eval_model.py
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import torch
import pandas as pd
import cxr_dataset as CXR
from torch.utils.data import Dataset, DataLoader
import sklearn.metrics as sklm
import numpy as np
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
def make_pred_multilabel(dataloader, model, save_as_csv=False, fine_tune=False):
"""
Gives predictions for test fold and calculates AUCs using previously trained model
Args:
data_transforms: torchvision transforms to preprocess raw images; same as validation transforms
model: densenet-121 from torchvision previously fine tuned to training data
PATH_TO_IMAGES: path at which NIH images can be found
Returns:
pred_df: dataframe containing individual predictions and ground truth for each test image
auc_df: dataframe containing aggregate AUCs by train/test tuples
"""
batch_size = dataloader.batch_size
# set model to eval mode; required for proper predictions given use of batchnorm
model.train(False)
# create empty dfs
pred_df = pd.DataFrame(columns=["Image Index"])
true_df = pd.DataFrame(columns=["Image Index"])
# iterate over dataloader
for i, data in enumerate(dataloader):
inputs, labels, _ = data
inputs, labels = inputs.to(device), labels.to(device)
true_labels = labels.cpu().data.numpy()
# batch_size = true_labels.shape
outputs = model(inputs)
outputs = torch.sigmoid(outputs)
probs = outputs.cpu().data.numpy()
# get predictions and true values for each item in batch
for j in range(0, true_labels.shape[0]):
thisrow = {}
truerow = {}
thisrow["Image Index"] = dataloader.dataset.df.index[batch_size * i + j]
truerow["Image Index"] = dataloader.dataset.df.index[batch_size * i + j]
# iterate over each entry in prediction vector; each corresponds to
# individual label
for k in range(len(dataloader.dataset.PRED_LABEL)):
thisrow["prob_" + dataloader.dataset.PRED_LABEL[k]] = probs[j, k]
truerow[dataloader.dataset.PRED_LABEL[k]] = true_labels[j, k]
pred_df = pred_df.append(thisrow, ignore_index=True)
true_df = true_df.append(truerow, ignore_index=True)
# if(i % 10 == 0):
# print(str(i * BATCH_SIZE))
auc_df = pd.DataFrame(columns=["label", "auc"])
# calc AUCs
for column in true_df:
if not fine_tune:
if column not in [
'Atelectasis',
'Cardiomegaly',
'Effusion',
'Infiltration',
'Mass',
'Nodule',
'Pneumonia',
'Pneumothorax',
'Consolidation',
'Edema',
'Emphysema',
'Fibrosis',
'Pleural_Thickening',
'Hernia']:
continue
else:
if column not in [
'Detector01',
'Detector2',
'Detector3']:
continue
actual = true_df[column]
pred = pred_df["prob_" + column]
thisrow = {}
thisrow['label'] = column
thisrow['auc'] = np.nan
thisrow['AP'] = np.nan
try:
thisrow['auc'] = sklm.roc_auc_score(actual.to_numpy().astype(int), pred.to_numpy())
thisrow['AP'] = sklm.average_precision_score(actual.to_numpy().astype(int), pred.to_numpy())
except BaseException:
print("can't calculate auc for " + str(column))
auc_df = auc_df.append(thisrow, ignore_index=True)
if save_as_csv:
pred_df.to_csv("results/preds.csv", index=False)
auc_df.to_csv("results/aucs.csv", index=False)
return pred_df, auc_df
def evaluate_mae(dataloader, model):
"""
Calculates MAE using previously trained model
Args:
data_transforms: torchvision transforms to preprocess raw images; same as validation transforms
model: densenet-121 from torchvision previously fine tuned to training data
Returns:
mae: MAE
"""
# calc preds in batches of 32, can reduce if your GPU has less RAM
batch_size = dataloader.batch_size
# set model to eval mode; required for proper predictions given use of batchnorm
model.train(False)
# create empty dfs
pred_df = pd.DataFrame(columns=["Image Index"])
true_df = pd.DataFrame(columns=["Image Index"])
# iterate over dataloader
for i, data in enumerate(dataloader):
inputs, ground_truths, _ = data
inputs, ground_truths = inputs.to(device), ground_truths.to(device)
true_scores = ground_truths.cpu().data.numpy()
outputs = model(inputs)
preds = outputs.cpu().data.numpy()
# get predictions and true values for each item in batch
for j in range(0, true_scores.shape[0]):
thisrow = {}
truerow = {}
thisrow["Image Index"] = dataloader.dataset.df.index[batch_size * i + j]
truerow["Image Index"] = dataloader.dataset.df.index[batch_size * i + j]
# iterate over each entry in prediction vector; each corresponds to
# individual label
thisrow["pred_score"] = preds[j]
truerow["true_score"] = true_scores[j]
pred_df = pred_df.append(thisrow, ignore_index=True)
true_df = true_df.append(truerow, ignore_index=True)
actual = true_df["true_score"]
pred = pred_df["pred_score"]
try:
mae = sklm.mean_absolute_error(actual.to_numpy().astype(int), pred.to_numpy())
return mae, true_df, pred_df
except BaseException:
print("can't calculate mae")