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various additions and improvements to data #83

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Nov 11, 2021
Merged

various additions and improvements to data #83

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206 changes: 129 additions & 77 deletions tidy3d/components/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,21 @@ def decode_bytes_array(array_of_bytes: Numpy) -> List[str]:
return list_of_str


""" Base Classes """
""" xarray subclasses """


class Tidy3dDataArray(xr.DataArray):
"""Subclass of xarray's DataArray that implements some custom functions."""

__slots__ = ()

@property
def abs(self):
"""Absolute value of complex-valued data."""
return abs(self)


""" Base data classes """


class Tidy3dData(Tidy3dBaseModel):
Expand All @@ -63,7 +77,7 @@ class Config: # pylint: disable=too-few-public-methods
json_encoders = { # how to write certain types to json files
np.ndarray: numpy_encoding, # use custom encoding defined in .types
np.int64: lambda x: int(x), # pylint: disable=unnecessary-lambda
xr.DataArray: lambda x: None, # dont write
Tidy3dDataArray: lambda x: None, # dont write
xr.Dataset: lambda x: None, # dont write
}

Expand Down Expand Up @@ -106,7 +120,7 @@ class MonitorData(Tidy3dData, ABC):
"""

@property
def data(self) -> xr.DataArray:
def data(self) -> Tidy3dDataArray:
# pylint:disable=line-too-long
"""Returns an xarray representation of the montitor data.

Expand All @@ -120,7 +134,7 @@ def data(self) -> xr.DataArray:

data_dict = self.dict()
coords = {dim: data_dict[dim] for dim in self._dims}
return xr.DataArray(self.values, coords=coords)
return Tidy3dDataArray(self.values, coords=coords)

def __eq__(self, other) -> bool:
"""Check equality against another MonitorData instance.
Expand Down Expand Up @@ -204,8 +218,8 @@ def data(self) -> xr.Dataset:
data_arrays = {name: arr.data for name, arr in self.data_dict.items()}

# make an xarray dataset
# return xr.Dataset(data_arrays) # datasets are annoying
return data_arrays
return xr.Dataset(data_arrays) # datasets are annoying
# return data_arrays

def __eq__(self, other):
"""Check for equality against other :class:`CollectionData` object."""
Expand Down Expand Up @@ -488,9 +502,11 @@ class SimulationData(Tidy3dBaseModel):
@property
def log(self):
"""Prints the server-side log."""
print(self.log_string if self.log_string else "no log stored")
if not self.log_string:
raise DataError("No log stored in SimulationData.")
return self.log_string

def __getitem__(self, monitor_name: str) -> Union[xr.DataArray, xr.Dataset]:
def __getitem__(self, monitor_name: str) -> Union[Tidy3dDataArray, xr.Dataset]:
"""Get the :class:`MonitorData` xarray representation by name (``sim_data[monitor_name]``).

Parameters
Expand All @@ -508,75 +524,111 @@ def __getitem__(self, monitor_name: str) -> Union[xr.DataArray, xr.Dataset]:
raise DataError(f"monitor {monitor_name} not found")
return monitor_data.data

# @add_ax_if_none
# def plot_field(
# self,
# field_monitor_name: str,
# field_name: str,
# x: float = None,
# y: float = None,
# z: float = None,
# freq: float = None,
# time: float = None,
# eps_alpha: pydantic.confloat(ge=0.0, le=1.0) = 0.5,
# ax: Ax = None,
# **kwargs,
# ) -> Ax:
# """Plot the field data for a monitor with simulation plot overlayed.

# Parameters
# ----------
# field_monitor_name : ``str``
# Name of :class:`FieldMonitor` or :class:`FieldTimeData` to plot.
# field_name : ``str``
# Name of `field` in monitor to plot (eg. 'Ex').
# x : ``float``, optional
# Position of plane in x direction.
# y : ``float``, optional
# Position of plane in y direction.
# z : ``float``, optional
# Position of plane in z direction.
# freq: ``float``, optional
# if monitor is a :class:`FieldMonitor`, specifies the frequency (Hz) to plot the field.
# time: ``float``, optional
# if monitor is a :class:`FieldTimeMonitor`, specifies the time (sec) to plot the field.
# cbar: `bool``, optional
# if True (default), will include colorbar
# ax : ``matplotlib.axes._subplots.Axes``, optional
# matplotlib axes to plot on, if not specified, one is created.
# **patch_kwargs
# Optional keyword arguments passed to ``add_artist(patch, **patch_kwargs)``.

