diff --git a/.gitignore b/.gitignore
index 3825a6ab5a89436ea58a3513859272e88abee742..764c5ec57cd932bc024ae62cff117e517559d4a3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,7 @@ dist
.vscode
.venv
.coverage
+.testmondata
report.xml
htmlcov
html
@@ -16,5 +17,7 @@ env
*.hdf5
*.mp4
+!tests/resources/*.hdf5
+
feature_requests.md
output_graph.png
diff --git a/src/robofish/evaluate/evaluate.py b/src/robofish/evaluate/evaluate.py
index d62c6ce49fd11273037e32358f89d2a69f18b4cb..aaa9645ecaba2afc8a91ed6990b566a557b40965 100644
--- a/src/robofish/evaluate/evaluate.py
+++ b/src/robofish/evaluate/evaluate.py
@@ -73,6 +73,8 @@ def evaluate_speed(
"""
files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
speeds = []
+ left_quantiles = []
+ right_quantiles = []
frequency = None
for k, files in enumerate(files_per_path):
@@ -82,19 +84,22 @@ def evaluate_speed(
frequency = file.frequency
for e_speeds_turns in file.entity_actions_speeds_turns:
- path_speeds = np.concatenate(
- [path_speeds, e_speeds_turns[:, 0] * frequency]
- )
+ path_speeds.extend(e_speeds_turns[:, 0] * frequency)
+
+ path_speeds = np.array(path_speeds)
+ left_quantiles.append(np.quantile(path_speeds, 0.001))
+ right_quantiles.append(np.quantile(path_speeds, 0.999))
speeds.append(path_speeds)
if labels is None:
labels = paths
- speeds = np.array(speeds)
-
- left_quantile = np.min(np.quantile(speeds, 0.001, axis=1))
- right_quantile = np.max(np.quantile(speeds, 0.999, axis=1))
- plt.hist(list(speeds), bins=20, label=labels, range=[left_quantile, right_quantile])
+ plt.hist(
+ list(speeds),
+ bins=20,
+ label=labels,
+ range=[min(left_quantiles), max(right_quantiles)],
+ )
plt.title("Agent speeds")
plt.xlabel("Speed [cm/s]")
plt.ylabel("Frequency")
@@ -132,25 +137,28 @@ def evaluate_turn(
for k, files in enumerate(files_per_path):
path_turns = []
+ left_quantiles, right_quantiles = [], []
for p, file in files.items():
assert frequency is None or frequency == file.frequency
frequency = file.frequency
for e_speeds_turns in file.entity_actions_speeds_turns:
path_turns.extend(np.rad2deg(e_speeds_turns[:, 1]))
+
+ path_turns = np.array(path_turns)
+ left_quantiles.append(np.quantile(path_turns, 0.001))
+ right_quantiles.append(np.quantile(path_turns, 0.999))
turns.append(path_turns)
if labels is None:
labels = paths
- left_quantile = np.min(np.quantile(np.array(turns), 0.005, axis=1))
- right_quantile = np.max(np.quantile(np.array(turns), 0.995, axis=1))
plt.hist(
turns,
bins=41,
label=labels,
density=True,
- range=[left_quantile, right_quantile],
+ range=[min(left_quantiles), max(right_quantiles)],
)
plt.title("Agent turns")
plt.xlabel("Change in orientation [Degree / timestep at %dhz]" % frequency)
@@ -697,6 +705,12 @@ def evaluate_all(
predicate: a lambda function, selecting entities
(example: lambda e: e.category == "fish")
"""
+ assert (
+ save_folder is not None and save_folder != ""
+ ), "Please provide a save_folder using --save_path"
+
+ save_folder.mkdir(exist_ok=True)
+
t = tqdm(fdict.items(), desc="Evaluation", leave=True)
for f_name, f_callable in t:
t.set_description(f_name)
diff --git a/tests/resources/valid.hdf5 b/tests/resources/valid_1.hdf5
similarity index 100%
rename from tests/resources/valid.hdf5
rename to tests/resources/valid_1.hdf5
diff --git a/tests/resources/valid_2.hdf5 b/tests/resources/valid_2.hdf5
new file mode 100644
index 0000000000000000000000000000000000000000..10caedaafa4d0d13c4be720f2c8d48dec184a092
Binary files /dev/null and b/tests/resources/valid_2.hdf5 differ
diff --git a/tests/robofish/evaluate/test_app_evaluate.py b/tests/robofish/evaluate/test_app_evaluate.py
index d7b783fe4bd764562337309ca1ae74e9eea5ce7f..ac3d8c084d85f5525ea48c45abcd2c58f5ddc3c7 100644
--- a/tests/robofish/evaluate/test_app_evaluate.py
+++ b/tests/robofish/evaluate/test_app_evaluate.py
@@ -9,7 +9,8 @@ np.seterr(all="raise")
logging.getLogger().setLevel(logging.INFO)
-h5py_file = utils.full_path(__file__, "../../resources/valid.hdf5")
+h5py_file_1 = utils.full_path(__file__, "../../resources/valid_1.hdf5")
+h5py_file_2 = utils.full_path(__file__, "../../resources/valid_2.hdf5")
def test_app_validate(tmp_path):
@@ -24,10 +25,10 @@ def test_app_validate(tmp_path):
for mode in app.function_dict().keys():
if mode == "all":
- app.evaluate(DummyArgs(mode, [h5py_file], tmp_path))
- app.evaluate(DummyArgs(mode, [h5py_file, h5py_file], tmp_path))
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path))
+ app.evaluate(DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path))
else:
- app.evaluate(DummyArgs(mode, [h5py_file], tmp_path / "image.png"))
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path / "image.png"))
app.evaluate(
- DummyArgs(mode, [h5py_file, h5py_file], tmp_path / "image.png")
+ DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path / "image.png")
