[Olena-patches] r3695: Various update for IGR demo and new fixed segmentation

21 Apr 2009

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

ChangeLog:
2009-04-21  Fabien Freling  <fabien.freling@lrde.epita.fr>

	Various update for IGR demo and new fixed segmentation.
	* fabien/igr/Makefile: Add 'seg_fixed' target.
	* fabien/igr/check.sh: Update.
	* fabien/igr/fun_labels.cc: Update.
	* fabien/igr/fun_labels.sh: Update.
	* fabien/igr/med.cc: Update.
	* fabien/igr/norm.cc: Update.
	* fabien/igr/seg_fixed.cc: New.
	* fabien/igr/space_smooth/Makefile: Update.
	* fabien/igr/space_smooth/linear.cc: Update.
	* fabien/igr/thres.cc: Update.
	* fabien/igr/time_max_norm.cc: New tool for tmax map.
	* fabien/igr/time_smooth/Makefile: Update.
	* fabien/igr/time_smooth/linear.cc: Update.

---
 TODO                       |   18 +++++-
 igr/Makefile               |   12 +++-
 igr/check.sh               |   11 ++-
 igr/fun_labels.cc          |   36 ++++++------
 igr/fun_labels.sh          |   36 +++++++++---
 igr/med.cc                 |   15 ++---
 igr/norm.cc                |   14 +---
 igr/seg_fixed.cc           |  135 +++++++++++++++++++++++++++++++++++++++++++++
 igr/space_smooth/Makefile  |    2 
 igr/space_smooth/linear.cc |   21 ++++---
 igr/thres.cc               |    2 
 igr/time_max_norm.cc       |  116 ++++++++++++++++++++++++++++++++++++++
 igr/time_smooth/Makefile   |    2 
 igr/time_smooth/linear.cc  |   42 ++++++++++----
 14 files changed, 388 insertions(+), 74 deletions(-)

Index: trunk/milena/sandbox/fabien/igr/seg_fixed.cc
===================================================================

