Added packaged version of bubble analysis GUI.

packaged-code/pacakged-gui/README.md

+# Bubble Analysis GUI
+`bubble_analysis_gui.py` is a GUI program written with PyQt5 that allows a series of readings to be inspected and analysed easily. A demonstration can be found [here](https://xorg.us/2018-07-18_12-07-23.mp4).
+
+#### Instructions
+1) On running the script a file selection prompt will appear. Select the folder that contains the index.csv file.
+2) Find as many readings in your data that contain the same geometry and have a common coordinate (for example a constant y). Navigate to an empty frame (no bubble) and click 'Add Frame' under 'Calibration'. If you select incorrect frames you can restart by clicking 'Clear Frames'. When you have selected a series of frames click 'Calibrate'. This will take a moment to run and will result in a 'mm/px' value being shown in the 'Calibration' status box.
+3) You can navigate through your data with the navigation buttons provided or slide the slider to advance through the frames.
+4) You can click on a frame to take measurements, left click once at the start of your measurement and again at the end. A red line will appear and the status box at the bottom of the window will show details about your measurement. The angle noted is measured from the positive horizontal (x) direction anti-clockwise (Note: the order in which you choose your points is important in angle measurement). Right clicking will clear your measurement.
+5) There are numerous other options for debugging and information.
+
+#### Recording Data
+To use this analysis tool data must be recorded in the correct format.
+- index.csv must be a CSV file with headers "x", "y", "idx" (names are not important but order is).
+- Each position index should have its own directory containing movies.
+It is suggested to view the existing data as a reference.
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packaged-code/pacakged-gui/run_bubble_analysis.bat

+python ./bubble_analysis_gui.py
+PAUSE
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packaged-code/pacakged-gui/util/calibration_utils.py

+import math
+
+import matplotlib.pyplot as plt
+import numpy as np
+import skimage.transform as tf
+from skimage.registration import phase_cross_correlation
+from skimage.filters import sobel, threshold_triangle
+from skimage.restoration import denoise_bilateral
+
+import util.plotting_utils as pu
+import util.file_utils as fu
+
+
+def calculate_offset(frame_1, frame_2, plot_compared_frames=False):
+    """
+    Calculates a required offset of frame_1 in direction dir such that it maps onto frame_2 as closely as possible.
+
+    :param frame_1: Frame to be moved.
+    :param frame_2: Frame to be mapped onto.
+    :param plot_compared_frames: Whether to plot the final frame comparison.
+    :return: Offset required in direction.
+    """
+    frame_1 = denoise_bilateral(frame_1, channel_axis=None, bins=2, mode='reflect', sigma_spatial=2.5)
+    frame_2 = denoise_bilateral(frame_2, channel_axis=None, bins=2, mode='reflect', sigma_spatial=2.5)
+    frame_1 = sobel(frame_1, mask=np.ones(frame_1.shape, dtype=bool))
+    frame_2 = sobel(frame_2, mask=np.ones(frame_1.shape, dtype=bool))
+
+    # thresh_1 = threshold_triangle(frame_1)
+    # thresh_2 = threshold_triangle(frame_2)
+    # thresh = (thresh_1 + thresh_2) / 2
+    # frame_1 = frame_1 > thresh
+    # frame_2 = frame_2 > thresh
+
+    offset, error, _ = phase_cross_correlation(frame_1, frame_2, normalization=None)
+    if plot_compared_frames:
+        tform = tf.SimilarityTransform(translation=[offset[1], offset[0]])
+        pu.plot_frame(tf.warp(frame_1, tform), show_immediately=False)
+        pu.plot_frame(frame_2, show_immediately=False)
+        plt.show()
+
+    return offset
+
+
+if __name__ == '__main__':
+    # cal_dir = "../../../Data/SidewaysSeries/w2.2h2.7/"
+    # print(calculate_mm_per_pixel(cal_dir, plot_compared_frames=True))
+    # mraw_1 = fu.get_mraw_from_dir("../../../../Data/SlotSweeps/w1h3/movie_S0013/")
+    # mraw_2 = fu.get_mraw_from_dir("../../../../Data/SlotSweeps/w1h3/movie_S0001/")
+    mraw_1 = fu.get_mraw_from_dir("C:/Users/eda1g15/OneDrive - University of Southampton/Research/Porous Materials/Data/~25VF/Purer water between 3 degassed again/movie_C001H001S0001/")
+    mraw_2 = fu.get_mraw_from_dir("C:/Users/eda1g15/OneDrive - University of Southampton/Research/Porous Materials/Data/~25VF/Purer water between 3 degassed again/movie_C001H001S0002/")
+    print(calculate_offset(mraw_1[0], mraw_2[0], True))