Add custom contrast window presets (window level and window width)

Common/ContrastXML.cxx

@@ -0,0 +1,150 @@
+/*=========================================================================
+
+  Program:   ITK-SNAP
+  Language:  C++
+
+  This file was created as part of the added functionality of the custom windowing.
+  We have added the option to set a custom contrast window preset using Contrast Menu.
+
+  This file is mostly based on Common\Registry.cxx
+
+=========================================================================*/
+#include "ContrastXML.h"
+#include "itkXMLFile.h"
+
+#include "itksys/SystemTools.hxx"
+#include "IRISException.h"
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+#include <Registry.cxx>
+
+using namespace std;
+
+
+int ContrastXMLFileReader::CanReadFile(const char* name)
+{
+    return GenericXMLFileReader::CanReadFile(name);
+}
+
+std::vector<std::shared_ptr<PresetStruct>> ContrastXMLFileReader::getPresetStack() const
+{
+  return m_PresetStack;
+}
+
+void ContrastXMLFileReader::StartElement(const char* name, const char** atts)
+{
+    // If this is the root-level element <contrast>, it can be ignored
+    if (strcmpi(name, "contrast") == 0)
+    {
+        return;
+    }
+
+    // Read the attributes into a map
+    typedef std::map<std::string, std::string> AttributeMap;
+    typedef AttributeMap::const_iterator AttrIter;
+    AttributeMap attrmap;
+
+    for (int i = 0; atts[i] != nullptr && atts[i + 1] != nullptr; i += 2)
+        attrmap[itksys::SystemTools::LowerCase(atts[i])] = atts[i + 1];
+
+    // Process tags
+    if (strcmpi(name, "preset") == 0)
+    {
+        const AttrIter itKey = attrmap.find("key");
+        if (itKey == attrmap.end())
+            throw IRISException("Missing 'key' attribute to <preset> element");
+
+        const auto preset_name = itKey->second;
+
+        // Create a new preset and place it on the stack
+        m_PresetStack.push_back(std::make_shared<PresetStruct>(PresetStruct{preset_name}));
+    }
+    else if (strcmpi(name, "contrastProperty") == 0)
+    {
+        const AttrIter itKey = attrmap.find("key");
+        if (itKey == attrmap.end())
+            throw IRISException("Missing 'key' attribute to <contrastProperty> element");
+
+        const AttrIter itValue = attrmap.find("value");
+        if (itValue == attrmap.end())
+            throw IRISException("Missing 'value' attribute to <contrastProperty> element");
+
+        const auto property_name = itKey->second;
+        const auto property_value = itValue->second;
+
+        if(property_name == "Window")
+        {
+            m_PresetStack.back()->window = stod(property_value);
+        }
+        if(property_name == "Level")
+        {
+          m_PresetStack.back()->level = stod(property_value);
+        }
+    }
+    else
+        throw IRISException("Unknown XML element <%s>", name);
+}
+
+void ContrastXMLFileReader::EndElement(const char* name)
+{
+}
+
+void ContrastXMLFileReader::CharacterDataHandler(const char* inData, int inLength)
+{
+}
+
+
+void
+Contrast
+::Clear()
+{
+    m_PresetMap.clear();
+}
+
+std::vector<std::string>
+Contrast::GetPresetNames()
+{
+    // get all keys from m_PresetMap and sort if needed
+    std::vector<std::string> presets;
+    for (const auto& map_entry : m_PresetMap)
+    {
+        presets.push_back(map_entry.first); // have to get all keys
+    }
+
+    return presets;
+}
+
+double Contrast::GetLevel(const std::string& tissue)
+{
+    return m_PresetMap.at(tissue).level;
+}
+
+double Contrast::GetWindow(const std::string& tissue)
+{
+    return m_PresetMap.at(tissue).window;
+}
+
+
+Contrast
+::Contrast()
+= default;
+
+Contrast::
+~Contrast()
+= default;
+
+void Contrast::ReadFromCustomContrastXMLFile(const char* pathname, SmartPtr<ContrastXMLFileReader>& reader)
+{
+    reader->SetOutputObject(this);
+    reader->SetFilename(pathname);
+
+    reader->GenerateOutputInformation();
+
+    // check if presets are populated
+    for (const auto& preset : reader->getPresetStack())
+    {
+        m_PresetMap.insert(std::pair<std::string, PresetStruct>(preset->preset_name, *preset));
+    }
+}

