Replace CntrlComparison with LeafGasComparison
This commit is contained in:
@@ -14,13 +14,13 @@ namespace LeafWeb.Core.Tests.Charter
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[Test]
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public void Convert_Valid()
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{
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var fileInfo = FileUtility.GetContentFile(ContentDirectory, "cntrlcomparison_Wild Capsicum.csv");
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CntrlComparison[] cntrlComparison;
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using (var parser = new CntrlComparisonParser(fileInfo))
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cntrlComparison = parser.Parse();
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var fileInfo = FileUtility.GetContentFile(ContentDirectory, "leafgascomparison.csv");
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LeafGasComparison[] leafGasComparisons;
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using (var parser = new LeafGasComparisonParser(fileInfo))
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leafGasComparisons = parser.Parse();
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var curves = CurveDataConverter.Convert(cntrlComparison);
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Assert.That(curves.Count(),Is.EqualTo(7));
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var curves = CurveDataConverter.Convert(leafGasComparisons);
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Assert.That(curves.Count(),Is.EqualTo(1));
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}
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}
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}
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@@ -45,7 +45,7 @@
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</ItemGroup>
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<ItemGroup>
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<Compile Include="Charter\CurveDataConverterTests.cs" />
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<Compile Include="Parsers\CntrlComparisonParserTests.cs" />
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<Compile Include="Parsers\LeafGasComparisonParserTests.cs" />
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<Compile Include="Parsers\FluxnetSiteCsvParserTests.cs" />
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<Compile Include="Properties\AssemblyInfo.cs" />
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<Compile Include="Parsers\LeafInputCsvParserTests.cs" />
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@@ -79,6 +79,9 @@
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<Content Include="Parsers\LeafOutputData\cntrlparameters_Wild Capsicum.csv">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</Content>
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<Content Include="Parsers\LeafOutputData\leafgascomparison.csv">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</Content>
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</ItemGroup>
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<ItemGroup />
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<ItemGroup>
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+6
-6
@@ -6,20 +6,20 @@ using NUnit.Framework;
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namespace LeafWeb.Core.Tests.Parsers
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{
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[TestFixture]
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public class CntrlComparisonParserTests
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public class LeafGasComparisonParserTests
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{
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private const string ContentDirectory = @"Parsers\LeafOutputData\";
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[Test]
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public void Parse_Valid()
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{
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var fileInfo = FileUtility.GetContentFile(ContentDirectory, "cntrlcomparison_Wild Capsicum.csv");
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var fileInfo = FileUtility.GetContentFile(ContentDirectory, "leafgascomparison.csv");
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CntrlComparison[] cntrlComparison;
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using (var parser = new CntrlComparisonParser(fileInfo))
