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brian-rose/climlab | climlab/process/process.py | get_axes | def get_axes(process_or_domain):
"""Returns a dictionary of all Axis in a domain or dictionary of domains.
:param process_or_domain: a process or a domain object
:type process_or_domain: :class:`~climlab.process.process.Process` or
:class:`~climlab.domain.domain._Domain... | python | def get_axes(process_or_domain):
"""Returns a dictionary of all Axis in a domain or dictionary of domains.
:param process_or_domain: a process or a domain object
:type process_or_domain: :class:`~climlab.process.process.Process` or
:class:`~climlab.domain.domain._Domain... | [
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brian-rose/climlab | climlab/process/process.py | Process.add_subprocesses | def add_subprocesses(self, procdict):
"""Adds a dictionary of subproceses to this process.
Calls :func:`add_subprocess` for every process given in the
input-dictionary. It can also pass a single process, which will
be given the name *default*.
:param procdict: a dictionary w... | python | def add_subprocesses(self, procdict):
"""Adds a dictionary of subproceses to this process.
Calls :func:`add_subprocess` for every process given in the
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brian-rose/climlab | climlab/process/process.py | Process.add_subprocess | def add_subprocess(self, name, proc):
"""Adds a single subprocess to this process.
:param string name: name of the subprocess
:param proc: a Process object
:type proc: :class:`~climlab.process.process.Process`
:raises: :exc:`ValueError`
... | python | def add_subprocess(self, name, proc):
"""Adds a single subprocess to this process.
:param string name: name of the subprocess
:param proc: a Process object
:type proc: :class:`~climlab.process.process.Process`
:raises: :exc:`ValueError`
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brian-rose/climlab | climlab/process/process.py | Process.remove_subprocess | def remove_subprocess(self, name, verbose=True):
"""Removes a single subprocess from this process.
:param string name: name of the subprocess
:param bool verbose: information whether warning message
should be printed [default: True]
:Example:
... | python | def remove_subprocess(self, name, verbose=True):
"""Removes a single subprocess from this process.
:param string name: name of the subprocess
:param bool verbose: information whether warning message
should be printed [default: True]
:Example:
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brian-rose/climlab | climlab/process/process.py | Process.set_state | def set_state(self, name, value):
"""Sets the variable ``name`` to a new state ``value``.
:param string name: name of the state
:param value: state variable
:type value: :class:`~climlab.domain.field.Field` or *array*
:raises: :exc:`ValueError`
... | python | def set_state(self, name, value):
"""Sets the variable ``name`` to a new state ``value``.
:param string name: name of the state
:param value: state variable
:type value: :class:`~climlab.domain.field.Field` or *array*
:raises: :exc:`ValueError`
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brian-rose/climlab | climlab/process/process.py | Process._add_field | def _add_field(self, field_type, name, value):
"""Adds a new field to a specified dictionary. The field is also added
as a process attribute. field_type can be 'input', 'diagnostics' """
try:
self.__getattribute__(field_type).update({name: value})
except:
raise Va... | python | def _add_field(self, field_type, name, value):
"""Adds a new field to a specified dictionary. The field is also added
as a process attribute. field_type can be 'input', 'diagnostics' """
try:
self.__getattribute__(field_type).update({name: value})
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raise Va... | [
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brian-rose/climlab | climlab/process/process.py | Process.add_diagnostic | def add_diagnostic(self, name, value=None):
"""Create a new diagnostic variable called ``name`` for this process
and initialize it with the given ``value``.
Quantity is accessible in two ways:
* as a process attribute, i.e. ``proc.name``
* as a member of the diagnostics... | python | def add_diagnostic(self, name, value=None):
"""Create a new diagnostic variable called ``name`` for this process
and initialize it with the given ``value``.
Quantity is accessible in two ways:
* as a process attribute, i.e. ``proc.name``
* as a member of the diagnostics... | [
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brian-rose/climlab | climlab/process/process.py | Process.add_input | def add_input(self, name, value=None):
'''Create a new input variable called ``name`` for this process
and initialize it with the given ``value``.
Quantity is accessible in two ways:
* as a process attribute, i.e. ``proc.name``
* as a member of the input dictionary,
... | python | def add_input(self, name, value=None):
'''Create a new input variable called ``name`` for this process
and initialize it with the given ``value``.
Quantity is accessible in two ways:
* as a process attribute, i.e. ``proc.name``
* as a member of the input dictionary,
... | [
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brian-rose/climlab | climlab/process/process.py | Process.remove_diagnostic | def remove_diagnostic(self, name):
""" Removes a diagnostic from the ``process.diagnostic`` dictionary
and also delete the associated process attribute.
:param str name: name of diagnostic quantity to be removed
:Example:
Remove diagnostic variable 'icelat' from energy ... | python | def remove_diagnostic(self, name):
""" Removes a diagnostic from the ``process.diagnostic`` dictionary
and also delete the associated process attribute.
:param str name: name of diagnostic quantity to be removed
:Example:
Remove diagnostic variable 'icelat' from energy ... | [
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brian-rose/climlab | climlab/process/process.py | Process.to_xarray | def to_xarray(self, diagnostics=False):
""" Convert process variables to ``xarray.Dataset`` format.
With ``diagnostics=True``, both state and diagnostic variables are included.
Otherwise just the state variables are included.
Returns an ``xarray.Dataset`` object with all spatial axes,... | python | def to_xarray(self, diagnostics=False):
""" Convert process variables to ``xarray.Dataset`` format.
With ``diagnostics=True``, both state and diagnostic variables are included.
Otherwise just the state variables are included.
