CntrlComparison parsing
This commit is contained in:
@@ -1,49 +1,15 @@
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using System;
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using System.Collections.Generic;
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using System.IO;
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using System.ComponentModel.DataAnnotations;
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namespace LeafWeb.Core.Models
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{
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[Serializable]
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/// <summary>
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/// The file 'cntrlcomparison.csv', which is in comma-separated-value format, contains outputs from PISCAL that
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/// facilitates examination of how well the fitting is.
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/// </summary>
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public class CntrlComparison
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{
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// Each element will be a PiscalCurve element that contains
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// all of the output data for one curve.
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private readonly List<CurveData> _curveData;
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public CntrlComparison()
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{
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_curveData = new List<CurveData>();
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}
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public bool ReadFromStream(StreamReader sr, ref String errorMsg)
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{
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// Skip the first two lines.
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sr.ReadLine();
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sr.ReadLine();
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var lineNbr = 2;
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// Now, there should be one or more rows, delimited by a row that has
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// CO2i in the first field. Read in all of these rows. The first field
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// in each row is the curve ID (input filename).
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var more = true;
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while (more)
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{
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var curve = new CurveData(sr, ref errorMsg, ref lineNbr);
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if (errorMsg.Length > 0)
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return false;
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_curveData.Add(curve);
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if (sr.EndOfStream)
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more = false;
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}
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return true;
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}
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public List<CurveData> GetCurveData()
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{
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return _curveData;
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}
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public virtual IEnumerable<CntrlComparisonFittingInfo> FittingInfo { get; set; }
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public virtual IEnumerable<CntrlComparisonPhotosyntheticInfo> PhotosyntheticInfo { get; set; }
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}
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}
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@@ -0,0 +1,118 @@
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using LeafWeb.Core.Parsers;
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using LeafWeb.Core.Utility;
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namespace LeafWeb.Core.Models
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{
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/// <summary>
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/// First model prediction is calculated at each sampling point.
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/// Then model prediction is calculated at many selected levels of intercelluar CO2 partial pressure
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/// levels under three limitation states to enable plotting curves.The same structure is then repeated for
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/// each fitting of the same curve with different parameters to be estimated and with different curves. Note
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/// that some common information about a curve is repeated for each data point to make the structure of the
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/// file as regular as possible.
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/// </summary>
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public class CntrlComparisonFittingInfo
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{
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/// <summary>
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/// the curve identifier, repeated for each point
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/// </summary>
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[ParseInfo(1)]
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public string CurveID { get; set; }
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/// <summary>
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/// whether or not chlorophyll fluorescence data are used for identifying the limitation states
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/// 0 = not used, 1 = used. (Currently this choice is still under evaluation and therefore ChlFlUse? = 0).
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/// </summary>
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[ParseInfo(2, alternateTitle: "ChlFlUse?")]
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public bool ChlFlUse {get; set; }
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/// <summary>
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/// whether or not the internal conductance (gi) is fitted for.
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/// 0 = not fitted and gi is either infinite or fixed at the value provided by the user.
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/// 1 = gi is estiamted, repeated for each point
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/// </summary>
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[ParseInfo(3, alternateTitle: "FitGi?")]
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public bool FitGi {get; set;}
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/// <summary>
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/// whether or not the chloroplastic CO2 partial pressure photocompensation point is
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/// fitted for. 0= not fitted, a prescribed value is used, repeated for each point
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/// </summary>
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[ParseInfo(4, alternateTitle: "FitGamma*?")]
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public bool FitGammaStar {get; set; }
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/// <summary>
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/// whether or not the apparent Michaelis - Menten constant Kco = Kc(1+O/Ko) is fitted for.
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/// 0= not fitted, a prescribed value is calculated from Kc, Ko and the oxygen partial pressure.
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/// 1= Fitted for, repeated for each point
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/// </summary>
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[ParseInfo(5, alternateTitle: "FitKco?")]
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public bool FitKco {get; set; }
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/// <summary>
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/// whether the dark respiration is fitted for. 0= not fitted for, a prescribed value is used.
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/// 1= fitted for. repeated for each point
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/// </summary>
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[ParseInfo(6, alternateTitle: "FitRd?")]
