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docs(core.annotations): adds docstrings
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@Oli4
Oli4 committed Mar 29, 2023
1 parent 9e47a09 commit 236c074
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Showing 2 changed files with 75 additions and 119 deletions.
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ upload_to_release = true
build_command = "pip install poetry && poetry build"

[tool.docformatter]
check = true
check = false
recursive = true
in-place = true
syntax = "google"
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192 changes: 74 additions & 118 deletions src/eyepy/core/annotations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
from collections import defaultdict
from collections.abc import Iterable
import logging
from typing import Optional, TYPE_CHECKING, Union
from typing import Any, Optional, TYPE_CHECKING, Union

from matplotlib import cm
from matplotlib import colors
Expand All @@ -25,7 +25,6 @@


class EyeVolumeLayerAnnotation:
""""""

def __init__(
self,
Expand All @@ -34,13 +33,16 @@ def __init__(
meta: Optional[dict] = None,
**kwargs,
) -> None:
"""
"""Layer annotation for a single layer in an EyeVolume.
Args:
volume:
data:
meta:
**kwargs:
volume: EyeVolume object
data: 2D array of shape (n_bscans, bscan_width) holding layer height values
meta: dict with additional meta data
**kwargs: additional meta data specified as parameters
Returns:
None
"""
self.volume = volume
if data is None:
Expand All @@ -67,11 +69,7 @@ def __init__(

@property
def name(self) -> str:
"""
Returns:
"""
"""Layer name."""
return self.meta['name']

@name.setter
Expand All @@ -80,11 +78,7 @@ def name(self, value: str) -> None:

@property
def knots(self) -> dict:
"""
Returns:
"""
"""Knots parameterizing the layer."""
return self.meta['knots']

def layer_indices(self) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
Expand Down Expand Up @@ -123,7 +117,6 @@ def layer_indices(self) -> tuple[np.ndarray, np.ndarray, np.ndarray]:


class EyeVolumePixelAnnotation:
""""""

def __init__(
self,
Expand All @@ -136,18 +129,21 @@ def __init__(
offsets: Iterable[int] = (0, 45),
center: Optional[tuple[float, float]] = None,
**kwargs,
):
"""
) -> None:
"""Pixel annotation for an EyeVolume.
Args:
volume:
data:
meta:
radii:
n_sectors:
offsets:
center:
**kwargs:
volume: EyeVolume object
data: 3D array of shape (n_bscans, bscan_height, bscan_width) holding boolean pixel annotations
meta: dict with additional meta data
radii: radii for quantification on circular grid
n_sectors: number of sectors for quantification on circular grid
offsets: offsets from x axis for first sector, for quantification on circular grid
center: center of circular grid for quantification
**kwargs: additional meta data specified as parameters
Returns:
None
"""
self.volume = volume

Expand Down Expand Up @@ -180,11 +176,7 @@ def __init__(

@property
def name(self) -> str:
"""
Returns:
"""
"""Annotation name."""
return self.meta['name']

@name.setter
Expand All @@ -197,11 +189,7 @@ def _reset(self) -> None:

@property
def radii(self) -> Iterable[float]:
"""
Returns:
"""
"""Radii for quantification on circular grid."""
return self.meta['radii']

@radii.setter
Expand All @@ -211,11 +199,7 @@ def radii(self, value: Iterable[float]) -> None:

@property
def n_sectors(self) -> Iterable[int]:
"""
Returns:
"""
"""Number of sectors for quantification on circular grid."""
return self.meta['n_sectors']

@n_sectors.setter
Expand All @@ -225,11 +209,8 @@ def n_sectors(self, value: Iterable[int]) -> None:

@property
def offsets(self) -> Iterable[int]:
"""
Returns:
"""
"""Offsets from x axis for first sector, for quantification on circular
grid."""
return self.meta['offsets']

@offsets.setter
Expand All @@ -239,11 +220,7 @@ def offsets(self, value: Iterable[int]) -> None:

@property
def center(self) -> tuple[float, float]:
"""
Returns:
"""
"""Center of circular grid for quantification."""
return self.meta['center']

@center.setter
Expand All @@ -253,22 +230,14 @@ def center(self, value: tuple[float, float]) -> None:

@property
def projection(self) -> np.ndarray:
"""
Returns:
"""
"""Projection of the annotation to the enface plane."""
# The flip is required because in the volume the bottom most B-scan has the lowest index
# while in the enface projection the bottom most position should have the biggest index.
return np.flip(np.nansum(self.data, axis=1), axis=0)

