Setting configurations in SpatialTis¶
[1]:
from spatialtis import CONFIG
To check the what configurations can be set and what’s the current value, just print the CONFIG
[2]:
print(CONFIG)
Current configurations of SpatialTis ┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┓ ┃ Options ┃ Value ┃ ┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━┩ │ OS │ Darwin │ │ MP │ True │ │ WORKING_ENV │ jupyter │ │ VERBOSE │ True │ │ PBAR │ True │ │ AUTO_SAVE │ False │ │ EXP_OBS │ None │ │ ROI_KEY │ None │ │ CELL_TYPE_KEY │ None │ │ MARKER_KEY │ marker │ │ NEIGHBORS_KEY │ cell_neighbors │ │ CENTROID_KEY │ centroid │ │ AREA_KEY │ area │ │ SHAPE_KEY │ cell_shape │ │ ECCENTRICITY_KEY │ eccentricity │ └──────────────────┴────────────────┘
There are a few points to be noticed!
<ol>
<li>
Options in CONFIG are all <strong>CAPITALIZED</strong>
</li>
<li>
The changes happen on the fly!
</li>
<li>
Can be overwritted by <strong>local parameter</strong>
</li>
</ol>
For example, If you turn on multi processing, every functions supported parallelism will execute using multi-CPUs afterwards. This happen on the fly.
[3]:
CONFIG.MP = True
However, if you don’t want to use parallelism in some analysis, you can turn it off only in that analysis.
import spatialtis as st
st.spatial_distribution(data, mp=False)
Or you want to turn it off for every function afterwards.
[4]:
CONFIG.MP = False
Setting CONFIG.EXP_OBS
and CONFIG.ROI_KEY
¶
EXP_OBS
represents experiment observations, this is used to tell SpatialTis how your data grouped.
[5]:
CONFIG.EXP_OBS = ['ROI', 'Patient', 'Stage']
However, SpatialTis has no idea which level is ROI. By default it will assume the last one is the ROI level, but this is not the case here.
[6]:
CONFIG.ROI_KEY
[6]:
'Stage'
We need to explicit set the key of ROI
[7]:
CONFIG.ROI_KEY = 'ROI'
print(f"ROI key: {CONFIG.ROI_KEY}", f"EXP_OBS: {CONFIG.EXP_OBS}", sep="\n")
ROI key: ROI
EXP_OBS: ['Patient', 'Stage', 'ROI']
Now SpatialTis got how your data grouped correctly!
Setting Keys¶
To work with analysis in SpatialTis, it’s very important to know where your data is stored.
Remember to specific those keys.
CELL_TYPE_KEY
MARKER_KEY
NEIGHBORS_KEY
CENTROID_KEY
AREA_KEY
SHAPE_KEY
ECCENTRICITY_KEY
Setting CONFIG.WORKING_ENV
¶
As of 0.3.0, SpatialTis will auto-detect your working environment. In jupyter
, terminal
or None
Settting CONFIG.VERBOSE
and CONFIG.PBAR
¶
This is to control the display of logging and progress bar,
If you don’t want SpatialTis to print anything
[8]:
CONFIG.VERBOSE = False
This will also turn off progress bar, if you just don’t want progress bar
[9]:
CONFIG.PBAR = False