Skip to content

Commit

Permalink
docs(annotations.py): adds type annotations to all objects in this mo…
Browse files Browse the repository at this point in the history 
…dule
  • Loading branch information
@Oli4
Oli4 committed Mar 15, 2023
1 parent 82a4af0 commit 986f9bc
Show file tree
Hide file tree
Showing 2 changed files with 61 additions and 61 deletions.
1 change: 1 addition & 0 deletions .github/workflows/ci.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,5 +41,6 @@ jobs:
mkdocs-literate-nav \
mkdocs-section-index \
pymdown-extensions \
mkdocs-macros-plugin \
eyepie
- run: mkdocs gh-deploy --force
121 changes: 60 additions & 61 deletions src/eyepy/core/annotations.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

from collections import defaultdict
import logging
from typing import List, Optional, Tuple, TYPE_CHECKING
from typing import Dict, Iterable, List, Optional, Tuple, TYPE_CHECKING, Union

from matplotlib import cm
from matplotlib import colors
Expand All @@ -15,6 +15,8 @@
from eyepy import config

if TYPE_CHECKING:
import matplotlib as mpl

from eyepy import EyeEnface
from eyepy import EyeVolume

Expand All @@ -30,7 +32,7 @@ def __init__(
data: Optional[npt.NDArray[np.float32]] = None,
meta: Optional[dict] = None,
**kwargs,
):
) -> None:
"""
Args:
Expand Down Expand Up @@ -63,7 +65,7 @@ def __init__(
self.meta["current_color"] = config.layer_colors[self.name]

@property
def name(self):
def name(self) -> str:
"""
Returns:
Expand All @@ -72,11 +74,11 @@ def name(self):
return self.meta["name"]

@name.setter
def name(self, value):
def name(self, value: str) -> None:
self.meta["name"] = value

@property
def knots(self):
def knots(self) -> Dict:
"""
Returns:
Expand Down Expand Up @@ -123,16 +125,16 @@ class EyeVolumePixelAnnotation:
""" """

def __init__(
self,
volume: EyeVolume,
# Type hint for an optional boolean numpy array
data: Optional[npt.NDArray[np.bool_]] = None,
meta: Optional[dict] = None,
radii=(1.5, 2.5),
n_sectors=(1, 4),
offsets=(0, 45),
center=None,
**kwargs,
self,
volume: EyeVolume,
# Type hint for an optional boolean numpy array
data: Optional[npt.NDArray[np.bool_]] = None,
meta: Optional[dict] = None,
radii: Iterable[float] = (1.5, 2.5),
n_sectors: Iterable[int] = (1, 4),
offsets: Iterable[int] = (0, 45),
center: Optional[Tuple[float, float]] = None,
**kwargs,
):
"""
Expand Down Expand Up @@ -176,7 +178,7 @@ def __init__(
self.meta["name"] = "Voxel Annotation"

@property
def name(self):
def name(self) -> str:
"""
Returns:
Expand All @@ -185,15 +187,15 @@ def name(self):
return self.meta["name"]

@name.setter
def name(self, value):
def name(self, value) -> None:
self.meta["name"] = value

def _reset(self):
def _reset(self) -> None:
self._masks = None
self._quantification = None

@property
def radii(self):
def radii(self) -> Iterable[float]:
"""
Returns:
Expand All @@ -202,12 +204,12 @@ def radii(self):
return self.meta["radii"]

@radii.setter
def radii(self, value):
def radii(self, value: Iterable[float]) -> None:
self._reset()
self.meta["radii"] = value

@property
def n_sectors(self):
def n_sectors(self) -> Iterable[int]:
"""
Returns:
Expand All @@ -216,12 +218,12 @@ def n_sectors(self):
return self.meta["n_sectors"]

@n_sectors.setter
def n_sectors(self, value):
def n_sectors(self, value: Iterable[int]) -> None:
self._reset()
self.meta["n_sectors"] = value

@property
def offsets(self):
def offsets(self) -> Iterable[int]:
"""
Returns:
Expand All @@ -230,12 +232,12 @@ def offsets(self):
return self.meta["offsets"]

@offsets.setter
def offsets(self, value):
def offsets(self, value: Iterable[int]) -> None:
self._reset()
self.meta["offsets"] = value

@property
def center(self):
def center(self) -> Tuple[float, float]:
"""
Returns:
Expand All @@ -244,12 +246,12 @@ def center(self):
return self.meta["center"]

@center.setter
def center(self, value):
def center(self, value: Tuple[float, float]) -> None:
self._reset()
self.meta["center"] = value

@property
def projection(self):
def projection(self) -> np.ndarray:
"""
Returns:
Expand All @@ -261,7 +263,7 @@ def projection(self):
return np.flip(np.nansum(self.data, axis=1), axis=0)

