Merge pull request #42 from jchevrie/Add_volume_processing

Add volume processing

modules/ustk_core/include/visp3/ustk_core/usImage3D.h

@@ -66,12 +66,21 @@ template <class Type> class usImage3D
   usImage3D();
 
   /**
-  * Constructor. Set the dimensions of the volume.
+  * Constructor. Set the dimensions of the volume. Initialize the data container with default value.
   * @param height Volume height.
   * @param width Volume width.
   * @param frameNumber Volume size in the third dimension (orthogonal to ultrasound 2D frames).
   */
   usImage3D(unsigned int height, unsigned int width, unsigned int frameNumber);
+
+  /**
+  * Constructor. Set the dimensions of the volume. Initialize the data container with the specified value.
+  * @param height Volume height.
+  * @param width Volume width.
+  * @param frameNumber Volume size in the third dimension (orthogonal to ultrasound 2D frames).
+  * @param initialValue The initial data
+  */
+  usImage3D(unsigned int height, unsigned int width, unsigned int frameNumber, Type initialValue);
 
   /**
   * Copy constructor. By default performs a deep copy.
@@ -176,11 +185,11 @@ template <class Type> class usImage3D
 
   /**
   * Resize the image if needed (if new dimensions differ from old ones).
-  * @param width The volume size along i axis.
-  * @param heigth The volume size along j axis.
+  * @param height The volume size along i axis.
+  * @param width The volume size along j axis.
   * @param numberOfFrames The volume size along k axis.
   */
-  void resize(unsigned int width, unsigned int heigth, unsigned int numberOfFrames);
+  void resize(unsigned int height, unsigned int width, unsigned int numberOfFrames);
 
   /**
   * Set the data container.
@@ -195,11 +204,11 @@ template <class Type> class usImage3D
 private:
   /**
   * Initiation of the image.
-  * @param heigth Volume height (number of voxels).
+  * @param height Volume height (number of voxels).
   * @param width Volume width (number of voxels).
   * @param numberOfFrames Volume size (number of voxels) in the third dimension (orthogonal to ultrasound 2D frames).
   */
-  void init(unsigned int heigth, unsigned int width, unsigned int numberOfFrames);
+  void init(unsigned int height, unsigned int width, unsigned int numberOfFrames);
 
   unsigned int m_width;          /**< Volume width in voxels (number of voxels on the j-axis)*/
   unsigned int m_height;         /**< Volume height in voxels (number of voxels on the i-axis)*/
@@ -246,9 +255,9 @@ inline void usImage3D<Type>::init(unsigned int height, unsigned int width, unsig
     }
   }
 
-  this->m_width = width;
-  this->m_height = height;
-  this->m_numberOfFrames = numberOfFrames;
+  m_width = width;
+  m_height = height;
+  m_numberOfFrames = numberOfFrames;
 
   m_size = m_width * m_height * m_numberOfFrames;
 
@@ -269,28 +278,34 @@ inline void usImage3D<Type>::init(unsigned int height, unsigned int width, unsig
 }
 
 template <class Type>
-usImage3D<Type>::usImage3D() : m_width(0), m_height(0), m_numberOfFrames(0), m_size(0), bitmap(NULL), framPointer(NULL)
+usImage3D<Type>::usImage3D()
+    : m_width(0), m_height(0), m_numberOfFrames(0), m_size(0), bitmap(NULL), framPointer(NULL)
 {
 }
 
 template <class Type>
 usImage3D<Type>::usImage3D(unsigned int height, unsigned int width, unsigned int frameNumber)
-  : m_width(width), m_height(height), m_numberOfFrames(frameNumber), m_size(width * height * frameNumber), bitmap(NULL),
-    framPointer(NULL)
+    : m_width(0), m_height(0), m_numberOfFrames(0), m_size(0), bitmap(NULL), framPointer(NULL)
 {
-  init(height, width, frameNumber);
-  initData(0);
+  this->init(height, width, frameNumber);
+  this->initData(Type());
 }
 
