diff --git a/src/robofish/io/app.py b/src/robofish/io/app.py
index 08bebc9c36180bd09333c08e57d5ee108d88d59d..cf33493e906bc76cee929ba95777d2278348988e 100644
--- a/src/robofish/io/app.py
+++ b/src/robofish/io/app.py
@@ -198,7 +198,8 @@ def render(args: argparse.Namespace = None) -> None:
"""
parser = argparse.ArgumentParser(
- description="This function shows the file as animation."
+ description="This function shows the file as animation.",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument(
"path",
@@ -248,14 +249,14 @@ def render(args: argparse.Namespace = None) -> None:
f"--{key}",
default=value,
action="store_true" if value is False else "store_false",
- help=f"Optional setter for video option {key}.\tDefault: {value}",
+ help=f"Optional setter for video option {key}.",
)
else:
parser.add_argument(
f"--{key}",
default=value,
type=type(value),
- help=f"Optional video option {key} with type {type(value)}.\tDefault: {value}",
+ help=f"Optional video option {key} with type {type(value)}.",
)
if args is None:
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 97026b6da13328b8fd293009296d80a374f3c5d0..66d3b5ae06bd8077656ff41e6994eefa35495c67 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -20,6 +20,7 @@ from __future__ import annotations
import datetime
import logging
import platform
+import re
import shutil
import tempfile
import types
@@ -1079,20 +1080,43 @@ class File(h5py.File):
ax.set_facecolor("gray")
plt.tight_layout(pad=0.05)
n_entities = len(self.entities)
+ categories = [entity.attrs.get("category", None) for entity in self.entities]
+ n_fish = len([c for c in categories if c == "organism"])
+
lines = [
plt.plot([], [], lw=options["linewidth"], zorder=0)[0]
for _ in range(n_entities)
]
- zone_sizes = (
- get_zone_sizes(self.attrs.get("guppy_model_rollout", ""))
- if options["render_zones"]
- else {}
- )
+ entity_colors = [lines[entity].get_color() for entity in range(n_entities)]
+ fish_colors = [
+ color
+ for i, color in enumerate(entity_colors)
+ if categories[i] == "organism"
+ ]
+
+ zone_sizes = [
+ (
+ get_zone_sizes(self.attrs.get("guppy_model_rollout", ""))
+ if options["render_zones"]
+ else {}
+ )
+ for _ in range(n_fish)
+ ]
zones = [
- plt.Circle((0, 0), zone_size, color="k", alpha=0.5, fill=False)
- for zone_size in zone_sizes.values()
+ [
+ plt.Circle(
+ (0, 0), zone_size, color=fish_colors[i], alpha=0.2, fill=False
+ )
+ for zone_size in zone_sizes_fish.values()
+ ]
+ for i, zone_sizes_fish in enumerate(zone_sizes)
]
- if options["render_swarm_center"] and len([e for e in self.entities if e.category == "organism"]) > 0:
+ zones_flat = []
+ for zones_fish in zones:
+ for zone in zones_fish:
+ ax.add_artist(zone)
+ zones_flat.append(zone)
+ if options["render_swarm_center"] and n_fish > 0:
swarm_center_position = np.stack(
[e.positions for e in self.entities if e.category == "organism"]
).mean(axis=0)
@@ -1101,8 +1125,6 @@ class File(h5py.File):
]
else:
swarm_center = []
- for zone in zones:
- ax.add_artist(zone)
annotations = []
if options["show_ids"]:
ids = None
@@ -1133,8 +1155,6 @@ class File(h5py.File):
plt.scatter([], [], marker="x", color="k"),
plt.plot([], [], linestyle="dotted", alpha=0.5, color="k", zorder=0)[0],
]
- categories = [entity.attrs.get("category", None) for entity in self.entities]
- entity_colors = [lines[entity].get_color() for entity in range(n_entities)]
entity_polygons = [
patches.Polygon(
@@ -1147,12 +1167,14 @@ class File(h5py.File):
alpha=0.8,
)
for edgecolor, color, entity in [
- ("k", "white", self.entities[entity])
- if category == "robot"
- else (
- entity_colors[entity],
- entity_colors[entity],
- self.entities[entity],
+ (
+ ("k", "white", self.entities[entity])
+ if category == "robot"
+ else (
+ entity_colors[entity],
+ entity_colors[entity],
+ self.entities[entity],
+ )
)
for entity, category in enumerate(categories)
]
@@ -1255,7 +1277,9 @@ class File(h5py.File):
for e_poly in entity_polygons:
ax.add_patch(e_poly)
ax.add_patch(border)
- return lines + entity_polygons + [border] + points + zones + swarm_center
+ return (
+ lines + entity_polygons + [border] + points + zones_flat + swarm_center
+ )
n_frames = self.entity_poses.shape[1]
@@ -1370,11 +1394,13 @@ class File(h5py.File):
poses_trails = entity_poses[
:, max(0, file_frame - options["trail"]) : file_frame
]
- for zone in zones:
- zone.center = (
- this_pose[0, 0],
- this_pose[0, 1],
- )
+ for i_entity in range(n_entities):
+ if categories[i_entity] == "organism":
+ for zone in zones[i_entity]:
+ zone.center = (
+ this_pose[i_entity, 0],
+ this_pose[i_entity, 1],
+ )
if options["render_swarm_center"]:
swarm_center[0].set_offsets(swarm_center_position[file_frame])
@@ -1403,7 +1429,7 @@ class File(h5py.File):
+ [border]
+ points
+ annotations
- + zones
+ + zones_flat
+ swarm_center
)
@@ -1437,3 +1463,29 @@ class File(h5py.File):
plt.close()
else:
plt.show()
+
+
+def get_zone_sizes(model: str):
+ zone_sizes = {}
+ for zone in [
+ "zor",
+ "zoa",
+ "zoo",
+ "preferred_d",
+ "neighbor_radius",
+ ]:
+ match = re.search(r"{}=(\d+(?:\.\d+)?)".format(zone), model)
+ if match:
+ value = float(match.group(1))
+ zone_sizes[zone] = value
+ else:
+ match = re.search(r"'{}': (\d+(?:\.\d+)?)".format(zone), model)
+ if match:
+ value = float(match.group(1))
+ zone_sizes[zone] = value
+
+ match = re.search(r"additive_zone_sizes[:,\'\" ]*(\b(?:True|False)\b)", model)
+ if match and match.group(1) == "True":
+ zone_sizes["zoo"] += zone_sizes["zor"]
+ zone_sizes["zoa"] += zone_sizes["zoo"]
+ return zone_sizes