relion.convert.convert_deprecated module¶
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relion.convert.convert_deprecated.
acquisitionToRow
(acquisition, ctfRow)[source]¶ Set labels values from acquisition to md row.
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relion.convert.convert_deprecated.
alignmentToRow
(alignment, alignmentRow, alignType)[source]¶ - is2D == True-> matrix is 2D (2D images alignment)
- otherwise matrix is 3D (3D volume alignment or projection)
- invTransform == True -> for xmipp implies projection
- -> for xmipp implies alignment
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relion.convert.convert_deprecated.
coordinateToRow
(coord, coordRow, copyId=True)[source]¶ Set labels values from Coordinate coord to md row.
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relion.convert.convert_deprecated.
copyOrLinkFileName
(imgRow, prefixDir, outputDir, copyFiles=False)[source]¶
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relion.convert.convert_deprecated.
ctfModelToRow
(ctfModel, ctfRow)[source]¶ Set labels values from ctfModel to md row.
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relion.convert.convert_deprecated.
matrixFromGeometry
(shifts, angles, inverseTransform)[source]¶ Create the transformation matrix from a given 2D shifts in X and Y…and the 3 euler angles.
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relion.convert.convert_deprecated.
objectToRow
(obj, row, attrDict, extraLabels=[])[source]¶ This function will convert an EMObject into a XmippMdRow. Params:
obj: the EMObject instance (input) row: the XmippMdRow instance (output) attrDict: dictionary with the map between obj attributes(keys) and
row MDLabels in Xmipp (values).- extraLabels: a list with extra labels that could be included
- as _xmipp_labelName
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relion.convert.convert_deprecated.
particleToRow
(part, partRow, **kwargs)[source]¶ Set labels values from Particle to md row.
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relion.convert.convert_deprecated.
readSetOfCoordinates
(coordSet, coordFiles, micList=None)[source]¶ Read a set of coordinates from given coordinate files associated to some SetOfMicrographs. Params:
micSet and coordFiles should have same length and same order. coordSet: empty SetOfCoordinates to be populated.
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relion.convert.convert_deprecated.
readSetOfParticles
(filename, imgSet, rowToFunc=<function rowToParticle>, **kwargs)[source]¶ read from Relion image meta filename: The metadata filename where the image are. imgSet: the SetOfParticles that will be populated. rowToParticle: this function will be used to convert the row to Object
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relion.convert.convert_deprecated.
rowToAcquisition
(acquisitionRow)[source]¶ Create an acquisition from a row of a meta
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relion.convert.convert_deprecated.
rowToAlignment
(alignmentRow, alignType)[source]¶ - is2D == True-> matrix is 2D (2D images alignment)
- otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
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relion.convert.convert_deprecated.
rowToCoordinate
(coordRow)[source]¶ Create a Coordinate from a row of a meta
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relion.convert.convert_deprecated.
rowToCtfModel
(ctfRow)[source]¶ Create a CTFModel from a row of a meta
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relion.convert.convert_deprecated.
rowToObject
(row, obj, attrDict, extraLabels=[])[source]¶ This function will convert from a XmippMdRow to an EMObject. Params:
row: the XmippMdRow instance (input) obj: the EMObject instance (output) attrDict: dictionary with the map between obj attributes(keys) and
row MDLabels in Xmipp (values).- extraLabels: a list with extra labels that could be included
- as properties with the label name such as: _rlnSomeThing
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relion.convert.convert_deprecated.
rowToParticle
(partRow, particleClass=<class 'pwem.objects.data.Particle'>, **kwargs)[source]¶ Create a Particle from a row of a meta
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relion.convert.convert_deprecated.
rowToVolume
(volRow, **kwargs)[source]¶ Create a Volume object from a row of metadata.
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relion.convert.convert_deprecated.
setOfImagesToMd
(imgSet, imgMd, imgToFunc, **kwargs)[source]¶ This function will fill Relion metadata from a SetOfMicrographs Params:
imgSet: the set of images to be converted to metadata md: metadata to be filled rowFunc: this function can be used to setup the row before
adding to meta
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relion.convert.convert_deprecated.
setPsdFiles
(ctfModel, ctfRow)[source]¶ Set the PSD files of CTF estimation related to this ctfModel. The values will be read from the ctfRow if present.
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relion.convert.convert_deprecated.
setupCTF
(imgRow, sampling)[source]¶ Do some validations and set some values for Relion import.
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relion.convert.convert_deprecated.
volumeToRow
(vol, volRow, **kwargs)[source]¶ Set labels values from Micrograph mic to md row.
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relion.convert.convert_deprecated.
writeReferences
(inputSet, outputRoot, useBasename=False, **kwargs)[source]¶ Write references star and stack files from SetOfAverages or SetOfClasses2D/3D. Params:
inputSet: the input SetOfParticles to be converted outputRoot: where to write the output files. basename: If True, use the basename of the stack for setting path.
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relion.convert.convert_deprecated.
writeSetOfImages
(imgSet, filename, imgToFunc, blockName='Images', **kwargs)[source]¶ This function will write a SetOfImages as metadata. Params:
imgSet: the set of images to be written (particles, micrographs or volumes) filename: the filename where to write the metadata.` rowFunc: this function can be used to setup the row before
adding to metadata.