Common/ContrastXML.h

@@ -0,0 +1,101 @@
+/*=========================================================================
+
+  Program:   ITK-SNAP
+  Language:  C++
+
+  This file was created as part of the added functionality of the custom windowing.
+  We have added the option to set a custom contrast window preset using Contrast Menu.
+
+  This file is mostly based on Common\Registry.h
+
+=========================================================================*/
+#ifndef __Contrast_h_
+#define __Contrast_h_
+
+#ifdef _MSC_VER
+# pragma warning(disable:4786)  // '255' characters in the debug information
+#endif //_MSC_VER
+
+#include <list>
+#include <map>
+#include <string>
+#include <cstdarg>
+#include <iomanip>
+
+#include <itksys/SystemTools.hxx>
+#include "itkXMLFile.h"
+
+#include "IRISException.h"
+
+struct PresetStruct
+{
+  std::string preset_name;
+  double level;
+  double window;
+};
+
+class Contrast;
+
+/** Reader for XML files */
+class ContrastXMLFileReader : public itk::XMLReader<Contrast>
+{
+public:
+
+    irisITKObjectMacro(ContrastXMLFileReader, itk::XMLReader<Contrast>)
+    int CanReadFile(const char* name) ITK_OVERRIDE;
+
+    std::vector<std::shared_ptr<PresetStruct>> getPresetStack() const;
+
+protected:
+
+    ContrastXMLFileReader()
+    = default;
+
+    void StartElement(const char* name, const char** atts) ITK_OVERRIDE;
+    void EndElement(const char* name) ITK_OVERRIDE;
+    void CharacterDataHandler(const char* inData, int inLength) ITK_OVERRIDE;
+
+    static int strcmpi(const char* str1, const char* str2)
+    {
+        return itksys::SystemTools::Strucmp(str1, str2);
+    }
+
+    // The preset stack
+    std::vector<std::shared_ptr<PresetStruct>> m_PresetStack;
+};
+
+/**
+ * \class Contrast
+ * \brief A tree of key-value pair maps
+ */
+class Contrast final
+{
+public:
+    /** Constructor initializes an empty contrast */
+    Contrast();
+
+    /** Destructor */
+    virtual ~Contrast();
+
+    /** Get a list of preset names*/
+    std::vector<std::string> GetPresetNames();
+
+    /** Get a level value*/
+    double GetLevel(const std::string& tissue);
+
+    /** Get a window value*/
+    double GetWindow(const std::string& tissue);
+
+    /** Empty the contents of the contrast */
+    void Clear();
+
+    /** Read from XML file */
+    void ReadFromCustomContrastXMLFile(const char* pathname, SmartPtr<ContrastXMLFileReader>& reader);
+
+private:
+
+    /** A hash table for the presets */
+    std::map<std::string, PresetStruct> m_PresetMap;
+};
+
+#endif

Common/Registry.cxx

@@ -50,6 +50,20 @@
 
 using namespace std;
 
+namespace GenericXMLFileReader
+{
+    static int CanReadFile(const char *name)
+    {
+        if ( !itksys::SystemTools::FileExists(name)
+            || itksys::SystemTools::FileIsDirectory(name)
+            || itksys::SystemTools::FileLength(name) == 0 )
+        {
+            return 0;
+        }
+
+        return 1;
+    }
+}
 
 
 /** Reader for XML files */
@@ -79,14 +93,7 @@ class RegistryXMLFileReader : public itk::XMLReader<Registry>
 
 int RegistryXMLFileReader::CanReadFile(const char *name)
 {
-  if ( !itksys::SystemTools::FileExists(name)
-       || itksys::SystemTools::FileIsDirectory(name)
-       || itksys::SystemTools::FileLength(name) == 0 )
-    {
-    return 0;
-    }
-
-  return 1;
+    return GenericXMLFileReader::CanReadFile(name);
 }
 
 void RegistryXMLFileReader::StartElement(const char *name, const char **atts)

