def process_node(i):
DeltaFrame = 300
winsize = 12 # pixels
searchsize = 12 #pixels
overlap = 6 # piexels
dt = DeltaFrame * 1. / fps # piexels
frame_a = tools.imread(fileNameList[i])
frame_b = tools.imread(fileNameList[i + DeltaFrame])
u0, v0, sig2noise = process.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
x, y = process.get_coordinates(image_size=frame_a.shape,
window_size=winsize,
overlap=overlap)
u1, v1, mask = validation.sig2noise_val(u0, v0, sig2noise, threshold=1.3)
u2, v2 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=5,
kernel_size=5)
u3, v3, mask1 = validation.local_median_val(u2, v2, 3, 3, 1)
u4, v4 = filters.replace_outliers(u3,
v3,
method='localmean',
max_iter=5,
kernel_size=5)
tools.save(x, y, u4, v4, mask1, '../testResult/' + str(i) + '.txt')
def openpiv_default_run(im1, im2):
""" default settings for OpenPIV analysis using
extended_search_area_piv algorithm for two images
Inputs:
im1,im2 : str,str = path of two image
"""
frame_a = tools.imread(im1)
frame_b = tools.imread(im2)
u, v, sig2noise = process.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=32,
overlap=8,
dt=1,
search_area_size=64,
sig2noise_method='peak2peak')
x, y = process.get_coordinates(image_size=frame_a.shape,
window_size=32,
overlap=8)
u, v, mask = validation.sig2noise_val(u, v, sig2noise, threshold=1.3)
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor=1)
tools.save(x, y, u, v, mask, list_of_images[0] + '.txt')
fig, ax = tools.display_vector_field(list_of_images[0] + '.txt',
on_img=True,
image_name=list_of_images[0],
scaling_factor=1,
ax=None)
def PIV(I0, I1, winsize, overlap, dt):
""" Normal PIV """
u0, v0, sig2noise = pyprocess.extended_search_area_piv(
I0.astype(np.int32),
I1.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=winsize,
sig2noise_method='peak2peak',
)
# get x, y
x, y = pyprocess.get_coordinates(image_size=I0.shape,
search_area_size=winsize,
overlap=overlap,
window_size=winsize)
u1, v1, mask_s2n = validation.sig2noise_val(
u0,
v0,
sig2noise,
threshold=1.05,
)
# replace_outliers
u2, v2 = filters.replace_outliers(
u1,
v1,
method='localmean',
max_iter=3,
kernel_size=3,
)
# median filter smoothing
u3 = medfilt2d(u2, 3)
v3 = medfilt2d(v2, 3)
return x, y, u3, v3
def func(args):
"""A function to process each image pair."""
# this line is REQUIRED for multiprocessing to work
# always use it in your custom function
file_a, file_b, counter = args
#####################
# Here goes you code
#####################
# read images into numpy arrays
frame_a = tools.imread(os.path.join(path, file_a))
frame_b = tools.imread(os.path.join(path, file_b))
frame_a = (frame_a * 1024).astype(np.int32)
frame_b = (frame_b * 1024).astype(np.int32)
# process image pair with extended search area piv algorithm.
u, v, sig2noise = pyprocess.extended_search_area_piv( frame_a, frame_b, \
window_size=64, overlap=32, dt=0.02, search_area_size=128, sig2noise_method='peak2peak')
u, v, mask = validation.sig2noise_val(u, v, sig2noise, threshold=1.5)
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
# get window centers coordinates
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
search_area_size=128,
overlap=32)
# save to a file
tools.save(x, y, u, v, mask, 'test2_%03d.txt' % counter)
tools.display_vector_field('test2_%03d.txt' % counter)
def test_replace_outliers():
""" test of replacing outliers """
v = np.ones((9, 9))
v[1:-1, 1:-1] = np.nan
u = v.copy()
uf, vf = filters.replace_outliers(u, v)
assert (np.sum(np.isnan(u)) == 7**2)
assert (np.allclose(np.ones((9, 9)), uf))
def run_piv(
frame_a,
frame_b,
):
winsize = 64 # pixels, interrogation window size in frame A
searchsize = 68 # pixels, search in image B
overlap = 32 # pixels, 50% overlap
dt = 0.0005 # sec, time interval between pulses
u0, v0, sig2noise = pyprocess.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
search_area_size=searchsize,
window_size=winsize,
overlap=overlap)
u1, v1, mask = validation.sig2noise_val(u0, v0, sig2noise, threshold=1.05)
u2, v2 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=10,
kernel_size=3)
x, y, u3, v3 = scaling.uniform(x, y, u2, v2,
scaling_factor=41.22) # 41.22 microns/pixel
mean_u = np.mean(u3)
mean_v = np.mean(v3)
deficit_u = u3 - mean_u
deficit_v = v3 - mean_v
u_prime = np.mean(np.sqrt(0.5 * (deficit_u**2 + deficit_v**2)))
u_avg = np.mean(np.sqrt(0.5 * (mean_u**2 + mean_v**2)))
turbulence_intensity = u_prime / u_avg
#save in the simple ASCII table format
fname = "./Tables/" + exp_string + ".txt"
# tools.save(x, y, u3, v3, mask, fname)
out = np.vstack([m.ravel() for m in [x, y, u3, v3]])
# print(out)
# np.savetxt(fname,out.T)
with open(fname, "ab") as f:
f.write(b"\n")
np.savetxt(f, out.T)
return turbulence_intensity
def two_images(image_1, image_2, search_area_size=64, window_size=32, overlap=16, dt=0.02):
with open("image_1.bmp", "wb") as fh1:
fh1.write(base64.b64decode(image_1))
with open("image_2.bmp", "wb") as fh2:
fh2.write(base64.b64decode(image_2))
frame_a = tools.imread( 'image_1.bmp' )
frame_b = tools.imread( 'image_2.bmp' )
frame_a = (frame_a*1024).astype(np.int32)
frame_b = (frame_b*1024).astype(np.int32)
if not search_area_size:
search_area_size = 64
if not window_size:
window_size = 32
if not overlap:
overlap = 16
if not dt:
dt = 0.02
u, v, sig2noise = process.extended_search_area_piv( frame_a, frame_b, window_size=window_size,
overlap=overlap, dt=dt, search_area_size=search_area_size, sig2noise_method='peak2peak' )
x, y = process.get_coordinates( image_size=frame_a.shape, window_size=window_size, overlap=overlap )
u, v, mask = validation.sig2noise_val( u, v, sig2noise, threshold = 1.3 )
u, v, mask = validation.global_val( u, v, (-1000, 2000), (-1000, 1000) )
u, v = filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2)
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
file_name_text = 'result.txt'
file_name_png = 'result.png'
if os.path.isfile(file_name_text):
os.remove(file_name_text)
if os.path.isfile(file_name_png):
os.remove(file_name_png)
tools.save(x, y, u, v, mask, file_name_text)
a = np.loadtxt(file_name_text)
fig = plt.figure()
invalid = a[:,4].astype('bool')
fig.canvas.set_window_title('Vector field, '+str(np.count_nonzero(invalid))+' wrong vectors')
valid = ~invalid
plt.quiver(a[invalid,0],a[invalid,1],a[invalid,2],a[invalid,3],color='r',scale=100, width=0.0025)
plt.quiver(a[valid,0],a[valid,1],a[valid,2],a[valid,3],color='b',scale=100, width=0.0025)
plt.draw()
plt.savefig(file_name_png, format="png")
with open(file_name_text, "rb") as resultFileText:
file_reader_text = resultFileText.read()
text_encode = base64.encodestring(file_reader_text)
base64_string_text = str(text_encode, 'utf-8')
with open(file_name_png, "rb") as resultFilePng:
file_reader_image = resultFilePng.read()
image_encode = base64.encodestring(file_reader_image)
base64_string_image = str(image_encode, 'utf-8')
return base64_string_text, base64_string_image
def _piv_frame(self, img1, img2, show=False, **kwargs):
"""
calculate velocity using piv method on two frames
"""
from openpiv.process import extended_search_area_piv, get_coordinates
# from openpiv.scaling import uniform
if self._debug:
print('... [PIV] window size: {}'.format(self._windowSize))
print('... [PIV] overlap: {}'.format(self._overlap))
print('... [PIV] search area size: {}'.format(self._searchArea))
print('... [PIV] threshold: {}'.format(self._piv_threshold))
u, v, sig2noise = extended_search_area_piv(
img1,
img2,
window_size=self._windowSize,
overlap=self._overlap,
dt=self._exposuretime,
search_area_size=self._searchArea,
sig2noise_method='peak2peak')
self._pivx, self._pivy = get_coordinates(image_size=img1.shape,
window_size=self._windowSize,
overlap=self._overlap)
#self._pivy = np.flipud(self._pivy)
#self._pivx, self._pivy, u, v = uniform(self._pivx, self._pivy, u, v, scaling_factor=self._mpp)
if show:
from openpiv.validation import sig2noise_val
from openpiv.filters import replace_outliers
u, v, mask = sig2noise_val(u,
v,
sig2noise,
threshold=self._piv_threshold)
u, v = replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
# show quiver plot
plt.figure(figsize=(12, 6))
plt.imshow(img1)
plt.quiver(self._pivx, self._pivy, u, v, color='w', pivot='mid')
plt.savefig(self._fname[:-4] + '_piv.png', dpi=100)
if self._debug:
print(
"... [PIV] mean velocity [um/sec]: ({:4.2f}, {:4.2f})".format(
np.mean(u) * self._mpp,
np.mean(v) * self._mpp))
print("... [PIV] mean velocity [pixel/frame]: ({:4.2f}, {:4.2f})".
