protected static speciesattrs species_Attrs = null;//Pointer to an attached set of species Attributes.
//Constructor. This constructor can only be used on the first creation
//instance of class species. It sets the number of different varieties of species in the model.
public species(uint n)
{
if (numSpec != 0)
{
throw new Exception("SPECIES::SPECIES(int)-> Number of species may only be set once at construction.");
}
all_species = new specie[n];
for (int i = 0; i < n; i++)
{
all_species[i] = new specie(i);
}
numSpec = n;
currentSpec = 0;
}
//start killing trees gradually at the 80 % longevity until they reach their longevity
// modified version of function : void SUCCESSION::kill(SPECIE *s, SPECIESATTR *sa)
public static void KillTrees(uint local_r, uint local_c)
{
site local_site = gl_sites[local_r, local_c];
for (int k = 1; k <= specAtNum; ++k)//sites.specNum
{
int longev = gl_spe_Attrs[k].Longevity;
int numYears = longev / 5;
float chanceMod = 0.8f / (numYears + 0.00000001f);
float chanceDeath = 0.2f;
int m_beg = (longev - numYears) / gl_sites.SuccessionTimeStep;
int m_end = longev / gl_sites.SuccessionTimeStep;
specie local_specie = local_site.SpecieIndex(k);
for (int m = m_beg; m <= m_end; m++)
{
int tmpTreeNum = (int)local_specie.getTreeNum(m, k);
int tmpMortality = 0;
if (tmpTreeNum > 0)
{
float local_threshold = chanceDeath * gl_sites.SuccessionTimeStep / 10;
for (int x = 1; x <= tmpTreeNum; x++)
{
if (system1.frand() < local_threshold)
{
tmpMortality++;
}
}
local_specie.setTreeNum(m, k, Math.Max(0, tmpTreeNum - tmpMortality));
}
chanceDeath += chanceMod;
}
}
}
//Constructor. Should be used on all instance constructions other than the
//first. This may be used on the first instance of construction but should
//be followed by a call to setNumber before the second construction instance.
public species()
{
if (numSpec == 0)
{
all_species = null;
currentSpec = 0;
}
else
{
all_species = new specie[numSpec];
currentSpec = 0;
for (int i = 0; i < numSpec; i++)
{
all_species[i] = new specie(i);
all_species[i].AGELISTAllocateVector(i);
}
}
}
public void copy(specie[] in_all_species, uint in_numSpec)
{
if (in_all_species == null)
{
return;
}
numSpec = in_numSpec;
all_species = new specie[numSpec];
for (int i = 0; i < numSpec; i++)
{
all_species[i] = new specie(i);
all_species[i].copy(in_all_species[i]);
}
currentSpec = 0;
}
public void copy(specie in_specie)
{
if (in_specie == null)
{
return;
}
vegPropagules = in_specie.vegPropagules;
disPropagules = in_specie.disPropagules;
availableSeed = in_specie.availableSeed;
treesFromVeg = in_specie.treesFromVeg;
matureTree = in_specie.MatureTree;
index = in_specie.index;
base.copy(in_specie.agevector);
}
//This will perform a reclassification based upon the oldest cohort upon a landis stand.
//The cohorts will be scaled into 16 age classes.
public static void ageReclass(map8 m)
{
m.dim(snr, snc);
m.rename("Age class representation");
for (uint j = 1; j < map8.MapmaxValue; j++)
{
m.assignLeg(j, "");
}
string str;
//J.Yang hard coding changing itr*sites.TimeStep to itr
//J.Yang maxLeg is defined as 256 in map8.h, therefore, maximum age cohorts it can output is 254
for (uint i = 1; i < map8.MaxValueforLegend - 4; i++)
{
str = string.Format("{0: } - {1: } yr", (i - 1) * time_step + 1, i * time_step);
m.assignLeg(i, str);
}
m.assignLeg(0, "NoSpecies");
m.assignLeg(map8.MaxValueforLegend - 1, "N/A");
m.assignLeg(map8.MaxValueforLegend - 2, "Water");
m.assignLeg(map8.MaxValueforLegend - 3, "NonForest");
str = string.Format(" >{0: } yr", (map8.MaxValueforLegend - 4 - 1) * time_step);
m.assignLeg(map8.MaxValueforLegend - 4, str);
for (uint i = snr; i >= 1; i--)
{
for (uint j = 1; j <= snc; j++)
{
if (PlugIn.gl_sites.locateLanduPt(i, j).active())
{
m[i, j] = 0;
uint myage = 0;
site local_site = PlugIn.gl_sites[i, j];
specie s = local_site.first();
while (s != null)
{
uint temp = s.oldest();
if (temp > myage)
{
myage = temp;
}
s = local_site.next();
}
m[i, j] = (ushort)(myage / time_step);
}
else if (PlugIn.gl_sites.locateLanduPt(i, j).lowland())
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 3);
}
else if (PlugIn.gl_sites.locateLanduPt(i, j).water())
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 2);
}
else
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 1);
}
}
}
}
//This will faciliate age output at 10 year step for species specified in species age index file.
//This will output age at 10 year step for each specified species.
