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python scripts to help process microCT data from the machine to a usable .csv file.

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annavalentine/mCT-Processing-CRREL

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MicroCT File Processing

work done w/ Cold Regions Research & Engineering Lab

Scratch Notes: I need to edit this for coherency, this is vars I found in an email:

['Scan Depth', 'Average Depth', 'Number of layers', 'Lower vertical position', 'Upper vertical position', 'Pixel size', 'Lower grey threshold', 'Upper grey threshold', 'Total VOI volume', 'Object volume', 'Percent object volume', 'Total VOI surface', 'Object surface', 'Intersection surface', 'Object surface / volume ratio', 'Object surface density', 'Surface convexity index', 'Centroid (x)', 'Centroid (y)', 'Centroid (z)', 'Moment of inertia (x)', 'Moment of inertia (y)', 'Moment of inertia (z)', 'Polar moment of inertia', 'Radius of gyration (x)', 'Radius of gyration (y)', 'Radius of gyration (z)', 'Polar radius of gyration', 'Product of inertia (xy)', 'Product of inertia (xz)', 'Product of inertia (yz)', 'Total orientation (theta)', 'Total orientation (phi)', 'Structure model index', 'Structure thickness', 'Structure linear density', 'Structure separation', 'Fractal dimension', 'Number of objects', 'Number of closed pores', 'Volume of closed pores', 'Surface of closed pores', 'Closed porosity (percent)', 'Volume of open pore space', 'Open porosity (percent)', 'Total volume of pore space', 'Total porosity (percent)', 'Euler number', 'Connectivity', 'Connectivity density', 'Degree of anisotropy', 'Eigenvalue 1', 'Eigenvalue 2', 'Eigenvalue 3']

Additionally, and perhaps more applicable to your .png calculates is the 2D pit data. The .csv files I have concatenates the 2D 20um slice .txt data files as it goes down each 2cm section scan. The 2D data has the following variables that the software spits out (for reference):

[Z position, Number of objects, Total ROI area, Object area, Percent object area, Total ROI perimeter, Object perimeter, Object perimeter / area ratio, Average object area, Average object area-equivalent circle diameter, Surface convexity index, Euler number, Number of closed pores, Area of closed pores, Perimeter of closed pores, Closed porosity (percent), Area of open pore space, Total area of pore space, Open porosity (percent), Total porosity (percent), Total orientation (phi), Eccentricity, Structure thickness (plate model), Structure separation (plate model), Structure linear density (plate model), Fractal dimension, Intersection perimeter]

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python scripts to help process microCT data from the machine to a usable .csv file.

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