#!/usr/bin/env python
# coding: utf-8

# # Bead segmentation and measurements
# This notebook shows how to detect hot spots / local maxima / beads in an image and how to measure their FWHM. To make the algorithm work, the beads should be sufficiently sparse.

# In[1]:


import pyclesperanto_prototype as cle

cle.get_device()


# Let's start by making an image showing local maxima.

# In[10]:


import numpy as np
from skimage.io import imshow

random_image = np.random.random([512,512])
binary_image = random_image > 0.9995

# push to GPU
input_image = cle.push(binary_image * random_image)

# blur the image
sigma = 3
starting_point = cle.gaussian_blur(input_image, sigma_x=sigma, sigma_y=sigma)

# show input image
cle.imshow(starting_point)


# ## Local maxima detection

# In[11]:


maxima = cle.detect_maxima_box(starting_point)

cle.imshow(maxima)


# ## Local threshold determination

# In[12]:


# Label maxima
labeled_maxima = cle.label_spots(maxima)

# read out intensities at the maxima
max_intensities = cle.read_intensities_from_map(labeled_maxima, starting_point)
print(max_intensities)

# calculate thresholds
thresholds = cle.multiply_image_and_scalar(max_intensities, scalar=0.5)


# ## Make a local threshold image

# In[13]:


# Extend labeled maxima until they touch
voronoi_label_image = cle.extend_labeling_via_voronoi(labeled_maxima)
cle.imshow(voronoi_label_image, labels=True)


# In[14]:


# Replace labels with thresholds
threshold_image = cle.replace_intensities(voronoi_label_image, thresholds)

cle.imshow(threshold_image)


# In[15]:


# Apply threshold
binary_segmented = cle.greater(starting_point, threshold_image)

cle.imshow(binary_segmented)


# ## Measure bounding boxes

# In[16]:


# Label objects
labels = cle.connected_components_labeling_box(binary_segmented)

cle.imshow(labels, labels=True)


# In[17]:


# Derive statistics
stats = cle.statistics_of_labelled_pixels(label_image=labels)

print('Bounding box widths', stats['bbox_width'])
print('Bounding box heights', stats['bbox_height'])


# The bounding box width and height should be approximately twice as large as the sigma used for bluring the image at the very beginning.

# In[18]:


print("Sigma", sigma)


# In[ ]: