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jizhang02 · Dec 22, 2023 · 9ea1456 · 9ea1456
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![Header Image](/code/figures/dream_codeworld.jpg)
+![Header Image](/figures/dream_codeworld.jpg)
 
 # Code 
 
@@ -10,17 +10,11 @@
 This repo collects the python code and jupyter notebooks.
 
 ## Code lists
-* [Cardiac images preprocessing](/code/cardiac-dataset-preprocess)
-* [Compute model memory](https://gist.github.com/jizhang02/ef8eb45450f3d943fea37c6544d3808c)
-* [Convert dcm to mhd](https://gist.github.com/jizhang02/6e395880c085f7c9884d9cec5490c710)
-* [DenseNet-FCN](/code/densenetfcn)
-* [Evaluation index](/code/basic-python-files/)
-* [Traditional image segmentation algorithms](/code/traditional-segmentation-algorithms/)
-* [U-Net](/code/u-net)
-* [V-Net](/code/vnet.py)
-* [plots](/code/basic-python-files/myplots.ipynb) 
-* [timm model list](/code/basic-python-files/timm_model_names.ipynb)
-* [DNN Marathon](/code/dnn_marathon.ipynb)
+* [Cardiac images preprocessing](/cardiac-dataset-preprocess)
+* [Deep learning based image segmentation](/segmentation-dl/)
+* [Image processing based image segmentation](/segmentation-mip/)
+* [Various utils](/utils/) 
+* [DNN Marathon](/dnn_marathon.ipynb)
 
 
 

diff --git a/...cardiac-dataset-preprocess/BoundingBox.py → cardiac-dataset-preprocess/BoundingBox.py b/...cardiac-dataset-preprocess/BoundingBox.py → cardiac-dataset-preprocess/BoundingBox.py
diff --git a/...ardiac-dataset-preprocess/Champ_train.txt → cardiac-dataset-preprocess/Champ_train.txt b/...ardiac-dataset-preprocess/Champ_train.txt → cardiac-dataset-preprocess/Champ_train.txt
diff --git a/code/cardiac-dataset-preprocess/Cropping.py → cardiac-dataset-preprocess/Cropping.py b/code/cardiac-dataset-preprocess/Cropping.py → cardiac-dataset-preprocess/Cropping.py
diff --git a/...iac-dataset-preprocess/FindBoundingbox.py → ...iac-dataset-preprocess/FindBoundingbox.py b/...iac-dataset-preprocess/FindBoundingbox.py → ...iac-dataset-preprocess/FindBoundingbox.py
diff --git a/code/cardiac-dataset-preprocess/ReadMe.md → cardiac-dataset-preprocess/ReadMe.md b/code/cardiac-dataset-preprocess/ReadMe.md → cardiac-dataset-preprocess/ReadMe.md
diff --git a/...diac-dataset-preprocess/UnifyingSlices.py → cardiac-dataset-preprocess/UnifyingSlices.py b/...diac-dataset-preprocess/UnifyingSlices.py → cardiac-dataset-preprocess/UnifyingSlices.py
diff --git a/...iac-dataset-preprocess/cropping_target.py → ...iac-dataset-preprocess/cropping_target.py b/...iac-dataset-preprocess/cropping_target.py → ...iac-dataset-preprocess/cropping_target.py
diff --git a/...c-dataset-preprocess/data_augmentation.py → ...c-dataset-preprocess/data_augmentation.py b/...c-dataset-preprocess/data_augmentation.py → ...c-dataset-preprocess/data_augmentation.py
diff --git a/...cardiac-dataset-preprocess/grid search.py → cardiac-dataset-preprocess/grid search.py b/...cardiac-dataset-preprocess/grid search.py → cardiac-dataset-preprocess/grid search.py
diff --git a/...ardiac-dataset-preprocess/metrics_acdc.py → cardiac-dataset-preprocess/metrics_acdc.py b/...ardiac-dataset-preprocess/metrics_acdc.py → cardiac-dataset-preprocess/metrics_acdc.py
diff --git a/...iac-dataset-preprocess/reading_slicese.py → ...iac-dataset-preprocess/reading_slicese.py b/...iac-dataset-preprocess/reading_slicese.py → ...iac-dataset-preprocess/reading_slicese.py
diff --git a/...iac-dataset-preprocess/slice_selection.py → ...iac-dataset-preprocess/slice_selection.py b/...iac-dataset-preprocess/slice_selection.py → ...iac-dataset-preprocess/slice_selection.py
diff --git a/code/.ipynb_checkpoints/dnn_marathon-checkpoint.ipynb b/code/.ipynb_checkpoints/dnn_marathon-checkpoint.ipynb
diff --git a/code/basic-python-files/ReadMe.md b/code/basic-python-files/ReadMe.md
diff --git a/code/basic-python-files/meanstd.py b/code/basic-python-files/meanstd.py
diff --git a/code/demo.pth b/code/demo.pth
diff --git a/code/u-net/readme.md b/code/u-net/readme.md
diff --git a/code/dnn_marathon.ipynb → dnn_marathon.ipynb b/code/dnn_marathon.ipynb → dnn_marathon.ipynb
@@ -1734,7 +1734,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   },
   "vscode": {
    "interpreter": {