Returns an ``xarray.Dataset`` object with all spatial axes,... | [
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brian-rose/climlab | climlab/process/process.py | Process.diagnostics | def diagnostics(self):
"""Dictionary access to all diagnostic variables
:type: dict
"""
diag_dict = {}
for key in self._diag_vars:
try:
#diag_dict[key] = getattr(self,key)
# using self.__dict__ doesn't count diagnostics defined ... | python | def diagnostics(self):
"""Dictionary access to all diagnostic variables
:type: dict
"""
diag_dict = {}
for key in self._diag_vars:
try:
#diag_dict[key] = getattr(self,key)
# using self.__dict__ doesn't count diagnostics defined ... | [
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brian-rose/climlab | climlab/process/process.py | Process.input | def input(self):
"""Dictionary access to all input variables
That can be boundary conditions and other gridded quantities
independent of the `process`
:type: dict
"""
input_dict = {}
for key in self._input_vars:
try:
input_dict[... | python | def input(self):
"""Dictionary access to all input variables
That can be boundary conditions and other gridded quantities
independent of the `process`
:type: dict
"""
input_dict = {}
for key in self._input_vars:
try:
input_dict[... | [
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brian-rose/climlab | climlab/solar/orbital/table.py | _get_Berger_data | def _get_Berger_data(verbose=True):
'''Read in the Berger and Loutre orbital table as a pandas dataframe, convert to xarray
'''
# The first column of the data file is used as the row index, and represents kyr from present
orbit91_pd, path = load_data_source(local_path = local_path,
r... | python | def _get_Berger_data(verbose=True):
'''Read in the Berger and Loutre orbital table as a pandas dataframe, convert to xarray
'''
# The first column of the data file is used as the row index, and represents kyr from present
orbit91_pd, path = load_data_source(local_path = local_path,
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brian-rose/climlab | climlab/utils/data_source.py | load_data_source | def load_data_source(local_path,
remote_source_list,
open_method,
open_method_kwargs=dict(),
remote_kwargs=dict(),
verbose=True):
'''Flexible data retreiver to download and cache the data files locally.
Usage example (this makes a local... | python | def load_data_source(local_path,
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open_method_kwargs=dict(),
remote_kwargs=dict(),
verbose=True):
'''Flexible data retreiver to download and cache the data files locally.
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.. code-block:: python
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from xarray import open_dataset
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brian-rose/climlab | climlab/radiation/transmissivity.py | tril | def tril(array, k=0):
'''Lower triangle of an array.
Return a copy of an array with elements above the k-th diagonal zeroed.
Need a multi-dimensional version here because numpy.tril does not
broadcast for numpy verison < 1.9.'''
try:
tril_array = np.tril(array, k=k)
except:
# hav... | python | def tril(array, k=0):
'''Lower triangle of an array.
Return a copy of an array with elements above the k-th diagonal zeroed.
Need a multi-dimensional version here because numpy.tril does not
broadcast for numpy verison < 1.9.'''
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brian-rose/climlab | climlab/radiation/transmissivity.py | Transmissivity.flux_up | def flux_up(self, fluxUpBottom, emission=None):
'''Compute downwelling radiative flux at interfaces between layers.
Inputs:
* fluxDownTop: flux down at top
* emission: emission from atmospheric levels (N)
defaults to zero if not given
Returns:
... | python | def flux_up(self, fluxUpBottom, emission=None):
'''Compute downwelling radiative flux at interfaces between layers.
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* fluxDownTop: flux down at top
* emission: emission from atmospheric levels (N)
defaults to zero if not given
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brian-rose/climlab | climlab/radiation/transmissivity.py | Transmissivity.flux_down | def flux_down(self, fluxDownTop, emission=None):
'''Compute upwelling radiative flux at interfaces between layers.
Inputs:
* fluxUpBottom: flux up from bottom
* emission: emission from atmospheric levels (N)
defaults to zero if not given
Returns:
... | python | def flux_down(self, fluxDownTop, emission=None):
'''Compute upwelling radiative flux at interfaces between layers.
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* fluxUpBottom: flux up from bottom
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defaults to zero if not given
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brian-rose/climlab | climlab/radiation/rrtm/rrtmg_lw.py | RRTMG_LW._compute_heating_rates | def _compute_heating_rates(self):
'''Prepare arguments and call the RRTGM_LW driver to calculate
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brian-rose/climlab | climlab/radiation/rrtm/utils.py | _prepare_general_arguments | def _prepare_general_arguments(RRTMGobject):
'''Prepare arguments needed for both RRTMG_SW and RRTMG_LW with correct dimensions.'''
tlay = _climlab_to_rrtm(RRTMGobject.Tatm)
tlev = _climlab_to_rrtm(interface_temperature(**RRTMGobject.state))
play = _climlab_to_rrtm(RRTMGobject.lev * np.ones_like(tlay))
... | python | def _prepare_general_arguments(RRTMGobject):
'''Prepare arguments needed for both RRTMG_SW and RRTMG_LW with correct dimensions.'''
tlay = _climlab_to_rrtm(RRTMGobject.Tatm)
tlev = _climlab_to_rrtm(interface_temperature(**RRTMGobject.state))
play = _climlab_to_rrtm(RRTMGobject.lev * np.ones_like(tlay))
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brian-rose/climlab | climlab/radiation/rrtm/utils.py | interface_temperature | def interface_temperature(Ts, Tatm, **kwargs):
'''Compute temperature at model layer interfaces.'''
# Actually it's not clear to me how the RRTM code uses these values
lev = Tatm.domain.axes['lev'].points
lev_bounds = Tatm.domain.axes['lev'].bounds
# Interpolate to layer interfaces
f = interp1... | python | def interface_temperature(Ts, Tatm, **kwargs):
'''Compute temperature at model layer interfaces.'''
