File "/mnt/home/stonnesen/yt-conda/yt/yt/units/yt_array.py", line 1391, in __array_ufunc__ inps, units, ufunc, ret_class) File "/mnt/home/stonnesen/yt-conda/yt/yt/units/yt_array.py", line 161, in handle_preserve_units any_nonzero = [np.any(inps[0]), np.any(inps[1])] File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 1970, in any return arr.any(axis=axis, out=out, **kwargs) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/numpy/core/_methods.py", line 38, in _any return umr_any(a, axis, dtype, out, keepdims) TypeError: cannot perform reduce with flexible type
-- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY
stonnes@gmail.com
Hi Stephanie,
The reason this is failing is that you're trying to represent 80 kpc as a tuple in your field definition. Tuples are just a shorthand way of representing unit-aware quantities in some of the function calls (e.g. ProjectionPlot(ds, 'x', width=(80, 'kpc')) ), but they don't work outside of these special functions.
To fix this, you can just make your function call:
from yt.units import kpc
def _zdisk(field,data): return data['index','z'] - 80*kpc
Also, it's worth mentioning that there was a discussion on slack last week about offering a series of "relative_position" fields, where after you define a "center" for your data object (in your case, all_data), "relative_position_z" would automatically return the desired position relative to that center. These fields already exist for velocity (e.g. for calculating radial velocities from a central point once a "bulk_velocity" is defined), and for particle fields, but not for grid-based position fields. I believe Corentin Cadiou was going to implement this, which may provide an easier alternative than you defining your own fields. And it would be used as:
ad = all_data() ad.set_field_parameter("center", [0.5, 0.5, 0.5]) ad[('gas', 'relative_position_z')].to('kpc')
For more info on the "relative" fields, grep for "relative" on the "Fields" page: http://yt-project.org/docs/dev/reference/field_list.html#gas-relative-veloci... For more on declaring units, please see Nathan's excellent primer in the docs: http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html
Cameron
On Sat, Jan 19, 2019 at 1:05 PM Stephanie Tonnesen stonnes@gmail.com wrote:
Hi all,
I am making a phaseplot where the x-axis is the distance along the z-axis and the y-axis is the velocity in the z direction. I am really, however, plotting distance above the disk, which is at [0.5,0.5,0.5] or [80,80,80] in kpc. Instead of my x-axis going from 70 to 120 where 80 is the disk position, I would like it to go from -10 to 40 where 0 is the disk position.
So, I thought I would define a new variable, zdisk, and use that, but have run into some problems. Since this plot works beautifully when I am not messing with the z-values, I am guessing that I have done something wrong defining my variable. Any help is much appreciated!!
Thanks, Stephanie
yt version:
Version = 3.5.dev0 Changeset = f7ac18f5bf99
Okay, so the code:
import sys import numpy as np import yt from yt.units import kpc
def _zdisk(field,data): return data['index','z'].in_units('kpc')-(80.,'kpc')
ds = yt.load("/mnt/ceph/users/stonnesen/data1/BPr16vs30arcfo/DD"+loop[i]+"/BPr16vs30arcfo"+loop[i])
yt.add_field(("gas","zdisk"), function=_zdisk,units="kpc") ad = ds.all_data() diska = ad.cut_region(["obj['Metal_Density']/obj['density'] > 0.25"]) profile = yt.create_profile(diska, ['zdisk','velocity_z'], 'cell_mass',n_bins=80,weight_field=None) histogram = profile.field_data['gas','cell_mass'] histogram[histogram < 1e37] = 0 plot2 = yt.PhasePlot.from_profile(profile) plot2.set_unit('zdisk','kpc') plot2.set_log('zdisk',False) plot2.set_unit('velocity_z','km/s') plot2.set_log('velocity_z',False) plot2.set_xlim(-10,40) plot2.set_ylim(-6e2,1.5e3) plot2.set_zlim('cell_mass',1e37,1e42) plot2.save('BPr16vs30arcfo'+loop[i]+'_tp25_alls_mcut_nbin80_zdisk')
and now the error: yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: current_time = 3119.9999022826 yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2019-01-19 15:55:25,745 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2019-01-19 15:55:25,746 Parameters: cosmological_simulation = 0.0 /mnt/home/stonnesen/yt-conda/yt/yt/fields/local_fields.py:46: UserWarning: Because 'sampling_type' not specified, yt will assume a cell 'sampling_type' warnings.warn("Because 'sampling_type' not specified, yt will "
Parsing Hierarchy : 0%| | 0/4284 [00:00<?, ?it/s] Parsing Hierarchy : 23%|██▎ | 968/4284 [00:00<00:00, 9672.70it/s] Parsing Hierarchy : 40%|███▉ | 1702/4284 [00:00<00:00, 8971.55it/s] Parsing Hierarchy : 62%|██████▏ | 2643/4284 [00:00<00:00, 9101.75it/s] Parsing Hierarchy : 77%|███████▋ | 3298/4284 [00:00<00:00, 8334.29it/s] Parsing Hierarchy : 99%|█████████▉| 4241/4284 [00:00<00:00, 8660.50it/s] Parsing Hierarchy : 100%|██████████| 4284/4284 [00:00<00:00, 8466.80it/s] yt : [INFO ] 2019-01-19 15:55:26,407 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "yt_allphaseplot_newz.py", line 40, in <module> profile = yt.create_profile(diska, ['zdisk','velocity_z'], 'cell_mass',n_bins=80,weight_field=None) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/profiles.py", line 1042, in create_profile bin_fields = data_source._determine_fields(bin_fields) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/data_containers.py", line 1165, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 756, in _get_field_info self.index File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 514, in index self.create_field_info() File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 571, in create_field_info self.field_info.load_all_plugins(self.default_fluid_type) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 276, in load_all_plugins self.find_dependencies(loaded) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 289, in find_dependencies deps, unavailable = self.check_derived_fields(loaded) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 362, in check_derived_fields fd = fi.get_dependencies(ds = self.ds) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/derived_field.py", line 216, in get_dependencies e[self.name] File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_detector.py", line 108, in __missing__ vv = finfo(self) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/derived_field.py", line 256, in __call__ dd = self._function(self, data) File "yt_allphaseplot_newz.py", line 21, in _zdisk return data['index','z'].in_units('kpc')-(80.,'kpc') File "/mnt/home/stonnesen/yt-conda/yt/yt/units/yt_array.py", line 1391, in __array_ufunc__ inps, units, ufunc, ret_class) File "/mnt/home/stonnesen/yt-conda/yt/yt/units/yt_array.py", line 161, in handle_preserve_units any_nonzero = [np.any(inps[0]), np.any(inps[1])] File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 1970, in any return arr.any(axis=axis, out=out, **kwargs) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/numpy/core/_methods.py", line 38, in _any return umr_any(a, axis, dtype, out, keepdims) TypeError: cannot perform reduce with flexible type
-- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY
stonnes@gmail.com _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
participants (2)
-
Cameron Hummels -
Stephanie Tonnesen