Fix tests

optimap/image/_core.py

@@ -68,10 +68,11 @@ def load_image(filename, as_gray=False, **kwargs):
     _print(f'loading image from {fn.absolute()} ... ')
 
     if fn.suffix == '.npy':
-        image = np.load(filename, **kwargs)
+        image = np.load(fn, **kwargs)
     else:
         # image = skimage.io.imread(filename, as_gray=as_gray, **kwargs)
-        image = cv2.imread(filename, cv2.IMREAD_ANYDEPTH | cv2.IMREAD_UNCHANGED)
+        image = cv2.imread(str(fn),
+                           cv2.IMREAD_ANYDEPTH | cv2.IMREAD_UNCHANGED)
         if as_gray and image.ndim == 3:
             if image.shape[2] == 3:
                 image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
@@ -131,7 +132,7 @@ def save_image(image, filename, **kwargs):
     _print(f"saving image to {Path(filename).absolute()}")
     fn = Path(filename)
     if fn.suffix == '.npy':
-        np.save(filename, image, **kwargs)
+        np.save(fn, image, **kwargs)
     else:
         # skimage.io.imsave(filename, image, **kwargs)
-        cv2.imwrite(filename, image, **kwargs)
+        cv2.imwrite(str(fn), image, **kwargs)

optimap/video/_load.py

@@ -41,7 +41,7 @@ def load_tiff(filename, start_frame=0, end_frame=None, step=1, use_mmap=False):
     )
     return video
 
-def load_image_folder(folder_path, prefix="", start_frame=0, end_frame=None, step=1):
+def load_image_folder(path, prefix="", start_frame=0, end_frame=None, step=1):
     """
     Loads a sequences of images from a folder as a video.
 
@@ -53,7 +53,7 @@ def load_image_folder(folder_path, prefix="", start_frame=0, end_frame=None, ste
 
     Parameters
     ----------
-    folder_path : str or pathlib.Path
+    path : str or pathlib.Path
         Path to folder containing .tiff images
     prefix : str, optional
         Prefix of the files to load
@@ -69,8 +69,8 @@ def load_image_folder(folder_path, prefix="", start_frame=0, end_frame=None, ste
     np.ndarray
         3D numpy array containing the loaded images
     """
-    _print(f"loading video from series of .tif/.tiff-images in folder '{folder_path}'")
-    path = Path(folder_path)
+    _print(f"loading video from series of images files in folder '{path}'")
+    path = Path(path)
     if not path.is_dir():
         raise ValueError(f"'{path}' is not a directory")
 

tests/test_image.py

@@ -1,28 +1,28 @@
 import optimap as om
 import numpy as np
-from tempfile import TemporaryDirectory
+from pathlib import Path
 
-def test_image_export():
+def test_image_export(tmpdir):
     img = np.random.rand(100, 100).astype(np.float32)
-    with TemporaryDirectory() as tmpdir:
-        fn = tmpdir + "/test.npy"
-        om.image.save_image(img, fn)
-        img2 = om.image.load_image(fn)
-        assert np.allclose(img, img2)
 
-    # Test if 16-bit PNG and TIFF export works
-    with TemporaryDirectory() as tmpdir:
-        img = (img * 65535).astype(np.uint16)
-        fn = tmpdir + "/test.png"
-        om.image.save_image(img, fn)
-        img2 = om.image.load_image(fn)
-        assert img.dtype == img2.dtype
-        assert np.allclose(img, img2)
+    fn = tmpdir / "test.npy"
+    om.image.save_image(img, Path(fn))
+    img2 = om.image.load_image(Path(fn))
+    assert np.allclose(img, img2)
 
-    with TemporaryDirectory() as tmpdir:
-        img = (img * 65535).astype(np.uint16)
-        fn = tmpdir + "/test.tiff"
-        om.image.save_image(img, fn)
-        img2 = om.image.load_image(fn)
-        assert img.dtype == img2.dtype
-        assert np.allclose(img, img2)
+def test_16bit_export(tmpdir):
+    """Test if 16-bit PNG and TIFF export works."""
+    img = np.random.rand(100, 100).astype(np.float32)
+    img = (img * 65535).astype(np.uint16)
+
+    fn = tmpdir / "test.png"
+    om.image.save_image(img, fn)
+    img2 = om.image.load_image(fn)
+    assert img.dtype == img2.dtype
+    assert np.allclose(img, img2)
+
+    fn = tmpdir / "test.tiff"
+    om.image.save_image(img, fn)
+    img2 = om.image.load_image(fn)
+    assert img.dtype == img2.dtype
+    assert np.allclose(img, img2)

tests/test_video_io.py

@@ -5,102 +5,99 @@
 import optimap as om
 
 
-def test_npy_video():
+def test_npy_video(tmpdir):
     vid = np.random.random((8, 4, 6)).astype(np.float32)
-    with TemporaryDirectory() as tmpdir:
-        filename = tmpdir + "/test.npy"
-        om.save_video(vid, filename)
-        assert Path(filename).exists()
 
-        video = om.load_video(filename)
-        assert video.shape == vid.shape
-        assert video.dtype == vid.dtype
-        assert np.all(video == vid)
+    filename = tmpdir / "test.npy"
+    om.save_video(vid, filename)
+    assert Path(filename).exists()
 
-        video = om.load_video(filename, start_frame=4)
-        assert video.shape == (4, 4, 6)
-        assert np.all(video == vid[4:])
+    video = om.load_video(filename)
+    assert video.shape == vid.shape
+    assert video.dtype == vid.dtype
+    assert np.all(video == vid)
 
-        video = om.load_video(filename, frames=4)
-        assert video.shape == (4, 4, 6)
-        assert np.all(video == vid[:4])
+    video = om.load_video(filename, start_frame=4)
+    assert video.shape == (4, 4, 6)
+    assert np.all(video == vid[4:])
 
