def main():
args = parser().parse_args()
img_paths = get_sorted_file_paths(args.img_paths, file_extension=".tif")
cells, non_cells = get_cell_arrays(args.cells_xml)
with napari.gui_qt():
v = napari.Viewer(title="Cellfinder cell viewer")
images = magic_imread(img_paths, use_dask=True, stack=True)
v.add_image(images)
v.add_points(
non_cells,
size=args.marker_size,
n_dimensional=True,
opacity=args.opacity,
symbol=args.symbol,
face_color="lightskyblue",
name="Non-Cells",
)
v.add_points(
cells,
size=args.marker_size,
n_dimensional=True,
opacity=args.opacity,
symbol=args.symbol,
face_color="lightgoldenrodyellow",
name="Cells",
)
def test_zarr():
image = np.random.random((10, 20, 20))
with TemporaryDirectory(suffix='.zarr') as fout:
z = zarr.open(fout, 'a', shape=image.shape)
z[:] = image
image_in = io.magic_imread([fout])
# Note: due to lazy loading, the next line needs to happen within
# the context manager. Alternatively, we could convert to NumPy here.
np.testing.assert_array_equal(image, image_in)
def test_zarr_nested(tmp_path):
image = np.random.random((10, 20, 20))
image_name = 'my_image'
root_path = tmp_path / 'dataset.zarr'
grp = zarr.open(str(root_path), mode='a')
grp.create_dataset(image_name, data=image)
image_in = io.magic_imread([str(root_path / image_name)])
np.testing.assert_array_equal(image, image_in)
def add_raw_image(viewer, image_path, name):
"""
Add a raw image (as a virtual stack) to the napari viewer
:param viewer: Napari viewer object
:param image_path: Path to the raw data
:param str name: Name to give the data
"""
paths = get_sorted_file_paths(image_path, file_extension=".tif")
images = magic_imread(paths, use_dask=True, stack=True)
viewer.add_image(images, name=name, opacity=0.6, blending="additive")
def test_irregular_images(irregular_images):
image_files = irregular_images
# Ideally, this would work "magically" with dask and irregular images,
# but there is no foolproof way to do this without reading in all the
# files. We need to be able to inspect the file shape without reading
# it in first, then we can automatically turn stacking off when shapes
# are irregular (and create proper dask arrays)
images = io.magic_imread(image_files, use_dask=False, stack=False)
assert isinstance(images, list)
assert len(images) == 2
assert tuple(image.shape for image in images) == ((512, 512), (303, 384))
def load_labels(self,
image_path,
use_dask=True,
stack=True,
name=None,
opacity=1):
labels = self.viewer.add_labels(
magic_imread(image_path, use_dask=use_dask, stack=stack),
name=name,
opacity=opacity,
)
return labels
def load_data(self, name="", visible=True):
try:
img_paths = get_sorted_file_paths(self.directory,
file_extension=".tif")
images = magic_imread(img_paths, use_dask=True, stack=True)
return self.viewer.add_image(images)
# return self.viewer.open(
# str(self.directory), name=name, visible=visible
# )
except ValueError:
print(f"The directory ({self.directory}) cannot be "
f"loaded, please try again.")
return
def load_raw_data_directory(self):
self.status_label.setText("Loading...")
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
directory = QFileDialog.getExistingDirectory(
self,
"Select data directory",
options=options,
)
# deal with existing dialog
if directory is not "":
directory = Path(directory)
img_paths = get_sorted_file_paths(directory,
file_extension=".tif*")
images = magic_imread(img_paths, use_dask=True, stack=True)
self.viewer.add_image(images, name=directory.stem)
self.status_label.setText("Ready")
def test_zarr_multiscale():
multiscale = [
np.random.random((20, 20)),
np.random.random((10, 10)),
np.random.random((5, 5)),
]
with TemporaryDirectory(suffix='.zarr') as fout:
root = zarr.open_group(fout, 'a')
for i in range(len(multiscale)):
shape = 20 // 2**i
z = root.create_dataset(str(i), shape=(shape, ) * 2)
z[:] = multiscale[i]
multiscale_in = io.magic_imread([fout])
assert len(multiscale) == len(multiscale_in)
