(0) Add camera group data structures

.conda/bld.bat

@@ -9,6 +9,10 @@ set PIP_IGNORE_INSTALLED=False
 @REM https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html)
 pip install --no-cache-dir -r .\requirements.txt
 
+@REM HACK(LM): (untested) Uninstall all opencv packages and install opencv-contrib-python
+for /f "tokens=1" %%a in ('conda list ^| findstr opencv') do pip uninstall %%a -y
+pip install "opencv-contrib-python<4.7.0"
+
 @REM Install sleap itself. This does not install the requirements, but will list which 
 @REM requirements are missing (see "install_requires") when user attempts to install.
 python setup.py install --single-version-externally-managed --record=record.txt

.conda/build.sh

@@ -9,6 +9,9 @@ export PIP_IGNORE_INSTALLED=False
 # https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html)
 pip install --no-cache-dir -r ./requirements.txt
 
+# HACK(LM): (untested) Uninstall all opencv packages and install opencv-contrib-python
+conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")}'
+pip install "opencv-contrib-python<4.7.0"
 
 # Install sleap itself. This does not install the requirements, but will list which 
 # requirements are missing (see "install_requires") when user attempts to install.

.conda_mac/build.sh

@@ -9,4 +9,8 @@ export PIP_IGNORE_INSTALLED=False
 
 pip install --no-cache-dir -r requirements.txt
 
+# HACK(LM): (untested) Uninstall all opencv packages and install opencv-contrib-python
+conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")}'
+pip install "opencv-contrib-python<4.7.0"
+
 python setup.py install --single-version-externally-managed --record=record.txt

.github/workflows/ci.yml

@@ -91,6 +91,14 @@ jobs:
             bash
             powershell
           post-cleanup: all
+
+      # HACK(LM): Install correct version of opencv
+      - name: Reinstall opencv
+        shell: bash -l {0}
+        run: |
+          pip freeze | grep opencv | awk '{system("pip uninstall " $1 " -y")}'
+          pip install "opencv-contrib-python<4.7.0"
+
 
       # Print environment info
       - name: Print environment info
@@ -101,7 +109,7 @@ jobs:
           micromamba list
           pip freeze
 
-      # Test environment
+      # Test the code and the environment
       - name: Test with pytest
         shell: bash -l {0}
         run: |

dev_requirements.txt

@@ -3,7 +3,7 @@
 pytest
 pytest-qt>=4.0.0
 pytest-cov<=3.0.0
-pytest-xvfb
+pytest-xvfb  # For running tests without UI
 ipython
 sphinx
 # furo

docs/installation.md

@@ -192,6 +192,12 @@ mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.3
    mamba env create -f environment_mac.yml -n sleap
    ```
 
