Merge pull request #11 from Rouast-Labs/prpy-update

Update prpy and add Dockerfile

Dockerfile

@@ -0,0 +1,14 @@
+FROM python:3.9-slim
+ENV PYTHONUNBUFFERED=1
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    git \
+    ffmpeg \
+    && rm -rf /var/lib/apt/lists/*
+WORKDIR /app
+COPY . /app
+RUN pip install --upgrade pip setuptools wheel
+RUN pip install .
+RUN pip install matplotlib pandas
+ENTRYPOINT ["python", "examples/test.py"]
+CMD ["--api_key", "", "--vitals_path", "examples/sample_vitals_1.csv", "--video_path", "examples/sample_video_1.mp4", "--method", "VITALLENS", "--input_str", "True"]

README.md

@@ -186,6 +186,51 @@ vl = VitalLens(method=Method.POS)
 result = vl(my_video_arr, fps=my_video_fps)
 ```
 
+### Example: Run example script with Docker
+
+If you encounter issues installing `vitallens-python` dependencies directly, you can use our Docker image, which contains all necessary tools and libraries.
+This docker image is set up to execute the example Python script in `examples/test.py` for you.
+Please note that the example script plots won't work when running them through Docker. 
+
+#### Prerequisites
+
+- [Docker](https://docs.docker.com/engine/install/) installed on your system.
+
+#### Usage
+
+1. Clone the repository
+
+```
+git clone https://github.com/Rouast-Labs/vitallens-python.git && cd vitallens-python
+```
+
+2. Build the Docker image
+
+```
+docker build -t vitallens .
+```
+
+3. Run the Docker container
+
+To run the example script on the sample video:
+
+```
+docker run vitallens \          
+  --api_key "your_api_key_here" \
+  --vitals_path "examples/sample_vitals_2.csv" \
+  --video_path "examples/sample_video_2.mp4" \
+  --method "VITALLENS"
+```
+
+You can also run it on your own video:
+
+```
+docker run vitallens \          
+  --api_key "your_api_key_here" \
+  --video_path "path/to/your/video.mp4" \
+  --method "VITALLENS"
+```
+
 ## 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. 

examples/test.py

@@ -57,6 +57,8 @@ def run(args=None):
   stop = timeit.default_timer()
   time_ms = (stop-start)*1000
   print("Inference time: {:.2f} ms".format(time_ms))
+  # Print the results
+  print(result)
   # Plot the results
   vital_signs = result[0]['vital_signs']
   if "respiratory_waveform" in vital_signs:

pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
     "importlib_resources",
     "numpy",
     "onnxruntime",
-    "prpy[ffmpeg,numpy_min]>=0.2.12",
+    "prpy[ffmpeg,numpy_min]>=0.2.15",
     "python-dotenv",
     "pyyaml",
     "requests",

tests/test_utils.py

@@ -19,13 +19,14 @@
 # SOFTWARE.
 
 import numpy as np
+from prpy.numpy.image import parse_image_inputs, probe_image_inputs
 import pytest
 
 import sys
 sys.path.append('../vitallens-python')
 
 from vitallens.client import Method
-from vitallens.utils import load_config, probe_video_inputs, parse_video_inputs
+from vitallens.utils import load_config
 from vitallens.utils import merge_faces, check_faces, check_faces_in_roi
 
 @pytest.mark.parametrize("method", [m for m in Method])
@@ -37,52 +38,47 @@ 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, i = probe_video_inputs(test_video_path)
+    video_shape, fps, i = probe_image_inputs(test_video_path)
   else:
     test_video_ndarray = request.getfixturevalue('test_video_ndarray')
     test_video_fps = request.getfixturevalue('test_video_fps')
-    video_shape, fps, i = probe_video_inputs(test_video_ndarray, fps=test_video_fps)
+    video_shape, fps, i = probe_image_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):
-    _ = probe_video_inputs("does_not_exist", fps="fps")
+    _ = probe_image_inputs("does_not_exist", fps="fps")
 
 def test_probe_video_inputs_wrong_fps(request):
   with pytest.raises(Exception):
     test_video_path = request.getfixturevalue('test_video_path')
-    _ = probe_video_inputs(test_video_path, fps="fps")
+    _ = probe_image_inputs(test_video_path, fps="fps")
 
 def test_probe_video_inputs_no_fps(request):
   test_video_ndarray = request.getfixturevalue('test_video_ndarray')
   with pytest.raises(Exception):
-    _ = probe_video_inputs(test_video_ndarray)
+    _ = probe_image_inputs(test_video_ndarray)
 
 def test_probe_video_inputs_wrong_dtype(request):
   test_video_ndarray = request.getfixturevalue('test_video_ndarray')
   with pytest.raises(Exception):
-    _ = probe_video_inputs(test_video_ndarray.astype(np.float32), fps=30.)