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cntrlComparison = parser.Parse();
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LeafGasComparison[] leafGasComparisons;
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using (var parser = new LeafGasComparisonParser(fileInfo))
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leafGasComparisons = parser.Parse();
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Assert.That(cntrlComparison.Length, Is.EqualTo(7 * 4));
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Assert.That(leafGasComparisons.Length, Is.EqualTo(6));
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}
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}
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}
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@@ -0,0 +1,218 @@
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CurveID,FitRwp|Rch|ha?,Fitha_Vcmax|Jmax|Tpu?,FitGamma*|ha?,FitKc|ha?,FitKo|ha?,FitRd|ha?,FitAlpha?,FitbetaPSII?,CO2i_obs,CO2i_Pred,CO2c,Anet_Obs,Anet_Pred,LimitState,RecycRate,CO2S,Pres_O2,Pres_H2O,Pres_Air,VPDL,PARi,LeafTemp,ChamberAirTemp,Trmmol,StomatalCond_H2O,ChlFlPHIPSII_Obs,ChlFlPHIPSII_Pred,CO2i_Pred_ChlFl,Anet_Pred_ChlFl,CO2c_CO2i_ChlFl,CO2c_Anet_ChlFl
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NA,1=No2=Yes,1=No2=Yes,1=No2=Yes,1=No2=Yes,1=No2=Yes,1=No2=Yes,1=No2=Yes,1=No2=Yes,Pa,Pa,Pa,umolm-2s-1,umolm-2s-1,Rubis1RUBP2TPU3,%,Pa,KPa,KPa,KPa,KPa,umolm-2s-1,oC,oC,mmolm-2s-1,molm-2s-1,NA,NA,Pa,umolm-2s-1,Pa,Pa
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|
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|
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|
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|
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|
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|
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|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,11.410662,11.410662,.160992,8.376207,8.119417,1,66.688585,36.968568,21.000000,1.902891,93.756218,1.774054,751.998169,27.642038,25.558516,1.231317,.063979,.229373,.201077,-9999.000000,7.335549,-9999.000000,.097864
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,15.457426,15.457426,.219858,12.050142,11.627775,1,67.306076,50.764352,21.000000,1.920236,93.760933,1.769423,751.566040,27.703815,25.577255,1.199540,.062463,.256533,.258436,-9999.000000,11.673508,-9999.000000,.229415
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,18.453370,18.453370,.393270,14.865519,14.595753,2,67.513450,64.606537,21.000000,1.936348,93.764381,1.772160,751.500244,27.793242,25.598539,1.188842,.061792,.282432,.286217,-9999.000000,14.648679,-9999.000000,.441160
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,22.087725,22.087725,2.429051,16.534050,16.754513,2,66.606703,78.529723,21.000000,1.941673,93.765282,1.778054,751.203430,27.845459,25.617878,1.134871,.058748,.285451,.287144,-9999.000000,16.671636,-9999.000000,2.531320
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,24.614529,24.614529,4.814654,17.634794,17.099773,2,66.655219,92.506767,21.000000,1.946412,93.768608,1.802464,751.009888,27.978724,25.633127,1.047879,.053442,.289946,.289307,-9999.000000,17.136238,-9999.000000,4.772492
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,26.640135,26.640135,6.800288,18.362624,17.215581,2,67.693060,111.245730,21.000000,1.951034,93.768127,1.809146,750.768982,28.030703,25.651936,.933403,.047362,.292079,.290216,-9999.000000,17.325240,-9999.000000,6.675248
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,31.772055,31.772055,11.921317,19.571966,17.475415,2,69.261094,148.710005,21.000000,1.966181,93.772064,1.838296,750.370056,28.232525,25.692453,.751472,.037435,.291893,.293555,-9999.000000,17.375343,-9999.000000,12.033064
|
||||
371Jeq2.csv,221,111,21,21,11,11,1,2,32.865828,32.865828,12.983979,19.783484,17.371967,2,65.992155,130.008366,21.000000,1.954853,93.769012,1.823533,750.677429,28.113436,25.661491,.830709,.041764,.291100,.291555,-9999.000000,17.344552,-9999.000000,13.014810
|
||||
CO2i,CO2cc,Ac,CO2cj,Aj,CO2ct,At
|
||||
1.000000,.014094,-.782969,.002231,-7.779976,-9999.000000,-9999.000000
|
||||
2.000000,.028214,.079421,.004709,-6.473019,-9999.000000,-9999.000000
|
||||
3.000000,.042361,.941788,.007476,-5.166441,-9999.000000,-9999.000000
|
||||
4.000000,.056536,1.804132,.010587,-3.860313,-9999.000000,-9999.000000
|
||||
5.000000,.070737,2.666451,.014108,-2.554723,-9999.000000,-9999.000000
|
||||
6.000000,.084966,3.528747,.018128,-1.249785,-9999.000000,-9999.000000
|
||||
8.500000,.120656,5.684382,.031190,2.008609,-9999.000000,-9999.000000
|
||||
