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Commit 92d24083 authored by Schneider Leo's avatar Schneider Leo
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antibio resistance label extraction

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data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx
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dataset/dataset.py
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import random
import numpy as np
import torch
import torchvision
......@@ -57,11 +55,9 @@ def load_data(base_dir, batch_size, shuffle=True, noise_threshold=0):
train_dataset = torchvision.datasets.ImageFolder(root=base_dir, transform=train_transform)
val_dataset = torchvision.datasets.ImageFolder(root=base_dir, transform=val_transform)
#Same seed to avoid overlap while having different transforms
seed = random.randint(0,1000)
train_dataset, _ = train_test_split(train_dataset, test_size=None, train_size=None, random_state=seed, shuffle=True,
train_dataset, _ = train_test_split(train_dataset, test_size=None, train_size=None, random_state=42, shuffle=True,
stratify=True)
_, val_dataset = train_test_split(val_dataset, test_size=None, train_size=None, random_state=seed, shuffle=True,
_, val_dataset = train_test_split(val_dataset, test_size=None, train_size=None, random_state=42, shuffle=True,
stratify=True)
data_loader_train = data.DataLoader(
......
image_processing/build_dataset.py
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......@@ -12,24 +12,129 @@ from build_image import build_image_ms1
find . -name '*.mzML' -exec cp -prv '{}' '/home/leo/PycharmProjects/pseudo_image/data/raw_data' ';'
copy des mzml depuis lecteur
"""
antibiotic_tests = ['AMC (disk)','AMK (disk)','AMK (mic)','AMK (vitek)','AMP (vitek)','AMX (disk)',
'AMX (vitek)','ATM (disk)','ATM (vitek)','CAZ (disk)','CAZ (mic)','CAZ (vitek)','CHL (vitek)','CIP (disk)',
'CIP (vitek)','COL (mic)','CRO (mic)','CRO (vitek)','CTX (disk)','CTX (mic)','CTX (vitek)',
'CXM (vitek)','CZA (disk)','CZA (vitek)','CZT (disk)','CZT (vitek)','ETP (disk)','ETP (mic)','ETP (vitek)',
'FEP (disk)','FEP (mic)','FEP (vitek)','FOS (disk)','FOX (disk)','FOX (vitek)','GEN (disk)','GEN (mic)',
'GEN (vitek)','IPM (disk)','IPM (mic)','IPM (vitek)','LVX (disk)','LVX (vitek)','MEC (disk)',
'MEM (disk)','MEM (mic)','MEM (vitek)','NAL (vitek)','NET (disk)','OFX (vitek)','PIP (vitek)','PRL (disk)',
'SXT (disk)','SXT (vitek)','TCC (disk)','TCC (vitek)','TGC (disk)','TGC (vitek)',
'TIC (disk)','TIC (vitek)','TOB (disk)','TOB (vitek)','TZP (disk)','TZP (mic)','TZP (vitek)']
antibiotic_enterrobacter_breakpoints = {
'AMC (disk)': {"S":14, "R":14 },
'AMK (disk)': {"S":18, "R":18 },
'AMK (mic)': {"S":8, "R":8 },
'AMK (vitek)': {"S":8, "R":8 },
'AMP (vitek)': {"S":8, "R":8 },
'AMX (disk)': {"S":14, "R":14 },
'AMX (vitek)': {"S":8, "R":8 },
'ATM (disk)': {"S":26, "R":21 },
'ATM (vitek)': {"S":1, "R":4 },
'CAZ (disk)': {"S":22, "R":22 },
'CAZ (mic)': {"S":1, "R":4 },
'CAZ (vitek)': {"S":1, "R":4 },
'CHL (vitek)': {"S":16, "R":16 },
'CIP (disk)': {"S":25, "R":22 },
'CIP (vitek)': {"S":0.25, "R":0.5 },
'COL (disk)': {"S":None, "R":None }, # : https://academic-oup-com.docelec.univ-lyon1.fr/cid/article/71/9/e523/5735218?login=true&token=eyJhbGciOiJub25lIn0.eyJleHAiOjE3NDU2NjA0NTgsImp0aSI6IjcxYzJmOWI1LTlhMWYtNGRiMy1iYmE0LTA0MGRlMTU3NjdmZSJ9.
