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tools.py
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tools.py
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#!/usr/bin/env python
"""The openpiv.tools module is a collection of utilities and tools.
"""
__licence__ = """
Copyright (C) 2011 www.openpiv.net
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import glob
import sys
import os.path
import multiprocessing
import numpy as np
from matplotlib.image import imsave as _imsave, imread as _imread
import matplotlib.pyplot as pl
import matplotlib.patches as pt
from builtins import range
def display_vector_field( filename, on_img=False, image_name='None', window_size=32, scaling_factor=1, **kw):
""" Displays quiver plot of the data stored in the file
Parameters
----------
filename : string
the absolute path of the text file
on_img : Bool, optional
if True, display the vector field on top of the image provided by image_name
image_name : string, optional
path to the image to plot the vector field onto when on_img is True
window_size : int, optional
when on_img is True, provide the interogation window size to fit the background image to the vector field
scaling_factor : float, optional
when on_img is True, provide the scaling factor to scale the background image to the vector field
Key arguments : (additional parameters, optional)
*scale*: [None | float]
*width*: [None | float]
See also:
---------
matplotlib.pyplot.quiver
Examples
--------
--- only vector field
>>> openpiv.tools.display_vector_field('./exp1_0000.txt',scale=100, width=0.0025)
--- vector field on top of image
>>> openpiv.tools.display_vector_field('./exp1_0000.txt', on_img=True, image_name='exp1_001_a.bmp', window_size=32, scaling_factor=70, scale=100, width=0.0025)
"""
a = np.loadtxt(filename)
fig=pl.figure()
if on_img: # plot a background image
im = imread(image_name)
im = negative(im) #plot negative of the image for more clarity
imsave('neg.tif', im)
im = imread('neg.tif')
xmax=np.amax(a[:,0])+window_size/(2*scaling_factor)
ymax=np.amax(a[:,1])+window_size/(2*scaling_factor)
implot = pl.imshow(im, origin='lower', cmap="Greys_r",extent=[0.,xmax,0.,ymax])
invalid = a[:,4].astype('bool')
fig.canvas.set_window_title('Vector field, '+str(np.count_nonzero(invalid))+' wrong vectors')
valid = ~invalid
pl.quiver(a[invalid,0],a[invalid,1],a[invalid,2],a[invalid,3],color='r',**kw)
pl.quiver(a[valid,0],a[valid,1],a[valid,2],a[valid,3],color='b',**kw)
pl.draw()
pl.show()
def imread( filename, flatten=0 ):
"""Read an image file into a numpy array
using imageio.imread
Parameters
----------
filename : string
the absolute path of the image file
flatten : bool
True if the image is RGB color or False (default) if greyscale
Returns
-------
frame : np.ndarray
a numpy array with grey levels
Examples
--------
>>> image = openpiv.tools.imread( 'image.bmp' )
>>> print image.shape
(1280, 1024)
"""
im = _imread(filename)
if np.ndim(im) > 2:
im = rgb2gray(im)
return im
def rgb2gray(rgb):
return np.dot(rgb[...,:3], [0.299, 0.587, 0.144])
def imsave( filename, arr ):
"""Write an image file from a numpy array
using imageio.imread
Parameters
----------
filename : string
the absolute path of the image file that will be created
arr : 2d np.ndarray
a 2d numpy array with grey levels
Example
--------
>>> image = openpiv.tools.imread( 'image.bmp' )
>>> image2 = openpiv.tools.negative(image)
>>> imsave( 'negative-image.tif', image2)
"""
if np.ndim(arr) > 2:
arr = rgb2gray(arr)
if np.amin(arr) < 0:
arr -= arr.min()
if np.amax(arr) > 255:
arr /= arr.max()
arr *= 255
if filename.endswith('tif'):
_imsave( filename, arr ,format='TIFF')
else:
_imsave( filename, arr)
def convert16bitsTIF( filename, save_name):
img = imread( filename )
img2 = np.zeros([img.shape[0],img.shape[1]], dtype = np.int32)
for I in range(img.shape[0]):
for J in range(img.shape[1]):
img2[I,J]=img[I,J,0]
imsave( save_name, img2)
def mark_background(threshold, list_img, filename):
list_frame = []
for I in range(len(list_img)):
list_frame.append(imread(list_img[I]))
mark = np.zeros(list_frame[0].shape, dtype=np.int32)
background = np.zeros(list_frame[0].shape, dtype=np.int32)
