From d2a08d197d628b7225e2d96714ffcaa7399317c2 Mon Sep 17 00:00:00 2001
From: Andi Gerken <andi.gerken@gmail.com>
Date: Mon, 14 Feb 2022 18:54:09 +0100
Subject: [PATCH] Fixed evaluate scripts to work with nan data. Additional
bugfixes.
---
src/robofish/evaluate/app.py | 14 +-
src/robofish/evaluate/evaluate.py | 150 ++++++++++++-------
src/robofish/io/file.py | 24 +--
src/robofish/io/utils.py | 10 +-
tests/resources/nan_test.hdf5 | Bin 0 -> 12296 bytes
tests/robofish/evaluate/test_app_evaluate.py | 24 +++
tests/robofish/io/test_app_io.py | 2 +-
tests/robofish/io/test_file.py | 7 +
tests/robofish/io/test_io.py | 4 +-
9 files changed, 160 insertions(+), 75 deletions(-)
create mode 100644 tests/resources/nan_test.hdf5
diff --git a/src/robofish/evaluate/app.py b/src/robofish/evaluate/app.py
index 183b5dd..a73fe46 100644
--- a/src/robofish/evaluate/app.py
+++ b/src/robofish/evaluate/app.py
@@ -26,7 +26,7 @@ def function_dict():
"tank_positions": base.evaluate_tankpositions,
"tracks": base.evaluate_tracks,
"tracks_distance": base.evaluate_tracks_distance,
- "evaluate_positionVec": base.evaluate_positionVec,
+ "socialVec": base.evaluate_socialVec,
"follow_iid": base.evaluate_follow_iid,
"individual_speeds": base.evaluate_individual_speeds,
"individual_iid": base.evaluate_individual_iid,
@@ -114,11 +114,11 @@ def evaluate(args=None):
print("\n".join([str(p) for p in save_paths]))
else:
fig = fdict[args.analysis_type](**params)
-
- if save_path is None:
- plt.show()
- else:
- fig.savefig(save_path)
- plt.close(fig)
+ if fig is not None:
+ if save_path is None:
+ plt.show()
+ else:
+ fig.savefig(save_path)
+ plt.close(fig)
else:
print(f"Evaluation function not found {args.analysis_type}")
diff --git a/src/robofish/evaluate/evaluate.py b/src/robofish/evaluate/evaluate.py
index eaf6acb..00fb7e5 100644
--- a/src/robofish/evaluate/evaluate.py
+++ b/src/robofish/evaluate/evaluate.py
@@ -7,6 +7,7 @@
# email andi.gerken@gmail.com
# Last doku update Feb 2021
+from cv2 import floodFill
import robofish.io
import robofish.evaluate
from pathlib import Path
@@ -87,7 +88,10 @@ def evaluate_speed(
path_speeds.extend(e_speeds_turns[:, 0] * frequency)
file.close()
+ # Exclude possible nans
path_speeds = np.array(path_speeds)
+ path_speeds = path_speeds[~np.isnan(path_speeds)]
+
left_quantiles.append(np.quantile(path_speeds, 0.001))
right_quantiles.append(np.quantile(path_speeds, 0.999))
speeds.append(path_speeds)
@@ -139,7 +143,10 @@ def evaluate_turn(
path_turns.extend(np.rad2deg(e_speeds_turns[:, 1]))
file.close()
+ # Exclude possible nans
path_turns = np.array(path_turns)
+ path_turns = path_turns[~np.isnan(path_turns)]
+
left_quantiles.append(np.quantile(path_turns, 0.001))
right_quantiles.append(np.quantile(path_turns, 0.999))
turns.append(path_turns)
@@ -254,13 +261,13 @@ def evaluate_relative_orientation(
poses = file.select_entity_poses(
None if predicate is None else predicate[k]
)
- all_poses = file.entity_poses
+
for i in range(len(poses)):
- for j in range(len(all_poses)):
- if (poses[i] != all_poses[j]).any():
+ for j in range(len(poses)):
+ if i != j:
ori_diff = (
- all_poses[j, :, 2] - poses[i, :, 2],
- all_poses[j, :, 3] - poses[i, :, 3],
+ poses[j, :, 2] - poses[i, :, 2],
+ poses[j, :, 3] - poses[i, :, 3],
)
path_orientations.extend(np.arctan2(ori_diff[1], ori_diff[0]))
file.close()
@@ -367,6 +374,10 @@ def evaluate_tankpositions(
predicate: a lambda function, selecting entities
(example: lambda e: e.category == "fish")
"""
+
+ # Parameter to set how many steps are skipped in the kde plot.