--- trunk/milena/sandbox/fabien/igr/seg_fixed.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/seg_fixed.cc	(revision 3695)
@@ -0,0 +1,135 @@
+#include <algorithm>
+
+#include <mln/core/image/image1d.hh>
+#include <mln/core/image/image2d.hh>
+#include <mln/core/alias/neighb2d.hh>
+#include <mln/core/image/image3d.hh>
+#include <mln/core/image/slice_image.hh>
+#include <mln/core/routine/duplicate.hh>
+
+#include <mln/io/dump/all.hh>
+
+#include <mln/value/int_u12.hh>
+
+#include <mln/accu/sum.hh>
+#include <mln/data/fill.hh>
+#include <mln/convert/from_to.hh>
+#include <mln/level/compute.hh>
+#include <mln/util/array.hh>
+
+
+using namespace mln;
+using value::int_u12;
+
+
+
+inline
+point2d
+get_edge_location(point2d p, point2d n)
+{
+  point2d res(p);
+
+  res.to_vec()[0] *= 2;
+  res.to_vec()[1] *= 2;
+
+  if (n.to_vec()[0] > p.to_vec()[0])
+    ++(res.to_vec()[0]);
+  if (n.to_vec()[0] < p.to_vec()[0])
+    --(res.to_vec()[0]);
+
+  if (n.to_vec()[1] > p.to_vec()[1])
+    ++(res.to_vec()[1]);
+  if (n.to_vec()[1] < p.to_vec()[1])
+    --(res.to_vec()[1]);
+
+  return res;
+}
+
+
+template <typename I>
+inline
+float
+compute_dist(image2d<util::array<I> > ima_arr,
+	     image2d<float> ima_sum,
+	     point2d p, point2d n)
+{
+  float res = 0.f;
+
+  for (unsigned i = 0; i < ima_arr(p).nelements(); ++i)
+    res += std::min(ima_arr(p)[i], ima_arr(n)[i]);
+  res /= std::max(ima_sum(p), ima_sum(n));
+
+  return res;
+}
+
+template <typename I>
+inline
+void
+compute_sum_arrays(image2d<float> ima_sum, image2d<util::array<I> > ima_arr)
+{
+  mln_piter(image2d<float>) p(ima_sum.domain());
+  for_all(p)
+  {
+    image1d<I> tmp_ima;
+    convert::from_to(ima_arr(p), tmp_ima);
+    accu::sum<I> accu_sum;
+    ima_sum(p) = level::compute(accu_sum, tmp_ima);
+  }
+}
+
+template <typename I>
+image2d<float>
+dist_on_edges(image2d<util::array<I> > ima_arr)
+{
+  image2d<float> edges(2 * ima_arr.nrows(), 2 * ima_arr.ncols());
+  data::fill(edges, -1.f);
+  image2d<float> ima_sum;
+  initialize(ima_sum, ima_arr);
+  compute_sum_arrays(ima_sum, ima_arr);
+
+  mln_piter(image2d<util::array<I> >) p(ima_arr.domain());
+  mln_niter(neighb2d) n(c4(), p);
+  for_all(p)
+    for_all(n)
+    {
+      point2d location = get_edge_location(p, n);
+      if (edges(location) != -1)
+	edges(location) = compute_dist(ima_arr, ima_sum, p, n);
+    }
+
+  return edges;
+}
+
+
+
+
+
+int usage(const char* bin)
+{
+  std::cout << "Usage: " << bin << " input.dump" << std::endl;
+  return 1;
+}
+
+int main(int argc, char* argv[])
+{
+  typedef int_u12 I;
+
+  if (argc != 2)
+    return usage(argv[0]);
+
+  image3d<I> input;
+  io::dump::save(input, argv[1]);
+  image2d<util::array<I> > ima_arr;
+  initialize(ima_arr, slice(input, 0));
+  for (unsigned int i = 0; i < input.nslices(); ++i)
+  {
+    image2d<I> tmp_slice = duplicate(slice(input, i));
+    mln_piter_(image2d<I>) p(tmp_slice.domain());
+    for_all(p)
+      ima_arr(p).append(tmp_slice(p));
+  }
+
+  image2d<float> edges = dist_on_edges(ima_arr);
+
+  return 0;
+}
Index: trunk/milena/sandbox/fabien/igr/time_max_norm.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/time_max_norm.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/time_max_norm.cc	(revision 3695)
@@ -0,0 +1,116 @@
+#include <sstream>
+
+#include <mln/core/image/image2d.hh>
+#include <mln/core/image/image3d.hh>
+#include <mln/core/image/image_if.hh>
+#include <mln/core/image/cast_image.hh>
+#include <mln/core/image/slice_image.hh>
+#include <mln/core/routine/duplicate.hh>
+
+#include <mln/value/int_u8.hh>
+#include <mln/value/int_u12.hh>
+
+#include <mln/io/dump/load.hh>
+#include <mln/io/pgm/save.hh>
+
+#include <mln/accu/count.hh>
+#include <mln/accu/mean.hh>
+#include <mln/accu/sum.hh>
+#include <mln/accu/image/all.hh>
+
+#include <mln/arith/minus.hh>
+#include <mln/arith/all.hh>
+
+#include <mln/data/fill.hh>
+#include <mln/data/paste.hh>
+
+#include <mln/level/compute.hh>
+#include <mln/level/stretch.hh>
+
+#include <mln/math/abs.hh>
+#include <mln/pw/all.hh>
+#include <mln/trait/concrete.hh>
+#include <mln/util/array.hh>
+
+#include <cmath>
+
+using namespace mln;
+using value::int_u8;
+
+
+
+// FIXME: Protoype is wrong. Should be Image<I>.
+template <typename I>
+inline
+void
+save_tmax_map(util::array<image2d<I> >& arr_ima, unsigned dim3, const char* desc)
+{
+  image2d<float> ima_c;
+  initialize(ima_c, arr_ima[0]);
+  data::fill(ima_c, 0.0);
+  image2d<unsigned> ima_t;
+  initialize(ima_t, ima_c);
+  data::fill(ima_t, 0);
+
+  mln_piter(image2d<float>) p(ima_c.domain());
+  for_all(p)
+    for (unsigned k = 0; k < dim3; ++k)
+      if (ima_c(p) < arr_ima[k](p))
+      {
+	ima_c(p) = arr_ima[k](p);
+	ima_t(p) = k;
+      }
+
+  std::ostringstream smax;
+  smax << desc << "_max.pgm";
+  std::ostringstream stime;
+  stime << desc << "_time.pgm";
+
+  image2d<int_u8> result_c = level::stretch(int_u8(), ima_c);
+  image2d<int_u8> result_t = level::stretch(int_u8(), ima_t);
+  io::pgm::save(result_c, smax.str());
+  io::pgm::save(result_t, stime.str());
+}
+
+
+int main(int argc, char* argv[])
+{
+  if (argc != 2)
+  {
+    std::cout << "Usage: " << argv[0] << " input" << std::endl;
+    return 1;
+  }
+
+  image3d<float> input;
+  io::dump::load(input, argv[1]);
+  util::array<image2d<float> > arr_ima;
+  for (unsigned int i = 0; i < input.nslices(); ++i)
+    arr_ima.append(duplicate(cast_image<float>(slice(input, i))));
+
+  unsigned dim3 = arr_ima.nelements();
+
+
+  /////////////
+  //	     //
+  // Lissage //
+  //	     //
+  /////////////
+
+  util::array<image2d<double> > arr_smooth;
+  arr_smooth.append(arr_ima[0] * 1.0);
+  for (unsigned k = 1; k < dim3 - 1; ++k)
+    arr_smooth.append(arr_ima[k] * 0.5 + arr_ima[k - 1] * 0.25 + arr_ima[k + 1] * 0.25);
+  arr_smooth.append(arr_ima[dim3 - 1] * 1.0);
+
+
+  ///////////////////////////////////
+  //				   //
+  // Calcul image max et temps max //
+  //				   //
+  ///////////////////////////////////
+
+  save_tmax_map(arr_ima, dim3, "tmax");
+  save_tmax_map(arr_smooth, dim3, "tmax_smooth");
+
+  return 0;
+}
Index: trunk/milena/sandbox/fabien/igr/check.sh
===================================================================
--- trunk/milena/sandbox/fabien/igr/check.sh	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/check.sh	(revision 3695)
@@ -2,19 +2,20 @@
 