diff --git a/code/figures/VGG16_networks.png → figures/VGG16_networks.png b/code/figures/VGG16_networks.png → figures/VGG16_networks.png
diff --git a/code/figures/dream_codeworld.jpg → figures/dream_codeworld.jpg b/code/figures/dream_codeworld.jpg → figures/dream_codeworld.jpg
diff --git a/code/figures/resnet50.png → figures/resnet50.png b/code/figures/resnet50.png → figures/resnet50.png
diff --git a/code/figures/transunet.png → figures/transunet.png b/code/figures/transunet.png → figures/transunet.png
diff --git a/code/figures/vgg16model.png → figures/vgg16model.png b/code/figures/vgg16model.png → figures/vgg16model.png
diff --git a/code/figures/vit.png → figures/vit.png b/code/figures/vit.png → figures/vit.png
diff --git a/code/densenetfcn/data.py → segmentation-dl/densenetfcn/data.py b/code/densenetfcn/data.py → segmentation-dl/densenetfcn/data.py
diff --git a/code/densenetfcn/densenet_fc.py → segmentation-dl/densenetfcn/densenet_fc.py b/code/densenetfcn/densenet_fc.py → segmentation-dl/densenetfcn/densenet_fc.py
diff --git a/code/densenetfcn/readme.md → segmentation-dl/densenetfcn/readme.md b/code/densenetfcn/readme.md → segmentation-dl/densenetfcn/readme.md
diff --git a/code/densenetfcn/utils.py → segmentation-dl/densenetfcn/utils.py b/code/densenetfcn/utils.py → segmentation-dl/densenetfcn/utils.py
diff --git a/code/u-net/ModelPara_load.py → segmentation-dl/u-net/ModelPara_load.py b/code/u-net/ModelPara_load.py → segmentation-dl/u-net/ModelPara_load.py
diff --git a/code/u-net/Weighted_hausdorff_distance.py → ...n-dl/u-net/Weighted_hausdorff_distance.py b/code/u-net/Weighted_hausdorff_distance.py → ...n-dl/u-net/Weighted_hausdorff_distance.py
diff --git a/code/u-net/binary.py → segmentation-dl/u-net/binary.py b/code/u-net/binary.py → segmentation-dl/u-net/binary.py
diff --git a/code/u-net/data.py → segmentation-dl/u-net/data.py b/code/u-net/data.py → segmentation-dl/u-net/data.py
diff --git a/code/u-net/image preprocess.py → segmentation-dl/u-net/image preprocess.py b/code/u-net/image preprocess.py → segmentation-dl/u-net/image preprocess.py
diff --git a/code/u-net/loss.py → segmentation-dl/u-net/loss.py b/code/u-net/loss.py → segmentation-dl/u-net/loss.py
diff --git a/code/u-net/main.py → segmentation-dl/u-net/main.py b/code/u-net/main.py → segmentation-dl/u-net/main.py
diff --git a/code/u-net/metrics.py → segmentation-dl/u-net/metrics.py b/code/u-net/metrics.py → segmentation-dl/u-net/metrics.py
diff --git a/code/u-net/model1.py → segmentation-dl/u-net/model1.py b/code/u-net/model1.py → segmentation-dl/u-net/model1.py
diff --git a/code/u-net/model2.py → segmentation-dl/u-net/model2.py b/code/u-net/model2.py → segmentation-dl/u-net/model2.py
diff --git a/code/u-net/predict.py → segmentation-dl/u-net/predict.py b/code/u-net/predict.py → segmentation-dl/u-net/predict.py
diff --git a/code/u-net/weighted_binary_crossentropy.py → ...-dl/u-net/weighted_binary_crossentropy.py b/code/u-net/weighted_binary_crossentropy.py → ...-dl/u-net/weighted_binary_crossentropy.py
diff --git a/code/vnet.py → segmentation-dl/vnet.py b/code/vnet.py → segmentation-dl/vnet.py
diff --git a/...tation-algorithms/Active Contour Model.py → segmentation-mip/Active Contour Model.py b/...tation-algorithms/Active Contour Model.py → segmentation-mip/Active Contour Model.py