# Returns
# -------
# ``matplotlib.axes._subplots.Axes``
# The supplied or created matplotlib axes.

# TODO: fully test and finalize arguments.
# """

# if field_monitor_name not in self.monitor_data:
# raise DataError(f"field_monitor_name {field_monitor_name} not found in SimulationData.")

# monitor_data = self.monitor_data.get(field_monitor_name)

# if not isinstance(monitor_data, FieldData):
# raise DataError(f"field_monitor_name {field_monitor_name} not a FieldData instance.")

# if field_name not in monitor_data.data_dict:
# raise DataError(f"field_name {field_name} not found in {field_monitor_name}.")

# xr_data = monitor_data.data_dict.get(field_name)
# if isinstance(monitor_data, FieldData):
# field_data = xr_data.sel(f=freq)
# else:
# field_data = xr_data.sel(t=time)

# ax = field_data.sel(x=x, y=y, z=z).real.plot.pcolormesh(ax=ax)
# ax = self.simulation.plot_structures_eps(
# freq=freq, cbar=False, x=x, y=y, z=z, alpha=eps_alpha, ax=ax
# )
# return ax
@add_ax_if_none
def plot_field(
self,
field_monitor_name: str,
field_name: str,
x: float = None,
y: float = None,
z: float = None,
val: Literal["real", "imag", "abs"] = "real",
freq: float = None,
time: float = None,
cbar: bool = None,
eps_alpha: float = 0.2,
ax: Ax = None,
**kwargs,
) -> Ax:
"""Plot the field data for a monitor with simulation plot overlayed.

Parameters
----------
field_monitor_name : str
Name of :class:`FieldMonitor` or :class:`FieldTimeData` to plot.
field_name : str
Name of `field` in monitor to plot (eg. 'Ex').
x : float = None
Position of plane in x direction.
y : float = None
Position of plane in y direction.
z : float = None
Position of plane in z direction.
val : Literal['real', 'imag', 'abs'] = 'real'
What part of the field to plot (in )
freq: float = None
If monitor is a :class:`FieldMonitor`, specifies the frequency (Hz) to plot the field.
time: float = None
if monitor is a :class:`FieldTimeMonitor`, specifies the time (sec) to plot the field.
cbar: bool = True
if True (default), will include colorbar
eps_alpha : float = 0.2
Opacity of the structure permittivity.
Must be between 0 and 1 (inclusive).
ax : matplotlib.axes._subplots.Axes = None
matplotlib axes to plot on, if not specified, one is created.
**patch_kwargs
Optional keyword arguments passed to ``add_artist(patch, **patch_kwargs)``.

Returns
-------
matplotlib.axes._subplots.Axes
The supplied or created matplotlib axes.
"""

# get the monitor data
if field_monitor_name not in self.monitor_data:
raise DataError(f"Monitor named '{field_monitor_name}' not found.")
monitor_data = self.monitor_data.get(field_monitor_name)
if not isinstance(monitor_data, FieldData):
raise DataError(f"field_monitor_name '{field_monitor_name}' not a FieldData instance.")

# get the field data component
if field_name not in monitor_data.data_dict:
raise DataError(f"field_name {field_name} not found in {field_monitor_name}.")
xr_data = monitor_data.data_dict.get(field_name).data

# select the frequency or time value
if "f" in monitor_data.coords:
if freq is None:
raise DataError("'freq' must be supplied to plot a FieldMonitor.")
field_data = xr_data.interp(f=freq)
elif "t" in monitor_data.coords:
if time is None:
raise DataError("'time' must be supplied to plot a FieldMonitor.")
field_data = xr_data.interp(t=time)
else:
raise DataError("Field data has neither time nor frequency data, something went wrong.")

