SMS_BP
Single Molecule Simulations -BP
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SMS_BP.simulate_cell Namespace Reference

Classes

class  Simulate_cells
 

Functions

 save_tiff (image, path, img_name=None)
 
 sub_segment (img, sub_frame_num, img_name=None, subsegment_type="mean")
 
 make_directory_structure (cd, img_name, img, subsegment_type, sub_frame_num, **kwargs)
 
 convert_lists_to_arrays (obj)
 
 convert_arrays_to_lists (obj)
 

Variables

 sim_new
 
 cd
 
 img_name
 
 subsegment_type
 
 sub_frame_num
 

Function Documentation

◆ convert_arrays_to_lists()

SMS_BP.simulate_cell.convert_arrays_to_lists ( obj)

◆ convert_lists_to_arrays()

SMS_BP.simulate_cell.convert_lists_to_arrays ( obj)

◆ make_directory_structure()

SMS_BP.simulate_cell.make_directory_structure ( cd,
img_name,
img,
subsegment_type,
sub_frame_num,
** kwargs )
 Docstring for make_directory_structure: make the directory structure for the simulation and save the image + the data and parameters
Also perform the subsegmentation and save the subsegments in the appropriate directory
Parameters:
-----------
cd : str
    directory to save the simulation
img_name : str
    name of the image
img : array-like
    image to be subsegmented
subsegment_type : str
    type of subsegmentation to be performed, currently only "mean" is supported
sub_frame_num : int
    number of subsegments to be created
**kwargs : dict
    dictionary of keyword arguments
KWARGS:
-------
data : dict, Default = None
    dictionary of data to be saved, Keys = "map","tracks","points_per_frame" Values = array-like.
    See the return of the function simulate_cell_tracks for more details
parameters : dict, Default = self.init_dict
Returns:
--------
array-like
    list of subsegment images

◆ save_tiff()

SMS_BP.simulate_cell.save_tiff ( image,
path,
img_name = None )
 Docstring for save_tiff: save the image as a tiff file
Parameters:
-----------
image : array-like
    image to be saved
path : str
    path to save the image
img_name : str, Default = None
    name of the image
Returns:
--------
None

◆ sub_segment()

SMS_BP.simulate_cell.sub_segment ( img,
sub_frame_num,
img_name = None,
subsegment_type = "mean" )
 Docstring for sub_segment: perform subsegmentation on the image
Parameters:
-----------
img : array-like
    image to be subsegmented
sub_frame_num : int
    number of subsegments to be created
img_name : str, Default = None
    name of the image
subsegment_type : str, Default = "mean"
    type of subsegmentation to be performed, currently only "mean" is supported
Returns:
--------
hold_img : list
    list of subsegments
hold_name : list
    list of names of the subsegments

Variable Documentation

◆ cd

SMS_BP.simulate_cell.cd

◆ img_name

SMS_BP.simulate_cell.img_name

◆ sim_new

SMS_BP.simulate_cell.sim_new
Initial value:
1= Simulate_cells(
2 init_dict_json="/Users/baljyot/Documents/CODE/GitHub_t2/PHD/SingleMoleculeSimulations_BP/SMS_BP/sim_config_testing.json")

◆ sub_frame_num

SMS_BP.simulate_cell.sub_frame_num

◆ subsegment_type

SMS_BP.simulate_cell.subsegment_type