MIC calculation

In its most minimal form, AIgarMIC can be used as a simple agar dilution MI calculator. Here, it is up to users to provide growth matrices for each agar dilution plate. Such users can then use aigarmic.Plate and aigarmic.PlateSet to calculate MICs:

>>> from aigarmic import Plate, PlateSet
>>> antibiotic = "amikacin"
>>> plate1 = Plate(drug=antibiotic,
...                 concentration=0,
...                 growth_code_matrix=[[2, 2, 2],
...                                [2, 2, 0],
...                                [0, 2, 2]])
>>> plate2 = Plate(drug=antibiotic,
...                 concentration=0.125,
...                 growth_code_matrix=[[0, 1, 2],
...                                [2, 2, 0],
...                                [0, 2, 2]])
>>> plate3 = Plate(drug=antibiotic,
...                 concentration=0.25,
...                 growth_code_matrix=[[0, 1, 2],
...                                [2, 2, 0],
...                                [0, 2, 1]])
>>> plate4 = Plate(drug=antibiotic,
...                 concentration=0.5,
...                 growth_code_matrix=[[0, 0, 2],
...                                [2, 0, 0],
...                                [0, 2, 0]])
>>> plate_set = PlateSet(plates_list=[plate1, plate2, plate3, plate4])
>>> plate_set.calculate_mic(no_growth_key_items=tuple([0, 1]))
array([[0.125, 0.125, 1.   ],
       [1.   , 0.5  , 0.125],
       [0.125, 1.   , 0.25 ]])

As we can see, aigarmic.PlateSet.calculate_mic() returns a numpy array with the MICs for each strain in the plate set. This is a ‘numerical’ MIC – strains with growth in the plate with highest antibiotic concentration are reported as double the highest concentration. To convert to a more classical string MIC format, with appropriate censoring (e.g., ‘<0.125’, ‘>0.5’), we can use aigarmic.PlateSet.convert_mic_matrix():

>>> plate_set.convert_mic_matrix(mic_format='string').tolist()
[['<0.125', '<0.125', '>0.5'], ['>0.5', '0.5', '<0.125'], ['<0.125', '>0.5', '0.25']]