diff --git a/...segmentation-algorithms/Active Contour.py → segmentation-mip/Active Contour.py b/...segmentation-algorithms/Active Contour.py → segmentation-mip/Active Contour.py
diff --git a/...onal-segmentation-algorithms/Chan-Vese.py → segmentation-mip/Chan-Vese.py b/...onal-segmentation-algorithms/Chan-Vese.py → segmentation-mip/Chan-Vese.py
diff --git a/...entation-algorithms/Clustering_K-Means.py → segmentation-mip/Clustering_K-Means.py b/...entation-algorithms/Clustering_K-Means.py → segmentation-mip/Clustering_K-Means.py
diff --git a/...l-segmentation-algorithms/Code_Eval.ipynb → segmentation-mip/Code_Eval.ipynb b/...l-segmentation-algorithms/Code_Eval.ipynb → segmentation-mip/Code_Eval.ipynb
diff --git a/...aditional-segmentation-algorithms/Dice.py → segmentation-mip/Dice.py b/...aditional-segmentation-algorithms/Dice.py → segmentation-mip/Dice.py
diff --git a/...ntation-algorithms/Edge_Canny_operator.py → segmentation-mip/Edge_Canny_operator.py b/...ntation-algorithms/Edge_Canny_operator.py → segmentation-mip/Edge_Canny_operator.py
diff --git a/...gorithms/Edge_Laplacian-gauss_operator.py → ...tion-mip/Edge_Laplacian-gauss_operator.py b/...gorithms/Edge_Laplacian-gauss_operator.py → ...tion-mip/Edge_Laplacian-gauss_operator.py
diff --git a/...thms/Energy_ActiveContour_FastMarching.py → ...-mip/Energy_ActiveContour_FastMarching.py b/...thms/Energy_ActiveContour_FastMarching.py → ...-mip/Energy_ActiveContour_FastMarching.py
diff --git a/...gorithms/Energy_ActiveContour_Levelset.py → ...tion-mip/Energy_ActiveContour_Levelset.py b/...gorithms/Energy_ActiveContour_Levelset.py → ...tion-mip/Energy_ActiveContour_Levelset.py
diff --git a/...-algorithms/Energy_ActiveContour_SNAKE.py → ...ntation-mip/Energy_ActiveContour_SNAKE.py b/...-algorithms/Energy_ActiveContour_SNAKE.py → ...ntation-mip/Energy_ActiveContour_SNAKE.py
diff --git a/...ional-segmentation-algorithms/Grab Cut.py → segmentation-mip/Grab Cut.py b/...ional-segmentation-algorithms/Grab Cut.py → segmentation-mip/Grab Cut.py
diff --git a/...ional-segmentation-algorithms/GrabCut.cpp → segmentation-mip/GrabCut.cpp b/...ional-segmentation-algorithms/GrabCut.cpp → segmentation-mip/GrabCut.cpp
diff --git a/...nal-segmentation-algorithms/Graph Cuts.py → segmentation-mip/Graph Cuts.py b/...nal-segmentation-algorithms/Graph Cuts.py → segmentation-mip/Graph Cuts.py
diff --git a/...-segmentation-algorithms/Graph_GrabCut.py → segmentation-mip/Graph_GrabCut.py b/...-segmentation-algorithms/Graph_GrabCut.py → segmentation-mip/Graph_GrabCut.py
diff --git a/...segmentation-algorithms/Graph_GraphCut.py → segmentation-mip/Graph_GraphCut.py b/...segmentation-algorithms/Graph_GraphCut.py → segmentation-mip/Graph_GraphCut.py
diff --git a/...on-algorithms/Graph_MarkovRandomFields.py → segmentation-mip/Graph_MarkovRandomFields.py b/...on-algorithms/Graph_MarkovRandomFields.py → segmentation-mip/Graph_MarkovRandomFields.py
diff --git a/...mentation-algorithms/Graph_Random walk.py → segmentation-mip/Graph_Random walk.py b/...mentation-algorithms/Graph_Random walk.py → segmentation-mip/Graph_Random walk.py
diff --git a/...itional-segmentation-algorithms/ReadMe.md → segmentation-mip/ReadMe.md b/...itional-segmentation-algorithms/ReadMe.md → segmentation-mip/ReadMe.md
