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

# # Phase separation tutorial
# In the first section, we load an artificial two-phase PIV image and then use different phase separation methods to discriminate the two phases and save them as separate images. This section aims to introduce different methods that are available.
# 
# In the second section, we demonstrate phase separation on real images followed by actual PIV process as a more realistic example.

# # Section 1 - Introducing different methods

# ## Loading image

# In[1]:


from openpiv import tools, phase_separation
import matplotlib.pyplot as plt
plt.gray()


# In[2]:


two_phase_image = tools.imread('../two_phase_piv/artificial_A.tif')
plt.figure(figsize=(10,10))
plt.imshow(two_phase_image)
plt.show()


# ## Opening method

# In[3]:


big_particles_image, small_particles_image = phase_separation.opening_method( two_phase_image, 11, thresh_factor=1.05 )
fig, ax = plt.subplots(1, 2, figsize=(16,10))
ax[0].imshow( big_particles_image, vmin=0, vmax=255 )
ax[1].imshow( small_particles_image, interpolation='bicubic', vmin=0, vmax=255 )
plt.show()


# ## Median filter method

# In[4]:


big_particles_image, small_particles_image = phase_separation.median_filter_method(two_phase_image, 11)
fig, ax = plt.subplots(1, 2, figsize=(16,10))
ax[0].imshow( big_particles_image)
ax[1].imshow( small_particles_image, vmin=0, vmax=255 )
plt.show()


# ## Khalitov-Longmire method

# ### Using a simple size limit

# In[5]:


# Plot size distribution
plt.hist( phase_separation.get_particles_size_array(two_phase_image), 30)
plt.yscale('log')
plt.title('Particle size distribution')
plt.show()


# In[6]:


# Choose size limit = 100 
big_particles_criteria = {'min_size' : 75}
small_particles_criteria = {'max_size' : 75}
big_particles_image, small_particles_image = \
    phase_separation.khalitov_longmire( two_phase_image, big_particles_criteria, small_particles_criteria ) 
fig, ax = plt.subplots(1, 2, figsize=(16,10))
ax[0].imshow( big_particles_image )
ax[1].imshow( small_particles_image )
plt.show()


# ### Using size and brightness limits

# In[7]:


# First plot size-brightness map
sb_map = phase_separation.get_size_brightness_map( two_phase_image ) # It is possible to sum over maps of multiple images
plt.figure(figsize=(10,8))
plt.imshow( sb_map, interpolation='nearest', aspect='auto', origin='lower', cmap='jet' )
plt.colorbar()
plt.xlabel('Brightness')
plt.ylabel('Size (px)')
plt.title('Signal density')
plt.show()


# In[8]:


# size-brightness rectangle regions 
big_particles_criteria = {
    'min_size' : 100 ,'max_size' : 350 , 'min_brightness' : 100 , 'max_brightness' : 180 }
small_particles_criteria = {
    'min_size' : 25 ,'max_size' : 100 , 'min_brightness' : 30 , 'max_brightness' : 100}
big_particles_image , small_particles_image = \
    phase_separation.khalitov_longmire( two_phase_image, big_particles_criteria, small_particles_criteria ) 
fig, ax = plt.subplots(1, 2, figsize=(16,10))
ax[0].imshow( big_particles_image )
ax[1].imshow( small_particles_image )
plt.show()


# # Section 2 - Practical example

# ## Loading image

# In[9]:


raw_A = tools.imread('../two_phase_piv/real_A.tif')
raw_B = tools.imread('../two_phase_piv/real_B.tif')
fig, ax = plt.subplots(1, 2, figsize=(16,10))
ax[0].imshow( raw_A )
ax[1].imshow( raw_B )
plt.show()


# ## Separating phases

# In[10]:


solid_A, carrier_A = phase_separation.opening_method( raw_A, 7, thresh_factor=1.05 )
solid_B, carrier_B = phase_separation.opening_method( raw_B, 7, thresh_factor=1.05 )
fig, ax = plt.subplots(2, 2, figsize=(16,10))
ax[0,0].imshow( solid_A, vmin=0, vmax=255 )
ax[0,1].imshow( carrier_A, vmin=0, vmax=255 )
ax[1,0].imshow( solid_B, vmin=0, vmax=255 )
ax[1,1].imshow( carrier_A, vmin=0, vmax=255 )
plt.show()


