r3536: Fix median threshold and add ImageMagick load support..

16 Mar 2009

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox

ChangeLog:
2009-03-16  Fabien Freling  <fabien.freling@lrde.epita.fr>

	Fix median threshold and add ImageMagick load support..
	* fabien/igr/Makefile: Update.
	* fabien/igr/check.sh: Update.
	* fabien/igr/med.cc: Fix median value.
	* fabien/magick/Makefile: Update.
	* fabien/magick/load.hh: Implement Magick support.
	* fabien/magick/magick.cc: Test file for Magick support.

---
 igr/Makefile     |    2 -
 igr/check.sh     |    7 ++--
 igr/med.cc       |   26 +++++++++++----
 magick/load.hh   |   95 ++++++++++++++++++++-----------------------------------
 magick/magick.cc |   19 +++++++----
 5 files changed, 74 insertions(+), 75 deletions(-)

Index: trunk/milena/sandbox/fabien/igr/check.sh
===================================================================

--- trunk/milena/sandbox/fabien/igr/check.sh	(revision 3535)
+++ trunk/milena/sandbox/fabien/igr/check.sh	(revision 3536)
@@ -12,11 +12,14 @@
     echo "  for lambda_closing = ${lambda_closing}";
     ./clo_vol grad.dump $dim ${lambda_closing}
     nbasins=`./wst clo_vol.dump $dim`
+    echo "    nbasins = $nbasins"
     ../bin/dumpl32_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm
     median=`./med wst.dump $dim $input $nbasins`
+    echo "    median = $median"
+    threshold=$(($median / 2))
     ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm
-    ./thres med.dump $dim $median
-    mv bin_result.pbm results/result_${3}_${lambda_closing}.pbm
+    ./thres med.dump $dim $threshold
+    mv result.pbm results/result_${3}_${lambda_closing}.pbm
 
 #if [ $2 -eq 2 ]; then
 #     if [ ${lambda_closing} -eq 100 ]; then
Index: trunk/milena/sandbox/fabien/igr/med.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/med.cc	(revision 3535)
+++ trunk/milena/sandbox/fabien/igr/med.cc	(revision 3536)
@@ -20,9 +20,12 @@
 #include <mln/core/routine/extend.hh>
 #include <mln/accu/mean.hh>
 #include <mln/accu/median_h.hh>
-#include <mln/morpho/elementary/dilation.hh>
+#include <mln/histo/array.hh>
+#include <mln/histo/compute.hh>
+#include <mln/labeling/compute.hh>
 #include <mln/labeling/mean_values.hh>
 #include <mln/level/compute.hh>
+#include <mln/morpho/elementary/dilation.hh>
 #include <mln/pw/all.hh>
 #include <mln/util/array.hh>
 
@@ -59,6 +62,8 @@
     return 1;
   }
 
+  unsigned median = 0;
+
   if (dim == 2)
   {
     image2d<L> labels;
@@ -70,18 +75,27 @@
     data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate);
     mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins));
 
-    accu::mean<float> accu_mean;
-    util::array<float> means = level::compute(accu_mean, wst_mean);
-
-    // FIXME: Take median value of means
+    histo::array<int_u12> histogram = histo::compute(wst_mean);
+    int j = 0;
+    int k = 0;
+    for (int i = 0; i < histogram.nvalues(); ++i)
+    {
+      if (histogram[i])
+	histogram[i] = i;
+    }
+    image1d<unsigned> ima_histo;
+    convert::from_to(histogram, ima_histo);
+    accu::median_h<int_u12> accu_med;
+    median = level::compute(accu_med, ima_histo | pw::value(ima_histo) != pw::cst(0));
 
     io::dump::save(wst_mean, "med.dump");
-    std::cout << median << std::endl;
   }
   else
   {
     // FIXME
   }
 
+  std::cout << median << std::endl;
+
   return 0;
 }
Index: trunk/milena/sandbox/fabien/igr/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/Makefile	(revision 3535)
+++ trunk/milena/sandbox/fabien/igr/Makefile	(revision 3536)
@@ -49,4 +49,4 @@
 	g++ -I../../../ ${CXXFLAGS} $^ -o thres
 	
 clean:
-	rm -rf *.dump *.p?m *.plot *.log *.csv
+	rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM
Index: trunk/milena/sandbox/fabien/TODO
===================================================================
Index: trunk/milena/sandbox/fabien/magick/magick.cc
===================================================================
--- trunk/milena/sandbox/fabien/magick/magick.cc	(revision 3535)
+++ trunk/milena/sandbox/fabien/magick/magick.cc	(revision 3536)
@@ -1,15 +1,22 @@
 #include <mln/core/image/image2d.hh>
-#include <mln/value/int_u8.hh>
+#include <mln/value/rgb8.hh>
 
 #include "load.hh"
 
-int main()
+int main(int argc, char* argv[])
 {
   using namespace mln;
-  using value::int_u8;
+  using value::rgb8;
 
-  image2d<int_u8> lena;
+  if (argc != 2)
+  {
+    std::cout << "Usage: " << argv[0] << " filename.ext" << std::endl;
+    return 1;
+  }
+
+  image2d<rgb8> lena;
+
+  io::magick::load(lena, argv[1]);
 