# Actually it's not clear to me how the RRTM code uses these values
lev = Tatm.domain.axes['lev'].points
lev_bounds = Tatm.domain.axes['lev'].bounds
# Interpolate to layer interfaces
f = interp1... | [
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brian-rose/climlab | climlab/dynamics/meridional_moist_diffusion.py | moist_amplification_factor | def moist_amplification_factor(Tkelvin, relative_humidity=0.8):
'''Compute the moisture amplification factor for the moist diffusivity
given relative humidity and reference temperature profile.'''
deltaT = 0.01
# slope of saturation specific humidity at 1000 hPa
dqsdTs = (qsat(Tkelvin+deltaT/2, 100... | python | def moist_amplification_factor(Tkelvin, relative_humidity=0.8):
'''Compute the moisture amplification factor for the moist diffusivity
given relative humidity and reference temperature profile.'''
deltaT = 0.01
# slope of saturation specific humidity at 1000 hPa
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brian-rose/climlab | climlab/solar/insolation.py | daily_insolation | def daily_insolation(lat, day, orb=const.orb_present, S0=const.S0, day_type=1):
"""Compute daily average insolation given latitude, time of year and orbital parameters.
Orbital parameters can be interpolated to any time in the last 5 Myears with
``climlab.solar.orbital.OrbitalTable`` (see example above).
... | python | def daily_insolation(lat, day, orb=const.orb_present, S0=const.S0, day_type=1):
"""Compute daily average insolation given latitude, time of year and orbital parameters.
Orbital parameters can be interpolated to any time in the last 5 Myears with
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brian-rose/climlab | climlab/solar/insolation.py | solar_longitude | def solar_longitude( day, orb=const.orb_present, days_per_year = None ):
"""Estimates solar longitude from calendar day.
Method is using an approximation from :cite:`Berger_1978` section 3
(lambda = 0 at spring equinox).
**Function-call arguments** \n
:param array day: Indicator of time... | python | def solar_longitude( day, orb=const.orb_present, days_per_year = None ):
"""Estimates solar longitude from calendar day.
Method is using an approximation from :cite:`Berger_1978` section 3
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**Function-call arguments** \n
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brian-rose/climlab | climlab/domain/domain.py | single_column | def single_column(num_lev=30, water_depth=1., lev=None, **kwargs):
"""Creates domains for a single column of atmosphere overlying a slab of water.
Can also pass a pressure array or pressure level axis object specified in ``lev``.
If argument ``lev`` is not ``None`` then function tries to build a level axi... | python | def single_column(num_lev=30, water_depth=1., lev=None, **kwargs):
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brian-rose/climlab | climlab/domain/domain.py | zonal_mean_surface | def zonal_mean_surface(num_lat=90, water_depth=10., lat=None, **kwargs):
"""Creates a 1D slab ocean Domain in latitude with uniform water depth.
Domain has a single heat capacity according to the specified water depth.
**Function-call argument** \n
:param int num_lat: number of latitude point... | python | def zonal_mean_surface(num_lat=90, water_depth=10., lat=None, **kwargs):
"""Creates a 1D slab ocean Domain in latitude with uniform water depth.
Domain has a single heat capacity according to the specified water depth.
**Function-call argument** \n
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brian-rose/climlab | climlab/domain/domain.py | surface_2D | def surface_2D(num_lat=90, num_lon=180, water_depth=10., lon=None,
lat=None, **kwargs):
"""Creates a 2D slab ocean Domain in latitude and longitude with uniform water depth.
Domain has a single heat capacity according to the specified water depth.
**Function-call argument** \n
:param i... | python | def surface_2D(num_lat=90, num_lon=180, water_depth=10., lon=None,
lat=None, **kwargs):
"""Creates a 2D slab ocean Domain in latitude and longitude with uniform water depth.
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brian-rose/climlab | climlab/domain/domain.py | _Domain._make_axes_dict | def _make_axes_dict(self, axes):
"""Makes an axes dictionary.
.. note::
In case the input is ``None``, the dictionary :code:`{'empty': None}`
is returned.
**Function-call argument** \n
:param axes: axes input
:type axes: dict or single instance ... | python | def _make_axes_dict(self, axes):
"""Makes an axes dictionary.
.. note::
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**Function-call argument** \n
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brian-rose/climlab | climlab/process/implicit.py | ImplicitProcess._compute | def _compute(self):
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To calculate the new state the :func:`_implicit_solver()` method is
called for daughter classes. This however returns the new state of the
variables, not just the tendencies. Therefore, the adj... | python | def _compute(self):
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brian-rose/climlab | climlab/utils/walk.py | walk_processes | def walk_processes(top, topname='top', topdown=True, ignoreFlag=False):
"""Generator for recursive tree of climlab processes
Starts walking from climlab process ``top`` and generates a complete
list of all processes and sub-processes that are managed from ``top`` process.
``level`` indicades the rank o... | python | def walk_processes(top, topname='top', topdown=True, ignoreFlag=False):
"""Generator for recursive tree of climlab processes
Starts walking from climlab process ``top`` and generates a complete
list of all processes and sub-processes that are managed from ``top`` process.
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brian-rose/climlab | climlab/utils/walk.py | process_tree | def process_tree(top, name='top'):
"""Creates a string representation of the process tree for process top.
This method uses the :func:`walk_processes` method to create the process tree.
:param top: top process for which process tree string should be
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:typ... | python | def process_tree(top, name='top'):
"""Creates a string representation of the process tree for process top.
This method uses the :func:`walk_processes` method to create the process tree.
:param top: top process for which process tree string should be
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brian-rose/climlab | climlab/radiation/greygas.py | GreyGas._compute_fluxes | def _compute_fluxes(self):
''' All fluxes are band by band'''
self.emission = self._compute_emission()
self.emission_sfc = self._compute_emission_sfc()
fromspace = self._from_space()
self.flux_down = self.trans.flux_down(fromspace, self.emission)
self.flux_reflected_up = ... | python | def _compute_fluxes(self):
''' All fluxes are band by band'''
self.emission = self._compute_emission()
self.emission_sfc = self._compute_emission_sfc()
fromspace = self._from_space()
self.flux_down = self.trans.flux_down(fromspace, self.emission)
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brian-rose/climlab | climlab/radiation/greygas.py | GreyGas.flux_components_top | def flux_components_top(self):
'''Compute the contributions to the outgoing flux to space due to
emissions from each level and the surface.'''