 process_file ()
 {
-  echo "Processing $3..."
+  echo "Processing $1..." | cowsay
   dist_max=10
   input=$1
   dim=$2
 
-  ./grad $input $dim
+  ./crop $input 0 50 90 149 230 170 crop.dump
+  ./grad crop.dump $dim
   for lambda_closing in 50 100 500 1000 5000 10000 50000; do
     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`
+    ../bin/dumpl16_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm
+    median=`./med wst.dump $dim crop.dump $nbasins`
     echo "    median = $median"
     threshold=$(($median / 2))
     ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm
@@ -38,6 +39,8 @@
 #  rm *.dump
 }
 
+make crop grad clo_vol wst med thres
+
 #process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0049.dcm" 2 "49"
 process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 "52"
 #process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0055.dcm" 2 "55"
Index: trunk/milena/sandbox/fabien/igr/fun_labels.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/fun_labels.cc	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/fun_labels.cc	(revision 3695)
@@ -71,7 +71,7 @@
     box3d slice = make::box3d(sli, min_row, min_col,
 			      sli, max_row, max_col);
     mln_VAR(slice_label, vol_label | slice);
-    accu::mean<int_u12> accu_mean;
+    accu::mean<mln_value(I)> accu_mean;
     float mean = level::compute(accu_mean, slice_label);
     arr.append(mean);
   }
@@ -148,14 +148,15 @@
 void plot_point(Image<I>& ima, Image<L>& ima_labels, point2d point, const char* desc)
 {
   util::array<float> arr;
-  label_16 prev_lbl;
+  mln_value(L) prev_lbl;
   int start = 0;
   int count = 1;
+  int nslices = geom::nslis(ima);
 
-  for (unsigned sli = 0; sli < geom::nslis(ima); ++sli)
+  for (unsigned sli = 0; sli < nslices; ++sli)
   {
-    image2d<int_u12> ima_slice = duplicate(slice(ima, sli));
-    image2d<label_16> lbl_slice = duplicate(slice(ima_labels, sli));
+    image2d<mln_value(I)> ima_slice = duplicate(slice(ima, sli));
+    image2d<mln_value(L)> lbl_slice = duplicate(slice(ima_labels, sli));
     if (sli == 0)
       prev_lbl = lbl_slice(point);
     if (lbl_slice(point) != prev_lbl)
@@ -166,13 +167,13 @@
       start = sli + 1;
     }
     // Taking the median value of the region.
-    accu::median_h<int_u12> accu_med;
-    int_u12 median = level::compute(accu_med, ima_slice | pw::value(lbl_slice) == pw::cst(lbl_slice(point)));
-    arr.append(median);
+    accu::mean<mln_value(I)> accu_mean;
+    mln_value(I) mean = level::compute(accu_mean, ima_slice | pw::value(lbl_slice) == pw::cst(lbl_slice(point)));
+    arr.append(mean);
     prev_lbl = lbl_slice(point);
 
