[Olena-patches] r3603: Create plot files depending on labels

3 Apr 2009

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

ChangeLog:
2009-04-03  Fabien Freling  <fabien.freling@lrde.epita.fr>

	Create plot files depending on labels.
	* fabien/igr/Makefile: Add new targets.
	* fabien/igr/check.sh: Update.
	* fabien/igr/clo_vol.cc: Minor update, helped for debug.
	* fabien/igr/fun_labels.cc: Create plot files with labels value.
	* fabien/igr/fun_labels.sh: New script file for testing fun_labels.
	* fabien/igr/time_smooth/linear.cc: Update tumeur point.

---
 TODO                      |    4 -
 igr/Makefile              |   13 +--
 igr/check.sh              |   12 +--
 igr/clo_vol.cc            |   14 +++
 igr/fun_labels.cc         |  163 ++++++++++++++++++++++++++++++++++++++++++++++
 igr/fun_labels.sh         |   20 +++++
 igr/time_smooth/linear.cc |    8 +-
 7 files changed, 211 insertions(+), 23 deletions(-)

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

--- trunk/milena/sandbox/fabien/igr/clo_vol.cc	(revision 3602)
+++ trunk/milena/sandbox/fabien/igr/clo_vol.cc	(revision 3603)
@@ -16,6 +16,13 @@
 
 
 
+
+
+#include <mln/canvas/morpho/attribute_filter.hh>
+#include <mln/morpho/attribute/volume.hh>
+
+
+
 ///////////////////
 //               //
 // Main Function //
@@ -53,9 +60,12 @@
   }
   else
   {
-    image3d<int_u12> input;
+    typedef image3d<int_u12> I;
+
+    I input;
     io::dump::load(input, argv[1]);
-    image3d<int_u12> clo = morpho::closing::volume(input, c6(), closure_lambda);
+
+    I clo = morpho::closing::volume(input, c6(), closure_lambda);
     io::dump::save(clo, "clo_vol.dump");
   }
 
Index: trunk/milena/sandbox/fabien/igr/fun_labels.sh
===================================================================
--- trunk/milena/sandbox/fabien/igr/fun_labels.sh	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/fun_labels.sh	(revision 3603)
@@ -0,0 +1,20 @@
+#!/bin/zsh
+
+process_file ()
+{
+  echo "Processing $3..."
+  input=$1
+  dim=$2
+
+  ./grad $input $dim
+  for lambda_closing in 5000; 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 $nbasins colorize_${3}_${lambda_closing}.ppm
+    ./fun_labels wst.dump $dim $input $nbasins
+  done
+}
+
+process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 "52"

Property changes on: trunk/milena/sandbox/fabien/igr/fun_labels.sh
___________________________________________________________________
Name: svn:executable
   + *

Index: trunk/milena/sandbox/fabien/igr/check.sh
===================================================================
--- trunk/milena/sandbox/fabien/igr/check.sh	(revision 3602)
+++ trunk/milena/sandbox/fabien/igr/check.sh	(revision 3603)
@@ -15,7 +15,7 @@
     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"
+    echo "    median = $median"
     threshold=$(($median / 2))
     ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm
     ./thres med.dump $dim $threshold
@@ -38,9 +38,9 @@
 #  rm *.dump
 }
 
-process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0049.dcm" 2 "49"
+#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"
-process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm" 2 "58"
-process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm" 3 "61"
-process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0064.dcm" 3 "64"
+#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0055.dcm" 2 "55"
+#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm" 2 "58"
+#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm" 3 "61"
+#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0064.dcm" 3 "64"
Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc	(revision 3602)
+++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc	(revision 3603)
@@ -66,11 +66,11 @@
   // Outputs //
   //	     //
   /////////////
-  io::plot::save(ima_arr(point2d(160, 120)), "ref_tumeur.plot");
-  io::plot::save(ima_linear(point2d(160, 120)), "linear_tumeur.plot");
-  io::plot::save(ima_arr(point2d(34, 94)), "ref_air.plot");
+  //io::plot::save(ima_arr(point2d(160, 120)), "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(122, 115)), "ref_poumon.plot");
+  //io::plot::save(ima_arr(point2d(122, 115)), "ref_poumon.plot");
   io::plot::save(ima_linear(point2d(122, 115)), "linear_poumon.plot");
 
