From a0875baa5ffffde3322b75839dd43e00296f63e5 Mon Sep 17 00:00:00 2001
From: Vivien Delmon <vivien.delmon@creatis.insa-lyon.fr>
Date: Mon, 25 Feb 2013 17:35:08 +0100
Subject: [PATCH] New tool to keep points in a mask

---
 tools/clitkMaskLandmarks.cxx | 104 +++++++++++++++++++++++++++++++++++
 tools/clitkMaskLandmarks.ggo |  10 ++++
 2 files changed, 114 insertions(+)
 create mode 100644 tools/clitkMaskLandmarks.cxx
 create mode 100644 tools/clitkMaskLandmarks.ggo

diff --git a/tools/clitkMaskLandmarks.cxx b/tools/clitkMaskLandmarks.cxx
new file mode 100644
index 0000000..a63c85f
--- /dev/null
+++ b/tools/clitkMaskLandmarks.cxx
@@ -0,0 +1,104 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================*/
+#include "clitkMaskLandmarks_ggo.h"
+
+#include <string>
+#include <vector>
+#include <iostream>
+#include <fstream>
+
+#include <clitkCommon.h>
+#include <clitkImageCommon.h>
+
+typedef itk::Point<double, 3> PointType;
+typedef std::vector<PointType> PointArrayType;
+
+static void read_points_pts(const std::string& fileName, PointArrayType& points, bool verbose)
+{
+  std::ifstream landmarksFile(fileName.c_str());
+  if (landmarksFile.fail())
+  {
+    std::cerr << "ERROR: could not open '" << fileName << "'" << std::endl;
+    exit(-2);
+  }
+
+  std::string line;
+  std::getline(landmarksFile, line);
+  if (line.find("#X") != 0)
+  {
+    std::cerr << "ERROR: invalid landmarks file '" << fileName << "'" << std::endl;
+    exit(-3);
+  }
+
+  PointType p;
+  while (!landmarksFile.eof())
+  {
+    landmarksFile >> p[0] >> p[1] >> p[2];
+    if (landmarksFile.fail())
+      break;
+    if (verbose)
+      std::cout << "point " << p << std::endl;
+    points.push_back(p);
+  }
+}
+
+void write_points_pts(const std::string& fileName, const PointArrayType& points, bool verbose)
+{
+  std::ofstream landmarksFile(fileName.c_str());
+
+  landmarksFile << "#X\tY\tZ" << std::endl;
+  for (size_t i = 0; i < points.size(); i++)
+    landmarksFile << points[i][0] << "\t" << points[i][1] << "\t" << points[i][2] << "\t" << std::endl;
+}
+
+int main(int argc, char** argv)
+{
+  typedef itk::Image<unsigned char, 3>  MaskType;
+  typedef MaskType::Pointer             MaskPointer;
+  GGO(clitkMaskLandmarks, args_info);
+
+  if (args_info.input_given != args_info.output_given)
+  {
+    std::cerr << "The number of inputs must be equal to the number of outputs" << std::endl;;
+    exit(1);
+  }
+
+  std::vector<PointArrayType> inputs(args_info.input_given);
+  for (unsigned i = 0; i < args_info.input_given; ++i)
+  {
+    read_points_pts(args_info.input_arg[i], inputs[i], args_info.verbose_flag);
+    if (inputs[i].size() != inputs[0].size())
+    {
+      std::cerr << "All input files must contain the same amount of points" << std::endl;
+      exit(2);
+    }
+  }
+
+  MaskPointer mask = clitk::readImage<MaskType>(args_info.mask_arg, args_info.verbose_flag);
+  std::vector<PointArrayType> outputs(args_info.input_given);
+  for (unsigned i = 0; i < inputs[0].size(); ++i)
+  {
+    MaskType::IndexType idx;
+    if (mask->TransformPhysicalPointToIndex(inputs[0][i], idx) && (*mask)[idx])
+      for (unsigned j = 0; j < args_info.input_given; j++)
+        outputs[j].push_back(inputs[j][i]);
+  }
+
+  for (unsigned i = 0; i < args_info.input_given; ++i)
+    write_points_pts(args_info.output_arg[i], outputs[i], args_info.verbose_flag);
+}
diff --git a/tools/clitkMaskLandmarks.ggo b/tools/clitkMaskLandmarks.ggo
new file mode 100644
index 0000000..82cfcc3
--- /dev/null
+++ b/tools/clitkMaskLandmarks.ggo
@@ -0,0 +1,10 @@
+package "clitkMaskLandmarks"
+version "1.0"
+purpose "Remove landmarks outside of a given mask also remove their corresponding points if multiple input are given."
+
+option "config"     - "Config file"       string    no
+option "verbose"    v     "Verbose"       flag    off
+
+option "input"  i   "Input landmarks filename"      string  yes     multiple
+option "mask"   m   "Input mask"                    string  yes
+option "output" o   "Output landmarks filename"	    string  yes     multiple
-- 
2.47.1