Merge pull request #8 from Rouast-Labs/video-read-fix

Video read fix

pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
     "importlib_resources",
     "numpy",
     "onnxruntime",
-    "prpy[ffmpeg,numpy_min]>=0.2.8",
+    "prpy[ffmpeg,numpy_min]==0.2.10",
     "python-dotenv",
     "pyyaml",
     "requests",

tests/conftest.py

@@ -52,7 +52,7 @@ def test_video_fps():
 
 @pytest.fixture(scope='session')
 def test_video_shape():
-  _, n, w, h, _, _, _ = probe_video(TEST_VIDEO_PATH)
+  _, n, w, h, *_ = probe_video(TEST_VIDEO_PATH)
   return (n, h, w, 3)
 
 @pytest.fixture(scope='session')

tests/test_ssd.py

@@ -19,7 +19,6 @@
 # SOFTWARE.
 
 import numpy as np
-from prpy.ffmpeg.probe import probe_video
 import pytest
 
 import sys

tests/test_utils.py

@@ -26,7 +26,7 @@
 
 from vitallens.client import Method
 from vitallens.utils import load_config, probe_video_inputs, parse_video_inputs
-from vitallens.utils import merge_faces, check_faces
+from vitallens.utils import merge_faces, check_faces, check_faces_in_roi
 
 @pytest.mark.parametrize("method", [m for m in Method])
 def test_load_config(method):
@@ -37,13 +37,14 @@ def test_load_config(method):
 def test_probe_video_inputs(request, file):
   if file:
     test_video_path = request.getfixturevalue('test_video_path')
-    video_shape, fps = probe_video_inputs(test_video_path)
+    video_shape, fps, i = probe_video_inputs(test_video_path)
   else:
     test_video_ndarray = request.getfixturevalue('test_video_ndarray')
     test_video_fps = request.getfixturevalue('test_video_fps')
-    video_shape, fps = probe_video_inputs(test_video_ndarray, fps=test_video_fps)
+    video_shape, fps, i = probe_video_inputs(test_video_ndarray, fps=test_video_fps)
   assert video_shape == (360, 480, 768, 3)
   assert fps == 30
+  assert i == False
 
 def test_probe_video_inputs_no_file():
   with pytest.raises(Exception):
@@ -152,4 +153,21 @@ def test_check_faces_n_frames_n_dets_not_matching_2():
 def test_check_faces_invalid_dets():
   with pytest.raises(Exception):
     _ = check_faces([1, 3, 2, 2], inputs_shape=(2, 10, 10, 3))
-
+
+@pytest.mark.parametrize("scenario", [([[0.4, 0.4, 0.6, 0.6], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.5), True), # Fully in ROI
+                                      ([[0.2, 0.4, 0.6, 0.6], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.5), True), # Slightly out to left but ok
+                                      ([[0.0, 0.4, 0.4, 0.6], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.5), False), # Too much out to left
+                                      ([[0.5, 0.4, 0.9, 0.6], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.2, 0.5), True), # Slightly out to right but ok
+                                      ([[0.5, 0.4, 0.9, 0.6], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.6, 0.5), False), # Too much out to right
+                                      ([[0.4, 0.2, 0.6, 0.5], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.5), True), # Slightly out to top but ok
+                                      ([[0.4, 0.1, 0.6, 0.5], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.6), False), # Too much out to top
+                                      ([[0.4, 0.5, 0.6, 0.8], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.5), True), # Slightly out to bottom but ok
+                                      ([[0.4, 0.6, 0.6, 0.9], [0.4, 0.4, 0.6, 0.6]], [0.3, 0.3, 0.7, 0.7], (0.5, 0.5), False), # Too much out to bottom
+                                      ])
+def test_check_faces_in_roi(scenario):
+  faces = np.asarray(scenario[0])
+  roi = np.asarray(scenario[1])
+  percentage_required_inside_roi = scenario[2]
+  expected = scenario[3]
+  actual = check_faces_in_roi(faces=faces, roi=roi, percentage_required_inside_roi=percentage_required_inside_roi)
+  assert expected == actual

