Module classes
Classes have been documented using sphinx.ext.autodoc and the docstring
style extension ‘sphinx.ext.napoleon’:
- class Modules.classes.AFMimg(xvalues, yvalues, zvalues, filename, directory)
A class that contains the x-, y-, z-values, filename and directory of the raw AFM file
- xvalues
N dimensional array with type float that contains the x-values of the igor pro height trace data
- Type
ndarray
- yvalues
N dimensional array with type float that contains the y-values of the igor pro height trace data
- Type
ndarray
- zvalues
N dimensional array with type float that contains the z-values of the igor pro height trace data
- Type
ndarray
- create_directory(directory, name)
Creates a new directory
- class Modules.classes.contAFMimg(xvalues, yvalues, zvalues, filename, directory, propAFMimg, rect_del, rect2_del, rect_exp, cnt_all, cnt_del, img_cnt, img_gr, img_rgb, coord, cdrawn)
A class which inherits from AFMimg and contains the contour and the rectangles covering the objects in the image
- rect_del
1 dimensional array with type rectangle that contains rectangles around contours
- Type
ndarray
- rect2_del
1 dimensional array with type int, rectangle that contains rectangles around clicked coordinates
- Type
ndarray
- rect_exp
1 dimensional array with type rectangle that contains the not selected expanded rectangles
- Type
ndarray
- cnt_all
1 dimensional array with type contours that were not selected manually
- Type
ndarray
- cnt_del
1 dimensional array with type contours that contains all not selected contours in the loop
- Type
ndarray
- img_cnt
N dimensional array with type int that contains all not selected contours
- Type
image
- img_gr
N dimensional array with type float that contains a greyscale image of the original image
- Type
ndarray
- img_rgb
N dimensional array with type float that contains img_gr as rgb image with detected contours
- Type
ndarray
- coord
N dimensional array with type float that contains the coordinates of points inside manually selected rectangles/contours
- Type
ndarray
- cdrawn
1 dimensional array with type int, int, float, float that contains the index of a rectangle with corresponding contour, the x- and y-coordinate of the contour
- Type
ndarray
- class Modules.classes.propAFMimg(xvalues, yvalues, zvalues, filename, directory, imgh, imgw, imgrh, imgrw, thr)
A class which inherits from AFMimg and contains size, threshold value and the expansion factor of the rectangles covering the objects in the image
- class Modules.classes.LMimg(orig, values, val_enh, filename, directory)
A class that contains the x-, y-, z-values, filename and directory of the raw LM file
- orig
N dimensional array with type int that contains the colour values of the LM image
- Type
ndarray
- values
N dimensional array with type int that contains the greyscale values of the LM image
- Type
ndarray
- val_enh
N dimensional array with type int that contains the enhanced LM image
- Type
ndarray
- create_directory(directory, name)
Creates a new directory
- class Modules.classes.contLMimg(orig, values, val_enh, filename, directory, propLMimg, rect_del, rect2_del, rect_exp, cnt_all, cnt_del, img_cnt, img_gr, img_rgb, coord, cdrawn)
A class which inherits from LMimg and contains the contour and the rectangles covering the objects in the image
- rect_del
1 dimensional array with type rectangle that contains rectangles around contours
- Type
ndarray
- rect2_del
1 dimensional array with type int, rectangle that contains rectangles around clicked coordinates
- Type
ndarray
- rect_exp
1 dimensional array with type rectangle that contains the not selected expanded rectangles
- Type
ndarray
- cnt_all
1 dimensional array with type contours that were not selected manually
- Type
ndarray
- cnt_del
1 dimensional array with type contours that contains all not selected contours in the loop
- Type
ndarray
- img_cnt
N dimensional array with type int that contains all not selected contours
- Type
image
- img_gr
N dimensional array with type float that contains a greyscale image of the original image
- Type
ndarray
- img_rgb
N dimensional array with type float that contains img_gr as rgb image with detected contours
- Type
ndarray
- coord
N dimensional array with type float that contains the coordinates of points inside manually selected rectangles/contours
- Type
ndarray
- cdrawn
1 dimensional array with type int, int, float, float that contains the index of a rectangle with corresponding contour, the x- and y-coordinate of the contour
- Type
ndarray
- class Modules.classes.propLMimg(orig, values, val_enh, filename, directory, imgh, imgw, imgrh, imgrw, thr)
A class which inherits from LMimg and contains size, threshold value of the LM image
- class Modules.classes.Cell(img, gfimg, zcut2, label, cntCell, centre, mcentre, radius, rectChange, offset)
A class that contains the geometric properties of a cell
- img
N x N x N dimensional array that contains the extracted cell images
- Type
ndarray
- gfimg
N x N x N dimensional array that contains the gaussian filtered images
- Type
ndarray
- zcut2
N x 2 dimensional array with type float that contains two extracted cuts
- Type
ndarray
- label
N dimensional array with type str that contains the labels of the images
- Type
ndarray
- cntCell
N x N X (1, 1) dimensional array with type (int, int) that contains the contour of the cells
- Type
ndarray
- centre
N x (1, 1) dimensional array with type (float, float) that contains the centre of the cell
- Type
ndarray
- mcentre
N x (1, 1) dimensional array with type (float, float) that contains the centre of mass of the cell
- Type
ndarray
- radius
N dimensional array with type float that contains the radius of the detected circle
- Type
ndarray
- rectChange
N x (1, 1, 1, 1, 1, 1, 1) dimensional array with type float that contains the bounding coordinates of the bounding rectangle around a cell
- Type
ndarray
- offset
N x (1, 1) dimensional array with type float that contains the x and y offset of the cropped image
- Type
ndarray
- calc_cellCnt(circle_found, img_hc, directory)
Calculates the coordinates of the cell contour
- Parameters
circle_found (ndarray) – N x (1, 1, 1) dimensional array with type float that contains the centre and the radius of the detected circle
img_hc (ndarray) – N x N dimensional array that contains the normalised zvalues
- calc_geomP()
Calculates the coordinates inside the cell, its centre, and its centre of mass
- extract_cut(circle_found, imgh, imgw, imgrh, imgrw)
Extracts cut from cell image
- Parameters
circle_found (ndarray) – N x (1, 1, 1) dimensional array with type float that contains the centre and the radius of the detected circle
imgh (float) – The height of the image in µm
imgw (float) – The width of the image in µm
imgrh (int) – The resolution of the yvalues
imgrw (int) – The resolution of the xvalues