//The cohorts can be up to 50 age classes, 0-500 years.
public static void speciesAgeMap(map8 m, string ageFile)
{
int curSp = PlugIn.gl_spe_Attrs.current(ageFile);
m.dim(snr, snc);
m.rename(ageFile);
string str;
for (uint i = 1; i < map8.maxLeg - 4; i++)
{
str = string.Format("{0: } - {1: } yr", (i - 1) * time_step + 1, i * time_step);
m.assignLeg(i, str);
}
m.assignLeg(0, "NotPresent");
m.assignLeg(map8.MaxValueforLegend - 1, "N/A");
m.assignLeg(map8.MaxValueforLegend - 2, "Water");
m.assignLeg(map8.MaxValueforLegend - 3, "NonForest");
str = string.Format(" >{0} yr", (map8.maxLeg - 4 - 1) * time_step);
m.assignLeg(map8.MaxValueforLegend - 4, str);
for (uint i = snr; i >= 1; i--)
{
for (uint j = 1; j <= snc; j++)
{
if (PlugIn.gl_sites.locateLanduPt(i, j) == null)
{
throw new Exception("Invalid landunit error\n");
}
if (PlugIn.gl_sites.locateLanduPt(i, j).active())
{
m[i, j] = 0; //where species not presents
if (PlugIn.gl_sites[i, j] == null)
{
throw new Exception("No site\n");
}
specie s = PlugIn.gl_sites[i, j].current(curSp);
if (s == null)
{
Console.WriteLine("{0}\n", curSp);
throw new Exception("No Species\n");
}
if (s.query())
{
m[i, j] = (ushort)(s.oldest() / time_step); //compare ageReclass which uses +3 there???
if (m[i, j] > map8.MaxValueforLegend - 4) //maximum longevity is 640 years// Notice 66 means 640 years
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 4);
}
}
}
else if (PlugIn.gl_sites.locateLanduPt(i, j).water())
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 2);
}
else if (PlugIn.gl_sites.locateLanduPt(i, j).lowland())
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 3);
}
else
{
m[i, j] = (ushort)(map8.MaxValueforLegend - 1);
}
}
}
}
//This will reclassify a singular site. M is the number of possible output classes.
private int reclassifySite(site site_in, int m)
{
float[] sval = new float[MAX_RECLASS];
specie local_specie = site_in.first();
int j = 1;
while (local_specie != null)
{
float c = (float)local_specie.oldest() / maximum[j - 1];
if (c > 1.0)
{
c = 1.0f;
}
for (int i = 1; i <= m; i++)
{
if (BOOL[i, j] != 0)
{
if (BOOL[i, j] > 0)
{
sval[i] += c;
}
else
{
sval[i] -= c;
}
if (sval[i] != 0)
{
if (sval[i] > 1.0)
{
sval[i] = 1.0f;
}
if (sval[i] < 0.0)
{
sval[i] = 0.0f;
}
}
}
}
j++;
local_specie = site_in.next();
}
int mx = 0;
float mxVal = 0.0f;
for (int i = 1; i <= m; i++)
{
if (sval[i] > mxVal)
{
mxVal = sval[i];
mx = i;
}
}
if (mxVal > 0.0)
{
return(mx);
}
else
{
return(m + 1);
}
}
//This will calculate the reclassification value given a specie list for a site.
private int reclassificationValue(specie s)
{
return(s.number());
}
//This will reclassify sites from user defined class file and the existing age
//maps. Class file is a file containing site descriptions for a set of class.
//Age maps involved in the reclassification need to be created before.
public static void reclassify(int timeStep, string[] ageMaps)
{
uint specAtNum = PlugIn.gl_spe_Attrs.NumAttrs;
uint yDim = PlugIn.gl_sites.numRows;
uint xDim = PlugIn.gl_sites.numColumns;
for (int i = 0; i < specAtNum; i++)
{
string str = ageMaps[i] + ".age";
string speciesName;
//read species name from ageIndex file
using (StreamReader inAgeIndex = new StreamReader(str))
{
speciesName = system1.read_string(inAgeIndex);
}
int curSp = PlugIn.gl_spe_Attrs.current(speciesName);
//read age map file from output directory
str = PlugIn.gl_param.OutputDir + "/" + ageMaps[i] + timeStep.ToString() + ".gis";
using (BinaryReader inAgeMap = new BinaryReader(File.Open(str, FileMode.Open)))
{
byte[] dest = new byte[128];
inAgeMap.Read(dest, 0, 128);
// read inAgeMap
for (uint k = yDim; k > 0; k--)
{
for (uint j = 1; j <= xDim; j++)
{
int coverType = inAgeMap.Read();
if (coverType == 255) //species absence
{
specie s = PlugIn.gl_sites[k, j].current(curSp);
s.clear();
}
else if (coverType >= 3) //0-empty 1-water 2-nonforest
{
specie s = PlugIn.gl_sites[k, j].current(curSp);
s.clear();
s.set((coverType - 2) * PlugIn.gl_sites.SuccessionTimeStep);
}
} //end for
} //end for
} //end using
} //end for
}
