Merge pull request #10 from alexlib/pyprocess_extended_search

Pyprocess extended search

openpiv/__init__.py

@@ -1,23 +0,0 @@
-import os.path as _osp
-
-# the root directory of the package when installed.
-# this is an os independent trick to know where the
-# package is installed, so we can access data files
-# we have provided with the python module
-__root__ = _osp.abspath(_osp.dirname(__file__))
-
-# this is the location of the default parameters file
-# which we have distributed with openpiv.
-__default_config_file__ = _osp.join( __root__, 'data/defaults-processing-parameters.cfg' )
-
-
-# import default modules
-import openpiv.preprocess
-import openpiv.tools
-import openpiv.pyprocess
-import openpiv.scaling
-import openpiv.validation
-import openpiv.filters
-# import openpiv.ui
-import openpiv.process
-import openpiv.lib

openpiv/examples/tutorial-part1/tutorial-part1.py

@@ -1,24 +1,43 @@
+#!/usr/bin/env python
 import sys
-sys.path.append('/Users/alex/Documents/OpenPIV/openpiv-python')
 
-import openpiv.tools
-import openpiv.process
-import openpiv.scaling
+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  = openpiv.tools.imread( 'exp1_001_a.bmp' )
-frame_b  = openpiv.tools.imread( 'exp1_001_b.bmp' )
+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 = 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, 'exp1_001.txt' )
+
+tools.display_vector_field('exp1_001.txt', scale=100, width=0.0025)
+
+
 
-u, v, sig2noise = openpiv.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' )
+u1, v1, sig2noise = pyprocess.piv( frame_a.astype(np.int32), 
+                                  frame_b.astype(np.int32), 
+window_size=24, overlap=12, dt=0.02, search_size=64, sig2noise_method='peak2peak' )
 
-x, y = openpiv.process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
+x, y = process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
 
-u, v, mask = openpiv.validation.sig2noise_val( u, v, sig2noise, threshold = 1.3 )
+u1, v1, mask = validation.sig2noise_val( u1, v1, sig2noise, threshold = 1.3 )
 
-u, v = openpiv.filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2)
+u1, v1 = filters.replace_outliers( u1, v1, method='localmean', max_iter=10, kernel_size=2)
 
-x, y, u, v = openpiv.scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
+x, y, u1, v1 = scaling.uniform(x, y, u1, v1, scaling_factor = 96.52 )
 
-openpiv.tools.save(x, y, u, v, mask, 'exp1_001.txt' )
+tools.save(x, y, u1, v1, mask, 'exp1_001_1.txt' )
 
-openpiv.tools.display_vector_field('exp1_001.txt', scale=100, width=0.0025)
+tools.display_vector_field('exp1_001_1.txt', scale=100, width=0.0025)

openpiv/examples/tutorial-part1/tutorial-part2.py

@@ -1,57 +1,44 @@
+#!/usr/bin/env ipython
 import sys
-sys.path.append('/Users/alex/Documents/OpenPIV/openpiv-python')
-
-import openpiv.tools
-import openpiv.process
-import openpiv.scaling
-import numpy as np
-
-frame_a  = openpiv.tools.imread( 'exp1_001_a.bmp' )
-frame_b  = openpiv.tools.imread( 'exp1_001_b.bmp' )
-
-u, v, sig2noise = openpiv.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 = openpiv.process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
-
-u, v, mask = openpiv.validation.sig2noise_val( u, v, sig2noise, threshold = 2.5 )
-
-u, v = openpiv.filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2)
-
-x, y, u, v = openpiv.scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
-
-openpiv.tools.save(x, y, u, v, mask, 'exp1_001.txt' )
-
-openpiv.tools.display_vector_field('exp1_001.txt', scale=100, width=0.0025)
 
+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
 
-u, v= openpiv.pyprocess.piv( frame_a, frame_b, corr_method='fft', window_size=24, overlap=12, dt=0.02, sig2noise_method='peak2peak' )
-x, y = openpiv.pyprocess.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
-
-
-u, v, mask = openpiv.validation.sig2noise_val( u, v, sig2noise, threshold = 2.5 )
-
-u, v = openpiv.filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2.5)
-
-x, y, u, v = openpiv.scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
-
-openpiv.tools.save(x, y, u, v, mask, 'exp1_002.txt' )
-
-openpiv.tools.display_vector_field('exp1_002.txt', scale=100, width=0.0025)
-
-
+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= openpiv.pyprocess.piv( frame_a, frame_b, corr_method='direct', window_size=24, overlap=12, dt=0.02, sig2noise_method='peak2peak' )
-x, y = openpiv.pyprocess.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
 
