xmipp3.convert.convert module

This module contains converter functions that will serve to: 1. Write from base classes to Xmipp specific files 2. Read from Xmipp files to base classes

xmipp3.convert.convert.acquisitionToRow(acquisition, ctfRow)

Set labels values from acquisition to md row.

xmipp3.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

xmipp3.convert.convert.class2DToRow(class2D, classRow)

Set labels values from Class2D to md row.

xmipp3.convert.convert.coordinateToRow(coord, coordRow, copyId=True)

Set labels values from Coordinate coord to md row.

xmipp3.convert.convert.createClassesFromImages(inputImages, inputMd, classesFn, ClassType, classLabel, classFnTemplate, alignType, iter, preprocessImageRow=None)

From an intermediate X.xmd file produced by xmipp, create the set of classes in which those images are classified. Params:

inputImages: the SetOfImages that were initially classified by relion. inputMd: the filename metadata. classesFn: filename where to write the classes. ClassType: the output type of the classes set

(usually SetOfClass2D or 3D)

classLabel: label that is the class reference. classFnTemplate: the template to get the classes averages filenames iter: the iteration number, just used in Class template

xmipp3.convert.convert.createClassesFromImages2(inputImages, inputMd, classesFn, ClassType, classLabel, alignType, getClassFn=None, preprocessImageRow=None)

From an intermediate X.xmd file produced by xmipp, create the set of classes in which those images are classified. Params:

inputImages: the SetOfImages that were initially classified by relion. inputMd: the filename metadata. classesFn: filename where to write the classes. ClassType: the output type of the classes set ( usually SetOfClass2D or 3D ) classLabel: label that is the class reference. classFnTemplate: the template to get the classes averages filenames iter: the iteration number, just used in Class template

xmipp3.convert.convert.createItemMatrix(item, row, align)

xmipp3.convert.convert.createParamPhantomFile(filename, dimX, partSetMd, phFlip=False, ctfCorr=False)

xmipp3.convert.convert.ctfModelToRow(ctfModel, ctfRow)

Set labels values from ctfModel to md row.

xmipp3.convert.convert.defocusGroupSetToRow(defocusGroup, defocusGroupRow)

Set labels values from ctfModel to md row.

xmipp3.convert.convert.fillClasses(clsSet, updateClassCallback=None)

Give an empty SetOfClasses (either 2D or 3D). Iterate over the input images and append to the corresponding class. It is important that each image has the classId properly set.

xmipp3.convert.convert.fixVolumeFileName(image)

This method will add :mrc to .mrc volumes because for mrc format is not possible to distinguish between 3D volumes and 2D stacks.

xmipp3.convert.convert.geometryFromMatrix(matrix, inverseTransform)

xmipp3.convert.convert.getImageLocation(image)

xmipp3.convert.convert.getMovieFileName(movie)

Add the :mrcs or :ems extensions to movie files to be recognized by Xmipp as proper stack files.

xmipp3.convert.convert.getScipionObj(value)

xmipp3.convert.convert.getXmippAttribute(obj, label, default=None)

Sets an attribute of an object prefixing it with xmipp

xmipp3.convert.convert.imageToRow(img, imgRow, imgLabel, **kwargs)

xmipp3.convert.convert.locationToXmipp(index, filename)

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

xmipp3.convert.convert.matrixFromGeometry(shifts, angles, inverseTransform)

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

xmipp3.convert.convert.mdToCTFModel(mdIn, mic)

xmipp3.convert.convert.micrographToCTFParam(mic, ctfparam)

This function is used to convert a Micrograph object to the .ctfparam metadata needed by some Xmipp programs. If the micrograph already comes from xmipp, the ctfparam will be returned, if not, the new file.

xmipp3.convert.convert.micrographToRow(mic, micRow, **kwargs)

Set labels values from Micrograph mic to md row.

xmipp3.convert.convert.objectToRow(obj, row, attrDict, extraLabels=[])

This function will convert an EMObject into a Row. Params:

obj: the EMObject instance (input) row: the Row instance (output) -see emlib.metadata.utils.Row()- 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

xmipp3.convert.convert.openMd(fn, state='Manual')

xmipp3.convert.convert.particleToRow(part, partRow, **kwargs)

Set labels values from Particle to md row.

xmipp3.convert.convert.prefixAttribute(attribute)

xmipp3.convert.convert.readAnglesFromMicrographs(micFile, anglesSet)

Read the angles from a micrographs Metadata.

xmipp3.convert.convert.readCTFModel(filename, mic)

Read from Xmipp .ctfparam and create a CTFModel object.

