phase

(Extension of the original program from European-XFEL team here)

Supported algorithms :

• ER (error reduction)
• DM (difference map)
• RAAR (relaxed averaged alternating reflections)

(1) spipy.phase.phase2d

--> " 2d pattern phase retrieval using iterative (projection-support) methods "

+ :void = new_project (data_mask_path:str, path:str/None, name:str/None)

+ :void = config (params:dict)

+ :void = run (num_proc:int/1, nohup:bool/False, cluster:bool/False)

+ :void = use_project (project_path:str)

All parameters, a dict :

• important :
  • 'input|shape' : input pattern shape, default='123,123'
  • 'input|padd_to_pow2' : zero padding to make the size of pattern to be a 2ⁿ number, default=True
  • 'input|inner_mask' : pixels whose radius<inner_mask are allowed to float while phasing, default=5
  • 'input|outer_mask' : pixels whose radius>outer_mask are set to zero, default=64
  • 'input|outer_outer_mask' : pixels whose radius are between outer_mask and outer_outer_mask are allowed to float, default=None
  • 'input|mask_edges' : a switch, whether allow pixels between outer_mask and outer_outer_mask to float, default=True
  • 'phasing|repeats' : how many times of independent phasing for every process, default=40
  • 'phasing|iters' : schedual iterations for 1 phasing loop, default='100RAAR 200DM 200ERA' which means '100 times relaxed averaged alternating reflections algorithm -> 200 times different map algorithm -> 300 times error reduction algorithm'
  • 'phasing_parameters|support_size' : set restriction to the number of pixels inside final support of shrinkwrap process, default=200 (pixels)
  • 'phasing_parameters|beta' : beta value for RAAR algorithm, float from 0 to 1, default=0.8
• optional (for most time you don't need to change them):
  • 'input|subtract_percentile' : subtract the ?th percentile value of data for all pixels, float value from 0 to 100, default=None
  • 'input|spherical_support' : radius of spherical support that added at the initiation, default=None
  • 'input|init_model' : filepath of initial REAL space model. Support .npy, .bin and .mat file formats. The size of init model should agree with 'input|shape' after 'input|padd_2_pow', default=None
  • 'phasing_parameters|background' : evaluate background while phasing, default=True

--

• new_project : create a new project at your given path, NO return
  • data_mask_path : [data_path, user_mask_path] , data_path is the path of pattern while user_mask_path is the path of mask file, inside the mask file there should be a 0/1 2d array and 1 means masked point
  • path : create work directory at your give path, set None to use current dir, default=None
  • name : give a name to your project, set None to let program choose one for you, default=None
  • [Notice] Your original intensity file should be 2D array '.npy' or '.mat' or '.bin', mask file must be 'npy'. Leave data_mask_path[1] to None if you don't have user mask

--

• config : edit configure file, NO return
  • params : dict, parameters that you want to modified. refer to example code

--

• run : start phasing, NO return
  • num_proc : number of processes, default=1
  • nohup : whether run in background, default=False
  • cluster : bool, whether you will submit jobs using job scheduling system, if True, the function will only generate a command file at your work path without submitting it; if False, the program will run directly. default=False

--

• show_result : show pahsing result, calling 'show_result.py' in your work_dir, NO return
  • outpath : IF you move output.h5 to another folder (not your project folder), please give me its path, default is None
  • exp_param : list detd, lambda, det_r, pix_size in a string. Used to calculate q value. e.g. '200,2.5,128,0.3', default=None

--

• use_project : switch to an existing project, NO return
  • project_path : path of the project directory that you want to use

(2) spipy.phase.phase3d

--> " 3d voxel model phase retrieval using iterative (projection-support) methods "

+ :void = new_project (data_path:str, mask_path/None, path:str/None, name:str/None)

+ :void = config (params:dict)

+ :void = run (num_proc:int/1, nohup:bool/False, cluster:bool/True)

+ :void = use_project (project_path:str)

+ :void = show_result (outpath:str/None, exp_param:str/None)

• All parameters
  • 'input|shape' : default='120,120,120'
  • There is no 'phasing_parameters|support_size', for replacement, there are 'phasing_parameters|voxel_number', default=2000
  • Others the same with phase2d parameters

--

• new_project : create a new project at your given path, NO return
  • data_path : path of your original 3d scattering intensity data, file that contains 3D voxel data should be '.npy' or '.mat', or Dragonfly output '.bin'
  • mask_path : path of user-defined mask file, a 0/1 numpy.2darray where 1 means masked point, default=None
  • path : create work directory at your give path, set None to use current dir, default=None
  • name : give a name to your project, set None to let program choose one for you, default=None

--

• config : edit configure file, NO return
  • params : dict, parameters that you want to modified. refer to example code

--

• run : start phasing, NO return
  • num_proc : this function maps multi-processes automatically, so you need to figure out how many processes to run in parallel, default=1
  • nohup : whether run in background, default=False
  • cluster : bool, whether you will submit jobs using job scheduling system, if True, the function will only generate a command file at your work path without submitting it; if False, the program will run directly. default=True

--

• show_result : show pahsing result, calling 'show_result.py' in your work_dir, NO return
  • outpath : IF you move output.h5 to another folder (not your project folder), please give me its path, default is None
  • exp_param : list detd, lambda, det_r, pix_size in a string. Used to calculate q value. e.g. '200,2.5,128,0.3', default=None

--

• use_project : switch to an existing project, NO return
  • project_path : path of the project directory that you want to use