Merge pull request #175 from OpenPIV/windef_default_settings

Windef default settings

Author: alexlib

openpiv/test/test_windef.py

@@ -9,6 +9,7 @@
 import numpy as np
 import openpiv.windef as windef
 from test_process import create_pair, shift_u, shift_v, threshold
+import pathlib
 
 frame_a, frame_b = create_pair(image_size=256)
 
@@ -60,7 +61,7 @@ def test_multi_pass_circ():
     print("\n", x, y, u_old, v_old, s2n)
     assert np.mean(np.abs(u_old - shift_u)) < threshold
     assert np.mean(np.abs(v_old - shift_v)) < threshold
-    for i in range(1, iterations ):
+    for i in range(1, iterations):
         x, y, u, v, s2n = windef.multipass_img_deform(
             frame_a,
             frame_b,
@@ -108,6 +109,109 @@ def test_first_pass_lin():
     assert np.mean(np.abs(v - shift_v)) < threshold
 
 
+def test_invert():
+    """ Test windef.piv with invert option """
+
+    file_a = pathlib.Path(__file__).parent / '../examples/test1/exp1_001_a.bmp'
+    file_b = pathlib.Path(__file__).parent / '../examples/test1/exp1_001_b.bmp'
+
+    settings = windef.Settings()
+    'Data related settings'
+    # Folder with the images to process
+    settings.filepath_images = pathlib.Path(__file__).parent / '../examples/test1'
+    settings.save_path = '.'
+    # Root name of the output Folder for Result Files
+    settings.save_folder_suffix = 'test'
+    # Format and Image Sequence
+    settings.frame_pattern_a = 'exp1_001_a.bmp'
+    settings.frame_pattern_b = 'exp1_001_a.bmp'
+
+    'Region of interest'
+    # (50,300,50,300) #Region of interest: (xmin,xmax,ymin,ymax) or 'full' for full image
+    settings.ROI = 'full'
+    # settings.ROI = (0,1024,200,500)
+
+    'Image preprocessing'
+
+    settings.invert = True
+    # 'None' for no masking, 'edges' for edges masking, 'intensity' for intensity masking
+    # WARNING: This part is under development so better not to use MASKS
+    settings.dynamic_masking_method = 'None'
+    settings.dynamic_masking_threshold = 0.005
+    settings.dynamic_masking_filter_size = 7
+
+    'Processing Parameters'
+    settings.correlation_method = 'circular'  # 'circular' or 'linear'
+    settings.normalized_correlation = 'True'
+
+    settings.deformation_method = 'symmetric'
+    settings.iterations = 3  # select the number of PIV passes
+    # add the interroagtion window size for each pass. 
+    # For the moment, it should be a power of 2 
+    settings.windowsizes = (64, 32, 16)  # if longer than n iteration the rest is ignored
+    # The overlap of the interroagtion window for each pass.
+    settings.overlap = (32, 16, 8)  # This is 50% overlap
+    # Has to be a value with base two. In general window size/2 is a good choice.
+    # methode used for subpixel interpolation: 'gaussian','centroid','parabolic'
+    settings.subpixel_method = 'gaussian'
+    # order of the image interpolation for the window deformation
+    settings.interpolation_order = 3
+    settings.scaling_factor = 1  # scaling factor pixel/meter
+    settings.dt = 1  # time between to frames (in seconds)
+    'Signal to noise ratio options (only for the last pass)'
+    # It is possible to decide if the S/N should be computed (for the last pass) or not
+    settings.extract_sig2noise = True  # 'True' or 'False' (only for the last pass)
+    # method used to calculate the signal to noise ratio 'peak2peak' or 'peak2mean'
+    settings.sig2noise_method = 'peak2peak'
+    # select the width of the masked to masked out pixels next to the main peak
+    settings.sig2noise_mask = 2
+    # If extract_sig2noise==False the values in the signal to noise ratio
+    # output column are set to NaN
+    'vector validation options'
+    # choose if you want to do validation of the first pass: True or False
+    settings.validation_first_pass = True
+    # only effecting the first pass of the interrogation the following passes
+    # in the multipass will be validated
+    'Validation Parameters'
+    # The validation is done at each iteration based on three filters.
+    # The first filter is based on the min/max ranges. Observe that these values are defined in
+    # terms of minimum and maximum displacement in pixel/frames.
+    settings.MinMax_U_disp = (-30, 30)
+    settings.MinMax_V_disp = (-30, 30)
+    # The second filter is based on the global STD threshold
+    settings.std_threshold = 4  # threshold of the std validation
+    # The third filter is the median test (not normalized at the moment)
+    settings.median_threshold = 3  # threshold of the median validation
+    # On the last iteration, an additional validation can be done based on the S/N.
+    settings.median_size = 1 #defines the size of the local median
+    'Validation based on the signal to noise ratio'
+    # Note: only available when extract_sig2noise==True and only for the last
+    # pass of the interrogation
+    # Enable the signal to noise ratio validation. Options: True or False
+    settings.do_sig2noise_validation = False # This is time consuming
+    # minmum signal to noise ratio that is need for a valid vector
+    settings.sig2noise_threshold = 1.2
+    'Outlier replacement or Smoothing options'
+    # Replacment options for vectors which are masked as invalid by the validation
+    settings.replace_vectors = True  # Enable the replacment. Chosse: True or False
+    settings.smoothn = True  # Enables smoothing of the displacemenet field
+    settings.smoothn_p = 0.5  # This is a smoothing parameter
+    # select a method to replace the outliers: 'localmean', 'disk', 'distance'
+    settings.filter_method = 'localmean'
+    # maximum iterations performed to replace the outliers
+    settings.max_filter_iteration = 10
+    settings.filter_kernel_size = 2  # kernel size for the localmean method
+    'Output options'
+    # Select if you want to save the plotted vectorfield: True or False
+    settings.save_plot = False
+    # Choose wether you want to see the vectorfield or not :True or False
+    settings.show_plot = False
+    settings.scale_plot = 10  # select a value to scale the quiver plot of the vectorfield
+    # run the script with the given settings
+    windef.piv(settings)
+
+
+
 def test_multi_pass_lin():
     """ test fot the multipass """
     window_size = (128, 64, 32)