def removeOverlaps(self): if not self.allowOverlaps: theGarden=self if theGarden.showProgressBar: print "***Removing overlapping objects***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 for obj in theGarden.soil[:]: ###seeds and or stems that overlap are violating physics. ##Rules about overlapping objects: #####1.) If 2 objects overlap, the more massive object remains. #####2.) If 2 seeds overlap and they have the same mass, the oldest seed remains. objectList=theGarden.checkForOverlap(obj) for overlappingObject in objectList: if obj.massTotal>overlappingObject.massTotal: overlappingObject.causeOfDeath="crushed" theGarden.kill(overlappingObject) break elif obj.massTotal<overlappingObject.massTotal: obj.causeOfDeath="crushed" theGarden.kill(obj) break elif obj.massTotal==overlappingObject.massTotal: if obj.timePlanted>overlappingObject.timePlanted: obj.causeOfDeath="overlap violation" theGarden.kill(obj) break else: obj.causeOfDeath="overlap violation" theGarden.kill(overlappingObject) break if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def removeOverlaps(self):
if not self.allowOverlaps:
theGarden = self
if theGarden.showProgressBar:
print "***Removing overlapping objects***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
for obj in theGarden.soil[:]:
###seeds and or stems that overlap are violating physics.
##Rules about overlapping objects:
#####1.) If 2 objects overlap, the more massive object remains.
#####2.) If 2 seeds overlap and they have the same mass, the oldest seed remains.
objectList = theGarden.checkForOverlap(obj)
for overlappingObject in objectList:
if obj.massTotal > overlappingObject.massTotal:
overlappingObject.causeOfDeath = "crushed"
theGarden.kill(overlappingObject)
break
elif obj.massTotal < overlappingObject.massTotal:
obj.causeOfDeath = "crushed"
theGarden.kill(obj)
break
elif obj.massTotal == overlappingObject.massTotal:
if obj.timePlanted > overlappingObject.timePlanted:
obj.causeOfDeath = "overlap violation"
theGarden.kill(obj)
break
else:
obj.causeOfDeath = "overlap violation"
theGarden.kill(overlappingObject)
break
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def checkDistanceMortality(self):
if self.allowDistanceFromMother and self.janzenConnell > 0.0:
theGarden = self
if theGarden.showProgressBar:
print "***Checking for mortality due to proximity to mother...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
#print "Name : Distance : Chance"
for obj in theGarden.soil[:]:
if not obj.isSeed:
twoPi = 2.0 * 3.14
stddev = self.janzenConnell
theAvg = 0.0
theDistance = geometry_utils.distBetweenPoints(
obj.motherPlant.x, obj.motherPlant.y, obj.x, obj.y)
if theDistance > 0.0:
theExponent = -(((theDistance - theAvg)**2.0) /
((2.0 * stddev)**2.0))
theDeathChance = ((1 / (stddev * (twoPi**0.5))) *
2.71)**theExponent
#print "%s : %s :%s" % (obj.name, theDistance, theDeathChance)
tooBad = random.random()
if tooBad < theDeathChance:
obj.causeOfDeath = "experimental death due to distance from mother"
theGarden.kill(obj)
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def checkSenescence(self): if self.allowSlowGrowthDeath: theGarden=self if theGarden.showProgressBar: print "***Checking for too slow growth...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 for obj in theGarden.soil[:]: if not obj.isSeed and obj.maxAvgHeightGrowthRate>0.0: #only look at growth if the object is a plant, not a seed. fractOfMaxHeightGrowth=obj.avgHeightGrowthRate/obj.maxAvgHeightGrowthRate if obj.randomSlowGrowth>fractOfMaxHeightGrowth or theGarden.randomSlowGrowth>fractOfMaxHeightGrowth: #the garden defines a value at which plants will start to stochastically die #each species also defines a value at which that species will start to stochastically die #this way the garden can have a 'bad' environment that triggers problems earlier than a species might define #to simulate a virus or something. tooBad=random.random() theRegion=theGarden if len(obj.subregion)>0: #if there are multiple regions, only the most recently made one is used. theRegion=obj.subregion[-1] chanceOfDeath=theRegion.randomDeath if tooBad<=chanceOfDeath: obj.causeOfDeath="growth too slow" theGarden.kill(obj) if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def checkSenescence(self):
if self.allowSlowGrowthDeath:
theGarden = self
if theGarden.showProgressBar:
print "***Checking for too slow growth...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
for obj in theGarden.soil[:]:
if not obj.isSeed and obj.maxAvgHeightGrowthRate > 0.0: #only look at growth if the object is a plant, not a seed.
