Advanced options
The Used dark value indicated in the entry box is the value used in the analysis to remove the small residual intensity of the stack. The default is the Calculated dark value indicated above the entry box. To change it, select the switch and enter the chosen value in the entry box. For 1PF, the minimum possible value is 480.
Method to compute the Calculated dark value: Each image of the stack is paved with non-overlapping cells of 20x20 pixels. The mean value of each cell is computed for the first image of the stack (first angle). The average over all angles of the cell with the smallest mean value is the Calculated dark value.
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The value of the offset angle used in the analysis is indicated. This angle (in degrees) is measured according to the convention mentioned in the Options tab. In order to manually change this value, the switch should be set to 'On'.
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or 
: click to select the polarization direction as clockwise or counter-clockwise. The direction shown on the button is the direction chosen in the analysis.
The offset angle and the polarization direction are saved in the MS Excel file (see Save output in the Options tab).
For 1PF: The drop down menu lists all the disk cones included in the app. If the disk cone to be used is not in the list, select otherand download the appropriate disk cone. The choice of disk cone also sets the value for the offset angle.
Click the button 
to visualize the disk cone used in the 1PF analysis. The name of the disk cone used in the analysis is displayed on the lower part of the panel. The name of the disk cone is saved in the MS Excel file (see Save output in the Options tab).
For 4POLAR: The upper drop down menu lists all the calibration data included in the app. If the calibration data to be used is not in the list, select other and download the appropriate calibration data. The calibration data is a .txt file with a name of the type Calib*.txt containing a 4x3 matrix for 4POLAR 2D (see template) or a 4x4 matrix for 4POLAR 3D (see template). The name of the calibration data used in the analysis is displayed on the lower part of the panel.
Select the distribution of the polarization angles (0°, 45°, 90°, 135°) using the lower drop down menu: UL (upper left), UR (upper right), LR (lower right) and LL (lower left). The choice of distribution is saved in the MS Excel file (see Save output in the Options tab).
This option is used to improve the quality of the stack if the signal is too weak. It performs a convolution of the stack with a kernel of 1's of size Bin width x Bin height. A side effect is a blurring of the stack as displayed in the intensity images. The binning values are saved in the MS Excel file (see Save output in the Options tab).
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Stick (deg): (editable) value of the angle (in degrees) to arbitrarily rotate the sticks (following the above-mentioned convention: positive=counter-clockwise, negative=clockwise) -
Figure (deg): (editable) value of the angle (in degrees) to arbitrarily rotate the entire figure (following the above-mentioned convention: positive=counter-clockwise, negative=clockwise) -
Reference (deg): (editable) value of the angle (in degrees) with respect to which ρ is normalized; if the change of reference angle is combined with a figure rotation, the reference angle has to be determined in the rotated figure.
This option is used to remove some intensity from the stack. First, define the size in pixels (Bin width and Bin height) of the patch in the part of the intensity image. Second, select a point (center of the patch of size Bin width x Bin height) in the intensity image by clicking the button 
. Third, choose the value Factor (between 0 and 1) for the fraction of the mean intensity of the patch to be removed from the stack. The mean value over the selected patch weighted by the chosen factor is removed from the entire stack. The value Removed intensity value which is substracted from the stack is indicated in the lower part of the panel.
PyPOLAR is developed under BSD 2-Clause License, Copyright(c) 2021 [email protected]