format(
np.mean(u) * self._exposuretime,
np.mean(v) * self._exposuretime))
return (u, v, sig2noise)
def test_replace_outliers():
""" test of replacing outliers """
v = np.ones((9,9))
v[1:-1,1:-1] = np.nan
u = v.copy()
uf,vf = filters.replace_outliers(u,v)
assert(np.sum(np.isnan(u))==7**2)
assert(np.allclose(np.ones((9,9)),uf))
def analyzer(frame_a, frame_b, text, plot, num_scene, pathout, scal, zre, xre,
dt):
winsize = 16 # pixels
searchsize = 32 # pixels, search in image b
overlap = 8 # pixels
frame_a = cv2.adaptiveThreshold(frame_a, 255, cv2.ADAPTIVE_THRESH_MEAN_C,
cv2.THRESH_BINARY, 5, 5)
frame_b = cv2.adaptiveThreshold(frame_b, 255, cv2.ADAPTIVE_THRESH_MEAN_C,
cv2.THRESH_BINARY, 5, 5)
#frame_a = cv2.adaptiveThreshold(frame_a,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,cv2.THRESH_BINARY,11,2)
#frame_b = cv2.adaptiveThreshold(frame_b,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,cv2.THRESH_BINARY,11,2)
plt.imshow(np.c_[frame_a, frame_b], cmap='gray')
plt.savefig(pathout + '/filtered' + str(num_scene) + '.png', dpi=800)
u0, v0, sig2noise = process.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
x, y = process.get_coordinates(image_size=frame_a.shape,
window_size=winsize,
overlap=overlap)
u1, v1, mask = validation.sig2noise_val(u0, v0, sig2noise, threshold=1.3)
u2, v2 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=10,
kernel_size=2)
x, y, u3, v3 = scaling.uniform(
x, y, u2, v2, scaling_factor=scal) # scaling_factor (pixel per meter)
u3 = np.flip(u3, axis=0)
v3 = np.flip(v3, axis=0)
xre = np.linspace(0, xre / 100, len(x[0, :]))
zre = np.linspace(0, zre / 100, len(x[:, 0]))
if plot == 1:
piv_plotting(xre, zre, u3, v3, num_scene, pathout)
if text == 0:
tools.save(x, y, u3, v3, mask,
pathout + '/piv' + str(num_scene) + '.txt')
def process(args, bga, bgb, reflection):
file_a, file_b, counter = args
# read images into numpy arrays
frame_a = tools.imread(file_a)
frame_b = tools.imread(file_b)
# removing background and reflections
frame_a = frame_a - bga
frame_b = frame_b - bgb
frame_a[reflection == 255] = 0
frame_b[reflection == 255] = 0
#applying a static mask (taking out the regions where we have walls)
yp = [580, 435, 0, 0, 580, 580, 0, 0, 435, 580]
xp = [570, 570, 680, 780, 780, 0, 0, 105, 230, 230]
pnts = draw.polygon(yp, xp, frame_a.shape)
frame_a[pnts] = 0
frame_b[pnts] = 0
# checking the resulting frame
#fig, ax = plt.subplots(2,2)
#ax[0,0].imshow(frame_a_org, cmap='gray')
#ax[0,1].imshow(frame_a, cmap='gray')
#ax[1,0].imshow(frame_b_org, cmap='gray')
#ax[1,1].imshow(frame_b, cmap='gray')
#plt.tight_layout()
#plt.show()
# main piv processing
u, v, sig2noise = pyprocess.extended_search_area_piv( frame_a, frame_b, \
window_size=48, overlap=16, dt=0.001094, search_area_size=64, sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
window_size=48,
overlap=16)
u, v, mask = validation.local_median_val(u, v, 2000, 2000, size=2)
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
u, *_ = smoothn(u, s=1.0)
v, *_ = smoothn(v, s=1.0)
# saving the results
save_file = tools.create_path(file_a, 'Analysis')
tools.save(x, y, u, v, mask, save_file + '.dat')
def two_images(image_1, image_2):
with open("image_1.bmp", "wb") as fh1:
fh1.write(base64.b64decode(image_1))
with open("image_2.bmp", "wb") as fh2:
fh2.write(base64.b64decode(image_2))
frame_a = tools.imread('image_1.bmp')
frame_b = tools.imread('image_2.bmp')
winsize = 32 # pixels
searchsize = 64 # pixels, search in image B
overlap = 12 # pixels
dt = 0.02 # sec
u, v, sig2noise = pyprocess.piv(frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_size=searchsize,
sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
window_size=searchsize,
overlap=overlap)
u, v, mask = validation.sig2noise_val(u, v, sig2noise, threshold=1.3)
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor=96.52)
file_name = 'result.txt'
if os.path.isfile(file_name):
os.remove(file_name)
tools.save(x, y, u, v, np.zeros_like(u),
file_name) # no masking, all values are valid
with open(file_name, "rb") as resultFile:
file_reader = resultFile.read()
image_encode = base64.encodestring(file_reader)
base64_string = str(image_encode, 'utf-8')
return base64_string
def ProcessPIV(args, bga, bgb, reflection, stg):
# read images into numpy arrays
file_a, file_b, counter = args
frame_a = tools.imread(file_a)
frame_b = tools.imread(file_b)
# removing background and reflections
if bgb is not None:
frame_a = frame_a - bga
frame_b = frame_b - bgb
frame_a[reflection == 255] = 0
frame_b[reflection == 255] = 0
#plt.imshow(frame_a, cmap='gray')
#plt.show()
# main piv processing
u, v, s2n = pyprocess.extended_search_area_piv( frame_a, frame_b, \
window_size=stg['WS'], overlap=stg['OL'], dt=stg['DT'], search_area_size=stg['SA'], sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
window_size=stg['WS'],
overlap=stg['OL'])
if stg['BVR'] == 'on':
u, v, mask = validation.local_median_val(u,
v,
stg['MF'][0],
stg['MF'][1],
size=2)
u, v, mask = validation.global_val(u,
v,
u_thresholds=stg['GF'][0],
v_thresholds=stg['GF'][1])
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
u, *_ = smoothn(u, s=0.5)
v, *_ = smoothn(v, s=0.5)
x, y, u, v = scaling.uniform(x, y, u, v, stg['SC'])
# saving the results
save_file = tools.create_path(file_a, 'Analysis')
tools.save(x, y, u, v, s2n, save_file + '.dat')
def PIV(image_0, image_1, winsize, searchsize, overlap, frame_rate,
scaling_factor):
frame_0 = image_0
# [0:600, :]
frame_1 = image_1
# [0:600, :]
# Processing the images with interrogation area and search area / cross correlation algortihm
u, v, sig2noise = pyprocess.extended_search_area_piv(
frame_0,
frame_1,
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
# Compute the coordinates of the centers of the interrogation windows
x, y = pyprocess.get_coordinates(image_size=frame_0.shape,
window_size=winsize,
overlap=overlap)
# This function actually sets to NaN all those vector for
# which the signal to noise ratio is below 1.3.
u, v, mask = validation.sig2noise_val(u, v, sig2noise, threshold=1.2)
# Function as described above, removing outliers deviating with more
# than twice the standard deviation
u, v, mask = remove_outliers(u, v, mask)
# Replacing the outliers with interpolation
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=50,
kernel_size=3)
# Apply an uniform scaling to the flow field to get dimensional units
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor=scaling_factor)
return x, y, u, v, mask
def repl_outliers(self):
'''Replace outliers.'''
result_fnames = []
for i, f in enumerate(self.p['fnames']):
data = np.loadtxt(f)
u, v = piv_flt.replace_outliers(np.array([data[:, 2]]),
np.array([data[:, 3]]),
method=self.p['repl_method'],
max_iter=self.p['repl_iter'],
kernel_size=self.p['repl_kernel'])
save_fname = create_save_vec_fname(path=f, postfix='_repl')
save(data[:, 0],
data[:, 1],
u,
v,
data[:, 4],
data[:, 5],
save_fname,
delimiter=delimiter)
result_fnames.append(save_fname)
return (result_fnames)
if 'OpenPIV' not in sys.path:
sys.path.append('/Users/alex/Documents/OpenPIV/alexlib/openpiv-python')
from openpiv import tools, validation, process, filters, scaling, pyprocess
import numpy as np
frame_a = tools.imread( 'exp1_001_a.bmp' )
frame_b = tools.imread( 'exp1_001_b.bmp' )
u, v, sig2noise = process.extended_search_area_piv( frame_a.astype(np.int32),
frame_b.astype(np.int32), window_size=24, overlap=12, dt=0.02, search_area_size=64,
sig2noise_method='peak2peak' )
x, y = process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
u, v, mask = validation.sig2noise_val( u, v, sig2noise, threshold = 2.5 )
u, v = filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2)
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
tools.save(x, y, u, v, mask, 'exp1_001.txt' )
tools.display_vector_field('exp1_001.txt', scale=100, width=0.0025)
u, v, s2n= pyprocess.piv(frame_a, frame_b, corr_method='fft', window_size=24, overlap=12,
dt=0.02, sig2noise_method='peak2peak' )
x, y = pyprocess.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
u, v, mask = validation.sig2noise_val( u, v, s2n, threshold = 2.5 )
u, v = filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2.5)
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
tools.save(x, y, u, v, mask, 'exp1_002.txt' )
tools.display_vector_field('exp1_002.txt', scale=100, width=0.0025)
def multipass_img_deform(
frame_a,
frame_b,
current_iteration,
x_old,
y_old,
u_old,
v_old,
settings,
mask_coords=[],
):
# window_size,
# overlap,
# iterations,
# current_iteration,
# x_old,
# y_old,
# u_old,
# v_old,
# correlation_method="circular",
# normalized_correlation=False,
# subpixel_method="gaussian",
# deformation_method="symmetric",
# sig2noise_method="peak2peak",
# sig2noise_threshold=1.0,
# sig2noise_mask=2,
# interpolation_order=1,
"""
Multi pass of the PIV evaluation.
This function does the PIV evaluation of the second and other passes.
