r3526: Find threshold value thanks to watershed

13 Mar 2009

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

ChangeLog:
2009-03-13  Fabien Freling  <fabien.freling@lrde.epita.fr>

	Find threshold value thanks to watershed.
	* fabien/bin/dumpi12_to_pgm.cc: New tool.
	* fabien/igr/Makefile: Update.
	* fabien/igr/check.sh: Update.
	* fabien/igr/graph.cc: Update.
	* fabien/igr/med.cc: Find median region value.
	* fabien/igr/thres.cc: Threshold image.

---
 TODO                  |    8 +++-
 bin/dumpi12_to_pgm.cc |   55 +++++++++++++++++++++++++++++++
 igr/Makefile          |    6 +++
 igr/check.sh          |   37 +++++++++++++--------
 igr/graph.cc          |   13 ++++++-
 igr/med.cc            |   87 ++++++++++++++++++++++++++++++++++++++++++++++++++
 igr/thres.cc          |   67 ++++++++++++++++++++++++++++++++++++++
 7 files changed, 256 insertions(+), 17 deletions(-)

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

--- trunk/milena/sandbox/fabien/igr/graph.cc	(revision 3525)
+++ trunk/milena/sandbox/fabien/igr/graph.cc	(revision 3526)
@@ -11,11 +11,13 @@
 #include <mln/io/dump/all.hh>
 #include <mln/io/dicom/load.hh>
 #include <mln/io/pgm/save.hh>
+#include <mln/io/ppm/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/value/rgb8.hh>
 
 #include <mln/morpho/watershed/flooding.hh>
 
@@ -53,6 +55,8 @@
 #include <mln/extract/all.hh>
 #include <mln/make/region_adjacency_graph.hh>
 
+#include <mln/debug/colorize.hh>
+
 
 
 
@@ -241,6 +245,7 @@
   using value::int_u12;
   using value::label_16;
   using value::label_32;
+  using value::rgb8;
   typedef label_32 L;
 
   if (argc != 6)
@@ -315,8 +320,12 @@
     mln_VAR(wsd2_, morpho::elementary::dilation(extend(wsd2 | (pw::value(wsd2) == 0u), wsd2), c8()));
     data::fill((wsd2 | (pw::value(wsd2) == 0u)).rw(), wsd2_);
 
-    io::pgm::save(level::stretch(int_u8(), labeling::mean_values(dcm, wshed, nbasins)), "wsd_original.pgm");
-    io::pgm::save(level::stretch(int_u8(), labeling::mean_values(dcm, wsd2, nbasins2)), "wsd_mean_colors.pgm");
+    mln_VAR(original, level::stretch(int_u8(), labeling::mean_values(dcm, wshed, nbasins)));
+    mln_VAR(mean, level::stretch(int_u8(), labeling::mean_values(dcm, wsd2, nbasins2)));
+    io::pgm::save(original, "wsd_original.pgm");
+    io::pgm::save(mean, "wsd_mean_colors.pgm");
+    io::ppm::save(debug::colorize(rgb8(), wshed, nbasins), "wsd_colorize_01.ppm");
+    io::ppm::save(debug::colorize(rgb8(), wsd2, nbasins2), "wsd_colorize_02.ppm");
   }
   else
   {
Index: trunk/milena/sandbox/fabien/igr/check.sh
===================================================================
--- trunk/milena/sandbox/fabien/igr/check.sh	(revision 3525)
+++ trunk/milena/sandbox/fabien/igr/check.sh	(revision 3526)
@@ -4,22 +4,33 @@
 {
   echo "Processing $3..."
   dist_max=10
+  input=$1
+  dim=$2
 
-  ./grad $1 $2
-  for lambda_closing in 10 50 100 500 1000 5000 10000 50000; do
+  ./grad $input $dim
+  for lambda_closing in 50 100 500 1000 5000 10000 50000; do
     echo "  for lambda_closing = ${lambda_closing}";
-    ./clo_vol grad.dump $2 ${lambda_closing}
-    nbasins=`./wst clo_vol.dump $2`
-    ../bin/dumpl32_to_colorize wst.dump $2 $nbasins results/colorize_${3}_${lambda_closing}.ppm
+    ./clo_vol grad.dump $dim ${lambda_closing}
+    nbasins=`./wst clo_vol.dump $dim`
+    ../bin/dumpl32_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm
+    median=`./med wst.dump $dim $input $nbasins`
+    ../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
 
