yt-dev January 2016

yt-dev@python.org

25 participants
40 discussions

Issue #1164: particle angular momentum profile error with attachment (the same as #1163) (yt_analysis/yt)

by Anonymous

New issue 1164: particle angular momentum profile error with attachment (the same as #1163) https://bitbucket.org/yt_analysis/yt/issues/1164/particle-angular-momentum-… Anonymous: I wrote the attach script to compute the particle angular momentum. This script result in following error message: ……………… Traceback (most recent call last): File "pang.py", line 26, in <module> profile = yt.Profile1D(sphere, 'partradiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field=None) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 411, in __init__ self.x_field = data_source._determine_fields(x_field)[0] File "/home/jhchoi/common/src/yt/yt/data_objects/data_containers.py", line 1001, in _determine_fields raise YTFieldNotFound((ftype,fname),self.ds) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'partradiuspc')' in DD0045. If I remove "particle_type=True" in add_field, it works. However, I am not sure that removing "particle_type=True" returns correct output. Thank you, Junhwan

5 years, 8 months

Issue #1163: particle angular momentum profile error (yt_analysis/yt)

by Anonymous

New issue 1163: particle angular momentum profile error https://bitbucket.org/yt_analysis/yt/issues/1163/particle-angular-momentum-… Anonymous: Hi yt developer I wrote the following script to compute the particle angular momentum =============================== import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _partradiuspc(field, data): return data[('all','particle_radius')].in_units('pc') yt.add_field('partradiuspc', function=_partradiuspc, particle_type=True, units="pc") index = 45 Nbin= 100 rmax = 3000 ds = yt.load("../DD%04d/DD%04d" % (index,index)) ds.index ad= ds.all_data() center = ds.find_max(("gas", "density"))[1] rmin = max([1.0e-3,2.0*ds.index.get_smallest_dx().in_units('pc')]) sphere = ds.sphere(center, rmax*units.pc) bulk_velocity = sphere.quantities['BulkVelocity']() sphere.set_field_parameter('bulk_velocity', bulk_velocity) profile = yt.Profile1D(sphere, 'partradiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field=None) profile.add_fields(('all', 'particle_angular_momentum_x')) profile.add_fields(('all', 'particle_angular_momentum_y')) profile.add_fields(('all', 'particle_angular_momentum_z')) PartAngularMomentum = np.sqrt(profile[('all', 'particle_angular_momentum_x')]**2 + profile[('all', 'particle_angular_momentum_y')]**2 + profile[('all', 'particle_angular_momentum_z')]**2) plt.plot(profile.x, PartAngularMomentum, label='Total',linestyle="-",color='r') plt.xlabel('r [pc]') plt.ylabel('pang') =================================== And, I got the following error message ……………… Traceback (most recent call last): File "pang.py", line 26, in <module> profile = yt.Profile1D(sphere, 'partradiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field=None) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 411, in __init__ self.x_field = data_source._determine_fields(x_field)[0] File "/home/jhchoi/common/src/yt/yt/data_objects/data_containers.py", line 1001, in _determine_fields raise YTFieldNotFound((ftype,fname),self.ds) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'partradiuspc')' in DD0045. If I remove "particle_type=True" in add_field, it works. However, I am not sure that removing "particle_type=True" return correct output. Thank you, Junhwan

5 years, 8 months

next yt team meeting: signups

by Britton Smith

Hey everyone, It's time once again to get together and talk about the state of the yt project. For those who haven't been to a yt team meeting before, this is where we get together and discuss things like new developments in the code, project management issues, and whatever's on our minds relating to yt. Like the PR Triage, we do these on google hangout, so anyone is welcome to come and speak up. Let's try to have the next yt team meeting during the week of February 1-5. To schedule this, I will do a doodle poll including everyone named in the project management document (YTEP-1776 <http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-1776.html>) and anyone else who is interested in participating. If you'd like to participate and are not named in the YTEP, just send me a message and I'll be sure to include you in the poll. Please, let me know by Thursday, January 28 if you want to be included. Britton

5 years, 8 months

mbox format of archives

by Matthew Turk

Hi folks, We're having issues with archiving again. If you have email messages from yt-users or yt-dev in mbox format (for instance, if you use thunderbird or apple mail) and a complete archive of the last couple months, *please* contact me off-list. Getting these from multiple folks is necessary to make sure we have all the messages sent to the list, and I can then de-duplicate and upload them to the server. And if you have them from last Spring, too, that'd be outstanding as well. Thanks, Matt