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public bool FitRd {get; set;}
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/// <summary>
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/// whether alpha (the non-returned fraction of the glycolate carbon
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/// recycled in the photorespiratory cycle) is fitted for.
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/// 0= not fitted for and alpha = 0
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/// 1= fitted for, repeated for each point
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/// </summary>
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[ParseInfo(7, alternateTitle: "FitAlpha?")]
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public bool FitAlpha {get; set;}
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/// <summary>
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/// the combination of limitation states present in the A/Ci dataset. Parameters
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/// are estimated for those limitation states that occur in the measured curve, repeated for each point
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/// Rubisco: Rubisco limitation(Vcmax, Kco)
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/// RuBP: RuBP regeneration limitation(J)
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/// Tpu: export limitation(TPU, alpha)
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/// </summary>
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[ParseInfo(8)]
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public string LimitCombina { get; set; }
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/// <summary>
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/// intercellular CO2 partial pressure
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/// </summary>
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[ParseInfo(9, units:"Pa")]
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public double PCO2i { get; set; }
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/// <summary>
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/// chloroplastic CO2 partial pressure corresponding to the PCO2i of a point.
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/// PCO2c=PCO2i-AnetCal/internal conductance
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/// </summary>
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[ParseInfo(10, units:"Pa")]
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public double PCO2c { get; set; }
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/// <summary>
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/// measured net assimilation rate
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/// </summary>
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[ParseInfo(11, units: "umol/m2/s")]
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public double AnetMeas { get; set; }
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/// <summary>
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/// calculated net assimilation rate
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/// </summary>
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[ParseInfo(12, units: "umol/m2/s")]
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public double AnetCal { get; set; }
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// TODO: readme has weitedrms, data file has PCOiCal
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// weitedrms - (umol/m2/s), root mean square error of the fitting (weiting coefficient =1)
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[ParseInfo(13)]
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public double PCOiCal { get; set; }
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/// <summary>
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/// 1 = point limited by rubisco
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/// 2 = point limited by RuBP regeneration
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/// 3 = point limited by TPU
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/// </summary>
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[ParseInfo(14, units:"1,2,3")]
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public int PointLimitType { get; set; }
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public virtual CntrlComparison CntrlComparison { get; set; }
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}
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}
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@@ -0,0 +1,56 @@
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using LeafWeb.Core.Parsers;
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using LeafWeb.Core.Utility;
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namespace LeafWeb.Core.Models
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{
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/// <summary>
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/// The second section gives photosynthesis for each of the three limitation states at selected values of intercellular
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/// partial pressure.Note that the corresponding values of chloraplastic CO2 partial pressure depend on the limitation state.
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/// </summary>
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public class CntrlComparisonPhotosyntheticInfo
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{
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/// <summary>
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/// intercellular CO2 partial pressure
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/// </summary>
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[ParseInfo(1, units:"Pa")]
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public double CO2i { get; set; }
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/// <summary>
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/// Chloraplastic CO2 partial pressure for Rubisco limited photosynthesis
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/// </summary>
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[ParseInfo(2, units: "Pa")]
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public double CO2cc { get; set; }
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/// <summary>
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/// Rubisco-limited net assimilation rate calculated with the optimized parameters
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/// </summary>
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[ParseInfo(3, units: "umol/m2/s")]
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public double Ac { get; set; }
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/// <summary>
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/// Chloraplastic CO2 partial pressure for RuBP regeneration limited photosynthesis
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/// </summary>
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[ParseInfo(4, units:"Pa")]
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public double CO2cj { get; set; }
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/// <summary>
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/// RuBP regeneration-limited net assimilation rate calculated with estimated parameters
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/// </summary>
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[ParseInfo(5, units: "umol/m2/s")]
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public double Aj { get; set; }
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/// <summary>
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/// Chloraplastic CO2 partial pressure for export limited photosynthesis
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/// </summary>
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[ParseInfo(6, units: "Pa")]
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public double CO2ct { get; set; }
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/// <summary>
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/// TPU-limited net assimilation rate calculated with estimated parameters
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/// </summary>
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[ParseInfo(7, units: "umol/m2/s")]
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public double At { get; set; }
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public virtual CntrlComparison CntrlComparison { get; set; }
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}
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}
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@@ -1,59 +0,0 @@
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using System;
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using System.IO;
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namespace LeafWeb.Core.Models
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{
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[Serializable]
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public class CurveData
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{
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private readonly string _curveId;
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private readonly CurveParamSet _paramSet1;
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private readonly CurveParamSet _paramSet2;
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private readonly CurveParamSet _paramSet3;
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private readonly CurveParamSet _paramSet4;
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public CurveData(StreamReader sr, ref string errMsg, ref int lineNbr)
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{
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// For each curve in the output file there are four sets of data.