for I in range(mark.shape[0]):
print((" row ", I , " / " , mark.shape[0]));
for J in range(mark.shape[1]):
sum1 = 0
for K in range(len(list_frame)):
sum1 = sum1 + list_frame[K][I, J]
if sum1 < threshold*len(list_img):
mark[I,J] = 0
else:
mark[I,J]=1
background[I,J]=mark[I,J]*255
imsave(filename, background)
print("done with background");
return background
def mark_background2(list_img, filename):
list_frame = []
for I in range(len(list_img)):
list_frame.append(imread(list_img[I]))
background = np.zeros(list_frame[0].shape, dtype=np.int32)
for I in range(background.shape[0]):
print((" row ", I , " / " , background.shape[0]));
for J in range(background.shape[1]):
min_1 = 255
for K in range(len(list_frame)):
if min_1 > list_frame[K][I,J]:
min_1 = list_frame[K][I,J]
background[I,J]=min_1
imsave(filename, background)
print("done with background");
return background
def edges(list_img, filename):
back = mark_background(30, list_img, filename)
edges = filter.canny(back, sigma=3)
imsave(filename, edges)
def find_reflexions(list_img, filename):
background = mark_background2(list_img, filename)
reflexion = np.zeros(background.shape, dtype=np.int32)
for I in range(background.shape[0]):
print((" row ", I , " / " , background.shape[0]));
for J in range(background.shape[1]):
if background[I,J] > 253:
reflexion[I,J] = 255
imsave(filename, reflexion)
print("done with reflexions");
return reflexion
def find_boundaries(threshold, list_img1, list_img2, filename, picname):
f = open(filename, 'w')
print("mark1..");
mark1 = mark_background(threshold, list_img1, "mark1.bmp")
print("[DONE]");
print((mark1.shape));
print("mark2..");
mark2 = mark_background(threshold, list_img2, "mark2.bmp")
print("[DONE]");
print("computing boundary");
print((mark2.shape));
list_bound = np.zeros(mark1.shape, dtype=np.int32)
for I in range(list_bound.shape[0]):
print(( "bound row ", I , " / " , mark1.shape[0]));
for J in range(list_bound.shape[1]):
list_bound[I,J]=0
if mark1[I,J]==0:
list_bound[I,J]=125
if I>1 and J>1 and I<list_bound.shape[0]-2 and J< list_bound.shape[1]-2:
for K in range(5):
for L in range(5):
if mark1[I-2+K,J-2+L] != mark2[I-2+K,J-2+L]:
list_bound[I,J]=255
else:
list_bound[I,J]=255
f.write(str(I)+'\t'+str(J)+'\t'+str(list_bound[I,J])+'\n')
print('[DONE]');
f.close()
imsave(picname, list_bound)
return list_bound
def save( x, y, u, v, mask, filename, fmt='%8.4f', delimiter='\t' ):
"""Save flow field to an ascii file.
Parameters
----------
x : 2d np.ndarray
a two dimensional array containing the x coordinates of the
interrogation window centers, in pixels.
y : 2d np.ndarray
a two dimensional array containing the y coordinates of the
interrogation window centers, in pixels.
u : 2d np.ndarray
a two dimensional array containing the u velocity components,
in pixels/seconds.
v : 2d np.ndarray
a two dimensional array containing the v velocity components,
in pixels/seconds.
mask : 2d np.ndarray
a two dimensional boolen array where elements corresponding to
invalid vectors are True.
filename : string
the path of the file where to save the flow field
fmt : string
a format string. See documentation of numpy.savetxt
for more details.
delimiter : string
character separating columns
Examples
--------
>>> openpiv.tools.save( x, y, u, v, 'field_001.txt', fmt='%6.3f', delimiter='\t')
"""
# build output array
out = np.vstack( [m.ravel() for m in [x, y, u, v, mask] ] )
# save data to file.
np.savetxt( filename, out.T, fmt=fmt, delimiter=delimiter )
def display( message ):
"""Display a message to standard output.
Parameters
----------
message : string
a message to be printed
"""
sys.stdout.write(message)
sys.stdout.write('\n')
sys.stdout.flush()
class Multiprocesser():
def __init__ ( self, data_dir, pattern_a, pattern_b = None ):
"""A class to handle and process large sets of images.
This class is responsible of loading image datasets
and processing them. It has parallelization facilities
to speed up the computation on multicore machines.
It currently support only image pair obtained from
conventional double pulse piv acquisition. Support
for continuos time resolved piv acquistion is in the
future.