5 years, 8 months

SPHGR

by Robert Thompson

Hi yt devs, I wanted to share a short introduction to my [WIP] PR for SPHGR. At the following link I detail what it does, how it does it, and how to use it: http://rthompsonj.github.io/yt-sphgr.html <http://rthompsonj.github.io/yt-sphgr.html> Questions, comments, and thoughts are all welcome! -Robert

5 years, 8 months

Issue #1162: Test failures under numpy 1.11 beta (yt_analysis/yt)

by Nathan Goldbaum

New issue 1162: Test failures under numpy 1.11 beta https://bitbucket.org/yt_analysis/yt/issues/1162/test-failures-under-numpy-… Nathan Goldbaum: Currently the following test failures are generated under the NumPy 1.11.0b1 release: They all seem to be variations on using a float as an index in different places. ``` Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/Users/goldbaum/Documents/yt-hg/yt/fields/tests/test_fields.py", line 211, in test_add_smoothed_particle_field ret = ad[fn] File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 323, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 343, in _generate_spatial_fluid ind += o.select(self.selector, self[field], rv, ind) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__ dd = self._function(self, data) File "/Users/goldbaum/Documents/yt-hg/yt/fields/particle_fields.py", line 792, in _vol_weight smooth_cutoff = data["index","cell_volume"]**(1./3) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 74, in __getitem__ tr = super(OctreeSubset, self).__getitem__(key) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__ dd = self._function(self, data) File "/Users/goldbaum/Documents/yt-hg/yt/geometry/coordinates/coordinate_handler.py", line 38, in _dds return data._reshape_vals(rv) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 107, in _reshape_vals arr = arr.reshape(new_shape, order="F") TypeError: 'float' object cannot be interpreted as an index ====================================================================== ERROR: Failure: TypeError ('float' object cannot be interpreted as an index) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate for test in g(): File "/Users/goldbaum/Documents/yt-hg/yt/frontends/sdf/tests/test_outputs.py", line 47, in test_scivis ProjectionPlot(ds, "z", _fields) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 1410, in __init__ field_parameters = field_parameters, method = method) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 258, in __init__ self.get_data(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 332, in get_data self._handle_chunk(chunk, fields, tree) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 432, in _handle_chunk d = chunk[field] * dl File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 323, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 343, in _generate_spatial_fluid ind += o.select(self.selector, self[field], rv, ind) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__ dd = self._function(self, data) File "/Users/goldbaum/Documents/yt-hg/yt/fields/particle_fields.py", line 141, in particle_cic d /= data["index", "cell_volume"] File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 74, in __getitem__ tr = super(OctreeSubset, self).__getitem__(key) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 268, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1181, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 1201, in _generate_fields fd = self._generate_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 305, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 325, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.py", line 182, in __call__ dd = self._function(self, data) File "/Users/goldbaum/Documents/yt-hg/yt/geometry/coordinates/coordinate_handler.py", line 38, in _dds return data._reshape_vals(rv) File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/octree_subset.py", line 107, in _reshape_vals arr = arr.reshape(new_shape, order="F") TypeError: 'float' object cannot be interpreted as an index ====================================================================== ERROR: Failure: TypeError (an integer is required) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate for test in g(): File "/Users/goldbaum/Documents/yt-hg/yt/frontends/stream/tests/test_stream_particles.py", line 30, in test_stream_particles amr0 = refine_amr(ug0, rc, fo, 3) File "/Users/goldbaum/Documents/yt-hg/yt/frontends/stream/data_structures.py", line 956, in refine_amr nsg = fg.find_subgrids() File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 54, in find_subgrids psg = ProtoSubgrid(self.flagged, self.left_index, self.dimensions) File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 88, in __init__ self.compute_signatures() File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 95, in compute_signatures self.sigs.append(self.flagged.sum(axis=d1).sum(axis=d2)) File "/Users/goldbaum/Documents/numpy/numpy/core/_methods.py", line 32, in _sum return umr_sum(a, axis, dtype, out, keepdims) TypeError: an integer is required ====================================================================== ERROR: Failure: TypeError ('float' object cannot be interpreted as an index) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate for test in g(): File "/Users/goldbaum/Documents/yt-hg/yt/geometry/tests/test_neighbor_search.py", line 28, in test_neighbor_search ds = fake_particle_ds(npart = 16**3) File "/Users/goldbaum/Documents/yt-hg/yt/testing.py", line 265, in fake_particle_ds v = np.random.normal(npart, 0.5, 0.25) File "mtrand.pyx", line 1897, in mtrand.RandomState.normal (numpy/random/mtrand/mtrand.c:18066) File "mtrand.pyx", line 234, in mtrand.cont2_array_sc (numpy/random/mtrand/mtrand.c:3089) TypeError: 'float' object cannot be interpreted as an index ====================================================================== ERROR: Failure: TypeError (an integer is required) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/loader.py", line 251, in generate for test in g(): File "/Users/goldbaum/Documents/yt-hg/yt/utilities/tests/test_particle_generator.py", line 27, in test_particle_generator ds = refine_amr(ug, rc, fo, 3) File "/Users/goldbaum/Documents/yt-hg/yt/frontends/stream/data_structures.py", line 956, in refine_amr nsg = fg.find_subgrids() File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 54, in find_subgrids psg = ProtoSubgrid(self.flagged, self.left_index, self.dimensions) File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 88, in __init__ self.compute_signatures() File "/Users/goldbaum/Documents/yt-hg/yt/utilities/flagging_methods.py", line 95, in compute_signatures self.sigs.append(self.flagged.sum(axis=d1).sum(axis=d2)) File "/Users/goldbaum/Documents/numpy/numpy/core/_methods.py", line 32, in _sum return umr_sum(a, axis, dtype, out, keepdims) TypeError: an integer is required ====================================================================== ERROR: test_stereoperspective_lens (yt.visualization.volume_rendering.tests.test_lenses.LensTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/tests/test_lenses.py", line 70, in test_stereoperspective_lens sc.render() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 163, in render bmp = self.composite(camera=camera) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 288, in composite im = source.render(camera, zbuffer=opaque) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 256, in render self.set_sampler(camera) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 228, in set_sampler sampler = new_volume_render_sampler(camera, self) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/utils.py", line 35, in new_volume_render_sampler params = camera._get_sampler_params(render_source) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/camera.py", line 197, in _get_sampler_params lens_params = self.lens._get_sampler_params(self, render_source) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/lens.py", line 287, in _get_sampler_params camera, -self.disparity) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/lens.py", line 337, in _get_positions_vectors dtype='float64', order='C') TypeError: 'numpy.float64' object cannot be interpreted as an index ====================================================================== ERROR: test_stereospherical_lens (yt.visualization.volume_rendering.tests.test_lenses.LensTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/tests/test_lenses.py", line 130, in test_stereospherical_lens sc.render() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 163, in render bmp = self.composite(camera=camera) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/scene.py", line 288, in composite im = source.render(camera, zbuffer=opaque) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 256, in render self.set_sampler(camera) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/render_source.py", line 228, in set_sampler sampler = new_volume_render_sampler(camera, self) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/utils.py", line 35, in new_volume_render_sampler params = camera._get_sampler_params(render_source) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/camera.py", line 197, in _get_sampler_params lens_params = self.lens._get_sampler_params(self, render_source) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/volume_rendering/lens.py", line 691, in _get_sampler_params dtype='float64', order='C') TypeError: 'numpy.float64' object cannot be interpreted as an index ====================================================================== ERROR: test suite for <class 'yt.visualization.tests.test_particle_plot.TestParticlePhasePlotSave'> ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run self.setUp() File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp self.setupContext(ancestor) File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext try_run(context, names) File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/tests/test_particle_plot.py", line 139, in setUpClass test_ds = fake_particle_ds() File "/Users/goldbaum/Documents/yt-hg/yt/testing.py", line 265, in fake_particle_ds v = np.random.normal(npart, 0.5, 0.25) File "mtrand.pyx", line 1897, in mtrand.RandomState.normal (numpy/random/mtrand/mtrand.c:18066) File "mtrand.pyx", line 234, in mtrand.cont2_array_sc (numpy/random/mtrand/mtrand.c:3089) TypeError: 'float' object cannot be interpreted as an index ====================================================================== ERROR: test suite for <class 'yt.visualization.tests.test_particle_plot.TestParticleProjectionPlotSave'> ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run self.setUp() File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp self.setupContext(ancestor) File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext try_run(context, names) File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/tests/test_particle_plot.py", line 192, in setUpClass test_ds = fake_particle_ds() File "/Users/goldbaum/Documents/yt-hg/yt/testing.py", line 265, in fake_particle_ds v = np.random.normal(npart, 0.5, 0.25) File "mtrand.pyx", line 1897, in mtrand.RandomState.normal (numpy/random/mtrand/mtrand.c:18066) File "mtrand.pyx", line 234, in mtrand.cont2_array_sc (numpy/random/mtrand/mtrand.c:3089) TypeError: 'float' object cannot be interpreted as an index ```