It returns the coordinates of the interrogation window centres,
the displacement u, v for each interrogation window as well as
the signal to noise ratio array (which is full of NaNs if opted out)
Parameters
----------
frame_a : 2d np.ndarray
the first image
frame_b : 2d np.ndarray
the second image
window_size : tuple of ints
the size of the interrogation window
overlap : tuple of ints
the overlap of the interrogation window, e.g. window_size/2
x_old : 2d np.ndarray
the x coordinates of the vector field of the previous pass
y_old : 2d np.ndarray
the y coordinates of the vector field of the previous pass
u_old : 2d np.ndarray
the u displacement of the vector field of the previous pass
in case of the image mask - u_old and v_old are MaskedArrays
v_old : 2d np.ndarray
the v displacement of the vector field of the previous pass
subpixel_method: string
the method used for the subpixel interpolation.
one of the following methods to estimate subpixel location of the peak:
'centroid' [replaces default if correlation map is negative],
'gaussian' [default if correlation map is positive],
'parabolic'
interpolation_order : int
the order of the spline interpolation used for the image deformation
mask_coords : list of x,y coordinates (pixels) of the image mask,
default is an empty list
Returns
-------
x : 2d np.array
array containg the x coordinates of the interrogation window centres
y : 2d np.array
array containg the y coordinates of the interrogation window centres
u : 2d np.array
array containing the horizontal displacement for every interrogation
window [pixels]
u : 2d np.array
array containing the vertical displacement for every interrogation
window it returns values in [pixels]
s2n : 2D np.array of signal to noise ratio values
"""
if not isinstance(u_old, np.ma.MaskedArray):
raise ValueError('Expected masked array')
# calculate the y and y coordinates of the interrogation window centres.
# Hence, the
# edges must be extracted to provide the sufficient input. x_old and y_old
# are the coordinates of the old grid. x_int and y_int are the coordinates
# of the new grid
window_size = settings.windowsizes[current_iteration]
overlap = settings.overlap[current_iteration]
x, y = get_coordinates(frame_a.shape, window_size, overlap)
# The interpolation function dont like meshgrids as input.
# plus the coordinate system for y is now from top to bottom
# and RectBivariateSpline wants an increasing set
y_old = y_old[:, 0]
# y_old = y_old[::-1]
x_old = x_old[0, :]
y_int = y[:, 0]
# y_int = y_int[::-1]
x_int = x[0, :]
# interpolating the displacements from the old grid onto the new grid
# y befor x because of numpy works row major
ip = RectBivariateSpline(y_old, x_old, u_old.filled(0.))
u_pre = ip(y_int, x_int)
ip2 = RectBivariateSpline(y_old, x_old, v_old.filled(0.))
v_pre = ip2(y_int, x_int)
# if settings.show_plot:
if settings.show_all_plots:
plt.figure()
plt.quiver(x_old, y_old, u_old, -1 * v_old, color='b')
plt.quiver(x_int, y_int, u_pre, -1 * v_pre, color='r', lw=2)
plt.gca().set_aspect(1.)
plt.gca().invert_yaxis()
plt.title('inside deform, invert')
plt.show()
# @TKauefer added another method to the windowdeformation, 'symmetric'
# splits the onto both frames, takes more effort due to additional
# interpolation however should deliver better results
old_frame_a = frame_a.copy()
old_frame_b = frame_b.copy()
# Image deformation has to occur in image coordinates
# therefore we need to convert the results of the
# previous pass which are stored in the physical units
# and so y from the get_coordinates
if settings.deformation_method == "symmetric":
# this one is doing the image deformation (see above)
x_new, y_new, ut, vt = create_deformation_field(
frame_a, x, y, u_pre, v_pre)
frame_a = scn.map_coordinates(frame_a,
((y_new - vt / 2, x_new - ut / 2)),
order=settings.interpolation_order,
mode='nearest')
frame_b = scn.map_coordinates(frame_b,
((y_new + vt / 2, x_new + ut / 2)),
order=settings.interpolation_order,
mode='nearest')
elif settings.deformation_method == "second image":
frame_b = deform_windows(
frame_b,
x,
y,
u_pre,
-v_pre,
interpolation_order=settings.interpolation_order)
else:
raise Exception("Deformation method is not valid.")
# if settings.show_plot:
if settings.show_all_plots:
if settings.deformation_method == 'symmetric':
plt.figure()
plt.imshow(frame_a - old_frame_a)
plt.show()
plt.figure()
plt.imshow(frame_b - old_frame_b)
plt.show()
# if do_sig2noise is True
# sig2noise_method = sig2noise_method
# else:
# sig2noise_method = None
# so we use here default circular not normalized correlation:
# if we did not want to validate every step, remove the method
if settings.sig2noise_validate is False:
settings.sig2noise_method = None
u, v, s2n = extended_search_area_piv(
frame_a,
frame_b,
window_size=window_size,
overlap=overlap,
width=settings.sig2noise_mask,
subpixel_method=settings.subpixel_method,
sig2noise_method=settings.sig2noise_method,
correlation_method=settings.correlation_method,
normalized_correlation=settings.normalized_correlation,
)
shapes = np.array(get_field_shape(frame_a.shape, window_size, overlap))
u = u.reshape(shapes)
v = v.reshape(shapes)
s2n = s2n.reshape(shapes)
u += u_pre
v += v_pre
# reapply the image mask to the new grid
if settings.image_mask:
grid_mask = preprocess.prepare_mask_on_grid(x, y, mask_coords)
u = np.ma.masked_array(u, mask=grid_mask)
v = np.ma.masked_array(v, mask=grid_mask)
else:
u = np.ma.masked_array(u, np.ma.nomask)
v = np.ma.masked_array(v, np.ma.nomask)
# validate in the multi-pass by default
u, v, mask = validation.typical_validation(u, v, s2n, settings)
if np.all(mask):
raise ValueError("Something happened in the validation")
if not isinstance(u, np.ma.MaskedArray):
raise ValueError('not a masked array anymore')
if settings.show_all_plots:
plt.figure()
nans = np.nonzero(mask)
plt.quiver(x[~nans], y[~nans], u[~nans], -v[~nans], color='b')
plt.quiver(x[nans], y[nans], u[nans], -v[nans], color='r')
plt.gca().invert_yaxis()
plt.gca().set_aspect(1.)
plt.title('After sig2noise, inverted')
plt.show()
# we have to replace outliers
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size,
)
# reapply the image mask to the new grid
if settings.image_mask:
grid_mask = preprocess.prepare_mask_on_grid(x, y, mask_coords)
u = np.ma.masked_array(u, mask=grid_mask)
v = np.ma.masked_array(v, mask=grid_mask)
else:
u = np.ma.masked_array(u, np.ma.nomask)
v = np.ma.masked_array(v, np.ma.nomask)
if settings.show_all_plots:
plt.figure()
plt.quiver(x, y, u, -v, color='r')
plt.quiver(x, y, u_pre, -1 * v_pre, color='b')
plt.gca().invert_yaxis()
plt.gca().set_aspect(1.)
plt.title(' after replaced outliers, red, invert')
plt.show()
return x, y, u, v, s2n, mask
def func(args):
"""A function to process each image pair."""
# this line is REQUIRED for multiprocessing to work
# always use it in your custom function
file_a, file_b, counter = args
# counter2=str(counter2)
#####################
# Here goes you code
#####################
" read images into numpy arrays"
frame_a = imread(os.path.join(settings.filepath_images, file_a))
frame_b = imread(os.path.join(settings.filepath_images, file_b))
# Miguel: I just had a quick look, and I do not understand the reason
# for this step.
# I propose to remove it.
# frame_a = (frame_a*1024).astype(np.int32)
# frame_b = (frame_b*1024).astype(np.int32)
" crop to ROI"
if settings.ROI == "full":
frame_a = frame_a
frame_b = frame_b
else:
frame_a = frame_a[settings.ROI[0]:settings.ROI[1],
settings.ROI[2]:settings.ROI[3]]
frame_b = frame_b[settings.ROI[0]:settings.ROI[1],
settings.ROI[2]:settings.ROI[3]]
if settings.invert is True:
frame_a = invert(frame_a)
frame_b = invert(frame_b)
if settings.show_all_plots:
fig, ax = plt.subplots(1, 1)
ax.imshow(frame_a, cmap=plt.get_cmap('Reds'))
ax.imshow(frame_b, cmap=plt.get_cmap('Blues'), alpha=.5)
plt.show()
if settings.dynamic_masking_method in ("edge", "intensity"):
frame_a, mask_a = preprocess.dynamic_masking(
frame_a,
method=settings.dynamic_masking_method,
filter_size=settings.dynamic_masking_filter_size,
threshold=settings.dynamic_masking_threshold,
)
frame_b, mask_b = preprocess.dynamic_masking(
frame_b,
method=settings.dynamic_masking_method,
filter_size=settings.dynamic_masking_filter_size,
threshold=settings.dynamic_masking_threshold,
)
# "first pass"
x, y, u, v, s2n = first_pass(frame_a, frame_b, settings)
if settings.show_all_plots:
plt.figure()
plt.quiver(x, y, u, -v, color='b')
# plt.gca().invert_yaxis()
# plt.gca().set_aspect(1.)
# plt.title('after first pass, invert')
# plt.show()
# " Image masking "
if settings.image_mask:
image_mask = np.logical_and(mask_a, mask_b)
mask_coords = preprocess.mask_coordinates(image_mask)
# mark those points on the grid of PIV inside the mask
grid_mask = preprocess.prepare_mask_on_grid(x, y, mask_coords)
# mask the velocity
u = np.ma.masked_array(u, mask=grid_mask)
v = np.ma.masked_array(v, mask=grid_mask)
else:
mask_coords = []
u = np.ma.masked_array(u, mask=np.ma.nomask)
v = np.ma.masked_array(v, mask=np.ma.nomask)
if settings.validation_first_pass:
u, v, mask = validation.typical_validation(u, v, s2n, settings)
if settings.show_all_plots:
# plt.figure()
plt.quiver(x, y, u, -v, color='r')
plt.gca().invert_yaxis()
plt.gca().set_aspect(1.)
