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Merged
merged 3 commits into from
Sep 10, 2024
Merged

Feat: improve cached method invocations #424

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a2e053b
feat(vispy): cast `axes_pos` to tuple to ensure it's a hashable object
sanjayankur31 Sep 10, 2024
755ffd2
chore(vispy): various type hint fixes
sanjayankur31 Sep 10, 2024
97b1c63
feat(vispy): use `detailed` as default visualisation style
sanjayankur31 Sep 10, 2024
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122 changes: 65 additions & 57 deletions pyneuroml/plot/PlotMorphologyVispy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,8 @@
import math
import random
import time
import typing
from functools import lru_cache
from typing import List, Optional, Tuple, Union
from typing import Any, Dict, List, Optional, Tuple, TypedDict, Union

import numpy
import progressbar
Expand Down Expand Up @@ -43,6 +42,18 @@
load_minimal_morphplottable__model,
)

# define special type for plot_spec dictionary
PlotSpec = TypedDict(
"PlotSpec",
{
"point_fraction": float,
"point_cells": List[str],
"schematic_cells": List[str],
"constant_cells": List[str],
"detailed_cells": List[str],
},
)

logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)

Expand Down Expand Up @@ -78,9 +89,9 @@

def add_text_to_vispy_3D_plot(
current_canvas: scene.SceneCanvas,
xv: typing.List[float],
yv: typing.List[float],
zv: typing.List[float],
xv: List[float],
yv: List[float],
zv: List[float],
color: str,
text: str,
):
Expand Down Expand Up @@ -120,18 +131,16 @@ def add_text_to_vispy_3D_plot(


def create_new_vispy_canvas(
view_min: typing.Optional[typing.List[float]] = None,
view_max: typing.Optional[typing.List[float]] = None,
view_min: Optional[List[float]] = None,
view_max: Optional[List[float]] = None,
title: str = "",
axes_pos: typing.Optional[
typing.Union[
typing.Tuple[float, float, float], typing.Tuple[int, int, int], str
]
axes_pos: Optional[
Union[Tuple[float, float, float], Tuple[int, int, int], str]
] = None,
axes_length: float = 100,
axes_width: int = 2,
theme=PYNEUROML_VISPY_THEME,
view_center: typing.Optional[typing.List[float]] = None,
view_center: Optional[List[float]] = None,
) -> Tuple[scene.SceneCanvas, ViewBox]:
"""Create a new vispy scene canvas with a view and optional axes lines

Expand Down Expand Up @@ -198,9 +207,9 @@ def create_new_vispy_canvas(
cam_index = 1
view.camera = cams[cam_index]

calc_axes_pos: typing.Optional[
typing.Union[typing.Tuple[float, float, float], typing.Tuple[int, int, int]]
] = None
calc_axes_pos: Optional[Union[Tuple[float, float, float], Tuple[int, int, int]]] = (
None
)

if view_min is not None and view_max is not None:
x_width = abs(view_min[0] - view_max[0])
Expand Down Expand Up @@ -329,24 +338,20 @@ def vispy_on_key_press(event):


def plot_interactive_3D(
nml_file: typing.Union[str, Cell, Morphology, NeuroMLDocument],
nml_file: Union[str, Cell, Morphology, NeuroMLDocument],
min_width: float = DEFAULTS["minWidth"],
verbose: bool = False,
plot_type: str = "constant",
axes_pos: typing.Optional[
typing.Union[
typing.Tuple[float, float, float], typing.Tuple[int, int, int], str
]
plot_type: str = "detailed",
axes_pos: Optional[
Union[Tuple[float, float, float], Tuple[int, int, int], str]
] = None,
title: typing.Optional[str] = None,
title: Optional[str] = None,
theme: str = "light",
nogui: bool = False,
plot_spec: typing.Optional[
typing.Dict[str, typing.Union[str, typing.List[int], float]]
] = None,
highlight_spec: typing.Optional[typing.Dict[typing.Any, typing.Any]] = None,
plot_spec: Optional[PlotSpec] = None,
highlight_spec: Optional[Dict[Any, Any]] = None,
upright: bool = False,
save_mesh_to: typing.Optional[str] = None,
save_mesh_to: Optional[str] = None,
):
"""Plot interactive plots in 3D using Vispy

Expand Down Expand Up @@ -417,9 +422,10 @@ def plot_interactive_3D(
- points_cells: list of cell ids to plot as point cells
- schematic_cells: list of cell ids to plot as schematics
- constant_cells: list of cell ids to plot as constant widths
- detailed_cells: list of cell ids to plot in full detail

The last three lists override the point_fraction setting. If a cell id
is not included in the spec here, it will follow the plot_type provided
The lists override the point_fraction setting. If a cell id is not
included in the spec here, it will follow the plot_type provided
before.
:type plot_spec: dict
:param highlight_spec: dictionary that allows passing some
Expand Down Expand Up @@ -486,6 +492,12 @@ def plot_interactive_3D(
if highlight_spec is None:
highlight_spec = {}

# convert axes_pos from list to tuple, it needs to be hashable for
# functions that use caching
if axes_pos:
if isinstance(axes_pos, list):
axes_pos = tuple(axes_pos)

if plot_type != "detailed" and len(highlight_spec.items()) > 0:
if plot_type == "constant":
logger.warning(
Expand Down Expand Up @@ -689,10 +701,10 @@ def plot_interactive_3D(
)

# process plot_spec
point_cells = []
schematic_cells = []
constant_cells = []
detailed_cells = []
point_cells: List[str] = []
schematic_cells: List[str] = []
constant_cells: List[str] = []
detailed_cells: List[str] = []
if plot_spec is not None:
try:
point_cells = plot_spec["point_cells"]
Expand All @@ -711,7 +723,7 @@ def plot_interactive_3D(
except KeyError:
pass

meshdata = [] # type: typing.List[typing.Any]
meshdata = [] # type: List[Any]

# do not show this pbar in jupyter notebooks
if not pynml_in_jupyter:
Expand Down Expand Up @@ -900,28 +912,26 @@ def plot_interactive_3D(

@lru_cache(maxsize=100)
def plot_3D_cell_morphology(
offset: typing.Optional[typing.Tuple[float, float, float]] = (0.0, 0.0, 0.0),
offset: Optional[Tuple[float, float, float]] = (0.0, 0.0, 0.0),
cell: Optional[Cell] = None,
color: typing.Optional[str] = None,
color: Optional[str] = None,
title: str = "",
verbose: bool = False,
current_canvas: Optional[scene.SceneCanvas] = None,
current_view: Optional[scene.ViewBox] = None,
min_width: float = DEFAULTS["minWidth"],
axis_min_max: typing.Tuple = (float("inf"), -1 * float("inf")),
axes_pos: typing.Optional[
typing.Union[
typing.Tuple[float, float, float], typing.Tuple[int, int, int], str
]
axis_min_max: Tuple = (float("inf"), -1 * float("inf")),
axes_pos: Optional[
Union[Tuple[float, float, float], Tuple[int, int, int], str]
] = None,
nogui: bool = False,
plot_type: str = "constant",
plot_type: str = "detailed",
theme: str = "light",
meshdata: typing.Optional[typing.List[typing.Any]] = None,
highlight_spec: typing.Optional[typing.Union[typing.Dict, frozendict]] = None,
meshdata: Optional[List[Any]] = None,
highlight_spec: Optional[Union[Dict, frozendict]] = None,
upright: bool = False,
save_mesh_to: typing.Optional[str] = None,
) -> typing.Optional[typing.List[typing.Any]]:
save_mesh_to: Optional[str] = None,
) -> Optional[List[Any]]:
"""Plot the detailed 3D morphology of a cell using vispy.
https://vispy.org/

Expand Down Expand Up @@ -1171,26 +1181,24 @@ def plot_3D_cell_morphology(
@lru_cache(maxsize=100)
def plot_3D_schematic(
cell: Cell,
segment_groups: typing.Optional[typing.List[SegmentGroup]] = None,
offset: typing.Optional[typing.Tuple[float, float, float]] = (0.0, 0.0, 0.0),
segment_groups: Optional[List[SegmentGroup]] = None,
offset: Optional[Tuple[float, float, float]] = (0.0, 0.0, 0.0),
labels: bool = False,
width: float = 5.0,
verbose: bool = False,
nogui: bool = False,
title: str = "",
current_canvas: Optional[scene.SceneCanvas] = None,
current_view: Optional[scene.ViewBox] = None,
axes_pos: typing.Optional[
typing.Union[
typing.Tuple[float, float, float], typing.Tuple[int, int, int], str
]
axes_pos: Optional[
Union[Tuple[float, float, float], Tuple[int, int, int], str]
] = None,
theme: str = "light",
color: typing.Optional[str] = "Cell",
meshdata: typing.Optional[typing.List[typing.Any]] = None,
color: Optional[str] = "Cell",
meshdata: Optional[List[Any]] = None,
upright: bool = False,
save_mesh_to: typing.Optional[str] = None,
) -> typing.Optional[typing.List[typing.Any]]:
save_mesh_to: Optional[str] = None,
) -> Optional[List[Any]]:
"""Plot a 3D schematic of the provided segment groups using vispy.
layer..

Expand Down Expand Up @@ -1489,7 +1497,7 @@ def compute_faces_of_cylindrical_mesh(rows: int, cols: int, closed: bool):
def create_cylindrical_mesh(
rows: int,
cols: int,
radius: typing.Union[float, typing.Tuple[float, float]] = (1.0, 1.0),
radius: Union[float, Tuple[float, float]] = (1.0, 1.0),
length: float = 1.0,
closed: bool = True,
):
Expand Down
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