11.000000,.156519,7.839868,.051349,5.257706,-9999.000000,-9999.000000
|
||||
13.500000,.192554,9.995202,.086388,8.487307,-9999.000000,-9999.000000
|
||||
16.000000,.228763,12.150384,.161197,11.664800,-9999.000000,-9999.000000
|
||||
18.500000,.265147,14.305413,.401097,14.625992,-9999.000000,-9999.000000
|
||||
21.000000,.301708,16.460287,1.524948,16.429027,-9999.000000,-9999.000000
|
||||
23.500000,.338447,18.615006,3.708712,16.843360,-9999.000000,-9999.000000
|
||||
26.000000,.375364,20.769568,6.119897,16.959726,2.217923,20.229132
|
||||
28.500000,.412462,22.923973,8.580469,17.011385,4.842059,20.229132
|
||||
31.000000,.449742,25.078218,11.058427,17.040265,7.377878,20.229132
|
||||
33.500000,.487204,27.232304,13.544392,17.058653,9.895239,20.229132
|
||||
36.000000,.524851,29.386229,16.034685,17.071372,12.405523,20.229132
|
||||
38.500000,.562683,31.539991,18.527575,17.080687,14.912332,20.229132
|
||||
41.000000,.600702,33.693589,21.022145,17.087802,17.417176,20.229132
|
||||
43.500000,.638910,35.847023,23.517863,17.093412,19.920799,20.229132
|
||||
|
||||
|
@@ -8,7 +8,7 @@ namespace LeafWeb.Core.Charter
|
||||
{
|
||||
public static class CurveDataConverter
|
||||
{
|
||||
public static IEnumerable<CurveData> Convert(IEnumerable<CntrlComparison> cntrlComparison)
|
||||
public static IEnumerable<CurveData> Convert(IEnumerable<LeafGasComparison> cntrlComparison)
|
||||
{
|
||||
var comparisonGroups =
|
||||
from comparison in cntrlComparison
|
||||
@@ -17,12 +17,12 @@ namespace LeafWeb.Core.Charter
|
||||
{
|
||||
CurveID = curves.Key,
|
||||
FitType = from curve in curves
|
||||
group curve by new {curve.FitGi, curve.FitGammaStar} into grp
|
||||
group curve by new {curve.FitRwp, curve.FitGammaStar} into grp
|
||||
select new
|
||||
{
|
||||
grp.Key.FitGi,
|
||||
grp.Key.FitRwp,
|
||||
grp.Key.FitGammaStar,
|
||||
Comparison = grp.SingleOrDefault()
|
||||
Comparison = grp.FirstOrDefault() // TODO: this may need to be SingleOrDefault
|
||||
}
|
||||
};
|
||||
|
||||
@@ -44,13 +44,13 @@ namespace LeafWeb.Core.Charter
|
||||
// gammastar = chloroplastic CO2 partial pressure photocompensation point = "Cmp"
|
||||
|
||||
// put each comparison into the correct curve location
|
||||
if (!fitType.FitGi && !fitType.FitGammaStar)
|
||||
if (!fitType.FitRwp && !fitType.FitGammaStar)
|
||||
curveData.FixedCndFixedCmp = paramSet;
|
||||
else if (!fitType.FitGi && fitType.FitGammaStar)
|
||||
else if (!fitType.FitRwp && fitType.FitGammaStar)
|
||||
curveData.FixedCndEstimatedCmp = paramSet;
|
||||
else if (fitType.FitGi && !fitType.FitGammaStar)
|
||||
else if (fitType.FitRwp && !fitType.FitGammaStar)
|
||||
curveData.EstimatedCndFixedCmp = paramSet;
|
||||
else if (fitType.FitGi && fitType.FitGammaStar)
|
||||
else if (fitType.FitRwp && fitType.FitGammaStar)
|
||||
curveData.EstimatedCndEstimatedCmp = paramSet;
|
||||
}
|
||||
|
||||
@@ -71,7 +71,7 @@ namespace LeafWeb.Core.Charter
|
||||
}
|
||||
}
|
||||
|
||||
private static CurveParamSet ConvertParamSet(CntrlComparison comparison)
|
||||
private static CurveParamSet ConvertParamSet(LeafGasComparison comparison)
|
||||
{
|
||||
var curveParamSet = new CurveParamSet();
|
||||
foreach (var fittingInfo in comparison.FittingInfo)
|
||||
@@ -85,7 +85,7 @@ namespace LeafWeb.Core.Charter
|
||||
return curveParamSet;
|
||||
}
|
||||
|
||||
private static void Set(CurveParamSet paramSet, CntrlComparisonPhotosyntheticInfo item)
|
||||
private static void Set(CurveParamSet paramSet, LeafGasComparisonPhotosyntheticInfo item)
|
||||
{
|
||||
AddXyIfInRange(item.CO2cc, item.Ac, paramSet.AcChloroData.Add); // Ac(y),CO2cc(x)
|
||||
AddXyIfInRange(item.CO2cj, item.Aj, paramSet.AjChloroData.Add); // Aj(y),CO2cj(x)
|
||||
@@ -103,12 +103,12 @@ namespace LeafWeb.Core.Charter
|
||||
set(xyPoint);
|
||||
}
|
||||
|
||||
private static void Set(CurveParamSet paramSet, CntrlComparisonFittingInfo fittingInfo)
|
||||
private static void Set(CurveParamSet paramSet, LeafGasComparisonFittingInfo fittingInfo)
|
||||
{
|
||||
var xyPoint1 = new XyPoint(fittingInfo.PCO2c, fittingInfo.AnetMeas); // AnetMeas(y), PCO2c(x)
|
||||
var xyPoint2 = new XyPoint(fittingInfo.PCO2i, fittingInfo.AnetMeas);
|
||||
var xyPoint1 = new XyPoint(fittingInfo.CO2c, fittingInfo.Anet_obs); // AnetMeas(y), PCO2c(x)
|
||||
var xyPoint2 = new XyPoint(fittingInfo.CO2i_obs, fittingInfo.Anet_obs);
|
||||
|
||||
switch (fittingInfo.PointLimitType)
|
||||
switch (fittingInfo.LimitState)
|
||||
{
|
||||
case 1:
|
||||
paramSet.AnetMeasChloro1Data.Add(xyPoint1);
|
||||
|
||||
+4
-4
@@ -76,13 +76,14 @@
|
||||
<Compile Include="DAL\DataService.cs" />
|
||||
<Compile Include="DAL\LeafWebContext.cs" />
|
||||