ContrastSettings.xml

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE contrast [
+<!ELEMENT contrast (contrastProperty*,preset*)>
+<!ELEMENT preset (contrastProperty*,preset*)>
+<!ELEMENT contrastProperty EMPTY>
+<!ATTLIST preset key CDATA #REQUIRED>
+<!ATTLIST contrastProperty key CDATA #REQUIRED>
+<!ATTLIST contrastProperty value CDATA #REQUIRED>
+]>
+<!--
+The contrast enhancement values are specifically prepared for CT analysis. 
+They are directly taken from: https://radiopaedia.org/articles/windowing-ct.
+
+To add a new preset, complete the file with the structure as in the examples below. 
+At "preset" change "key" to the name of the preset to be added, and at "contrastProperty" set custom "value".
+-->
+<contrast>
+  <preset key="Abdomen-SoftTissues" >
+    <contrastProperty key="Window" value="400" />
+    <contrastProperty key="Level" value="50" />
+  </preset>
+  <preset key="Brain" >
+    <contrastProperty key="Window" value="80" />
+    <contrastProperty key="Level" value="40" />
+  </preset>
+  <preset key="Lungs" >
+    <contrastProperty key="Window" value="1500" />
+    <contrastProperty key="Level" value="-600" />
+  </preset>
+  <preset key="Mediastinum" >
+    <contrastProperty key="Window" value="350" />
+    <contrastProperty key="Level" value="50" />
+  </preset>
+  <preset key="Spine-Bone" >
+    <contrastProperty key="Window" value="1800" />
+    <contrastProperty key="Level" value="400" />
+  </preset>
+</contrast>

GUI/Model/GlobalUIModel.cxx

@@ -399,6 +399,12 @@ void GlobalUIModel::ResetContrastAllLayers()
     }
 }
 
+void GlobalUIModel::AdjustContrastAllLayers(double level, double window)
+{
+    IntensityCurveModel *curve_model = GetIntensityCurveModel();
+    curve_model->OnAdjustCustomContrast(level, window);
+}
+
 void GlobalUIModel::ToggleOverlayVisibility()
 {
   // Are we in tiled mode or in stack mode?
@@ -510,6 +516,7 @@ void GlobalUIModel::LoadUserPreferences()
   m_AppearanceSettings->LoadFromRegistry(
         si->Folder("UserInterface.Appearance"));
 
+
   // Read the default behaviors
   dbs->ReadFromRegistry(
         si->Folder("UserInterface.DefaultBehavior"));

GUI/Model/GlobalUIModel.h

@@ -326,9 +326,12 @@ class GlobalUIModel : public AbstractModel
   /** Auto-adjust contrast in all image layers */
   void AutoContrastAllLayers();
 
-  /** Auto-adjust contrast in all image layers */
+  /** Reset contrast in all image layers */
   void ResetContrastAllLayers();
 
+  /** Adjust custom contrast in all image layers */
+  void AdjustContrastAllLayers(double level, double window);
+
   /** A function for switching between segmentation layers when there multiple */
   void CycleSelectedSegmentationLayer(int direction);
 

GUI/Model/IntensityCurveModel.cxx

@@ -637,6 +637,15 @@ void IntensityCurveModel::OnAutoFitWindow()
   dmp->AutoFitContrast();
 }
 
+void IntensityCurveModel::OnAdjustCustomContrast(double custom_level, double custom_window)
+{
+  int index_level = 2;
+  int index_window = 3;
+
+  SetIntensityRangeIndexedValue(index_level, custom_level);
+  SetIntensityRangeIndexedValue(index_window, custom_window);
+}
+
 bool
 IntensityCurveModel
 ::GetHistogramBinSizeValueAndRange(

GUI/Model/IntensityCurveModel.h

@@ -172,6 +172,7 @@ class IntensityCurveModel : public IntensityCurveModelBase
       IntensityRangePropertyType index) const;
 
   void OnAutoFitWindow();
+  void OnAdjustCustomContrast(double custom_level, double custom_window);
 protected:
 
   IntensityCurveModel();

GUI/Qt/Windows/MainControlPanel.cxx

@@ -184,6 +184,7 @@ MainControlPanel::MainControlPanel(MainImageWindow *parent) :
 void MainControlPanel::SetModel(GlobalUIModel *model)
 {
   m_Model = model;
+
   ui->pageCursorInspector->SetModel(m_Model->GetCursorInspectionModel());
   ui->pageZoomInspector->SetModel(m_Model);
   ui->pageDisplayInspector->SetModel(m_Model->GetDisplayLayoutModel());