#____________________________________________________________ # August 2, 2023 #____________________________________________________________ import os import numpy as np import gradio as gr import SimpleITK as sitk import seaborn as sns import matplotlib.pyplot as plt def LoadImage(path_img): try: img_itk, voxel_size= Load_itk_image(path_img) except FileNotFoundError: print('ERROR: File not found', path_img) img_numpy = sitk.GetArrayFromImage(img_itk[0]) img_load=img_numpy.transpose() #remove background = 0 img_load[img_load==0]=np.nan return img_load def Load_itk_image(path_img): #Read header file_reader = sitk.ImageFileReader() file_reader.SetFileName(path_img) file_reader.ReadImageInformation() dim_total = file_reader.GetSize() img_vol_ITK = [] if len(dim_total)==4: dim_vol = (dim_total[0:3]) # make volume for all images img_load_all = sitk.ReadImage(path_img, sitk.sitkFloat32) img_vol_ITK = [] for vol_n in range(dim_total[3]): #Extract vol out of object size = list(dim_total) size[3] = 0 index = [0,0,0,vol_n] extractor = sitk.ExtractImageFilter() extractor.SetSize(size) extractor.SetIndex(index) img_vol_ITK.append(extractor.Execute(img_load_all)) else: img_ITK = sitk.ReadImage(path_img, sitk.sitkFloat32) img_vol_ITK.append(img_ITK) dim_vol = dim_total #Voxelsize in mm. forth dimension has no meaning in spacing. voxel_size = img_vol_ITK[0].GetSpacing() return img_vol_ITK, voxel_size def NormalizeMinMax(img): #Normalization for Volumes minVal = np.nanmin(img) maxVal = np.nanmax(img) img_normalized = (img - minVal)/(maxVal- minVal) return img_normalized def NormalizePercentile(img, minP, maxP): #Normalization for Volumes minVal = np.nanpercentile(img, minP) maxVal = np.nanpercentile(img, maxP) img_normalized = (img - minVal)/(maxVal- minVal) return img_normalized def NormalizeZScore(img): #Normalization for Volumes meanVal = np.nanmean(img) stdVal = np.nanstd(img) img_normalized = (img-meanVal)/stdVal return img_normalized def PrepImage(pathName): img_load = LoadImage(pathName) img_normalized = NormalizeMinMax(img_load) img_normalized_per =NormalizePercentile(img_load, 10, 90) img_normalized_per98 =NormalizePercentile(img_load, 2, 98) img_normalized_zscore= (NormalizeZScore(img_load) ) return img_load.flatten(),img_normalized.flatten(),img_normalized_per.flatten(),img_normalized_zscore.flatten(), img_normalized_per98.flatten() def Norm_image(vol_path,normalization_technique): imglist = [] imgClist=[] imgNlist=[] imgNPlist=[] imgNZlist=[] imgNPer98list=[] print(len(vol_path)) for file in vol_path: pathName = file.name img_load = LoadImage(pathName) imglist.append(img_load.flatten()) gr.Info('The volumes are succesfully loaded.') if 'MinMax' in normalization_technique: imgNlist.append(NormalizeMinMax(img_load).flatten()) if 'Z-Score' in normalization_technique: imgNZlist.append(NormalizeZScore(img_load).flatten()) if 'Percentile (2th - 98th)'in normalization_technique: imgNPer98list.append(NormalizePercentile(img_load, 2, 98).flatten()) if 'Percentile (10th - 90th)' in normalization_technique: imgNPlist.append(NormalizePercentile(img_load, 10, 90).flatten()) gr.Info('The different normalization techniques are calculted.') plt.figure(11) fig, ax = plt.subplots(1,1) for i, file in enumerate(vol_path): sns.histplot(data=imglist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=False,element="step", fill=False,bins=500,legend=True).set(title='Original') ax.legend() plt.savefig("Original.png") plots=["Original.png"] if 'MinMax' in normalization_technique: fig, ax = plt.subplots(1,1) for i, file in enumerate(vol_path): sns.histplot(data=imgNlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=False,element="step", fill=False,bins=500,legend=True).set(title='Min-Max') ax.legend() plt.savefig("MinMax.png") plots.append("MinMax.png") if 'Z-Score' in normalization_technique: fig, ax = plt.subplots(1,1) for i, file in enumerate(vol_path): sns.histplot(data=imgNZlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=False,element="step", fill=False,bins=500,legend=True).set(title='Z-Score') ax.legend() plt.savefig("Zscore.png") plots.append("Zscore.png") if 'Percentile (2th - 98th)'in normalization_technique: fig, ax = plt.subplots(1,1) for i, file in enumerate(vol_path): sns.histplot(data=imgNPer98list[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=False,element="step", fill=False,bins=500,legend=True).set(title='Percentile 2-98') ax.legend() plt.savefig("Per98.png") plots.append("Per98.png") if 'Percentile (10th - 90th)' in normalization_technique: fig, ax = plt.subplots(1,1) for i, file in enumerate(vol_path): sns.histplot(data=imgNPlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=False,element="step", fill=False,bins=500,legend=True).set(title='Percentile 10 - 90') ax.legend() plt.savefig("Per90.png") plots.append("Per90.png") gr.Info('The histograms are produced.') return plots description = 'You can upload mutiple image volumes (recommonded 3-5) in *.nii or *.nii.gz to see their histograms for multiple normalization techniques. Depending on file size and selected techniques it might take a while to do the calculations. \n The uploaded data is not stored and gets deleted once closing the window. ' inputs = [gr.File(file_count="multiple", label=None),gr.CheckboxGroup(["MinMax", "Z-Score", "Percentile (2th - 98th)", "Percentile (10th - 90th)"])] demo = gr.Interface(fn=Norm_image, inputs=inputs, outputs=[gr.Gallery(label="Profiling Dashboard")], #.style(grid=(2,3))], description=description, ) demo.launch().queue()