diff --git a/...-algorithms/Region_SeededRegionGrowing.py → ...ntation-mip/Region_SeededRegionGrowing.py b/...-algorithms/Region_SeededRegionGrowing.py → ...ntation-mip/Region_SeededRegionGrowing.py
diff --git a/...gmentation-algorithms/Region_Watershed.py → segmentation-mip/Region_Watershed.py b/...gmentation-algorithms/Region_Watershed.py → segmentation-mip/Region_Watershed.py
diff --git a/...ntation-algorithms/SeededRegionGrowing.py → segmentation-mip/SeededRegionGrowing.py b/...ntation-algorithms/SeededRegionGrowing.py → segmentation-mip/SeededRegionGrowing.py
diff --git a/...tion-algorithms/SegmentationEvaluation.py → segmentation-mip/SegmentationEvaluation.py b/...tion-algorithms/SegmentationEvaluation.py → segmentation-mip/SegmentationEvaluation.py
diff --git a/...segmentation-algorithms/Threshold_Otsu.py → segmentation-mip/Threshold_Otsu.py b/...segmentation-algorithms/Threshold_Otsu.py → segmentation-mip/Threshold_Otsu.py
diff --git a/...egmentation-algorithms/chan-vese model.py → segmentation-mip/chan-vese model.py b/...egmentation-algorithms/chan-vese model.py → segmentation-mip/chan-vese model.py
diff --git a/...ional-segmentation-algorithms/chanvese.py → segmentation-mip/chanvese.py b/...ional-segmentation-algorithms/chanvese.py → segmentation-mip/chanvese.py
diff --git a/...egmentation-algorithms/data/Andbru.nii.gz → segmentation-mip/data/Andbru.nii.gz b/...egmentation-algorithms/data/Andbru.nii.gz → segmentation-mip/data/Andbru.nii.gz
diff --git a/...gmentation-algorithms/data/CONTOUR.nii.gz → segmentation-mip/data/CONTOUR.nii.gz b/...gmentation-algorithms/data/CONTOUR.nii.gz → segmentation-mip/data/CONTOUR.nii.gz
diff --git a/...al-segmentation-algorithms/data/GT.nii.gz → segmentation-mip/data/GT.nii.gz b/...al-segmentation-algorithms/data/GT.nii.gz → segmentation-mip/data/GT.nii.gz
diff --git a/...segmentation-algorithms/data/GT_axial.png → segmentation-mip/data/GT_axial.png b/...segmentation-algorithms/data/GT_axial.png → segmentation-mip/data/GT_axial.png
diff --git a/...gmentation-algorithms/data/GT_coronal.png → segmentation-mip/data/GT_coronal.png b/...gmentation-algorithms/data/GT_coronal.png → segmentation-mip/data/GT_coronal.png
diff --git a/...mentation-algorithms/data/GT_sagittal.png → segmentation-mip/data/GT_sagittal.png b/...mentation-algorithms/data/GT_sagittal.png → segmentation-mip/data/GT_sagittal.png
diff --git a/...ntation-algorithms/data/contour_axial.png → segmentation-mip/data/contour_axial.png b/...ntation-algorithms/data/contour_axial.png → segmentation-mip/data/contour_axial.png
diff --git a/...ation-algorithms/data/contour_coronal.png → segmentation-mip/data/contour_coronal.png b/...ation-algorithms/data/contour_coronal.png → segmentation-mip/data/contour_coronal.png
diff --git a/...tion-algorithms/data/contour_sagittal.png → segmentation-mip/data/contour_sagittal.png b/...tion-algorithms/data/contour_sagittal.png → segmentation-mip/data/contour_sagittal.png
diff --git a/...al-segmentation-algorithms/data/gourd.bmp → segmentation-mip/data/gourd.bmp b/...al-segmentation-algorithms/data/gourd.bmp → segmentation-mip/data/gourd.bmp
diff --git a/...onal-segmentation-algorithms/data/gt1.png → segmentation-mip/data/gt1.png b/...onal-segmentation-algorithms/data/gt1.png → segmentation-mip/data/gt1.png