plt.title('after first pass validation new, inverted')
plt.show()
# "filter to replace the values that where marked by the validation"
if settings.num_iterations == 1 and settings.replace_vectors:
# for multi-pass we cannot have holes in the data
# after the first pass
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size,
)
# don't even check if it's true or false
elif settings.num_iterations > 1:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size,
)
# "adding masks to add the effect of all the validations"
if settings.smoothn:
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
if settings.image_mask:
grid_mask = preprocess.prepare_mask_on_grid(x, y, mask_coords)
u = np.ma.masked_array(u, mask=grid_mask)
v = np.ma.masked_array(v, mask=grid_mask)
else:
u = np.ma.masked_array(u, np.ma.nomask)
v = np.ma.masked_array(v, np.ma.nomask)
if settings.show_all_plots:
plt.figure()
plt.quiver(x, y, u, -v)
plt.gca().invert_yaxis()
plt.gca().set_aspect(1.)
plt.title('before multi pass, inverted')
plt.show()
if not isinstance(u, np.ma.MaskedArray):
raise ValueError("Expected masked array")
""" Multi pass """
for i in range(1, settings.num_iterations):
if not isinstance(u, np.ma.MaskedArray):
raise ValueError("Expected masked array")
x, y, u, v, s2n, mask = multipass_img_deform(
frame_a,
frame_b,
i,
x,
y,
u,
v,
settings,
mask_coords=mask_coords)
# If the smoothing is active, we do it at each pass
# but not the last one
if settings.smoothn is True and i < settings.num_iterations - 1:
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
if not isinstance(u, np.ma.MaskedArray):
raise ValueError('not a masked array anymore')
if hasattr(settings, 'image_mask') and settings.image_mask:
grid_mask = preprocess.prepare_mask_on_grid(x, y, mask_coords)
u = np.ma.masked_array(u, mask=grid_mask)
v = np.ma.masked_array(v, mask=grid_mask)
else:
u = np.ma.masked_array(u, np.ma.nomask)
v = np.ma.masked_array(v, np.ma.nomask)
if settings.show_all_plots:
plt.figure()
plt.quiver(x, y, u, -1 * v, color='r')
plt.gca().set_aspect(1.)
plt.gca().invert_yaxis()
plt.title('end of the multipass, invert')
plt.show()
if settings.show_all_plots and settings.num_iterations > 1:
plt.figure()
plt.quiver(x, y, u, -v)
plt.gca().invert_yaxis()
plt.gca().set_aspect(1.)
plt.title('after multi pass, before saving, inverted')
plt.show()
# we now use only 0s instead of the image
# masked regions.
# we could do Nan, not sure what is best
u = u.filled(0.)
v = v.filled(0.)
# "scales the results pixel-> meter"
x, y, u, v = scaling.uniform(x,
y,
u,
v,
scaling_factor=settings.scaling_factor)
if settings.image_mask:
grid_mask = preprocess.prepare_mask_on_grid(x, y, mask_coords)
u = np.ma.masked_array(u, mask=grid_mask)
v = np.ma.masked_array(v, mask=grid_mask)
else:
u = np.ma.masked_array(u, np.ma.nomask)
v = np.ma.masked_array(v, np.ma.nomask)
# before saving we conver to the "physically relevant"
# right-hand coordinate system with 0,0 at the bottom left
# x to the right, y upwards
# and so u,v
x, y, u, v = transform_coordinates(x, y, u, v)
# import pdb; pdb.set_trace()
# "save to a file"
tools.save(x,
y,
u,
v,
mask,
os.path.join(save_path, "field_A%03d.txt" % counter),
delimiter="\t")
# "some other stuff that one might want to use"
if settings.show_plot or settings.save_plot:
Name = os.path.join(save_path, "Image_A%03d.png" % counter)
fig, _ = display_vector_field(
os.path.join(save_path, "field_A%03d.txt" % counter),
scale=settings.scale_plot,
)
if settings.save_plot is True:
fig.savefig(Name)
if settings.show_plot is True:
plt.show()
print(f"Image Pair {counter + 1}")
print(file_a.rsplit('/')[-1], file_b.rsplit('/')[-1])
def multipass_img_deform(frame_a,
frame_b,
window_size,
overlap,
iterations,
current_iteration,
x_old,
y_old,
u_old,
v_old,
correlation_method='circular',
subpixel_method='gaussian',
do_sig2noise=False,
sig2noise_method='peak2peak',
sig2noise_mask=2,
MinMaxU=(-100, 50),
MinMaxV=(-50, 50),
std_threshold=5,
median_threshold=2,
median_size=1,
filter_method='localmean',
max_filter_iteration=10,
filter_kernel_size=2,
interpolation_order=3):
"""
First pass of the PIV evaluation.
This function does the PIV evaluation of the first pass. It returns
the coordinates of the interrogation window centres, the displacment
u and v for each interrogation window as well as the mask which indicates
wether the displacement vector was interpolated or not.
Parameters
----------
frame_a : 2d np.ndarray
the first image
frame_b : 2d np.ndarray
the second image
window_size : tuple of ints
the size of the interrogation window
overlap : tuple of ints
the overlap of the interrogation window normal for example window_size/2
x_old : 2d np.ndarray
the x coordinates of the vector field of the previous pass
y_old : 2d np.ndarray
the y coordinates of the vector field of the previous pass
u_old : 2d np.ndarray
the u displacement of the vector field of the previous pass
v_old : 2d np.ndarray
the v displacement of the vector field of the previous pass
subpixel_method: string
the method used for the subpixel interpolation.
one of the following methods to estimate subpixel location of the peak:
'centroid' [replaces default if correlation map is negative],
'gaussian' [default if correlation map is positive],
'parabolic'
MinMaxU : two elements tuple
sets the limits of the u displacment component
Used for validation.
MinMaxV : two elements tuple
sets the limits of the v displacment component
Used for validation.
std_threshold : float
sets the threshold for the std validation
median_threshold : float
sets the threshold for the median validation
filter_method : string
the method used to replace the non-valid vectors
Methods:
'localmean',
'disk',
'distance',
max_filter_iteration : int
maximum of filter iterations to replace nans
filter_kernel_size : int
size of the kernel used for the filtering
interpolation_order : int
the order of the spline interpolation used for the image deformation
Returns
-------
x : 2d np.array
array containg the x coordinates of the interrogation window centres
y : 2d np.array
array containg the y coordinates of the interrogation window centres
u : 2d np.array
array containing the u displacement for every interrogation window
u : 2d np.array
array containing the u displacement for every interrogation window
mask : 2d np.array
array containg the mask values (bool) which contains information if
the vector was filtered
"""
x, y = get_coordinates(np.shape(frame_a), window_size, overlap)
'calculate the y and y coordinates of the interrogation window centres'
y_old = y_old[:, 0]
# y_old = y_old[::-1]
x_old = x_old[0, :]
y_int = y[:, 0]
# y_int = y_int[::-1]
x_int = x[0, :]
'''The interpolation function dont like meshgrids as input. Hence, the the edges
must be extracted to provide the sufficient input. x_old and y_old are the
are the coordinates of the old grid. x_int and y_int are the coordiantes
of the new grid'''
ip = RectBivariateSpline(y_old, x_old, u_old)
u_pre = ip(y_int, x_int)
ip2 = RectBivariateSpline(y_old, x_old, v_old)
v_pre = ip2(y_int, x_int)
''' interpolating the displacements from the old grid onto the new grid
y befor x because of numpy works row major
'''
frame_b_deform = frame_interpolation(
frame_b, x, y, u_pre, -v_pre, interpolation_order=interpolation_order)
'''this one is doing the image deformation (see above)'''
cor_win_1 = pyprocess.moving_window_array(frame_a, window_size, overlap)
cor_win_2 = pyprocess.moving_window_array(frame_b_deform, window_size,
overlap)
'''Filling the interrogation window. They windows are arranged
in a 3d array with number of interrogation window *window_size*window_size
this way is much faster then using a loop'''
correlation = correlation_func(cor_win_1,
cor_win_2,
correlation_method=correlation_method,
normalized_correlation=False)
'do the correlation'
disp = np.zeros((np.size(correlation, 0), 2))
for i in range(0, np.size(correlation, 0)):
''' determine the displacment on subpixel level '''
disp[i, :] = find_subpixel_peak_position(
correlation[i, :, :], subpixel_method=subpixel_method)
'this loop is doing the displacment evaluation for each window '
disp = np.array(disp) - np.floor(np.array(correlation[0, :, :].shape) / 2)
'reshaping the interrogation window to vector field shape'
shapes = np.array(
pyprocess.get_field_shape(np.shape(frame_a), window_size, overlap))
u = disp[:, 1].reshape(shapes)
v = -disp[:, 0].reshape(shapes)
'adding the recent displacment on to the displacment of the previous pass'
u = u + u_pre
v = v + v_pre
'validation using gloabl limits and local median'
u, v, mask_g = validation.global_val(u, v, MinMaxU, MinMaxV)
u, v, mask_s = validation.global_std(u, v, std_threshold=std_threshold)
u, v, mask_m = validation.local_median_val(u,
v,
u_threshold=median_threshold,
v_threshold=median_threshold,
size=median_size)
mask = mask_g + mask_m + mask_s
'adding masks to add the effect of alle the validations'
#mask=np.zeros_like(u)
'filter to replace the values that where marked by the validation'
if current_iteration != iterations:
'filter to replace the values that where marked by the validation'
u, v = filters.replace_outliers(u,
v,
method=filter_method,
max_iter=max_filter_iteration,
kernel_size=filter_kernel_size)
if do_sig2noise == True and current_iteration == iterations and iterations != 1:
sig2noise_ratio = sig2noise_ratio_function(
correlation,
sig2noise_method=sig2noise_method,
width=sig2noise_mask)
sig2noise_ratio = sig2noise_ratio.reshape(shapes)
else:
sig2noise_ratio = np.full_like(u, np.nan)
return x, y, u, v, sig2noise_ratio, mask
def func(args):
"""A function to process each image pair."""
