xmipp3.protocols.protocol_structure_map_zernike3d module

class xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D(**args)[source]

Bases: pwem.protocols.protocol_3d.ProtAnalysis3D

Protocol for structure mapping based on Zernike3D.

ALIGNED_VOL = 'vol%dAligned.mrc'
OUTPUT_SUFFIX = '_%d_crop.mrc'
alignStep(inputVolFn, refVolFn, i, j)[source]
computeCorr(vol1, vol2, i, j)[source]
convertStep(volFn, volDim, volSr, minDim, maxSr, nVoli)[source]
convolution(Xr, kernel, sigma, R, C, D)[source]
correlationMatrix(volList)[source]
deformStep(inputVolFn, refVolFn, i, j, step_id)[source]
deformationMatrix(volList)[source]
entropyConsensus()[source]
gatherResultsStepCorr()[source]
gatherResultsStepDef()[source]
gaussianKernel(sigma, i)[source]
rigidAlignmentMapping(i)[source]
saveCorrelation(matrix, fnRoot, label='')[source]
saveDeformation(matrix, fnRoot, label='')[source]
split(array, nrows, ncols)[source]

Split a matrix into sub-matrices.

validate()[source]

Try to find errors on define params.

xmipp3.protocols.protocol_structure_map_zernike3d.mds(d, dimensions=2)[source]

Multidimensional Scaling - Given a matrix of interpoint distances, find a set of low dimensional points that have similar interpoint distances.

xmipp3.protocols.protocol_structure_map_zernike3d.rigidRegistration(X, Y)[source]