tests/test_vitallens.py

@@ -94,8 +94,9 @@ def create_mock_api_response(
 @pytest.mark.parametrize("file", [True, False])
 @pytest.mark.parametrize("override_fps_target", [None, 15, 10])
 @pytest.mark.parametrize("long", [False, True])
+@pytest.mark.parametrize("override_global_parse", [False, True])
 @patch('requests.post', side_effect=create_mock_api_response)
-def test_VitalLensRPPGMethod_mock(mock_post, request, file, override_fps_target, long):
+def test_VitalLensRPPGMethod_mock(mock_post, request, file, long, override_fps_target, override_global_parse):
   if long and file:
     pytest.skip("Skip because parameter combination does not work")
   config = load_config("vitallens.yaml")
@@ -108,15 +109,17 @@ def test_VitalLensRPPGMethod_mock(mock_post, request, file, override_fps_target,
   if file:
     data, unit, conf, note, live = method(
       frames=test_video_path, faces=test_video_faces,
-      override_fps_target=override_fps_target)
-  else: 
+      override_fps_target=override_fps_target,
+      override_global_parse=override_global_parse)
+  else:
     if long:
       n_repeats = (API_MAX_FRAMES * 3) // test_video_ndarray.shape[0] + 1
       test_video_ndarray = np.repeat(test_video_ndarray, repeats=n_repeats, axis=0)
       test_video_faces = np.repeat(test_video_faces, repeats=n_repeats, axis=0)
     data, unit, conf, note, live = method(
       frames=test_video_ndarray, faces=test_video_faces,
-      fps=test_video_fps, override_fps_target=override_fps_target)
+      fps=test_video_fps, override_fps_target=override_fps_target,
+      override_global_parse=override_global_parse)
   assert all(key in data for key in method.signals)
   assert all(key in unit for key in method.signals)
   assert all(key in conf for key in method.signals)

vitallens/client.py

@@ -107,6 +107,7 @@ def __call__(
       faces: Union[np.ndarray, list] = None,
       fps: float = None,
       override_fps_target: float = None,
+      override_global_parse: bool = None,
       export_filename: str = None
     ) -> list:
     """Run rPPG inference.
@@ -124,6 +125,8 @@ def __call__(
       fps: Sampling frequency of the input video. Required if type(video) == np.ndarray. 
       override_fps_target: Target fps at which rPPG inference should be run (optional).
         If not provided, will use default of the selected method.
+      override_global_parse: If True, always use global parse. If False, don't use global parse.
+        If None, choose based on video.
       export_filename: Filename for json export if applicable.
     Returns:
       result: Analysis results as a list of faces in the following format:
@@ -169,7 +172,7 @@ def __call__(
         ]
     """
     # Probe inputs
-    inputs_shape, fps = probe_video_inputs(video=video, fps=fps)
+    inputs_shape, fps, _ = probe_video_inputs(video=video, fps=fps)
     # TODO: Optimize performance of simple rPPG methods for long videos
     # Warning if using long video
     target_fps = override_fps_target if override_fps_target is not None else self.rppg.fps_target
@@ -194,7 +197,9 @@ def __call__(
     for face in faces:
       # Run selected rPPG method
       data, unit, conf, note, live = self.rppg(
-        frames=video, faces=face, fps=fps, override_fps_target=override_fps_target)
+        frames=video, faces=face, fps=fps,
+        override_fps_target=override_fps_target,
+        override_global_parse=override_global_parse)
       # Parse face results
       face_result = {'face': {
         'coordinates': face,

vitallens/constants.py

@@ -38,5 +38,8 @@
 if 'API_URL' in os.environ:
   API_URL = os.getenv('API_URL')
 
+# Video error message
+VIDEO_PARSE_ERROR = "Unable to parse input video. There may be an issue with the video file."
+
 # Disclaimer message
 DISCLAIMER = "The provided values are estimates and should be interpreted according to the provided confidence levels ranging from 0 to 1. The VitalLens API is not a medical device and its estimates are not intended for any medical purposes."

vitallens/methods/simple_rppg_method.py

@@ -57,7 +57,8 @@ def __call__(
       frames: Union[np.ndarray, str],
       faces: np.ndarray,
       fps: float,
-      override_fps_target: float = None
+      override_fps_target: float = None,
+      override_global_parse: float = None,
     ) -> Tuple[dict, dict, dict, dict, np.ndarray]:
     """Estimate pulse signal from video frames using the subclass algorithm.
 
