The keypoint coordinates are extracted from the heatmap via:

The indices returned by np.where, respectively np.nonzero are in order of the dimensions. In a NumPy array, the first dimension is along the rows (i.e. the y coordinates in an image), the second dimension is along the columns (i.e. the x coordinates in an image).

Hence, syntactically this should be:

ys, xs = np.where(heatmap >= self.conf_thresh) # Confidence threshold.
# [...]
pts[0, :] = xs
pts[1, :] = ys
pts[2, :] = heatmap[ys, xs]

The actual variable name does not matter later, as those values are correctly normalised.