cryosparc2.convert.convert module

cryosparc2.convert.convert.acquisitionToRow(acquisition, ctfRow)

Set labels values from acquisition to md row.

cryosparc2.convert.convert.addRandomSubset(img, imgRow)

cryosparc2.convert.convert.alignmentToRow(alignment, alignmentRow, alignType)

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

cryosparc2.convert.convert.convertBinaryFiles(imgSet, outputDir, extension='mrcs')

Convert binary images files to a format read by Cryosparc. Params:

imgSet: input image set to be converted. outputDir: where to put the converted file(s)

Return:

A dictionary with old-file as key and new-file as value If empty, not conversion was done.

cryosparc2.convert.convert.convertBinaryVol(vol, outputDir)

Convert binary volume to a format read by Cryosparc. Params:

vol: input volume object to be converted. outputDir: where to put the converted file(s)

Return:

new file name of the volume (converted or not).

cryosparc2.convert.convert.convertCs2Star(args)

cryosparc2.convert.convert.coordinateToRow(coord, coordRow, copyId=True)

Set labels values from Coordinate coord to md row.

cryosparc2.convert.convert.createItemMatrix(item, row, align)

cryosparc2.convert.convert.cryosPARCwriteSetOfParticles(imgSet, starFile, outputDir, **kwargs)

cryosparc2.convert.convert.cryosparcToLocation(filename)

Return a location (index, filename) given a cryoSPARC filename with the index@filename structure.

cryosparc2.convert.convert.ctfModelToRow(ctfModel, ctfRow)

Set labels values from ctfModel to md row.

cryosparc2.convert.convert.defineArgs()

cryosparc2.convert.convert.geometryFromMatrix(matrix, inverseTransform)

cryosparc2.convert.convert.imageToRow(img, imgRow, imgLabel='rlnImageName', **kwargs)

cryosparc2.convert.convert.locationToCryosparc(index, filename)

Convert an index and filename location to a string with @ as expected in cryoSPARC.

cryosparc2.convert.convert.matrixFromGeometry(shifts, angles, inverseTransform)

Create the transformation matrix from a given 2D shifts in X and Y…and the 3 euler angles.

cryosparc2.convert.convert.objectToRow(obj, row, attrDict, extraLabels=[])

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

cryosparc2.convert.convert.particleToRow(part, partRow, **kwargs)

Set labels values from Particle to md row.

cryosparc2.convert.convert.readSetOfParticles(filename, partSet, **kwargs)

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

cryosparc2.convert.convert.rowToAcquisition(acquisitionRow)

Create an acquisition from a row of a meta

cryosparc2.convert.convert.rowToAlignment(alignmentRow, alignType)

is2D == True-> matrix is 2D (2D images alignment)

otherwise matrix is 3D (3D volume alignment or projection)

invTransform == True -> for xmipp implies projection

cryosparc2.convert.convert.rowToCoordinate(coordRow)

Create a Coordinate from a row of a meta

cryosparc2.convert.convert.rowToCtfModel(ctfRow)

Create a CTFModel from a row of a meta

cryosparc2.convert.convert.rowToObject(row, obj, attrDict, extraLabels=[])

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

cryosparc2.convert.convert.rowToParticle(partRow, particleClass=<class 'pwem.objects.data.Particle'>, **kwargs)

Create a Particle from a row of a meta

cryosparc2.convert.convert.setCryosparcAttributes(obj, objRow, *labels)

Set an attribute to obj from a label that is not basic ones. The new attribute will be named _rlnLabelName and the datatype will be set correctly.

cryosparc2.convert.convert.setObjId(obj, mdRow, label='rlnImageId')

cryosparc2.convert.convert.setOfImagesToMd(imgSet, imgMd, imgToFunc, **kwargs)

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

cryosparc2.convert.convert.setPsdFiles(ctfModel, ctfRow)

Set the PSD files of CTF estimation related to this ctfModel. The values will be read from the ctfRow if present.

cryosparc2.convert.convert.setRowId(mdRow, obj, label='rlnImageId')

cryosparc2.convert.convert.strip_path_uids1(df, inplace=False, count=- 1)

cryosparc2.convert.convert.writeSetOfParticles(imgSet, fileName, extraPath)