Virtual Dark/Bright Field (VDF/VBF) Imaging

This example demonstrates how to acquire a VDF/VBF image using DE API.

The virtual images are created by summing or subtracting the pixel values of the input image based on the values of the virtual masks. The virtual masks are 8-bit images with values: - 0: Negative Mask, pixel values subtracted - 1: Default value, pixels not accounted for - 2: Positive Mask, pixel values added

Here we will

1. Connect to the DE server

2. Set the hardware ROI

3. Acquire a single diffraction pattern for guiding the virtual imaging

4. Automatically generate the virtual birght field (VBF) and virtual dark field (VDF) images by finding the brightest disk in the diffraction pattern and measuring the extent of the disk in the diffraction pattern.

5. Acquire the VDF/VBF images and plot them.

import numpy as np

from deapi import Client
import time
from scipy.ndimage import gaussian_filter
from skimage.segmentation import flood
from skimage.morphology import dilation, disk
import matplotlib.pyplot as plt

client = Client()
client.usingMmf = False  # True if on same machine as DE Server and a Windows machine
client.connect(port=13241)  # connect to the running DE Server

Get A Single Diffraction Pattern

We will acquire a single diffraction pattern to guide the virtual masks. We can then use the brightest disk in the diffraction pattern to generate the VDF/VBF masks.

client.start_acquisition(1)

# wait for the acquisition to finish
while client.acquiring:
    time.sleep(1)

img = client.get_result("singleframe_integrated")[0]

Define a function to automatically find the bright field in the diffraction pattern

def auto_find_bf(img, threshold=0.5, sigma=10, dilation_rad=30):
    filtered = gaussian_filter(img, sigma=sigma)
    center = np.unravel_index(np.argmax(filtered), shape=filtered.shape)
    val = img[center]
    mask = img > (val * threshold)
    mask = flood(mask, center)  # only the center
    mask = dilation(mask, footprint=disk(dilation_rad))
    return mask


mask = auto_find_bf(img)

Create the Virtual Masks

We will create the VDF and VBF masks by setting the pixel values in the masks.

client.virtual_masks[1].calculation = "Sum"
client.virtual_masks[1].name = "VBF"
client.virtual_masks[1][:] = 1  # Set to 1
client.virtual_masks[1][mask] = 2  # Set mask to 2
client.virtual_masks[1].plot()

client.virtual_masks[2].calculation = "Sum"
client.virtual_masks[2].name = "VDF"
client.virtual_masks[2][:] = 2
client.virtual_masks[2][mask] = 1
client.virtual_masks[2].plot()

• 
• 

/home/runner/work/deapi/deapi/deapi/data_types.py:537: UserWarning: Virtual mask shape is not set to Arbitrary. Setting to Arbitrary.
  warnings.warn(

<Axes: >

Acquire the Virtual Images

We will then acquire the virtual images using the virtual masks and plot the results.

client["Frames Per Second"] = 5000  # 5000 frames per second
client.scan(enable="On", size_x=128, size_y=128)
client.start_acquisition()

while client.acquiring:  # wait for acquisition to finish and then plot the results
    time.sleep(1)

fig, axs = plt.subplots(1, 3)
for a, virt in zip(axs, ["virtual_image0", "virtual_image1", "virtual_image2"]):
    data, _, _, _ = client.get_result(virt)
    a.imshow(data)
    a.set_title(virt)