     // Saving a image of the selected label in the current slice for debug.
-    data::fill((ima_slice | pw::value(lbl_slice) == pw::cst(prev_lbl)).rw(), 1750);
+    /*data::fill((ima_slice | pw::value(lbl_slice) == pw::cst(prev_lbl)).rw(), 1750);
     std::ostringstream str_ima;
     str_ima << "debug_" << desc << "_";
     if (sli < 100)
@@ -180,7 +181,7 @@
     if (sli < 10)
       str_ima << "0";
     str_ima << sli << ".pgm";
-    io::pgm::save(level::stretch(int_u8(), ima_slice), str_ima.str());
+    io::pgm::save(level::stretch(int_u8(), ima_slice), str_ima.str());*/
   }
 
   if (!arr.is_empty())
@@ -198,6 +199,7 @@
 int main(int argc, char *argv[])
 {
   typedef label_16 L;
+  typedef float I;
 
   if (argc != 4)
   {
@@ -208,8 +210,8 @@
 
   L nlabels = atoi(argv[3]);
 
-  point2d p_tumeur(156, 114);
-  point2d p_air(34, 94);
+  point2d p_tumeur(163, 114);
+  point2d p_air(54, 94);
   point2d p_poumon(122, 115);
   image3d<L> ima_labels;
   io::dump::load(ima_labels, argv[1]);
@@ -220,15 +222,15 @@
 
   //plot_all_labels(ima, ima_labels, nlabels);
 
-  L l = 0;
+  /*L l = 0;
   for (unsigned i = 0; i < nlabels; ++i, l = i)
-    plot_label(ima, ima_labels, l);
+    plot_label(ima, ima_labels, l);*/
 
   io::dump::save(ima_labels, "labels.dump");
 
-  //plot_point(ima, ima_labels, p_tumeur, "tumeur");
-  //plot_point(ima, ima_labels, p_air, "air");
-  //plot_point(ima, ima_labels, p_poumon, "poumon");
+  plot_point(ima, ima_labels, p_tumeur, "tumeur");
+  plot_point(ima, ima_labels, p_air, "air");
+  plot_point(ima, ima_labels, p_poumon, "poumon");
 
   /*util::set<L> lbl_set;
     for (int sli = 0; sli < geom::nslis(ima_labels); ++sli)
Index: trunk/milena/sandbox/fabien/igr/norm.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/norm.cc	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/norm.cc	(revision 3695)
@@ -18,6 +18,8 @@
 #include <mln/data/paste.hh>
 
 // DEBUG
+#include <mln/core/var.hh>
+#include <mln/estim/min_max.hh>
 /*#include <mln/accu/min.hh>
 #include <mln/accu/max.hh>
 #include <mln/level/compute.hh>*/
@@ -60,18 +62,10 @@
   image2d<float> ima_ini = mean_slices(ima_f, first, last);
 
   image3d<float> ima_result;
-  initialize(ima_result, ima_f);
+  initialize(ima_result, ima);
 
   for (int i = min_sli; i <= max_sli; ++i)
-    data::paste((slice(ima_f, i) - ima_ini), slice(ima_result, i).rw());
-
-  // DEBUG
-  /*accu::min<float> accu_min;
-  accu::max<float> accu_max;
-  float min = level::compute(accu_min, ima_ini);
-  float max = level::compute(accu_max, ima_ini);
-  std::cout << "min = " << min << std::endl;
-  std::cout << "max = " << max << std::endl;*/
+    data::paste((slice(ima_f, i) - ima_ini) / ima_ini, slice(ima_result, i).rw());
 
   return ima_result;
 }
Index: trunk/milena/sandbox/fabien/igr/thres.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/thres.cc	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/thres.cc	(revision 3695)
@@ -34,7 +34,7 @@
   using value::int_u12;
   using value::label_16;
   using value::label_32;
-  typedef label_32 L;
+  typedef label_16 L;
 
   if (argc != 4)
   {
Index: trunk/milena/sandbox/fabien/igr/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/Makefile	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/Makefile	(revision 3695)
@@ -28,7 +28,7 @@
 	${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o graph
 	
 med: med.cc
-	${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o med
+	${CXX} -I../../../ ${CXXFLAGS} $^ -o med
 	
 thres: thres.cc
 	${CXX} -I../../../ ${CXXFLAGS} $^ -o thres
@@ -39,6 +39,9 @@
 time_max: time_max.cc
 	${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o time_max
 	