<Compile Include="DAL\LeafWebInitializer.cs" />
|
||||
<Compile Include="Entities\LeafGasComparisonPhotosyntheticInfo.cs" />
|
||||
<Compile Include="Entities\LeafGasComparisonFittingInfo.cs" />
|
||||
<Compile Include="Entities\LeafGasComparison.cs" />
|
||||
<Compile Include="Entities\LeafInputStatusType.cs" />
|
||||
<Compile Include="Entities\LeafOutputFile.cs" />
|
||||
<Compile Include="Entities\PhotosynthesisType.cs" />
|
||||
<Compile Include="Parsers\LeafGasComparisonParser.cs" />
|
||||
<Compile Include="Remote\IPiscalClient.cs" />
|
||||
<Compile Include="Entities\CntrlComparison.cs" />
|
||||
<Compile Include="Entities\CntrlComparisonFittingInfo.cs" />
|
||||
<Compile Include="Entities\CntrlComparisonPhotosyntheticInfo.cs" />
|
||||
<Compile Include="Entities\FluxnetSite.cs" />
|
||||
<Compile Include="Entities\LeafInput.cs" />
|
||||
<Compile Include="Entities\LeafInputData.cs" />
|
||||
@@ -100,7 +101,6 @@
|
||||
<Compile Include="Remote\PiscalStatus.cs" />
|
||||
<Compile Include="Remote\PiscalUtility.cs" />
|
||||
<Compile Include="Utility\BoolTypeConverter.cs" />
|
||||
<Compile Include="Parsers\CntrlComparisonParser.cs" />
|
||||
<Compile Include="Parsers\CsvParserBase.cs" />
|
||||
<Compile Include="Properties\AssemblyInfo.cs" />
|
||||
<Compile Include="Utility\FileUtility.cs" />
|
||||
|
||||
@@ -1,22 +0,0 @@
|
||||
using System.Collections.Generic;
|
||||
using System.Linq;
|
||||
|
||||
namespace LeafWeb.Core.Entities
|
||||
{
|
||||
/// <summary>
|
||||
/// Part of LeafOutput
|
||||
/// The file 'cntrlcomparison.csv', which is in comma-separated-value format, contains outputs from PISCAL that
|
||||
/// facilitates examination of how well the fitting is.
|
||||
/// </summary>
|
||||
public class CntrlComparison
|
||||
{
|
||||
public virtual IEnumerable<CntrlComparisonFittingInfo> FittingInfo { get; set; }
|
||||
public virtual IEnumerable<CntrlComparisonPhotosyntheticInfo> PhotosyntheticInfo { get; set; }
|
||||
|
||||
public string CurveID => FittingInfo.First().CurveID;
|
||||
|
||||
public bool FitGi => FittingInfo.First().FitGi;
|
||||
|
||||
public bool FitGammaStar => FittingInfo.First().FitGammaStar;
|
||||
}
|
||||
}
|
||||
@@ -1,117 +0,0 @@
|
||||
using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Entities
|
||||
{
|
||||
/// <summary>
|
||||
/// First model prediction is calculated at each sampling point.
|
||||
/// Then model prediction is calculated at many selected levels of intercelluar CO2 partial pressure
|
||||
/// levels under three limitation states to enable plotting curves.The same structure is then repeated for
|
||||
/// each fitting of the same curve with different parameters to be estimated and with different curves. Note
|
||||
/// that some common information about a curve is repeated for each data point to make the structure of the
|
||||
/// file as regular as possible.
|
||||
/// </summary>
|
||||
public class CntrlComparisonFittingInfo
|
||||
{
|
||||
/// <summary>
|
||||
/// the curve identifier, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(1)]
|
||||
public string CurveID { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// whether or not chlorophyll fluorescence data are used for identifying the limitation states
|
||||
/// 0 = not used, 1 = used. (Currently this choice is still under evaluation and therefore ChlFlUse? = 0).
|
||||
/// </summary>
|
||||
[ParseInfo(2, alternateTitle: "ChlFlUse?")]
|
||||
public bool ChlFlUse {get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// whether or not the internal conductance (gi) is fitted for.
|
||||
/// 0 = not fitted and gi is either infinite or fixed at the value provided by the user.
|
||||
/// 1 = gi is estiamted, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(3, alternateTitle: "FitGi?")]
|
||||
public bool FitGi {get; set;}
|
||||
|
||||
/// <summary>
|
||||
/// whether or not the chloroplastic CO2 partial pressure photocompensation point is
|
||||
/// fitted for. 0= not fitted, a prescribed value is used, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(4, alternateTitle: "FitGamma*?")]
|
||||
public bool FitGammaStar {get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// whether or not the apparent Michaelis - Menten constant Kco = Kc(1+O/Ko) is fitted for.
|
||||
/// 0= not fitted, a prescribed value is calculated from Kc, Ko and the oxygen partial pressure.
|
||||
/// 1= Fitted for, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(5, alternateTitle: "FitKco?")]
|
||||
public bool FitKco {get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// whether the dark respiration is fitted for. 0= not fitted for, a prescribed value is used.