+   Followed by a terrible hack that should never reach the real docs:
+
+   ```bash
+   conda activate sleap && conda list | grep opencv | awk '{system("conda uninstall " $1 " -y")}' && pip install "opencv-contrib-python<4.7.0"
+   ```
+
    This is the **recommended method for development**.
 
 ```{note}

environment.yml

@@ -12,12 +12,12 @@ dependencies:
     # Packages SLEAP uses directly
     - conda-forge::attrs >=21.2.0  #,<=21.4.0
     - conda-forge::cattrs ==1.1.1
-    - conda-forge::imgaug ==0.4.0
+    - conda-forge::imgaug ==0.4.0  # Uses opencv-python, but sleap-anipose needs contrib
     - conda-forge::jsmin
     - conda-forge::jsonpickle ==1.2
     - conda-forge::networkx
     - anaconda::numpy >=1.19.5,<1.23.0
-    - conda-forge::opencv
+    # - conda-forge::opencv  # Uses opencv-python, but sleap-anipose needs contrib
     - conda-forge::pandas
     - conda-forge::pip
     - conda-forge::pillow #>=8.3.1,<=8.4.0
@@ -46,4 +46,6 @@ dependencies:
 
     - pip:  
         - "--editable=.[conda_dev]"
-
+
+# HACK(LM): Uninstall all opencv packages and install opencv-contrib-python
+# conda activate sleap && conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")}' && pip install "opencv-contrib-python<4.7.0"

environment_no_cuda.yml

@@ -41,3 +41,7 @@ dependencies:
 
     - pip:  
         - "--editable=.[conda_dev]"
+
+# HACK(LM): Uninstall all opencv packages and install opencv-contrib-python
+# conda activate sleap && conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")} && pip install "opencv-contrib-python<4.7.0"
+

requirements.txt

@@ -6,9 +6,23 @@ ndx-pose
 nixio>=1.5.3  # Constrain put on by @jgrewe from G-Node
 qimage2ndarray  # ==1.9.0
 segmentation-models
+sleap-anipose
 tensorflow-macos==2.9.2; sys_platform == 'darwin' and platform_machine == 'arm64'
 tensorflow-metal==0.5.0; sys_platform == 'darwin' and platform_machine == 'arm64'
 
 # Conda installing results in https://github.com/h5py/h5py/issues/2037
 h5py<3.2; sys_platform == 'win32'  # Newer versions result in error above, linking issue in Linux
 pynwb>=2.3.3  # 2.0.0 required by ndx-pose, 2.3.3 fixes importlib-metadata incompatibility
+
+# HACK(LM): Uninstall all opencv packages and install opencv-contrib-python
+# Run after installing conda environment
+#
+# conda activate sleap
+#
+# if on Windows, then
+#   for /f "tokens=1" %a in ('conda list ^| findstr opencv') do pip uninstall %a -y
+# otherwise, run
+#   conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")}'
+#
+# everybody, run
+#   pip install "opencv-contrib-python<4.7.0"

sleap/io/cameras.py

@@ -0,0 +1,116 @@
+"""Module for storing information for camera groups."""
+
+from typing import List, Optional, Union, Iterator
+
+from attrs import define, field
+from aniposelib.cameras import Camera, FisheyeCamera, CameraGroup
+import numpy as np
+
+
+@define
+class Camcorder:
+    """Wrapper for `Camera` and `FishEyeCamera` classes.
+
+    Attributes:
+        camera: `Camera` or `FishEyeCamera` object.
+    """
+
+    camera: Optional[Union[Camera, FisheyeCamera]] = field(default=None)
+
+    def __eq__(self, other):
+        if not isinstance(other, Camcorder):
+            return NotImplemented
+
+        for attr in vars(self):
+            other_attr = getattr(other, attr)
+            if isinstance(other_attr, np.ndarray):
+                if not np.array_equal(getattr(self, attr), other_attr):
+                    return False
+            elif getattr(self, attr) != other_attr:
+                return False
+
+        return True
+
+    def __getattr__(self, attr):
+        """Used to grab methods from `Camera` or `FishEyeCamera` objects."""