diff --git a/...onal-segmentation-algorithms/data/gt2.png → segmentation-mip/data/gt2.png b/...onal-segmentation-algorithms/data/gt2.png → segmentation-mip/data/gt2.png
diff --git a/...onal-segmentation-algorithms/data/gt3.png → segmentation-mip/data/gt3.png b/...onal-segmentation-algorithms/data/gt3.png → segmentation-mip/data/gt3.png
diff --git a/...gmentation-algorithms/data/marked2_v2.jpg → segmentation-mip/data/marked2_v2.jpg b/...gmentation-algorithms/data/marked2_v2.jpg → segmentation-mip/data/marked2_v2.jpg
diff --git a/...entation-algorithms/data/original2_v1.jpg → segmentation-mip/data/original2_v1.jpg b/...entation-algorithms/data/original2_v1.jpg → segmentation-mip/data/original2_v1.jpg
diff --git a/...al-segmentation-algorithms/data/skin1.jpg → segmentation-mip/data/skin1.jpg b/...al-segmentation-algorithms/data/skin1.jpg → segmentation-mip/data/skin1.jpg
diff --git a/...al-segmentation-algorithms/data/skin2.jpg → segmentation-mip/data/skin2.jpg b/...al-segmentation-algorithms/data/skin2.jpg → segmentation-mip/data/skin2.jpg
diff --git a/...al-segmentation-algorithms/data/skin3.jpg → segmentation-mip/data/skin3.jpg b/...al-segmentation-algorithms/data/skin3.jpg → segmentation-mip/data/skin3.jpg
diff --git a/...mentation-algorithms/data/verbe_axial.png → segmentation-mip/data/verbe_axial.png b/...mentation-algorithms/data/verbe_axial.png → segmentation-mip/data/verbe_axial.png
diff --git a/...ntation-algorithms/data/verbe_coronal.png → segmentation-mip/data/verbe_coronal.png b/...ntation-algorithms/data/verbe_coronal.png → segmentation-mip/data/verbe_coronal.png
diff --git a/...tation-algorithms/data/verbe_sagittal.png → segmentation-mip/data/verbe_sagittal.png b/...tation-algorithms/data/verbe_sagittal.png → segmentation-mip/data/verbe_sagittal.png
diff --git a/...nal-segmentation-algorithms/drlse_algo.py → segmentation-mip/drlse_algo.py b/...nal-segmentation-algorithms/drlse_algo.py → segmentation-mip/drlse_algo.py
diff --git a/...mentation-algorithms/evaluation method.py → segmentation-mip/evaluation method.py b/...mentation-algorithms/evaluation method.py → segmentation-mip/evaluation method.py
diff --git a/...l-segmentation-algorithms/level set cv.py → segmentation-mip/level set cv.py b/...l-segmentation-algorithms/level set cv.py → segmentation-mip/level set cv.py
diff --git a/...egmentation-algorithms/morphologysnake.py → segmentation-mip/morphologysnake.py b/...egmentation-algorithms/morphologysnake.py → segmentation-mip/morphologysnake.py
diff --git a/...ditional-segmentation-algorithms/snake.py → segmentation-mip/snake.py b/...ditional-segmentation-algorithms/snake.py → segmentation-mip/snake.py
diff --git a/code/basic-python-files/csvread_write.py → utils/file_csv.py b/code/basic-python-files/csvread_write.py → utils/file_csv.py
@@ -1,12 +1,21 @@
+'''
+-----------------------------------------------
+File Name: file_csv.py
+Description: 
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
+
 from tqdm import tqdm # progress bar
 import numpy as np
 import matplotlib.pyplot as plt
 from PIL import Image,ImageChops
-
 import pandas as pd
 import math
 import glob
 import os
+
 def angle(a, b, c):
   """
   Return angle between lines ab, bc