# this line is REQUIRED for multiprocessing to work
# always use it in your custom function
file_a, file_b, counter = args
# counter2=str(counter2)
#####################
# Here goes you code
#####################
' read images into numpy arrays'
frame_a = tools.imread(os.path.join(settings.filepath_images, file_a))
frame_b = tools.imread(os.path.join(settings.filepath_images, file_b))
## Miguel: I just had a quick look, and I do not understand the reason for this step.
# I propose to remove it.
#frame_a = (frame_a*1024).astype(np.int32)
#frame_b = (frame_b*1024).astype(np.int32)
' crop to ROI'
if settings.ROI == 'full':
frame_a = frame_a
frame_b = frame_b
else:
frame_a = frame_a[settings.ROI[0]:settings.ROI[1],
settings.ROI[2]:settings.ROI[3]]
frame_b = frame_b[settings.ROI[0]:settings.ROI[1],
settings.ROI[2]:settings.ROI[3]]
if settings.dynamic_masking_method == 'edge' or 'intensity':
frame_a = preprocess.dynamic_masking(
frame_a,
method=settings.dynamic_masking_method,
filter_size=settings.dynamic_masking_filter_size,
threshold=settings.dynamic_masking_threshold)
frame_b = preprocess.dynamic_masking(
frame_b,
method=settings.dynamic_masking_method,
filter_size=settings.dynamic_masking_filter_size,
threshold=settings.dynamic_masking_threshold)
'''%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'''
'first pass'
x, y, u, v, sig2noise_ratio = first_pass(
frame_a,
frame_b,
settings.windowsizes[0],
settings.overlap[0],
settings.iterations,
correlation_method=settings.correlation_method,
subpixel_method=settings.subpixel_method,
do_sig2noise=settings.extract_sig2noise,
sig2noise_method=settings.sig2noise_method,
sig2noise_mask=settings.sig2noise_mask,
)
'validation using gloabl limits and std and local median'
'''MinMaxU : two elements tuple
sets the limits of the u displacment component
Used for validation.
MinMaxV : two elements tuple
sets the limits of the v displacment component
Used for validation.
std_threshold : float
sets the threshold for the std validation
median_threshold : float
sets the threshold for the median validation
filter_method : string
the method used to replace the non-valid vectors
Methods:
'localmean',
'disk',
'distance',
max_filter_iteration : int
maximum of filter iterations to replace nans
filter_kernel_size : int
size of the kernel used for the filtering'''
mask = np.full_like(x, False)
if settings.validation_first_pass == True:
u, v, mask_g = validation.global_val(u, v, settings.MinMax_U_disp,
settings.MinMax_V_disp)
u, v, mask_s = validation.global_std(
u, v, std_threshold=settings.std_threshold)
u, v, mask_m = validation.local_median_val(
u,
v,
u_threshold=settings.median_threshold,
v_threshold=settings.median_threshold,
size=settings.median_size)
if settings.extract_sig2noise == True and settings.iterations == 1 and settings.do_sig2noise_validation == True:
u, v, mask_s2n = validation.sig2noise_val(
u,
v,
sig2noise_ratio,
threshold=settings.sig2noise_threshold)
mask = mask + mask_g + mask_m + mask_s + mask_s2n
else:
mask = mask + mask_g + mask_m + mask_s
'filter to replace the values that where marked by the validation'
if settings.iterations > 1:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
'adding masks to add the effect of all the validations'
if settings.smoothn == True:
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
elif settings.iterations == 1 and settings.replace_vectors == True:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
'adding masks to add the effect of all the validations'
if settings.smoothn == True:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
i = 1
'all the following passes'
for i in range(2, settings.iterations + 1):
x, y, u, v, sig2noise_ratio, mask = multipass_img_deform(
frame_a,
frame_b,
settings.windowsizes[i - 1],
settings.overlap[i - 1],
settings.iterations,
i,
x,
y,
u,
v,
correlation_method=settings.correlation_method,
subpixel_method=settings.subpixel_method,
do_sig2noise=settings.extract_sig2noise,
sig2noise_method=settings.sig2noise_method,
sig2noise_mask=settings.sig2noise_mask,
MinMaxU=settings.MinMax_U_disp,
MinMaxV=settings.MinMax_V_disp,
std_threshold=settings.std_threshold,
median_threshold=settings.median_threshold,
median_size=settings.median_size,
filter_method=settings.filter_method,
max_filter_iteration=settings.max_filter_iteration,
filter_kernel_size=settings.filter_kernel_size,
interpolation_order=settings.interpolation_order)
# If the smoothing is active, we do it at each pass
if settings.smoothn == True:
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
'''%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'''
if settings.extract_sig2noise == True and i == settings.iterations and settings.iterations != 1 and settings.do_sig2noise_validation == True:
u, v, mask_s2n = validation.sig2noise_val(
u, v, sig2noise_ratio, threshold=settings.sig2noise_threshold)
mask = mask + mask_s2n
if settings.replace_vectors == True:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
'pixel/frame->pixel/sec'
u = u / settings.dt
v = v / settings.dt
'scales the results pixel-> meter'
x, y, u, v = scaling.uniform(x,
y,
u,
v,
scaling_factor=settings.scaling_factor)
'save to a file'
save(x,
y,
u,
v,
sig2noise_ratio,
mask,
os.path.join(save_path, 'field_A%03d.txt' % counter),
delimiter='\t')
'some messages to check if it is still alive'
'some other stuff that one might want to use'
if settings.show_plot == True or settings.save_plot == True:
plt.close('all')
plt.ioff()
Name = os.path.join(save_path, 'Image_A%03d.png' % counter)
display_vector_field(os.path.join(save_path,
'field_A%03d.txt' % counter),
scale=settings.scale_plot)
if settings.save_plot == True:
plt.savefig(Name)
if settings.show_plot == True:
plt.show()
print('Image Pair ' + str(counter + 1))
status_message(u)
# In[33]:
# "filter to replace the values that where marked by the validation"
# if settings.iterations > 1:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size,
)
# In[34]:
# mask the velocity maps
tmp = np.zeros_like(x,dtype=bool)
tmp.flat[xymask] = 1
u = np.ma.masked_array(u, mask = tmp)
v = np.ma.masked_array(v, mask = tmp)
dt = DeltaFrame * 1. / fps # piexels
u0, v0, sig2noise = process.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
x, y = process.get_coordinates(image_size=frame_a.shape,
window_size=winsize,
overlap=overlap)
u1, v1, mask = validation.sig2noise_val(u0, v0, sig2noise, threshold=1.3)
u2, v2 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=5,
kernel_size=5)
u3, v3, mask1 = validation.local_median_val(u2, v2, 3, 3, 1)
u4, v4 = filters.replace_outliers(u3,
v3,
method='localmean',
max_iter=5,
kernel_size=5)
tools.save(x, y, u4, v4, mask1, '../testResult/test.txt')
tools.display_vector_field('../testResult/test.txt', scale=500, width=0.0025)
#%% define node
def process_node(i):
def piv_frames(self, topn=-1, show=True):
from openpiv.validation import sig2noise_val
from openpiv.filters import replace_outliers
frames = self._frames[::2]
topn = np.min([len(frames), topn])
frames = frames[:topn]
(ut, vt, s2nt) = self.piv_frame(frame=0, show=False)
for i in tqdm.tqdm(frames[1:]):
(u, v, s2n) = self.piv_frame(frame=i, show=False)
ut += u
vt += v
s2nt += s2n
#print(np.max(u), np.min(u), u.size)
#print(np.max(v), np.max(v), v.size)
ut /= len(frames)
vt /= len(frames)
s2nt /= len(frames)
ut, vt, mask = sig2noise_val(ut,
vt,
s2nt,
threshold=self._piv_threshold)
ut, vt = replace_outliers(ut,
vt,
method='localmean',
max_iter=10,
kernel_size=2)
self._pivu = ut
self._pivv = vt
self._pivs2n = s2nt
self.save_piv()
if show:
fig = plt.figure(figsize=(12, 6))
ax1 = fig.add_subplot(121)
ax1.imshow(self.mean())
ax1.quiver(self._pivx, self._pivy, ut, vt, pivot='mid', color='w')
ax2 = fig.add_subplot(122)
n_u, bins, patches = ax2.hist(ut.flatten() * self._mpp,
bins=20,
normed=1,
facecolor='blue',
alpha=0.75,
label='u')
n_v, bins, patches = ax2.hist(vt.flatten() * self._mpp,
bins=20,
normed=1,
facecolor='green',
alpha=0.75,
label='v')
ax2.annotate(np.mean(ut) * self._mpp,
xy=(np.mean(ut) * self._mpp, np.max(n_u)))
ax2.annotate(np.mean(vt) * self._mpp,
xy=(np.mean(vt) * self._mpp, np.max(n_v)))
plt.legend(loc='best')
plt.tight_layout()
plt.savefig(self._fname[:-4] + '_piv_t.png', dpi=150)
print("... frames: {}, {}".format(frames[0], frames[-1]))
print("... mean velocity [um/sec]: ({:4.2f}, {:4.2f})".format(
np.mean(ut) * self._umtopixel,
np.mean(vt) * self._umtopixel))
print("... mean velocity [pixel/frame]: ({:4.2f}, {:4.2f})".format(
np.mean(ut) * self._dt,
np.mean(vt) * self._dt))
def process(self, args):
"""
Process chain as configured in the GUI.
