Macenko et al Walkthrough.m

(* ::Package:: *)

(************************************************************************)
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(* ::Input::Initialization:: *)
options[verbose] = True;
options[alpha]=0.01;
options[beta] = 0.15;


(* ::Input::Initialization:: *)
(* Convert the data in an image to a matrix of RGB tuples. This function removes the row/column structure from the image data.
Input: img -- an image file. Assumed to be an RGB image.
Output: an array of RGB tuples with byte data elements.*)
convertToRgbTuples[img_]:= Flatten[ImageData[img, "Byte"], 1];


(* ::Input::Initialization:: *)
(* Convert a short integer (8-bit byte) in the range of 0 to 255 to absorbance. Assumes that a value of 0 represents 0% transmittance and that 255 represents 100% transmittance. Handles special cases of 0% and 100% transmittance for numerical stability. Forces the result to a numerical value (as opposed to symbolic) using default machine precision. *)
convertRgbToOD[trans_]:=Module[
{recip},
recip=trans/255;
Switch[recip, 255, 0.000000001, 0, 3.0, _, N[-Log10[recip]]]
];


(* ::Input::Initialization:: *)
(* Convert an RGB tuple (a list with 3 elements in the range of 0 to 255) to an absorbance tuple.*)
convertRgbTupleToOD[tuple_]:=odTable[[#+1]]&/@tuple;


(* ::Input::Initialization:: *)
(* Convert a list of RGB tuples to absorbance. The input is a list of 3-element lists where each element is a value between 0 and 255.*)convertRgbTupleArrayToOD[tuples_]:=convertRgbTupleToOD /@ tuples;


(* ::Input::Initialization:: *)
tupleAboveThresholdQ[tuple_]:=Module[
{b},
b=options[beta];
Or[tuple[[1]]>b,tuple[[2]]>b, tuple[[3]]>b]
]


(* ::Input::Initialization:: *)
thresholdByBeta[odPixels_]:=Select[odPixels, tupleAboveThresholdQ];


(* ::Input::Initialization:: *)
calcSingularValues[a_]:= N[Sqrt[Sort[Eigenvalues[Transpose[a].a],Greater]]]