diff --git a/code/basic-python-files/h5file.py → utils/file_h5.py b/code/basic-python-files/h5file.py → utils/file_h5.py
@@ -1,3 +1,11 @@
+'''
+-----------------------------------------------
+File Name: file_h5.py
+Description: read h5 file.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
 # python 2
 #coding=utf-8
 import datetime

diff --git a/code/basic-python-files/mat2img.py → utils/file_mat.py b/code/basic-python-files/mat2img.py → utils/file_mat.py
@@ -1,3 +1,12 @@
+'''
+-----------------------------------------------
+File Name: file_mat.py
+Description: Processing mat file.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
+
 import cv2
 import scipy.io as scio
 from PIL import Image

diff --git a/code/basic-python-files/npyfile.py → utils/file_npy.py b/code/basic-python-files/npyfile.py → utils/file_npy.py
@@ -1,3 +1,12 @@
+'''
+-----------------------------------------------
+File Name: file_npy.py
+Description: npy file reading and writing.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
+
 import numpy as np
 import random
 import math

diff --git a/code/basic-python-files/tiff.py → utils/file_tiff.py b/code/basic-python-files/tiff.py → utils/file_tiff.py
@@ -1,3 +1,12 @@
+'''
+-----------------------------------------------
+File Name: file_tiff.py
+Description: tiff file processing.
+Author: Jing
+Date: 9/28/2021
+-----------------------------------------------
+'''
+
 import numpy as np
 import tifffile as tiff
 import matplotlib.image as mpimg # mpimg 用于读取图片
@@ -50,5 +59,4 @@ def readoneimg(imagepath):
     im1[np.where(im1==170)]=2
     im1[np.where(im1==255)]=3
     im = Image.fromarray(im1)
-    im.save('new.png')
-
+    im.save('new.png')
diff --git a/code/basic-python-files/HC_para.py → utils/image_HC_para.py b/code/basic-python-files/HC_para.py → utils/image_HC_para.py
@@ -1,9 +1,9 @@
 '''
 -----------------------------------------------
-File Name: HC_para$
+File Name: image_HC_para.py
 Description: Draw the parameters of an ellipse; Sum up the number of pixels of an ellipse
-Author: Jing$
-Date: 7/21/2021$
+Author: Jing
+Date: 7/21/2021
 -----------------------------------------------
 '''
 import glob

diff --git a/code/basic-python-files/NIQE.py → utils/image_NIQE.py b/code/basic-python-files/NIQE.py → utils/image_NIQE.py
@@ -1,4 +1,11 @@
-# Natural Image Quality Evaluator
+'''
+-----------------------------------------------
+File Name: image_NIQE.py
+Description: Natural Image Quality Evaluator.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
 
 import numpy as np
 import scipy.misc

diff --git a/code/basic-python-files/image-enhence.py → utils/image_enhence.py b/code/basic-python-files/image-enhence.py → utils/image_enhence.py
@@ -1,3 +1,11 @@
+'''
+-----------------------------------------------
+File Name: image_enhence.py
+Description: Different image enhence methods.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
 import numpy as np
 import cv2
 

diff --git a/code/basic-python-files/image preprocess.py → utils/image_process.py b/code/basic-python-files/image preprocess.py → utils/image_process.py
@@ -1,3 +1,12 @@
+'''
+-----------------------------------------------
+File Name: image_process.py
+Description: Different image processing methods.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
+
 from PIL import Image,ImageChops
 import os, sys
 import numpy as np

