imod.utils module

This module contains utils functions for IMOD protocols

imod.utils.format3DCoordinatesList(coordFilePath, xDim, yDim)[source]

This method takes the IMOD-based fiducial coordinates file path and returns a list containing each coordinate for each fiducial belonging to the tilt-series

imod.utils.formatAngleFile(inputTs, angleFilePath)[source]

This method takes a list containing the angles for each tilt-image belonging to the tilt-series and writes the IMOD-based angle file at the given location

imod.utils.formatAngleList(tltFilePath)[source]

This method takes the IMOD-based angle file path and returns a list containing the angles for each tilt-image belonging to the tilt-series

imod.utils.formatFiducialList(fiducialFilePath)[source]

This method takes the IMOD-based fiducial model file path and returns a list containing the coordinates of each fiducial for each tilt-image belonging to the tilt-series

imod.utils.formatFiducialResidList(fiducialFilePath)[source]

This method takes the IMOD-based fiducial residual model file path and returns a list containing the coordinates and residual values of each fiducial for each tilt-image belonging to the tilt-series. Since IMOD establishes a float value for each coordinate the are parsed to int

imod.utils.formatTransformFile(ts, transformFilePath)[source]

This method takes a tilt series and the output transformation file path and creates an IMOD-based transform file in the location indicated

imod.utils.formatTransformationMatrix(matrixFile)[source]

This method takes the IMOD-based transformation matrix file path and returns a 3D matrix containing the transformation matrices for each tilt-image belonging to the tilt-series