5 years, 8 months

Fwd: [astropy-dev] A word on GSoC and new contributors

by Matthew Turk

I thought this email from Erik Bray was thoughtful and well-written, and might be of interest to folks here. ---------- Forwarded message ---------- From: Erik Bray <erik.m.bray(a)gmail.com> Date: Mon, Jan 25, 2016 at 1:01 PM Subject: [astropy-dev] A word on GSoC and new contributors To: astropy-dev(a)googlegroups.com Hi all, Just a few thoughts jumbling around in my head lately that I need to get out--this is me speaking for myself. This in particular should be read by anyone interesting in applying for a Google Summer of Code internship with the Astropy project (under the assumption that Astropy will participate this year, and will receive funding from Google under the program). But even if you're not looking to participate in GSoC, there's a point I want novices interested in contributing to understand: That's great that you're excited to contribute to open source. We welcome and deeply appreciate contributions from all comers. [just see the number of open issues Astropy has on GitHub]. We should (and as far as I've seen do) strive to guide and work with each other to move Astropy forward whether you're a student or professional astronomer, or of any other background, and regardless of your experience contributing to open source projects like Astropy. This is in accordance with Astropy's Code of Conduct [1]. This involves mutual respect between newcomers, and long-time contributors. This means that new contributors must also respect the time and availability of existing contributors. To this end, it is the responsibility of new contributors to discover on their own the contribution directions [2], and show some self-direction on their part. Because unless otherwise stated (such as at a code sprint), nobody has explicitly volunteered, at this stage, to be anyone else's personal mentor. We will always provide respectful feedback and advice on your contributions. And if you have *specific* ideas on what kinds of issues you would like to work on we'll also provide feedback on that. But otherwise it is helpful to show initiative. Finally a few additional tips: Aside from the introduction for contributors linked to in [2], another useful resource that might be easy to miss is the contributing guidelines [3], useful for anyone ready to work on a specific issue. Most people seem to do a good job following that so it isn't a problem--just always worth pointing out. Make sure also not to miss the "development workflow" guide linked to from the contributing guidelines. There *are* some things in there that new contributors often miss, such as advice to not make a pull request from your "master" branch (always start a new branch for new work). Also, if you have any general questions about contributing, please ask here, on this mailing list, or via one of the other communication channels listed in [2]. Please do not, if you can help it, ask general questions in GitHub issues--unless the question or comment is specifically related to that issue it is noise that can make issues hard to follow. Thanks for reading, and keep up the good work, Erik [1] http://www.astropy.org/about.html#codeofconduct [2] http://www.astropy.org/contribute.html [3] https://github.com/astropy/astropy/blob/master/CONTRIBUTING.md -- You received this message because you are subscribed to the Google Groups "astropy-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to astropy-dev+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