-template <class Type> usImage3D<Type>::usImage3D(const usImage3D<Type> &volume, const bool copy)
+template <class Type>
+usImage3D<Type>::usImage3D(unsigned int height, unsigned int width, unsigned int frameNumber, Type initialValue)
+    : m_width(0), m_height(0), m_numberOfFrames(0), m_size(0), bitmap(NULL), framPointer(NULL)
 {
-  init(volume.getWidth(), volume.getHeight(), volume.getNumberOfFrames());
+  this->init(height, width, frameNumber);
+  this->initData(initialValue);
+}
 
-  m_size = m_width * m_height * m_numberOfFrames;
+template <class Type> usImage3D<Type>::usImage3D(const usImage3D<Type> &volume, const bool copy)
+    : m_width(0), m_height(0), m_numberOfFrames(0), m_size(0), bitmap(NULL), framPointer(NULL)
+{
+  this->init(volume.getHeight(), volume.getWidth(), volume.getNumberOfFrames());
 
   // deep copy
-  if (copy)
-    memcpy(bitmap, volume.bitmap, m_size * sizeof(Type));
+  if(copy) memcpy(bitmap, volume.bitmap, m_size * sizeof(Type));
 }
 
 template <class Type> usImage3D<Type>::~usImage3D()
@@ -307,7 +322,7 @@ template <class Type> usImage3D<Type>::~usImage3D()
 
 template <class Type> usImage3D<Type> &usImage3D<Type>::operator=(const usImage3D<Type> &other)
 {
-  init(other.m_width, other.m_height, other.m_numberOfFrames);
+  this->init(other.m_height, other.m_width, other.m_numberOfFrames);
 
   memcpy(bitmap, other.bitmap, m_size * sizeof(Type));
   return *this;
@@ -338,7 +353,6 @@ template <class Type> std::ostream &operator<<(std::ostream &out, const usImage3
 template <class Type> void usImage3D<Type>::setData(Type *data, int numberOfVoxels)
 {
   try {
-    m_size = numberOfVoxels;
     if (m_size != numberOfVoxels) {
       throw(vpException(vpException::fatalError, "usImage3D::setData() error, bitmap dimensions mismatch."));
     }
@@ -360,6 +374,6 @@ template <class Type> void usImage3D<Type>::initData(Type value)
 
 template <class Type> void usImage3D<Type>::resize(unsigned int height, unsigned int width, unsigned int numberOfFrames)
 {
-  init(height, width, numberOfFrames);
+    this->init(height, width, numberOfFrames);
 }
 #endif // __usImage3D_h_

modules/ustk_core/include/visp3/ustk_core/usImagePreScan3D.h

@@ -271,7 +271,7 @@ template <class Type> void usImagePreScan3D<Type>::setData(const usImage3D<Type>
  */
 template <class Type> void usImagePreScan3D<Type>::setScanLineNumber(unsigned int scanLineNumber)
 {
-  usImage3D<Type>::resize(scanLineNumber, usImage3D<Type>::getHeight(), usImage3D<Type>::getNumberOfFrames());
+  usImage3D<Type>::resize(usImage3D<Type>::getHeight(), scanLineNumber, usImage3D<Type>::getNumberOfFrames());
   usTransducerSettings::setScanLineNumber(scanLineNumber);
 }
 
@@ -283,7 +283,7 @@ template <class Type> void usImagePreScan3D<Type>::setScanLineNumber(unsigned in
  */
 template <class Type> void usImagePreScan3D<Type>::setFrameNumber(unsigned int frameNumber)
 {
-  usImage3D<Type>::resize(usImage3D<Type>::getWidth(), usImage3D<Type>::getHeight(), frameNumber);
+  usImage3D<Type>::resize(usImage3D<Type>::getHeight(), usImage3D<Type>::getWidth(), frameNumber);
   usMotorSettings::setFrameNumber(frameNumber);
 }
 

