def test_reader_plugin_can_return_null_layer_sentinel(test_plugin_manager,
add_implementation):
from napari_plugin_engine import napari_hook_implementation
from napari.plugins import hook_specifications
test_plugin_manager.project_name = 'napari'
test_plugin_manager.add_hookspecs(hook_specifications)
with pytest.raises(ValueError) as e:
read_data_with_plugins('')
assert 'No plugin found capable of reading' in str(e)
@napari_hook_implementation(tryfirst=True)
def napari_get_reader(path):
def _reader(path):
return [(None, )]
return _reader
add_implementation(napari_get_reader)
layer_data, _ = read_data_with_plugins('',
plugin_manager=test_plugin_manager)
assert layer_data is not None
assert len(layer_data) == 0
def test_iter_reader_plugins(plugin_manager):
"""Test safe iteration through reader plugins even with errors.
`napari_bad_plugin2` is a plugin that loads fine but throws an error during
file-reading. this tests that we can gracefully handle that.
"""
# the plugin loads fine, so there should be no exceptions yet.
assert 'napari_bad_plugin2' not in plugin_manager._exceptions
# we want 'napari_bad_plugin2' to be the first plugin called. But
# `napari_test_plugin` will be in line first... Until we can
# reorder the call-order of plugins, (#1023), this line serves to prevent
# that good plugin from running.
plugin_manager.set_blocked('napari_test_plugin')
# but when we try to read an image path, it will raise an IOError.
# we want to catch and store that IOError, and then move on to give other
# plugins chance to return layer_data
layer_data = read_data_with_plugins('image.ext', plugin_manager)
# the good plugins (like "napari_test_plugin") should return layer_data
assert layer_data
# but the exception from `bad_plugin2` should now be stored.
assert 'napari_bad_plugin2' in plugin_manager._exceptions
# we can print out a string that should have the explanation of the error.
exception_string = plugin_manager.format_exceptions('napari_bad_plugin2')
assert 'IOError' in exception_string
assert "napari_get_reader" in exception_string
def test_iter_reader_plugins(plugin_manager):
"""Test safe iteration through reader plugins even with errors.
`napari_bad_plugin2` is a plugin that loads fine but throws an error during
file-reading. this tests that we can gracefully handle that.
"""
# the plugin loads fine, so there should be no exceptions yet.
assert 'napari_bad_plugin2' not in PLUGIN_ERRORS
# make sure 'napari_bad_plugin2' gets called first
plugin_manager.hooks.napari_get_reader.bring_to_front(
['napari_bad_plugin2'])
# but when we try to read an image path, it will raise an IOError.
# we want to catch and store that IOError, and then move on to give other
# plugins chance to return layer_data
layer_data = read_data_with_plugins('image.ext', plugin_manager)
# the good plugins (like "napari_test_plugin") should return layer_data
assert layer_data
# but the exception from `bad_plugin2` should now be stored.
assert 'napari_bad_plugin2' in PLUGIN_ERRORS
# we can print out a string that should have the explanation of the error.
exception_string = format_exceptions('napari_bad_plugin2')
assert 'IOError' in exception_string
assert "napari_get_reader" in exception_string
def test_builtin_reader_plugin_url(builtins):
layer_data, _ = io.read_data_with_plugins(
['https://samples.fiji.sc/FakeTracks.tif'])
assert layer_data is not None
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
def test_reader_plugin_can_return_null_layer_sentinel(napari_plugin_manager, ):
from napari_plugin_engine import napari_hook_implementation
with pytest.raises(ValueError) as e:
read_data_with_plugins('/')
assert 'No plugin found capable of reading' in str(e)
class sample_plugin:
@napari_hook_implementation(tryfirst=True)
def napari_get_reader(path):
def _reader(path):
return [(None, )]
return _reader
napari_plugin_manager.register(sample_plugin)
layer_data, _ = read_data_with_plugins('')
assert layer_data is not None
assert len(layer_data) == 0
def test_builtin_reader_plugin(viewer_factory, builtin_plugin_manager):
"""Test the builtin reader plugin reads a temporary file."""