N = self.lev.size
flux_up_bottom = self.flux_from_sfc
emission = np.zeros_like(self.emission)
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'''Compute the contributions to the outgoing flux to space due to
emissions from each level and the surface.'''
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flux_up_bottom = self.flux_from_sfc
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brian-rose/climlab | climlab/radiation/greygas.py | GreyGas.flux_components_bottom | def flux_components_bottom(self):
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N = self.lev.size
atmComponents = np.zeros_like(self.Tatm)
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# same comment as above... would be ni... | python | def flux_components_bottom(self):
'''Compute the contributions to the downwelling flux to surface due to
emissions from each level.'''
N = self.lev.size
atmComponents = np.zeros_like(self.Tatm)
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brian-rose/climlab | climlab/surface/turbulent.py | LatentHeatFlux._compute | def _compute(self):
'''Overides the _compute method of EnergyBudget'''
tendencies = self._temperature_tendencies()
if 'q' in self.state:
# in a model with active water vapor, this flux should affect
# water vapor tendency, NOT air temperature tendency!
tenden... | python | def _compute(self):
'''Overides the _compute method of EnergyBudget'''
tendencies = self._temperature_tendencies()
if 'q' in self.state:
# in a model with active water vapor, this flux should affect
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brian-rose/climlab | climlab/utils/legendre.py | Pn | def Pn(x):
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:param float x: argument to calculate Legendre polynomials
:return Pn: dictionary which contains order of Legendre polynomials
(from 0 to 28) as keys and the corresponding ... | python | def Pn(x):
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brian-rose/climlab | climlab/utils/legendre.py | Pnprime | def Pnprime(x):
"""Calculates first derivatives of Legendre polynomials and returns them
in a dictionary ``Pnprime``.
:param float x: argument to calculate first derivate of Legendre polynomials
:return Pn: dictionary which contains order of Legendre polynomials
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"""Calculates first derivatives of Legendre polynomials and returns them
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:param float x: argument to calculate first derivate of Legendre polynomials
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brian-rose/climlab | climlab/model/ebm.py | EBM.inferred_heat_transport | def inferred_heat_transport(self):
"""Calculates the inferred heat transport by integrating the TOA
energy imbalance from pole to pole.
The method is calculating
.. math::
H(\\varphi) = 2 \pi R^2 \int_{-\pi/2}^{\\varphi} cos\phi \ R_{TOA} d\phi
where :math:`R_{TOA... | python | def inferred_heat_transport(self):
"""Calculates the inferred heat transport by integrating the TOA
energy imbalance from pole to pole.
The method is calculating
.. math::
H(\\varphi) = 2 \pi R^2 \int_{-\pi/2}^{\\varphi} cos\phi \ R_{TOA} d\phi
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brian-rose/climlab | climlab/radiation/rrtm/_rrtmg_lw/setup.py | rrtmg_lw_gen_source | def rrtmg_lw_gen_source(ext, build_dir):
'''Add RRTMG_LW fortran source if Fortran 90 compiler available,
if no compiler is found do not try to build the extension.'''
thispath = config.local_path
module_src = []
for item in modules:
fullname = join(thispath,'rrtmg_lw_v4.85','gcm_model','mod... | python | def rrtmg_lw_gen_source(ext, build_dir):
'''Add RRTMG_LW fortran source if Fortran 90 compiler available,
if no compiler is found do not try to build the extension.'''
thispath = config.local_path
module_src = []
for item in modules:
fullname = join(thispath,'rrtmg_lw_v4.85','gcm_model','mod... | [
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess.compute | def compute(self):
"""Computes the tendencies for all state variables given current state
and specified input.
The function first computes all diagnostic processes. They don't produce
any tendencies directly but they may affect the other processes (such as
change in solar distri... | python | def compute(self):
"""Computes the tendencies for all state variables given current state
and specified input.
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess._compute_type | def _compute_type(self, proctype):
"""Computes tendencies due to all subprocesses of given type
``'proctype'``. Also pass all diagnostics up to parent process."""
tendencies = {}
for varname in self.state:
tendencies[varname] = 0. * self.state[varname]
for proc in sel... | python | def _compute_type(self, proctype):
"""Computes tendencies due to all subprocesses of given type
``'proctype'``. Also pass all diagnostics up to parent process."""
tendencies = {}
for varname in self.state:
tendencies[varname] = 0. * self.state[varname]
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess._compute | def _compute(self):
"""Where the tendencies are actually computed...
Needs to be implemented for each daughter class
Returns a dictionary with same keys as self.state"""
tendencies = {}
for name, value in self.state.items():
tendencies[name] = value * 0.
ret... | python | def _compute(self):
"""Where the tendencies are actually computed...
Needs to be implemented for each daughter class
Returns a dictionary with same keys as self.state"""
tendencies = {}
for name, value in self.state.items():
tendencies[name] = value * 0.
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess._build_process_type_list | def _build_process_type_list(self):
"""Generates lists of processes organized by process type.
Following object attributes are generated or updated:
:ivar dict process_types: a dictionary with entries:
``'diagnostic'``, ``'explicit'``,
... | python | def _build_process_type_list(self):
"""Generates lists of processes organized by process type.
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:ivar dict process_types: a dictionary with entries:
``'diagnostic'``, ``'explicit'``,
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess.step_forward | def step_forward(self):
"""Updates state variables with computed tendencies.
Calls the :func:`compute` method to get current tendencies for all
process states. Multiplied with the timestep and added up to the state
variables is updating all model states.