+ poses_step = 5
+
files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
x_pos, y_pos = [], []
world_bounds = []
@@ -378,11 +389,18 @@ def evaluate_tankpositions(
)
world_bounds.append(file.attrs["world_size_cm"])
for e_poses in poses:
- path_x_pos.extend(e_poses[:, 0])
- path_y_pos.extend(e_poses[:, 1])
+ path_x_pos.extend(e_poses[::poses_step, 0])
+ path_y_pos.extend(e_poses[::poses_step, 1])
file.close()
- x_pos.append(np.array(path_x_pos))
- y_pos.append(np.array(path_y_pos))
+
+ # Exclude possible nans
+ path_x_pos = np.array(path_x_pos)
+ path_y_pos = np.array(path_y_pos)
+ path_x_pos = path_x_pos[~np.isnan(path_x_pos)]
+ path_y_pos = path_y_pos[~np.isnan(path_y_pos)]
+
+ x_pos.append(path_x_pos)
+ y_pos.append(path_y_pos)
fig, ax = plt.subplots(1, len(x_pos), figsize=(8 * len(x_pos), 8))
if len(x_pos) == 1:
@@ -396,12 +414,12 @@ def evaluate_tankpositions(
ax[i].set_xlabel("x [cm]")
ax[i].set_ylabel("y [cm]")
- sns.kdeplot(x=x_pos[i], y=y_pos[i], n_levels=25, shade=True, ax=ax[i])
+ sns.kdeplot(x=x_pos[i], y=y_pos[i], n_levels=20, shade=True, ax=ax[i])
return fig
-def evaluate_positionVec(
+def evaluate_socialVec(
paths: Iterable[str],
labels: Iterable[str] = None,
predicate=None,
@@ -416,42 +434,55 @@ def evaluate_positionVec(
(example: lambda e: e.category == "fish")
"""
files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
- posVec = []
+ socialVec = []
worldBoundsX, worldBoundsY = [], []
for k, files in enumerate(files_per_path):
- path_posVec = []
+ path_socialVec = []
for p, file in files.items():
worldBoundsX.append(file.attrs["world_size_cm"][0])
worldBoundsY.append(file.attrs["world_size_cm"][1])
poses = file.select_entity_poses(
None if predicate is None else predicate[k]
)
- all_poses = file.entity_poses
- # calculate posVec for every fish combination
+
+ if poses.shape[0] != 2:
+ print(
+ "The positionVec can only be calculated when there are exactly 2 fish."
+ )
+ return
+ # calculate socialVec for every fish combination
for i in range(len(poses)):
- for j in range(len(all_poses)):
- if (poses[i] != all_poses[j]).any():
- posVec_input = np.append(
- poses[i, :, [0, 1]].T, all_poses[j, :, [0, 1]].T, axis=1
+ for j in range(len(poses)):
+ if i != j:
+ socialVec_input = np.append(
+ poses[i, :, [0, 1]].T, poses[j, :, [0, 1]].T, axis=1
)
- path_posVec.append(
- calculate_posVec(
- posVec_input, np.arctan2(poses[i, :, 3], poses[i, :, 2])
+
+ path_socialVec.append(
+ calculate_socialVec(
+ socialVec_input,
+ np.arctan2(poses[i, :, 3], poses[i, :, 2]),
)
)
file.close()
- posVec.append(np.concatenate(path_posVec, axis=0))
+
+ # Concatenate and exclude possible nans
+ path_socialVec = np.concatenate(path_socialVec, axis=0)
+ path_socialVec = path_socialVec[~np.isnan(path_socialVec).any(axis=1)]
+
+ socialVec.append(path_socialVec)
grids = []
worldBoundsX, worldBoundsY = max(worldBoundsX), max(worldBoundsY)
- for i in range(len(posVec)):
- df = pd.DataFrame({"x": posVec[i][:, 0], "y": posVec[i][:, 1]})
- grid = sns.displot(df, x="x", y="y", binwidth=(10, 10), cbar=True)
+ for i in range(len(socialVec)):
+ df = pd.DataFrame({"x": socialVec[i][:, 0], "y": socialVec[i][:, 1]})
+ grid = sns.displot(df, x="x", y="y", binwidth=(1, 1), cbar=True)
grid.axes[0, 0].set_xlabel("x [cm]")
grid.axes[0, 0].set_ylabel("y [cm]")
- grid.set(xlim=(-worldBoundsX, worldBoundsX))
- grid.set(ylim=(-worldBoundsY, worldBoundsY))
+ # Limits set by educated guesses. If it doesnt work for your data adjust it.