5 years, 8 months

Re: [yt-dev] yt-dev Digest, Vol 85, Issue 33

by Gilbert, Austin B

The middle and right colormaps are the two best options in my mind because they have several unique colors in the interval between the two extremum, thus enabling a fuller range of data to be absorbed--especially in the phase plots and high resolution projections. ________________________________________ From: yt-dev <yt-dev-bounces(a)lists.spacepope.org> on behalf of yt-dev-request(a)lists.spacepope.org <yt-dev-request(a)lists.spacepope.org> Sent: Thursday, January 21, 2016 2:05 PM To: yt-dev(a)lists.spacepope.org Subject: yt-dev Digest, Vol 85, Issue 32 Send yt-dev mailing list submissions to yt-dev(a)lists.spacepope.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org or, via email, send a message with subject or body 'help' to yt-dev-request(a)lists.spacepope.org You can reach the person managing the list at yt-dev-owner(a)lists.spacepope.org When replying, please edit your Subject line so it is more specific than "Re: Contents of yt-dev digest..." Today's Topics: 1. Re: Default colormap (Matthew Turk) ---------------------------------------------------------------------- Message: 1 Date: Thu, 21 Jan 2016 13:05:07 -0600 From: Matthew Turk <matthewturk(a)gmail.com> To: "yt-dev(a)lists.spacepope.org" <yt-dev(a)lists.spacepope.org> Subject: Re: [yt-dev] Default colormap Message-ID: <CALO3=5HASX+DekU1xW2zRoTPkLd6csho2Mg7+JqUWsFGbXi+5A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Sounds good, but before we do that, I think we should have a suitable waiting period for others to propose them. I'll send an email out to yt-users asking for ideas on it. On Thu, Jan 21, 2016 at 12:10 PM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: > I think we should probably put it up for a vote and we should send an > e-mail to yt-users about it. > > On Thu, Jan 21, 2016 at 12:06 PM, Matthew Turk <matthewturk(a)gmail.com> > wrote: > >> Hi folks, >> >> I've put up a comparison image: >> >> http://i.imgur.com/Afxdb0G.jpg >> >> Left is Kacper, middle is me, right is Nathan. >> >> Honestly I think all could go in, but we should pick a default -- whether >> it's one of these or a different one. Anyone have a strong opinion? >> >> -Matt >> >> On Mon, Jan 18, 2016 at 10:19 AM, B.W. Keller <kellerbw(a)mcmaster.ca> >> wrote: >> >>> Wow, all of these look great. I think I like Matt's best for painting >>> our bikeshed, but I would be happy with any of them. >>> >>> On Mon, Jan 18, 2016 at 11:10 AM, Kacper Kowalik < >>> xarthisius.kk(a)gmail.com> wrote: >>> >>>> On 01/18/2016 09:45 AM, Matthew Turk wrote: >>>> > Hi all, >>>> > >>>> > I've experimented a bit and come up with this: >>>> > >>>> > https://images.hub.yt/u/fido/m/9bbe3cf6-png/ >>>> > >>>> > The script: >>>> > >>>> > http://paste.yt-project.org/show/6151/ >>>> > >>>> > This was designed with the viscm project, which is awfully cool. What >>>> > do folks think? I think Kacper and Nathan also experimented with >>>> > viscm and have some ideas too, so maybe we should put it up for an >>>> > eventual vote. >>>> >>>> This is my experiment: >>>> >>>> https://images.hub.yt/u/fido/m/f180a901-png/ >>>> >>>> Source: >>>> >>>> http://paste.yt-project.org/show/6166/ >>>> >>>> Cheers, >>>> Kacper >>>> >>>> >>>> > >>>> > Also, I would campaign for calling whatever our new colormap turns out >>>> > to be one of these three things, in increasing order of my preference: >>>> > >>>> > agar >>>> > kelp >>>> > kanten >>>> > >>>> > -Matt >>>> > >>>> > On Thu, Jan 14, 2016 at 10:57 AM, Matthew Turk <matthewturk(a)gmail.com> >>>> wrote: >>>> >> Hi Stuart and everyone else, >>>> >> >>>> >> This is great info. I appreciate everyone's thoughtful replies. >>>> >> >>>> >> Having both a sequential colormap (which would replace algae) and a >>>> >> diverging colormap, would be awesome. The Paraview devs shipped the >>>> >> new matplotlib ones (like Inferno) in 5.0. I think it would be a fun >>>> >> experiment to see if we can come up with something sufficiently >>>> >> "branded" or different. And then if we can't, fall back on something >>>> >> like Inferno? >>>> >> >>>> >> -Matt >>>> >> >>>> >> On Wed, Jan 6, 2016 at 12:48 PM, Levy, Stuart A <salevy(a)illinois.edu> >>>> wrote: >>>> >>> There was a fair bit of discussion about colormaps - terrible, >>>> useful, >>>> >>> beautiful - at IEEE Vis last October. The