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Commit 826b3d33 authored by blia's avatar blia
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update bash script

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...@@ -10,22 +10,26 @@ ...@@ -10,22 +10,26 @@
```bash ```bash
git clone https://lab.compute.dtu.dk/s161488/region_active_learning.git git clone https://lab.compute.dtu.dk/s161488/region_active_learning.git
cd Region_Active_Learning cd region_active_learning
chmod +x requirement.sh
chmod +x produce_figure.sh
``` ```
2. Prepare the Dataset and pertained resnet-50 ckpt 2. Create a virtual env with the required packages
```bash ```bash
./requirement.sh conda env create -f active_learning.yaml
source activate act
``` ```
3. Create a virtual env with the required packages
2. Prepare the Dataset and pertained resnet-50 ckpt
```bash ```bash
conda env create --act active_learning.yaml ./requirement.sh
source activate act
``` ```
#### Evaluate the model #### Evaluate the model
In order to evaluate the model at each acquisition step, run In order to evaluate the model at each acquisition step, run
......
...@@ -17,7 +17,7 @@ from skimage.morphology import dilation, disk ...@@ -17,7 +17,7 @@ from skimage.morphology import dilation, disk
from scipy import ndimage from scipy import ndimage
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
path_mom = "/home/blia/Region_Active_Learning/DATA/" # the directory for saving data path_mom = "DATA/" # the directory for saving data
# path_mom = "/Users/bo/Documents/Exp_Data/" # path_mom = "/Users/bo/Documents/Exp_Data/"
path_use = path_mom + 'Data' path_use = path_mom + 'Data'
if not os.path.exists(path_use): if not os.path.exists(path_use):
...@@ -167,6 +167,7 @@ def transfer_data_to_dict(): ...@@ -167,6 +167,7 @@ def transfer_data_to_dict():
print("Saving the data in path:", filename.split(".")[0]) print("Saving the data in path:", filename.split(".")[0])
else: else:
print("Oh, this is the first time of creating this file") print("Oh, this is the first time of creating this file")
print("Creating the training data npy for GlaS")
np.save(filename.split(".")[0], data) np.save(filename.split(".")[0], data)
...@@ -235,12 +236,10 @@ def transfer_data_to_dict_test(): ...@@ -235,12 +236,10 @@ def transfer_data_to_dict_test():
print("Remove the existing data file", os.remove(filename)) print("Remove the existing data file", os.remove(filename))
print("Saving the data in path:", filename.split(".")[0]) print("Saving the data in path:", filename.split(".")[0])
else: else:
print("The file is not existed") print("Creating GlaS test data (benign)")
print("Saving the data in path:", filename.split(".")[0]) print("Saving the data in path:", filename.split(".")[0])
np.save(filename.split(".")[0], data) np.save(filename.split(".")[0], data)
data1 = defaultdict(list) data1 = defaultdict(list)
data1['image'] = image_mali data1['image'] = image_mali
data1['label'] = label_mali data1['label'] = label_mali
...@@ -252,6 +251,6 @@ def transfer_data_to_dict_test(): ...@@ -252,6 +251,6 @@ def transfer_data_to_dict_test():
print("Remove the existing data file", os.remove(filename)) print("Remove the existing data file", os.remove(filename))
print("Saving the data in path:", filename.split(".")[0]) print("Saving the data in path:", filename.split(".")[0])
else: else:
print("The file is not existed") print("Creating GlaS test data (malignant)")
print("Saving the data in path:", filename.split(".")[0])
np.save(filename.split(".")[0], data1) np.save(filename.split(".")[0], data1)
...@@ -10,7 +10,7 @@ import tensorflow as tf ...@@ -10,7 +10,7 @@ import tensorflow as tf
import cv2 import cv2
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
path_mom = "/home/blia/Region_Active_Learning/DATA/" # NOTE, NEED TO BE MANUALLY DEFINED path_mom = "DATA/" # NOTE, NEED TO BE MANUALLY DEFINED
def prepare_train_data(path, select_benign_train, select_mali_train): def prepare_train_data(path, select_benign_train, select_mali_train):
......