|
||||
/// 1= fitted for. repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(6, alternateTitle: "FitRd?")]
|
||||
public bool FitRd {get; set;}
|
||||
|
||||
/// <summary>
|
||||
/// whether alpha (the non-returned fraction of the glycolate carbon
|
||||
/// recycled in the photorespiratory cycle) is fitted for.
|
||||
/// 0= not fitted for and alpha = 0
|
||||
/// 1= fitted for, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(7, alternateTitle: "FitAlpha?")]
|
||||
public bool FitAlpha {get; set;}
|
||||
|
||||
/// <summary>
|
||||
/// the combination of limitation states present in the A/Ci dataset. Parameters
|
||||
/// are estimated for those limitation states that occur in the measured curve, repeated for each point
|
||||
/// Rubisco: Rubisco limitation(Vcmax, Kco)
|
||||
/// RuBP: RuBP regeneration limitation(J)
|
||||
/// Tpu: export limitation(TPU, alpha)
|
||||
/// </summary>
|
||||
[ParseInfo(8)]
|
||||
public string LimitCombina { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// intercellular CO2 partial pressure
|
||||
/// </summary>
|
||||
[ParseInfo(9, units:"Pa")]
|
||||
public double PCO2i { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// chloroplastic CO2 partial pressure corresponding to the PCO2i of a point.
|
||||
/// PCO2c=PCO2i-AnetCal/internal conductance
|
||||
/// </summary>
|
||||
[ParseInfo(10, units:"Pa")]
|
||||
public double PCO2c { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// measured net assimilation rate
|
||||
/// </summary>
|
||||
[ParseInfo(11, units: "umol/m2/s")]
|
||||
public double AnetMeas { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// calculated net assimilation rate
|
||||
/// </summary>
|
||||
[ParseInfo(12, units: "umol/m2/s")]
|
||||
public double AnetCal { get; set; }
|
||||
|
||||
// TODO: readme has weitedrms, data file has PCOiCal
|
||||
// weitedrms - (umol/m2/s), root mean square error of the fitting (weiting coefficient =1)
|
||||
[ParseInfo(13)]
|
||||
public double PCOiCal { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// 1 = point limited by rubisco
|
||||
/// 2 = point limited by RuBP regeneration
|
||||
/// 3 = point limited by TPU
|
||||
/// </summary>
|
||||
[ParseInfo(14, units:"1,2,3")]
|
||||
public int PointLimitType { get; set; }
|
||||
|
||||
public virtual CntrlComparison CntrlComparison { get; set; }
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,22 @@
|
||||
using System.Collections.Generic;
|
||||
using System.Linq;
|
||||
|
||||
namespace LeafWeb.Core.Entities
|
||||
{
|
||||
/// <summary>
|
||||
/// Part of LeafOutput
|
||||
/// The file 'leafgascomparison.csv', which is in comma-separated-value format, contains outputs from PISCAL that
|
||||
/// facilitates examination of how well the fitting is.
|
||||
/// </summary>
|
||||
public class LeafGasComparison
|
||||
{
|
||||
public virtual IEnumerable<LeafGasComparisonFittingInfo> FittingInfo { get; set; }
|
||||
public virtual IEnumerable<LeafGasComparisonPhotosyntheticInfo> PhotosyntheticInfo { get; set; }
|
||||
|
||||
public string CurveID => FittingInfo.First().CurveID;
|
||||
|
||||
public bool FitRwp => FittingInfo.First().FitRwp;
|
||||
|
||||
public bool FitGammaStar => FittingInfo.First().FitGammaStar;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,65 @@
|
||||
using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Entities
|
||||
{
|
||||
/// <summary>
|
||||
/// First model prediction is calculated at each sampling point.
|
||||
/// Then model prediction is calculated at many selected levels of intercelluar CO2 partial pressure
|
||||
/// levels under three limitation states to enable plotting curves.The same structure is then repeated for
|
||||
/// each fitting of the same curve with different parameters to be estimated and with different curves. Note
|
||||
/// that some common information about a curve is repeated for each data point to make the structure of the
|
||||
/// file as regular as possible.
|
||||
/// </summary>
|
||||
public class LeafGasComparisonFittingInfo
|
||||
{
|
||||
/// <summary>
|
||||
/// the curve identifier, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(1)]
|
||||
public string CurveID { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// whether or not the internal conductance (gi) is fitted for.
|
||||
/// 0 = not fitted and gi is either infinite or fixed at the value provided by the user.
|
||||
/// 1 = gi is estiamted, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(2, boolEncodedPosition: 1, alternateTitle: "FitRwp|Rch|ha?")] // formerly FitGi
|
||||
public bool FitRwp {get; set;}
|
||||
|
||||
/// <summary>
|
||||
/// whether or not the chloroplastic CO2 partial pressure photocompensation point is
|
||||
/// fitted for. 0= not fitted, a prescribed value is used, repeated for each point
|
||||
/// </summary>
|
||||
[ParseInfo(4, boolEncodedPosition: 1, alternateTitle: "FitGamma*?")]
