r3512: Create watershed images in 3D..

11 Mar 2009

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

ChangeLog:
2009-03-11  Fabien Freling  <fabien.freling@lrde.epita.fr>

	Create watershed images in 3D..
	* fabien/bin/dump2pgm8b.cc: Fix.
	* fabien/igr/Makefile: Update.
	* fabien/igr/nbasins_check.sh: New test file.
	* fabien/igr/nbasins_finder.cc: New file for finding optimal parameters.
	* fabien/igr/watershed3d.cc: Update.

---
 TODO                  |    4 +-
 bin/dump2pgm8b.cc     |    5 ---
 igr/Makefile          |    5 ++-
 igr/nbasins_check.sh  |   17 ++++++++++
 igr/nbasins_finder.cc |   80 ++++++++++++++++++++++++++++++++++++++++++++++++++
 igr/watershed3d.cc    |    1 
 6 files changed, 105 insertions(+), 7 deletions(-)

Index: trunk/milena/sandbox/fabien/igr/watershed3d.cc
===================================================================

--- trunk/milena/sandbox/fabien/igr/watershed3d.cc	(revision 3511)
+++ trunk/milena/sandbox/fabien/igr/watershed3d.cc	(revision 3512)
@@ -277,6 +277,7 @@
   // Watershed
   label_32 nbasins;
   image3d<label_32> wshed = morpho::meyer_wst(clo, c6(), nbasins);
+  std::cout << "nbasins = " << nbasins << std::endl;
 
   // Debug
   io::dump::save(level::stretch(int_u8(), clo), "wsd_02.dump");
Index: trunk/milena/sandbox/fabien/igr/nbasins_check.sh
===================================================================
--- trunk/milena/sandbox/fabien/igr/nbasins_check.sh	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/nbasins_check.sh	(revision 3512)
@@ -0,0 +1,17 @@
+#!/bin/zsh
+
+process_file ()
+{
+  echo "Processing $2..."
+
+  for lambda_closure in 500 1000 5000 10000 50000; do
+    echo "  for lambda_closure = ${lambda_closure}";
+    ./nbasins_finder $1 $lambda_closure
+    ../bin/dump2ppm result_nbasins.dump results/nbasins_${2}_${lambda_closure}.ppm
+  done
+}
+
+#make nbasins
+#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" "52"
+process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm" "61"
+process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0064.dcm" "64"

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

Index: trunk/milena/sandbox/fabien/igr/nbasins_finder.cc
===================================================================
--- trunk/milena/sandbox/fabien/igr/nbasins_finder.cc	(revision 0)
+++ trunk/milena/sandbox/fabien/igr/nbasins_finder.cc	(revision 3512)
@@ -0,0 +1,80 @@
+#include <iostream>
+#include <mln/core/image/image3d.hh>
+
+#include <mln/core/alias/neighb3d.hh>
+#include <mln/core/alias/window3d.hh>
+#include <mln/core/image/image_if.hh>
+
+#include <mln/io/pgm/load.hh>
+#include <mln/io/dicom/load.hh>
+#include <mln/io/pgm/save.hh>
+#include <mln/io/dump/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/labeling/regional_minima.hh>
+
+#include <mln/level/transform.hh>
+#include <mln/level/stretch.hh>
+
+#include <mln/morpho/elementary/gradient.hh>
+#include <mln/morpho/closing/volume.hh>
+#include <mln/morpho/watershed/flooding.hh>
+
+#include <mln/fun/l2l/wrap.hh>
+
+#include <mln/debug/colorize.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;
+  using value::rgb8;
+
+  if (argc != 3)
+  {
+    std::cout << "Usage: " << argv[0] << " <ima.dcm> <closure_lambda>"
+	      << std::endl;
+    return 1;
+  }
+
+  unsigned closure_lambda = atoi(argv[2]);
+
+  image3d<int_u12> dcm;
+  io::dicom::load(dcm, argv[1]);
+
+  // Gradient
+  image3d<int_u12> grad = morpho::elementary::gradient(dcm, c6());
+
+  // Closure
+  image3d<int_u12> clo = morpho::closing::volume(grad, c6(), closure_lambda);
+
+  // Watershed
+  label_32 nbasins;
+  image3d<label_32> wshed = morpho::watershed::flooding(clo, c6(), nbasins);
+  //image3d<label_32> wshed = morpho::watershed::flooding(clo, c6(), nbasins);
+
+  // Visualization
+  std::cout << "    nbasins = " << nbasins << std::endl;
+  //io::dump::save(level::transform(wshed, fun::l2l::wrap<int_u8>()), "result_nbasins.dump");
+  //io::dump::save(level::stretch(int_u8(), wshed), "result_nbasins.dump");
+  io::dump::save(debug::colorize(rgb8(), wshed, nbasins), "result_nbasins.dump");
+
+  return 0;
+}
Index: trunk/milena/sandbox/fabien/igr/Makefile
===================================================================
--- trunk/milena/sandbox/fabien/igr/Makefile	(revision 3511)
+++ trunk/milena/sandbox/fabien/igr/Makefile	(revision 3512)
@@ -23,7 +23,10 @@
 	g++ -I../../../ ${DICOM_INC} ${DICOM_LIB} ${CXXFLAGS} $^ -o wsd3d
 
 wsd3dg: watershed.hh watershed3d.cc
-	g++ -I../../../ ${DICOM_INC} ${DICOM_LIB} -DNDEBUG -g $^ -o wsd3dg
+	g++ -I../../../ ${DICOM_INC} ${DICOM_LIB} -g $^ -o wsd3dg
+
+nbasins: nbasins_finder.cc
+	g++ -I../../../ ${DICOM_INC} ${DICOM_LIB} ${CXXFLAGS} $^ -o nbasins_finder
 	
 clean:
 	rm -rf *.dump *.p?m *.plot *.log *.csv
Index: trunk/milena/sandbox/fabien/TODO
===================================================================
--- trunk/milena/sandbox/fabien/TODO	(revision 3511)
+++ trunk/milena/sandbox/fabien/TODO	(revision 3512)
@@ -25,4 +25,6 @@
 [X] US: projection of internal gradient
 [X] Create 3D US morpho with 2D stack
 [ ] Create macro for_all_slice
-[ ] Batch process watershed with 2D, 3D and any combination of parameters
+[X] Batch process watershed with 2D, 3D and any combination of parameters
+[ ] Cut into small tools
+[ ] Test 3D workflow on 2D images
Index: trunk/milena/sandbox/fabien/bin/dump2pgm8b.cc
===================================================================
--- trunk/milena/sandbox/fabien/bin/dump2pgm8b.cc	(revision 3511)
+++ trunk/milena/sandbox/fabien/bin/dump2pgm8b.cc	(revision 3512)
@@ -3,12 +3,9 @@
 #include <mln/debug/slices_2d.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/literal/colors.hh>
-
 
 int usage(char* argv[])
 {
@@ -21,7 +18,6 @@
 int main(int argc, char* argv[])
 {
   using namespace mln;
-  using value::rgb8;
   using value::int_u8;
 
   if (argc != 3)
@@ -30,7 +26,6 @@
   image3d<int_u8> vol;
   io::dump::load(vol, argv[1]);
 
-  rgb8 bg = literal::black;
   image2d<int_u8> ima = debug::slices_2d(vol, 1.f, 0);
   io::pgm::save(ima, argv[2]);

    

Fabien Freling

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