   return 0;
Index: trunk/milena/sandbox/fabien/igr/fun_labels.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/fun_labels.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/fun_labels.cc	(revision 3603)
@@ -0,0 +1,163 @@
+#include <iostream>
+#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/slice_image.hh>
+#include <mln/core/routine/duplicate.hh>
+
+#include <mln/core/alias/neighb2d.hh>
+#include <mln/core/alias/window2d.hh>
+#include <mln/core/alias/neighb3d.hh>
+#include <mln/core/alias/window3d.hh>
+
+#include <mln/geom/nslis.hh>
+
+#include <mln/io/dump/all.hh>
+#include <mln/io/dicom/load.hh>
+#include <mln/io/plot/save.hh>
+
+#include <mln/value/int_u8.hh>
+#include <mln/value/int_u12.hh>
+#include <mln/value/label_16.hh>
+#include <mln/value/label_32.hh>
+
+#include <mln/accu/mean.hh>
+#include <mln/accu/median_h.hh>
+#include <mln/level/compute.hh>
+#include <mln/pw/all.hh>
+#include <mln/util/array.hh>
+#include <mln/util/set.hh>
+
+
+
+using namespace mln;
+using value::int_u8;
+using value::int_u12;
+using value::label_16;
+using value::label_32;
+
+
+template <typename I, typename L, typename V>
+inline
+void plot_label(I ima, L ima_labels, V lbl)
+{
+  I ima_spe = duplicate(ima | pw::value(ima_labels) == pw::cst(lbl));
+  util::array<float> arr;
+  for (int i = 0; i < ima_spe.domain().pmin().sli(); ++i)
+    arr.append(0.0);
+  for (int sli = ima_spe.domain().pmin().sli(); sli <= ima_spe.domain().pmax().sli(); ++sli)
+  {
+    image2d<int_u12> tmp_slice = duplicate(slice(ima_spe, sli));
+    accu::mean<int_u12> accu_mean;
+    float mean = level::compute(accu_mean, tmp_slice);
+    arr.append(mean);
+  }
+  for (int i = ima_spe.domain().pmax().sli() + 1; i <= ima.domain().pmax().sli(); ++i)
+    arr.append(0.0);
+  std::ostringstream slabel;
+  slabel << "label_" << lbl << ".plot";
+  io::plot::save(arr, slabel.str());
+}
+
+
+template <typename I, typename L>
+inline
+void plot_point(I ima, L ima_labels, point2d point, const char* desc)
+{
+  util::array<float> arr;
+  label_32 prev_lbl;
+  int start = 0;
+  int count = 1;
+  for (unsigned sli = 0; sli < geom::nslis(ima); ++sli)
+  {
+    image2d<int_u12> ima_slice = duplicate(slice(ima, sli));
+    image2d<label_32> lbl_slice = duplicate(slice(ima_labels, sli));
+    if (sli == 0)
+      prev_lbl = lbl_slice(point);
+    if (lbl_slice(point) != prev_lbl)
+    {
+      std::ostringstream slabel;
+      slabel << desc << "_" << count << "_label_" << prev_lbl << ".plot";
+      count++;
+      io::plot::save(arr, slabel.str(), start);
+      arr.clear();
+      start = sli + 1;
+    }
+    // Taking the mean value of the region.
+    accu::mean<int_u12> accu_mean;
+    float mean = level::compute(accu_mean, ima_slice | pw::value(lbl_slice) == pw::cst(lbl_slice(point)));
+    arr.append(mean);
+    prev_lbl = lbl_slice(point);
+  }
+  if (!arr.is_empty())
+  {
+    std::ostringstream slabel;
+    slabel << desc << "_" << count << "_label_" << prev_lbl << ".plot";
+    io::plot::save(arr, slabel.str(), start);
+  }
+}
+
+
+///////////////////
+//               //
+// Main Function //
+//               //
+///////////////////
+
+
+int main(int argc, char *argv[])
+{
+  typedef label_32 L;
+
+  if (argc != 5)
+  {
+    std::cout << "Usage: " << argv[0] << " <ima.dump> <dimensions> <ima.dcm> <nbasins>"
+	      << std::endl;
+    return 1;
+  }
+
+  unsigned dim = atoi(argv[2]);
+  if (dim != 2 && dim != 3)
+  {
+    std::cout << "<dimensions> invalid" << std::endl;
+    return 1;
+  }
+
+  L nlabels = atoi(argv[4]);
+
+  if (dim == 2)
+  {
+    // FIXME
+  }
+  else
+  {
+    point2d p_tumeur(156, 114);
+    point2d p_air(34, 94);
+    point2d p_poumon(122, 115);
+    image3d<L> ima_labels;
+    io::dump::load(ima_labels, argv[1]);
+    image3d<int_u12> ima;
+    io::dicom::load(ima, argv[3]);
+
+    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)
+    {
+      image2d<L> tmp_slice = duplicate(slice(ima_labels, sli));
+      lbl_set.insert(tmp_slice(p_tumeur));
+      lbl_set.insert(tmp_slice(p_air));
+      lbl_set.insert(tmp_slice(p_poumon));
+    }
+
+    util::set_fwd_iter<L> siter(lbl_set);
+    for_all(siter)
+    {
+      plot_label(ima, ima_labels, siter.element());
+    }*/
+  }
+
+  return 0;
+}
Index: trunk/milena/sandbox/fabien/igr/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/Makefile	(revision 3602)
+++ trunk/milena/sandbox/fabien/igr/Makefile	(revision 3603)
@@ -1,12 +1,4 @@
-CXX = llvm-g++
-CXXFLAGS = -DNDEBUG -O4
-
-DICOM_INC = -I/usr/local/include/gdcm-2.0
-DICOM_LIBS = -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib \
-	     -framework CoreFoundation
-DICOM = ${DICOM_INC} ${DICOM_LIBS}
-
-MAGICK = `Magick++-config --cppflags --ldflags --libs`
+include Makefile.rules
 
 seg2d: seg_vol_irm.hh seg2d.cc
 	${CXX} -I../../../ ${DICOM} ${CXXFLAGS} seg2d.cc -o seg2d
@@ -50,6 +42,9 @@
 first_slice_dicom: first_slice_dicom.cc
 	${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o first_slice_dicom
 
+fun_labels: fun_labels.cc
+	${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o fun_labels
+
 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/TODO
===================================================================
--- trunk/milena/sandbox/fabien/TODO	(revision 3602)
+++ trunk/milena/sandbox/fabien/TODO	(revision 3603)
@@ -38,9 +38,9 @@
 [ ] Profile for performance
 [X] ImageMagick support
 [ ] Integrate external libraries (GDCM, IM)
-[ ] Send result images to lrde account
+[X] Send result images to lrde account
 [X] Translate Matlab code
 [X] Subsample binary images
 [X] Fast projected histogram
 [ ] Triple histogram
-[ ] Create plot for each kind of point with each method
+[X] Create plot for each kind of point with each method

    