|
||||
public bool FitGammaStar {get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// intercellular CO2 partial pressure
|
||||
/// </summary>
|
||||
[ParseInfo(10, units:"Pa")]
|
||||
public double CO2i_obs { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// chloroplastic CO2 partial pressure corresponding to the PCO2i of a point.
|
||||
/// PCO2c=PCO2i-AnetCal/internal conductance
|
||||
/// </summary>
|
||||
[ParseInfo(12, units:"Pa")]
|
||||
public double CO2c { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// measured net assimilation rate
|
||||
/// </summary>
|
||||
[ParseInfo(13, units: "umol/m2/s")]
|
||||
public double Anet_obs { get; set; }
|
||||
|
||||
/// <summary>
|
||||
/// 1 = point limited by rubisco
|
||||
/// 2 = point limited by RuBP regeneration
|
||||
/// 3 = point limited by TPU
|
||||
/// </summary>
|
||||
[ParseInfo(15, units:"1,2,3")]
|
||||
public int LimitState { get; set; }
|
||||
|
||||
public virtual LeafGasComparison LeafGasComparison { get; set; }
|
||||
}
|
||||
}
|
||||
+2
-2
@@ -6,7 +6,7 @@ namespace LeafWeb.Core.Entities
|
||||
/// The second section gives photosynthesis for each of the three limitation states at selected values of intercellular
|
||||
/// partial pressure.Note that the corresponding values of chloraplastic CO2 partial pressure depend on the limitation state.
|
||||
/// </summary>
|
||||
public class CntrlComparisonPhotosyntheticInfo
|
||||
public class LeafGasComparisonPhotosyntheticInfo
|
||||
{
|
||||
/// <summary>
|
||||
/// intercellular CO2 partial pressure
|
||||
@@ -50,6 +50,6 @@ namespace LeafWeb.Core.Entities
|
||||
[ParseInfo(7, units: "umol/m2/s")]
|
||||
public double At { get; set; }
|
||||
|
||||
public virtual CntrlComparison CntrlComparison { get; set; }
|
||||
public virtual LeafGasComparison LeafGasComparison { get; set; }
|
||||
}
|
||||
}
|
||||
@@ -12,7 +12,7 @@ namespace LeafWeb.Core.Entities
|
||||
public byte[] Contents { get; set; }
|
||||
|
||||
// convention for the filename which LeafCharter uses
|
||||
public bool IsLeafChartFile => Filename?.StartsWith("cntrlcomparison") ?? false;
|
||||
public bool IsLeafChartFile => Filename?.Contains("leafgascomparison") ?? false;
|
||||
public bool IsErrorMessage => Filename?.Contains("errormessage") ?? false;
|
||||
public bool IsWarningMessage => Filename?.Contains("warningmessage") ?? false;
|
||||
}
|
||||
|
||||
@@ -6,17 +6,17 @@ using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Parsers
|
||||
{
|
||||
public class CntrlComparisonParser : CsvParserBase
|
||||
public class LeafGasComparisonParser : CsvParserBase
|
||||
{
|
||||
public CntrlComparisonParser(FileSystemInfo csvFile) : base(csvFile)
|
||||
public LeafGasComparisonParser(FileSystemInfo csvFile) : base(csvFile)
|
||||
{
|
||||
}
|
||||
|
||||
public CntrlComparisonParser(byte[] fileContents) : base(fileContents)
|
||||
public LeafGasComparisonParser(byte[] fileContents) : base(fileContents)
|
||||
{
|
||||
}
|
||||
|
||||
public CntrlComparison[] Parse()
|
||||
public LeafGasComparison[] Parse()
|
||||
{
|
||||
var fittingTitles = GetNextCsvRowValues();
|
||||
if (fittingTitles == null)
|
||||
@@ -25,10 +25,10 @@ namespace LeafWeb.Core.Parsers
|
||||
if (fitUnits == null)
|
||||
throw new ParseException($"Could not read data units row on line number {CsvReader.Row}");
|
||||
|
||||
return ParseCntrlComparisonSet(fittingTitles).ToArray();
|
||||
return ParseLeafGasComparisonSet(fittingTitles).ToArray();
|
||||
}
|
||||
|
||||
private IEnumerable<CntrlComparison> ParseCntrlComparisonSet(string[] fittingTitles)
|
||||
private IEnumerable<LeafGasComparison> ParseLeafGasComparisonSet(string[] fittingTitles)
|
||||
{
|
||||
var endOfFile = false;
|
||||
while (!endOfFile)
|
||||
@@ -43,7 +43,7 @@ namespace LeafWeb.Core.Parsers
|
||||