+        if self.camera is None:
+            raise AttributeError(
+                f"No camera has been specified. "
+                f"This is likely because the `Camcorder.from_dict` method was not used to initialize this object. "
+                f"Please use `Camcorder.from_dict` to recreate the object."
+            )
+        return getattr(self.camera, attr)
+
+    def __repr__(self):
+        return f"{self.__class__.__name__}(name={self.name}, size={self.size})"
+
+    @classmethod
+    def from_dict(cls, d) -> "Camcorder":
+        """Creates a `Camcorder` object from a dictionary.
+
+        Args:
+            d: Dictionary with keys for matrix, dist, size, rvec, tvec, and name.
+
+        Returns:
+            `Camcorder` object.
+        """
+        if "fisheye" in d and d["fisheye"]:
+            cam = FisheyeCamera.from_dict(d)
+        else:
+            cam = Camera.from_dict(d)
+        return Camcorder(cam)
+
+
+@define
+class CameraCluster(CameraGroup):
+    """Class for storing information for camera groups.
+
+    Attributes:
+        cameras: List of `Camcorder`s.
+        metadata: Set of metadata.
+    """
+
+    cameras: List[Camcorder] = field(factory=list)
+    metadata: set = field(factory=set)
+
+    def __attrs_post_init__(self):
+        super().__init__(cameras=self.cameras, metadata=self.metadata)
+
+    def __len__(self):
+        return len(self.cameras)
+
+    def __getitem__(self, idx):
+        return self.cameras[idx]
+
+    def __iter__(self) -> Iterator[List[Camcorder]]:
+        return iter(self.cameras)
+
+    def __contains__(self, item):
+        return item in self.cameras
+
+    def __repr__(self):
+        message = f"{self.__class__.__name__}(len={len(self)}: "
+        for cam in self:
+            message += f"{cam.name}, "
+        return f"{message[:-2]})"
+
+    @classmethod
+    def load(cls, filename) -> "CameraCluster":
+        """Loads cameras as `Camcorder`s from a calibration.toml file.
+
+        Args:
+            filename: Path to calibration.toml file.
+
+        Returns:
+            `CameraCluster` object.
+        """
+
+        try:
+            cam_group: CameraGroup = super().load(filename)
+        except FileNotFoundError as e:
+            raise FileNotFoundError(
+                f"Could not find calibration file at {filename}."
+            ) from e
+
+        cameras = [Camcorder(cam) for cam in cam_group.cameras]
+        return cls(cameras=cameras, metadata=cam_group.metadata)

sleap/io/video.py

@@ -12,7 +12,7 @@
 import logging
 import multiprocessing
 
-from typing import Iterable, List, Optional, Tuple, Union, Text
+from typing import Iterable, List, Optional, Tuple, Union
 
 from sleap.util import json_loads, json_dumps
 
@@ -999,8 +999,7 @@ def get_frame(self, idx: int, grayscale: bool = None) -> np.ndarray:
 
 @attr.s(auto_attribs=True, eq=False, order=False)
 class Video:
-    """
-    The top-level interface to any Video data used by SLEAP.
+    """The top-level interface to any Video data used by SLEAP.
 
     This class provides a common interface for various supported video data
     backends. It provides the bare minimum of properties and methods that

tests/conftest.py

@@ -11,3 +11,4 @@
 from tests.fixtures.datasets import *
 from tests.fixtures.videos import *
 from tests.fixtures.models import *
+from tests.fixtures.cameras import *

tests/data/cameras/minimal_session/calibration.toml

@@ -0,0 +1,33 @@
+[cam_0]
+name = "back"
+size = [ 1280, 1024,]
+matrix = [ [ 769.8864926727645, 0.0, 639.5,], [ 0.0, 769.8864926727645, 511.5,], [ 0.0, 0.0, 1.0,],]
+distortions = [ -0.2853406116327607, 0.0, 0.0, 0.0, 0.0,]