:Example:
... | python | def step_forward(self):
"""Updates state variables with computed tendencies.
Calls the :func:`compute` method to get current tendencies for all
process states. Multiplied with the timestep and added up to the state
variables is updating all model states.
:Example:
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess._update_time | def _update_time(self):
"""Increments the timestep counter by one.
Furthermore ``self.time['days_elapsed']`` and
``self.time['num_steps_per_year']`` are updated.
The function is called by the time stepping methods.
"""
self.time['steps'] += 1
# time in days sin... | python | def _update_time(self):
"""Increments the timestep counter by one.
Furthermore ``self.time['days_elapsed']`` and
``self.time['num_steps_per_year']`` are updated.
The function is called by the time stepping methods.
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self.time['steps'] += 1
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess.integrate_years | def integrate_years(self, years=1.0, verbose=True):
"""Integrates the model by a given number of years.
:param float years: integration time for the model in years
[default: 1.0]
:param bool verbose: information whether model time details
... | python | def integrate_years(self, years=1.0, verbose=True):
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:param float years: integration time for the model in years
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess.integrate_days | def integrate_days(self, days=1.0, verbose=True):
"""Integrates the model forward for a specified number of days.
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:func:`integrate_years`.
:param float days: integration time for the model in days
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brian-rose/climlab | climlab/process/time_dependent_process.py | TimeDependentProcess.integrate_converge | def integrate_converge(self, crit=1e-4, verbose=True):
"""Integrates the model until model states are converging.
:param crit: exit criteria for difference of iterated
solutions [default: 0.0001]
:type crit: float
:param bool verbos... | python | def integrate_converge(self, crit=1e-4, verbose=True):
"""Integrates the model until model states are converging.
:param crit: exit criteria for difference of iterated
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:type crit: float
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brian-rose/climlab | climlab/radiation/cam3/setup.py | cam3_gen_source | def cam3_gen_source(ext, build_dir):
'''Add CAM3 fortran source if Fortran 90 compiler available,
if no compiler is found do not try to build the extension.'''
# Fortran 90 sources in order of compilation
fort90source = ['pmgrid.F90',
'prescribed_aerosols.F90',
'shr_kind... | python | def cam3_gen_source(ext, build_dir):
'''Add CAM3 fortran source if Fortran 90 compiler available,
if no compiler is found do not try to build the extension.'''
# Fortran 90 sources in order of compilation
fort90source = ['pmgrid.F90',
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brian-rose/climlab | climlab/domain/field.py | global_mean | def global_mean(field):
"""Calculates the latitude weighted global mean of a field
with latitude dependence.
:param Field field: input field
:raises: :exc:`ValueError` if input field has no latitude axis
:return: latitude weighted global mean of the field
:rtype: float
:Example:
i... | python | def global_mean(field):
"""Calculates the latitude weighted global mean of a field
with latitude dependence.
:param Field field: input field
:raises: :exc:`ValueError` if input field has no latitude axis
:return: latitude weighted global mean of the field
:rtype: float
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i... | [
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brian-rose/climlab | climlab/domain/field.py | to_latlon | def to_latlon(array, domain, axis = 'lon'):
"""Broadcasts a 1D axis dependent array across another axis.
:param array input_array: the 1D array used for broadcasting
:param domain: the domain associated with that
array
:param axis: the axis ... | python | def to_latlon(array, domain, axis = 'lon'):
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brian-rose/climlab | climlab/domain/xarray.py | Field_to_xarray | def Field_to_xarray(field):
'''Convert a climlab.Field object to xarray.DataArray'''
dom = field.domain
dims = []; dimlist = []; coords = {};
for axname in dom.axes:
dimlist.append(axname)
try:
assert field.interfaces[dom.axis_index[axname]]
bounds_name = axname +... | python | def Field_to_xarray(field):
'''Convert a climlab.Field object to xarray.DataArray'''
dom = field.domain
dims = []; dimlist = []; coords = {};
for axname in dom.axes:
dimlist.append(axname)
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brian-rose/climlab | climlab/domain/xarray.py | state_to_xarray | def state_to_xarray(state):
'''Convert a dictionary of climlab.Field objects to xarray.Dataset
Input: dictionary of climlab.Field objects
(e.g. process.state or process.diagnostics dictionary)
Output: xarray.Dataset object with all spatial axes,
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'''Convert a dictionary of climlab.Field objects to xarray.Dataset
Input: dictionary of climlab.Field objects
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brian-rose/climlab | climlab/domain/xarray.py | to_xarray | def to_xarray(input):
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adamrehn/slidingwindow | slidingwindow/SlidingWindow.py | generate | def generate(data, dimOrder, maxWindowSize, overlapPercent, transforms = []):
"""
Generates a set of sliding windows for the specified dataset.
"""
# Determine the dimensions of the input data
width = data.shape[dimOrder.index('w')]
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return gene... | python | def generate(data, dimOrder, maxWindowSize, overlapPercent, transforms = []):
"""
Generates a set of sliding windows for the specified dataset.
"""
# Determine the dimensions of the input data
width = data.shape[dimOrder.index('w')]
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adamrehn/slidingwindow | slidingwindow/SlidingWindow.py | generateForSize | def generateForSize(width, height, dimOrder, maxWindowSize, overlapPercent, transforms = []):
"""
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adamrehn/slidingwindow | slidingwindow/SlidingWindow.py | SlidingWindow.apply | def apply(self, matrix):
"""
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"""
Slices the supplied matrix and applies any transform bound to this window
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adamrehn/slidingwindow | slidingwindow/SlidingWindow.py | SlidingWindow.indices | def indices(self, includeChannel=True):
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adamrehn/slidingwindow | slidingwindow/Batching.py | batchWindows | def batchWindows(windows, batchSize):
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originX = width / 2
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# Determine the number of bytes required to store the array
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kwikteam/phy | phy/cluster/views/base.py | ManualClusteringView.set_state | def set_state(self, state):
"""Set the view state.
