SMS_BP
Single Molecule Simulations -BP
|
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 | |
SMS_BP.simulate_cell.convert_arrays_to_lists | ( | obj | ) |
SMS_BP.simulate_cell.convert_lists_to_arrays | ( | obj | ) |
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
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
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
SMS_BP.simulate_cell.cd |
SMS_BP.simulate_cell.img_name |
SMS_BP.simulate_cell.sim_new |
SMS_BP.simulate_cell.sub_frame_num |
SMS_BP.simulate_cell.subsegment_type |