Parameters
----------
args : tuple
Tuple as expected by the inherited run method:
file_a (str) -- image file a
file_b (str) -- image file b
counter (int) -- index pointing to an element of the filename
list
"""
file_a, file_b, counter = args
frame_a = piv_tls.imread(file_a)
frame_b = piv_tls.imread(file_b)
# Smoothning script borrowed from openpiv.windef
s = self.p['smoothn_val']
def smoothn(u, s):
s = s
u, _, _, _ = piv_smt.smoothn(u, s=s, isrobust=self.p['robust'])
return (u)
# delimiters placed here for safety
delimiter = self.p['separator']
if delimiter == 'tab':
delimiter = '\t'
if delimiter == 'space':
delimiter = ' '
# preprocessing
print('\nPre-pocessing image pair: {}'.format(counter + 1))
if self.p['background_subtract'] \
and self.p['background_type'] == 'minA - minB':
self.background = gen_background(self.p, frame_a, frame_b)
frame_a = frame_a.astype(np.int32)
frame_a = process_images(self,
frame_a,
self.GUI.preprocessing_methods,
background=self.background)
frame_b = frame_b.astype(np.int32)
frame_b = process_images(self,
frame_b,
self.GUI.preprocessing_methods,
background=self.background)
print('Evaluating image pair: {}'.format(counter + 1))
# evaluation first pass
start = time.time()
passes = 1
# setup custom windowing if selected
if self.parameter['custom_windowing']:
corr_window_0 = self.parameter['corr_window_1']
overlap_0 = self.parameter['overlap_1']
for i in range(2, 8):
if self.parameter['pass_%1d' % i]:
passes += 1
else:
break
else:
passes = self.parameter['coarse_factor']
if self.parameter['grid_refinement'] == 'all passes' \
and self.parameter['coarse_factor'] != 1:
corr_window_0 = self.parameter['corr_window'] * \
2**(self.parameter['coarse_factor'] - 1)
overlap_0 = self.parameter['overlap'] * \
2**(self.parameter['coarse_factor'] - 1)
# Refine all passes after first when there are more than 1 pass.
elif self.parameter['grid_refinement'] == '2nd pass on' \
and self.parameter['coarse_factor'] != 1:
corr_window_0 = self.parameter['corr_window'] * \
2**(self.parameter['coarse_factor'] - 2)
overlap_0 = self.parameter['overlap'] * \
2**(self.parameter['coarse_factor'] - 2)
# If >>none<< is selected or something goes wrong, the window
# size would remain the same.
else:
corr_window_0 = self.parameter['corr_window']
overlap_0 = self.parameter['overlap']
overlap_percent = overlap_0 / corr_window_0
sizeX = corr_window_0
u, v, sig2noise = piv_wdf.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=corr_window_0,
overlap=overlap_0,
search_area_size=corr_window_0,
width=self.parameter['s2n_mask'],
subpixel_method=self.parameter['subpixel_method'],
sig2noise_method=self.parameter['sig2noise_method'],
correlation_method=self.parameter['corr_method'],
normalized_correlation=self.parameter['normalize_correlation'])
x, y = piv_prc.get_coordinates(frame_a.shape, corr_window_0, overlap_0)
# validating first pass
mask = np.full_like(x, 0)
if self.parameter['fp_vld_global_threshold']:
u, v, Mask = piv_vld.global_val(
u,
v,
u_thresholds=(self.parameter['fp_MinU'],
self.parameter['fp_MaxU']),
v_thresholds=(self.parameter['fp_MinV'],
self.parameter['fp_MaxV']))
# consolidate effects of mask
mask += Mask
if self.parameter['fp_local_med']:
u, v, Mask = piv_vld.local_median_val(
u,
v,
u_threshold=self.parameter['fp_local_med'],
v_threshold=self.parameter['fp_local_med'],
size=self.parameter['fp_local_med_size'])
mask += Mask
if self.parameter['adv_repl']:
u, v = piv_flt.replace_outliers(
u,
v,
method=self.parameter['adv_repl_method'],
max_iter=self.parameter['adv_repl_iter'],
kernel_size=self.parameter['adv_repl_kernel'])
print('Validated first pass result of image pair: {}.'.format(counter +
1))
# smoothning before deformation if 'each pass' is selected
if self.parameter['smoothn_each_pass']:
if self.parameter['smoothn_first_more']:
s *= 2
u = smoothn(u, s)
v = smoothn(v, s)
print('Smoothned pass 1 for image pair: {}.'.format(counter + 1))
s = self.parameter['smoothn_val1']
print('Finished pass 1 for image pair: {}.'.format(counter + 1))
print("window size: " + str(corr_window_0))
print('overlap: ' + str(overlap_0), '\n')
# evaluation of all other passes
if passes != 1:
iterations = passes - 1
for i in range(2, passes + 1):
# setting up the windowing of each pass
if self.parameter['custom_windowing']:
corr_window = self.parameter['corr_window_%1d' % i]
overlap = int(corr_window * overlap_percent)
else:
if self.parameter['grid_refinement'] == 'all passes' or \
self.parameter['grid_refinement'] == '2nd pass on':
corr_window = self.parameter['corr_window'] * \
2**(iterations - 1)
overlap = self.parameter['overlap'] * \
2**(iterations - 1)
else:
corr_window = self.parameter['corr_window']
overlap = self.parameter['overlap']
sizeX = corr_window
# translate settings to windef settings object
piv_wdf_settings = piv_wdf.Settings()
piv_wdf_settings.correlation_method = \
self.parameter['corr_method']
piv_wdf_settings.normalized_correlation = \
self.parameter['normalize_correlation']
piv_wdf_settings.windowsizes = (corr_window, ) * (passes + 1)
piv_wdf_settings.overlap = (overlap, ) * (passes + 1)
piv_wdf_settings.num_iterations = passes
piv_wdf_settings.subpixel_method = \
self.parameter['subpixel_method']
piv_wdf_settings.deformation_method = \
self.parameter['deformation_method']
piv_wdf_settings.interpolation_order = \
self.parameter['interpolation_order']
piv_wdf_settings.sig2noise_validate = True,
piv_wdf_settings.sig2noise_method = \
self.parameter['sig2noise_method']
piv_wdf_settings.sig2noise_mask = self.parameter['s2n_mask']
# do the correlation
x, y, u, v, sig2noise, mask = piv_wdf.multipass_img_deform(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
i, # current iteration
x,
y,
u,
v,
piv_wdf_settings)
# validate other passes
if self.parameter['sp_vld_global_threshold']:
u, v, Mask = piv_vld.global_val(
u,
v,
u_thresholds=(self.parameter['sp_MinU'],
self.parameter['sp_MaxU']),
v_thresholds=(self.parameter['sp_MinV'],
self.parameter['sp_MaxV']))
mask += Mask # consolidate effects of mask
if self.parameter['sp_vld_global_threshold']:
u, v, Mask = piv_vld.global_std(
u, v, std_threshold=self.parameter['sp_std_threshold'])
mask += Mask
if self.parameter['sp_local_med_validation']:
u, v, Mask = piv_vld.local_median_val(
u,
v,
u_threshold=self.parameter['sp_local_med'],
v_threshold=self.parameter['sp_local_med'],
size=self.parameter['sp_local_med_size'])
mask += Mask
if self.parameter['adv_repl']:
u, v = piv_flt.replace_outliers(
u,
v,
method=self.parameter['adv_repl_method'],
max_iter=self.parameter['adv_repl_iter'],
kernel_size=self.parameter['adv_repl_kernel'])
print('Validated pass {} of image pair: {}.'.format(
i, counter + 1))
# smoothning each individual pass if 'each pass' is selected
if self.parameter['smoothn_each_pass']:
u = smoothn(u, s)
v = smoothn(v, s)
print('Smoothned pass {} for image pair: {}.'.format(
i, counter + 1))
print('Finished pass {} for image pair: {}.'.format(
i, counter + 1))
print("window size: " + str(corr_window))
print('overlap: ' + str(overlap), '\n')
iterations -= 1
if self.p['flip_u']:
u = np.flipud(u)
if self.p['flip_v']:
v = np.flipud(v)
if self.p['invert_u']:
u *= -1
if self.p['invert_v']:
v *= -1
# scaling
u = u / self.parameter['dt']
v = v / self.parameter['dt']
x, y, u, v = piv_scl.uniform(x,
y,
u,
v,
scaling_factor=self.parameter['scale'])
end = time.time()
