update readme

README.md

@@ -1,9 +1,11 @@
-Atlas guided em algorithm
+Atlas guided EM Algorithm
 ---------------------------------
 
-## About this repository
+This implementation is based on [Shimizu, A., Ohno, R., Ikegami, T. et al. (2007) Segmentation of multiple organs in non-contrast 3D abdominal CT images, Int J CARS 2: 135. https://doi.org/10.1007/s11548-007-0135-z](https://link.springer.com/article/10.1007/s11548-007-0135-z).
 
-This implementation is based on [Shimizu, A., Ohno, R., Ikegami, T. et al. (2007) Segmentation of multiple organs in non-contrast 3D abdominal CT images, Int J CARS 2: 135. https://doi.org/10.1007/s11548-007-0135-z](https://link.springer.com/article/10.1007/s11548-007-0135-z)
+Note this is not official implementation.
+
+Please use at your own responsibility.
 
 ## Requirements
 
@@ -13,9 +15,9 @@ Nuget package
 
 - Boost
 
-- Itk
+- ITK
 
-Another library
+Another library (already contained)
 
 - [mist](https://github.com/mist-team/mist)
 
@@ -25,5 +27,124 @@ Another library
 
 - Visual Studio 2015
 
-#### Note
-In development
+- Release x64
+
+## Detail of data
+
+Data I used is as follow:
+
+Label correspondense
+
+| Organs | Label number |
+|:---:|:---:|
+|others|0|
+|liver|1|
+|spleen|2|
+|kidneyL|3|
+|kidneyR|4|
+|heart|5|
+|gallbladder|6|
+|pancreas|7|
+|aorta|8|
+|IVC|9|
+|portal|10|
+|stomachWall|11|
+|oesophagus|12|
+
+Note:
+In this case, i didnt use heart label since it is not included in mask image region.
+
+Example:
+
+|Original|Label|Mask|
+|:---:|:---:|:---:|
+|<img src='assets/img/resize/fig1.png' width=75%>|<img src='assets/img/resize/fig2.png' width=75%>|<img src='assets/img/resize/fig3.png' width=75%>|
+
+## How to use
+
+First of all, please build all project.
+
+And then, please put your data into `data/preprocessed` folder.
+
+```
+data
+└─preprocessed
+   ├─abdominal_cavity_mask        <--- mask image e.g. region of interest image
+   ├─label                        <--- label image
+   └─org                          <--- original image
+```
+
+I show flow chart as bellow:
+
+<img src='assets/img/fig4.png' width=75%>
+
+[Cite](https://www.jstage.jst.go.jp/article/mit/24/3/24_153/_pdf)
+
+#### 1. generate_atlas
+
+Generate atlas.
+
+This program outputs into `results/generate_atlas`.
+
+```
+bat\generate_atlas.bat
+```
+
+#### 2. compute_features
+
+Compute features each original image.
+
+In this case, we calculate median image.
+
+```
+bat\compute_features.bat
+```
+
+#### 3. calc_init_val
+
+Compute initial value for em algorithm using training data.
+
+```
+bat\calc_init_val.bat
+```
+
+#### 4. apply_em_algorithm
+
+Apply em algorithm to test data
+
+```
+bat\apply_em_algorithm_using_atlas.bat
+```
+
+#### 5. apply_maximum_a_posteriori
+
+Apply maximum a posteriori to test data
+
+```
+bat\apply_maximum_a_posteriori.bat
+```
+
+## Results
+
+I show example of result.
+
+|Predict|Ground truth|Original|
+|:---:|:---:|:---:|
+|<img src='assets/img/resize/fig6.png' width=75%>|<img src='assets/img/resize/fig7.png' width=75%>|<img src='assets/img/resize/fig5.png' width=75%>|
+
+I evaluate my result in terms of Jaccard Index.
+
+|organs|JI|
+|:---:|:---:|
+|liver|0.873291|
+|spleen|0.561109|
+|kidneyL|0.33408|
+|kidneyR|0.0138403|
+|gallbladder|0|
+|pancreas|0|
+|aorta|0.412388|
+|IVC|0|
+|portal|0|
+|stomachWall|0.116285|
+|oesophagus|0|
+|other|	0.673242|

apply_em_algorithm/main.cpp

@@ -155,6 +155,8 @@ int main(int argc, char **argv) {
 		for (int l = 0; l < TESTTIME_NUM_LABELS; l++) {
 			std::string result_dir = output_dir + TESTTIME_LABEL_NAMES[l];
 			make_dir(result_dir);
+			save_param_as_csv(mean[l], result_dir + "/estimated_mean_param.csv");
+			save_param_as_csv(covariance[l], result_dir + "/estimated_covariance_param.csv");
 			write_raw_and_txt(mean[l], result_dir + "/estimated_mean_param");
 			write_raw_and_txt(covariance[l], result_dir + "/estimated_covariance_param");
 		} /* Label loop */

calc_init_val/main.cpp

@@ -140,6 +140,8 @@ int main(int argc, char **argv) {
 		std::cout << "----- Save param -----" << std::endl;
 		std::string result_dir = output_dir + LABEL_NAMES[l];
 		make_dir(result_dir);
+		save_param_as_csv(total_feat_mean, result_dir + "/mean_param.csv");
+		save_param_as_csv(total_feat_covariance, result_dir + "/covariance_param.csv");
 		write_raw_and_txt(total_feat_mean, result_dir + "/mean_param");
 		write_raw_and_txt(total_feat_covariance, result_dir + "/covariance_param");
 

headers/dataIO.h

@@ -180,3 +180,12 @@ void read_raw_to_eigen(Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>& eigen,
 	eigen = Eigen::Map<Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>>(&v[0], row_size, col_size);
 }
 
+template <class T>
+void save_param_as_csv(Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic> &eigen, std::string filename) {
+
+	std::ofstream ofs(filename);
+	ofs << eigen;
+	ofs.close();
+
+	return;
+}