update maxflow for multiple channels

Author: taigw

LICENSE

@@ -0,0 +1,11 @@
+Copyright 2019 University of Electronic Science and Technology of China
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,14 @@
+include maxflow_python/*h
+include densecrf_python/*h
+include dependency/maxflow-v3.0/*h
+include dependency/maxflow-v3.0/*inc
+recursive-include dependency/densecrf/include/ *
+recursive-include dependency/densecrf/external/liblbfgs *
+include dependency/densecrf/src/*h
+include dependency/densecrf/external/liblbfgs/include/*h
+recursive-include dependency/densecrf3d/include/ *
+recursive-include dependency/densecrf3d/external/liblbfgs *
+include dependency/densecrf3d/src/*h
+include dependency/densecrf3d/external/liblbfgs/include/*h
+
+

examples/demo_maxflow.py

@@ -8,6 +8,7 @@
 def demo_maxflow():
     I = Image.open('../data/brain.png')
     Iq = np.asarray(I.convert('L'), np.float32)
+    # Iq = np.asarray(I, np.float32)
     P = np.asarray(Image.open('../data/brain_mask.png').convert('L'), np.float32) / 255
 
     fP = 0.5 + (P - 0.5) * 0.8
@@ -24,7 +25,8 @@ def demo_maxflow():
 
 def demo_interactive_maxflow():
     I = Image.open('../data/brain.png')
-    Iq = np.asarray(I.convert('L'), np.float32)
+    # Iq = np.asarray(I.convert('L'), np.float32)
+    Iq = np.asarray(I, np.float32)
     P = np.asarray(Image.open('../data/brain_mask.png').convert('L'), np.float32) / 255
 
     fP = 0.5 + (P - 0.5) * 0.8

maxflow_python/maxflow.cpp

@@ -317,9 +317,3 @@ static PyMethodDef Methods[] = {
     {"interactive_max_flow3d",  interactive_max_flow3d_wrapper, METH_VARARGS, "computing max flow 3d"},
     {NULL, NULL, 0, NULL}
 };
-
-//PyMODINIT_FUNC
-//initmax_flow3d(void) {
-//    (void) Py_InitModule("max_flow3d", Methods);
-//    import_array();
-//}

maxflow_python/maxflow3d.cpp

@@ -0,0 +1,114 @@
+#include "util.h"
+#include <iostream>
+#include <cmath>
+
+// for 2d images
+template<typename T>
+T get_pixel(const T * data, int height, int width, int h, int w)
+{
+    return data[h * width + w];
+}
+
+template<typename T>
+std::vector<T> get_pixel_vector(const T * data, int height, int width, int channel, int h, int w)
+{
+    std::vector<T> pixel_vector(channel);
+    for (int c = 0; c < channel; c++){
+        pixel_vector[c]= data[h * width * channel + w * channel + c];
+    }
+    return pixel_vector;
+}
+
+template<typename T>
+void set_pixel(T * data,  int height, int width, int h, int w, T value)
+{
+    data[h * width + w] = value;
+}
+
+template<typename T>
+float get_l2_distance(std::vector<T> p1, std::vector<T> p2)
+{
+    T sq_sum = 0.0;
+    for(int d = 0; d < p1.size(); d++)
+    {
+        sq_sum = sq_sum + (p1[d] - p2[d]) * (p1[d] - p2[d]);
+    }
+    float dis = sqrt(sq_sum);
+    return dis;
+}
+
+template
+float get_pixel<float>(const float * data, int height, int width, int h, int w);
+
+template
+int get_pixel<int>(const int * data, int height, int width, int h, int w);
+
+template
+std::vector<float> get_pixel_vector<float>(const float * data, int height, int width, int channel, int h, int w);
+
+template
+unsigned char get_pixel<unsigned char>(const unsigned char * data, int height, int width, int h, int w);
+
+
+template
+void set_pixel<float>(float * data, int height, int width, int h, int w, float value);
+
+template
+void set_pixel<int>(int * data, int height, int width, int h, int w, int value);
+
+template
+void set_pixel<unsigned char>(unsigned char * data, int height, int width, int h, int w, unsigned char value);
+
+template
+float get_l2_distance(std::vector<float> p1, std::vector<float> p2);
+
+
+// for 3d images
+template<typename T>
+T get_pixel(const T * data, int depth, int height, int width, int d, int h, int w)
+{
+    return data[(d*height + h) * width + w];
+}
+
+template<typename T>
+std::vector<T> get_pixel_vector(const T * data, int depth,  int height, int width, int channel, int d, int h, int w)
+{
+    std::vector<T> pixel_vector(channel);
+    for (int c = 0; c < channel; c++){
+        pixel_vector[c]= data[d*height*width*channel +  h * width * channel + w * channel + c];
+    }
+    return pixel_vector;
+}
+
+template<typename T>
+void set_pixel(T * data, int depth, int height, int width, int d, int h, int w, T value)
+{
+    data[(d*height + h) * width + w] = value;
+}
+
+template
+float get_pixel<float>(const float * data, int depth, int height, int width, int d, int h, int w);
+
+template
+std::vector<float> get_pixel_vector<float>(const float * data, int depth, int height, int width, int channel, int d, int h, int w);
+
+template
+int get_pixel<int>(const int * data, int depth, int height, int width, int d, int h, int w);
+
+template
+unsigned char get_pixel<unsigned char>(const unsigned char * data,
+                                       int depth, int height, int width,
+                                       int d, int h, int w);
+
+
+template
+void set_pixel<float>(float * data, int depth, int height, int width, int d, int h, int w, float value);
+
+template
+void set_pixel<int>(int * data, int depth, int height, int width, int d, int h, int w, int value);
+
+template
+void set_pixel<unsigned char>(unsigned char * data,
+                              int depth, int height, int width,
+                              int d, int h, int w, unsigned char value);
+

maxflow_python/util.cpp

@@ -0,0 +1,25 @@
+#include <vector>
+using namespace std;
+
+// for 2d images
+template<typename T>
+T get_pixel(const T * data, int height, int width, int h, int w);
+
+template<typename T>
+std::vector<T> get_pixel_vector(const T * data, int height, int width, int channel, int h, int w);
+
+template<typename T>
+void set_pixel(T * data,  int height, int width, int h, int w, T value);
+
+template<typename T>
+float get_l2_distance(std::vector<T> p1, std::vector<T> p2);
+
+// for 3d images
+template<typename T>
+T get_pixel(const T * data, int depth, int height, int width, int d, int h, int w);
+
+template<typename T>
+std::vector<T> get_pixel_vector(const T * data, int depth, int height, int width, int channel, int d, int h, int w);
+
+template<typename T>
+void set_pixel(T * data,  int depth, int height, int width, int d, int h, int w, T value);