def ProcessHandler(stg):
# setting up the path and grabbing the files
analysis_path = tools.create_directory(stg['DP'])
task = tools.Multiprocesser(data_dir=stg['DP'], pattern_a='frame*.jpg')
# finding background and reflections in the images
if stg['BR'] == 'on':
print('preprocessing:')
bg_a, bg_b = task.find_background(50, 10, 6)
reflection = tools.mark_reflection(180, task.files_a)
#tools.imsave(os.path.join(stg['DP'], 'Analysis/reflection.jpg'), reflection)
else:
bg_a, bg_b, reflection = tools.imread(
os.path.join(stg['DP'], 'avg.jpg')), None, None
#tools.imsave(os.path.join(stg['DP'], 'Analysis/background.jpg'), bg_a)
# start processing data
print('main process:\nprocessing images...')
#task.n_files = 6
main_process = partial(ProcessPIV,
bga=bg_a,
bgb=bg_b,
reflection=reflection,
stg=stg)
task.run(func=main_process, n_cpus=6)
print('- done processing')
'''
fig, ax = plt.subplots(2,2)
img = tools.imread(task.files_a[0])
bg = bg_a
ax[0,0].imshow(img, cmap='gray')
ax[0,1].imshow(bg, cmap='gray')
ax[1,0].imshow(reflection, cmap='gray')
img = img - bg
img[reflection==255] = 0
ax[1,1].imshow(img, cmap='gray')
plt.show()
'''
return bg_a
def piv(settings):
# '''the func fuction is the "frame" in which the PIV evaluation is done'''
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))
'Below is code to read files and create a folder to store the results'
save_path = os.path.join(
settings.save_path, 'Open_PIV_results_' +
str(settings.windowsizes[settings.iterations - 1]) + '_' +
settings.save_folder_suffix)
if not os.path.exists(save_path):
os.makedirs(save_path)
task = tools.Multiprocesser(data_dir=settings.filepath_images,
pattern_a=settings.frame_pattern_a,
pattern_b=settings.frame_pattern_b)
task.run(func=func, n_cpus=1)
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)
path = os.path.dirname(os.path.abspath(__file__))
path = os.path.join(path, '../test2/')
task = tools.Multiprocesser(data_dir=path,
pattern_a='2image_*0.tif',
pattern_b='2image_*1.tif')
task.run(func=func, n_cpus=1)
def process(args):
file_a, file_b, counter = args
# read images into numpy arrays
frame_a = tools.imread(file_a)
frame_b = tools.imread(file_b)
print(counter + 1)
# process image pair with piv algorithm.
u, v, sig2noise = pyprocess.extended_search_area_piv( frame_a, frame_b, \
window_size=32, overlap=16, dt=0.0015, search_area_size=32, sig2noise_method='peak2peak')
x, y = pyprocess.get_coordinates(image_size=frame_a.shape,
window_size=32,
overlap=16)
u, v, mask1 = validation.sig2noise_val(u, v, sig2noise, threshold=1.0)
u, v, mask2 = validation.global_val(u, v, (-2000, 2000), (-2000, 4000))
u, v, mask3 = validation.local_median_val(u, v, 400, 400, size=2)
#u, v, mask4 = validation.global_std(u, v, std_threshold=3)
mask = mask1 | mask2 | mask3
#u, v = filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2)
save_file = tools.create_path(file_a, 'Analysis')
tools.save(x, y, u, v, mask, save_file + '.dat')
run_path = ''
raw_data_path = os.path.join(run_path, 'Images')
Analysis_path = tools.create_directory(run_path)
task = tools.Multiprocesser(data_dir=raw_data_path, pattern_a='*.bmp')
task.run(func=process, n_cpus=1)