-    if [ ${lambda_closing} -eq 100 ]; then
-      for lambda_dist in 10 50 100; do
-	nbasins_after=`./graph wst.dump $2 $1 $lambda_dist $nbasins`
-	mv wsd_original.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_01.pgm
-	mv wsd_mean_colors.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_02.pgm
-	echo "nbasins was" $nbasins "and now is" $nbasins_after "( diff =" $(($nbasins - $nbasins_after)) ")"
-      done
-    fi
+#if [ $2 -eq 2 ]; then
+#     if [ ${lambda_closing} -eq 100 ]; then
+#	for lambda_dist in 50 100 120 130 140 150; do
+#	  nbasins_after=`./graph wst.dump $2 $1 $lambda_dist $nbasins`
+#	  mv wsd_original.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_01.pgm
+#	  mv wsd_mean_colors.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_02.pgm
+#	  mv wsd_colorize_01.ppm results/graph_${3}_${lambda_closing}_${lambda_dist}_03.ppm
+#	  mv wsd_colorize_02.ppm results/graph_${3}_${lambda_closing}_${lambda_dist}_04.ppm
+#	  diff=$(($nbasins - $nbasins_after))
+#	  echo "    dist = $lambda_dist | $nbasins -> $nbasins_after (diff = $diff ) $(($diff * 100 / $nbasins))%"
+#	done
+#     fi
+#   fi
   done
 #  rm *.dump
 }
Index: trunk/milena/sandbox/fabien/igr/med.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/med.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/med.cc	(revision 3526)
@@ -0,0 +1,87 @@
+#include <iostream>
+#include <mln/core/image/image2d.hh>
+#include <mln/core/image/image3d.hh>
+#include <mln/core/image/image_if.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/io/dump/all.hh>
+#include <mln/io/dicom/load.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/core/var.hh>
+#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/labeling/mean_values.hh>
+#include <mln/level/compute.hh>
+#include <mln/pw/all.hh>
+#include <mln/util/array.hh>
+
+
+
+///////////////////
+//               //
+// Main Function //
+//               //
+///////////////////
+
+
+int main(int argc, char *argv[])
+{
+  using namespace mln;
+  using value::int_u8;
+  using value::int_u12;
+  using value::label_16;
+  using value::label_32;
+  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]);
+  L nbasins = atoi(argv[4]);
+  if (dim != 2 && dim != 3)
+  {
+    std::cout << "<dimensions> invalid" << std::endl;
+    return 1;
+  }
+
+  if (dim == 2)
+  {
+    image2d<L> labels;
+    io::dump::load(labels, argv[1]);
+    image2d<int_u12> dcm;
+    io::dicom::load(dcm, 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));
+
+    accu::mean<float> accu_mean;
+    util::array<float> means = level::compute(accu_mean, wst_mean);
+
+    // FIXME: Take median value of means
+
+    io::dump::save(wst_mean, "med.dump");
+    std::cout << median << std::endl;
+  }
+  else
+  {
+    // FIXME
+  }
+
+  return 0;
+}
Index: trunk/milena/sandbox/fabien/igr/thres.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/thres.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/thres.cc	(revision 3526)
@@ -0,0 +1,67 @@
+#include <iostream>
+#include <mln/core/image/image2d.hh>
+#include <mln/core/image/image3d.hh>
+#include <mln/core/image/image_if.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/io/dump/all.hh>
+#include <mln/io/pbm/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/binarization/threshold.hh>
+
+
+
+///////////////////
+//               //
+// Main Function //
+//               //
+///////////////////
+
+
+int main(int argc, char *argv[])
+{
+  using namespace mln;
+  using value::int_u8;
+  using value::int_u12;
+  using value::label_16;
+  using value::label_32;
+  typedef label_32 L;
+
+  if (argc != 4)
+  {
+    std::cout << "Usage: " << argv[0] << " <ima.dump> <dimensions> <threshold>"
+	      << std::endl;
+    return 1;
+  }
+
+  unsigned dim = atoi(argv[2]);
+  unsigned threshold = atoi(argv[3]);
+  if (dim != 2 && dim != 3)
+  {
+    std::cout << "<dimensions> invalid" << std::endl;
+    return 1;
+  }
+
+  if (dim == 2)
+  {
+    image2d<int_u12> input;
+    io::dump::load(input, argv[1]);
+    image2d<bool> bin_result = binarization::threshold(input, threshold);
+    io::pbm::save(bin_result, "result.pbm");
+  }
+  else
+  {
+    // FIXME
+  }
+
+  return 0;
+}
Index: trunk/milena/sandbox/fabien/igr/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/Makefile	(revision 3525)
+++ trunk/milena/sandbox/fabien/igr/Makefile	(revision 3526)
@@ -42,5 +42,11 @@
 graph: graph.cc
 	g++ -I../../../ ${DICOM_INC} ${DICOM_LIBS} ${CXXFLAGS} $^ -o graph
 	