xmipp3.convert.convert.readCoordinates(mic, fileName, coordsSet, outputDir, readDiscarded=False, scale=1)

xmipp3.convert.convert.readPosCoordinates(posFile, readDiscarded=False)

Read the coordinates in .pos file and return corresponding metadata. There are two possible blocks with particles: particles: with manual/supervised particles particles_auto: with automatically picked particles. If posFile doesn’t exist, the metadata will be empty readDiscarded: read only the coordinates in the particles_auto DB

with the MDL_ENABLE set at -1 and a positive cost

xmipp3.convert.convert.readSetOfClasses(classesSet, filename, classesBlock='classes', **kwargs)

xmipp3.convert.convert.readSetOfClasses2D(classes2DSet, filename, classesBlock='classes', **kwargs)

Just a wrapper to readSetOfClasses.

xmipp3.convert.convert.readSetOfClasses3D(classes3DSet, filename, classesBlock='classes', **kwargs)

Just a wrapper to readSetOfClasses.

xmipp3.convert.convert.readSetOfClassesVol(classesVolSet, filename, classesBlock='classes', **kwargs)

read from Xmipp image metadata. fnImages: The metadata filename where the particles properties are. imgSet: the SetOfParticles that will be populated. hasCtf: is True if the ctf information exists.

xmipp3.convert.convert.readSetOfCoordinates(outputDir, micSet, coordSet, readDiscarded=False, scale=1)

Read from Xmipp .pos files. Params:

outputDir: the directory where the .pos files are.

It is also expected a file named: config.xmd in this directory where the box size can be read.

micSet: the SetOfMicrographs to associate the .pos, which

name should be the same of the micrographs.

coordSet: the SetOfCoordinates that will be populated. readDiscarded: read only the coordinates with the MDL_ENABLE set at -1 scale: Factor to scale ONLY x,y coordinates, you are supposed to use an appropiate boxsize (you created the set)

xmipp3.convert.convert.readSetOfImages(filename, imgSet, rowToFunc, **kwargs)

read from Xmipp image metadata. filename: The metadata filename where the image are. imgSet: the SetOfParticles that will be populated. rowToFunc: this function will be used to convert the row to Object

xmipp3.convert.convert.readSetOfMicrographs(filename, micSet, **kwargs)

xmipp3.convert.convert.readSetOfMovieParticles(filename, partSet, **kwargs)

xmipp3.convert.convert.readSetOfParticles(filename, partSet, **kwargs)

xmipp3.convert.convert.readSetOfVolumes(filename, volSet, **kwargs)

xmipp3.convert.convert.readShiftsMovieAlignment(xmdFn)

xmipp3.convert.convert.rowFromMd(mdIn, objId)

xmipp3.convert.convert.rowToAcquisition(acquisitionRow)

Create an acquisition from a row of a metadata.

xmipp3.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

xmipp3.convert.convert.rowToClass(classRow, classItem)

Method base to create a class2D, class3D or classVol from a row of a metadata

xmipp3.convert.convert.rowToCoordinate(coordRow)

Create a Coordinate from a row of a metadata.

xmipp3.convert.convert.rowToCtfModel(ctfRow)

Create a CTFModel from a row of a metadata.

xmipp3.convert.convert.rowToImage(imgRow, imgLabel, imgClass, **kwargs)

Create an Image from a row of a metadata.

xmipp3.convert.convert.rowToMicrograph(micRow, **kwargs)

Create a Micrograph object from a row of Xmipp metadata.

xmipp3.convert.convert.rowToMovieParticle(partRow, **kwargs)

xmipp3.convert.convert.rowToObject(row, obj, attrDict, extraLabels=[])

This function will convert from a Row to an EMObject. Params:

row: the Row instance (input) -see emlib.metadata.utils.Row()- 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 _xmipp_labelName

xmipp3.convert.convert.rowToParticle(partRow, **kwargs)

xmipp3.convert.convert.rowToVolume(volRow, **kwargs)

Create a Volume object from a row of Xmipp metadata.

xmipp3.convert.convert.setObjId(obj, mdRow, label=186)

xmipp3.convert.convert.setOfImagesToMd(imgSet, mdIn, imgToFunc, **kwargs)

This function will fill Xmipp metadata from a SetOfMicrographs Params:

imgSet: the set of images to be converted to metadata mdIn: metadata to be filled rowFunc: this function can be used to setup the row before

adding to metadata.

xmipp3.convert.convert.setOfMicrographsToMd(imgSet, mdMics, **kwargs)

xmipp3.convert.convert.setOfParticlesToMd(imgSet, mdParts, **kwargs)

xmipp3.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.