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_paramSet1 = new CurveParamSet(sr, ref errMsg, ref lineNbr, ref _curveId);
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if (errMsg.Length > 0)
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return;
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_paramSet2 = new CurveParamSet(sr, ref errMsg, ref lineNbr, ref _curveId);
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if (errMsg.Length > 0)
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return;
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_paramSet3 = new CurveParamSet(sr, ref errMsg, ref lineNbr, ref _curveId);
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if (errMsg.Length > 0)
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return;
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_paramSet4 = new CurveParamSet(sr, ref errMsg, ref lineNbr, ref _curveId);
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}
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public string GetCurveId()
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{
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return _curveId;
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}
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public CurveParamSet CndctFixedCmpPntFixedParams()
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{
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return _paramSet1;
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}
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public CurveParamSet CndctFixedCmpPntEstimatedParams()
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{
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return _paramSet2;
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}
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public CurveParamSet CndctEstimatedCmpPntFixedParams()
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{
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return _paramSet3;
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}
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public CurveParamSet CndctEstimatedCmpPntEstimatedParams()
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{
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return _paramSet4;
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}
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}
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}
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@@ -1,238 +0,0 @@
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using System;
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using System.Collections.Generic;
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using System.IO;
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using System.Text;
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namespace LeafWeb.Core.Models
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{
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[Serializable]
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public class CurveParamSet
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{
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private readonly List<XyPoint> _anetMeasChloro1Data; // y=AnetMeas column, x=PCO2c, for PointLimitType=1
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private readonly List<XyPoint> _anetMeasChloro2Data; // y=AnetMeas column, x=PCO2c, for PointLimitType=2
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private readonly List<XyPoint> _anetMeasChloro3Data; // y=AnetMeas column, x=PCO2c, for PointLimitType=3
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private readonly List<XyPoint> _anetMeasInter1Data; // y=AnetMeas column, x=PCO2i, for PointLimitType=1
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private readonly List<XyPoint> _anetMeasInter2Data; // y=AnetMeas column, x=PCO2i, for PointLimitType=2
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private readonly List<XyPoint> _anetMeasInter3Data; // y=AnetMeas column, x=PCO2i, for PointLimitType=3
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private readonly List<XyPoint> _acChloroData; // y=Ac column, x=CO2cc column
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private readonly List<XyPoint> _ajChloroData; // y=Aj column, x=CO2cj column
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private readonly List<XyPoint> _atChloroData; // y=At column, x=CO2ct column
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private readonly List<XyPoint> _acInterData; // y=Ac column, x=CO2i column
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private readonly List<XyPoint> _ajInterData; // y=Aj column, x=CO2i column
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private readonly List<XyPoint> _atInterData; // y=At column, x=CO2i column
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public CurveParamSet()
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{
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}
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public CurveParamSet(StreamReader sr, ref String errMsg, ref int lineNbr, ref String curveId)
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{
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bool curveIdSet = false, doneWithAnet = false;
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String line;
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var errorMsg = new StringBuilder("");
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List<string> phrases;
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XyPoint xyPoint1;
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_anetMeasChloro1Data = new List<XyPoint>();
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_anetMeasChloro2Data = new List<XyPoint>();
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_anetMeasChloro3Data = new List<XyPoint>();
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_anetMeasInter1Data = new List<XyPoint>();
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_anetMeasInter2Data = new List<XyPoint>();
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_anetMeasInter3Data = new List<XyPoint>();
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_acChloroData = new List<XyPoint>();
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_ajChloroData = new List<XyPoint>();
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_atChloroData = new List<XyPoint>();
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_acInterData = new List<XyPoint>();
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_ajInterData = new List<XyPoint>();
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_atInterData = new List<XyPoint>();
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while (!doneWithAnet)
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{
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lineNbr++;
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line = sr.ReadLine();
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if (line == null)
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{
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errorMsg.Append("Unexpected end-of-file at line " + lineNbr);
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sr.Close();
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errMsg = errorMsg.ToString();
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return;
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}
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phrases = SplitCsvLine(line);
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String firstField = phrases[0];
