pysted.base.Datamap

class pysted.base.Datamap(whole_datamap, datamap_pixelsize)

This class implements a datamap, containing a disposition of molecules and a ROI to image.

The Datamap can be a composition of multiple parts, for instance, a ‘base’, which is static, a ‘flashes’ part, which represents only the flashes occuring in the Datamap, or a ‘diffusing’ part, which would represent only the moving molecules in the Datamap. The ROI represents the portion of the Datamap that will be imaged. Since the microscope’s lasers are represented by arrays, we must ensure that the laser array’s edges are contained within the whole Datamap array for every pixel of the ROI. To facilitated this, the ROI can be set to ‘max’, which will simply 0 pad the passed whole_datamap so the laser stays confined when scanning over the pixels of the whole_datamap.

Parameters:

• whole_datamap – The disposition of the molecules in the sample. This represents the whole sample, from which only a region will be imaged (roi). (numpy array)

• datamap_pixelsize – The size of a pixel of the datamap. (m)

Datamap.set_bleached_datamap(bleached_datamap)	Updates the datamap.
Datamap.set_roi(laser[, intervals])	Sets the Region of Interest for the acquisition.