def test_builtin_reader_plugin(viewer_factory):
"""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)
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(tmp.name, plugin='builtins')
assert np.allclose(viewer.layers[0].data, data)
def test_builtin_reader_plugin_stacks(viewer_factory):
"""Test the builtin reader plugin reads multiple files as a stack."""
data = np.random.rand(5, 20, 20)
tmps = []
for plane in data:
tmp = NamedTemporaryFile(suffix='.tif', delete=False)
io.imsave(tmp.name, plane)
tmp.seek(0)
tmps.append(tmp)
_, viewer = viewer_factory()
# open should take both strings and Path object, so we make one of the
# pathnames a Path object
names = [tmp.name for tmp in tmps]
names[0] = Path(names[0])
viewer.open(names, stack=True, plugin='builtins')
assert np.allclose(viewer.layers[0].data, data)
for tmp in tmps:
tmp.close()
os.unlink(tmp.name)
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 animate(
self,
path,
fps=20,
quality=5,
format=None,
canvas_only=True,
scale_factor=None,
):
"""Create a movie based on key-frames
Parameters
-------
path : str
path to use for saving the movie (can also be a path). Extension
should be one of .gif, .mp4, .mov, .avi, .mpg, .mpeg, .mkv, .wmv
If no extension is provided, images are saved as a folder of PNGs
interpolation_steps : int
Number of steps for interpolation.
fps : int
frames per second
quality: float
number from 1 (lowest quality) to 9
only applies to non-gif extensions
format: str
The format to use to write the file. By default imageio selects the appropriate for you based on the filename.
canvas_only : bool
If True include just includes the canvas, otherwise include the full napari viewer.
scale_factor : float
Rescaling factor for the image size. Only used without
viewer (with_viewer = False).
"""
self._validate_animation()
# create a frame generator
frame_gen = self._frame_generator(canvas_only=canvas_only)
# create path object
path_obj = Path(path)
folder_path = path_obj.absolute().parent.joinpath(path_obj.stem)
# if path has no extension, save as fold of PNG
save_as_folder = False
if path_obj.suffix == "":
save_as_folder = True
# try to create an ffmpeg writer. If not installed default to folder creation
if not save_as_folder:
try:
# create imageio writer. Handle separately imageio-ffmpeg extensions and
# gif extension which doesn't accept the quality parameter.
if path_obj.suffix in [
".mov",
".avi",
".mpg",
".mpeg",
".mp4",
".mkv",
".wmv",
]:
writer = imageio.get_writer(
path,
fps=fps,
quality=quality,
format=format,
)
else:
writer = imageio.get_writer(path, fps=fps, format=format)
except ValueError as err:
print(err)
print("Your file will be saved as a series of PNG files")
save_as_folder = True
if save_as_folder:
# if movie is saved as series of PNG, create a folder
if folder_path.is_dir():
for f in folder_path.glob("*.png"):
os.remove(f)
else:
folder_path.mkdir(exist_ok=True)
# save frames
for ind, frame in enumerate(frame_gen):
if scale_factor is not None:
frame = ndi.zoom(frame, (scale_factor, scale_factor, 1))
frame = frame.astype(np.uint8)
if not save_as_folder:
writer.append_data(frame)
else:
fname = folder_path / (path_obj.stem + "_" + str(ind) + ".png")
imsave(fname, frame)
if not save_as_folder:
writer.close()