sphire.convert module¶
- class sphire.convert.CoordBoxReader(boxSize, yFlipHeight=None, boxSizeEstimated=False)[source]¶
Bases:
object
Helper class to read coordinates from .BOX files.
- class sphire.convert.CoordBoxWriter(boxSize, yFlipHeight=None)[source]¶
Bases:
object
Helper class to write a .BOX file for cryolo.
- sphire.convert.convertMicrographs(micList, micDir, prefix='mic')[source]¶
Convert (or simply link) input micrographs into the given directory in a format that is compatible with crYOLO.
- sphire.convert.getFlipYHeight(filename)[source]¶
Return y-Height if flipping is needed, None otherwise
- sphire.convert.getMicIdName(mic, prefix='mic', suffix='')[source]¶
Return a name for the micrograph based on its IDs.
- sphire.convert.readSetOfCoordinates3D(tomogram, coord3DSetDict, coordsFile, boxSize, origin=None)[source]¶
- sphire.convert.roundInputSize(inputSize)[source]¶
Returns the closest value to inputSize th is multiple of 32
- sphire.convert.roundTo(number, base=1.0)[source]¶
Returns the closest int value to number that is multiple of base
- sphire.convert.writeSetOfCoordinates(boxDir, coordSet, micList=None)[source]¶
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.