Add a helloworld example

Add a simple "hello world" example program to show how to set up a
project that builds against MIRTK.

Examples/helloworld/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.9)
+project(flip)
+
+find_package(VTK)
+
+find_package(MIRTK REQUIRED
+	PointSet
+	Common 
+	Numerics 
+	IO 
+	Image 
+	Transformation 
+	Registration
+	)
+
+include(MIRTKTargets)
+
+add_executable(flip flip.cc)
+target_include_directories(flip PUBLIC "${MIRTK_INCLUDE_DIRS}")
+target_link_libraries(flip mirtk::LibCommon mirtk::LibPointSet)
+install(TARGETS flip DESTINATION bin)

Examples/helloworld/README.md

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+# MIRTK helloworld
+
+`flip.cc` is just `Applications/src/flip-image.cc` renamed, and is supposed to
+be an example program that you might try to build against 
+[MIRTK](https://github.com/BioMedIA/MIRTK).
+
+# Setting up MIRTK as a build dependency
+
+Set `MIRTK_ROOT` to point to your MIRTK install area, and make sure the bin
+directory is on your `PATH` and the lib area is on your library path. For
+example, on Linux you might append these lines to your `.bashrc`:
+
+```
+export MIRTK_ROOT=/opt/mirtk
+export PATH="$MIRTK_ROOT/bin:$PATH"
+export LD_LIBRARY_PATH="$MIRTK_ROOT/lib:$LD_LIBRARY_PATH"
+```
+
+Then build this program with:
+
+```
+$ cd MIRTK/Examples/helloworld
+$ mkdir build
+$ cd build
+$ cmake -D CMAKE_MODULE_PATH:PATH=$MIRTK_ROOT/lib/cmake/mirtk ..
+$ make
+$ make install
+```
+
+And run with:
+
+```
+$ ./flip
+```

Examples/helloworld/flip.cc

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+/*
+ * Medical Image Registration ToolKit (MIRTK)
+ *
+ * Copyright 2008-2017 Imperial College London
+ * Copyright 2008-2013 Daniel Rueckert, Julia Schnabel
+ * Copyright 2013-2017 Andreas Schuh
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#include "mirtk/Common.h"
+#include "mirtk/Options.h"
+
+#include "mirtk/IOConfig.h"
+#include "mirtk/BaseImage.h"
+
+using namespace mirtk;
+
+
+// =============================================================================
+// Help
+// =============================================================================
+
+// -----------------------------------------------------------------------------
+void PrintHelp(const char *name)
+{
+  cout << "\n";
+  cout << "Usage: " << name << " <input> <output> [options]\n";
+  cout << "\n";
+  cout << "Description:\n";
+  cout << "  Swaps the two image dimensions at a time, in the order of the input\n";
+  cout << "  options. Both, the image data and the coordinates of the image origin\n";
+  cout << "  are swapped each time an input option is processed. To swap the image\n";
+  cout << "  axes instead of the origin, use the :option:`-axes` option before the\n";
+  cout << "  swap options. This option should be used to reorder the image dimensions\n";
+  cout << "  without changing the world coordinates of the voxels. When swapping of\n";
+  cout << "  the coordinate axes is enabled, the coordinates of the image origin are\n";
+  cout << "  kept the same, i.e., :option:`-origin` is ignored. The default behavior\n";
+  cout << "  is to swap the image data and the coordinates of the image origin. This\n";
+  cout << "  may in many cases not have the desired effect, but has been this way\n";
+  cout << "  already for some time.\n";
+  cout << "\n";
+  cout << "Options:\n";
+  cout << "  -axes [on|off]     Enable/disable swapping of the coordinate axes. (default: off)\n";
+  cout << "  -noaxes            Disable swapping of the coordinate axes.\n";
+  cout << "  -origin [on|off]   Enable/disable swapping of the origin coordinates. (default: on)\n";
+  cout << "  -noorigin          Disable swapping of the origin coordinates.\n";
+  cout << "  -xy, -yx           Swap x and y dimension.\n";
+  cout << "  -xz, -zx           Swap x and z dimension.\n";
+  cout << "  -xt, -tx           Swap x and t dimension.\n";
+  cout << "  -yz, -zy           Swap y and z dimension.\n";
+  cout << "  -yt, -ty           Swap y and t dimension.\n";
+  cout << "  -zt, -tz           Swap z and t dimension.\n";
+  PrintStandardOptions(cout);
+  cout << endl;
+}
+
+// =============================================================================
+// Main
+// =============================================================================
+
+// -----------------------------------------------------------------------------
+int main(int argc, char **argv)
+{
+  EXPECTS_POSARGS(2);
+
+  const char *input_name  = POSARG(1);
+  const char *output_name = POSARG(2);
+
+  InitializeIOLibrary();
+  UniquePtr<BaseImage> image(BaseImage::New(input_name));
+  bool modify_origin = true;
+  bool modify_axes   = false;
+
+  for (ALL_OPTIONS) {
+    if (OPTION("-xy") || OPTION("-yx")) {
+      if (modify_axes) {
+        image->SwapXY(true);
+      } else {
+        image->FlipXY(modify_origin);
+      }
+    }
+    else if (OPTION("-xz") || OPTION("-zx")) {
+      if (modify_axes) {
+        image->SwapXZ(true);
+      } else {
+        image->FlipXZ(modify_origin);
+      }
+    }
+    else if (OPTION("-xt") || OPTION("-tx")) {
+      if (modify_axes) {
+        image->SwapXT(true);
+      } else {
+        image->FlipXT(modify_origin);
+      }
+    }
+    else if (OPTION("-yz") || OPTION("-zy")) {
+      if (modify_axes) {
+        image->SwapYZ(true);
+      } else {
+        image->FlipYZ(modify_origin);
+      }
+    }
+    else if (OPTION("-yt") || OPTION("-ty")) {
+      if (modify_axes) {
+        image->SwapYT(true);
+      } else {
+        image->FlipYT(modify_origin);
+      }
+    }
+    else if (OPTION("-zt") || OPTION("-tz")) {
+      if (modify_axes) {
+        image->SwapZT(true);
+      } else {
+        image->FlipZT(modify_origin);
+      }
+    }
+    else if (OPTION("-axes")) {
+      modify_axes = true;
+      if (HAS_ARGUMENT) {
+        PARSE_ARGUMENT(modify_axes);
+      }
+    }
+    else if (OPTION("-noaxes")) {
+      modify_axes = false;
+    }
+    else if (OPTION("-origin")) {
+      modify_origin = true;
+      if (HAS_ARGUMENT) {
+        PARSE_ARGUMENT(modify_origin);
+      }
+    }
+    else if (OPTION("-noorigin")) {
+      modify_origin = false;
+    }
+    else HANDLE_COMMON_OR_UNKNOWN_OPTION();
+  }
+
+  image->Write(output_name);
+
+  return 0;
+}