with NamedTemporaryFile(suffix='.tif', delete=False) as tmp:
data = np.random.rand(20, 20)
io.imsave(tmp.name, data)
tmp.seek(0)
layer_data = read_data_with_plugins(tmp.name, builtin_plugin_manager)
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert np.allclose(data, layer_data[0][0])
view, viewer = viewer_factory()
viewer.add_path(tmp.name)
assert np.allclose(viewer.layers[0].data, data)
def test_reader_plugin_can_return_null_layer_sentinel(napari_plugin_manager,
monkeypatch):
from napari_plugin_engine import napari_hook_implementation
class sample_plugin:
@napari_hook_implementation(tryfirst=True)
def napari_get_reader(path):
def _reader(path):
return [(None, )]
return _reader
napari_plugin_manager.register(sample_plugin)
monkeypatch.setattr(io, 'plugin_manager', napari_plugin_manager)
layer_data, _ = io.read_data_with_plugins([''], stack=False)
assert layer_data is not None
assert len(layer_data) == 0
def test_builtin_reader_plugin_npy():
"""Test the builtin reader plugin reads a temporary npy file."""
with NamedTemporaryFile(suffix='.npy', delete=False) as tmp:
data = np.random.rand(20, 20)
np.save(tmp.name, data)
tmp.seek(0)
layer_data, _ = io.read_data_with_plugins(tmp.name, 'builtins')
assert layer_data is not None
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert np.allclose(data, layer_data[0][0])
viewer = ViewerModel()
viewer.open(tmp.name, plugin='builtins')
assert np.allclose(viewer.layers[0].data, data)
def test_builtin_reader_plugin_csv(viewer_factory, tmpdir):
"""Test the builtin reader plugin reads a temporary file."""
tmp = os.path.join(tmpdir, 'test.csv')
column_names = ['index', 'axis-0', 'axis-1']
table = np.random.random((5, 3))
data = table[:, 1:]
# Write csv file
io.write_csv(tmp, table, column_names=column_names)
layer_data = read_data_with_plugins(tmp)
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert layer_data[0][2] == 'points'
assert np.allclose(data, layer_data[0][0])
view, viewer = viewer_factory()
viewer.open(tmp, plugin='builtins')
assert np.allclose(viewer.layers[0].data, data)
def test_builtin_reader_plugin(builtins: DynamicPlugin):
"""Test the builtin reader plugin reads a temporary file."""
with NamedTemporaryFile(suffix='.tif', delete=False) as tmp:
data = np.random.rand(20, 20)
utils.io.imsave(tmp.name, data)
tmp.seek(0)
layer_data, _ = io.read_data_with_plugins([tmp.name],
builtins.name,
stack=False)
assert layer_data is not None
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert np.allclose(data, layer_data[0][0])
viewer = ViewerModel()
viewer.open(tmp.name, plugin=builtins.name)
assert np.allclose(viewer.layers[0].data, data)
def test_builtin_reader_plugin(viewer_factory):
"""Test the builtin reader plugin reads a temporary file."""
from napari.plugins import plugin_manager
plugin_manager.hooks.napari_get_reader.bring_to_front(['builtins'])
with NamedTemporaryFile(suffix='.tif', delete=False) as tmp:
data = np.random.rand(20, 20)
io.imsave(tmp.name, data)
tmp.seek(0)
layer_data = read_data_with_plugins(tmp.name)
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert np.allclose(data, layer_data[0][0])
view, viewer = viewer_factory()
viewer.open_path(tmp.name)
assert np.allclose(viewer.layers[0].data, data)
def test_builtin_reader_plugin_csv(tmpdir, builtins: DynamicPlugin):
"""Test the builtin reader plugin reads a temporary file."""
tmp = os.path.join(tmpdir, 'test.csv')
column_names = ['index', 'axis-0', 'axis-1']
table = np.random.random((5, 3))
data = table[:, 1:]
# Write csv file
utils.io.write_csv(tmp, table, column_names=column_names)
layer_data, _ = io.read_data_with_plugins([tmp],
builtins.name,
stack=False)
assert layer_data is not None
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert layer_data[0][2] == 'points'
assert np.allclose(data, layer_data[0][0])
viewer = ViewerModel()
viewer.open(tmp, plugin=builtins.name)
assert np.allclose(viewer.layers[0].data, data)
def test_nonsense_path_is_ok(plugin_manager):
"""Test that a path with no readers doesn't throw an exception."""
layer_data = read_data_with_plugins('image.NONsense', plugin_manager)
assert not layer_data
