from ._version import get_versions
__version__ = get_versions()['version']
del get_versions
import pint
from pint import UnitRegistry
from importlib_resources import files
from distutils.version import LooseVersion
# Create ureg here so it is only created once
if LooseVersion(pint.__version__) < LooseVersion('0.10'):
# Bohr, unified_atomic_mass_unit not defined in pint 0.9, so load
# pint 0.16.1 definition file
ureg = UnitRegistry(str(files('euphonic.data') / 'default_en.txt'))
else:
ureg = UnitRegistry()
ureg.enable_contexts('spectroscopy')
Quantity = ureg.Quantity
from .spectra import Spectrum1D, Spectrum1DCollection, Spectrum2D
from .crystal import Crystal
from .debye_waller import DebyeWaller
from .qpoint_frequencies import QpointFrequencies
from .structure_factor import StructureFactor
from .qpoint_phonon_modes import QpointPhononModes
from .force_constants import ForceConstants
def image(self):
source = files(
'jaraco.site') / 'static' / 'images' / f'{self.name}.svg'
return source.read_text()
import sys
from deprecated import deprecated
if sys.version_info < (3, 9):
import importlib_resources as resources
else:
import importlib.resources as resources
__all__ = ("basepath", "open_text")
basepath = resources.files(__name__)
open_text = deprecated(version="0.12.0",
reason="Use decaylanguage.data.basepath instead.")(
resources.open_text)
def copy_scaffold() -> List[Path]:
dir_path = ir.files("datapane.resources.templates") / scaffold_name
copy_tree(dir_path, ".")
return [Path(x.name) for x in dir_path.iterdir()]
def template_to_head(info,
space,
coord_frame='auto',
unit='auto',
verbose=None):
"""Transform a BIDS standard template montage to the head coordinate frame.
Parameters
----------
%(info_not_none)s The info is modified in place.
space : str
The name of the BIDS standard template. See
https://bids-specification.readthedocs.io/en/stable/99-appendices/08-coordinate-systems.html#standard-template-identifiers
for a list of acceptable spaces.
coord_frame : 'mri' | 'mri_voxel' | 'ras'
BIDS template coordinate systems do not specify a coordinate frame,
so this must be determined by inspecting the documentation for the
dataset or the ``electrodes.tsv`` file. If ``'auto'``, the coordinate
frame is assumed to be ``'mri_voxel'`` if the coordinates are strictly
positive, and ``'ras'`` (``"scanner RAS"``) otherwise.
.. warning::
``scanner RAS`` and ``surface RAS`` coordinates frames are similar
so be very careful not to assume a BIDS dataset's coordinates are
in one when they are actually in the other. The only way to tell
for template coordinate systems, currently, is if it is specified
in the dataset documentation.
unit : 'm' | 'mm' | 'auto'
The unit that was used in the coordinate system specification.
If ``'auto'``, ``'m'`` will be inferred if the montage
spans less than ``-1`` to ``1``, and ``'mm'`` otherwise. If the
``coord_frame`` is ``'mri_voxel'``, ``unit`` will be ignored.
%(verbose)s
Returns
-------
%(info_not_none)s The modified ``Info`` object.
trans : mne.transforms.Transform
The data transformation matrix from ``'head'`` to ``'mri'``
coordinates.
"""
_validate_type(info, mne.io.Info)
_check_option('space', space, BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS)
_check_option('coord_frame', coord_frame,
('auto', 'mri', 'mri_voxel', 'ras'))
_check_option('unit', unit, ('auto', 'm', 'mm'))
# XXX: change to after 0.11 release
# montage = info.get_montage()
montage = _get_montage(info)
if montage is None:
raise RuntimeError('No montage found in the `raw` object')
montage.remove_fiducials() # we will add fiducials so remove any
pos = montage.get_positions()
if pos['coord_frame'] not in ('mni_tal', 'unknown'):
raise RuntimeError(
"Montage coordinate frame '{}' not expected for a template "
"montage, should be 'unknown' or 'mni_tal'".format(
pos['coord_frame']))
locs = np.array(list(pos['ch_pos'].values()))
locs = locs[~np.any(np.isnan(locs), axis=1)] # only channels with loc
if locs.size == 0:
raise RuntimeError('No channel locations found in the montage')
if unit == 'auto':
unit = 'm' if abs(locs - locs.mean(axis=0)).max() < 1 else 'mm'
if coord_frame == 'auto':
coord_frame = 'mri_voxel' if locs.min() >= 0 else 'ras'
# transform montage to head
data_dir = files('mne_bids.data')
# set to the right coordinate frame as specified by the user
for d in montage.dig: # ensure same coordinate frame
d['coord_frame'] = MNE_STR_TO_FRAME[coord_frame]
# do the transforms, first ras -> vox if needed
if montage.get_positions()['coord_frame'] == 'ras':
ras_vox_trans = mne.read_trans(data_dir /
f'space-{space}_ras-vox_trans.fif')
if unit == 'm': # must be in mm here
for d in montage.dig:
d['r'] *= 1000
montage.apply_trans(ras_vox_trans)
if montage.get_positions()['coord_frame'] == 'mri_voxel':
vox_mri_trans = mne.read_trans(data_dir /
f'space-{space}_vox-mri_trans.fif')
montage.apply_trans(vox_mri_trans)
assert montage.get_positions()['coord_frame'] == 'mri'
if not (unit == 'm' and coord_frame == 'mri'): # if so, already in m
for d in montage.dig:
d['r'] /= 1000 # mm -> m
# now add fiducials (in mri coordinates)
fids = mne.io.read_fiducials(data_dir / f'space-{space}_fiducials.fif')[0]
montage.dig = fids + montage.dig # add fiducials
for fid in fids: # ensure also in mri
fid['coord_frame'] = MNE_STR_TO_FRAME['mri']
info.set_montage(montage) # transform to head
# finally return montage
return info, mne.read_trans(data_dir / f'space-{space}_trans.fif')
from psaw import PushshiftAPI
from typing import Iterator, List
from pathlib import Path
import importlib_resources
import re
import praw
import uwb.src.util as u
T = PushshiftAPI
_test_posts_folder = (importlib_resources.files(
'uwb') / "resources" / "test_posts")
def eprint(x: str) -> None:
u.eprint(f"reddit.py: {x}")
class Post:
def __init__(self, *, _id: str, subreddit: str, title: str, content: str):
self._id = _id
self.subreddit = subreddit
self.title = title
self.content = content
def init(test=False) -> T:
if test:
return None
return PushshiftAPI()
True,
'server.socket_port':
int(os.environ.get('PORT', 8080)),
'server.socket_host':
os.environ.get('SOCKET_HOST', '::'),
'tools.encode.on':
True,
'tools.encode.encoding':
'utf-8',
'tools.decode.on':
True,
'tools.sessions.on':
True,
'tools.trailing_slash.on':
True,
'tools.staticdir.root':
os.fspath(files('jaraco.site')),
'tools.proxy.on':
True,
})
config = {
'/static': {
'tools.staticdir.on': True,
'tools.staticdir.dir': 'static',
'tools.staticdir.content_types': dict(svg='image/svg+xml'),
}
}
app = cherrypy.tree.mount(Root(), '/', config)