+    _ = probe_image_inputs(test_video_ndarray.astype(np.float32), fps=30.)
 
 def test_probe_video_inputs_wrong_shape_1(request):
   test_video_ndarray = request.getfixturevalue('test_video_ndarray')
   with pytest.raises(Exception):
-    _ = probe_video_inputs(test_video_ndarray[np.newaxis], fps=30.)
+    _ = probe_image_inputs(test_video_ndarray[np.newaxis], fps=30.)
 
 def test_probe_video_inputs_wrong_shape_2(request):
   test_video_ndarray = request.getfixturevalue('test_video_ndarray')
   with pytest.raises(Exception):
-    _ = probe_video_inputs(test_video_ndarray[...,0:1], fps=30.)
-
-def test_probe_video_inputs_wrong_shape_3(request):
-  test_video_ndarray = request.getfixturevalue('test_video_ndarray')
-  with pytest.raises(Exception):
-    _ = probe_video_inputs(test_video_ndarray[:10], fps=30.)
+    _ = probe_image_inputs(test_video_ndarray[...,0:1], fps=30.)
 
 def test_probe_video_inputs_wrong_type():
   with pytest.raises(Exception):
-    _ = probe_video_inputs(12345, fps=30.)
+    _ = probe_image_inputs(12345, fps=30.)
 
 @pytest.mark.parametrize("file", [True, False])
 @pytest.mark.parametrize("roi", [None, (200, 0, 500, 350)])
@@ -91,13 +87,13 @@ def test_probe_video_inputs_wrong_type():
 def test_parse_video_inputs(request, file, roi, target_size, target_fps):
   if file:
     test_video_path = request.getfixturevalue('test_video_path')
-    parsed, fps_in, video_shape_in, ds_factor, idxs = parse_video_inputs(
-      test_video_path, roi=roi, target_size=target_size, target_fps=target_fps)
+    parsed, fps_in, video_shape_in, ds_factor, idxs = parse_image_inputs(
+      inputs=test_video_path, roi=roi, target_size=target_size, target_fps=target_fps)
   else:
     test_video_ndarray = request.getfixturevalue('test_video_ndarray')
     test_video_fps = request.getfixturevalue('test_video_fps')
-    parsed, fps_in, video_shape_in, ds_factor, idxs = parse_video_inputs(
-      test_video_ndarray, fps=test_video_fps, roi=roi, target_size=target_size,
+    parsed, fps_in, video_shape_in, ds_factor, idxs = parse_image_inputs(
+      inputs=test_video_ndarray, fps=test_video_fps, roi=roi, target_size=target_size,
       target_fps=target_fps)
   assert parsed.shape == (360 if target_fps is None else 360 // 2,
                           200 if target_size is not None else (350 if roi is not None else 480),
@@ -110,11 +106,11 @@ def test_parse_video_inputs(request, file, roi, target_size, target_fps):
 
 def test_parse_video_inputs_no_file():
   with pytest.raises(Exception):
-    _ = parse_video_inputs("does_not_exist")
+    _ = parse_image_inputs("does_not_exist")
 
 def test_parse_video_inputs_wrong_type():
   with pytest.raises(Exception):
-    _ = parse_video_inputs(12345, fps=30.)
+    _ = parse_image_inputs(12345, fps=30.)
