xmipp3.protocols.protocol_structure_map_zernike3d module

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

Bases: 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]