Gets absolute intensity threshold from config file. OMP will only be run on
pixels with absolute intensity greater than this.
Parameters:
| Name |
Type |
Description |
Default |
config |
dict
|
omp section of config file.
|
required
|
nbp |
NotebookPage
|
call_spots NotebookPage
|
required
|
Returns:
| Type |
Description |
float
|
Either config['initial_intensity_thresh'] or
nbp.abs_intensity_percentile[config['initial_intensity_thresh_percentile']]. |
Source code in coppafish/omp/base.py
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28 | def get_initial_intensity_thresh(config: dict, nbp: NotebookPage) -> float:
"""
Gets absolute intensity threshold from config file. OMP will only be run on
pixels with absolute intensity greater than this.
Args:
config: `omp` section of config file.
nbp: `call_spots` *NotebookPage*
Returns:
Either `config['initial_intensity_thresh']` or
`nbp.abs_intensity_percentile[config['initial_intensity_thresh_percentile']]`.
"""
initial_intensity_thresh = config['initial_intensity_thresh']
if initial_intensity_thresh is None:
config['initial_intensity_thresh'] = \
round_any(nbp.abs_intensity_percentile[config['initial_intensity_thresh_percentile']],
config['initial_intensity_precision'])
initial_intensity_thresh = \
float(np.clip(config['initial_intensity_thresh'], config['initial_intensity_thresh_min'],
config['initial_intensity_thresh_max']))
return initial_intensity_thresh
|