- remove all readers but bioformats

- open folder with sequence

tests/test_open.py

@@ -1,27 +1,21 @@
 import pickle
-from multiprocessing import active_children
 from pathlib import Path
 
 import pytest
 
-from ndbioimage import Imread, ReaderNotFoundError
+from ndbioimage import Imread
 
 
-@pytest.mark.parametrize('file', (Path(__file__).parent / 'files').iterdir())
+@pytest.mark.parametrize('file',
+                         [file for file in (Path(__file__).parent / 'files').iterdir() if not file.suffix == '.pzl'])
 def test_open(file):
-    try:
-        with Imread(file) as im:
-            mean = im[dict(c=0, z=0, t=0)].mean()
-            b = pickle.dumps(im)
-            jm = pickle.loads(b)
-            assert jm[dict(c=0, z=0, t=0)].mean() == mean
-            v = im.view()
-            assert v[dict(c=0, z=0, t=0)].mean() == mean
-            b = pickle.dumps(v)
-            w = pickle.loads(b)
-            assert w[dict(c=0, z=0, t=0)].mean() == mean
-    except ReaderNotFoundError:
-        assert len(Imread.__subclasses__()), 'No subclasses for Imread found.'
-
-    for child in active_children():
-        child.kill()
+    with Imread(file) as im:
+        mean = im[dict(c=0, z=0, t=0)].mean()
+        b = pickle.dumps(im)
+        jm = pickle.loads(b)
+        assert jm[dict(c=0, z=0, t=0)].mean() == mean
+        v = im.view()
+        assert v[dict(c=0, z=0, t=0)].mean() == mean
+        b = pickle.dumps(v)
+        w = pickle.loads(b)
+        assert w[dict(c=0, z=0, t=0)].mean() == mean

tests/test_slicing.py

@@ -1,20 +1,32 @@
+import tempfile
 from itertools import combinations_with_replacement
 from numbers import Number
+from pathlib import Path
 
 import numpy as np
 import pytest
+from tiffwrite import tiffwrite
 
 from ndbioimage import Imread
 
-r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
-im = Imread(r)
-a = np.array(im)
+
+@pytest.fixture
+def array():
+    return np.random.randint(0, 255, (64, 64, 2, 3, 4), 'uint8')
+
+@pytest.fixture()
+def image(array):
+    with tempfile.TemporaryDirectory() as folder:
+        file = Path(folder) / "test.tif"
+        tiffwrite(file, array, 'yxczt')
+        with Imread(file, axes='yxczt') as im:
+            yield im
 
 
 @pytest.mark.parametrize('s', combinations_with_replacement(
     (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5))
-def test_slicing(s):
-    s_im, s_a = im[s], a[s]
+def test_slicing(s, image, array):
+    s_im, s_a = image[s], array[s]
     if isinstance(s_a, Number):
         assert isinstance(s_im, Number)
         assert s_im == s_a

tests/test_ufuncs.py

@@ -1,19 +1,31 @@
+import tempfile
 from itertools import product
+from pathlib import Path
 
 import numpy as np
 import pytest
+from tiffwrite import tiffwrite
 
 from ndbioimage import Imread
 
-r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
-im = Imread(r)
-a = np.array(im)
+
+@pytest.fixture
+def array():
+    return np.random.randint(0, 255, (64, 64, 2, 3, 4), 'uint16')
+
+@pytest.fixture()
+def image(array):
+    with tempfile.TemporaryDirectory() as folder:
+        file = Path(folder) / "test.tif"
+        tiffwrite(file, array, 'yxczt')
+        with Imread(file, axes='yxczt') as im:
+            yield im
 
 
 @pytest.mark.parametrize('fun_and_axis', product(
     (np.sum, np.nansum, np.min, np.nanmin, np.max, np.nanmax, np.argmin, np.argmax,
      np.mean, np.nanmean, np.var, np.nanvar, np.std, np.nanstd), (None, 0, 1, 2, 3, 4)))
-def test_ufuncs(fun_and_axis):
+def test_ufuncs(fun_and_axis, image, array):
     fun, axis = fun_and_axis
-    assert np.all(np.isclose(fun(im, axis), fun(a, axis))), \
+    assert np.all(np.isclose(fun(image, axis), fun(array, axis))), \
         f'function {fun.__name__} over axis {axis} does not give the correct result'