-        video = om.load_video(filename, step=2)
-        assert video.shape == (4, 4, 6)
-        assert np.all(video == vid[::2])
+    video = om.load_video(filename, frames=4)
+    assert video.shape == (4, 4, 6)
+    assert np.all(video == vid[:4])
 
-        video = om.load_video(filename, use_mmap=True)
-        assert np.all(video == vid)
-        assert video.flags["WRITEABLE"] == False
+    video = om.load_video(filename, step=2)
+    assert video.shape == (4, 4, 6)
+    assert np.all(video == vid[::2])
 
+    video = om.load_video(filename, use_mmap=True)
+    assert np.all(video == vid)
+    assert video.flags["WRITEABLE"] == False
 
-def test_tiff_folder():
+
+def test_tiff_folder(tmpdir):
     vid = np.random.random((10, 4, 6)).astype(np.float32)
 
-    with TemporaryDirectory() as tmpdir:
-        om.save_image_sequence(vid, directory=tmpdir, suffix=".tiff")
-        assert len(list(Path(tmpdir).glob("*.tiff"))) == 10
+    om.save_image_sequence(vid, directory=tmpdir, suffix=".tiff")
+    assert len(list(Path(tmpdir).glob("*.tiff"))) == 10
 
-        video = om.load_video(tmpdir)
-        assert video.shape == vid.shape
-        assert video.dtype == vid.dtype
-        assert np.all(video == vid)
+    video = om.load_video(tmpdir)
+    assert video.shape == vid.shape
+    assert video.dtype == vid.dtype
+    assert np.all(video == vid)
 
-        video = om.load_video(tmpdir, start_frame=1, frames=3, step=2)
-        assert video.shape == (3, 4, 6)
-        assert np.all(video == vid[1:6:2])
+    video = om.load_video(tmpdir, start_frame=1, frames=3, step=2)
+    assert video.shape == (3, 4, 6)
+    assert np.all(video == vid[1:6:2])
 
 
-def test_png_folder():
+def test_png_folder(tmpdir):
     vid = np.random.random((10, 4, 6)) * 16535
     vid = vid.astype(np.uint16)
 
-    with TemporaryDirectory() as tmpdir:
-        om.save_image_sequence(vid, directory=tmpdir, suffix=".png")
-        assert len(list(Path(tmpdir).glob("*.png"))) == 10
+    om.save_image_sequence(vid, directory=tmpdir, suffix=".png")
+    assert len(list(Path(tmpdir).glob("*.png"))) == 10
 
-        video = om.load_video(tmpdir)
-        assert video.shape == vid.shape
-        assert video.dtype == vid.dtype
-        assert np.all(video == vid)
+    video = om.load_video(tmpdir)
+    assert video.shape == vid.shape
+    assert video.dtype == vid.dtype
+    assert np.all(video == vid)
 
-        video = om.load_video(tmpdir, start_frame=1, frames=3, step=2)
-        assert video.shape == (3, 4, 6)
-        assert np.all(video == vid[1:6:2])
+    video = om.load_video(tmpdir, start_frame=1, frames=3, step=2)
+    assert video.shape == (3, 4, 6)
+    assert np.all(video == vid[1:6:2])
 
 
-def test_tiff_stack():
+def test_tiff_stack(tmpdir):
     vid = np.random.random((10, 4, 6)).astype(np.float32)
-    with TemporaryDirectory() as tmpdir:
-        filename = tmpdir + "/test.tiff"
-        om.save_video(vid, filename)
-        assert Path(filename).exists()
-        assert Path(filename).is_file()
+    filename = tmpdir / "test.tiff"
+    om.save_video(vid, filename)
+    assert Path(filename).exists()
+    assert Path(filename).is_file()
 
-        video = om.load_video(filename)
-        assert video.shape == vid.shape
-        assert video.dtype == vid.dtype
-        assert np.all(video == vid)
+    video = om.load_video(filename)
+    assert video.shape == vid.shape
+    assert video.dtype == vid.dtype
+    assert np.all(video == vid)
 
-        video = om.load_video(filename, start_frame=1, frames=3, step=2, use_mmap=True)
-        assert video.shape == (3, 4, 6)
-        assert np.all(video == vid[1:6:2])
-        assert video.flags["WRITEABLE"] == False
+    video = om.load_video(filename, start_frame=1, frames=3, step=2, use_mmap=True)
+    assert video.shape == (3, 4, 6)
+    assert np.all(video == vid[1:6:2])
+    assert video.flags["WRITEABLE"] == False
 
 
-def test_matlab():
+def test_matlab(tmpdir):
     vid = np.random.random((10, 4, 6)).astype(np.float32)
-    with TemporaryDirectory() as tmpdir:
-        filename = tmpdir + "/test.mat"
-        om.save_video(vid, filename)
-        assert Path(filename).exists()
-        assert Path(filename).is_file()
-
-        video = om.load_video(filename)
-        assert video.shape == vid.shape
-        assert video.dtype == vid.dtype
-        assert np.all(video == vid)
-
-        video = om.load_video(filename, start_frame=1, frames=3, step=2)
-        assert video.shape == (3, 4, 6)
-        assert np.all(video == vid[1:6:2])
+
+    filename = tmpdir / "test.mat"
+    om.save_video(vid, filename)
+    assert Path(filename).exists()
+    assert Path(filename).is_file()
+
+    video = om.load_video(filename)
+    assert video.shape == vid.shape
+    assert video.dtype == vid.dtype
+    assert np.all(video == vid)
+
+    video = om.load_video(filename, start_frame=1, frames=3, step=2)
+    assert video.shape == (3, 4, 6)
+    assert np.all(video == vid[1:6:2])