imod.utils module

This module contains utils functions for IMOD protocols

imod.utils.calculateRotationAngleFromTM(ts)

This method calculates que average tilt image rotation angle from its associated transformation matrix.

imod.utils.format3DCoordinatesList(coordFilePath)

This method takes an 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)

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)

This method takes an 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)

This method takes an 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)

This method takes an 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.formatGoldBead3DCoordinatesList(coordFilePath)

This method takes the IMOD-based gold bead 3D coordinates obtained with find3dbeads program file path and returns a list containing each coordinate for each bead belonging to the tilt-series

imod.utils.formatTransformFile(ts, transformFilePath)

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.formatTransformFileFromTransformList(transformMatrixList, transformFilePath)

This method takes a list of Transform matrices and the output transformation file path and creates an IMOD-based transform file in the location indicated. :param transformMatrixList: list of transformation matrices to be writter in file. :param transformFilePath: output location of the file.

imod.utils.formatTransformationMatrix(matrixFile)

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

imod.utils.generateCutOnFreqDictionary(ctfTomoSeries)

This method generates a dictionary containing the cut-on frequency estimation information from a ctfTomoSeries object.

imod.utils.generateDefocusAngleDictionary(ctfTomoSeries)

This method generates a dictionary containing the defocus angle estimation information from a ctfTomoSeries object.

imod.utils.generateDefocusIMODFileFromObject(ctfTomoSeries, defocusFilePath, isRelion=False)

This methods takes a ctfTomoSeries object a generate a defocus information file in IMOD formatting containing the same information in the specified location.

imod.utils.generateDefocusUDictionary(ctfTomoSeries)

This method generates a dictionary containing the defocus U estimation information from a ctfTomoSeries object.

imod.utils.generateDefocusVDictionary(ctfTomoSeries)

This method generates a dictionary containing the defocus V estimation information from a ctfTomoSeries object.

imod.utils.generateDoseFileFromAccDoseTS(ts, doseFileOutputPath)

This method generates a file containing the dose information of a tilt series in the specified location from the accumulated dose per tilt information. The format file consist in a single column with one dose value per line that must coincide with each image from the tilt-series

imod.utils.generateDoseFileFromDoseTS(ts, doseFileOutputPath)

This method generates a file containing the dose information of a tilt series in the specified location from the dose per tilt information. The format file consist in a single column with one dose value per line that must coincide with each image from the tilt-series

imod.utils.generateIMODFiducialTextFile(landmarkModel, outputFilePath)

This method takes a Scipion LandmarkModel object and generates a text file in the sepecified location in IMOD convention that contains the information of the position of each fiducial through the tilt-series. :param landmarkModel: landmarkModel Scipion object. :param outputFilePath: location where the output file must be saved.

imod.utils.generatePhaseShiftDictionary(ctfTomoSeries)

This method generates a dictionary containing the phase shift estimation information from a ctfTomoSeries object.

imod.utils.getDefocusFileFlag(defocusFilePath)

This method returns the flag that indicate the information contained in an IMOD defocus file. The flag value “is the sum of:

1 if the file has astigmatism values 2 if the astigmatism axis angle is in radians, not degrees 4 if the file has phase shifts 8 if the phase shifts are in radians, not degrees

16 if tilt angles need to be inverted to match what the

program expects (what Ctfplotter would produce) with the -invert option

32 if the file has cut-on frequencies attenuating the phase

at low frequencies”

from https://bio3d.colorado.edu/imod/doc/man/ctfphaseflip.html

imod.utils.readCTFEstimationInfoFile(defocusFilePath, flag)

This method takes an IMOD-based file path containing the information associated to a CTF estimation and produces a set of dictionaries containing the information of each parameter for each tilt-image belonging to the tilt-series. These dictionaries are readable information for Scipion, useful to generate the corresponding output CTFTomoSeries object.

imod.utils.readDefocusFileAsTable(defocusFilePath)

This method takes an IMOD-based ctf estimation file path and returns a table containing the CTF estimation information of each tilt-image (per line) belonging to the tilt-series.

imod.utils.readExcludeViewsFile(excludeViewsFilePath)

Thie method retrieves from a input exclude views file path a matrix with two columns containing the tsId of tilt-series from which exlude the views in the first column and in the second a string with the pattern of the excluded views

imod.utils.refactorCTFDefocusAstigmatismPhaseShiftCutOnFreqEstimationInfo(ctfInfoIMODTable)

This method takes a table containing the information of an IMOD-based CTF estimation containing defocus, astigmatism, phase shift information and cut-on frequency (8 columns) and produces a new set of dictionaries containing the same information in a format readable for Scipion. Flag 37.

imod.utils.refactorCTFDefocusAstigmatismPhaseShiftEstimationInfo(ctfInfoIMODTable)

This method takes a table containing the information of an IMOD-based CTF estimation containing defocus, astigmatism and phase shift information (8 columns) and produces a new set of dictionaries containing the same information in a format readable for Scipion. Flag 5.

imod.utils.refactorCTFDefocusEstimationInfo(ctfInfoIMODTable)

This method takes a table containing the information of an IMOD-based CTF estimation containing only defocus information (5 columns) and produces a new dictionary containing the same information in a format readable for Scipion. Flag 0.

imod.utils.refactorCTFDefocusPhaseShiftEstimationInfo(ctfInfoIMODTable)

This method takes a table containing the information of an IMOD-based CTF estimation containing defocus, and phase shift information (6 columns) and produces a new set of dictionaries containing the same information in a format readable for Scipion. Flag 4.

imod.utils.refactorCTFDesfocusAstigmatismEstimationInfo(ctfInfoIMODTable)

This method takes a table containing the information of an IMOD-based CTF estimation containing defocus and astigmatism information (7 columns) and produces a set of dictionaries table containing the same information in a format readable for Scipion. Flag 1.