viridis colormap was a >>>> featured >>>> >>> one. So was the traditional rainbow, which lots of info-vis and >>>> perceptual >>>> >>> people piled on to criticize. >>>> >>> >>>> >>> Among design criteria for a continuous-valued colormap is whether >>>> it's >>>> >>> "sequential" (like the typical yt colormap, or viridis) or >>>> "diverging". >>>> >>> You'd want a diverging colormap to show signed deviations from a >>>> norm - >>>> >>> where the eye should be caught by places where a value is either >>>> much less >>>> >>> than, or much more than, something in the middle. Is it worth >>>> offering a >>>> >>> typical divergent colormap, as well as a new typical sequential >>>> one, in yt? >>>> >>> >>>> >>> Note that among the Stefan van der Walt & Nathaniel Smith writeup ( >>>> >>> http://bids.github.io/colormap/ ) on their development of better >>>> cmaps, they >>>> >>> use Nathan Goldbaum's galaxy evolution as a test case for six >>>> (sequential) >>>> >>> examples! => >>>> http://vorpus.org/~njs/goldbaum-galaxies-all-colormaps.mkv >>>> >>> >>>> >>> A neat web site with sample colormaps - aimed at mapping discrete >>>> values on >>>> >>> geographic maps, so not directly applicable but cool - is this, by >>>> Cynthia >>>> >>> Brewer and Mark Harrower at PSU: >>>> >>> http://colorbrewer2.org/ >>>> >>> It has a library of predesigned cmaps, and lets you sift them by >>>> being >>>> >>> colorblind-safe, photocopy safe, etc. >>>> >>> ________________________________ >>>> >>> From: yt-dev [yt-dev-bounces(a)lists.spacepope.org] on behalf of >>>> B.W. Keller >>>> >>> [kellerbw(a)mcmaster.ca] >>>> >>> Sent: Wednesday, January 06, 2016 12:13 >>>> >>> To: yt-dev(a)lists.spacepope.org >>>> >>> Subject: Re: [yt-dev] Default colormap >>>> >>> >>>> >>> There is a really excellent paper on designing color maps called >>>> "Color >>>> >>> Sequences for Univariate Maps: Theory, Experiments, and Principles" >>>> that you >>>> >>> can get here: >>>> >>> >>>> http://ccom.unh.edu/sites/default/files/publications/Ware_1988_CGA_Color_se… >>>> >>> >>>> >>> If we design a new colormap, this would be a good reference along >>>> with those >>>> >>> scipy resources. I personally would love to have an accessible, >>>> yt-custom >>>> >>> colormap. >>>> >>> >>>> >>> On Wed, Jan 6, 2016 at 11:50 AM, Erik Schnetter < >>>> schnetter(a)gmail.com> wrote: >>>> >>>> >>>> >>>> I think there are several colourmaps that were created when Viridis >>>> >>>> was invented. I personally like Inferno. >>>> >>>> >>>> >>>> -erik >>>> >>>> >>>> >>>> On Wed, Jan 6, 2016 at 11:34 AM, Nathan Goldbaum < >>>> nathan12343(a)gmail.com> >>>> >>>> wrote: >>>> >>>>> I would also be for coming up with our own colormap. That said, I >>>> think >>>> >>>>> simply modifying algae won't be enough, since it is too >>>> perceptually >>>> >>>>> nonlinear. >>>> >>>>> >>>> >>>>> On Wed, Jan 6, 2016 at 10:32 AM, John ZuHone <jzuhone(a)gmail.com> >>>> wrote: >>>> >>>>>> >>>> >>>>>> I would go for modifying algae. >>>> >>>>>> >>>> >>>>>>> On Jan 6, 2016, at 11:30 AM, Matthew Turk < >>>> matthewturk(a)gmail.com> >>>> >>>>>>> wrote: >>>> >>>>>>> >>>> >>>>>>> Hi folks, >>>> >>>>>>> >>>> >>>>>>> For a long time we've used "algae," which was designed by >>>> Britton >>>> >>>>>>> about eight years ago, as the default colormap. This has been >>>> really >>>> >>>>>>> nice for "branding" yt -- if you see an algae plot, it's >>>> probably >>>> >>>>>>> (not >>>> >>>>>>> definitely) made with yt. But it's also not accessible from a >>>> >>>>>>> colorblindness perspective. Stefan van der Walt has been >>>> giving some >>>> >>>>>>> really great talks lately about building a better colormap for >>>> >>>>>>> matplotlib (e.g., https://www.youtube.com/watch?v=xAoljeRJ3lU >>>> ) which >>>> >>>>>>> culminated in viridis, which is shipping in recent versions of >>>> >>>>>>> matplotlib and will become the default. >>>> >>>>>>> >>>> >>>>>>> In support of this, he built a tool called viscm which can >>>> generate >>>> >>>>>>> reduced versions of colormaps to show what they would be like >>>> with >>>> >>>>>>> varying degrees of insensitivity to color. I've generated >>>> outputs >>>> >>>>>>> from viscm of three of the custom colormaps we ship with yt: >>>> >>>>>>> >>>> >>>>>>> Algae: https://images.hub.yt/u/fido/m/d275d5e1-png/ >>>> >>>>>>> Cubehelix: https://images.hub.yt/u/fido/m/8e698928-png/ (I >>>> believe >>>> >>>>>>> this is now also shipped with MPL) >>>> >>>>>>> Kamae: https://images.hub.yt/u/fido/m/e0e40efa-png/ >>>> >>>>>>> >>>> >>>>>>> I love algae, but it's not the best from an accessibility >>>> >>>>>>> perspective. >>>> >>>>>>> >>>> >>>>>>> I'd like to propose that we use a new default colormap. If we >>>> do >>>> >>>>>>> this, I see two options: >>>> >>>>>>> >>>> >>>>>>> * Retain a "branding" by developing a new one either by using >>>> the >>>> >>>>>>> techniques used by matplotlib (or one of the maps they opted >>>> not to >>>> >>>>>>> use) or by modifying algae to be more accessible; looking at the >>>> >>>>>>> response functions, I suspect it would be reasonably possible to >>>> >>>>>>> modify it. (Modifying algae is my preference.) >>>> >>>>>>> * Use viridis (which we may then have to ship if we have older >>>> >>>>>>> versions of matplotlib to support) >>>> >>>>>>> >>>> >>>>>>> -Matt >>>> >>>>>>> _______________________________________________ >>>> >>>>>>> yt-dev mailing list >>>> >>>>>>> yt-dev(a)lists.spacepope.org >>>> >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>>>>> >>>> >>>>>> _______________________________________________ >>>> >>>>>> yt-dev mailing list >>>> >>>>>> yt-dev(a)lists.spacepope.org >>>> >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> _______________________________________________ >>>> >>>>> yt-dev mailing list >>>> >>>>> yt-dev(a)lists.spacepope.org >>>> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> >>>> Erik Schnetter <schnetter(a)gmail.com> >>>> >>>> http://www.perimeterinstitute.ca/personal/eschnetter/ >>>> >>>> _______________________________________________ >>>> >>>> yt-dev mailing list >>>> >>>> yt-dev(a)lists.spacepope.org >>>> >>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>> >>>> >>> >>>> >>> >>>> >>> _______________________________________________ >>>> >>> yt-dev mailing list >>>> >>> yt-dev(a)lists.spacepope.org >>>> >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>> >>>> > _______________________________________________ >>>> > yt-dev mailing list >>>> > yt-dev(a)lists.spacepope.org >>>> > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> > >>>> >>>> >>>> >>>> _______________________________________________ >>>> yt-dev mailing list >>>> yt-dev(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>>> >>> >>> _______________________________________________ >>> yt-dev mailing list >>> yt-dev(a)lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >>> >> >> _______________________________________________ >> yt-dev mailing list >> yt-dev(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >> >> > > _______________________________________________ > yt-dev mailing list > yt-dev(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/attachments/20160…> ------------------------------ Subject: Digest Footer _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org ------------------------------ End of yt-dev Digest, Vol 85, Issue 32 ************************************** _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

5 years, 8 months

Issue #1161: YTArray does not return scalar item in correct dtype (yt_analysis/yt)

by Yi-Hao Chen

New issue 1161: YTArray does not return scalar item in correct dtype https://bitbucket.org/yt_analysis/yt/issues/1161/ytarray-does-not-return-sc… Yi-Hao Chen: The default dtype for YTArray is float64. If a YTArray is in integer or other dtype, it will still return an item in float64 if the returned item is a scalar. This can be clearly demonstrated in the following example. ``` #!python >>> import yt >>> mark = yt.YTArray([1,3,0]).astype('int') >>> mark YTArray([1, 3, 0]) (dimensionless) >>> mark.dtype dtype('int64') >>> mark[0] 1.0 dimensionless >>> mark[0].dtype dtype('float64') ``` This bug affects the function ```_find_field_values_at_points``` in ```GridIndex```. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

5 years, 8 months

yt 3.2.3 bugfix release?

by Nathan Goldbaum

Hi all, Tom Robitaille just pointed out on bitbucket that there are some python3 fixes that should be backported to the stable branch. I'd like to do a yt 3.2.3 release next week. Is that ok? Does anyone have anything incoming they'd like me to wait on? -Nathan _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

5 years, 8 months

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yt-dev January 2016