The architecture of spipy package is shown as below:

• analyse : diffraction experiment data analysis
  • q
    • cal_q : calculate q values in k-space
    • cal_q_pat : calculate q values of a pattern
    • cal_r : calculate radius list on detector corresponding to a q-list
    • oversamp_rate : calculate oversampling rate
    • ewald_mapping : map detector pixels onto ewald sphere
  • saxs
    • grid : calculate grid of a pattern
    • friedel_search : return the central point (zero frequency) of a pattern
    • center_refine : refine the center coordinates from ‘friedel_search’
    • inten_profile_vaccurate : the averaged intensity radial profile
    • inten_profile_vfast : fast calculation of intensity profile
    • cal_saxs : calculate saxs/powder pattern of a dataset
    • centering : shift the input pattern to make its geometry center as q=0 point
    • particle_size : estimate particle size through saxs pattern
    • particle_size_sp : fit the diameter of spherical-like samples by using Iq curve of diffraction patterns
  • orientation
    • Sphere_randp : return random/uniform distributed points on a spherical surface
    • proc_Hammer : transfer quaternions to Aitoff-Hammer projection coordinates
    • draw_Hammer : plot Aitoff-Hammer projection coordinates
    • draw_ori_Df : draw figure to show orientation distribution of DragonFly output
  • criterion
    • r_factor : overall r-factor between two models
    • r_factor_shell : r-factor on different q values between two models
    • fsc : Fourier Shell Correlation between two models (in reciprocal space)
    • r_split : r-split factors between two models (in reciprocal space)
    • Pearson_cc : Pearson correlation coefficient between two arrays
    • PRTF : Phase Retrieval Transfer Function of phased dataset
  • rotate
    • eul2rotm : transfer euler angles to rotation matrix in intrinsic order
    • rot_ext : do an extrinsic rotation to a 3D voxel model
    • align : Using grid search (euler angles) to align two models
  • SH_expan
    • sp_harmonics : spherical harmonics expansion of a 3D model
• image : diffraction pattern processing and I/O
  • radp
    • radial_profile : calculate intensity radial profile of a pattern/volume
    • shells : return indices of pixels in a pattern/volume which forms a shell at radius r
    • radp_norm : scaling pattern/volume intensities referring to a given radial profile
    • circle : generates a circle/sphere area with given radius, centered by (0,0)
  • quat
    • invq : calculate the inverse of a quaternion
    • quat_mul : multiply two quaternions
    • conj : conjugate quaternion
    • quat2rot : transfer quaternion to 3D rotation matrix
    • rot2quat : transfer 3D rotation matrix to quaternion
    • quat2azi : transfer quaternion to azimuth angle
    • azi2quat : transfer azimuth angle to quaternion
    • rotv : rotate a 3D vector using a quaternion
    • Slerp : linear interpolation on spherical surface between two quaternions
  • classify
    • cluster_fSpec ： single-nonsingle hits clustering using linear/non-linear decomposition and spectural clustering
    • cluster_fTSNE : single-nonsingle hits clustering using t-SNE decomposition and KNN clustering
    • diffusion_map : diffusion map embedding and decomposition
  • preprocess
    • fix_artifact : reduces artifacts in dataset, the positions of bad pixels are needed
    • fix_artifact_auto : detect and fix artifacts automatically without providing bad pixel positions
    • adu2photon : evaluate adu value per photon and transfer adu to photon counts
    • hit_find : hit finding based on chi-square testing
    • hit_find_pearson : hit finding based on pearson cc score testing
    • cal_correction_factor : calculate polarization and solid angle correction factors
    • avg_pooling : downsample patterns by a given factor
  • io
    • readccp4 : read ccp4/mrc files
    • writeccp4 : write intensity volume into a ccp4/mrc file
    • pdb2density : read pdb file and return electron density map
    • cxi_parser : print cxi/h5 inner path structures
    • xyz2pdb : write xyz-coordinates into a pdb file
    • readpdb_full : read pdb files and return full infomation
• merge : orientation recovery and merging
  • emc
    • new_project : create a new project
    • config : configuration
    • run : run emc
    • use_project : switch to an existing project
  • tools
    • get_slice : generate slices from a 3D model according to given orientations
    • merge_slice : merge slices into a 3D model according to given orientations
    • poisson_likelihood : calculate poisson likelihood between a model slice and a diffraction pattern
    • maximization : calculate updated slice of orientation j after likelihood maximization
    • get_quaternion : calculate quaternions which are uniformly distributed in orientation space
• phase : phase retrieval network framework (PRNF) or traditional phasing
  • phmodel
    • pInput,pOutput,pMerge,ERA,HIO,DM,RAAR,HPR : different types of nodes (algorithms) to build phase retrieval network (PRNF)
  • phexec
    • Runner : class, used for execuating phase retrieval network
  • phase2d (deprecated)
    • new_project : create a new project
    • config_project : edit configuration file
    • run_project : start phasing
    • use_project : switch to an existing project
  • phase3d (deprecated)
    • the same as phase2d
• simulate : diffraction simulation
  • sim_adu
    • go_magic : diffraction simulation of PDB file using atom reflection or FFT method