plot_gmx_densmap

Read up to three matrices from text files and plot them as one RGB matrix with matplotlib.axes.Axes.imshow().

Each matrix must be stored in a separate text file. The first column of the text files must contain the x values and the first row the y values (note that this is opposed to the standard matrix convention). The value in the upper left corner will be ignored. The remaining elements of the matrix must contain the z values for each (x,y) pair. The file may contain comment lines starting with ‘#’, which will be ignored.

Options

-r

File containing the matrix that shall be represented as red levels in the final RGB matrix.

-g

File containing the matrix that shall be represented as green levels in the final RGB matrix.

-b

File containing the matrix that shall be represented as blue levels in the final RGB matrix.

Note that at least one of the -r, -g and -b flag must be provided. If multiple matrices are given, all matrices must have the same shape and the same x and y values. The input matrices must not contain negative values.

-o

Output filename.

-c

Eliminate values below a certain cutoff in the final RGB matrix to suppress noise. The values of each RGB channel are normalized to the interval [0, 1] (not [0,255] as usual). Default: 0.

--Otsu

Use Otsu’s binarization[1] to automatically calculate a cutoff. If --Otsu is set, -c will be ignored. This option requires the opencv-python package.

--xylabel

x- and y-axis label. Default: [r'$x$ / nm', r'$y$ / nm'].

--xlim

Left and right limit of the x-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. Default: [None, None].

--ylim

Lower and upper limit of the y-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. Default: [None, None].

--xticks-at-yticks

Set x-ticks at the same positions as y-ticks.