def test_complex_workflow(make_napari_viewer):
viewer = make_napari_viewer()
initial = _init_test()
assistant_gui = napari_pyclesperanto_assistant.napari_plugin(viewer)
root = Path(napari_pyclesperanto_assistant.__file__).parent
filename = str(root / 'data' / 'Lund_000500_resampled-cropped.tif')
layer = viewer.open(filename)
assistant_gui._activate(StatefulFunctionFactory(magic_denoise))
assistant_gui._activate(StatefulFunctionFactory(magic_background_removal))
assistant_gui._activate(StatefulFunctionFactory(magic_filter))
assistant_gui._activate(StatefulFunctionFactory(magic_binarize))
assistant_gui._activate(StatefulFunctionFactory(magic_label))
assistant_gui._activate(StatefulFunctionFactory(magic_label_processing))
assistant_gui._activate(StatefulFunctionFactory(magic_map))
assistant_gui._activate(StatefulFunctionFactory(magic_combine))
assistant_gui._activate(StatefulFunctionFactory(magic_transform))
assistant_gui._activate(StatefulFunctionFactory(magic_projection))
#assistant_gui._export_jython_code_to_clipboard()
assistant_gui._export_notebook(filename="test.ipynb")
_finalize_test(initial, viewer)
def main():
import napari
from skimage.io import imread
import pyclesperanto_prototype as cle
from napari_pyclesperanto_assistant._gui._Assistant import Assistant
import sys
if len(sys.argv) > 1:
filename = str(sys.argv[1])
image = imread(filename)
else:
# make some artificial cell image
filename = "undefined.tif"
labels = cle.artificial_tissue_2d(width=512,
height=512,
delta_x=48,
delta_y=32,
random_sigma_x=6,
random_sigma_y=6)
membranes = cle.detect_label_edges(labels)
eroded = cle.maximum_sphere(membranes, radius_x=3, radius_y=3)
blurred = cle.gaussian_blur(eroded, sigma_x=3, sigma_y=3)
image = cle.pull_zyx(blurred)
#image = imread('https://samples.fiji.sc/blobs.png')
#image = imread('C:/structure/data/lund_000500_resampled.tif')
#filename = 'data/Lund_000500_resampled-cropped.tif'
#filename = str(Path(__file__).parent) + '/data/CalibZAPWfixed_000154_max-16.tif'
print("Available GPUs: " + str(cle.available_device_names()))
cle.select_device("rtx")
print("Used GPU: " + str(cle.get_device()))
with napari.gui_qt():
# create a viewer and add some image
viewer = napari.Viewer()
layer = viewer.add_image(image, metadata={'filename': filename})
from napari_pyclesperanto_assistant import napari_plugin
napari_plugin(viewer)
import napari
import napari_pyclesperanto_assistant
from pathlib import Path
<<<<<<< HEAD
root = Path(napari_pyclesperanto_assistant.__file__).parent
img_path = str(root / 'data' / 'Lund_000500_resampled-cropped.tif')
=======
root = Path(napari_pyclesperanto_assistant.__file__).parent
filename = str(root / 'data' / 'Lund_000500_resampled-cropped.tif')
# filename = str(root / 'data' / 'CalibZAPWfixed_000154_max-16.tif')
>>>>>>> 1b6b7d026ee5cd1714ce3e62d8722aff7bff89ba
# create Qt GUI context
with napari.gui_qt():
# start napari
viewer = napari.Viewer()
<<<<<<< HEAD
viewer.open(img_path)
=======
layer = viewer.open(filename)
layer[0].metadata['filename'] = filename
>>>>>>> 1b6b7d026ee5cd1714ce3e62d8722aff7bff89ba
# attach the assistant
assistant_gui = napari_pyclesperanto_assistant.napari_plugin(viewer)