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if (firstField.Equals("CO2i"))
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{
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doneWithAnet = true;
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}
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else
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{
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// The fields on the line:
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// Column Name
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// 0 CurveID
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// 1 ChlFlUse
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// 2 FitGi
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// 3 FitGamma
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// 4 FitKco
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// 5 FitRd
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// 6 FitAlpha
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// 7 LimitCombina
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// 8 PCO2i
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// 9 PCO2c
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// 10 AnetMeas
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// 11 AnetCal
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// 12 weitedrms
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// 13 PointLimitType
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if (!curveIdSet)
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{
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curveId = firstField;
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curveIdSet = true;
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}
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xyPoint1 = new XyPoint(phrases[9], phrases[10]); // AnetMeas(y), PCO2c(x)
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var xyPoint2 = new XyPoint(phrases[8], phrases[10]);
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var pointLimitType = Int32.Parse(phrases[13]);
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switch (pointLimitType)
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{
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case 1:
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_anetMeasChloro1Data.Add(xyPoint1);
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_anetMeasInter1Data.Add(xyPoint2);
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break;
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case 2:
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_anetMeasChloro2Data.Add(xyPoint1);
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_anetMeasInter2Data.Add(xyPoint2);
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break;
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case 3:
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_anetMeasChloro3Data.Add(xyPoint1);
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_anetMeasInter3Data.Add(xyPoint2);
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break;
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}
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}
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}
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// The next set of lines will have three pairs of x,y-coordinates to save.
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// A blank line signals the end of the data.
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var moreData = true;
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while (moreData)
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{
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// The fields on the line:
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// Column Name
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// 0 CO2i
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// 1 CO2cc
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// 2 Ac
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// 3 CO2cj
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// 4 Aj
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// 5 CO2ct
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// 6 At
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lineNbr++;
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line = sr.ReadLine();
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if (line == null)
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{
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errorMsg.Append("Unexpected end-of-file at line " + lineNbr);
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sr.Close();
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errMsg = errorMsg.ToString();
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return;
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}
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if (line.Length == 0)
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moreData = false;
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else
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{
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phrases = SplitCsvLine(line);
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xyPoint1 = new XyPoint(phrases[1],phrases[2]); // Ac(y),CO2cc(x)
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if (xyPoint1.YIsInRange(-20.0, 50.0))
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_acChloroData.Add(xyPoint1);
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xyPoint1 = new XyPoint(phrases[3], phrases[4]); // Aj(y),CO2cj(x)
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if (xyPoint1.YIsInRange(-20.0, 50.0))
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_ajChloroData.Add(xyPoint1);
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xyPoint1 = new XyPoint(phrases[5], phrases[6]); // At(y),CO2ct(x)
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if (xyPoint1.YIsInRange(-20.0, 50.0))
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_atChloroData.Add(xyPoint1);
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xyPoint1 = new XyPoint(phrases[0], phrases[2]); // Ac(y),CO2i(x)
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if (xyPoint1.YIsInRange(-20.0, 50.0))
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_acInterData.Add(xyPoint1);
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xyPoint1 = new XyPoint(phrases[0], phrases[4]); // Aj(y),CO2i(x)
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if (xyPoint1.YIsInRange(-20.0, 50.0))
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_ajInterData.Add(xyPoint1);
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xyPoint1 = new XyPoint(phrases[0], phrases[6]); // At(y),CO2i(x)
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if (xyPoint1.YIsInRange(-20.0, 50.0))
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_atInterData.Add(xyPoint1);
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}
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}
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}
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/// <summary>
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||||
/// This method assumes that the argument is a comma-, blank-, or
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||||
/// tab-separated set of strings. It returns an ArrayList of those
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||||
/// quantities. Consecutive commas will be returned as an empty string,
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||||
/// but all empty strings at the end of the line will be thrown away.