+med: med.cc
+	g++ -I../../../ ${DICOM_INC} ${DICOM_LIBS} ${CXXFLAGS} $^ -o med
+	
+thres: thres.cc
+	g++ -I../../../ ${CXXFLAGS} $^ -o thres
+	
 clean:
 	rm -rf *.dump *.p?m *.plot *.log *.csv
Index: trunk/milena/sandbox/fabien/TODO
===================================================================
--- trunk/milena/sandbox/fabien/TODO	(revision 3525)
+++ trunk/milena/sandbox/fabien/TODO	(revision 3526)
@@ -28,5 +28,9 @@
 [X] Batch process watershed with 2D, 3D and any combination of parameters
 [X] Cut into small tools
 [X] Test 3D workflow on 2D images
-[ ] Create colorized colors for graph
-[ ] Diff with %
+[X] Create colorized colors for graph
+[X] Diff with %
+[ ] Find biggest dark regions (threshold value or median accu - median / 2 - )
+ [ ] Learn regions value
+  [ ] Threshold
+[ ] Profile for performance
Index: trunk/milena/sandbox/fabien/bin/dumpi12_to_pgm.cc
===================================================================
--- trunk/milena/sandbox/fabien/bin/dumpi12_to_pgm.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/bin/dumpi12_to_pgm.cc	(revision 3526)
@@ -0,0 +1,55 @@
+#include <mln/core/image/image2d.hh>
+#include <mln/make/image3d.hh>
+#include <mln/debug/slices_2d.hh>
+
+#include <mln/value/int_u8.hh>
+#include <mln/value/int_u12.hh>
+#include <mln/value/label_32.hh>
+
+#include <mln/io/dump/load.hh>
+#include <mln/io/pgm/save.hh>
+
+#include <mln/level/stretch.hh>
+
+
+int usage(char* argv[])
+{
+  std::cerr << "usage: " << argv[0] << " input.dump dim output.pgm" << std::endl;
+  return 1;
+}
+
+
+
+int main(int argc, char* argv[])
+{
+  using namespace mln;
+  using value::int_u8;
+  using value::int_u12;
+  using value::label_32;
+  using value::rgb8;
+
+  if (argc != 4)
+    return usage(argv);
+
+  unsigned dim = atoi(argv[2]);
+  unsigned nbasins = atoi(argv[3]);
+  if (dim != 2 && dim != 3)
+  {
+    std::cout << "<dimensions> invalid" << std::endl;
+    return 1;
+  }
+
+  if (dim == 2)
+  {
+    image2d<int_u12> ima2d;
+    io::dump::load(ima2d, argv[1]);
+    image2d<int_u8> ima_pgm = level::stretch(int_u8(), ima2d);
+    io::pgm::save(ima_pgm, argv[3]);
+  }
+  else
+  {
+    // FIXME
+  }
+
+  return 0;
+}

    

Fabien Freling

tags

participants (1)