Implemented tests; Debugging

.github/workflows/main.yml

@@ -36,5 +36,7 @@ jobs:
         run: |
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
       - name: Test with pytest
+        env:
+          VITALLENS_DEV_API_KEY: ${{ secrets.VITALLENS_DEV_API_KEY }}
         run: |
           pytest

README.md

@@ -65,8 +65,8 @@ This can also be configured using the following parameters:
 
 | Parameter           | Description                                                                           | Default |
 |---------------------|---------------------------------------------------------------------------------------|---------|
-| video               | The video to analyze. Either a path to a video file or `np.ndarray`. [More info here.](https://github.com/Rouast-Labs/vitallens-python/blob/2a674a22e910c432a7c9c135d5f7cc9f2cdb566c/vitallens/client.py#L99)    |         |
-| faces               | Face detections. Ignored unless `detect_faces=False`. [More info here.](https://github.com/Rouast-Labs/vitallens-python/blob/2a674a22e910c432a7c9c135d5f7cc9f2cdb566c/vitallens/client.py#L102) | `None`  |
+| video               | The video to analyze. Either a path to a video file or `np.ndarray`. [More info here.](https://github.com/Rouast-Labs/vitallens-python/blob/ddcf48f29a2765fd98a7029c0f10075a33e44247/vitallens/client.py#L98)    |         |
+| faces               | Face detections. Ignored unless `detect_faces=False`. [More info here.](https://github.com/Rouast-Labs/vitallens-python/blob/ddcf48f29a2765fd98a7029c0f10075a33e44247/vitallens/client.py#L101) | `None`  |
 | fps                 | Sampling frequency of the input video. Required if video is `np.ndarray`.             | `None`  |
 | override_fps_target | Target frequency for inference (optional - use methods's default otherwise).          | `None`  |
 
