- Author:
- Randall Britten <r.britten@auckland.ac.nz>
- Date:
- 2014-03-10 12:37:50+13:00
- Desc:
- Snapshot of partial progress towards a CellML representation, based on the BM file.
At this stage, this aimed just at the Respiration component, and without physical units, or any work to validate that the simulation results are correct.
A more detailed version history to this point is available at https://github.com/codecurve/Ikeda-et-al-1979
- Permanent Source URI:
- https://models.cellml.org/workspace/193/rawfile/e837300b086b879f3016fa777f83b9199afd1ee8/daeml2bmadonna2.xsl
<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet version="1.0"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
xmlns:math="http://www.w3.org/1998/Math/MathML"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:fo="http://www.w3.org/1999/XSL/Format">
<!-- This xsl file converts (partially for now) a DAEML xml file into a Berkeley Madonna model file. -->
<!-- 24April2008: used Alfredo's cellml2hppv2.xsl -->
<xsl:output method="text" encoding="UTF-8" indent="no"/>
<xsl:strip-space elements="*"/>
<xsl:template match="/">
<xsl:text>METHOD stiff </xsl:text>
<xsl:text>STARTTIME = 0 </xsl:text>
<xsl:text>STOPTIME = 100 </xsl:text>
<xsl:text>DT = 0.002 </xsl:text>
<xsl:text> </xsl:text>
<xsl:text>{ </xsl:text>
<xsl:text> * </xsl:text>
<xsl:text> * Test of DAEML translation to Berkeley Madonna </xsl:text>
<xsl:text> * </xsl:text>
<xsl:text>} </xsl:text>
<xsl:text> </xsl:text>
<xsl:text>{ *** Model description*** </xsl:text>
<xsl:value-of select="daeml/model/description"/>
<xsl:text> } </xsl:text>
<!--
<xsl:call-template name="units"/>
<xsl:call-template name="parameters"/>
<xsl:call-template name="variables"/>
<xsl:call-template name="odes"/>
-->
<xsl:apply-templates select="daeml/model/list_of_units"/>
<xsl:apply-templates select="daeml/model/parameters"/>
<xsl:apply-templates select="daeml/model/variables"/>
<xsl:apply-templates select="daeml/model/system_equations/derivative_equations"/>
</xsl:template> <!-- End of main template -->
<!--
Now list the various templates.
-->
<xsl:template match="list_of_units" name="units">
<xsl:text> ; ***Units list goes here*** </xsl:text>
</xsl:template>
<xsl:template match="parameters" name="parameters">
<xsl:text> { Parameter list (values don't change during the simulation): </xsl:text>
<xsl:for-each select="parameter">
<xsl:text>	 </xsl:text><!-- tabulation -->
<xsl:value-of select="@name"/>
<xsl:text> (</xsl:text>
<xsl:value-of select="@units"/>
<xsl:text>), types: </xsl:text>
<xsl:for-each select="type">
<xsl:value-of select="."/>
</xsl:for-each>
<xsl:text>; </xsl:text>
<xsl:value-of select="comment"/>
<xsl:text> </xsl:text>
</xsl:for-each>
<xsl:text>} </xsl:text>
<xsl:text> ; ***Parameter values: </xsl:text>
<xsl:for-each select="parameter">
<xsl:choose>
<xsl:when test="init_value/eq_code/text()">
<xsl:value-of select="init_value/eq_code"/>
<xsl:text> </xsl:text>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="definition/eq_code"/>
<xsl:text> </xsl:text>
</xsl:otherwise>
</xsl:choose>
</xsl:for-each>
</xsl:template>
<xsl:template match="variables" name="variables">
<!-- First, list the variables in a comment. -->
<xsl:text> { Variables (values may change during the simulation): </xsl:text>
<xsl:for-each select="variable">
<xsl:text>	 </xsl:text><!-- tabulation -->
<xsl:value-of select="@name"/>
<xsl:text> (</xsl:text>
<xsl:value-of select="@units"/>
<xsl:text>), types: </xsl:text>
<xsl:if test="@state_var='true'">
<xsl:text>state </xsl:text>
</xsl:if>
<xsl:for-each select="type">
<xsl:value-of select="."/>
<xsl:text> </xsl:text>
</xsl:for-each>
<xsl:text>; </xsl:text>
<xsl:value-of select="comment"/>
<xsl:text> </xsl:text>
</xsl:for-each>
<xsl:text>} </xsl:text>
<!-- Next, give the variable values and definitions. -->
<xsl:text> ; ***Variable values and definitions: </xsl:text>
<xsl:for-each select="variable">
<xsl:choose>
<xsl:when test="not(@state_var='true')">
<xsl:choose>
<xsl:when test="init_value/eq_code/text()">
<xsl:value-of select="init_value/eq_code"/>
<xsl:text> </xsl:text>
</xsl:when>
<xsl:when test="definition/eq_code/text()">
<xsl:value-of select="definition/eq_code"/>
<xsl:text> </xsl:text>
</xsl:when>
<xsl:when test="definition/function_call">
<xsl:apply-templates match="definition/function_call">
<xsl:with-param name="func_name" select="definition/function_call/@name"/>
<xsl:with-param name="caller_index" select="position()"/>
</xsl:apply-templates>
</xsl:when>
</xsl:choose>
</xsl:when>
</xsl:choose>
</xsl:for-each>
<xsl:text> </xsl:text>
<!-- Next, initialize the state variables. -->
<xsl:text>; *** initialize state variables *** </xsl:text>
<xsl:for-each select="variable">
<xsl:if test="@state_var='true'">
<xsl:text>INIT </xsl:text>
<xsl:value-of select="init_value/eq_code"/>
<xsl:text> </xsl:text>
</xsl:if>
</xsl:for-each>
<xsl:text> </xsl:text>
<!-- Finally, set limits, if any, for the state variables. -->
<xsl:text>; *** range conditions for the state variables *** </xsl:text>
<xsl:for-each select="variable">
<xsl:if test="@state_var='true'">
<xsl:for-each select="condition">
<xsl:text>LIMIT </xsl:text>
<xsl:value-of select="eq_code"/>
<xsl:text> </xsl:text>
</xsl:for-each>
</xsl:if>
</xsl:for-each>
<xsl:text> </xsl:text>
</xsl:template>
<xsl:template match="derivative_equations" name="odes">
<xsl:text>; *** ODEs *** </xsl:text>
<xsl:for-each select="ode">
<xsl:value-of select="eq_code"/>
<xsl:text> </xsl:text>
</xsl:for-each>
</xsl:template>
<!-- NB: put function definitions off for later:
<xsl:template match="definition/function_call">
<xsl:param name="func_name"/>
<xsl:param name="caller_index"/>
<xsl:for-each select="map">
<xsl:variable name="
<if test="/daeml/function/@functionName=$func_name">
<if test="daeml/function/variable/@name=
</xsl:template>
-->
</xsl:stylesheet>