# Note: due to lazy loading, the next line needs to happen within
# the context manager. Alternatively, we could convert to NumPy here.
for images, images_in in zip(multiscale, multiscale_in):
np.testing.assert_array_equal(images, images_in)
def test_no_files_raises(tmp_path, two_pngs):
with pytest.raises(ValueError) as e:
io.magic_imread(tmp_path)
assert "No files found in" in str(e.value)
def test_multi_png_no_stack(two_pngs):
image_files = two_pngs
images = io.magic_imread(image_files, stack=False)
assert isinstance(images, list)
assert len(images) == 2
assert all(a.shape == (512, 512) for a in images)
def test_multi_png_no_dask(two_pngs):
image_files = two_pngs
images = io.magic_imread(image_files, use_dask=False)
assert isinstance(images, np.ndarray)
assert images.shape == (2, 512, 512)
def test_multi_png_pathlib(two_pngs):
image_files = [Path(png) for png in two_pngs]
images = io.magic_imread(image_files)
assert isinstance(images, da.Array)
assert images.shape == (2, 512, 512)
def test_multi_png_defaults(two_pngs):
image_files = two_pngs
images = io.magic_imread(image_files)
assert isinstance(images, da.Array)
assert images.shape == (2, 512, 512)
def test_single_png_pathlib(single_png):
image_files = Path(single_png[0])
images = io.magic_imread(image_files)
assert isinstance(images, np.ndarray)
assert images.shape == (512, 512)
def test_single_png_defaults(single_png):
image_files = single_png
images = io.magic_imread(image_files)
assert isinstance(images, np.ndarray)
assert images.shape == (512, 512)
def test_tiff(single_tiff):
image_files = single_tiff
images = io.magic_imread(image_files)
assert isinstance(images, np.ndarray)
assert images.shape == (2, 15, 10)
assert images.dtype == np.uint8
def test_single_filename(single_tiff):
image_files = single_tiff[0]
images = io.magic_imread(image_files)
assert images.shape == (2, 15, 10)
def main():
args = parser().parse_args()
args = define_pixel_sizes(args)
if args.output is None:
output = Path(args.cells_xml)
output_directory = output.parent
print(f"No output directory given, so setting output "
f"directory to: {output_directory}")
else:
output_directory = args.output
ensure_directory_exists(output_directory)
output_filename = output_directory / OUTPUT_NAME
img_paths = get_sorted_file_paths(args.signal_image_paths,
file_extension=".tif")
cells, labels = get_cell_labels_arrays(args.cells_xml)
properties = {"cell": labels}
with napari.gui_qt():
viewer = napari.Viewer(title="Cellfinder cell curation")
images = magic_imread(img_paths, use_dask=True, stack=True)
viewer.add_image(images)
face_color_cycle = ["lightskyblue", "lightgoldenrodyellow"]
points_layer = viewer.add_points(
cells,
properties=properties,
symbol=args.symbol,
n_dimensional=True,
size=args.marker_size,
face_color="cell",
face_color_cycle=face_color_cycle,
name="Cell candidates",
)
@viewer.bind_key("t")
def toggle_point_property(viewer):
"""Toggle point type"""
selected_points = viewer.layers[1].selected_data
if selected_points:
selected_properties = viewer.layers[1].properties["cell"][
selected_points]
toggled_properties = np.logical_not(selected_properties)
viewer.layers[1].properties["cell"][
selected_points] = toggled_properties
# Add curated cells to list
CURATED_POINTS.extend(selected_points)
print(f"{len(selected_points)} points "
f"toggled and added to the list ")
# refresh the properties colour
viewer.layers[1].refresh_colors(update_color_mapping=False)
@viewer.bind_key("c")
def confirm_point_property(viewer):
"""Confirm point type"""
selected_points = viewer.layers[1].selected_data
if selected_points:
# Add curated cells to list
CURATED_POINTS.extend(selected_points)
print(f"{len(selected_points)} points "
f"confirmed and added to the list ")
@viewer.bind_key("Control-S")
def save_curation(viewer):
"""Save file"""
if not CURATED_POINTS:
print("No cells have been confirmed or toggled, not saving")
else:
unique_cells = unique_elements_lists(CURATED_POINTS)
points = viewer.layers[1].data[unique_cells]
labels = viewer.layers[1].properties["cell"][unique_cells]
labels = labels.astype("int")
labels = labels + 1
cells_to_save = []
for idx, point in enumerate(points):
cell = Cell([point[2], point[1], point[0]], labels[idx])
cells_to_save.append(cell)
print(f"Saving results to: {output_filename}")
save_cells(cells_to_save, output_filename)
@viewer.bind_key("Alt-E")
def start_cube_extraction(viewer):
"""Extract cubes for training"""
if not output_filename.exists():
print("No curation results have been saved. "
"Please save before extracting cubes")
else:
print(f"Saving cubes to: {output_directory}")
run_extraction(
output_filename,
output_directory,
args.signal_image_paths,
args.background_image_paths,
args.cube_depth,
args.cube_width,
args.cube_height,
args.x_pixel_um,
args.y_pixel_um,
args.z_pixel_um,
args.x_pixel_um_network,
args.y_pixel_um_network,
args.z_pixel_um_network,
args.max_ram,
args.n_free_cpus,
args.save_empty_cubes,
)
print("Saving yaml file to use for training")
save_yaml_file(output_directory)
print("Closing window")
QApplication.closeAllWindows()
print("Finished! You may now annotate more "
"datasets, or go straight to training")
def test_many_tiffs(single_tiff):
image_files = single_tiff * 3
images = io.magic_imread(image_files)
assert isinstance(images, da.Array)
assert images.shape == (3, 2, 15, 10)
assert images.dtype == np.uint8
non_cells = df[df["type"] == Cell.UNKNOWN]
cells = df[df["type"] == Cell.CELL]
cells = cells_df_as_np(cells)
non_cells = cells_df_as_np(non_cells)
return cells, non_cells
# def main():
args = parser().parse_args()
img_paths = get_sorted_file_paths(args.img_paths, file_extension=".tif")
cells, non_cells = get_cell_arrays(args.cells_xml)
with napari.gui_qt():
v = napari.Viewer(title="Cellfinder cell viewer")
images = magic_imread(img_paths, use_dask=True, stack=True)
v.add_image(images)
points_layer_non_cells = v.add_points(
non_cells,
size=args.marker_size,
n_dimensional=True,
opacity=args.opacity,
symbol=args.symbol,
face_color="lightskyblue",
name="Non-Cells",
)
points_layer_cells = v.add_points(
cells,
size=args.marker_size,
n_dimensional=True,