)
diff --git a/tests/robofish/evaluate/test_evaluate.py b/tests/robofish/evaluate/test_evaluate.py
index 65aa7271cff6a82026cf38620a1fd68220656446..0476c18985fe065ee8f7566e0581461ed6666379 100644
--- a/tests/robofish/evaluate/test_evaluate.py
+++ b/tests/robofish/evaluate/test_evaluate.py
@@ -5,7 +5,7 @@ import numpy as np
def test_get_all_poses_from_paths():
- valid_file_path = utils.full_path(__file__, "../../resources/valid.hdf5")
+ valid_file_path = utils.full_path(__file__, "../../resources/valid_1.hdf5")
poses, frequency = robofish.evaluate.get_all_poses_from_paths([valid_file_path])
# (1 input array, 1 file, 2 fishes, 100 timesteps, 4 poses)
diff --git a/tests/robofish/io/test_app_io.py b/tests/robofish/io/test_app_io.py
index 6ac95611137f8de5634cc622ff05e8be4cfb5e0f..31ca2ded7b17b39049745ff43f8f13f9d185dcac 100644
--- a/tests/robofish/io/test_app_io.py
+++ b/tests/robofish/io/test_app_io.py
@@ -7,34 +7,32 @@ from pathlib import Path
logging.getLogger().setLevel(logging.INFO)
+resources_path = utils.full_path(__file__, "../../resources")
+h5py_file = utils.full_path(__file__, "../../resources/valid_1.hdf5")
+
+
def test_app_validate():
- """ This tests the function of the robofish-io-validate command """
+ """This tests the function of the robofish-io-validate command"""
class DummyArgs:
def __init__(self, path, output_format):
self.path = path
self.output_format = output_format
- raw_output = app.validate(
- DummyArgs(utils.full_path(__file__, "../../resources"), "raw")
- )
+ 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) == 2
- app.validate(DummyArgs(utils.full_path(__file__, "../../resources"), "human"))
+ assert len(raw_output) == 3
+ app.validate(DummyArgs(resources_path, "human"))
def test_app_print():
- """ This tests the function of the robofish-io-validate command """
+ """This tests the function of the robofish-io-validate command"""
class DummyArgs:
def __init__(self, path, output_format):
self.path = path
self.output_format = output_format
- app.print_file(
- DummyArgs(utils.full_path(__file__, "../../resources/valid.hdf5"), "full")
- )
- app.print_file(
- DummyArgs(utils.full_path(__file__, "../../resources/valid.hdf5"), "shape")
- )
+ app.print_file(DummyArgs(h5py_file, "full"))
+ app.print_file(DummyArgs(h5py_file, "shape"))
diff --git a/tests/robofish/io/test_file.py b/tests/robofish/io/test_file.py
index 97e2aa18bf7888143046a4302745de0d8b907554..2ec1f26b2d0804f20c70d685c7576a3fe4a6bc05 100644
--- a/tests/robofish/io/test_file.py
+++ b/tests/robofish/io/test_file.py
@@ -10,7 +10,7 @@ import logging
LOGGER = logging.getLogger(__name__)
-valid_file_path = utils.full_path(__file__, "../../resources/valid.hdf5")
+valid_file_path = utils.full_path(__file__, "../../resources/valid_1.hdf5")
def test_constructor():
diff --git a/tests/robofish/io/test_io.py b/tests/robofish/io/test_io.py
index 3a7bb32390223adfbd4e7f2f1f9a3454c93bdfa4..0cd1c80b65b23b53a914acba090ec99f19ae67ca 100644
--- a/tests/robofish/io/test_io.py
+++ b/tests/robofish/io/test_io.py
@@ -5,6 +5,10 @@ from pathlib import Path
import numpy as np
+resources_path = utils.full_path(__file__, "../../resources/")
+h5py_file = utils.full_path(__file__, "../../resources/valid_1.hdf5")
+
+
def test_now_iso8061():
# Example time: 2021-01-05T14:33:40.401000+00:00
time = robofish.io.now_iso8061()
@@ -13,12 +17,12 @@ def test_now_iso8061():
def test_read_multiple_single():
- path = utils.full_path(__file__, "../../resources/valid.hdf5")
+ path = h5py_file
# Variants path as posix path or as string
for sf in [
- robofish.io.read_multiple_files(path),
- robofish.io.read_multiple_files(str(path)),
+ robofish.io.read_multiple_files(h5py_file),
+ robofish.io.read_multiple_files(str(h5py_file)),
]:
assert len(sf) == 1
for p, f in sf.items():
@@ -27,27 +31,23 @@ def test_read_multiple_single():
def test_read_multiple_folder():
- path = utils.full_path(__file__, "../../resources/")
-
# Variants path as posix path or as string
for sf in [
- robofish.io.read_multiple_files(path),
- robofish.io.read_multiple_files(str(path)),
+ 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) == 2
+ assert len(sf) == 3
for p, f in sf.items():
print(p)
assert type(f) == robofish.io.File
-path = utils.full_path(__file__, "../../resources/valid.hdf5")
-
# TODO read from folder of valid files
-@pytest.mark.parametrize("_path", [path, str(path)])
-def test_read_poses_rad_from_multiple_folder(_path):
+@pytest.mark.parametrize("param_path", [h5py_file, str(h5py_file)])
+def test_read_poses_rad_from_multiple_folder(param_path):
poses = robofish.io.read_property_from_multiple_files(
- [_path, _path], robofish.io.entity.Entity.poses_rad
+ [param_path, param_path], robofish.io.entity.Entity.poses_rad
)
# Should find the 3 presaved hdf5 files
assert len(poses) == 2