+time_max_norm: time_max_norm.cc
+	${CXX} -I../../../ ${CXXFLAGS} -lm $^ -o time_max_norm
+	
 first_slice_dicom: first_slice_dicom.cc
 	${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o first_slice_dicom
 
@@ -57,6 +60,13 @@
 norm: norm.cc
 	${CXX} -I../../../ ${CXXFLAGS} $^ -o norm
 
+#####################
+
+seg_fixed: seg_fixed.cc
+	${CXX} -I../../../ ${CXXFLAGS} $^ -o seg_fixed
+	
+#####################
+
 clean:
 	rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM
 	rm seg2d seg3d wsd2d wsd3d nbasins_finder grad clo_vol wst graph med thres matlab time_max first_slice_dicom
Index: trunk/milena/sandbox/fabien/igr/fun_labels.sh
===================================================================
--- trunk/milena/sandbox/fabien/igr/fun_labels.sh	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/fun_labels.sh	(revision 3695)
@@ -1,5 +1,9 @@
 #!/bin/zsh
 
+#########
+# Plots #
+#########
+
 reconstruct_plot ()
 {
   rm -f ${1}_${2}.plot
@@ -10,11 +14,16 @@
 
 rename_label_plots ()
 {
-  for i in label_*.plot; do
+  for i in *_label_*.plot; do
     mv $i ${1}_$i
   done
 }
 
+
+#############
+# Animation #
+#############
+
 create_anim ()
 {
   echo "      Creating ${1} animation..."
@@ -43,15 +52,25 @@
   rm debug_${1}_*.png
 }
 
+
+
+
+
+
+
+
+
+
 process_file ()
 {
-  echo "Processing $3..."
+  echo "Processing $1..." | cowsay
   input=$1
   dim=$2
 
   ./crop $input 0 50 90 149 230 170 crop.dump
+  ./norm crop.dump norm.dump
   ./grad crop.dump $dim
-  for lambda_closing in 10000; do
+  for lambda_closing in 1000; do
     echo "  for lambda_closing = ${lambda_closing}";
     ./clo_vol grad.dump $dim ${lambda_closing}
     nbasins=`./wst clo_vol.dump $dim`
@@ -61,24 +80,25 @@
 #../bin/dumpi12_to_png mean_slices.dump $dim mean_slices_${3}_${lambda_closing}.png
 #../bin/dumpi12_to_pgm mean_slices.dump $dim mean_slices_${3}_${lambda_closing}.pgm
 
-    ./norm crop.dump norm.dump
     ./fun_labels wst.dump norm.dump $nbasins
-    rename_label_plots ${lambda_closing}
 
 #./all_labels2gif.sh crop.dump labels.dump $nbasins ${lambda_closing}
 
 #mv *.gif results/
 #mv *.plot results/plots/
 
-#reconstruct_plot tumeur ${lambda_closing}
+    reconstruct_plot tumeur ${lambda_closing}
+    reconstruct_plot air ${lambda_closing}
+    reconstruct_plot poumon ${lambda_closing}
+    rename_label_plots ${lambda_closing}
 #create_anim tumeur ${lambda_closing}
-#reconstruct_plot air ${lambda_closing}
 #create_anim air ${lambda_closing}
-#reconstruct_plot poumon ${lambda_closing}
 #create_anim poumon ${lambda_closing}
 
   done
 }
 
+make crop grad clo_vol fun_labels norm label2gif
+
 # 3D (2D + t) images only
 process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 52
Index: trunk/milena/sandbox/fabien/igr/space_smooth/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/space_smooth/Makefile	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/space_smooth/Makefile	(revision 3695)
@@ -2,7 +2,7 @@
 
 
 linear: linear.cc
-	${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o linear
+	${CXX} -I../../../../ ${CXXFLAGS} $^ -o linear
 	
 median: median.cc
 	${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o median
Index: trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc	(revision 3695)
@@ -7,7 +7,7 @@
 