The passed object is the persisted `self.state` bunch.
May be overriden.
"""
for k, v in state.items():
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The passed object is the persisted `self.state` bunch.
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kwikteam/phy | phy/utils/_misc.py | _fullname | def _fullname(o):
"""Return the fully-qualified name of a function."""
return o.__module__ + "." + o.__name__ if o.__module__ else o.__name__ | python | def _fullname(o):
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kwikteam/phy | phy/cluster/views/feature.py | FeatureView._get_axis_label | def _get_axis_label(self, dim):
"""Return the channel id from a dimension, if applicable."""
if u(dim[:-1]).isdecimal():
n = len(self.channel_ids)
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"""Return the channel id from a dimension, if applicable."""
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n = len(self.channel_ids)
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kwikteam/phy | phy/cluster/views/feature.py | FeatureView._get_axis_data | def _get_axis_data(self, bunch, dim, cluster_id=None, load_all=None):
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bunch is returned by the features() function.
dim is the string specifying the dimensions to extract for the data.
"""
if dim in self.attributes:
... | python | def _get_axis_data(self, bunch, dim, cluster_id=None, load_all=None):
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kwikteam/phy | phy/cluster/views/feature.py | FeatureView._plot_labels | def _plot_labels(self):
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# kth column in bottom row:
br = self.n_cols - 1 # bottom row
for k in range(0, self.n_cols):
dim_x, _ = self.grid_dim[0]... | python | def _plot_labels(self):
"""Plot feature labels along left and bottom edge of subplots"""
# iterate simultaneously over kth row in left column and
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br = self.n_cols - 1 # bottom row
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kwikteam/phy | phy/cluster/views/feature.py | FeatureView.on_channel_click | def on_channel_click(self, channel_id=None, key=None, button=None):
"""Respond to the click on a channel."""
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return
assert len(channels) >= 2
... | python | def on_channel_click(self, channel_id=None, key=None, button=None):
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kwikteam/phy | phy/cluster/views/feature.py | FeatureView.on_request_split | def on_request_split(self):
"""Return the spikes enclosed by the lasso."""
if (self.lasso.count < 3 or
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return np.array([], dtype=np.int64)
assert len(self.channel_ids)
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"""Return the spikes enclosed by the lasso."""
if (self.lasso.count < 3 or
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return np.array([], dtype=np.int64)
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kwikteam/phy | phy/plot/interact.py | Boxed.get_closest_box | def get_closest_box(self, pos):
"""Get the box closest to some position."""
pos = np.atleast_2d(pos)
d = np.sum((np.array(self.box_pos) - pos) ** 2, axis=1)
idx = np.argmin(d)
return idx | python | def get_closest_box(self, pos):
"""Get the box closest to some position."""
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kwikteam/phy | phy/plot/interact.py | Boxed.update_boxes | def update_boxes(self, box_pos, box_size):
"""Set the box bounds from specified box positions and sizes."""
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kwikteam/phy | phy/gui/qt.py | require_qt | def require_qt(func):
"""Specify that a function requires a Qt application.
Use this decorator to specify that a function needs a running
Qt application before it can run. An error is raised if that is not
the case.
"""
@wraps(func)
def wrapped(*args, **kwargs):
if not QApplication... | python | def require_qt(func):
"""Specify that a function requires a Qt application.
Use this decorator to specify that a function needs a running
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"""
@wraps(func)
def wrapped(*args, **kwargs):
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kwikteam/phy | phy/gui/qt.py | create_app | def create_app():
"""Create a Qt application."""
global QT_APP
QT_APP = QApplication.instance()
if QT_APP is None: # pragma: no cover
QT_APP = QApplication(sys.argv)
return QT_APP | python | def create_app():
"""Create a Qt application."""
global QT_APP
QT_APP = QApplication.instance()
if QT_APP is None: # pragma: no cover
QT_APP = QApplication(sys.argv)
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kwikteam/phy | phy/gui/qt.py | AsyncCaller.set | def set(self, f):
"""Call a function after a delay, unless another function is set
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self.stop()
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self.start() | python | def set(self, f):
"""Call a function after a delay, unless another function is set
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self.stop()
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kwikteam/phy | phy/gui/qt.py | AsyncCaller.stop | def stop(self):
"""Stop the current timer if there is one and cancel the async call."""
if self._timer:
self._timer.stop()
self._timer.deleteLater() | python | def stop(self):
"""Stop the current timer if there is one and cancel the async call."""
if self._timer:
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kwikteam/phy | phy/gui/actions.py | _wrap_callback_args | def _wrap_callback_args(f, docstring=None): # pragma: no cover
"""Display a Qt dialog when a function has arguments.
The user can write function arguments as if it was a snippet.
"""
def wrapped(checked, *args):
if args:
return f(*args)
if isinstance(f, partial):
... | python | def _wrap_callback_args(f, docstring=None): # pragma: no cover
"""Display a Qt dialog when a function has arguments.
The user can write function arguments as if it was a snippet.