@@ -120,3 +120,21 @@ my_video_fps = 30
 vl = VitalLens(method=Method.POS)
 result = vl(my_video_arr, fps=my_video_fps)
 ```
+
+## Linting and tests
+
+Before running tests, please make sure that you have an environment variable `VITALLENS_DEV_API_KEY` set to a valid API Key. 
+To lint and run tests:
+
+```
+flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+pytest
+```
+
+## Build
+
+To build:
+
+```
+python -m build
+```

examples/test.py

@@ -7,6 +7,7 @@
 from prpy.ffmpeg.readwrite import read_video_from_path
 
 input_str = True
+# TODO: Select a better test video
 video_path = "examples/test.mp4"
 
 if input_str:
@@ -20,7 +21,7 @@
   print("Video shape: {}".format(video.shape))
 
 vl = vitallens.VitalLens(
-  method=vitallens.Method.POS,
+  method=vitallens.Method.VITALLENS,
   api_key="INSERT_API_KEY_HERE")
 start = timeit.default_timer()
 result = vl(video=video, fps=fps, override_fps_target=30.0)
@@ -29,6 +30,6 @@
 print("Inference time: {:.2f} ms".format((stop-start)*1000))
 
 import matplotlib.pyplot as plt
-if 'pulse' in result[0]: plt.plot(result[0]['pulse']['sig'])
-if 'resp' in result[0]: plt.plot(result[0]['resp']['sig'])
+if 'pulse' in result[0]: plt.plot(result[0]['pulse']['val'])
+if 'resp' in result[0]: plt.plot(result[0]['resp']['val'])
 plt.show()

tests/conftest.py

@@ -0,0 +1,67 @@
+# Copyright (c) 2024 Philipp Rouast
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import os
+from prpy.ffmpeg.probe import probe_video
+from prpy.ffmpeg.readwrite import read_video_from_path
+import pytest
+
+import sys
+sys.path.append('../vitallens-python')
+
+from vitallens.ssd import FaceDetector
+
+# TODO: Select a better test video
+TEST_VIDEO_PATH = "examples/test.mp4"
+
+@pytest.fixture(scope='session')
+def test_video_path():
+  return TEST_VIDEO_PATH
+
+@pytest.fixture(scope='session')
+def test_video_ndarray():
+  video, _ = read_video_from_path(path=TEST_VIDEO_PATH, pix_fmt='rgb24')
+  return video
+
+@pytest.fixture(scope='session')
+def test_video_fps():
+  fps, *_ = probe_video(TEST_VIDEO_PATH)
+  return fps
+
+@pytest.fixture(scope='session')
+def test_video_faces(request):
+  det = FaceDetector(
+    max_faces=1, fs=1.0, iou_threshold=0.45, score_threshold=0.9)
+  test_video_ndarray = request.getfixturevalue('test_video_ndarray')
+  test_video_fps = request.getfixturevalue('test_video_fps')
+  boxes, _ = det(test_video_ndarray, fps=test_video_fps)
+  boxes = (boxes * [test_video_ndarray.shape[2], test_video_ndarray.shape[1], test_video_ndarray.shape[2], test_video_ndarray.shape[1]]).astype(int)
+  return boxes[:,0]
+
+@pytest.fixture(scope='session')
+def test_dev_api_key():
+  api_key = os.getenv('VITALLENS_DEV_API_KEY')
+  if not api_key:
+    raise pytest.UsageError(
+        "VITALLENS_DEV_API_KEY environment variable is not set. Please set this variable "
+        "to a valid VitalLens API Key to run the tests. You can do this by exporting the "
+        "variable in your shell or adding it to your conda environment configuration."
+    )
+  return api_key

tests/test_client.py

@@ -0,0 +1,59 @@
+# Copyright (c) 2024 Philipp Rouast
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import numpy as np
+import pytest
+
+import sys
+sys.path.append('../vitallens-python')
+
+from vitallens.client import VitalLens, Method
+
+@pytest.mark.parametrize("method", [Method.G, Method.CHROM, Method.POS])
+@pytest.mark.parametrize("detect_faces", [True, False])
+@pytest.mark.parametrize("file", [True, False])
+def test_VitalLens(request, method, detect_faces, file):
+  vl = VitalLens(method=method, detect_faces=detect_faces)
+  if file:
+    test_video_path = request.getfixturevalue('test_video_path')
+    result = vl(test_video_path, faces = None if detect_faces else [425, 116, 671, 433])
+  else:
+    test_video_ndarray = request.getfixturevalue('test_video_ndarray')
+    test_video_fps = request.getfixturevalue('test_video_fps')
+    result = vl(test_video_ndarray, fps=test_video_fps, faces = None if detect_faces else [425, 116, 671, 433])
+  assert len(result) == 1
+  assert result[0]['face'].shape == (139, 4)
+  assert result[0]['pulse']['val'].shape == (139,)
+  np.testing.assert_allclose(result[0]['hr']['val'], 71.5, atol=2)
+
+def test_VitalLens_API(request):
+  api_key = request.getfixturevalue('test_dev_api_key')
+  vl = VitalLens(method=Method.VITALLENS, api_key=api_key, detect_faces=True)
+  test_video_ndarray = request.getfixturevalue('test_video_ndarray')
+  test_video_fps = request.getfixturevalue('test_video_fps')
+  result = vl(test_video_ndarray, fps=test_video_fps, faces=None)
+  assert len(result) == 1
+  assert result[0]['face'].shape == (139, 4)
+  assert result[0]['pulse']['val'].shape == (139,)
+  assert result[0]['pulse']['conf'].shape == (139,)
+  assert result[0]['resp']['val'].shape == (139,)
+  assert result[0]['resp']['conf'].shape == (139,)
+  np.testing.assert_allclose(result[0]['hr']['val'], 73, atol=0.5)
+  np.testing.assert_allclose(result[0]['rr']['val'], 15, atol=0.5)

tests/test_simple_rppg_method.py

@@ -0,0 +1,84 @@
+# Copyright (c) 2024 Philipp Rouast
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import numpy as np
+import pytest
+
+import sys
+sys.path.append('../vitallens-python')
+
+from vitallens.methods.chrom import CHROMRPPGMethod
+from vitallens.methods.g import GRPPGMethod
+from vitallens.methods.pos import POSRPPGMethod
+from vitallens.utils import load_config
+
+@pytest.mark.parametrize("override_fps_target", [None, 15])
+def test_CHROMRPPGMethod(request, override_fps_target):
+  config = load_config("chrom.yaml")
+  method = CHROMRPPGMethod(config)
+  res = method.algorithm(np.random.rand(100, 3), fps=30.)
+  assert res.shape == (100,)
+  res = method.pulse_filter(res, fps=30.)
+  assert res.shape == (100,)
+  test_video_ndarray = request.getfixturevalue('test_video_ndarray')
+  test_video_fps = request.getfixturevalue('test_video_fps')
+  test_video_faces = request.getfixturevalue('test_video_faces')
+  sig, conf, live = method(
+    frames=test_video_ndarray, faces=test_video_faces,
+    fps=test_video_fps, override_fps_target=override_fps_target)
+  assert sig.shape == (1, test_video_ndarray.shape[0])
+  np.testing.assert_equal(conf, np.ones((1, test_video_ndarray.shape[0]), np.float32))
+  np.testing.assert_equal(live, np.ones((test_video_ndarray.shape[0],), np.float32))
+
+@pytest.mark.parametrize("override_fps_target", [None, 15])
+def test_GRPPGMethod(request, override_fps_target):
+  config = load_config("g.yaml")
+  method = GRPPGMethod(config)
+  res = method.algorithm(np.random.rand(100, 3), fps=30.)
+  assert res.shape == (100,)
+  res = method.pulse_filter(res, fps=30.)
+  assert res.shape == (100,)
+  test_video_ndarray = request.getfixturevalue('test_video_ndarray')
+  test_video_fps = request.getfixturevalue('test_video_fps')
+  test_video_faces = request.getfixturevalue('test_video_faces')
+  sig, conf, live = method(
+    frames=test_video_ndarray, faces=test_video_faces,
+    fps=test_video_fps, override_fps_target=override_fps_target)
+  assert sig.shape == (1, test_video_ndarray.shape[0])
+  np.testing.assert_equal(conf, np.ones((1, test_video_ndarray.shape[0]), np.float32))
+  np.testing.assert_equal(live, np.ones((test_video_ndarray.shape[0],), np.float32))
+
+@pytest.mark.parametrize("override_fps_target", [None, 15])
+def test_POSRPPGMethod(request, override_fps_target):
+  config = load_config("pos.yaml")
+  method = POSRPPGMethod(config)
+  res = method.algorithm(np.random.rand(100, 3), fps=30.)
+  assert res.shape == (100,)
+  res = method.pulse_filter(res, fps=30.)
+  assert res.shape == (100,)
+  test_video_ndarray = request.getfixturevalue('test_video_ndarray')
+  test_video_fps = request.getfixturevalue('test_video_fps')
+  test_video_faces = request.getfixturevalue('test_video_faces')
+  sig, conf, live = method(
+    frames=test_video_ndarray, faces=test_video_faces,
+    fps=test_video_fps, override_fps_target=override_fps_target)
+  assert sig.shape == (1, test_video_ndarray.shape[0])
+  np.testing.assert_equal(conf, np.ones((1, test_video_ndarray.shape[0]), np.float32))
+  np.testing.assert_equal(live, np.ones((test_video_ndarray.shape[0],), np.float32))