sphire.convert module

class sphire.convert.CoordBoxReader(boxSize, yFlipHeight=None, boxSizeEstimated=False)

Bases: object

Helper class to read coordinates from .BOX files.

close()

iter3DCoords()

iterCoords()

open(filename)

Open a new filename to write, close previous one if open.

class sphire.convert.CoordBoxWriter(boxSize, yFlipHeight=None)

Bases: object

Helper class to write a .BOX file for cryolo.

close()

open(filename)

Open a new filename to write, close previous one if open.

writeCoord(coord)

sphire.convert.convertMicrographs(micList, micDir, prefix='mic')

Convert (or simply link) input micrographs into the given directory in a format that is compatible with crYOLO.

sphire.convert.convertTomograms(micList, micDir)

sphire.convert.getFlipYHeight(filename)

Return y-Height if flipping is needed, None otherwise

sphire.convert.getMicIdName(mic, prefix='mic', suffix='')

Return a name for the micrograph based on its IDs.

sphire.convert.needToFlipOnY(filename)

Returns true if need to flip coordinates on Y

sphire.convert.readSetOfCoordinates3D(tomogram, coord3DSetDict, coordsFile, boxSize, origin=None)

sphire.convert.roundInputSize(inputSize)

Returns the closest value to inputSize th is multiple of 32

sphire.convert.roundTo(number, base=1.0)

Returns the closest int value to number that is multiple of base

sphire.convert.writeSetOfCoordinates(boxDir, coordSet, micList=None)

Convert a SetOfCoordinates to Cryolo box files. Params:

boxDir: the output directory where to generate the files. coordSet: the input SetOfCoordinates that will be converted. micList: if not None, only coordinates from this micrographs

will be written.