fractOfMaxHeightGrowth = obj.avgHeightGrowthRate / obj.maxAvgHeightGrowthRate
if obj.randomSlowGrowth > fractOfMaxHeightGrowth or theGarden.randomSlowGrowth > fractOfMaxHeightGrowth:
#the garden defines a value at which plants will start to stochastically die
#each species also defines a value at which that species will start to stochastically die
#this way the garden can have a 'bad' environment that triggers problems earlier than a species might define
#to simulate a virus or something.
tooBad = random.random()
theRegion = theGarden
if len(obj.subregion) > 0:
#if there are multiple regions, only the most recently made one is used.
theRegion = obj.subregion[-1]
chanceOfDeath = theRegion.randomDeath
if tooBad <= chanceOfDeath:
obj.causeOfDeath = "growth too slow"
theGarden.kill(obj)
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def removeEulerGreenhillViolaters(self): if not self.allowEulerGreenhillViolations: theGarden=self if theGarden.showProgressBar: print "***Checking for Greenhill-Euler violations...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 for obj in theGarden.soil[:]: if theGarden.checkEulerGreenhillViolation(obj)==1: obj.causeOfDeath="violated Euler-Greenhill" theGarden.kill(obj) if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def removeEulerGreenhillViolaters(self):
if not self.allowEulerGreenhillViolations:
theGarden = self
if theGarden.showProgressBar:
print "***Checking for Greenhill-Euler violations...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
for obj in theGarden.soil[:]:
if theGarden.checkEulerGreenhillViolation(obj) == 1:
obj.causeOfDeath = "violated Euler-Greenhill"
theGarden.kill(obj)
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def removeOffWorldViolaters(self): if not self.allowOffWorld: theGarden=self if theGarden.showProgressBar: print "***Removing plants growing off world...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 ###see if plants or seeds extend over the edge of the world ### if so, kill them off for obj in theGarden.soil[:]: if theGarden.outOfBounds(obj)==1: obj.causeOfDeath="stem off world" theGarden.kill(obj) if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def removeOffWorldViolaters(self):
if not self.allowOffWorld:
theGarden = self
if theGarden.showProgressBar:
print "***Removing plants growing off world...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
###see if plants or seeds extend over the edge of the world
### if so, kill them off
for obj in theGarden.soil[:]:
if theGarden.outOfBounds(obj) == 1:
obj.causeOfDeath = "stem off world"
theGarden.kill(obj)
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def causeRandomDeath(self): if self.allowRandomDeath: theGarden=self if theGarden.showProgressBar: print "***A time to die...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 for obj in theGarden.soil[:]: tooBad=random.random() theRegion=theGarden if len(obj.subregion)>0: #if there are multiple regions, only the most recently made one is used. theRegion=obj.subregion[-1] if tooBad<theRegion.randomDeath: obj.causeOfDeath="random death" theGarden.kill(obj) if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def causeRandomDeath(self):
if self.allowRandomDeath:
theGarden = self
if theGarden.showProgressBar:
print "***A time to die...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
for obj in theGarden.soil[:]:
tooBad = random.random()
theRegion = theGarden
if len(obj.subregion) > 0:
#if there are multiple regions, only the most recently made one is used.
theRegion = obj.subregion[-1]
if tooBad < theRegion.randomDeath:
obj.causeOfDeath = "random death"
theGarden.kill(obj)
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def checkDistanceMortality(self): if self.allowDistanceFromMother: theGarden=self if theGarden.showProgressBar: print "***Checking for mortality due to proximity to mother...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") #print "Name : Distance : Chance" for obj in theGarden.soil[:]: if not obj.isSeed: twoPi=2.0*3.14 stddev=0.9 theAvg=0.0 theDistance=geometry_utils.distBetweenPoints(obj.motherPlant.x, obj.motherPlant.y, obj.x, obj.y) if theDistance>0.0: theExponent=-(((theDistance-theAvg)**2.0)/((2.0*stddev)**2.0)) theDeathChance=((1/(stddev*(twoPi**0.5)))*2.71)**theExponent #print "%s : %s :%s" % (obj.name, theDistance, theDeathChance) tooBad=random.random() if tooBad<theDeathChance: obj.causeOfDeath="experimental death due to distance from mother" theGarden.kill(obj) if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def determineShade(theGarden):
if theGarden.showProgressBar:
print "***Generating lists of overlapping plants. This could take a while...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
###populate the overlap list
theIndex = 0
for plantOne in theGarden.soil:
if plantOne.isSeed == 0 or (plantOne.isSeed and
plantOne.minimumLightForGermination > 0.0):
plantOne.overlapList = []
plantOne.areaCovered = 0.0
plantOne.colourLeaf[2] = 1.0
###the following might be able to be used to speed things up
#for overlappingItem in plantOne.overlapList:
# if not overlappingItem in theGarden.soil or not overlappingItem.z>plantOne.z:
# ###make sure the overlapping item is still alive
# ###and that overlapping item is still taller
# plantOne.overlapList.remove(overlappingItem)
###need to insert something so tallest plant looks at all the other plants of exactly the same size
###if they are the same size and overlapping, they need to share shading
for plantTwo in range(theIndex):
plantTwo = theGarden.soil[plantTwo]
###is plant two overlapping you?