diff --git a/...sic-python-files/image reading methods.py → utils/image_reading.py b/...sic-python-files/image reading methods.py → utils/image_reading.py
@@ -1,3 +1,12 @@
+'''
+-----------------------------------------------
+File Name: image_reading.py
+Description: Different image reading methods.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
+
 #encoding=utf8
 from PIL import Image
 import numpy as np

diff --git a/code/basic-python-files/Seg_evaluation.py → utils/image_seg_evaluation.py b/code/basic-python-files/Seg_evaluation.py → utils/image_seg_evaluation.py
@@ -1,9 +1,12 @@
 '''
-Title: Calculate Dice score, hausdorff distance, assd
+-----------------------------------------------
+File Name: image_seg_evaluation.py
+Description: Calculate Dice score, hausdorff distance, assd
 between segmented images and ground truth images.
 Compute p-value between two same metrics.
-Author: Jing Zhang ([email protected])
+Author: Jing ([email protected])
 Date: 2021-04-23
+-----------------------------------------------
 '''
 
 from PIL import Image

diff --git a/code/basic-python-files/binary.py → utils/lib_binary.py b/code/basic-python-files/binary.py → utils/lib_binary.py
diff --git a/...basic-python-files/timm_model_names.ipynb → utils/lib_timm_model_names.ipynb b/...basic-python-files/timm_model_names.ipynb → utils/lib_timm_model_names.ipynb
diff --git a/code/basic-python-files/analysis.py → utils/plots_analysis.py b/code/basic-python-files/analysis.py → utils/plots_analysis.py
@@ -1,17 +1,12 @@
 '''
 -----------------------------------------------
-File Name: log_curve$
-Description:
-Author: Jing$
-Date: 7/5/2021$
+File Name: plots_analysis.py
+Description: Drawing learning curve in training,
+validation, test stage from log file.
+Author: Jing ([email protected])
+Date: 7/5/2021
 -----------------------------------------------
 '''
-'''
-Title: Drawing learning curve in training, validation, test stage
-from log file.
-Author: Jing Zhang
-Date: 2021-04-23
-'''
 
 import glob
 import cv2

diff --git a/code/basic-python-files/log_curve.py → utils/plots_curvefromcsv.py b/code/basic-python-files/log_curve.py → utils/plots_curvefromcsv.py
@@ -1,17 +1,12 @@
 '''
 -----------------------------------------------
-File Name: log_curve$
-Description:
-Author: Jing$
-Date: 7/5/2021$
+File Name: plots_curvefromcsv.py
+Description: Drawing learning curve in training,
+validation, test stage from log file.
+Author: Jing ([email protected])
+Date: 7/5/2021
 -----------------------------------------------
 '''
-'''
-Title: Drawing learning curve in training, validation, test stage
-from log file.
-Author: Jing Zhang
-Date: 2021-04-23
-'''
 
 import os
 import pandas as pd

diff --git a/code/basic-python-files/curvefromjson.py → utils/plots_curvefromjson.py b/code/basic-python-files/curvefromjson.py → utils/plots_curvefromjson.py
@@ -1,3 +1,13 @@
+'''
+-----------------------------------------------
+File Name: plots_curvefromjson.py
+Description: Drawing learning curve in training,
+validation, test stage from log file.
+Author: Jing ([email protected])
+Date: 7/5/2021
+-----------------------------------------------
+'''
+
 import matplotlib.pyplot as plt
 import os
 from sklearn.preprocessing import MinMaxScaler

diff --git a/code/basic-python-files/error_bar.py → utils/plots_errorbar.py b/code/basic-python-files/error_bar.py → utils/plots_errorbar.py
@@ -1,9 +1,9 @@
 '''
 -----------------------------------------------
-File Name: error_bar$
-Description:
-Author: Jing$
-Date: 8/20/2021$
+File Name: plots_errorbar.py
+Description: Drawing error bar.
+Author: Jing ([email protected])
+Date: 7/5/2021
 -----------------------------------------------
 '''
 import matplotlib.pyplot as plt

diff --git a/code/basic-python-files/myplots.ipynb → utils/plots_myplots.ipynb b/code/basic-python-files/myplots.ipynb → utils/plots_myplots.ipynb