"""
def wrapped(checked, *args):
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kwikteam/phy | phy/gui/actions.py | _get_shortcut_string | def _get_shortcut_string(shortcut):
"""Return a string representation of a shortcut."""
if shortcut is None:
return ''
if isinstance(shortcut, (tuple, list)):
return ', '.join([_get_shortcut_string(s) for s in shortcut])
if isinstance(shortcut, string_types):
if hasattr(QKeySeque... | python | def _get_shortcut_string(shortcut):
"""Return a string representation of a shortcut."""
if shortcut is None:
return ''
if isinstance(shortcut, (tuple, list)):
return ', '.join([_get_shortcut_string(s) for s in shortcut])
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kwikteam/phy | phy/gui/actions.py | _get_qkeysequence | def _get_qkeysequence(shortcut):
"""Return a QKeySequence or list of QKeySequence from a shortcut string."""
if shortcut is None:
return []
if isinstance(shortcut, (tuple, list)):
return [_get_qkeysequence(s) for s in shortcut]
assert isinstance(shortcut, string_types)
if hasattr(QKe... | python | def _get_qkeysequence(shortcut):
"""Return a QKeySequence or list of QKeySequence from a shortcut string."""
if shortcut is None:
return []
if isinstance(shortcut, (tuple, list)):
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kwikteam/phy | phy/gui/actions.py | _show_shortcuts | def _show_shortcuts(shortcuts, name=None):
"""Display shortcuts."""
name = name or ''
print('')
if name:
name = ' for ' + name
print('Keyboard shortcuts' + name)
for name in sorted(shortcuts):
shortcut = _get_shortcut_string(shortcuts[name])
if not name.startswith('_'):
... | python | def _show_shortcuts(shortcuts, name=None):
"""Display shortcuts."""
name = name or ''
print('')
if name:
name = ' for ' + name
print('Keyboard shortcuts' + name)
for name in sorted(shortcuts):
shortcut = _get_shortcut_string(shortcuts[name])
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kwikteam/phy | phy/gui/actions.py | Actions.add | def add(self, callback=None, name=None, shortcut=None, alias=None,
docstring=None, menu=None, verbose=True):
"""Add an action with a keyboard shortcut."""
if callback is None:
# Allow to use either add(func) or @add or @add(...).
return partial(self.add, name=name, sh... | python | def add(self, callback=None, name=None, shortcut=None, alias=None,
docstring=None, menu=None, verbose=True):
"""Add an action with a keyboard shortcut."""
if callback is None:
# Allow to use either add(func) or @add or @add(...).
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kwikteam/phy | phy/gui/actions.py | Actions.separator | def separator(self, menu=None):
"""Add a separator"""
self.gui.get_menu(menu or self.menu).addSeparator() | python | def separator(self, menu=None):
"""Add a separator"""
self.gui.get_menu(menu or self.menu).addSeparator() | [
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kwikteam/phy | phy/gui/actions.py | Actions.disable | def disable(self, name=None):
"""Disable one or all actions."""
if name is None:
for name in self._actions_dict:
self.disable(name)
return
self._actions_dict[name].qaction.setEnabled(False) | python | def disable(self, name=None):
"""Disable one or all actions."""
if name is None:
for name in self._actions_dict:
self.disable(name)
return
self._actions_dict[name].qaction.setEnabled(False) | [
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kwikteam/phy | phy/gui/actions.py | Actions.enable | def enable(self, name=None):
"""Enable one or all actions."""
if name is None:
for name in self._actions_dict:
self.enable(name)
return
self._actions_dict[name].qaction.setEnabled(True) | python | def enable(self, name=None):
"""Enable one or all actions."""
if name is None:
for name in self._actions_dict:
self.enable(name)
return
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kwikteam/phy | phy/gui/actions.py | Actions.run | def run(self, name, *args):
"""Run an action as specified by its name."""
assert isinstance(name, string_types)
# Resolve the alias if it is an alias.
name = self._aliases.get(name, name)
# Get the action.
action = self._actions_dict.get(name, None)
if not action:... | python | def run(self, name, *args):
"""Run an action as specified by its name."""
assert isinstance(name, string_types)
# Resolve the alias if it is an alias.
name = self._aliases.get(name, name)
# Get the action.
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kwikteam/phy | phy/gui/actions.py | Actions.remove | def remove(self, name):
"""Remove an action."""
self.gui.removeAction(self._actions_dict[name].qaction)
del self._actions_dict[name]
delattr(self, name) | python | def remove(self, name):
"""Remove an action."""
self.gui.removeAction(self._actions_dict[name].qaction)
del self._actions_dict[name]
delattr(self, name) | [
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kwikteam/phy | phy/gui/actions.py | Actions.remove_all | def remove_all(self):
"""Remove all actions."""
names = sorted(self._actions_dict.keys())
for name in names:
self.remove(name) | python | def remove_all(self):
"""Remove all actions."""
names = sorted(self._actions_dict.keys())
for name in names:
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kwikteam/phy | phy/gui/actions.py | Actions.shortcuts | def shortcuts(self):
"""A dictionary of action shortcuts."""
return {name: action.shortcut
for name, action in self._actions_dict.items()} | python | def shortcuts(self):
"""A dictionary of action shortcuts."""
return {name: action.shortcut
for name, action in self._actions_dict.items()} | [
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kwikteam/phy | phy/gui/actions.py | Actions.show_shortcuts | def show_shortcuts(self):
"""Print all shortcuts."""
gui_name = self.gui.name
actions_name = self.name
name = ('{} - {}'.format(gui_name, actions_name)
if actions_name else gui_name)
_show_shortcuts(self.shortcuts, name) | python | def show_shortcuts(self):
"""Print all shortcuts."""
gui_name = self.gui.name
actions_name = self.name
name = ('{} - {}'.format(gui_name, actions_name)
if actions_name else gui_name)
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kwikteam/phy | phy/gui/actions.py | Snippets.command | def command(self):
"""This is used to write a snippet message in the status bar.
A cursor is appended at the end.
"""
msg = self.gui.status_message
n = len(msg)
n_cur = len(self.cursor)
return msg[:n - n_cur] | python | def command(self):
"""This is used to write a snippet message in the status bar.
A cursor is appended at the end.
