Add GUI changes and tinyxml2 thirdparty package.

Code/CMake/SimVascularInternals.cmake

@@ -70,6 +70,7 @@ set(SV_LIBS ${SV_LIBS}
  THIRDPARTY_VMTK
  THIRDPARTY_ZLIB
  THIRDPARTY_TINYXML
+ THIRDPARTY_TINYXML2
  THIRDPARTY_SOLVERIO)
 
 # Module libs

Code/CMake/SimVascularOptions.cmake

@@ -145,6 +145,7 @@ option(SV_USE_TETGEN "Enable Tetgen Meshing Plugin" ON)
 option(SV_USE_TETGEN_ADAPTOR "Option to use open source mesh adaption" ON)
 
 option(SV_USE_TINYXML "Use TinyXML" ON)
+option(SV_USE_TINYXML2 "Use TinyXML2" ON)
 
 option(SV_USE_PYTHON "Use Python" ON)
 

Code/CMake/SimVascularThirdParty.cmake

@@ -82,6 +82,10 @@ if(SV_USE_TINYXML)
 else()
  unset(TINYXML_LIBRARY CACHE)
 endif()
+
+simvascular_third_party(tinyxml2)
+set(TINYXML2_LIBRARY ${SV_LIB_THIRDPARTY_TINYXML2_NAME})
+
 #-----------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------

Code/Source/sv4gui/Plugins/org.sv.gui.qt.svfsi/sv4gui_svFSIView.cxx

@@ -1402,11 +1402,16 @@ void sv4guisvFSIView::SaveRemesher()
  DataChanged();
 }
 
-
+//-----------------
+// CreateInputFile
+//-----------------
+// Create a text or XML input file of solver commands.
+//
 void sv4guisvFSIView::CreateInputFile()
 {
- if(!m_MitkJob)
+ if (!m_MitkJob) {
  return;
+ }
 
  QString jobPath=GetJobPath();
  if(jobPath=="" || !QDir(jobPath).exists())
@@ -1415,14 +1420,33 @@ void sv4guisvFSIView::CreateInputFile()
  return;
  }
 
- std::string mfsFileName=m_JobNode->GetName()+".txt";
- std::string mfsFullFilePath=jobPath.toStdString()+"/"+mfsFileName;
 
- if(m_Job->WriteFile(mfsFullFilePath))
- {
- m_MitkJob->SetStatus("Input file created");
- m_JobNode->SetBoolProperty("dummy",true);//trigger NodeChanged to update job status
- mitk::StatusBar::GetInstance()->DisplayText("Input file (.msf) have been created.");
+ // If the 'xml_format_radioButton' is selected then write
+ // out an XML format file for svFSIplus.
+ //
+ bool xml_format = ui->xml_format_radioButton->isChecked();
+
+ if (xml_format) { 
+ std::string mfsFileName=m_JobNode->GetName()+".xml";
+ std::string mfsFullFilePath=jobPath.toStdString()+"/"+mfsFileName;
+
+ if (m_Job->WriteXmlFile(mfsFullFilePath)) {
+ m_MitkJob->SetStatus("Input XML file created");
+ m_JobNode->SetBoolProperty("dummy",true);//trigger NodeChanged to update job status
+ mitk::StatusBar::GetInstance()->DisplayText("Input file (.msf) have been created.");
+ }
+
+ // Write out a plain text format file for svFSI.
+ //
+ } else {
+ std::string mfsFileName=m_JobNode->GetName()+".txt";
+ std::string mfsFullFilePath=jobPath.toStdString()+"/"+mfsFileName;
+
+ if (m_Job->WriteFile(mfsFullFilePath)) {
+ m_MitkJob->SetStatus("Input file created");
+ m_JobNode->SetBoolProperty("dummy",true);//trigger NodeChanged to update job status
+ mitk::StatusBar::GetInstance()->DisplayText("Input file (.msf) have been created.");
+ }
  }
 }
 

Code/Source/sv4gui/Plugins/org.sv.gui.qt.svfsi/sv4gui_svFSIView.ui

@@ -275,7 +275,7 @@
  <rect>
  <x>0</x>
  <y>0</y>
- <width>434</width>
+ <width>449</width>
  <height>581</height>
  </rect>
  </property>
@@ -1929,7 +1929,7 @@
  <rect>
  <x>0</x>
  <y>0</y>
- <width>434</width>
+ <width>449</width>
  <height>609</height>
  </rect>
  </property>
@@ -2436,6 +2436,26 @@
  </property>
  </spacer>
  </item>
+ <item row="2" column="0">
+ <widget class="QPushButton" name="btnStopSim">
+ <property name="text">
+ <string>Stop</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <spacer name="verticalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
  <item row="1" column="0">
  <widget class="QWidget" name="widgetRun" native="true">
  <layout class="QGridLayout" name="gridLayout_42">
@@ -2454,17 +2474,30 @@
  <property name="spacing">
  <number>5</number>
  </property>
- <item row="2" column="1">
- <widget class="ctkSliderWidget" name="sliderNumProcs" native="true"/>
+ <item row="0" column="1">
+ <widget class="QRadioButton" name="xml_format_radioButton">
+ <property name="toolTip">
+ <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;If selected then write the solver commands in XML format used by svFSIplus.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+ </property>
+ <property name="text">
+ <string>XML Format</string>
+ </property>
+ </widget>
  </item>
- <item row="0" column="0" colspan="2">
+ <item row="0" column="0">
  <widget class="QPushButton" name="btnCreateInputFile">
+ <property name="toolTip">
+ <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+ </property>
  <property name="text">
  <string>Create Input File</string>
  </property>
  </widget>
  </item>
- <item row="2" column="0">
+ <item row="1" column="1">
+ <widget class="ctkSliderWidget" name="sliderNumProcs" native="true"/>
+ </item>
+ <item row="1" column="0">
  <widget class="QLabel" name="label_5">
  <property name="sizePolicy">
  <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
@@ -2477,7 +2510,7 @@
  </property>
  </widget>
  </item>
- <item row="6" column="0" colspan="2">
+ <item row="2" column="0" colspan="2">
  <widget class="QPushButton" name="btnRunSim">
  <property name="sizePolicy">
  <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
@@ -2496,26 +2529,6 @@
  </layout>
  </widget>
  </item>
- <item row="4" column="0">
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="2" column="0">
- <widget class="QPushButton" name="btnStopSim">
- <property name="text">
- <string>Stop</string>
- </property>
- </widget>
- </item>
  </layout>
  </widget>
  </widget>

Code/ThirdParty/tinyxml2/CMakeLists.txt

@@ -0,0 +1,31 @@
+# Copyright (c) Stanford University, The Regents of the University of
+# California, and others.
+#
+# All Rights Reserved.
+#
+# See Copyright-SimVascular.txt for additional details.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject
+# to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+#simvascular_third_party(tinyxml)

Code/ThirdParty/tinyxml2/Makefile

@@ -0,0 +1,64 @@
+# Hey emacs, this is a -*- makefile -*-
+
+# Copyright (c) Stanford University, The Regents of the University of
+# California, and others.
+#
+# All Rights Reserved.
+#
+# See Copyright-SimVascular.txt for additional details.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject
+# to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+TOP=../../../BuildWithMake
+
+include $(TOP)/include.mk
+
+TINYXML_SUBDIRS = simvascular_tinyxml
+
+lib: createHeaderFile libsubdirs
+
+shared:
+
+libsubdirs:
+ @for i in ${TINYXML_SUBDIRS}; do ( \
+ cd $$i; \
+ $(MAKE)) ; done
+
+clean:
+ for i in ${TINYXML_SUBDIRS}; do ( \
+ cd $$i; \
+ $(MAKE) clean ) ; done
+
+veryclean: clean
+ rm -f simvascular_tinyxml.h
+ for i in ${TINYXML_SUBDIRS}; do ( \
+ cd $$i; \
+ $(MAKE) veryclean ) ; done
+
+createHeaderFile:
+ rm -f simvascular_tinyxml.h
+ @echo "#ifndef __simvascular_tinyxml_h" > simvascular_tinyxml.h
+ @echo "#define __simvascular_tinyxml_h" >> simvascular_tinyxml.h
+ @echo "#include <simvascular_tinyxml/tinyxml.h>" >> simvascular_tinyxml.h
+ @echo "#endif" >> simvascular_tinyxml.h

Code/ThirdParty/tinyxml2/simvascular_tinyxml2.h.in

@@ -0,0 +1,43 @@
+/* Copyright (c) Stanford University, The Regents of the University of
+ * California, and others.
+ *
+ * All Rights Reserved.
+ *
+ * See Copyright-SimVascular.txt for additional details.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#ifndef __simvascular_tinyxml2_h
+#define __simvascular_tinyxml2_h
+
+/* Use the tinyxml library configured for SimVascular. */
+#cmakedefine SV_USE_SYSTEM_TINYXML2
+#ifdef SV_USE_SYSTEM_TINYXML2
+# include <tinyxml.h>2
+#else
+# include <simvascular_tinyxml2/tinyxml2.h>
+#endif
+
+#endif