#deleted since method is not accurate (DO NOT USE IT)
'COL (mic)': {"S":2, "R":2 },
'CRO (mic)': {"S":1, "R":2 },
'CRO (vitek)': {"S":1, "R":2 },
'CTX (disk)': {"S":20, "R":17 },
'CTX (mic)': {"S":1, "R":2 },
'CTX (vitek)': {"S":1, "R":2 },
'CXM (vitek)': {"S":0.001, "R":8 },
'CZA (disk)': {"S":13, "R":13 },
'CZA (vitek)': {"S":8, "R":8 },
'CZT (disk)': {"S":22, "R":22 },
'CZT (vitek)': {"S":2, "R":2 },
'ETP (disk)': {"S":23, "R":23 },
'ETP (mic)': {"S":0.5, "R":0.5 },
'ETP (vitek)': {"S":0.5, "R":0.5 },
'FEP (disk)': {"S":27, "R":24 },
'FEP (mic)': {"S":1, "R":4 },
'FEP (vitek)': {"S":1, "R":4 },
'FOS (disk)': {"S":24, "R":24 },#pas clair ?
'FOX (disk)': {"S":19, "R":19 },#screen only ?
'FOX (vitek)': {"S":8, "R":8 },#screen only ? high sensitivity but poor specificity for identification of AmpC-producing Enterobacterales
'GEN (disk)': {"S":17, "R":17 },
'GEN (mic)': {"S":2, "R":2 }, #entre parenthèse
'GEN (vitek)': {"S":2, "R":2 }, #entre parenthèse cf https://www.eucast.org/eucastguidancedocuments/ ?
'IPM (disk)': {"S":22, "R":19 },
'IPM (mic)': {"S":2, "R":4 },
'IPM (vitek)': {"S":2, "R":4 },
'LTM (disk)': {"S":None, "R":None }, # Lactimidomycin ?
'LVX (disk)': {"S":23, "R":19 },
'LVX (vitek)': {"S":0.5, "R":1 },
'MEC (disk)': {"S":15, "R":15 },
'MEM (disk)': {"S":22, "R":16 },
'MEM (mic)': {"S":2, "R":8 },
'MEM (vitek)': {"S":2, "R":8 },
'NAL (vitek)': {"S":2, "R":8 }, #pas présent dans EUCAST, trouvé dans CLSI M100 (for uninary tract only)
'NET (disk)': {"S":15, "R":12 }, #insuffisant evidencence for EUCAST, found in CLSI M100
'OFX (vitek)': {"S":0.25, "R":0.5 },
'PIP (vitek)': {"S":8, "R":8 },
'PRL (disk)': {"S":20, "R":20 },
'SXT (disk)': {"S":14, "R":11 },
'SXT (vitek)': {"S":2, "R":4 },
'TCC (disk)': {"S":8, "R":16 },
'TCC (vitek)': {"S":23, "R":20 },
'TEM (disk)': {"S":None, "R":None },#Abréviation non standard
'TEM (vitek)': {"S":None, "R":None },#Abréviation non standard
'TGC (disk)': {"S":18, "R":18 }, #pour E.coli et C.koseri seulement
'TGC (vitek)': {"S":0.5, "R":0.5 },
'TIC (disk)': {"S":13, "R":20 },
'TIC (vitek)': {"S":8, "R":16 },
'TOB (disk)': {"S":16, "R":16 }, #entre parenthèse cf https://www.eucast.org/eucastguidancedocuments/ ?
'TOB (vitek)': {"S":2, "R":2 }, #entre parenthèse cf https://www.eucast.org/eucastguidancedocuments/ ?
'TZP (disk)': {"S":20, "R":20 },
'TZP (mic)': {"S":8, "R":8 },
'TZP (vitek)': {"S":8, "R":8 },
}
def create_antibio_dataset(path='../data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx',suffix='-d200'):
"""
Extract and organise labels from raw excel file
Extract and build file name corresponding to each sample
:param path: excel path
:return: dataframe
"""
df = pd.read_excel(path, header=1)
df = df[['sample_name','species','AMC (disk)','AMK (disk)','AMK (mic)','AMK (vitek)','AMP (vitek)','AMX (disk)',
'AMX (vitek)','ATM (disk)','ATM (vitek)','CAZ (disk)','CAZ (mic)','CAZ (vitek)','CHL (vitek)','CIP (disk)',
'CIP (vitek)','COL (disk)','COL (mic)','CRO (mic)','CRO (vitek)','CTX (disk)','CTX (mic)','CTX (vitek)',
'CIP (vitek)','COL (mic)','CRO (mic)','CRO (vitek)','CTX (disk)','CTX (mic)','CTX (vitek)',
'CXM (vitek)','CZA (disk)','CZA (vitek)','CZT (disk)','CZT (vitek)','ETP (disk)','ETP (mic)','ETP (vitek)',
'FEP (disk)','FEP (mic)','FEP (vitek)','FOS (disk)','FOX (disk)','FOX (vitek)','GEN (disk)','GEN (mic)',
'GEN (vitek)','IPM (disk)','IPM (mic)','IPM (vitek)','LTM (disk)','LVX (disk)','LVX (vitek)','MEC (disk)',