"""
msg = self.gui.status_message
n = len(msg)
n_cur = len(self.cursor)
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kwikteam/phy | phy/gui/actions.py | Snippets._backspace | def _backspace(self):
"""Erase the last character in the snippet command."""
if self.command == ':':
return
logger.log(5, "Snippet keystroke `Backspace`.")
self.command = self.command[:-1] | python | def _backspace(self):
"""Erase the last character in the snippet command."""
if self.command == ':':
return
logger.log(5, "Snippet keystroke `Backspace`.")
self.command = self.command[:-1] | [
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] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/gui/actions.py#L390-L395 | train |
kwikteam/phy | phy/gui/actions.py | Snippets._enter | def _enter(self):
"""Disable the snippet mode and execute the command."""
command = self.command
logger.log(5, "Snippet keystroke `Enter`.")
# NOTE: we need to set back the actions (mode_off) before running
# the command.
self.mode_off()
self.run(command) | python | def _enter(self):
"""Disable the snippet mode and execute the command."""
command = self.command
logger.log(5, "Snippet keystroke `Enter`.")
# NOTE: we need to set back the actions (mode_off) before running
# the command.
self.mode_off()
self.run(command) | [
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kwikteam/phy | phy/gui/actions.py | Snippets._create_snippet_actions | def _create_snippet_actions(self):
"""Add mock Qt actions for snippet keystrokes.
Used to enable snippet mode.
"""
# One action per allowed character.
for i, char in enumerate(self._snippet_chars):
def _make_func(char):
def callback():
... | python | def _create_snippet_actions(self):
"""Add mock Qt actions for snippet keystrokes.
Used to enable snippet mode.
"""
# One action per allowed character.
for i, char in enumerate(self._snippet_chars):
def _make_func(char):
def callback():
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kwikteam/phy | phy/gui/actions.py | Snippets.run | def run(self, snippet):
"""Executes a snippet command.
May be overridden.
"""
assert snippet[0] == ':'
snippet = snippet[1:]
snippet_args = _parse_snippet(snippet)
name = snippet_args[0]
logger.info("Processing snippet `%s`.", snippet)
try:
... | python | def run(self, snippet):
"""Executes a snippet command.
May be overridden.
"""
assert snippet[0] == ':'
snippet = snippet[1:]
snippet_args = _parse_snippet(snippet)
name = snippet_args[0]
logger.info("Processing snippet `%s`.", snippet)
try:
... | [
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kwikteam/phy | phy/traces/waveform.py | _before_after | def _before_after(n_samples):
"""Get the number of samples before and after."""
if not isinstance(n_samples, (tuple, list)):
before = n_samples // 2
after = n_samples - before
else:
assert len(n_samples) == 2
before, after = n_samples
n_samples = before + after
as... | python | def _before_after(n_samples):
"""Get the number of samples before and after."""
if not isinstance(n_samples, (tuple, list)):
before = n_samples // 2
after = n_samples - before
else:
assert len(n_samples) == 2
before, after = n_samples
n_samples = before + after
as... | [
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kwikteam/phy | phy/traces/waveform.py | _slice | def _slice(index, n_samples, margin=None):
"""Return a waveform slice."""
if margin is None:
margin = (0, 0)
assert isinstance(n_samples, (tuple, list))
assert len(n_samples) == 2
before, after = n_samples
assert isinstance(margin, (tuple, list))
assert len(margin) == 2
margin_be... | python | def _slice(index, n_samples, margin=None):
"""Return a waveform slice."""
if margin is None:
margin = (0, 0)
assert isinstance(n_samples, (tuple, list))
assert len(n_samples) == 2
before, after = n_samples
assert isinstance(margin, (tuple, list))
assert len(margin) == 2
margin_be... | [
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] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/traces/waveform.py#L164-L179 | train |
kwikteam/phy | phy/traces/waveform.py | WaveformLoader._load_at | def _load_at(self, time, channels=None):
"""Load a waveform at a given time."""
if channels is None:
channels = slice(None, None, None)
time = int(time)
time_o = time
ns = self.n_samples_trace
if not (0 <= time_o < ns):
raise ValueError("Invalid ti... | python | def _load_at(self, time, channels=None):
"""Load a waveform at a given time."""
if channels is None:
channels = slice(None, None, None)
time = int(time)
time_o = time
ns = self.n_samples_trace
if not (0 <= time_o < ns):
raise ValueError("Invalid ti... | [
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kwikteam/phy | phy/traces/waveform.py | WaveformLoader.get | def get(self, spike_ids, channels=None):
"""Load the waveforms of the specified spikes."""
if isinstance(spike_ids, slice):
spike_ids = _range_from_slice(spike_ids,
start=0,
stop=self.n_spikes,
... | python | def get(self, spike_ids, channels=None):
"""Load the waveforms of the specified spikes."""
if isinstance(spike_ids, slice):
spike_ids = _range_from_slice(spike_ids,
start=0,
stop=self.n_spikes,
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kwikteam/phy | phy/stats/clusters.py | get_waveform_amplitude | def get_waveform_amplitude(mean_masks, mean_waveforms):
"""Return the amplitude of the waveforms on all channels."""
assert mean_waveforms.ndim == 2
n_samples, n_channels = mean_waveforms.shape
assert mean_masks.ndim == 1
assert mean_masks.shape == (n_channels,)
mean_waveforms = mean_waveform... | python | def get_waveform_amplitude(mean_masks, mean_waveforms):
"""Return the amplitude of the waveforms on all channels."""
assert mean_waveforms.ndim == 2
n_samples, n_channels = mean_waveforms.shape
assert mean_masks.ndim == 1
assert mean_masks.shape == (n_channels,)
mean_waveforms = mean_waveform... | [
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kwikteam/phy | phy/stats/clusters.py | get_mean_masked_features_distance | def get_mean_masked_features_distance(mean_features_0,
mean_features_1,
mean_masks_0,
mean_masks_1,
n_features_per_channel=None,
)... | python | def get_mean_masked_features_distance(mean_features_0,
mean_features_1,
mean_masks_0,
mean_masks_1,
n_features_per_channel=None,
)... | [
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] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/stats/clusters.py#L58-L80 | train |
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