 
 def test_merge_faces():
   np.testing.assert_equal(

tests/test_vitallens.py

@@ -21,6 +21,7 @@
 import base64
 import json
 import numpy as np
+from prpy.numpy.image import parse_image_inputs
 import pytest
 import requests
 from unittest.mock import Mock, patch
@@ -30,7 +31,7 @@
 
 from vitallens.constants import API_MAX_FRAMES, API_MIN_FRAMES, API_URL
 from vitallens.methods.vitallens import VitalLensRPPGMethod
-from vitallens.utils import load_config, parse_video_inputs
+from vitallens.utils import load_config
 
 def create_mock_response(
     status_code: int,
@@ -137,8 +138,8 @@ def test_VitalLens_API_valid_response(request, process_signals):
   test_video_ndarray = request.getfixturevalue('test_video_ndarray')
   test_video_fps = request.getfixturevalue('test_video_fps')
   test_video_faces = request.getfixturevalue('test_video_faces')
-  frames, *_ = parse_video_inputs(
-    video=test_video_ndarray, fps=test_video_fps, target_size=config['input_size'],
+  frames, *_ = parse_image_inputs(
+    inputs=test_video_ndarray, fps=test_video_fps, target_size=config['input_size'],
     roi=test_video_faces[0].tolist(), library='prpy', scale_algorithm='bilinear')
   headers = {"x-api-key": api_key}
   payload = {"video": base64.b64encode(frames[:16].tobytes()).decode('utf-8')}
@@ -168,8 +169,8 @@ def test_VitalLens_API_wrong_api_key(request):
   test_video_ndarray = request.getfixturevalue('test_video_ndarray')
   test_video_fps = request.getfixturevalue('test_video_fps')
   test_video_faces = request.getfixturevalue('test_video_faces')
-  frames, *_ = parse_video_inputs(
-    video=test_video_ndarray, fps=test_video_fps, target_size=config['input_size'],
+  frames, *_ = parse_image_inputs(
+    inputs=test_video_ndarray, fps=test_video_fps, target_size=config['input_size'],
     roi=test_video_faces[0].tolist(), library='prpy', scale_algorithm='bilinear')
   headers = {"x-api-key": "WRONG_API_KEY"}
   payload = {"video": base64.b64encode(frames[:16].tobytes()).decode('utf-8')}

vitallens/client.py

@@ -25,6 +25,7 @@
 import numpy as np
 import os
 from prpy.constants import SECONDS_PER_MINUTE
+from prpy.numpy.image import probe_image_inputs
 from typing import Union
 
 from vitallens.constants import DISCLAIMER
@@ -36,7 +37,7 @@
 from vitallens.methods.vitallens import VitalLensRPPGMethod
 from vitallens.signal import windowed_freq, windowed_mean
 from vitallens.ssd import FaceDetector
-from vitallens.utils import load_config, probe_video_inputs, check_faces, convert_ndarray_to_list
+from vitallens.utils import load_config, check_faces, convert_ndarray_to_list
 
 class Method(IntEnum):
   VITALLENS = 1
@@ -118,10 +119,10 @@ def __call__(
         video file. Note that aggressive video encoding destroys the rPPG signal.
       faces: Face boxes in flat point form, containing [x0, y0, x1, y1] coords.
         Ignored unless detect_faces=False. Pass a list or np.ndarray of
-        shape (n_faces, n_frames, 4) for multiple faces detected on multiple frames,
-        shape (n_frames, 4) for single face detected on mulitple frames, or
-        shape (4,) for a single face detected globally, or
-        `None` to assume all frames already cropped to the same single face detection.
+        - shape (n_faces, n_frames, 4) for multiple faces detected on multiple frames,
+        - shape (n_frames, 4) for single face detected on mulitple frames, or
+        - shape (4,) for a single face detected globally, or
+        - `None` to assume all frames already cropped to the same single face detection.
       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.