@@ -66,6 +67,7 @@ def __call__(
       faces: The face detection boxes as np.int64. Shape (n_frames, 4) in form (x0, y0, x1, y1)
       fps: The rate at which video was sampled.
       override_fps_target: Override the method's default inference fps (optional).
+      override_global_parse: Has no effect here.
     Returns:
       data: A dictionary with the values of the estimated vital signs.
       unit: A dictionary with the units of the estimated vital signs.

vitallens/methods/vitallens.py

@@ -26,6 +26,7 @@
 from prpy.numpy.face import get_roi_from_det
 from prpy.numpy.signal import detrend, moving_average, standardize
 from prpy.numpy.signal import interpolate_cubic_spline, estimate_freq
+from prpy.numpy.utils import enough_memory_for_ndarray
 import json
 import logging
 import requests
@@ -38,7 +39,7 @@
 from vitallens.signal import detrend_lambda_for_hr_response, detrend_lambda_for_rr_response
 from vitallens.signal import moving_average_size_for_hr_response, moving_average_size_for_rr_response
 from vitallens.signal import reassemble_from_windows
-from vitallens.utils import probe_video_inputs, parse_video_inputs
+from vitallens.utils import probe_video_inputs, parse_video_inputs, check_faces_in_roi
 
 class VitalLensRPPGMethod(RPPGMethod):
   def __init__(
@@ -56,7 +57,8 @@ def __call__(
       frames: Union[np.ndarray, str],
       faces: np.ndarray,
       fps: float = None,
-      override_fps_target: float = None
+      override_fps_target: float = None,
+      override_global_parse: bool = None
     ) -> Tuple[dict, dict, dict, dict, np.ndarray]:
     """Estimate vitals from video frames using the VitalLens API.
 