throw new ParseException($"Encountered empty line while readding fitting info on line {CsvReader.Row}");
|
||||
if (values == null) // end of file
|
||||
yield break;
|
||||
if (ParsedObjectFactory<CntrlComparisonPhotosyntheticInfo>.IsPropertiesTitlesMatch(values))
|
||||
if (ParsedObjectFactory<LeafGasComparisonPhotosyntheticInfo>.IsPropertiesTitlesMatch(values))
|
||||
{
|
||||
photosyntheticTitles = values;
|
||||
break;
|
||||
@@ -66,13 +66,13 @@ namespace LeafWeb.Core.Parsers
|
||||
}
|
||||
|
||||
var fittingInfo =
|
||||
ParsedObjectFactory<CntrlComparisonFittingInfo>
|
||||
ParsedObjectFactory<LeafGasComparisonFittingInfo>
|
||||
.Create(fittingTitles, fittingValues.ToArray());
|
||||
var photosyntheticInfo =
|
||||
ParsedObjectFactory<CntrlComparisonPhotosyntheticInfo>
|
||||
ParsedObjectFactory<LeafGasComparisonPhotosyntheticInfo>
|
||||
.Create(photosyntheticTitles, photosyntheticValues.ToArray());
|
||||
|
||||
yield return new CntrlComparison
|
||||
yield return new LeafGasComparison
|
||||
{
|
||||
FittingInfo = fittingInfo,
|
||||
PhotosyntheticInfo = photosyntheticInfo
|
||||
@@ -24,6 +24,8 @@ namespace LeafWeb.Core.Utility
|
||||
|
||||
public override object ConvertTo(ITypeDescriptorContext context, CultureInfo culture, object value, Type destinationType)
|
||||
{
|
||||
if (value is bool)
|
||||
return value;
|
||||
if (value is string)
|
||||
{
|
||||
var s = value as string;
|
||||
|
||||
@@ -8,6 +8,7 @@ namespace LeafWeb.Core.Utility
|
||||
public class ParseInfoAttribute : Attribute
|
||||
{
|
||||
public int Position { get; private set; }
|
||||
public int? BoolEncodedPosition { get; private set; }
|
||||
public string Units { get; private set; }
|
||||
public string Title { get; private set; }
|
||||
public string AlterateTitle { get; private set; }
|
||||
@@ -23,13 +24,16 @@ namespace LeafWeb.Core.Utility
|
||||
}
|
||||
}
|
||||
|
||||
public ParseInfoAttribute(int position, [CallerMemberName]string title = null, string units = null, string alternateTitle = null, string exampleValue = null)
|
||||
public ParseInfoAttribute(int position, [CallerMemberName]string title = null,
|
||||
string units = null, string alternateTitle = null, string exampleValue = null,
|
||||
int boolEncodedPosition = -1)
|
||||
{
|
||||
AlterateTitle = alternateTitle;
|
||||
ExampleValue = exampleValue;
|
||||
Title = title;
|
||||
Position = position;
|
||||
Units = units;
|
||||
BoolEncodedPosition = boolEncodedPosition == -1 ? (int?)null : boolEncodedPosition;
|
||||
}
|
||||
|
||||
public bool IsTitleMatch(string title)
|
||||
|
||||
@@ -132,6 +132,7 @@ namespace LeafWeb.Core.Utility
|
||||
return string.IsNullOrEmpty(value) || value == "NA" || value == "-9999";
|
||||
}
|
||||
|
||||
// TODO: this call maybe could be cached
|
||||
private static PropertyInfo MatchProperty(PropertyInfo[] properties, string title, int position)
|
||||
{
|
||||
return
|
||||
@@ -139,6 +140,7 @@ namespace LeafWeb.Core.Utility
|
||||
properties.FirstOrDefault(p => p.Attribute<ParseInfoAttribute>().IsPositionMatch(position));
|
||||
}
|
||||
|
||||
// TODO: this call maybe could be cached
|
||||
private static PropertyInfo MatchPropertyExact(PropertyInfo[] properties, string title, int position)
|
||||
{
|
||||
return
|
||||
@@ -180,6 +182,7 @@ namespace LeafWeb.Core.Utility
|
||||
{
|
||||
// http://stackoverflow.com/questions/3531318/convert-changetype-fails-on-nullable-types
|
||||
var t = Nullable.GetUnderlyingType(property.PropertyType) ?? property.PropertyType;
|
||||
value = HandleBoolEncodedProperty(property, value);
|
||||
// convertedValue = Convert.ChangeType(value, t);
|
||||
var converter = TypeDescriptor.GetConverter(t);
|
||||
convertedValue = converter.ConvertTo(value, t);
|
||||
@@ -191,5 +194,26 @@ namespace LeafWeb.Core.Utility
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