 #include <mln/value/int_u12.hh>
 
-#include <mln/io/dicom/load.hh>
+#include <mln/io/dump/load.hh>
 #include <mln/io/plot/save.hh>
 
 #include <mln/accu/median_h.hh>
@@ -29,17 +29,19 @@
     return 1;
   }
 
+  typedef float I;
+
   ///////////////////
   //		   //
   // Image loading //
   //		   //
   ///////////////////
-  image3d<int_u12> input;
-  io::dicom::load(input, argv[1]);
-  util::array<image2d<int_u12> > arr_ima;
-  for (int i = 0; i < input.nslices(); ++i)
+  image3d<I> input;
+  io::dump::load(input, argv[1]);
+  util::array<image2d<I> > arr_ima;
+  for (unsigned int i = 0; i < input.nslices(); ++i)
   {
-    image2d<int_u12> tmp_slice = duplicate(slice(input, i));
+    image2d<I> tmp_slice = duplicate(slice(input, i));
     arr_ima.append(tmp_slice);
   }
 
@@ -61,14 +63,15 @@
   // Outputs //
   //	     //
   /////////////
-  image2d<util::array<float> > ima_result(input.nrows(), input.ncols());
+  image2d<util::array<float> > ima_result;
+  initialize(ima_result, slice(input, 0));
   mln_piter_(image2d<util::array<float> >) p(ima_linear[0].domain());
   for_all(p)
-    for (int i = 0; i < ima_linear.nelements(); ++i)
+    for (unsigned int i = 0; i < ima_linear.nelements(); ++i)
       ima_result(p).append(ima_linear[i](p));
 
   io::plot::save(ima_result(point2d(156, 114)), "linear_tumeur.plot");
-  io::plot::save(ima_result(point2d(34, 94)), "linear_air.plot");
+  io::plot::save(ima_result(point2d(54, 94)), "linear_air.plot");
   io::plot::save(ima_result(point2d(122, 115)), "linear_poumon.plot");
 
   return 0;
Index: trunk/milena/sandbox/fabien/igr/time_smooth/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/time_smooth/Makefile	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/time_smooth/Makefile	(revision 3695)
@@ -2,7 +2,7 @@
 
 
 linear: linear.cc
-	${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o linear
+	${CXX} -I../../../../ ${CXXFLAGS} $^ -o linear
 	
 median: median.cc
 	${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o median
Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc	(revision 3695)
@@ -7,11 +7,13 @@
 
 #include <mln/value/int_u12.hh>
 
-#include <mln/io/dicom/load.hh>
+#include <mln/io/dump/all.hh>
 #include <mln/io/plot/save.hh>
 
 #include <mln/accu/median_h.hh>
 #include <mln/util/array.hh>
+#include <mln/linear/convolve.hh>
+#include <mln/make/w_window3d.hh>
 
 
 using namespace mln;
@@ -26,33 +28,48 @@
     return 1;
   }
 
+  typedef float I;
+
   ///////////////////
   //		   //
   // Image loading //
   //		   //
   ///////////////////
-  image3d<int_u12> input;
-  io::dicom::load(input, argv[1]);
-  image2d<util::array<int_u12> > ima_arr(input.nrows(), input.ncols());
-  for (int i = 0; i < input.nslices(); ++i)
+  image3d<I> input;
+  io::dump::load(input, argv[1]);
+  image2d<util::array<I> > ima_arr;
+  initialize(ima_arr, duplicate(slice(input, 0)));
+  for (unsigned int i = 0; i < input.nslices(); ++i)
   {
-    image2d<int_u12> tmp_slice = duplicate(slice(input, i));
-    mln_piter_(image2d<int_u12>) p(tmp_slice.domain());
+    image2d<I> tmp_slice = duplicate(slice(input, i));
+    mln_piter_(image2d<I>) p(tmp_slice.domain());
     for_all(p)
     {
       ima_arr(p).append(tmp_slice(p));
     }
   }
+  /*image3d<I> output;
+  initialize(output, input);*/
 