'GEN (vitek)','IPM (disk)','IPM (mic)','IPM (vitek)','LVX (disk)','LVX (vitek)','MEC (disk)',
'MEM (disk)','MEM (mic)','MEM (vitek)','NAL (vitek)','NET (disk)','OFX (vitek)','PIP (vitek)','PRL (disk)',
'SXT (disk)','SXT (vitek)','TCC (disk)','TCC (vitek)','TEM (disk)','TEM (vitek)','TGC (disk)','TGC (vitek)',
'SXT (disk)','SXT (vitek)','TCC (disk)','TCC (vitek)','TGC (disk)','TGC (vitek)',
'TIC (disk)','TIC (vitek)','TOB (disk)','TOB (vitek)','TZP (disk)','TZP (mic)','TZP (vitek)']]
for test in antibiotic_tests :# S - Susceptible R - Resistant U- Uncertain
#convert to string and transform >8 to 8
df[test] = df[test].map(lambda x :float(str(x).replace('>','').replace('<','')))
df[test+' cat']= 'NA'
if 'mic' in test or 'vitek' in test :
try :
df.loc[df[test] <= antibiotic_enterrobacter_breakpoints[test]['S'], test+ ' cat'] = 'S'
df.loc[df[test] >= antibiotic_enterrobacter_breakpoints[test]['R'], test + ' cat'] = 'R'
df.loc[(antibiotic_enterrobacter_breakpoints[test]['S'] < df[test]) & (df[test] < antibiotic_enterrobacter_breakpoints[test]['R']), test + ' cat'] = 'U'
except:
pass
elif 'disk' in test:
try :
df.loc[df[test] >= antibiotic_enterrobacter_breakpoints[test]['S'], test + ' cat'] = 'S'
df.loc[df[test] <= antibiotic_enterrobacter_breakpoints[test]['R'], test + ' cat'] = 'R'
df.loc[
(antibiotic_enterrobacter_breakpoints[test]['S'] > df[test]) & (df[test] > antibiotic_enterrobacter_breakpoints[test][
'R']), test + ' cat'] = 'U'
except:
pass
def split_before_number(s):
return re.split(r'(\d+)', s)
......@@ -98,5 +203,26 @@ def create_dataset():
np.save(directory_path_npy + "/" + name + '_' + analyse + '.npy', mat)
def extract_antio_res_labels():
"""
Extract and organise labels from raw excel file
:param
path: excel
path
:return: dataframe
"""
path = '../data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx'
df = pd.read_excel(path, header=1)
df = df[['sample_name','species','AMC (disk)','AMK (disk)','AMK (mic)','AMK (vitek)','AMP (vitek)','AMX (disk)',
'AMX (vitek)','ATM (disk)','ATM (vitek)','CAZ (disk)','CAZ (mic)','CAZ (vitek)','CHL (vitek)','CIP (disk)',
'CIP (vitek)','COL (disk)','COL (mic)','CRO (mic)','CRO (vitek)','CTX (disk)','CTX (mic)','CTX (vitek)',
'CXM (vitek)','CZA (disk)','CZA (vitek)','CZT (disk)','CZT (vitek)','ETP (disk)','ETP (mic)','ETP (vitek)',
'FEP (disk)','FEP (mic)','FEP (vitek)','FOS (disk)','FOX (disk)','FOX (vitek)','GEN (disk)','GEN (mic)',
'GEN (vitek)','IPM (disk)','IPM (mic)','IPM (vitek)','LTM (disk)','LVX (disk)','LVX (vitek)','MEC (disk)',
'MEM (disk)','MEM (mic)','MEM (vitek)','NAL (vitek)','NET (disk)','OFX (vitek)','PIP (vitek)','PRL (disk)',
'SXT (disk)','SXT (vitek)','TCC (disk)','TCC (vitek)','TEM (disk)','TEM (vitek)','TGC (disk)','TGC (vitek)',
'TIC (disk)','TIC (vitek)','TOB (disk)','TOB (vitek)','TZP (disk)','TZP (mic)','TZP (vitek)']]
if __name__ =='__main__' :
create_dataset()
\ No newline at end of file
df = create_antibio_dataset()
\ No newline at end of file
models/model.py
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......@@ -296,7 +296,7 @@ class Classification_model_duo(nn.Module):
self.predictor = nn.Linear(in_features=self.n_class*2,out_features=self.n_class)
def forward(self, input_aer, input_ana):
def forward(self, input_aer, input_ana, input_ref):
out_aer = self.im_encoder(input_aer)
out_ana = self.im_encoder(input_ana)
out = torch.concat([out_aer,out_ana],dim=1)
......
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