private static object HandleBoolEncodedProperty(PropertyInfo property, object value)
|
||||
{
|
||||
var boolEncodedPosition = property.Attribute<ParseInfoAttribute>().BoolEncodedPosition;
|
||||
if (boolEncodedPosition == null) return value;
|
||||
|
||||
var v = (value as string)?.Substring(boolEncodedPosition.Value -1, 1);
|
||||
switch (v)
|
||||
{
|
||||
// these values are False=1, True=2
|
||||
case "1":
|
||||
value = false;
|
||||
break;
|
||||
case "2":
|
||||
value = true;
|
||||
break;
|
||||
default:
|
||||
throw new ArgumentOutOfRangeException($"{property.Name} {boolEncodedPosition} {value} {v}");
|
||||
}
|
||||
return value;
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -34,20 +34,20 @@ namespace LeafWeb.Web.Controllers
|
||||
.FirstOrDefault(f => f.IsLeafChartFile);
|
||||
|
||||
if (leafOutputFile == null)
|
||||
return View(); // TODO: break
|
||||
throw new ArgumentOutOfRangeException(); // TODO: break
|
||||
|
||||
return File(GetChartImage(leafOutputFile.Contents, number), "image/png", "mychart.png");
|
||||
}
|
||||
|
||||
private byte[] GetChartImage(byte[] fileContents, int number, ChartImageFormat format = ChartImageFormat.Png)
|
||||
{
|
||||
CntrlComparison[] cntrlComparison;
|
||||
using (var parser = new CntrlComparisonParser(fileContents))
|
||||
cntrlComparison = parser.Parse();
|
||||
LeafGasComparison[] leafGasComparisons;
|
||||
using (var parser = new LeafGasComparisonParser(fileContents))
|
||||
leafGasComparisons = parser.Parse();
|
||||
|
||||
var curveData = CurveDataConverter.Convert(cntrlComparison).ToArray();
|
||||
var curveData = CurveDataConverter.Convert(leafGasComparisons).ToArray();
|
||||
|
||||
var charts = LeafWebCharter.ProduceCharts(curveData[2]);
|
||||
var charts = LeafWebCharter.ProduceCharts(curveData[0]);
|
||||
|
||||
//Image.FromFile()
|
||||
|
||||
|
||||
@@ -13,6 +13,7 @@ namespace LeafWeb.Web.ViewModels.ResultStatus
|
||||
public string LeafInputIdentifier { get; set; }
|
||||
public string LeafInputSiteId { get; set; }
|
||||
public string LeafInputPhotosynthesisType { get; set; }
|
||||
public bool HasLeafChart { get; set; }
|
||||
public string CurrentStatus { get; set; }
|
||||
public string[] ErrorMessages { get; set; }
|
||||
//public string[] LeafOutputFilenames { get; set; }
|
||||
@@ -25,6 +26,7 @@ namespace LeafWeb.Web.ViewModels.ResultStatus
|
||||
{
|
||||
cfg.CreateMap<Core.Entities.LeafInput, ResultStatusViewModel>()
|
||||
.ForMember(dest => dest.LeafInputId, opt => opt.MapFrom(src => src.Id))
|
||||
.ForMember(dest => dest.HasLeafChart, opt => opt.ResolveUsing(src => src.OutputFiles.Any(o => o.IsLeafChartFile)))
|
||||
//.ForMember(dest => dest.LeafOutputFilenames,
|
||||
// opt => opt.ResolveUsing(
|
||||
// src =>
|
||||
|
||||
@@ -3,5 +3,5 @@
|
||||
|
||||
@for (int i = 0; i < 8; i++)
|
||||
{
|
||||
<img src="@Url.Action("LeafCharts", new {leafInputFileId = Model, number=@i})" alt="image" height="@LeafWebCharter.ChartHeight" width="@LeafWebCharter.ChartWidth" />
|
||||
<img src="@Url.Action("LeafCharts", new {leafInputId = Model, number=@i})" alt="image" height="@LeafWebCharter.ChartHeight" width="@LeafWebCharter.ChartWidth" />
|
||||
}
|
||||
@@ -12,7 +12,11 @@
|
||||
grid.Column("LeafInputIdentifier", "Identifier"),
|
||||
grid.Column("LeafInputSiteId", "Site Id"),
|
||||
grid.Column("LeafInputName", "Submitted By"),
|
||||
grid.Column("CurrentStatus", "Status")
|
||||
),
|
||||
grid.Column("CurrentStatus", "Status"),
|
||||
grid.Column("Chart", "Chart", item =>
|
||||
item.HasLeafChart
|
||||
? Html.ActionLink("Chart", "Index", "LeafCharter", new {leafInputId = item.LeafInputId}, new {})
|
||||
: Html.Raw(""))
|
||||
),
|
||||
htmlAttributes: new { @class = "table table-striped table-bordered table-hover table-condensed" }
|
||||
)
|
||||
|
||||
Reference in New Issue
Block a user