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||||
/// </summary>
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||||
/// <param name="line"></param>
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||||
/// <returns></returns>
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private static List<string> SplitCsvLine(String line)
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||||
{
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||||
int i;
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var separator = new [] {',', ' ', '\t'};
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||||
var phrases = line.Split(separator);
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||||
//int lastNonBlank = -1;
|
||||
var retPhrases = new List<string>();
|
||||
for (i = 0; i < phrases.Length; i++)
|
||||
{
|
||||
var phrase = phrases[i].Trim();
|
||||
if (phrase.Length > 0)
|
||||
// lastNonBlank = i;
|
||||
retPhrases.Add(phrase);
|
||||
}
|
||||
|
||||
return retPhrases;
|
||||
}
|
||||
|
||||
public List<List<XyPoint>> GetAnetMeasData()
|
||||
{
|
||||
var list = new List<List<XyPoint>>
|
||||
{
|
||||
_anetMeasChloro1Data,
|
||||
_anetMeasChloro2Data,
|
||||
_anetMeasChloro3Data,
|
||||
_anetMeasInter1Data,
|
||||
_anetMeasInter2Data,
|
||||
_anetMeasInter3Data
|
||||
};
|
||||
|
||||
return list;
|
||||
}
|
||||
|
||||
public List<XyPoint> GetAcChloroData()
|
||||
{
|
||||
return _acChloroData;
|
||||
}
|
||||
|
||||
public List<XyPoint> GetAjChloroData()
|
||||
{
|
||||
return _ajChloroData;
|
||||
}
|
||||
|
||||
public List<XyPoint> GetAtChloroData()
|
||||
{
|
||||
return _atChloroData;
|
||||
}
|
||||
|
||||
public List<XyPoint> GetAcInterData()
|
||||
{
|
||||
return _acInterData;
|
||||
}
|
||||
|
||||
public List<XyPoint> GetAjInterData()
|
||||
{
|
||||
return _ajInterData;
|
||||
}
|
||||
|
||||
public List<XyPoint> GetAtInterData()
|
||||
{
|
||||
return _atInterData;
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -1,6 +1,7 @@
|
||||
using System.Collections.Generic;
|
||||
using System.ComponentModel.DataAnnotations;
|
||||
using LeafWeb.Core.Services;
|
||||
using LeafWeb.Core.Parsers;
|
||||
using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Models
|
||||
{
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
using System.ComponentModel.DataAnnotations;
|
||||
using LeafWeb.Core.Services;
|
||||
using LeafWeb.Core.Parsers;
|
||||
using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Models
|
||||
{
|
||||
|
||||
@@ -1,4 +1,5 @@
|
||||
using LeafWeb.Core.Services;
|
||||
using LeafWeb.Core.Parsers;
|
||||
using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Models
|
||||
{
|
||||
|
||||
@@ -1,4 +1,5 @@
|
||||
using LeafWeb.Core.Services;
|
||||
using LeafWeb.Core.Parsers;
|
||||
using LeafWeb.Core.Utility;
|
||||
|
||||
namespace LeafWeb.Core.Models
|
||||
{
|
||||
|
||||
@@ -1,23 +0,0 @@
|
||||
using System;
|
||||
|
||||
namespace LeafWeb.Core.Models
|
||||
{
|
||||
[Serializable]
|
||||
public class XyPoint
|
||||
{
|
||||
public XyPoint(String x, String y)
|
||||
{
|
||||
X = Double.Parse(x);
|
||||
Y = Double.Parse(y);
|
||||
}
|
||||
|
||||
public double X { get; private set; }
|
||||
|
||||
public double Y { get; private set; }
|
||||
|
||||
public bool YIsInRange(double lowEnd, double highEnd)
|
||||
{
|
||||
return (Y >= lowEnd) && (Y <= highEnd);
|
||||
}
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user