+ grid.set(xlim=(-worldBoundsX / 7.0, worldBoundsX / 7.0))
+ grid.set(ylim=(-worldBoundsY / 7.0, worldBoundsY / 7.0))
grids.append(grid)
fig = plt.figure(figsize=(8 * len(grids), 8))
@@ -492,16 +523,22 @@ def evaluate_follow_iid(
poses = file.select_entity_poses(
None if predicate is None else predicate[k]
)
- all_poses = file.entity_poses
+
+ if poses.shape[0] < 2:
+ print(
+ "The FollowIID can only be calculated when there are at least 2 fish."
+ )
+ return
+
for i in range(len(poses)):
- for j in range(len(all_poses)):
- if (poses[i] != all_poses[j]).any():
+ for j in range(len(poses)):
+ if i != j and (poses[i] != poses[j]).any():
path_iid.append(
- calculate_iid(poses[i, :-1, 0:2], all_poses[j, :-1, 0:2])
+ calculate_iid(poses[i, :-1, 0:2], poses[j, :-1, 0:2])
)
path_follow.append(
- calculate_follow(poses[i, :, 0:2], all_poses[j, :, 0:2])
+ calculate_follow(poses[i, :, 0:2], poses[j, :, 0:2])
)
file.close()
follow.append(np.array(path_follow))
@@ -513,6 +550,10 @@ def evaluate_follow_iid(
follow_flat = np.concatenate([f.flatten() for f in follow])
iid_flat = np.concatenate([i.flatten() for i in iid])
+ # Exclude possible nans
+ follow_flat = follow_flat[~np.isnan(follow_flat)]
+ iid_flat = iid_flat[~np.isnan(iid_flat)]
+
# Find the 0.5%/ 99.5% quantiles as min and max for the axis
follow_range = np.max(
[-1 * np.quantile(follow_flat, 0.005), np.quantile(follow_flat, 0.995)]
@@ -671,7 +712,7 @@ def evaluate_individuals(
files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
fig = plt.figure(figsize=(10, 4))
- small_iid_files = []
+ # small_iid_files = []
offset = 0
for k, files in enumerate(files_per_path):
all_avg = []
@@ -682,12 +723,18 @@ def evaluate_individuals(
metric = file.entity_actions_speeds_turns[..., 0] * file.frequency
elif mode == "iid":
poses = file.entity_poses_rad
+ if poses.shape[0] != 2:
+ print(
+ "The evaluate_individual_iid function only works when there are exactly 2 individuals."