@property
def enface(self):
def enface(self) -> np.ndarray:
"""
Returns:
Expand All @@ -279,13 +281,13 @@ def enface(self):

def plot(
self,
ax=None,
region=np.s_[...],
cmap="Reds",
vmin=None,
vmax=None,
cbar=True,
alpha=1,
ax: Optional[plt.Axes] = None,
region: Union[slice, Tuple[slice, slice]] = np.s_[:, :],
cmap: Union[str, mpl.colors.Colormap] = "Reds",
vmin: Optional[float] = None,
vmax: Optional[float] = None,
cbar: bool = True,
alpha: float = 1,
):
"""
Expand All @@ -303,8 +305,7 @@ def plot(
"""
enface_projection = self.enface

if ax is None:
ax = plt.gca()
ax = plt.gca() if ax is None else ax

if vmin is None:
vmin = 1
Expand Down Expand Up @@ -333,10 +334,11 @@ def plot(
)

@property
def masks(self):
def masks(self) -> Dict[str, np.ndarray]:
"""
Returns:
A dictionary of masks with the keys being the names of the masks.
"""
from eyepy.core.grids import grid
Expand All @@ -355,7 +357,7 @@ def masks(self):
return self._masks

@property
def quantification(self):
def quantification(self) -> Dict[str, Union[float, str]]:
"""
Returns:
Expand All @@ -366,7 +368,7 @@ def quantification(self):

return self._quantification

def _quantify(self):
def _quantify(self) -> Dict[str, Union[float, str]]:
enface_voxel_size_ym3 = (self.volume.localizer.scale_x * 1e3 *
self.volume.localizer.scale_y * 1e3 *
self.volume.scale_y * 1e3)
Expand Down Expand Up @@ -435,13 +437,13 @@ def _quantify(self):

def plot_quantification(
self,
ax=None,
region=np.s_[...],
alpha=0.5,
vmin=None,
vmax=None,
cbar=True,
cmap="YlOrRd",
ax: Optional[plt.Axes] = None,
region: Union[slice, Tuple[slice, slice]] = np.s_[:, :],
alpha: float = 0.5,
vmin: Optional[float] = None,
vmax: Optional[float] = None,
cbar: bool = True,
cmap: Union[str, mpl.colors.Colormap] = "YlOrRd",
):
"""
Expand All @@ -458,8 +460,7 @@ def plot_quantification(
"""

if ax is None:
ax = plt.gca()
ax = plt.gca() if ax is None else ax

mask_img = np.zeros(self.volume.localizer.shape, dtype=float)[region]
visible = np.zeros_like(mask_img)
Expand All @@ -468,10 +469,8 @@ def plot_quantification(
self.quantification[mask_name + " [mm³]"])
visible += self.masks[mask_name][region]

if vmin is None:
vmin = mask_img[visible.astype(int)].min()
if vmax is None:
vmax = max([mask_img.max(), vmin])
vmin = mask_img[visible.astype(int)].min() if vmin is None else vmin
vmax = max([mask_img.max(), vmin]) if vmax is None else vmax

if cbar:
divider = make_axes_locatable(ax)
Expand Down Expand Up @@ -507,7 +506,7 @@ def __init__(self, eyevolumelayerannotation: EyeVolumeLayerAnnotation,
self.index = index

@property
def name(self):
def name(self) -> str:
"""
Returns:
Expand All @@ -516,11 +515,11 @@ def name(self):
return self.eyevolumelayerannotation.meta["name"]

@name.setter
def name(self, value: str):
def name(self, value: str) -> None:
self.eyevolumelayerannotation.meta["name"] = value

@property
def data(self):
def data(self) -> npt.NDArray[np.float_]:
"""
Returns:
Expand All @@ -529,11 +528,11 @@ def data(self):
return self.eyevolumelayerannotation.data[self.index, :]

@data.setter
def data(self, value):
def data(self, value: npt.NDArray[np.float_]) -> None:
self.eyevolumelayerannotation.data[self.index, :] = value

@property
def knots(self):
def knots(self) -> List:
"""
Returns:
Expand All @@ -542,7 +541,7 @@ def knots(self):
return self.eyevolumelayerannotation.knots[self.index]

@knots.setter
def knots(self, value: List):
def knots(self, value: List) -> None:
self.eyevolumelayerannotation.knots[self.index] = value


Expand Down Expand Up @@ -583,7 +582,7 @@ def __init__(
self.meta["name"] = "Pixel Annotation"

@property
def name(self):
def name(self) -> str:
"""
Returns:
Expand All @@ -592,5 +591,5 @@ def name(self):
return self.meta["name"]

@name.setter
def name(self, value):
def name(self, value: str) -> None:
self.meta["name"] = value

0 comments on commit 986f9bc

Please sign in to comment.