spider.convert module

spider.convert.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
spider.convert.convertEndian(stackFn, stackSize)[source]

Convert the stack file generated by Xmipp to one that Spider likes more. Params:

stackFn: the filename of the images stack stackSize: the number of particles in the stack
spider.convert.createItemMatrix(item, row, align)[source]
spider.convert.geometryFromMatrix(matrix, inverseTransform)[source]
spider.convert.locationToSpider(index, filename)[source]

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

spider.convert.matrixFromGeometry(shifts, angles, inverseTransform)[source]

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

spider.convert.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

spider.convert.spiderToLocation(spiderFilename)[source]

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

spider.convert.writeSetOfImages(imgSet, stackFn, selFn)[source]

Write a SetOfMicrographs as a Spider stack and selfile. Params:

imgSet: the SetOfMicrograph instance. stackFn: the filename where to write the stack. selFn: the filename of the Spider selection file.