Parameters
----------
data_dir : str
the path where image files are located
pattern_a : str
a shell glob patter to match the first
frames.
pattern_b : str
a shell glob patter to match the second
frames. if None, then the list is sequential, 001.tif, 002.tif
Examples
--------
>>> multi = openpiv.tools.Multiprocesser( '/home/user/images', 'image_*_a.bmp', 'image_*_b.bmp')
"""
# load lists of images
self.files_a = sorted( glob.glob( os.path.join( os.path.abspath(data_dir), pattern_a ) ) )
if pattern_b is None:
self.files_b = self.files_a[1:]
self.files_a = self.files_a[:-1]
else:
self.files_b = sorted( glob.glob( os.path.join( os.path.abspath(data_dir), pattern_b ) ) )
# number of images
self.n_files = len(self.files_a)
# check if everything was fine
if not len(self.files_a) == len(self.files_b):
raise ValueError('Something failed loading the image file. There should be an equal number of "a" and "b" files.')
if not len(self.files_a):
raise ValueError('Something failed loading the image file. No images were found. Please check directory and image template name.')
def run( self, func, n_cpus=1 ):
"""Start to process images.
Parameters
----------
func : python function which will be executed for each
image pair. See tutorial for more details.
n_cpus : int
the number of processes to launch in parallel.
For debugging purposes use n_cpus=1
"""
# create a list of tasks to be executed.
image_pairs = [ (file_a, file_b, i) for file_a, file_b, i in zip( self.files_a, self.files_b, range(self.n_files) ) ]
# for debugging purposes always use n_cpus = 1,
# since it is difficult to debug multiprocessing stuff.
if n_cpus > 1:
pool = multiprocessing.Pool( processes = n_cpus )
res = pool.map( func, image_pairs )
else:
for image_pair in image_pairs:
func( image_pair )
def negative( image):
""" Return the negative of an image
Parameter
----------
image : 2d np.ndarray of grey levels
Returns
-------
(255-image) : 2d np.ndarray of grey levels
"""
return (255-image)
def display_windows_sampling( x, y, window_size, skip=0, method='standard'):
""" Displays a map of the interrogation points and windows
Parameters
----------
x : 2d np.ndarray
a two dimensional array containing the x coordinates of the
interrogation window centers, in pixels.
y : 2d np.ndarray
a two dimensional array containing the y coordinates of the
interrogation window centers, in pixels.
window_size : the interrogation window size, in pixels
skip : the number of windows to skip on a row during display.
Recommended value is 0 or 1 for standard method, can be more for random method
-1 to not show any window
method : can be only <standard> (uniform sampling and constant window size)
<random> (pick randomly some windows)
Examples
--------
>>> openpiv.tools.display_windows_sampling(x, y, window_size=32, skip=0, method='standard')
"""
fig=pl.figure()
if skip < 0 or skip +1 > len(x[0])*len(y):
fig.canvas.set_window_title('interrogation points map')
pl.scatter(x, y, color='g') #plot interrogation locations
else:
nb_windows = len(x[0])*len(y)/(skip+1)
#standard method --> display uniformly picked windows
if method == 'standard':
pl.scatter(x, y, color='g')#plot interrogation locations (green dots)
fig.canvas.set_window_title('interrogation window map')
#plot the windows as red squares
for i in range(len(x[0])):
for j in range(len(y)):
if j%2 == 0:
if i%(skip+1) == 0:
x1 = x[0][i] - window_size/2
y1 = y[j][0] - window_size/2
pl.gca().add_patch(pt.Rectangle((x1, y1), window_size, window_size, facecolor='r', alpha=0.5))
else:
if i%(skip+1) == 1 or skip==0:
x1 = x[0][i] - window_size/2
y1 = y[j][0] - window_size/2
pl.gca().add_patch(pt.Rectangle((x1, y1), window_size, window_size, facecolor='r', alpha=0.5))
#random method --> display randomly picked windows
elif method == 'random':
pl.scatter(x, y, color='g')#plot interrogation locations
fig.canvas.set_window_title('interrogation window map, showing randomly '+str(nb_windows)+' windows')
for i in range(nb_windows):
k=np.random.randint(len(x[0])) #pick a row and column index
l=np.random.randint(len(y))
x1 = x[0][k] - window_size/2
y1 = y[l][0] - window_size/2
pl.gca().add_patch(pt.Rectangle((x1, y1), window_size, window_size, facecolor='r', alpha=0.5))
else:
raise ValueError('method not valid: choose between standard and random')
pl.draw()
pl.show()