#!/usr/bin/env python # coding: utf-8 # # Importing the Required Libraries. # In[1]: from IPython import get_ipython import keras import os os.environ['SM_FRAMEWORK'] = 'tf.keras' import segmentation_models as sm import glob import matplotlib.pyplot as plt from scipy import ndimage from scipy.ndimage import label, generate_binary_structure import radiomics import cv2 import SimpleITK as sitk import six import numpy as np import pandas as pd import seaborn as sns import matplotlib.pyplot as plt from sklearn.model_selection import train_test_split from sklearn.feature_selection import SelectKBest from sklearn.feature_selection import mutual_info_classif from sklearn.ensemble import RandomForestClassifier from sklearn.feature_selection import RFE from sklearn.metrics import roc_auc_score from sklearn.feature_selection import SelectFromModel from sklearn.linear_model import Lasso, LogisticRegression from sklearn.preprocessing import StandardScaler from sklearn.decomposition import PCA from sklearn.svm import LinearSVC from sklearn.datasets import load_iris from sklearn.feature_selection import SelectFromModel from sklearn.feature_selection import mutual_info_classif as MIC from sklearn.feature_selection import mutual_info_classif, mutual_info_regression from sklearn.feature_selection import SelectKBest, SelectPercentile from sklearn.feature_selection import SequentialFeatureSelector from sklearn.neighbors import KNeighborsClassifier from sklearn.linear_model import LogisticRegression from sklearn.ensemble import RandomForestClassifier from sklearn.svm import SVC from sklearn.metrics import f1_score from sklearn.model_selection import cross_validate from sklearn.tree import DecisionTreeClassifier from sklearn.linear_model import Perceptron from sklearn.model_selection import RandomizedSearchCV from sklearn.model_selection import GridSearchCV os.environ["CUDA_VISIBLE_DEVICES"] = "1" # # Defining the path to Model and Images # In[2]: IMAGE_SIZE = (256,256,3) path_base_model = './/models//' # # Loading the models # In[4]: BACKBONE = 'efficientnetb0' model1 = sm.Unet(BACKBONE, input_shape = (IMAGE_SIZE[0],IMAGE_SIZE[1],IMAGE_SIZE[2]),classes=1, activation='sigmoid',encoder_weights='imagenet') model2 = sm.Unet(BACKBONE, input_shape = (IMAGE_SIZE[0],IMAGE_SIZE[1],IMAGE_SIZE[2]),classes=1, activation='sigmoid',encoder_weights='imagenet') model3 = sm.Unet(BACKBONE, input_shape = (IMAGE_SIZE[0],IMAGE_SIZE[1],IMAGE_SIZE[2]),classes=1, activation='sigmoid',encoder_weights='imagenet') BACKBONE = 'efficientnetb7' model4 = sm.Unet(BACKBONE, input_shape = (IMAGE_SIZE[0],IMAGE_SIZE[1],IMAGE_SIZE[2]),classes=1, activation='sigmoid',encoder_weights='imagenet') model5 = sm.Unet(BACKBONE, input_shape = (IMAGE_SIZE[0],IMAGE_SIZE[1],IMAGE_SIZE[2]),classes=1, activation='sigmoid',encoder_weights='imagenet') preprocess_input = sm.get_preprocessing(BACKBONE) model1.load_weights(path_base_model + 'model1.hdf5') model2.load_weights(path_base_model + 'model2.hdf5') model3.load_weights(path_base_model + 'model3.hdf5') model4.load_weights(path_base_model + 'model4.hdf5') model5.load_weights(path_base_model + 'model5.hdf5') # # Defining Required Functions # In[5]: def preprocessing_HE(img_): hist, bins = np.histogram(img_.flatten(), 256,[0,256]) cdf = hist.cumsum() cdf_m = np.ma.masked_equal(cdf,0) cdf_m = (cdf_m - cdf_m.min())*255/(cdf_m.max()-cdf_m.min()) cdf = np.ma.filled(cdf_m,0).astype('uint8') img_2 = cdf[img_] return img_2 def get_binary_mask (mask_, th_ = 0.5): mask_[mask_>th_] = 1 mask_[mask_<=th_] = 0 return mask_ def ensemble_results (mask1_, mask2_, mask3_, mask4_, mask5_): mask1_ = get_binary_mask (mask1_) mask2_ = get_binary_mask (mask2_) mask3_ = get_binary_mask (mask3_) mask4_ = get_binary_mask (mask4_) mask5_ = get_binary_mask (mask5_) ensemble_mask = mask1_ + mask2_ + mask3_ + mask4_ + mask5_ ensemble_mask[ensemble_mask<=2.0] = 0 ensemble_mask[ensemble_mask> 2.0] = 1 return ensemble_mask def postprocessing_HoleFilling (mask_): ensemble_mask_post_temp = ndimage.binary_fill_holes(mask_).astype(int) return ensemble_mask_post_temp def get_maximum_index (labeled_array): ind_nums = [] for i in range (len(np.unique(labeled_array)) - 1): ind_nums.append ([0, i+1]) for i in range (1, len(np.unique(labeled_array))): ind_nums[i-1][0] = len(np.where (labeled_array == np.unique(labeled_array)[i])[0]) ind_nums = sorted(ind_nums) return ind_nums[len(ind_nums)-1][1], ind_nums[len(ind_nums)-2][1] def postprocessing_EliminatingIsolation (ensemble_mask_post_temp): labeled_array, num_features = label(ensemble_mask_post_temp) ind_max1, ind_max2 = get_maximum_index (labeled_array) ensemble_mask_post_temp2 = np.zeros (ensemble_mask_post_temp.shape) ensemble_mask_post_temp2[labeled_array == ind_max1] = 1 ensemble_mask_post_temp2[labeled_array == ind_max2] = 1 return ensemble_mask_post_temp2.astype(int) def get_prediction(model_, img_org_): img_org_resize = cv2.resize(img_org_,(IMAGE_SIZE[0],IMAGE_SIZE[1]),cv2.INTER_AREA) img_org_resize_HE = preprocessing_HE (img_org_resize) img_ready = preprocess_input (img_org_resize_HE) img_ready = np.expand_dims(img_ready, axis=0) pr_mask = model_.predict(img_ready) pr_mask = np.squeeze(pr_mask) pr_mask = np.expand_dims(pr_mask, axis=-1) return pr_mask[:,:,0] # ## Create and intantiate Feature Extractor and enable the required features # In[9]: extractor = radiomics.featureextractor.RadiomicsFeatureExtractor(force2D=True) extractor.enableImageTypeByName('Original') # extract features from the original image extractor.enableFeatureClassByName('firstorder') # extract first-order features extractor.enableFeatureClassByName('glcm') # extract GLCM features extractor.enableFeatureClassByName('gldm') # extract GLDM features extractor.enableFeatureClassByName('glszm') # extract GLSZM features extractor.enableFeatureClassByName('ngtdm') # extract NGTDM features features_name = ['diagnostics_Versions_PyRadiomics', 'diagnostics_Versions_Numpy', 'diagnostics_Versions_SimpleITK', 'diagnostics_Versions_PyWavelet', 'diagnostics_Versions_Python', 'diagnostics_Configuration_Settings', 'diagnostics_Configuration_EnabledImageTypes', 'diagnostics_Image-original_Hash', 'diagnostics_Image-original_Dimensionality', 'diagnostics_Image-original_Spacing', 'diagnostics_Image-original_Size', 'diagnostics_Image-original_Mean', 'diagnostics_Image-original_Minimum', 'diagnostics_Image-original_Maximum', 'diagnostics_Mask-original_Hash', 'diagnostics_Mask-original_Spacing', 'diagnostics_Mask-original_Size', 'diagnostics_Mask-original_BoundingBox', 'diagnostics_Mask-original_VoxelNum', 'diagnostics_Mask-original_VolumeNum', 'diagnostics_Mask-original_CenterOfMassIndex', 'diagnostics_Mask-original_CenterOfMass', 'original_firstorder_10Percentile', 'original_firstorder_90Percentile', 'original_firstorder_Energy', 'original_firstorder_Entropy', 'original_firstorder_InterquartileRange', 'original_firstorder_Kurtosis', 'original_firstorder_Maximum', 'original_firstorder_MeanAbsoluteDeviation', 'original_firstorder_Mean', 'original_firstorder_Median', 'original_firstorder_Minimum', 'original_firstorder_Range', 'original_firstorder_RobustMeanAbsoluteDeviation', 'original_firstorder_RootMeanSquared', 'original_firstorder_Skewness', 'original_firstorder_TotalEnergy', 'original_firstorder_Uniformity', 'original_firstorder_Variance', 'original_glcm_Autocorrelation', 'original_glcm_ClusterProminence', 'original_glcm_ClusterShade', 'original_glcm_ClusterTendency', 'original_glcm_Contrast', 'original_glcm_Correlation', 'original_glcm_DifferenceAverage', 'original_glcm_DifferenceEntropy', 'original_glcm_DifferenceVariance', 'original_glcm_Id', 'original_glcm_Idm', 'original_glcm_Idmn', 'original_glcm_Idn', 'original_glcm_Imc1', 'original_glcm_Imc2', 'original_glcm_InverseVariance', 'original_glcm_JointAverage', 'original_glcm_JointEnergy', 'original_glcm_JointEntropy', 'original_glcm_MCC', 'original_glcm_MaximumProbability', 'original_glcm_SumAverage', 'original_glcm_SumEntropy', 'original_glcm_SumSquares', 'original_gldm_DependenceEntropy', 'original_gldm_DependenceNonUniformity', 'original_gldm_DependenceNonUniformityNormalized', 'original_gldm_DependenceVariance', 'original_gldm_GrayLevelNonUniformity', 