-  //io::magick::load(lena, "/Users/HiSoKa/Work/LRDE/Olena/resources/CardiacCT/178562160.dcm");
-  io::magick::load(lena, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm");
+  return 0;
 }
Index: trunk/milena/sandbox/fabien/magick/Makefile
===================================================================
Index: trunk/milena/sandbox/fabien/magick/load.hh
===================================================================
--- trunk/milena/sandbox/fabien/magick/load.hh	(revision 3535)
+++ trunk/milena/sandbox/fabien/magick/load.hh	(revision 3536)
@@ -37,6 +37,7 @@
  */
 
 # include <mln/core/image/image2d.hh>
+# include <mln/value/rgb8.hh>
 # include <Magick++.h>
 
 
@@ -59,58 +60,19 @@
       void load(Image<I>& ima,
 		const std::string& filename);
 
-      /*! Load a magick image in a Milena image. To use this routine, you
-       *  should specialize the template whith the value type of the
-       *  image loaded. (ex : load<value::int_u8>("...") )
-       *
-       * \param[in] filename The image source.
-       *
-       * \return An image2d which contains loaded data.
-       */
-      template <typename V>
-      image2d<V> load(const std::string& filename);
-
-      /*! Load a magick image in a Milena image. To use this routine, you
-       *  should specialize the template whith the value type of the
-       *  image loaded. (ex : load<value::int_u8>("...") )
-       *
-       * \param[in] filename The image source.
-       *
-       * \return An image2d which contains loaded data.
-       */
-      template <typename V>
-      image3d<V> load(const std::string& filename);
 
 # ifndef MLN_INCLUDE_ONLY
 
-      template <typename V>
-      inline
-      image2d<V> load(const std::string& filename)
-      {
-	trace::entering("mln::io::magick::load");
-	image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename);
-	trace::exiting("mln::io::magick::load");
-	return ima;
-      }
-
-      template <typename V>
-      inline
-      image3d<V> load(const std::string& filename)
-      {
-	trace::entering("mln::io::magick::load");
-	image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename);
-	trace::exiting("mln::io::magick::load");
-	return ima;
-      }
-
 
       template <typename I>
       inline
-      void load(Image<I>& ima,
+      void load(Image<I>& ima_,
 		const std::string& filename)
       {
 	trace::entering("mln::io::magick::load");
 
+	I& ima = exact(ima_);
+
 	//std::ifstream file(filename.c_str());
 	//if (! file)
 	//{
@@ -118,24 +80,37 @@
 	//  abort();
 	//}
 
-	Magick::Image file(filename);
-	//std::cout << "file attribute: " << file.attribute() << std::endl;
-	std::cout << "width: " << file.columns() << std::endl;
-	std::cout << "height: " << file.rows() << std::endl;
-	std::cout << "x resolution: " << file.xResolution() << std::endl;
-	std::cout << "y resolution: " << file.yResolution() << std::endl;
-	std::cout << "depth: " << file.depth() << std::endl;
-	//std::cout << "packets: " << file.packets() << std::endl;
-	//std::cout << "packet size: " << file.packetSize() << std::endl;
-	std::cout << "comment: " << file.comment() << std::endl;
-	std::cout << "format: " << file.format() << std::endl;
-	std::cout << "number of scenes: " << file.imageInfo()->number_scenes << std::endl;
-	std::cout << "scene: " << file.imageInfo()->scene << std::endl;
-	std::cout << "filename: " << file.imageInfo()->filename << std::endl;
-
-	//Magick::Pixels::Pixels pixels(file);
-	//std::cout << "sizeof PixelPacket: " << sizeof (pixel_cache) << std::endl;
-	//std::cout << "sizeof *PixelPacket: " << sizeof (*pixel_cache) << std::endl;
+	Magick::Image im_file(filename);
+	im_file.modifyImage();
+	im_file.type(Magick::TrueColorType);
+	int columns = im_file.columns();
+	int rows = im_file.rows();
+	/*std::cout << "width: " <<columns << std::endl;
+	std::cout << "height: " <<rows << std::endl;
+	std::cout << "depth: " <<im_file.depth() << std::endl;
+	std::cout << "comment: " <<im_file.comment() << std::endl;
+	std::cout << "format: " <<im_file.format() << std::endl;
+	std::cout << "filename: " <<im_file.imageInfo()->filename << std::endl;*/
+
+	const Magick::PixelPacket *pixel_cache = im_file.getConstPixels(0, 0, columns, rows);
+
+	algebra::vec<mln_site_(I)::dim, unsigned int> vmin;
+        algebra::vec<mln_site_(I)::dim, unsigned int> vmax;
+	vmin[0] = 0;
+	vmin[1] = 0;
+	vmax[0] = rows - 1;
+	vmax[1] = columns - 1;
+	mln_site(I) pmin(vmin);
+        mln_site(I) pmax(vmax);
+        mln_concrete(I) result(box<mln_site(I)>(pmin, pmax));
+        initialize(ima, result);
+        mln_piter(I) p(ima.domain());
+	for_all(p)
+	{
+	  const Magick::PixelPacket *pixel = pixel_cache + (int) p.to_site().to_vec()[0] * columns
+							 + (int) p.to_site().to_vec()[1];
+	  ima(p) = value::rgb8(pixel->red % 256, pixel->green % 256, pixel->blue % 256); // WARNING: Quantum = 16bits but rgb is 8bits
+	}
 
 	trace::exiting("mln::io::magick::load");
       }

    

Fabien Freling

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