 
-u, v, mask = openpiv.validation.sig2noise_val( u, v, sig2noise, threshold = 2.5 )
+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)
 
-u, v = openpiv.filters.replace_outliers( u, v, method='localmean', max_iter=10, kernel_size=2.5)
 
-x, y, u, v = openpiv.scaling.uniform(x, y, u, v, scaling_factor = 96.52 )
 
-openpiv.tools.save(x, y, u, v, mask, 'exp1_002.txt' )
 
-openpiv.tools.display_vector_field('exp1_002.txt', scale=100, width=0.0025)
+u,v,s2n = pyprocess.piv( frame_a, frame_b, corr_method='direct', 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, sig2noise, 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)

openpiv/examples/tutorial-part1/tutorial-part2small.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+import sys
+
+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
+import matplotlib.pyplot as plt
+
+frame_a  = tools.imread('exp1_001_a.bmp')
+frame_b  = tools.imread('exp1_001_b.bmp' )
+
+
+frame_a = frame_a[:128,:128]
+frame_b = frame_b[:128,:128]
+
+from pylab import *
+imshow(np.c_[frame_a,frame_b],cmap=cm.gray)
+show()
+
+
+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=32, 
+    sig2noise_method='peak2peak' )
+
+x, y = process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=12 )
+
+
+plt.figure()
+plt.quiver(x,y,u,v)
+plt.show()
+
+
+u, v, s2n = pyprocess.piv( frame_a, frame_b, corr_method='fft', 
+                            window_size=32, overlap=12, dt=0.02, sig2noise_method='peak2peak' )
+x, y = pyprocess.get_coordinates( image_size=frame_a.shape, window_size=32, overlap=12 )
+
+plt.figure()
+plt.quiver(x,y,u,v)
+plt.show()
+
+
+u, v, s2n = pyprocess.piv( frame_a, frame_b, corr_method='direct', 
+                            window_size=24, overlap=12, dt=0.02, 
+                            sig2noise_method='peak2peak',
+                            search_size = 32)
+x, y = pyprocess.get_coordinates( image_size=frame_a.shape, 
+                                         window_size=24, overlap=12 )
+
+plt.figure()
+plt.quiver(x,y,u,v)
+plt.show()

openpiv/examples/tutorial-part1/tutorial-part3.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+import sys
+
+if 'OpenPIV' not in sys.path:
+    sys.path.append('/Users/alex/Documents/OpenPIV/alexlib/openpiv-python')
+
+from openpiv import tools, process, pyprocess
+import numpy as np
+import matplotlib.pyplot as plt
+
+from skimage.transform import resize
+from skimage import img_as_ubyte
+
+
+frame_a  = tools.imread( 'test001.png')
+frame_b  = tools.imread( 'test002.png')
+
+
+# frame_a = img_as_ubyte(resize(frame_a,(1024,256)))
+# frame_b = img_as_ubyte(resize(frame_b,(1024,256)))
+
+frame_a = frame_a[:512,-200:]
+frame_b = frame_b[:512,-200:]
+
+#frame_a = frame_a[:256,:]
+#frame_b = frame_b[:256,:]
+
+plt.figure()
+plt.imshow(np.c_[frame_a,frame_b],cmap=plt.cm.gray)
+plt.show()
+
+
+u, v = process.extended_search_area_piv(frame_a.astype(np.int32), 
+frame_b.astype(np.int32), window_size=24, overlap=12, search_area_size=32, dt = 1.)
+
+plt.figure()
+plt.quiver(u,v)
+plt.axis('equal')
+plt.show()
+
+u1, v1 = pyprocess.piv(frame_a, frame_b, window_size=32, search_size=48, overlap=24)
+
+# x, y = process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=0)
+
+plt.figure()
+plt.quiver(u1,v1,v1)
+plt.axis('equal')
+plt.show()
+
+
+u2, v2 = pyprocess.piv(frame_a, frame_b, corr_method = 'direct', window_size=32)
+
+# x, y = process.get_coordinates( image_size=frame_a.shape, window_size=24, overlap=0)
+
+plt.figure()
+plt.quiver(u2,v2,v2)
+plt.axis('equal')
+plt.show()