xmipp3.convert.convert.setRowId(mdRow, obj, label=186)

xmipp3.convert.convert.setXmippAttribute(obj, label, value)

Sets an attribute of an object prefixing it with xmipp

xmipp3.convert.convert.setXmippAttributes(obj, objRow, *labels, **kwargs)

Set the labels attribute(s) to obj from a objRow (those not basic ones). More than one label can be set and default can also be a list of same number of entries. The new attribute will be named _xmipp_LabelName and the datatype will be set correctly. If obj doesn’t contain a label and a default value is in kwargs, it’s set in its corresponding Scipion datatype.

xmipp3.convert.convert.volumeToRow(vol, volRow, **kwargs)

Set labels values from Micrograph mic to md row.

xmipp3.convert.convert.writeCTFModel(ctfModel, ctfFile)

Given a CTFModel object write as Xmipp ctfparam

xmipp3.convert.convert.writeCoordsConfig(configFn, boxSize, state)

Write the config.xmd file needed for Xmipp picker. Params:

configFn: The filename were to store the configuration. boxSize: the box size in pixels for extraction. state: picker state

xmipp3.convert.convert.writeMicCoordinates(mic, coordList, outputFn, isManual=True, getPosFunc=None)

Write the pos file as expected by Xmipp with the coordinates of a given micrograph. Params:

mic: input micrograph. coordList: list of (x, y) pairs of the mic coordinates. outputFn: output filename for the pos file . isManual: if the coordinates are ‘Manual’ or ‘Supervised’ getPosFunc: a function to get the positions from the coordinate,

it can be useful for scaling the coordinates if needed.

xmipp3.convert.convert.writeMovieMd(movie, outXmd, f1, fN, useAlignment=False)

xmipp3.convert.convert.writeSetOfCTFs(ctfSet, mdCTF)

Write a ctfSet on metadata format. Params:

ctfSet: the SetOfCTF that will be read. mdCTF: The file where metadata should be written.

xmipp3.convert.convert.writeSetOfClasses2D(classes2DSet, filename, classesBlock='classes', writeParticles=True)

This function will write a SetOfClasses2D as Xmipp metadata. Params:

classes2DSet: the SetOfClasses2D instance. filename: the filename where to write the metadata.

xmipp3.convert.convert.writeSetOfClassesVol(classesVolSet, filename, classesBlock='classes')

This function will write a SetOfClassesVol as Xmipp metadata. Params:

classesVolSet: the SetOfClassesVol instance. filename: the filename where to write the metadata.

xmipp3.convert.convert.writeSetOfCoordinates(posDir, coordSet, ismanual=True, scale=1)

xmipp3.convert.convert.writeSetOfCoordinatesWithState(posDir, coordSet, state, scale=1)

Write a pos file on metadata format for each micrograph on the coordSet. Params:

posDir: the directory where the .pos files will be written. coordSet: the SetOfCoordinates that will be read.

xmipp3.convert.convert.writeSetOfDefocusGroups(defocusGroupSet, fnDefocusGroup)

Write a defocuGroupSet on metadata format. Params:

defocusGroupSet: the SetOfDefocus that will be read. fnDefocusGroup: The file where defocusGroup should be written.

xmipp3.convert.convert.writeSetOfImages(imgSet, filename, imgToFunc, blockName='Images', **kwargs)

This function will write a SetOfImages as a Xmipp 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.

xmipp3.convert.convert.writeSetOfMicrographs(micSet, filename, blockName='Micrographs', **kwargs)

xmipp3.convert.convert.writeSetOfMicrographsPairs(uSet, tSet, filename)

This function will write a MicrographsTiltPair as Xmipp metadata. Params:

uSet: the untilted set of micrographs to be written tSet: the tilted set of micrographs to be written filename: the filename where to write the metadata.

xmipp3.convert.convert.writeSetOfMovies(moviesSet, filename, moviesBlock='movies')

This function will write a SetOfMovies as Xmipp metadata. Params:

moviesSet: the SetOfMovies instance. filename: the filename where to write the metadata.

xmipp3.convert.convert.writeSetOfParticles(imgSet, filename, blockName='Particles', **kwargs)

xmipp3.convert.convert.writeSetOfVolumes(volSet, filename, blockName='Volumes', **kwargs)

xmipp3.convert.convert.writeShiftsMovieAlignment(movie, xmdFn, s0, sN)

xmipp3.convert.convert.xmippToLocation(xmippFilename)

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