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2D Snapshot Readibility of centroid circles and labels #87

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Merged
Hendrik-code merged 1 commit into from
Jun 11, 2025
Merged

2D Snapshot Readibility of centroid circles and labels #87

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93 changes: 82 additions & 11 deletions TPTBox/spine/snapshot2D/snapshot_modular.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from matplotlib.axes import Axes
from matplotlib.colors import ListedColormap, Normalize
from matplotlib.patches import Circle, FancyArrow
from matplotlib.patheffects import withStroke
from scipy import ndimage
from scipy.interpolate import RegularGridInterpolator, interp1d
from scipy.signal import savgol_filter
Expand Down Expand Up @@ -427,6 +428,14 @@ def make_isotropic2dpluscolor(arr3d, zms2d, msk=False):
return img


def get_contrasting_stroke_color(rgb):
# Convert RGBA to RGB if necessary
if len(rgb) == 4:
rgb = rgb[:3]
luminance = 0.299 * rgb[0] + 0.587 * rgb[1] + 0.114 * rgb[2]
return "gray" if luminance < 0.3 else "black"


def create_figure(dpi, planes: list, has_title=True):
fig_h = round(2 * planes[0].shape[0] / dpi, 2) + (0.5 if has_title else 0)
plane_w = [p.shape[1] for p in planes]
Expand Down Expand Up @@ -461,11 +470,32 @@ def plot_sag_centroids(
if show_these_subreg_poi is not None:
ctd2 = ctd.extract_subregion(*show_these_subreg_poi)
for k1, k2, v in ctd2.items():
color = cmap((k1 - 1) % LABEL_MAX % cmap.N)
backgroundcolor = get_contrasting_stroke_color(color)
# print(k, v, (v[1] * zms[1], v[0] * zms[0]), zms)
try:
axs.add_patch(Circle((v[1] * zms[1], v[0] * zms[0]), 2, color=cmap((k1 - 1) % LABEL_MAX % cmap.N)))
circle = Circle(
(v[1] * zms[1], v[0] * zms[0]),
3,
edgecolor=backgroundcolor,
facecolor=color,
linewidth=0.5,
)
axs.add_patch(circle)
if not hide_centroid_labels and k2 == curve_location.value and k1 in poi_labelmap:
axs.text(4, v[0] * zms[0], poi_labelmap[k1], fontdict={"color": cmap(k1 - 1), "weight": "bold"})
axs.text(
4,
v[0] * zms[0],
poi_labelmap[k1],
fontdict={
"color": color,
"weight": "bold",
"fontsize": 18,
},
# bbox=dict(boxstyle="square,pad=0.2", facecolor="gray", edgecolor="none"),
path_effects=[withStroke(linewidth=3.0, foreground=backgroundcolor)],
zorder=2,
)
except Exception as e:
print(e)
if "line_segments_sag" in ctd.info:
Expand All @@ -478,6 +508,7 @@ def plot_sag_centroids(
axs.add_patch(FancyArrow(v[1] * zms[1], v[0] * zms[0], c, d, color=cmap(color - 1 % LABEL_MAX % cmap.N)))
if "text_sag" in ctd.info:
for color, x in ctd.info["text_sag"]:
backgroundcolor = get_contrasting_stroke_color(color)
if not isinstance(color, int) and len(color) == 2:
color, curve_location = color # noqa: PLW2901
if isinstance(x, str) or len(x) == 1:
Expand All @@ -489,7 +520,19 @@ def plot_sag_centroids(
elif len(x) == 2:
(text, a) = x
b = zms[0] * ctd[color, curve_location][0]
axs.text(a, b, text, fontdict={"color": cmap(color - 1), "weight": "bold"})
axs.text(
a,
b,
text,
fontdict={
"color": color,
"weight": "bold",
"fontsize": 18,
},
# bbox=dict(boxstyle="square,pad=0.2", facecolor="gray", edgecolor="none"),
path_effects=[withStroke(linewidth=3.0, foreground=backgroundcolor)],
zorder=2,
)


def plot_cor_centroids(
Expand All @@ -508,16 +551,31 @@ def plot_cor_centroids(

# requires v_dict = dictionary of mask labels
for k1, k2, v in ctd2.items():
color = cmap((k1 - 1) % LABEL_MAX % cmap.N)
backgroundcolor = get_contrasting_stroke_color(color)
try:
axs.add_patch(
Circle(
(v[2] * zms[2], v[0] * zms[0]),
2,
color=cmap((k1 - 1) % LABEL_MAX % cmap.N),
)
circle = Circle(
(v[2] * zms[2], v[0] * zms[0]),
3,
edgecolor=backgroundcolor,
facecolor=color,
linewidth=0.5,
)
axs.add_patch(circle)
if not hide_centroid_labels and k2 == curve_location.value and k1 in poi_labelmap:
axs.text(4, v[0] * zms[0], poi_labelmap[k1], fontdict={"color": cmap(k1 - 1), "weight": "bold"})
axs.text(
4,
v[0] * zms[0],
poi_labelmap[k1],
fontdict={
"color": color,
"weight": "bold",
"fontsize": 18,
},
# bbox=dict(boxstyle="square,pad=0.2", facecolor="gray", edgecolor="none"),
path_effects=[withStroke(linewidth=3.0, foreground=backgroundcolor)],
zorder=2,
)
except Exception:
pass
if "line_segments_cor" in ctd.info:
Expand All @@ -529,6 +587,7 @@ def plot_cor_centroids(
axs.add_patch(FancyArrow(v[2] * zms[2], v[0] * zms[0], c, d, color=cmap(color - 1 % LABEL_MAX % cmap.N)))
if "text_cor" in ctd.info:
for color, x in ctd.info["text_cor"]:
backgroundcolor = get_contrasting_stroke_color(color)
if isinstance(color, Sequence) and len(color) == 2:
color, curve_location = color # noqa: PLW2901
if isinstance(x, str) or len(x) == 1:
Expand All @@ -540,7 +599,19 @@ def plot_cor_centroids(
elif len(x) == 2:
(text, a) = x
b = zms[0] * ctd[color, curve_location][0]
axs.text(a, b, text, fontdict={"color": cmap(color - 1), "weight": "bold"})
axs.text(
a,
b,
text,
fontdict={
"color": color,
"weight": "bold",
"fontsize": 18,
},
# bbox=dict(boxstyle="square,pad=0.2", facecolor="gray", edgecolor="none"),
path_effects=[withStroke(linewidth=3.0, foreground=backgroundcolor)],
zorder=2,
)


def make_2d_slice(
Expand Down