@@ -172,7 +173,7 @@ def __call__(
         ]
     """
     # Probe inputs
-    inputs_shape, fps, _ = probe_video_inputs(video=video, fps=fps)
+    inputs_shape, fps, _ = probe_image_inputs(video, fps=fps, allow_image=False)
     # 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

vitallens/methods/rppg_method.py

@@ -19,7 +19,6 @@
 # SOFTWARE.
 
 import abc
-import numpy as np
 
 class RPPGMethod(metaclass=abc.ABCMeta):
   """Abstract superclass for rPPG methods"""

vitallens/methods/simple_rppg_method.py

@@ -22,13 +22,13 @@
 import numpy as np
 from prpy.constants import SECONDS_PER_MINUTE
 from prpy.numpy.face import get_roi_from_det
-from prpy.numpy.image import reduce_roi
+from prpy.numpy.image import reduce_roi, parse_image_inputs
 from prpy.numpy.signal import interpolate_cubic_spline, estimate_freq
 from typing import Union, Tuple
 
 from vitallens.constants import CALC_HR_MIN, CALC_HR_MAX
 from vitallens.methods.rppg_method import RPPGMethod
-from vitallens.utils import parse_video_inputs, merge_faces
+from vitallens.utils import merge_faces
 
 class SimpleRPPGMethod(RPPGMethod):
   """A simple rPPG method using a handcrafted algorithm based on RGB signal trace"""
@@ -89,9 +89,11 @@ def __call__(
     u_roi = merge_faces(faces)
     faces = faces - [u_roi[0], u_roi[1], u_roi[0], u_roi[1]]
     # Parse the inputs
-    frames_ds, fps, inputs_shape, ds_factor, _ = parse_video_inputs(
-      video=frames, fps=fps, target_size=None, roi=u_roi,
-      target_fps=override_fps_target if override_fps_target is not None else self.fps_target)   
+    frames_ds, fps, inputs_shape, ds_factor, _ = parse_image_inputs(
+      inputs=frames, fps=fps, roi=u_roi, target_size=None,
+      target_fps=override_fps_target if override_fps_target is not None else self.fps_target,
+      preserve_aspect_ratio=False, library='prpy', scale_algorithm='bilinear', 
+      trim=None, allow_image=False, videodims=True)
     assert inputs_shape[0] == faces.shape[0], "Need same number of frames as face detections"
     faces_ds = faces[0::ds_factor]
     assert frames_ds.shape[0] == faces_ds.shape[0], "Need same number of frames as face detections"

vitallens/methods/vitallens.py

@@ -24,6 +24,7 @@
 import numpy as np
 from prpy.constants import SECONDS_PER_MINUTE
 from prpy.numpy.face import get_roi_from_det
+from prpy.numpy.image import probe_image_inputs, parse_image_inputs
 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
@@ -39,7 +40,7 @@
 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, check_faces_in_roi
+from vitallens.utils import check_faces_in_roi
 
 class VitalLensRPPGMethod(RPPGMethod):
   """RPPG method using the VitalLens API for inference"""
@@ -83,17 +84,18 @@ def __call__(
        - 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)
+       - live: The face live confidence. Shape (n_frames,)
     """
-    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)
+    inputs_shape, fps, video_issues = probe_image_inputs(frames, fps=fps)
     # 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)
     # Check if we can parse the video globally
+    video_fits_in_memory = enough_memory_for_ndarray(
+      shape=(expected_ds_n, self.input_size, self.input_size, 3), dtype=np.uint8,
+      max_fraction_of_available_memory_to_use=0.1)
     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]))
@@ -102,9 +104,10 @@ def __call__(
     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))
+      frames, _, _, _, idxs = parse_image_inputs(
+        inputs=frames, fps=fps, roi=global_roi, target_size=self.input_size, target_fps=fps_target,
+        preserve_aspect_ratio=False, library='prpy', scale_algorithm='bilinear', 
+        trim=None, allow_image=False, videodims=True)
     # 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)
@@ -228,10 +231,11 @@ def process_api_batch(
         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,
+      frames_ds, _, _, ds_factor, idxs = parse_image_inputs(
+        inputs=inputs, fps=fps, roi=roi, target_size=self.input_size, target_fps=fps_target,
+        preserve_aspect_ratio=False, library='prpy', scale_algorithm='bilinear', 
         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))
+        allow_image=False, videodims=True)
     # 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: