some working code to generate gds from pickle file

pickle2gds.py

import pickle
import numpy as np
import matplotlib.pyplot as plt
import gdspy
import cv2

index_low = 1.445*1.445
index_hi = 3.48*3.48
thr = 0.5
SizePerPixel = 0.04
offset_x = 0.0
offset_y = -0.04

index_thr = index_low * (1 - thr) + index_hi * thr

a = open("step82.pkl", "rb")
b = pickle.load(a)
epsilon = b["monitor_data"]["epsilon"]
epsilon0 = epsilon[0].real
epsshape = epsilon0.shape
epsilon0 = np.transpose(np.reshape(epsilon0, [epsshape[0], epsshape[1]]))
[rows, cols] = epsilon0.shape
plt.matshow(epsilon0)
plt.show()

left = -SizePerPixel * cols / 2 + offset_x
bottom = -SizePerPixel * rows / 2 + offset_y

for i in range(rows):
	for j in range(cols):
		if epsilon0[i][j] >= index_thr:
			epsilon0[i][j] = index_hi
		else:
			epsilon0[i][j] = index_low
plt.matshow(epsilon0)
plt.show()

rect_list = []
for i in range(rows):
	for j in range(cols):
		if epsilon0[i][j] >= index_thr:
			y1 = bottom + SizePerPixel * i
			x1 = left + SizePerPixel * j
			x2 = x1 + SizePerPixel
			y2 = y1 + SizePerPixel
			r = gdspy.Rectangle((x1, y1), (x2, y2), layer=100)
			rect_list.append(r)

joined = gdspy.boolean(rect_list, None, 'or', precision=0.001, max_points=100000000, layer = 100)

cell = gdspy.Cell('FIRST')
cell.add(joined)

# Save all created cells in file 'first.gds'.
gdspy.write_gds('first.gds')

# Optionally, display all cells using the internal viewer.
gdspy.LayoutViewer()