tomo.convert package

Module contents

tomo.convert.getAnglesFromHeader(tsImage)[source]

Extract the tilt angles from the tilt-series stack using the IMOD program: extracttilts.

tomo.convert.getAnglesFromMdoc(mdocFn)[source]

Return only the angles from the given mdoc file.

tomo.convert.getAnglesFromTlt(tltFn)[source]

Parse the tilt-angles from tlt file.

tomo.convert.parseMdoc(mdocFn)[source]

Parse the mdoc file and return a list with a dict key=value for each of the [Zvalue = X] sections :param mdocFn: Path to the mdoc file :return: list of dictonaries

tomo.convert.writeTiStack(inputTiList, outputStackFn, outputTltFn=None, excludeList=None)[source]

Write a given list of tilt images as a single stack Params:

inputTiList: input list of tilted images. outputStackFn: output path where to write the stack. orderBy: column to sort by, by default tilt angle (ascending) excludeList: a list of indexes of the images to skip (starting at 1)
Results:
A new stack file will be created and also a tlt file with tilt-angles