refactor: 项目目录结构重组

- 中文目录名改为英文：cDNA图像处理实例→examples，参考资料→references
- web→app（Flask应用标准命名）
- 输出目录平移到 data/output/simple/ 和 data/output/full/
- 输入图像统一到 data/input/
- 构建脚本移到 scripts/
- 源码文件改用 snake_case 命名
- 更新所有文件路径引用和文档

references/matlab/checkstop.m

@@ -0,0 +1,37 @@
+function indicator = checkstop(old,new,dt)
+% indicate whether we should performance further iteraions or stop
+
+% Copyright (c) 2009, 
+% Yue Wu @ ECE Department, Tufts University
+% All Rights Reserved  
+
+layer = size(new,3);
+
+for i = 1:layer
+    old_{i} = old(:,:,i);
+    new_{i} = new(:,:,i);
+end
+
+if layer
+    ind = find(abs(new)<=.5);
+    M = length(ind);
+    Q = sum(abs(new(ind)-old(ind)))./M;
+    if Q<=dt*.18^2
+        indicator = 1;
+    else
+        indicator = 0;
+    end
+else
+    ind1 = find(abs(old_{1})<1);
+    ind2 = find(abs(old_{2})<1);
+    M1 = length(ind1);
+    M2 = length(ind2);
+    Q1 = sum(abs(new_{1}(ind1)-old_{1}(ind1)))./M1;
+    Q2 = sum(abs(new_{2}(ind2)-old_{2}(ind2)))./M2;
+    if Q1<=dt*.18^2 && Q2<=dt*.18^2
+        indicator = 1;
+    else
+        indicator = 0;
+    end
+end
+return