@@ -66,44 +68,54 @@ def __call__(
       faces: The face detection boxes as np.int64. Shape (n_frames, 4) in form (x0, y0, x1, y1)
       fps: The rate at which video was sampled.
       override_fps_target: Override the method's default inference fps (optional).
+      override_global_parse: If True, always use global parse. If False, don't use global parse.
+        If None, choose based on video.
     Returns:
       out_data: The estimated data/value for each signal.
       out_unit: The estimation unit for each signal.
       out_conf: The estimation confidence for each signal.
       out_note: An explanatory note for each signal.
       live: The face live confidence. Shape (1, n_frames)
     """
-    inputs_shape, fps = probe_video_inputs(video=frames, fps=fps)
+    inputs_shape, fps, video_issues = probe_video_inputs(video=frames, fps=fps)
+    video_fits_in_memory = enough_memory_for_ndarray(
+      shape=(inputs_shape[0], self.input_size, self.input_size, 3), dtype=np.uint8)
     # Check the number of frames to be processed
     inputs_n = inputs_shape[0]
     fps_target = override_fps_target if override_fps_target is not None else self.fps_target
     expected_ds_factor = round(fps / fps_target)
     expected_ds_n = math.ceil(inputs_n / expected_ds_factor)
-    if expected_ds_n <= API_MAX_FRAMES:
-      # API supports up to MAX_FRAMES at once - process all frames
-      sig_ds, conf_ds, live_ds, idxs = self.process_api_batch(
-        batch=1, n_batches=1, inputs=frames, inputs_shape=inputs_shape,
-        faces=faces, fps_target=fps_target, fps=fps)
-    else:
-      # Longer videos are split up with small overlaps
-      n_splits = math.ceil((expected_ds_n - API_MAX_FRAMES) / (API_MAX_FRAMES - API_OVERLAP)) + 1
-      split_len = math.ceil((inputs_n + (n_splits-1) * API_OVERLAP * expected_ds_factor) / n_splits)
-      # start_idxs = [i for i in range(0, expected_ds_len - n_splits * API_OVERLAP, split_len - API_OVERLAP)]
-      start_idxs = [i * (split_len - API_OVERLAP * expected_ds_factor) for i in range(n_splits)]      
-      end_idxs = [min(start + split_len, inputs_n) for start in start_idxs]
-      start_idxs = [max(0, end - split_len) for end in end_idxs]
-      logging.info("Running inference for {} frames using {} requests...".format(expected_ds_n, n_splits))
-      # Process the splits in parallel
-      with concurrent.futures.ThreadPoolExecutor() as executor:
-        results = list(executor.map(lambda i: self.process_api_batch(
-          batch=i, n_batches=n_splits, inputs=frames, inputs_shape=inputs_shape,
-          faces=faces, fps_target=fps_target, start=start_idxs[i], end=end_idxs[i],
-          fps=fps), range(n_splits)))
-      # Aggregate the results
-      sig_results, conf_results, live_results, idxs_results = zip(*results)
-      sig_ds, idxs = reassemble_from_windows(x=sig_results, idxs=idxs_results)
-      conf_ds, _ = reassemble_from_windows(x=conf_results, idxs=idxs_results)
-      live_ds = reassemble_from_windows(x=np.asarray(live_results)[:,np.newaxis], idxs=idxs_results)[0][0]
+    # Check if we can parse the video globally
+    global_face = faces[np.argmin(np.linalg.norm(faces - np.median(faces, axis=0), axis=1))]
+    global_roi = get_roi_from_det(
+      global_face, roi_method=self.roi_method, clip_dims=(inputs_shape[2], inputs_shape[1]))
+    global_faces_in_roi = check_faces_in_roi(faces=faces, roi=global_roi)
+    global_parse = isinstance(frames, str) and video_fits_in_memory and (video_issues or global_faces_in_roi)
+    if override_global_parse is not None: global_parse = override_global_parse
+    if global_parse:
+      # Parse entire video for inference globally
+      frames, _, _, _, idxs = parse_video_inputs(
+        video=frames, fps=fps, target_size=self.input_size, roi=global_roi, target_fps=fps_target,
+        library='prpy', scale_algorithm='bilinear', dim_deltas=(API_OVERLAP, 0, 0))
+    # Longer videos are split up with small overlaps
+    n_splits = 1 if expected_ds_n <= API_MAX_FRAMES else math.ceil((expected_ds_n - API_MAX_FRAMES) / (API_MAX_FRAMES - API_OVERLAP)) + 1
+    split_len = expected_ds_n if n_splits == 1 else math.ceil((inputs_n + (n_splits-1) * API_OVERLAP * expected_ds_factor) / n_splits)
+    start_idxs = [i * (split_len - API_OVERLAP * expected_ds_factor) for i in range(n_splits)]      
+    end_idxs = [min(start + split_len, inputs_n) for start in start_idxs]
+    start_idxs = [max(0, end - split_len) for end in end_idxs]
+    logging.info("Running inference for {} frames using {} request(s)...".format(expected_ds_n, n_splits))
+    # Process the splits in parallel
+    with concurrent.futures.ThreadPoolExecutor() as executor:
+      results = list(executor.map(lambda i: self.process_api_batch(
+        batch=i, n_batches=n_splits, inputs=frames, inputs_shape=inputs_shape,
+        faces=faces, fps_target=fps_target, fps=fps, global_parse=global_parse,
+        start=None if n_splits == 1 else start_idxs[i],
+        end=None if n_splits == 1 else end_idxs[i]), range(n_splits)))
+    # Aggregate the results
+    sig_results, conf_results, live_results, idxs_results = zip(*results)
+    sig_ds, idxs = reassemble_from_windows(x=sig_results, idxs=idxs_results)
+    conf_ds, _ = reassemble_from_windows(x=conf_results, idxs=idxs_results)
+    live_ds = reassemble_from_windows(x=np.asarray(live_results)[:,np.newaxis], idxs=idxs_results)[0][0]
     # Interpolate to original sampling rate (n_frames,)
     sig = interpolate_cubic_spline(
       x=idxs, y=sig_ds, xs=np.arange(inputs_n), axis=1)
@@ -159,7 +171,8 @@ def process_api_batch(
       fps_target: float,
       start: int = None,
       end: int = None,
-      fps: float = None
+      fps: float = None,
+      global_parse: bool = False
     ) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
     """Process a batch of frames with the VitalLens API.
 