#!/bin/bash #!/bin/bash
cd Exp_Stat expdir=Exp_Stat
if [ -d "$expdir" ]; then
echo "folder $expdir already exists"
echo "next step, download the statistics to reproduce figures"
else
mkdir $expdir
echo "make folder $expdir for saving statistics"
fi
cd $expdir
filename=calibration_score filename=calibration_score
if [ -d "$filename" ]; then if [ -d "$filename" ]; then
echo "$filename exists" echo "YEAH! $filename exists"
echo "-----next step, reproducing the figures...................."
else else
echo "$filename does not exist" echo "$filename does not exist"
echo "Download the file-------------------" echo "Download the file..................................."
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /t$ wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1fu7RcqOMCCjz65VwFlTPg5qlLg2K7l1g' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1fu7RcqOMCCjz65VwFlTPg5qlLg2K7l1g" -O calibration_score.tar.gz && rm -rf /tmp/cookies.txt
echo "-----unziping the datafile" echo "-----unziping the datafile"
tar -xzvf calibration_score.tar.gz tar -xzvf calibration_score.tar.gz
mv use_stat calibration_score mv use_stat calibration_score
rm calibration_score.tar.gz rm calibration_score.tar.gz
fi fi
cd .. cd ..
echo "Start to reproduce figures"
python3 visualize_calibration_score.py --save True --path Exp_Stat/calibration_score/ python3 visualize_calibration_score.py --save True --path Exp_Stat/calibration_score/
echo "-----------------------------------"
echo "YEAH, FINISH REPRODUCING FIGURES :)"
echo "-----------------------------------"
\ No newline at end of file
#!/bin/bash #!/bin/bash
cd DATA cd DATA
datafolder=gland_data
if [ -d "$datafolder" ]; then
echo "YEAH, $datafolder exist"
echo "next download the resnet-v2-50 pretrained weight from tensorflow website..............."
else
echo "download the GlaS dataset ...................................."
wget https://warwick.ac.uk/fac/sci/dcs/research/tia/glascontest/download/warwick_qu_dataset_released_2016_07_08.zip wget https://warwick.ac.uk/fac/sci/dcs/research/tia/glascontest/download/warwick_qu_dataset_released_2016_07_08.zip
unzip warwick_qu_dataset_released_2016_07_08.zip unzip warwick_qu_dataset_released_2016_07_08.zip
mv 'Warwick QU Dataset (Released 2016_07_08)' gland_data mv 'Warwick QU Dataset (Released 2016_07_08)' gland_data
rm -rf warwick_qu_dataset_released_2016_07_08.zip rm -rf warwick_qu_dataset_released_2016_07_08.zip
rm -rf __MACOSX rm -rf __MACOSX
fi
cd .. cd ..
pwd
echo "download the resnet-v2-50 pretrained weight............."
pretrainfolder=pretrain_model
if [ -d "$pretrainfolder" ]; then
echo "YEAH, folder $pretrainfolder exists"
else
echo "create the folder to save resnet-v2-50 pretrained weight"
mkdir $pretrainfolder
fi
resnetname=resnet_v2_50.ckpt
cd pretrain_model cd pretrain_model
if [ -f "$resnetname" ]; then
echo "YEAH, $resnetname exists"
echo "next prepare the dataset ...................."
else
echo "download the resnet-v2-50 pretrained weight............."
wget http://download.tensorflow.org/models/resnet_v2_50_2017_04_14.tar.gz wget http://download.tensorflow.org/models/resnet_v2_50_2017_04_14.tar.gz
tar -xvf resnet_v2_50_2017_04_14.tar.gz tar -xvf resnet_v2_50_2017_04_14.tar.gz
rm resnet_v2_50_2017_04_14.tar.gz rm resnet_v2_50_2017_04_14.tar.gz
rm train.graph rm train.graph
rm eval.graph rm eval.graph
fi
cd .. cd ..
echo "print current directory"
pwd
echo "prepare the dataset"
python3 -c 'import data_utils.glanddata as gd;gd.transfer_data_to_dict()' python3 -c 'import data_utils.glanddata as gd;gd.transfer_data_to_dict()'
python3 -c 'import data_utils.glanddata as gd;gd.transfer_data_to_dict_test()' python3 -c 'import data_utils.glanddata as gd;gd.transfer_data_to_dict_test()'
echo "-------------------------------"
echo "YEAH, FINISH PREPARING THE DATA"
echo "-------------------------------"
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