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Refactored transformations implementation #162

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merged 8 commits into from
Oct 13, 2023
Merged

Refactored transformations implementation #162

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0313bb1
Refactored transformations implementation
timtreis Sep 5, 2023
b91449f
Now using new get_extent function
timtreis Sep 6, 2023
26b9e81
Updated to new get_extent function
timtreis Sep 8, 2023
8060c63
fix and format
timtreis Oct 2, 2023
77aad64
Merge branch 'main' into bugfix/103-wrong-spatialplot-of-affine-trans…
timtreis Oct 11, 2023
454e307
Removed unneeded code; refactor
timtreis Oct 13, 2023
5e7c13d
Threw out more old code
timtreis Oct 13, 2023
c85cc15
Updated changelog
timtreis Oct 13, 2023
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8 changes: 8 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,14 @@ and this project adheres to [Semantic Versioning][].

## [0.1.0] - tbd

### Added

- Pushed `get_extent` functionality upstream to `spatialdata` (#162)

### Fixed

-

## [0.0.5] - 2023-10-02

### Added
Expand Down
190 changes: 93 additions & 97 deletions src/spatialdata_plot/pl/basic.py
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Expand Up @@ -19,7 +19,8 @@
from multiscale_spatial_image.multiscale_spatial_image import MultiscaleSpatialImage
from pandas.api.types import is_categorical_dtype
from spatial_image import SpatialImage
from spatialdata._logging import logger as logg
from spatialdata._core.data_extent import get_extent
from spatialdata.transformations.operations import get_transformation

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot.pl.render import (
Expand All @@ -40,12 +41,10 @@
)
from spatialdata_plot.pl.utils import (
_get_cs_contents,
_get_extent,
_maybe_set_colors,
_mpl_ax_contains_elements,
_prepare_cmap_norm,
_prepare_params_plot,
_robust_transform,
_set_outline,
save_fig,
)
Expand Down Expand Up @@ -216,6 +215,8 @@ def render_shapes(
na_color=na_color, # type: ignore[arg-type]
**kwargs,
)
if isinstance(elements, str):
elements = [elements]
outline_params = _set_outline(outline, outline_width, outline_color)
sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
elements=elements,
Expand Down Expand Up @@ -285,12 +286,15 @@ def render_points(
sdata = self._copy()
sdata = _verify_plotting_tree(sdata)
n_steps = len(sdata.plotting_tree.keys())

cmap_params = _prepare_cmap_norm(
cmap=cmap,
norm=norm,
na_color=na_color, # type: ignore[arg-type]
**kwargs,
)
if isinstance(elements, str):
elements = [elements]
sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
elements=elements,
color=color,
Expand Down Expand Up @@ -370,6 +374,8 @@ def render_images(
**kwargs,
)

if isinstance(elements, str):
elements = [elements]
sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
elements=elements,
channel=channel,
Expand Down Expand Up @@ -450,6 +456,8 @@ def render_labels(
na_color=na_color, # type: ignore[arg-type]
**kwargs,
)
if isinstance(elements, str):
elements = [elements]
sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
elements=elements,
color=color,
Expand Down Expand Up @@ -552,12 +560,12 @@ def show(
raise TypeError("All titles must be strings.")

# get original axis extent for later comparison
x_min_orig, x_max_orig = (np.inf, -np.inf)
y_min_orig, y_max_orig = (np.inf, -np.inf)
ax_x_min, ax_x_max = (np.inf, -np.inf)
ax_y_min, ax_y_max = (np.inf, -np.inf)

if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
x_min_orig, x_max_orig = ax.get_xlim()
y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
ax_x_min, ax_x_max = ax.get_xlim()
ax_y_max, ax_y_min = ax.get_ylim() # (0, 0) is top-left

# handle coordinate system
coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
Expand All @@ -568,50 +576,6 @@ def show(
if cs not in sdata.coordinate_systems:
raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")

# Check if user specified only certain elements to be plotted
cs_contents = _get_cs_contents(sdata)
elements_to_be_rendered = []
for cmd, params in render_cmds.items():
if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
if params.elements is not None:
elements_to_be_rendered += (
[params.elements] if isinstance(params.elements, str) else params.elements
)
elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
if params.elements is not None:
elements_to_be_rendered += (
[params.elements] if isinstance(params.elements, str) else params.elements
)
elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
if params.elements is not None:
elements_to_be_rendered += (
[params.elements] if isinstance(params.elements, str) else params.elements
)
elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
if params.elements is not None:
elements_to_be_rendered += (
[params.elements] if isinstance(params.elements, str) else params.elements
)

extent = _get_extent(
sdata=sdata,
has_images="render_images" in render_cmds,
has_labels="render_labels" in render_cmds,
has_points="render_points" in render_cmds,
has_shapes="render_shapes" in render_cmds,
elements=elements_to_be_rendered,
coordinate_systems=coordinate_systems,
)

# Use extent to filter out coordinate system without the relevant elements
valid_cs = []
for cs in coordinate_systems:
if cs in extent:
valid_cs.append(cs)
else:
logg.info(f"Dropping coordinate system '{cs}' since it doesn't have relevant elements.")
coordinate_systems = valid_cs

# set up canvas
fig_params, scalebar_params = _prepare_params_plot(
num_panels=len(coordinate_systems),
Expand All @@ -633,32 +597,25 @@ def show(
colorbar=colorbar,
)

cs_contents = _get_cs_contents(sdata)