@@ -168,12 +181,13 @@ def process_api_batch(
       n_batches: The total number of batches.
       inputs: The video to analyze. Either a np.ndarray of shape (n_frames, h, w, 3)
         with a sequence of frames in unscaled uint8 RGB format, or a path to a video file.
-      inputs_shape: The shape of the inputs.
+      inputs_shape: The original shape of the inputs.
       faces: The face detection boxes as np.int64. Shape (n_frames, 4) in form (x0, y0, x1, y1)
       fps_target: The target frame rate at which to run inference.
       start: The index of first frame of the video to analyze in this batch.
       end: The index of the last frame of the video to analyze in this batch.
       fps: The frame rate of the input video. Required if type(video) == np.ndarray
+      global_parse: Flag that indicates whether video has already been parsed.
     Returns:
       sig: Estimated signals. Shape (n_sig, n_frames)
       conf: Estimation confidences. Shape (n_sig, n_frames)
@@ -188,16 +202,31 @@ def process_api_batch(
     face = faces[np.argmin(np.linalg.norm(faces - np.median(faces, axis=0), axis=1))]
     roi = get_roi_from_det(
       face, roi_method=self.roi_method, clip_dims=(inputs_shape[2], inputs_shape[1]))
-    if np.any(np.logical_or(
-      (faces[:,2] - faces[:,0]) * 0.5 < np.maximum(0, faces[:,0] - roi[0]) + np.maximum(0, faces[:,2] - roi[2]),
-      (faces[:,3] - faces[:,1]) * 0.5 < np.maximum(0, faces[:,1] - roi[1]) + np.maximum(0, faces[:,3] - roi[3]))):
+    if not check_faces_in_roi(faces=faces, roi=roi):
       logging.warning("Large face movement detected")
-    # Parse the inputs
-    frames_ds, fps, inputs_shape, _, idxs = parse_video_inputs(
-      video=inputs, fps=fps, target_size=self.input_size, roi=roi, target_fps=fps_target,
-      trim=(start, end) if start is not None and end is not None else None,
-      library='prpy', scale_algorithm='bilinear')
-    assert frames_ds.shape[0] <= API_MAX_FRAMES
+    if global_parse:
+      # Inputs have already been parsed globally.
+      assert isinstance(inputs, np.ndarray)
+      frames_ds = inputs
+      ds_factor = math.ceil(inputs_shape[0] / frames_ds.shape[0])
+      # Trim frames to batch if necessary
+      if start is not None and end is not None:
+        start_ds = start // ds_factor
+        end_ds = math.ceil((end-start)/ds_factor) + start_ds
+        frames_ds = frames_ds[start_ds:end_ds]
+        idxs = list(range(start, end, ds_factor))
+      else:
+        idxs = list(range(0, inputs_shape[0], ds_factor))
+    else:
+      # Inputs have not been parsed globally. Parse the inputs
+      frames_ds, _, _, ds_factor, idxs = parse_video_inputs(
+        video=inputs, fps=fps, target_size=self.input_size, roi=roi, target_fps=fps_target,
+        trim=(start, end) if start is not None and end is not None else None,
+        library='prpy', scale_algorithm='bilinear', dim_deltas=(API_OVERLAP, 0, 0))
+    # Make sure we have the correct number of frames
+    expected_n = math.ceil(((end-start) if start is not None and end is not None else inputs_shape[0]) / ds_factor)
+    if frames_ds.shape[0] != expected_n or len(idxs) != expected_n:
+      raise ValueError("Unexpected number of frames returned. Try to set `override_global_parse` to `True` or `False`.")
     # Prepare API header and payload
     headers = {"x-api-key": self.api_key}
     payload = {"video": base64.b64encode(frames_ds.tobytes()).decode('utf-8')}