# save data to file.
out = np.vstack([m.ravel() for m in [x, y, u, v, mask, sig2noise]])
np.savetxt(self.save_fnames[counter],
out.T,
fmt='%8.4f',
delimiter=delimiter)
print('Processed image pair: {}'.format(counter + 1))
sizeY = sizeX
sizeX = ((int(frame_a.shape[0] - sizeX) //
(sizeX - (sizeX * overlap_percent))) + 1)
sizeY = ((int(frame_a.shape[1] - sizeY) //
(sizeY - (sizeY * overlap_percent))) + 1)
time_per_vec = _round((((end - start) * 1000) / ((sizeX * sizeY) - 1)),
3)
print('Process time: {} second(s)'.format((_round((end - start), 3))))
print('Number of vectors: {}'.format(int((sizeX * sizeY) - 1)))
print('Time per vector: {} millisecond(s)'.format(time_per_vec))
# correcting stage drift between the field of views
u -= np.nanmean(u)
v -= np.nanmean(v)
w -= np.nanmean(w)
# %%
# filtering
uf, vf, wf, mask = sig2noise_val(u,
v,
w=w,
sig2noise=sig2noise,
threshold=signoise_filter)
uf, vf, wf = replace_outliers(uf,
vf,
wf,
max_iter=1,
tol=100,
kernel_size=2,
method='disk')
# %%
# plotting
# representation of the image stacks by maximums projections. The red circle marks the position of the cell
def update_plot(i, ims, ax):
a1 = ax.imshow(ims[i])
a2 = ax.add_patch(plt.Circle((330, 140), 100, color="red", fill=False))
return [a1, a2]
# %%
u, v, sig2noise = process.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=32,
overlap=8,
dt=.1,
sig2noise_method='peak2peak')
x, y = process.get_coordinates(image_size=frame_a.shape,
window_size=32,
overlap=8)
u, v, mask = validation.sig2noise_val(u, v, sig2noise, threshold=1.3)
u, v = filters.replace_outliers(u,
v,
method='localmean',
max_iter=10,
kernel_size=2)
x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor=96.52)
tools.save(x, y, u, v, mask, 'Y4-S3_Camera000398_a.txt')
# %%
# Use Python version, pyprocess:
u, v, sig2noise = pyprocess.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=32,
overlap=8,
dt=.1,
def func(args):
file_a, file_b, counter = args
# read the iamges
frame_a = tools.imread(os.path.join(settings.filepath_images, file_a))
frame_b = tools.imread(os.path.join(settings.filepath_images, file_b))
if counter == settings.fall_start:
settings.ROI[1] = frame_a.shape[0]
"""Here we check if the interface has reached the top of the roi yet
by comparing it to the index in the observation_periods file. If it has
not reached the roi yet we skip this part, if it did then we shift the
roi for each pair after the initial one """
if counter >= settings.roi_shift_start:
# set the roi to the image height for the first frame
# if counter == settings.roi_shift_start :
# settings.current_pos = 0
# shift the roi for each pair (this is not done for the first one)
settings.ROI[0] = int(settings.current_pos)
# crop to roi
if settings.ROI == 'full':
frame_a = frame_a
frame_b = frame_b
else:
frame_a = frame_a[settings.ROI[0]:settings.ROI[1],
settings.ROI[2]:settings.ROI[3]]
frame_b = frame_b[settings.ROI[0]:settings.ROI[1],
settings.ROI[2]:settings.ROI[3]]
if settings.dynamic_masking_method == 'edge' or settings.dynamic_masking_method == 'intensity':
frame_a = preprocess.dynamic_masking(
frame_a,
method=settings.dynamic_masking_method,
filter_size=settings.dynamic_masking_filter_size,
threshold=settings.dynamic_masking_threshold)
frame_b = preprocess.dynamic_masking(
frame_b,
method=settings.dynamic_masking_method,
filter_size=settings.dynamic_masking_filter_size,
threshold=settings.dynamic_masking_threshold)
#%%
""" Here we do the first pass of the piv interrogation """
x, y, u, v, sig2noise_ratio = first_pass(
frame_a,
frame_b,
settings.window_width[0],
settings.window_height[0],
settings.overlap_width[0],
settings.overlap_height[0],
settings.iterations,
correlation_method=settings.correlation_method,
subpixel_method=settings.subpixel_method,
do_sig2noise=settings.extract_sig2noise,
sig2noise_method=settings.sig2noise_method,
sig2noise_mask=settings.sig2noise_mask,
)
mask = np.full_like(x, False)
if settings.validation_first_pass == True:
u, v, mask_g = validation.global_val(u, v, settings.MinMax_U_disp,
settings.MinMax_V_disp)
u, v, mask_s = validation.global_std(
u, v, std_threshold=settings.std_threshold)
u, v, mask_m = validation.local_median_val(
u,
v,
u_threshold=settings.median_threshold,
v_threshold=settings.median_threshold,
size=settings.median_size)
if settings.extract_sig2noise == True and settings.iterations == 1 and settings.do_sig2noise_validation == True:
u, v, mask_s2n = validation.sig2noise_val(
u,
v,
sig2noise_ratio,
threshold=settings.sig2noise_threshold)
mask = mask + mask_g + mask_m + mask_s + mask_s2n
else:
mask = mask + mask_g + mask_m + mask_s
'filter to replace the values that where marked by the validation'
if settings.iterations > 1:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
'adding masks to add the effect of all the validations'
if settings.smoothn == True:
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
elif settings.iterations == 1 and settings.replace_vectors == True:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
'adding masks to add the effect of all the validations'
if settings.smoothn == True:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
#%%
i = 1
""" Do the multipass until the maximum iterations are reached """
for i in range(2, settings.iterations + 1):
x, y, u, v, sig2noise_ratio, mask = multipass_img_deform(
frame_a,
frame_b,
settings.window_width[i - 1],
settings.window_height[i - 1],
settings.overlap_width[i - 1],
settings.overlap_height[i - 1],
settings.iterations,
i,
x,
y,
u,
v,
correlation_method=settings.correlation_method,
subpixel_method=settings.subpixel_method,
do_sig2noise=settings.extract_sig2noise,
sig2noise_method=settings.sig2noise_method,
sig2noise_mask=settings.sig2noise_mask,
MinMaxU=settings.MinMax_U_disp,
MinMaxV=settings.MinMax_V_disp,
std_threshold=settings.std_threshold,
median_threshold=settings.median_threshold,
median_size=settings.median_size,
filter_method=settings.filter_method,
max_filter_iteration=settings.max_filter_iteration,
filter_kernel_size=settings.filter_kernel_size,
interpolation_order=settings.interpolation_order)
# smooth on each pass in case this is wanted
if settings.smoothn == True:
u, dummy_u1, dummy_u2, dummy_u3 = smoothn.smoothn(
u, s=settings.smoothn_p)
v, dummy_v1, dummy_v2, dummy_v3 = smoothn.smoothn(
v, s=settings.smoothn_p)
# extract the sig2noise ratio in case it is desired and replace the vectors
if settings.extract_sig2noise == True and i == settings.iterations and settings.iterations != 1 and settings.do_sig2noise_validation == True:
u, v, mask_s2n = validation_patch.sig2noise_val(
u,
v,
sig2noise_ratio,
threshold_low=settings.sig2noise_threshold)
mask = mask + mask_s2n
if settings.replace_vectors == True:
u, v = filters.replace_outliers(
u,
v,
method=settings.filter_method,
max_iter=settings.max_filter_iteration,
kernel_size=settings.filter_kernel_size)
if counter >= settings.roi_shift_start:
settings.current_pos = settings.current_pos - calc_disp(
x, v, frame_b.shape[1])
if ((settings.ROI[1] - settings.current_pos) < 300):
return settings.current_pos, True
# scale the result timewise and lengthwise
u = u / settings.dt
v = v / settings.dt
x, y, u, v = scaling.uniform(x,
y,
u,
v,
scaling_factor=settings.scaling_factor)
# save the result
save(x,
y,
u,
v,
sig2noise_ratio,
mask,
os.path.join(save_path_txts, 'field_%06d.txt' % (counter)),
delimiter='\t')
# disable the grid in the rcParams file
plt.rcParams['axes.grid'] = False
# show and save the plot if it is desired
if settings.show_plot == True or settings.save_plot == True:
plt.ioff()
Name = os.path.join(save_path_images, 'Image_%06d.png' % (counter))
display_vector_field(os.path.join(save_path_txts,
'field_%06d.txt' % (counter)),
scale=settings.scale_plot)
if settings.save_plot == True:
plt.savefig(Name, dpi=100)
if settings.show_plot == True:
plt.show()
plt.close('all')
print('Image Pair ' + str(counter) + ' of ' +
settings.save_folder_suffix)
if settings.current_pos == np.nan:
return settings.current_pos, True
return settings.current_pos, False
def quick_piv(self, search_dict, index_a=100, index_b=101, folder=None):
self.show_piv_param()
ns = Namespace(**self.piv_param)
if folder == None:
img_a, img_b = self.read_two_images(search_dict,
index_a=index_a,
index_b=index_b)
location_path = [
x['path'] for x in self.piv_dict_list
if search_dict.items() <= x.items()
]
results_path = os.path.join(self.results_path, *location_path)
try:
os.makedirs(results_path)
except FileExistsError:
pass
else:
try:
file_a_path = os.path.join(self.path, folder,
'frame_%06d.tiff' % index_a)
file_b_path = os.path.join(self.path, folder,
'frame_%06d.tiff' % index_b)
img_a = np.array(Image.open(file_a_path))
img_b = np.array(Image.open(file_b_path))
except:
return None
# crop
img_a = img_a[ns.crop[0]:-ns.crop[1] - 1, ns.crop[2]:-ns.crop[3] - 1]
img_b = img_b[ns.crop[0]:-ns.crop[1] - 1, ns.crop[2]:-ns.crop[3] - 1]
u0, v0, sig2noise = pyprocess.extended_search_area_piv(
img_a.astype(np.int32),
img_b.astype(np.int32),
window_size=ns.winsize,
overlap=ns.overlap,
dt=ns.dt,
search_area_size=ns.searchsize,
sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=img_a.shape,
search_area_size=ns.searchsize,
overlap=ns.overlap)
x, y, u0, v0 = scaling.uniform(
x, y, u0, v0,
scaling_factor=ns.pixel_density) # no. pixel per distance