# go through tree

for i, cs in enumerate(coordinate_systems):
sdata = self._copy()
# properly transform all elements to the current coordinate system
members = cs_contents.query(f"cs == '{cs}'")

if members["has_images"].values[0]:
for key in sdata.images:
sdata.images[key] = _robust_transform(sdata.images[key], cs)

if members["has_labels"].values[0]:
for key in sdata.labels:
sdata.labels[key] = _robust_transform(sdata.labels[key], cs)

if members["has_points"].values[0]:
for key in sdata.points:
sdata.points[key] = _robust_transform(sdata.points[key], cs)

if members["has_shapes"].values[0]:
for key in sdata.shapes:
sdata.shapes[key] = _robust_transform(sdata.shapes[key], cs)

_, has_images, has_labels, has_points, has_shapes = (
cs_contents.query(f"cs == '{cs}'").iloc[0, :].values.tolist()
)
ax = fig_params.ax if fig_params.axs is None else fig_params.axs[i]

wants_images = False
wants_labels = False
wants_points = False
wants_shapes = False
wanted_elements = []

for cmd, params in render_cmds.items():
if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]:
if cmd == "render_images" and has_images:
_render_images(
sdata=sdata,
render_params=params,
Expand All @@ -667,9 +624,18 @@ def show(
fig_params=fig_params,
scalebar_params=scalebar_params,
legend_params=legend_params,
# extent=extent[cs],
)
elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]:
wants_images = True
wanted_images = params.elements if params.elements is not None else list(sdata.images.keys())
wanted_elements.extend(
[
image
for image in wanted_images
if cs in set(get_transformation(sdata.images[image], get_all=True).keys())
]
)

elif cmd == "render_shapes" and has_shapes:
_render_shapes(
sdata=sdata,
render_params=params,
Expand All @@ -679,8 +645,17 @@ def show(
scalebar_params=scalebar_params,
legend_params=legend_params,
)
wants_shapes = True
wanted_shapes = params.elements if params.elements is not None else list(sdata.shapes.keys())
wanted_elements.extend(
[
shape
for shape in wanted_shapes
if cs in set(get_transformation(sdata.shapes[shape], get_all=True).keys())
]
)

elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]:
elif cmd == "render_points" and has_points:
_render_points(
sdata=sdata,
render_params=params,
Expand All @@ -690,8 +665,17 @@ def show(
scalebar_params=scalebar_params,
legend_params=legend_params,
)
wants_points = True
wanted_points = params.elements if params.elements is not None else list(sdata.points.keys())
wanted_elements.extend(
[
point
for point in wanted_points
if cs in set(get_transformation(sdata.points[point], get_all=True).keys())
]
)

elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]:
elif cmd == "render_labels" and has_labels:
if sdata.table is not None and isinstance(params.color, str):
colors = sc.get.obs_df(sdata.table, params.color)
if is_categorical_dtype(colors):
Expand All @@ -710,33 +694,46 @@ def show(
scalebar_params=scalebar_params,
legend_params=legend_params,
)
wants_labels = True
wanted_labels = params.elements if params.elements is not None else list(sdata.labels.keys())
wanted_elements.extend(
[
label
for label in wanted_labels
if cs in set(get_transformation(sdata.labels[label], get_all=True).keys())
]
)

if title is not None:
if len(title) == 1:
t = title[0]
else:
try:
t = title[i]
except IndexError as e:
raise IndexError("The number of titles must match the number of coordinate systems.") from e
else:
if title is None:
t = cs
elif len(title) == 1:
t = title[0]
else:
try:
t = title[i]
except IndexError as e:
raise IndexError("The number of titles must match the number of coordinate systems.") from e
ax.set_title(t)
ax.set_aspect("equal")

if any(
[
cs_contents.query(f"cs == '{cs}'")["has_images"][0],
cs_contents.query(f"cs == '{cs}'")["has_labels"][0],
cs_contents.query(f"cs == '{cs}'")["has_points"][0],
cs_contents.query(f"cs == '{cs}'")["has_shapes"][0],
]
):
extent = get_extent(
sdata,
coordinate_system=cs,
has_images=has_images and wants_images,
has_labels=has_labels and wants_labels,
has_points=has_points and wants_points,
has_shapes=has_shapes and wants_shapes,
elements=wanted_elements,
)
cs_x_min, cs_x_max = extent["x"]
cs_y_min, cs_y_max = extent["y"]

if any([has_images, has_labels, has_points, has_shapes]):
# If the axis already has limits, only expand them but not overwrite
x_min = min(x_min_orig, extent[cs][0]) - pad_extent
x_max = max(x_max_orig, extent[cs][1]) + pad_extent
y_min = min(y_min_orig, extent[cs][2]) - pad_extent
y_max = max(y_max_orig, extent[cs][3]) + pad_extent
x_min = min(ax_x_min, cs_x_min) - pad_extent
x_max = max(ax_x_max, cs_x_max) + pad_extent
y_min = min(ax_y_min, cs_y_min) - pad_extent
y_max = max(ax_y_max, cs_y_max) + pad_extent
ax.set_xlim(x_min, x_max)
ax.set_ylim(y_max, y_min) # (0, 0) is top-left

Expand All @@ -747,5 +744,4 @@ def show(
# https://stackoverflow.com/a/64523765
if not hasattr(sys, "ps1"):
plt.show()

return (fig_params.ax if fig_params.axs is None else fig_params.axs) if return_ax else None # shuts up ruff
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