+rotation = [ -0.01620434170631696, 0.00243953661952865, -0.0008482754607133058,]
+translation = [ 0.11101046010648573, -5.942766688873288, -122.27936818948484,]
+
+[cam_1]
+name = "mid"
+size = [ 1280, 1024,]
+matrix = [ [ 759.1049091821777, 0.0, 639.5,], [ 0.0, 759.1049091821777, 511.5,], [ 0.0, 0.0, 1.0,],]
+distortions = [ -0.3019598217075406, 0.0, 0.0, 0.0, 0.0,]
+rotation = [ -0.5899610967415617, -1.4541149329590473, -2.6096557771132054,]
+translation = [ -117.01279148208383, -335.68277970969496, 87.84524145188074,]
+
+[cam_2]
+name = "side"
+size = [ 1280, 1024,]
+matrix = [ [ 964.7203950924776, 0.0, 639.5,], [ 0.0, 964.7203950924776, 511.5,], [ 0.0, 0.0, 1.0,],]
+distortions = [ -0.2939343017698909, 0.0, 0.0, 0.0, 0.0,]
+rotation = [ 0.5133644577490065, 0.4933577839393885, 2.712950645410121,]
+translation = [ -137.65379909555472, -91.75965072441964, -19.01274966036669,]
+
+[cam_3]
+name = "top"
+size = [ 1280, 1024,]
+matrix = [ [ 964.7203950924776, 0.0, 639.5,], [ 0.0, 964.7203950924776, 511.5,], [ 0.0, 0.0, 1.0,],]
+distortions = [ -0.2939343017698909, 0.0, 0.0, 0.0, 0.0,]
+rotation = [ 0.5133644577490065, 0.4933577839393885, 2.712950645410121,]
+translation = [ -137.65379909555472, -91.75965072441964, -19.01274966036669,]
+
+[metadata]

tests/fixtures/cameras.py

@@ -0,0 +1,8 @@
+"""Camera fixtures for pytest."""
+
+import pytest
+
+
+@pytest.fixture
+def min_session_calibration_toml_path():
+    return "tests/data/cameras/minimal_session/calibration.toml"

tests/gui/test_app.py

@@ -1,9 +1,18 @@
+import os
+
 import pytest
+from qtpy.QtCore import QLibraryInfo
 from qtpy.QtWidgets import QApplication
 
 from sleap.gui.app import MainWindow
 from sleap.gui.commands import *
 
+# TODO(LM): Remove when sleap-anipose, aniposelib, and imgaug use headless opencv
+# https://github.com/pytest-dev/pytest-qt/issues/396#issuecomment-1060193720
+os.environ["QT_QPA_PLATFORM_PLUGIN_PATH"] = QLibraryInfo.location(
+    QLibraryInfo.PluginsPath
+)
+
 
 def test_app_workflow(
     qtbot, centered_pair_vid, small_robot_mp4_vid, min_tracks_2node_labels: Labels

tests/io/test_cameras.py

@@ -0,0 +1,49 @@
+"""Module to test functions in `sleap.io.cameras`."""
+
+import numpy as np
+import pytest
+from sleap.io.cameras import Camcorder, CameraCluster
+
+
+def test_camcorder(min_session_calibration_toml_path):
+    """Test `Camcorder` data structure."""
+    calibration = min_session_calibration_toml_path
+    cameras = CameraCluster.load(calibration)
+    cam: Camcorder = cameras[0]
+
+    # Test from_dict
+    cam_dict = cam.get_dict()
+    cam2 = Camcorder.from_dict(cam_dict)
+
+    # Test __repr__
+    assert f"{cam.__class__.__name__}(" in repr(cam)
+
+    # Check that attributes are the same
+    assert np.array_equal(cam.matrix, cam2.matrix)
+    assert np.array_equal(cam.dist, cam2.dist)
+    assert np.array_equal(cam.size, cam2.size)
+    assert np.array_equal(cam.rvec, cam2.rvec)
+    assert np.array_equal(cam.tvec, cam2.tvec)
+    assert cam.name == cam2.name
+    assert cam.extra_dist == cam2.extra_dist
+
+    # Test __eq__
+    assert cam == cam2
+
+
+def test_camera_cluster(min_session_calibration_toml_path):
+    """Test `CameraCluster` data structure."""
+    calibration = min_session_calibration_toml_path
+    cameras = CameraCluster.load(calibration)
+
+    # Test __len__
+    assert len(cameras) == len(cameras.cameras)
+    assert len(cameras) == 4
+
+    # Test __getitem__, __iter__, and __contains__
+    for idx, cam in enumerate(cameras):
+        assert cam == cameras[idx]
+        assert cam in cameras
+
+    # Test __repr__
+    assert f"{cameras.__class__.__name__}(" in repr(cameras)