+ )
+ return
metric = calculate_iid(poses[0], poses[1])[None]
- mean = np.mean(metric, axis=1)[0]
- if mean < 7:
- small_iid_files.append(str(file.path))
- all_avg.append(np.mean(metric, axis=1))
- all_std.append(np.std(metric, axis=1))
+ # mean = np.mean(metric, axis=1)[0]
+ # if mean < 7:
+ # small_iid_files.append(str(file.path))
+
+ all_avg.append(np.nanmean(metric, axis=1))
+ all_std.append(np.nanstd(metric, axis=1))
file.close()
all_avg = np.concatenate(all_avg, axis=0)
all_std = np.concatenate(all_std, axis=0)
@@ -724,15 +771,15 @@ def evaluate_individuals(
plt.ylabel(this_text["ylabel"])
plt.tight_layout()
- np.random.shuffle(small_iid_files)
-
- train_part = int(len(small_iid_files) * 0.8)
+ # This can be used to return a test data and training data split
+ # np.random.shuffle(small_iid_files)
+ # train_part = int(len(small_iid_files) * 0.8)
- print("TRAINING DATA:")
- print(" ".join(small_iid_files[:train_part]))
+ # print("TRAINING DATA:")
+ # print(" ".join(small_iid_files[:train_part]))
- print("TEST DATA:")
- print(" ".join(small_iid_files[train_part:]))
+ # print("TEST DATA:")
+ # print(" ".join(small_iid_files[train_part:]))
return fig
@@ -773,9 +820,10 @@ def evaluate_all(
t.refresh() # to show immediately the update
save_path = save_folder / (f_name + ".png")
fig = f_callable(paths=paths, labels=labels, predicate=predicate)
- fig.savefig(save_path)
- plt.close(fig)
- save_paths.append(save_path)
+ if fig is not None:
+ fig.savefig(save_path)
+ plt.close(fig)
+ save_paths.append(save_path)
return save_paths
@@ -825,8 +873,8 @@ def normalize_series(x):
return (x.T / np.linalg.norm(x, axis=-1)).T
-def calculate_posVec(data, angle):
- """Calculate position vectors.
+def calculate_socialVec(data, angle):
+ """Calculate social vectors.
Data should be of the form (n, (x1, y1, x2, y2)) and angle of the form (n, 1)
returns x, y distance from fish1 to fish2 with respect to the direction
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index cc75d52..d5ba5f9 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -767,7 +767,7 @@ class File(h5py.File):
lw=lw,
)
# Plotting outside of the figure to have the label
- ax.plot([55, 60], [55, 60], lw=5, c=this_c, label=fish_id)
+ ax.plot([550, 600], [550, 600], lw=5, c=this_c, label=fish_id)
ax.scatter(
[poses[:, skip_timesteps, 0]],
[poses[:, skip_timesteps, 1]],
@@ -930,23 +930,27 @@ class File(h5py.File):
this_pose = entity_poses[:, file_frame]
if not options["fixed_view"]:
- self.middle_of_swarm = options[
- "slow_view"
- ] * self.middle_of_swarm + (1 - options["slow_view"]) * np.mean(
- this_pose, axis=0
- )
# Find the maximal distance between the entities in x or y direction
min_view = np.max(
(np.max(this_pose, axis=0) - np.min(this_pose, axis=0))[:2]
)
+
new_view_size = np.max(
[options["view_size"], min_view + options["margin"]]
)
- self.view_size = (
- options["slow_zoom"] * self.view_size
- + (1 - options["slow_zoom"]) * new_view_size
- )
+
+ if not np.isnan(min_view).any() and not new_view_size is np.nan:
+ self.middle_of_swarm = options[
+ "slow_view"
+ ] * self.middle_of_swarm + (1 - options["slow_view"]) * np.mean(
+ this_pose, axis=0
+ )
+
+ self.view_size = (
+ options["slow_zoom"] * self.view_size
+ + (1 - options["slow_zoom"]) * new_view_size
+ )
ax.set_xlim(
self.middle_of_swarm[0] - self.view_size / 2,
diff --git a/src/robofish/io/utils.py b/src/robofish/io/utils.py
index 1992dc3..50be83f 100644
--- a/src/robofish/io/utils.py
+++ b/src/robofish/io/utils.py
@@ -29,10 +29,12 @@ def limit_angle_range(angle: Union[float, Iterable], _range=(-np.pi, np.pi)):
"""
assert np.isclose(_range[1] - _range[0], 2 * np.pi)
- def limit_one(value):
- return (value - _range[0]) % (2 * np.pi) + _range[0]
+ def limit_simple(a):
+ return (a - _range[0]) % (2 * np.pi) + _range[0]
if isinstance(angle, Iterable):
- return np.array([limit_one(v) for v in angle])
+ nan = np.isnan(angle)
+ angle[~nan] = limit_simple(angle[~nan])
else:
- return limit_one(angle)
+ angle = limit_simple(angle)
+ return angle
diff --git a/tests/resources/nan_test.hdf5 b/tests/resources/nan_test.hdf5
new file mode 100644
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GIT binary patch
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diff --git a/tests/robofish/evaluate/test_app_evaluate.py b/tests/robofish/evaluate/test_app_evaluate.py
index 5a89d39..d8b1d69 100644
--- a/tests/robofish/evaluate/test_app_evaluate.py
+++ b/tests/robofish/evaluate/test_app_evaluate.py
@@ -11,6 +11,30 @@ logging.getLogger().setLevel(logging.INFO)
h5py_file_1 = utils.full_path(__file__, "../../resources/valid_1.hdf5")
h5py_file_2 = utils.full_path(__file__, "../../resources/valid_2.hdf5")
+nan_file_path = utils.full_path(__file__, "../../resources/nan_test.hdf5")
+
+
+def test_app_validate(tmp_path):
+ """This tests the function of the robofish-io-validate command"""
+
+ class DummyArgs:
+ def __init__(self, analysis_type, paths, save_path):
+ self.paths = paths
+ self.names = None
+ self.analysis_type = analysis_type
+ self.save_path = save_path
+ self.labels = None
+
+ for mode in app.function_dict().keys():
+ if mode == "all":
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path))
+ app.evaluate(DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path))
+ app.evaluate(DummyArgs(mode, [nan_file_path], tmp_path))
+ else:
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path / "image.png"))
+ app.evaluate(
+ DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path / "image.png")
+ )
def test_app_validate(tmp_path):
diff --git a/tests/robofish/io/test_app_io.py b/tests/robofish/io/test_app_io.py
index 31ca2de..7d5ffd8 100644
--- a/tests/robofish/io/test_app_io.py
+++ b/tests/robofish/io/test_app_io.py
@@ -22,7 +22,7 @@ def test_app_validate():
raw_output = app.validate(DummyArgs(resources_path, "raw"))
# The three files valid.hdf5, almost_valid.hdf5, and invalid.hdf5 should be found.
- assert len(raw_output) == 3
+ assert len(raw_output) == 4
app.validate(DummyArgs(resources_path, "human"))
diff --git a/tests/robofish/io/test_file.py b/tests/robofish/io/test_file.py
index aa30a26..04d4b98 100644
--- a/tests/robofish/io/test_file.py
+++ b/tests/robofish/io/test_file.py
@@ -11,6 +11,7 @@ import logging
LOGGER = logging.getLogger(__name__)
valid_file_path = utils.full_path(__file__, "../../resources/valid_1.hdf5")
+nan_file_path = utils.full_path(__file__, "../../resources/nan_test.hdf5")
def test_constructor():
@@ -243,6 +244,12 @@ def test_file_plot():
f.plot(lw_distances=True)
+def test_file_plot():
+ with robofish.io.File(nan_file_path) as f:
+ f.plot()
+ f.plot(lw_distances=True)
+
+
if __name__ == "__main__":
# Find all functions in this module and execute them
all_functions = inspect.getmembers(sys.modules[__name__], inspect.isfunction)
diff --git a/tests/robofish/io/test_io.py b/tests/robofish/io/test_io.py
index 0cd1c80..ad0f68f 100644
--- a/tests/robofish/io/test_io.py
+++ b/tests/robofish/io/test_io.py
@@ -36,8 +36,8 @@ def test_read_multiple_folder():
robofish.io.read_multiple_files(resources_path),
robofish.io.read_multiple_files(str(resources_path)),
]:
- # Should find the 3 presaved hdf5 files
- assert len(sf) == 3
+ # Should find the 4 available hdf5 files
+ assert len(sf) == 4
for p, f in sf.items():
print(p)
assert type(f) == robofish.io.File
--
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