xmipp3.protocols.protocol_preprocess.protocol_preprocess module
- class xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippPreprocessHelper[source]
Bases:
objectHelper class that contains some Protocol utilities methods used by both XmippProtPreprocessParticles and XmippProtPreprocessVolumes.
- class xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles(**kwargs)[source]
Bases:
XmippProcessParticlesPreprocesses particle images by applying the optional steps: dust removal, randomize phase, normalize, center images, phase flip images, invert contrast, threshold, fill with below, abs_bellow or above, a threshold grey value below which all voxels should be set to 0, fill value or substitute by value binarize or average. This cleaning stage improves particle quality and consistency for downstream tasks.
- NORM_NEW = 1
- NORM_OLD = 0
- NORM_RAMP = 2
- class xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes(**kwargs)[source]
Bases:
XmippProcessVolumesPreprocesses 3D volumes using Xmipp tools to prepare them for further analysis. Operations include: normalization, change hand, change icosahedral orientation, randomize phase, symmetry, symmetry group, aggregation mode, wrap, apply Laplacian, mask volume. adjust gray value, segment, normalize background, invert contrast and threshold.
- AGG_AVERAGE = 0
- AGG_SUM = 1
- SEG_AMIN = 1
- SEG_AUTO = 3
- SEG_DALTON = 2
- SEG_VOXEL = 0