modules/ustk_grabber/src/usNetworkGrabberPreScan3D.cpp

@@ -247,26 +247,23 @@ void usNetworkGrabberPreScan3D::includeFrameInVolume()
             m_grabbedImage.getHeight()) { // m_grabbedImage is "turned" so the height corresponds to the scanline numer.
       throw(vpException(vpException::badValue, "Transducer settings changed during acquisition, somethink went wrong"));
     }
+    if (m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->getMotorSettings() != m_motorSettings)
+      throw(vpException(vpException::badValue, "Motor settings changed during acquisition, somethink went wrong"));
   } else { // init case
     m_outputBuffer.at(OUTPUT_FRAME_POSITION_IN_VEC)->setImagePreScanSettings(m_grabbedImage);
     m_outputBuffer.at(OUTPUT_FRAME_POSITION_IN_VEC)->setScanLineNumber(m_grabbedImage.getHeight());
     m_outputBuffer.at(MOST_RECENT_FRAME_POSITION_IN_VEC)->setImagePreScanSettings(m_grabbedImage);
     m_outputBuffer.at(MOST_RECENT_FRAME_POSITION_IN_VEC)->setScanLineNumber(m_grabbedImage.getHeight());
-  }
-  m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->setImagePreScanSettings(m_grabbedImage);
-  m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->setScanLineNumber(m_grabbedImage.getHeight());
-
-  if (m_firstFrameAvailable) {
-    if (m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->getMotorSettings() != m_motorSettings)
-      throw(vpException(vpException::badValue, "Motor settings changed during acquisition, somethink went wrong"));
-  } else { // init case
+    m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->setImagePreScanSettings(m_grabbedImage);
+    m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->setScanLineNumber(m_grabbedImage.getHeight());
+
     m_outputBuffer.at(OUTPUT_FRAME_POSITION_IN_VEC)->setMotorSettings(m_motorSettings);
     m_outputBuffer.at(MOST_RECENT_FRAME_POSITION_IN_VEC)->setMotorSettings(m_motorSettings);
+    m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->setMotorSettings(m_motorSettings);
   }
-  m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)->setMotorSettings(m_motorSettings);
-
+
   m_outputBuffer.at(CURRENT_FILLED_FRAME_POSITION_IN_VEC)
-      ->resize(m_grabbedImage.getHeight(), m_grabbedImage.getWidth(), m_motorSettings.getFrameNumber());
+      ->resize(m_grabbedImage.getWidth(), m_grabbedImage.getHeight(), m_motorSettings.getFrameNumber());
 
   // Inserting frame in volume by inverting rows and cols voxels (along x and y axis), to match ustk volume storage
   int volumeIndex = (m_grabbedImage.getFrameCount() / m_grabbedImage.getFramesPerVolume());    // from 0

modules/ustk_image_processing/ustk_volume_processing/CMakeLists.txt

@@ -0,0 +1,40 @@
+#############################################################################
+#
+# This file is part of the ustk software.
+# Copyright (C) 2016 - 2017 by Inria. All rights reserved.
+#
+# This software is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# ("GPL") version 2 as published by the Free Software Foundation.
+# See the file LICENSE.txt at the root directory of this source
+# distribution for additional information about the GNU GPL.
+#
+# For using ustk with software that can not be combined with the GNU
+# GPL, please contact Inria about acquiring a ViSP Professional
+# Edition License.
+#
+# This software was developed at:
+# Inria Rennes - Bretagne Atlantique
+# Campus Universitaire de Beaulieu
+# 35042 Rennes Cedex
+# France
+#
+# If you have questions regarding the use of this file, please contact
+# Inria at [email protected]
+#
+# This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+# WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+#
+# Authors:
+# Fabien Spindler
+#
+#############################################################################
+
+vp_add_module(ustk_volume_processing visp_core visp_ustk_core)
+
+vp_glob_module_sources()
+vp_module_include_directories()
+vp_create_module()
+
+vp_add_tests(DEPENDS_ON visp_ustk_volume_processing)
+