'original_gldm_GrayLevelVariance', 'original_gldm_HighGrayLevelEmphasis', 'original_gldm_LargeDependenceEmphasis', 'original_gldm_LargeDependenceHighGrayLevelEmphasis', 'original_gldm_LargeDependenceLowGrayLevelEmphasis', 'original_gldm_LowGrayLevelEmphasis', 'original_gldm_SmallDependenceEmphasis', 'original_gldm_SmallDependenceHighGrayLevelEmphasis', 'original_gldm_SmallDependenceLowGrayLevelEmphasis', 'original_glrlm_GrayLevelNonUniformity', 'original_glrlm_GrayLevelNonUniformityNormalized', 'original_glrlm_GrayLevelVariance', 'original_glrlm_HighGrayLevelRunEmphasis', 'original_glrlm_LongRunEmphasis', 'original_glrlm_LongRunHighGrayLevelEmphasis', 'original_glrlm_LongRunLowGrayLevelEmphasis', 'original_glrlm_LowGrayLevelRunEmphasis', 'original_glrlm_RunEntropy', 'original_glrlm_RunLengthNonUniformity', 'original_glrlm_RunLengthNonUniformityNormalized', 'original_glrlm_RunPercentage', 'original_glrlm_RunVariance', 'original_glrlm_ShortRunEmphasis', 'original_glrlm_ShortRunHighGrayLevelEmphasis', 'original_glrlm_ShortRunLowGrayLevelEmphasis', 'original_glszm_GrayLevelNonUniformity', 'original_glszm_GrayLevelNonUniformityNormalized', 'original_glszm_GrayLevelVariance', 'original_glszm_HighGrayLevelZoneEmphasis', 'original_glszm_LargeAreaEmphasis', 'original_glszm_LargeAreaHighGrayLevelEmphasis', 'original_glszm_LargeAreaLowGrayLevelEmphasis', 'original_glszm_LowGrayLevelZoneEmphasis', 'original_glszm_SizeZoneNonUniformity', 'original_glszm_SizeZoneNonUniformityNormalized', 'original_glszm_SmallAreaEmphasis', 'original_glszm_SmallAreaHighGrayLevelEmphasis', 'original_glszm_SmallAreaLowGrayLevelEmphasis', 'original_glszm_ZoneEntropy', 'original_glszm_ZonePercentage', 'original_glszm_ZoneVariance', 'original_ngtdm_Busyness', 'original_ngtdm_Coarseness', 'original_ngtdm_Complexity', 'original_ngtdm_Contrast', 'original_ngtdm_Strength'] # In[12]: df = pd.read_csv('final_dataset.csv') df.shape # In[13]: X_train, X_test, y_train, y_test = train_test_split( df.drop(labels=['Label'], axis=1), df['Label'], test_size=0.2, random_state=23) # In[16]: RF = RandomForestClassifier(criterion = 'entropy',max_depth = None, max_features = 'log2', max_leaf_nodes = None, min_samples_leaf = 1,min_samples_split = 4, min_weight_fraction_leaf = 0.0, n_estimators = 200) RF.fit(X_train,y_train) # In[17]: import pickle # create an iterator object with write permission - model.pkl with open('model_pkl', 'wb') as files: pickle.dump(RF, files) # In[19]: model = pickle.load(open('model_pkl', 'rb')) # In[42]: def pneumonia(image): img_ = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY) resized_img = cv2.resize(img_,(256,256)) original_image = 'original.jpeg' cv2.imwrite(original_image,resized_img) img = cv2.imread(original_image) pr_mask1 = get_prediction (model1, img); pr_mask2 = get_prediction (model2, img); pr_mask3 = get_prediction (model3, img); pr_mask4 = get_prediction (model4, img); pr_mask5 = get_prediction (model5, img); ensemble_mask = ensemble_results (pr_mask1, pr_mask2, pr_mask3, pr_mask4, pr_mask5) ensemble_mask_post_HF = postprocessing_HoleFilling (ensemble_mask) ensemble_mask_post_HF_EI = postprocessing_EliminatingIsolation (ensemble_mask_post_HF) mask = 'mask.jpeg' cv2.imwrite(mask,ensemble_mask_post_HF_EI*255) features = {} df = pd.DataFrame(columns=features_name) image_ = sitk.ReadImage(original_image, sitk.sitkInt8) mask = sitk.ReadImage(mask, sitk.sitkInt8) features = extractor.execute(image_, mask) data = [] values = [] for key in features: values.append(features[key]) data.extend([values]) df.loc[0] = data[0] cols = df.columns[22:] # Create new dataframe with selected columns DataFrame = df[cols] model.fit(DataFrame) prediction = model.predict(DataFrame) if prediction == 0: # Determine the predicted class Label = "Normal" elif prediction == 1: Label = "Pneumonia" return Label # In[43]: import gradio as gr iface =gr.Interface(fn = pneumonia, inputs = "image", outputs = [gr.outputs.Textbox(label="Prediction")], title = "Pnuemonia Detection from Chest X ray images", description = "Upload a Chest X ray image") iface.launch()