   ////////////////////////
   //			//
   // Linear convolution //
   //			//
   ////////////////////////
-  image2d<util::array<int_u12> > ima_linear;
+  /*float ws[][] = {{0, 0,    0,
+		   0, 0.25, 0,
+		   0, 0,    0},
+		  {0, 0,    0,
+		   0, 0.5,  0,
+		   0, 0,    0},
+		  {0, 0,    0,
+		   0, 0.25, 0,
+		   0, 0,    0}};
+
+  output = linear::convolve(input, make::w_window3d(ws));*/
+  image2d<util::array<I> > ima_linear;
   initialize(ima_linear, ima_arr);
-  mln_piter_(image2d<int_u12>) p(ima_linear.domain());
-  accu::median_h<int_u12> accu_med;
+  mln_piter_(image2d<I>) p(ima_linear.domain());
   for_all(p)
   {
     ima_linear(p).append(ima_arr(p)[0]);
@@ -66,10 +83,11 @@
   // Outputs //
   //	     //
   /////////////
+  //io::dump::save(output, "time_linear.dump");
   io::plot::save(ima_arr(point2d(156, 114)), "ref_tumeur.plot");
   io::plot::save(ima_linear(point2d(156, 114)), "linear_tumeur.plot");
-  io::plot::save(ima_arr(point2d(34, 94)), "ref_air.plot");
-  io::plot::save(ima_linear(point2d(34, 94)), "linear_air.plot");
+  io::plot::save(ima_arr(point2d(54, 94)), "ref_air.plot");
+  io::plot::save(ima_linear(point2d(54, 94)), "linear_air.plot");
   io::plot::save(ima_arr(point2d(122, 115)), "ref_poumon.plot");
   io::plot::save(ima_linear(point2d(122, 115)), "linear_poumon.plot");
 
Index: trunk/milena/sandbox/fabien/igr/med.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/med.cc	(revision 3694)
+++ trunk/milena/sandbox/fabien/igr/med.cc	(revision 3695)
@@ -9,7 +9,6 @@
 #include <mln/core/alias/window3d.hh>
 
 #include <mln/io/dump/all.hh>
-#include <mln/io/dicom/load.hh>
 
 #include <mln/value/int_u8.hh>
 #include <mln/value/int_u12.hh>
@@ -45,7 +44,7 @@
   using value::int_u12;
   using value::label_16;
   using value::label_32;
-  typedef label_32 L;
+  typedef label_16 L;
 
   if (argc != 5)
   {
@@ -70,12 +69,12 @@
   {
     image2d<L> labels;
     io::dump::load(labels, argv[1]);
-    image2d<int_u12> dcm;
-    io::dicom::load(dcm, argv[3]);
+    image2d<int_u12> input;
+    io::dump::load(input, argv[3]);
 
     mln_VAR(wst_dilate, morpho::elementary::dilation(extend(labels | (pw::value(labels) == 0u), labels), c8()));
     data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate);
-    mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins));
+    mln_VAR(wst_mean, labeling::mean_values(input, labels, nbasins));
 
     histo::array<int_u12> histogram = histo::compute(wst_mean);
     int j = 0;
@@ -106,12 +105,12 @@
   {
     image3d<L> labels;
     io::dump::load(labels, argv[1]);
-    image3d<int_u12> dcm;
-    io::dicom::load(dcm, argv[3]);
+    image3d<int_u12> input;
+    io::dump::load(input, argv[3]);
 
     mln_VAR(wst_dilate, morpho::elementary::dilation(extend(labels | (pw::value(labels) == 0u), labels), c26()));
     data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate);
-    mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins));
+    mln_VAR(wst_mean, labeling::mean_values(input, labels, nbasins));
 
     histo::array<int_u12> histogram = histo::compute(wst_mean);
     int j = 0;
Index: trunk/milena/sandbox/fabien/TODO
===================================================================
--- trunk/milena/sandbox/fabien/TODO	(revision 3694)
+++ trunk/milena/sandbox/fabien/TODO	(revision 3695)
@@ -47,6 +47,20 @@
 [ ] Fix mean slices values
 [X] Compatibility Windows
 [X] Fix spatial smooth
-[ ] Crop volume 52
-[ ] Plot all labels (3, 4 labels for tumeur)
+[X] Crop volume 52
+[X] Plot all labels (3, 4 labels for tumeur)
 [ ] Prepare data for IGR
+   [X] crop->norm->tmax
+   [X] crop->norm->space_smooth->tmax
+
+  (comparo normalisé)
+  1)brut
+  2)time_smooth
+  3)space_smooth
+  4)current_label_smooth (lambda faible, pas de ligne watershed)
+
+   [X] plot label
+   [X] gif animés labels
+
+   [X] fausses couleurs watershed
+   [X] images moyennes

    