# ## Carrier phase PIV

# In[11]:


from openpiv import tools, validation, filters, scaling, pyprocess
import numpy as np 


# In[12]:


winsize = 48 # pixels
searchsize = 128  # pixels, search in image B
overlap = 24 # pixels
dt = 20e-6 # sec
scaling_factor = 2500 # pixels/meter

u0, v0, sig2noise = pyprocess.extended_search_area_piv( carrier_A.astype(np.int32), carrier_B.astype(np.int32),
                subpixel_method ='parabolic', window_size=winsize, 
                overlap=overlap, dt=dt, search_area_size=searchsize, 
                sig2noise_method='peak2peak' )
x, y = pyprocess.get_coordinates(carrier_A.shape,searchsize,overlap)


# In[13]:


u1, v1, mask = validation.sig2noise_val( u0, v0, sig2noise, w=None, threshold=3.2 )
u2, v2 = filters.replace_outliers( u1, v1, method='localmean', max_iter=5, kernel_size=2 )
x, y, u3, v3 = scaling.uniform( x, y, u2, v2, scaling_factor=scaling_factor )
x, y, u3, v3 = tools.transform_coordinates(x, y, u3, v3)
tools.save( x, y, u3, v3, mask, 'data.txt' )
tools.save( x[::5, ::5], y[::5, ::5], u3[::5, ::5], v3[::5, ::5], mask[::5, ::5], 'preview.txt' )


# In[14]:


fig, ax = plt.subplots(figsize=(16,10))
tools.display_vector_field( 'preview.txt', on_img=True, 
                           image_name='../two_phase_piv/real_A.tif', 
                           scaling_factor=scaling_factor, ax=ax )


# ## Solid phase PTV

# In[15]:


# Note that this is an over-simplified PTV code, just for demonstration.
# Please use OpenPTV or other PTV software for meaningful results.

get_ipython().run_line_magic('matplotlib', 'inline')
get_ipython().run_line_magic('config', 'InlineBackend.close_figures=False')

import numpy as np
from skimage.measure import label, regionprops
from scipy.spatial.distance import cdist
from IPython.display import clear_output

centers_A = np.asarray([ p.centroid for p in regionprops( label( solid_A > 2 * np.mean(solid_A))) ])
centers_B = np.asarray([ p.centroid for p in regionprops( label( solid_B > 2 * np.mean(solid_B))) ])

cross_distance = cdist( centers_B, centers_A )

PTV_X = []
PTV_Y = []
PTV_U = []
PTV_V = []
for i in range(1, len(centers_A)):
    if np.min(cross_distance, 0)[i] < 5:
        j = np.argmin(cross_distance, 0)[i]
        PTV_X.append( centers_A[i,1]/scaling_factor )
        PTV_Y.append( centers_A[i,0]/scaling_factor )
        PTV_U.append( (centers_B[j,1] - centers_A[i,1])/(scaling_factor * dt) )
        PTV_V.append( -(centers_B[j,0] - centers_A[i,0])/(scaling_factor * dt) )

PTV_X = np.asarray(PTV_X)
PTV_Y = np.asarray(PTV_Y)
PTV_U = np.asarray(PTV_U)
PTV_V = np.asarray(PTV_V)

width = solid_A.shape[1] / scaling_factor 
height = solid_A.shape[0] / scaling_factor 
fig2, ax2 = plt.subplots(figsize=(16,10))
ax2.imshow( solid_A, extent=[0, width, 0, height], origin='lower' )
tools.display_vector_field( 'preview.txt', scaling_factor=scaling_factor, ax=ax2 )
ax2.invert_yaxis()
ax2.quiver( PTV_X, PTV_Y, PTV_U, PTV_V, color='yellow', width=0.003)
ax2.invert_yaxis()
clear_output(wait=True)
plt.show()


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