# select the cross section data
axis, pos = self.simulation.parse_xyz_kwargs(x=x, y=y, z=z)
axis_label = "xyz"[axis]
sel_kwarg = {axis_label: pos}
try:
field_data = field_data.sel(**sel_kwarg)
except Exception as e:
raise DataError(f"Could not select data at {axis_label}={pos}.") from e

# select the field value
if val not in ("real", "imag", "abs"):
raise DataError(f"'val' must be one of ``{'real', 'imag', 'abs'}``, given {val}")
if val == "real":
field_data = field_data.real
elif val == "imag":
field_data = field_data.imag
elif val == "real":
field_data = abs(field_data)

# plot the field
xy_coords = list("xyz")
xy_coords.pop(axis)
field_data.plot(ax=ax, x=xy_coords[0], y=xy_coords[1])

# plot the simulation epsilon
ax = self.simulation.plot_structures_eps(
freq=freq, cbar=cbar, x=x, y=y, z=z, alpha=eps_alpha, ax=ax
)
return ax

def export(self, fname: str) -> None:
"""Export :class:`SimulationData` to single hdf5 file including monitor data.
Expand Down
10 changes: 5 additions & 5 deletions tidy3d/components/geometry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -208,7 +208,7 @@ def plot(
# pylint:disable=line-too-long

# find shapes that intersect self at plane
axis, position = self._parse_xyz_kwargs(x=x, y=y, z=z)
axis, position = self.parse_xyz_kwargs(x=x, y=y, z=z)
shapes_intersect = self.intersections(x=x, y=y, z=z)

# for each intersection, plot the shape
Expand Down Expand Up @@ -328,7 +328,7 @@ def unpop_axis(ax_coord: Any, plane_coords: Tuple[Any, Any], axis: int) -> Tuple
return tuple(coords)

@staticmethod
def _parse_xyz_kwargs(**xyz) -> Tuple[Axis, float]:
def parse_xyz_kwargs(**xyz) -> Tuple[Axis, float]:
"""Turns x,y,z kwargs into index of the normal axis and position along that axis.

Parameters
Expand Down Expand Up @@ -380,7 +380,7 @@ def intersections(self, x: float = None, y: float = None, z: float = None):
For more details refer to
`Shapely's Documentaton <https://shapely.readthedocs.io/en/stable/project.html>`_.
"""
axis, position = self._parse_xyz_kwargs(x=x, y=y, z=z)
axis, position = self.parse_xyz_kwargs(x=x, y=y, z=z)
if axis == self.axis:
z0, _ = self.pop_axis(self.center, axis=self.axis)
if (position < z0 - self.length / 2) or (position > z0 + self.length / 2):
Expand Down Expand Up @@ -529,7 +529,7 @@ def intersections(self, x: float = None, y: float = None, z: float = None):
For more details refer to
`Shapely's Documentaton <https://shapely.readthedocs.io/en/stable/project.html>`_.
"""
axis, position = self._parse_xyz_kwargs(x=x, y=y, z=z)
axis, position = self.parse_xyz_kwargs(x=x, y=y, z=z)
z0, (x0, y0) = self.pop_axis(self.center, axis=axis)
Lz, (Lx, Ly) = self.pop_axis(self.size, axis=axis)
dz = np.abs(z0 - position)
Expand Down Expand Up @@ -647,7 +647,7 @@ def intersections(self, x: float = None, y: float = None, z: float = None):
For more details refer to
`Shapely's Documentaton <https://shapely.readthedocs.io/en/stable/project.html>`_.
"""
axis, position = self._parse_xyz_kwargs(x=x, y=y, z=z)
axis, position = self.parse_xyz_kwargs(x=x, y=y, z=z)
z0, (x0, y0) = self.pop_axis(self.center, axis=axis)
intersect_dist = self._intersect_dist(position, z0)
if not intersect_dist:
Expand Down
9 changes: 5 additions & 4 deletions tidy3d/components/medium.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from .viz import add_ax_if_none
from .validators import validate_name_str

from ..constants import C_0, inf, pec_val
from ..constants import C_0, pec_val
from ..log import log


Expand All @@ -23,15 +23,16 @@ class AbstractMedium(ABC, Tidy3dBaseModel):

Parameters
----------
frequeuncy_range : Tuple[float, float] = (-inf, inf)
frequeuncy_range : Tuple[float, float] = None
Range of validity for the medium in Hz.
If None, then all frequencies are valid.
If simulation or plotting functions use frequency out of this range, a warning is thrown.
name : str = None
Optional name for the medium.
"""

name: str = None
frequency_range: Tuple[FreqBound, FreqBound] = (-inf, inf)
frequency_range: Tuple[FreqBound, FreqBound] = None

_name_validator = validate_name_str()

Expand Down Expand Up @@ -88,7 +89,7 @@ def _eps_model(self, frequency: float) -> complex:
"""New eps_model function."""

# if frequency is none, don't check, return original function
if frequency is None:
if frequency is None or self.frequency_range is None:
return eps_model(self, frequency)

fmin, fmax = self.frequency_range
Expand Down
4 changes: 2 additions & 2 deletions tidy3d/components/simulation.py
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Expand Up @@ -637,7 +637,7 @@ def plot_grid(self, x: float = None, y: float = None, z: float = None, ax: Ax =
The supplied or created matplotlib axes.
"""
cell_boundaries = self.grid.boundaries
axis, _ = self._parse_xyz_kwargs(x=x, y=y, z=z)
axis, _ = self.parse_xyz_kwargs(x=x, y=y, z=z)
_, (axis_x, axis_y) = self.pop_axis([0, 1, 2], axis=axis)
boundaries_x = cell_boundaries.dict()["xyz"[axis_x]]
boundaries_y = cell_boundaries.dict()["xyz"[axis_y]]
Expand Down Expand Up @@ -668,7 +668,7 @@ def _set_plot_bounds(self, ax: Ax, x: float = None, y: float = None, z: float =
The axes after setting the boundaries.
"""

axis, _ = self._parse_xyz_kwargs(x=x, y=y, z=z)
axis, _ = self.parse_xyz_kwargs(x=x, y=y, z=z)
_, ((xmin, ymin), (xmax, ymax)) = self._pop_bounds(axis=axis)
_, (pml_thick_x, pml_thick_y) = self.pop_axis(self.pml_thicknesses, axis=axis)

Expand Down
8 changes: 4 additions & 4 deletions tidy3d/components/viz.py
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Expand Up @@ -81,15 +81,15 @@ class SourceParams(PatchParamSwitcher):

def get_plot_params(self) -> PatchParams:
"""Returns :class:`PatchParams` based on user-supplied args."""
return PatchParams(alpha=0.7, facecolor="blueviolet", edgecolor="blueviolet")
return PatchParams(alpha=0.4, facecolor="blueviolet", edgecolor="blueviolet")


class MonitorParams(PatchParamSwitcher):
"""Patch plotting parameters for :class:`Monitor`."""

def get_plot_params(self) -> PatchParams:
"""Returns :class:`PatchParams` based on user-supplied args."""
return PatchParams(alpha=0.7, facecolor="crimson", edgecolor="crimson")
return PatchParams(alpha=0.4, facecolor="crimson", edgecolor="crimson")


class StructMediumParams(PatchParamSwitcher):
Expand Down Expand Up @@ -140,9 +140,9 @@ class SymParams(PatchParamSwitcher):
def get_plot_params(self) -> PatchParams:
"""Returns :class:`PatchParams` based on user-supplied args."""
if self.sym_value == 1:
return PatchParams(alpha=0.5, facecolor="lightsteelblue", edgecolor="lightsteelblue")
return PatchParams(alpha=0.3, facecolor="lightsteelblue", edgecolor="lightsteelblue")
if self.sym_value == -1:
return PatchParams(alpha=0.5, facecolor="lightgreen", edgecolor="lightgreen")
return PatchParams(alpha=0.3, facecolor="lightgreen", edgecolor="lightgreen")
return PatchParams()


Expand Down
2 changes: 1 addition & 1 deletion tidy3d/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
HBAR = 6.582119569e-16

# infinity (very large)
inf = 1e20
inf = 1e10

# floating point precisions
dp_eps = np.finfo(np.float64).eps
Expand Down
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