@property
def enface(self) -> np.ndarray:
"""
Returns:
"""
"""Transformed projection of the annotation to the enface plane."""
return transform.warp(
self.projection,
self.volume.localizer_transform.inverse,
Expand All @@ -288,20 +257,20 @@ def plot(
vmax: Optional[float] = None,
cbar: bool = True,
alpha: float = 1,
):
"""
) -> None:
"""Plot the annotation on the enface plane.
Args:
ax:
region:
cmap:
vmin:
vmax:
cbar:
alpha:
ax: matplotlib axes object
region: region of the enface projection to plot
cmap: colormap
vmin: minimum value for colorbar
vmax: maximum value for colorbar
cbar: whether to plot a colorbar
alpha: alpha value for the annotation
Returns:
None
"""
enface_projection = self.enface

Expand Down Expand Up @@ -335,11 +304,10 @@ def plot(

@property
def masks(self) -> dict[str, np.ndarray]:
"""
"""Masks for quantification on circular grid.
Returns:
A dictionary of masks with the keys being the names of the masks.
"""
from eyepy.core.grids import grid

Expand All @@ -358,10 +326,10 @@ def masks(self) -> dict[str, np.ndarray]:

@property
def quantification(self) -> dict[str, Union[float, str]]:
"""
"""Quantification of the annotation on the specified circular grid.
Returns:
A dictionary of quantifications with the keys being the names of the regions.
"""
if self._quantification is None:
self._quantification = self._quantify()
Expand Down Expand Up @@ -444,20 +412,20 @@ def plot_quantification(
vmax: Optional[float] = None,
cbar: bool = True,
cmap: Union[str, mpl.colors.Colormap] = 'YlOrRd',
):
"""
) -> None:
"""Plot circular grid quantification of the annotation (like ETDRS)
Args:
ax:
region:
alpha:
vmin:
vmax:
cbar:
cmap:
ax: Matplotlib axes to plot on
region: Region to plot
alpha: Alpha value of the mask
vmin: Minimum value for the colorbar
vmax: Maximum value for the colorbar
cbar: Whether to plot a colorbar
cmap: Colormap to use
Returns:
None
"""

ax = plt.gca() if ax is None else ax
Expand Down Expand Up @@ -491,27 +459,25 @@ def plot_quantification(


class EyeBscanLayerAnnotation:
""""""

def __init__(self, eyevolumelayerannotation: EyeVolumeLayerAnnotation,
index: int) -> None:
"""
"""Layer annotation for a single B-scan.
Args:
eyevolumelayerannotation:
index:
eyevolumelayerannotation: EyeVolumeLayerAnnotation object
index: Index of the B-scan
Returns:
None
"""
self.eyevolumelayerannotation = eyevolumelayerannotation
self.volume = eyevolumelayerannotation.volume
self.index = index

@property
def name(self) -> str:
"""
Returns:
"""
"""Name of the layer annotation."""
return self.eyevolumelayerannotation.meta['name']

@name.setter
Expand All @@ -520,11 +486,7 @@ def name(self, value: str) -> None:

@property
def data(self) -> npt.NDArray[np.float_]:
"""
Returns:
"""
"""Layer heights."""
return self.eyevolumelayerannotation.data[self.index, :]

@data.setter
Expand All @@ -533,11 +495,7 @@ def data(self, value: npt.NDArray[np.float_]) -> None:

@property
def knots(self) -> list:
"""
Returns:
"""
"""Knots parameterizing the layer heights."""
return self.eyevolumelayerannotation.knots[self.index]

@knots.setter
Expand All @@ -546,22 +504,24 @@ def knots(self, value: list) -> None:


class EyeEnfacePixelAnnotation:
""""""

def __init__(
self,
enface: EyeEnface,
data: Optional[npt.NDArray[np.bool_]] = None,
meta: Optional[dict] = None,
**kwargs,
):
"""
) -> None:
"""Pixel annotation for an enface image.
Args:
enface:
data:
meta:
**kwargs:
enface: EyeEnface object
data: Pixel annotation data
meta: Metadata
**kwargs: Additional metadata specified as keyword arguments
Returns:
None
"""
self.enface = enface

Expand All @@ -583,11 +543,7 @@ def __init__(

@property
def name(self) -> str:
"""
Returns:
"""
"""Name of the pixel annotation."""
return self.meta['name']

@name.setter
Expand Down

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