napari_line_profile_layer.py

#%%
import matplotlib.pyplot as plt
from matplotlib.backends.backend_qt5agg import FigureCanvas
from skimage import measure
from skimage import io
import numpy as np
import os
import napari

#%%
# # create image
# x = np.linspace(0, 5, 256)
# y = np.linspace(0, 5, 256)[:, np.newaxis]
# img = np.sin(x) ** 10 + np.cos(10 + y * x) * np.cos(x)
#%%
# add it to the viewer
imgName = os.path.expanduser("~/Dev/images/Bars-G10-P15-stack.tif")
img = io.imread(imgName)
viewer = napari.view_image(img, name="Image", colormap="viridis")
line = np.array([[11, 13], [111, 113]])
line_prof_layer = viewer.add_shapes(
    line, shape_type="line", edge_color="red", name="Line Profile"
)
line_prof_layer.mode = "select"


#%%
def line_profile(image, line_prof_layer):
    slice = viewer.layers["Image"]._data_raw
    if line_prof_layer.data:
        if line_prof_layer.shape_type[-1] == "line":
            linescan = measure.profile_line(
                slice,
                line_prof_layer.data[-1][0],
                line_prof_layer.data[-1][1],
                mode="reflect",
            )
        else:
            print("no line")
    else:
        print("No data")
    return linescan


#%%
# create mpl figure with subplots
plt.rcParams.update({"font.size": 11})
mpl_fig = plt.figure()
ax = mpl_fig.add_subplot(1, 1, 1)
linescan = line_profile(img, line_prof_layer)
(line,) = ax.plot(linescan)
line.figure.canvas.draw()

#%%
# add the figure to the viewer as a FigureCanvas widget
viewer.window.add_dock_widget(FigureCanvas(mpl_fig), area="bottom")

# connect a callback that updates the line plot when
@line_prof_layer.mouse_drag_callbacks.append
def profile_lines_drag(shapes_layer, event):
    linescan = line_profile(img, shapes_layer)
    ax.clear()
    (line,) = ax.plot(linescan)
    line.figure.canvas.draw()
    yield
    while event.type == "mouse_move":
        linescan = line_profile(img, shapes_layer)
        ax.clear()
        (line,) = ax.plot(linescan)
        line.figure.canvas.draw()
        # the yield statement allows the mouse UI to keep working while
        # this loop is executed repeatedly
        yield
        
#%%
# try to connect to slider
@viewer.dims.events.current_step.connect
def profile_lines_slice(event):
    linescan = line_profile(img, line_prof_layer)
    ax.clear()
    (line,) = ax.plot(linescan)
    line.figure.canvas.draw()