u0, v0, mask = validation.global_val(
u0, v0, (ns.u_lower_bound, ns.u_upper_bound),
(ns.v_lower_bound, ns.v_upper_bound))
u1, v1, mask = validation.sig2noise_val(u0,
v0,
sig2noise,
threshold=1.01)
u3, v3 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=500,
kernel_size=3)
#save in the simple ASCII table format
tools.save(x, y, u3, v3, sig2noise, mask,
os.path.join(results_path, ns.text_export_name))
if ns.image_check == True:
fig, ax = plt.subplots(2, 1, figsize=(24, 12))
ax[0].imshow(img_a)
ax[1].imshow(img_b)
io.imwrite(os.path.join(results_path, ns.figure_export_name), img_a)
if ns.show_result == True:
fig, ax = plt.subplots(figsize=(24, 12))
tools.display_vector_field(
os.path.join(results_path, ns.text_export_name),
ax=ax,
scaling_factor=ns.pixel_density,
scale=ns.scale_factor, # scale defines here the arrow length
width=ns.arrow_width, # width is the thickness of the arrow
on_img=True, # overlay on the image
image_name=os.path.join(results_path, ns.figure_export_name))
fig.savefig(os.path.join(results_path, ns.figure_export_name))
if ns.show_vertical_profiles:
field_shape = pyprocess.get_field_shape(
image_size=img_a.shape,
search_area_size=ns.searchsize,
overlap=ns.overlap)
vertical_profiles(ns.text_export_name, field_shape)
print('Mean of u: %.3f' % np.mean(u3))
print('Std of u: %.3f' % np.std(u3))
print('Mean of v: %.3f' % np.mean(v3))
print('Std of v: %.3f' % np.std(v3))
output = np.array([np.mean(u3), np.std(u3), np.mean(v3), np.std(v3)])
# if np.absolute(np.mean(v3)) < 50:
# output = self.quick_piv(search_dict,index_a = index_a + 1, index_b = index_b + 1)
return x, y, u3, v3
def run_piv(
frame_a,
frame_b,
winsize=16, # pixels, interrogation window size in frame A
searchsize=20, # pixels, search in image B
overlap=8, # pixels, 50% overlap
dt=0.0001, # sec, time interval between pulses
image_check=False,
show_vertical_profiles=False,
figure_export_name='_results.png',
text_export_name="_results.txt",
scale_factor=1,
pixel_density=36.74,
arrow_width=0.001,
show_result=True,
u_bounds=(-100, 100),
v_bounds=(-100, 100)):
u0, v0, sig2noise = pyprocess.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
search_area_size=searchsize,
overlap=overlap)
x, y, u0, v0 = scaling.uniform(
x, y, u0, v0, scaling_factor=pixel_density) # no. pixel per distance
u0, v0, mask = validation.global_val(u0, v0, u_bounds, v_bounds)
u1, v1, mask = validation.sig2noise_val(u0, v0, sig2noise, threshold=1.05)
u3, v3 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=10,
kernel_size=3)
#save in the simple ASCII table format
if np.std(u3) < 480:
tools.save(x, y, u3, v3, sig2noise, mask, text_export_name)
if image_check == True:
fig, ax = plt.subplots(2, 1, figsize=(24, 12))
ax[0].imshow(frame_a)
ax[1].imshow(frame_b)
io.imwrite(figure_export_name, frame_a)
if show_result == True:
fig, ax = plt.subplots(figsize=(24, 12))
tools.display_vector_field(
text_export_name,
ax=ax,
scaling_factor=pixel_density,
scale=scale_factor, # scale defines here the arrow length
width=arrow_width, # width is the thickness of the arrow
on_img=True, # overlay on the image
image_name=figure_export_name)
fig.savefig(figure_export_name)
if show_vertical_profiles:
field_shape = pyprocess.get_field_shape(image_size=frame_a.shape,
search_area_size=searchsize,
overlap=overlap)
vertical_profiles(text_export_name, field_shape)
print('Std of u3: %.3f' % np.std(u3))
print('Mean of u3: %.3f' % np.mean(u3))
return np.std(u3)
def run(self):
self.is_to_stop = False
self.piv.piv_results_list = []
for i in range(0, len(self.frames_list) - 1, abs(self.jump)):
if self.piv.xy_zoom[0][0] and self.piv.xy_zoom[1][0]:
"""try:"""
frame_a = self.frames_list[i][2][
int(self.piv.xy_zoom[1][0]):int(self.piv.xy_zoom[1][1]),
int(self.piv.xy_zoom[0][0]):int(self.piv.xy_zoom[0][1])]
frame_b = self.frames_list[i + 1][2][
int(self.piv.xy_zoom[1][0]):int(self.piv.xy_zoom[1][1]),
int(self.piv.xy_zoom[0][0]):int(self.piv.xy_zoom[0][1])]
"""
except ValueError:
frame_a = self.frames_list[i][2][int(self.frames_list[i][2].shape[1] - self.piv.xy_zoom[1][0]): int(
self.frames_list[i][2].shape[1] - self.piv.xy_zoom[1][1]),
int(self.piv.xy_zoom[0][0]): int(
self.piv.xy_zoom[0][1])]
frame_b = self.frames_list[i + 1][2][
int(self.frames_list[i + 1][2].shape[1] - self.piv.xy_zoom[1][0]): int(
self.frames_list[i + 1][2].shape[1] - self.piv.xy_zoom[1][1]),
int(self.piv.xy_zoom[0][0]): int(
self.piv.xy_zoom[0][1])]
"""
else:
frame_a = self.frames_list[i][2]
frame_b = self.frames_list[i + 1][2]
try:
self.u, self.v, self.sig2noise = extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=self.winsize,
overlap=self.overlap,
dt=self.dt,
search_area_size=self.searchsize,
sig2noise_method='peak2peak')
self.x, self.y = get_coordinates(image_size=frame_a.shape,
window_size=self.winsize,
overlap=self.overlap)
self.u, self.v, self.mask = sig2noise_val(self.u,
self.v,
self.sig2noise,
threshold=1.0)
self.u, self.v = replace_outliers(self.u,
self.v,
method='localmean',
max_iter=10,
kernel_size=2)
# self.x, self.y, self.u, self.v = uniform(self.x, self.y, self.u, self.v, scaling_factor=5)
if self.piv.xy_zoom[0][0] and self.piv.xy_zoom[1][0]:
self.x += int(self.piv.xy_zoom[0][0])
self.y += int(self.piv.xy_zoom[1][0])
self.y = np.flip(self.y, 0)
self.x = np.flip(self.x, 0)
except ValueError:
if self.searchsize < self.winsize:
print("0")
self.error_message.setText(
"the search size cannot be smaller than the window size"
)
elif self.overlap > self.winsize:
print("1")
self.error_message.setText(
"Overlap has to be smaller than the window_size")
else:
print("2")
self.error_message.setText("ROI window to small")
self.error_message.exec()
break
self.piv.piv_results_list.append(
[self.x, self.y, self.u, self.v, self.mask])
self.piv.piv_images_list[i][3] = self.piv.piv_results_list[
i // abs(self.jump)]
# data = np.zeros((len(np.ravel(self.u)), 5))
# res_list = [np.ravel(self.x), np.ravel(self.y), np.ravel(self.u), np.ravel(self.v), np.ravel(self.mask)]
# for j in range(0, 4):
# for k in range(len(res_list[j])):
# data[k][j] = res_list[j][k]
# self.piv.piv_images_list[i][4] = data
# save_openpiv_vec(self.piv.piv_images_list[i][1].split('.')[0], data, 'pix', 'dt',
# len(data[0]), len(data))
self.piv.show_plot(i, self.piv.bit, True)
if i == len(self.frames_list) - 2 and self.jump == 1:
self.piv.piv_results_list.append(
[self.x, self.y, self.u, self.v, self.mask])
self.piv.piv_images_list[i +
1][3] = self.piv.piv_results_list[i +
1]
# self.piv.piv_images_list[i + 1][4] = data
self.piv.show_plot(i + 1, self.piv.bit, True)
if self.is_to_stop:
break
self.piv_finished_signal.emit()
ax[0].imshow(frame_a,cmap=plt.cm.gray)
ax[1].imshow(frame_b,cmap=plt.cm.gray)
# %%
winsize = 24 # pixels
searchsize = 64 # pixels, search in image B
overlap = 12 # pixels
dt = 0.02 # sec
u0, v0, sig2noise = process.extended_search_area_piv( frame_a.astype(np.int32), frame_b.astype(np.int32), window_size=winsize, overlap=overlap, dt=dt, search_area_size=searchsize, sig2noise_method='peak2peak' )
# %%
x, y = process.get_coordinates( image_size=frame_a.shape, window_size=winsize, overlap=overlap )
# %%
u1, v1, mask = validation.sig2noise_val( u0, v0, sig2noise, threshold = 1.3 )
# %%
u2, v2 = filters.replace_outliers( u1, v1, method='localmean', max_iter=10, kernel_size=2)
# %%
x, y, u3, v3 = scaling.uniform(x, y, u2, v2, scaling_factor = 96.52 )
# %%
tools.save(x, y, u3, v3, mask, 'exp1_001.txt' )
# %%
tools.display_vector_field('exp1_001.txt', scale=100, width=0.0025)
def calc_piv_2_images(frame_a, frame_b, idx, dir_name):
'''
Performs Particle Image Velocimetry (PIV) of two images, and saves an image with PIV on it.
:param frame_a: first image
:param frame_b: consecutive image
:param idx: index of the first frame, for saving and ordering the images
:param dir_name: directory to save the image to
:return: -
'''
u0, v0, sig2noise = pyprocess.extended_search_area_piv(
frame_a.astype(np.int32),
frame_b.astype(np.int32),
window_size=winsize,
overlap=overlap,
dt=dt,
search_area_size=searchsize,
sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
search_area_size=searchsize,
overlap=overlap)
u1, v1, mask = validation.sig2noise_val(u0, v0, sig2noise, threshold=1.05)
# to see where is a reasonable limit filter out
# outliers that are very different from the neighbours
u2, v2 = filters.replace_outliers(u1,
v1,
method='localmean',
max_iter=3,
kernel_size=3)
# convert x,y to mm; convert u,v to mm/sec
x, y, u3, v3 = scaling.uniform(
x, y, u2, v2, scaling_factor=scaling_factor) # 96.52 microns/pixel
# 0,0 shall be bottom left, positive rotation rate is counterclockwise
x, y, u3, v3 = tools.transform_coordinates(x, y, u3, v3)
fig, ax = plt.subplots()
im = np.negative(frame_a) # plot negative of the image for more clarity
xmax = np.amax(x) + winsize / (2 * scaling_factor)
ymax = np.amax(y) + winsize / (2 * scaling_factor)
ax.imshow(im, cmap="Greys_r", extent=[0.0, xmax, 0.0, ymax])
invalid = mask.astype("bool")
valid = ~invalid
plt.quiver(x[invalid],
y[invalid],
u3[invalid],
v3[invalid],
color="r",
width=width)
plt.quiver(x[valid],
y[valid],
u3[valid],
v3[valid],
color="b",
width=width)
ax.set_aspect(1.)
plt.title(r'Velocity Vectors Field (Frame #%d) $(\frac{\mu m}{hour})$' %
idx)
plt.savefig(dir_name + "/" + "vec_page%d.png" % idx, dpi=200)
plt.show()
plt.close()