overlapStatus = geometry_utils.checkOverlap(
plantOne.x, plantOne.y, plantOne.r, plantTwo.x, plantTwo.y,
plantTwo.r)
if overlapStatus > 0:
if not plantTwo in plantOne.overlapList:
if not plantTwo == plantOne:
plantOne.overlapList.append(plantTwo)
###sort the overlap list by height of the plants. Ordered shortest to tallest
plantOne.overlapList = list_utils.sort_by_attr(
plantOne.overlapList, "heightStem")
###flip the list so it's ordered tallest to shortest
plantOne.overlapList.reverse()
theIndex = theIndex + 1
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
###take the overlap list and start dropping photons onto it.
if theGarden.showProgressBar:
print "***Determining shading. This could take a while...***"
theProgressBar = progressBarClass.progressbarClass(
len(theGarden.soil), "*")
i = 0
for plant in theGarden.soil:
if plant.isSeed == 0 or (plant.isSeed
and plant.minimumLightForGermination > 0.0):
fractionExposed = 1.0
if len(plant.subregion) > 0:
theRegion = plant.subregion[-1]
else:
theRegion = theGarden
if len(plant.overlapList) > 0:
thePlantAreaTotal = geometry_utils.areaCircle(plant.r)
if thePlantAreaTotal == 0.0:
print "name:%s r:%f isSeed:%i massSeed:%f massTotal:%f" % (
plant.name, plant.r, plant.isSeed, plant.massSeed,
plant.massTotal)
if len(
plant.overlapList
) == 1: ###if you are covered by just 1 other, do a direct calc
overPlant = plant.overlapList[0]
areaCovered = geometry_utils.areaOverlappingCircles(
plant.x, plant.y, plant.r, overPlant.x, overPlant.y,
overPlant.r)
areaCovered = areaCovered - (areaCovered *
plantTwo.canopyTransmittance)
thePlantAreaExposed = thePlantAreaTotal - areaCovered
#plant.areaCovered=areaCovered
fractionExposed = thePlantAreaExposed / thePlantAreaTotal
#fractionExposed=fractionExposed*theGarden.lightIntensity #try and take into account overall world light intensity
fractionExposed = fractionExposed * theRegion.lightIntensity #try and take into account overall world light intensity
thePlantAreaExposed = thePlantAreaTotal * fractionExposed
plant.areaCovered = thePlantAreaTotal - thePlantAreaExposed
elif len(plant.overlapList
) > 1: ###if you are covered by 2, use monte-carlo
numbPhotons = int(thePlantAreaTotal)
if numbPhotons == 0:
numbPhotons = 1
numbPhotons = numbPhotons * 100
if numbPhotons > 750: #we don't need monster numbers
numbPhotons = 750
hitCount = 0
for photon in range(numbPhotons):
#####consider moving this to geometry_utils
###pick uniformly distributed point in a circle
randr = (random.random() * (plant.r - 0)
) + 0 #random between 0 and the radius
twoPi = math.pi * 2
randAngle = random.random() * twoPi
#randr =math.sqrt(randr) #if you don't use sqrt, you get clustering in the center
randr = randr**0.5 #if you don't use sqrt, you get clustering in the center
photonX = (randr * math.cos(randAngle)) + plant.x
photonY = (randr * math.sin(randAngle)) + plant.y
######
for overPlant in plant.overlapList:
if not photonX == "gone":
if geometry_utils.pointInsideCircle(
overPlant.x, overPlant.y, overPlant.r,
photonX, photonY):
randomValue = random.random()
if randomValue > overPlant.canopyTransmittance:
###these points are where the overlap is
photonX = "gone"
break
if not photonX == "gone":
hitCount = hitCount + 1
if numbPhotons == 0:
fractionExposed = 0.0
else:
fractionExposed = float(hitCount) / float(numbPhotons)
#fractionExposed=fractionExposed*theGarden.lightIntensity #try and take into account overall world light intensity
fractionExposed = fractionExposed * theRegion.lightIntensity #try and take into account overall world light intensity
thePlantAreaExposed = thePlantAreaTotal * fractionExposed
plant.areaCovered = thePlantAreaTotal - thePlantAreaExposed
else: #if you are not covered at all
thePlantAreaTotal = geometry_utils.areaCircle(plant.r)
fractionExposed = 1.0
#fractionExposed=fractionExposed*theGarden.lightIntensity #try and take into account overall world light intensity
fractionExposed = fractionExposed * theRegion.lightIntensity #try and take into account overall world light intensity
thePlantAreaExposed = thePlantAreaTotal * fractionExposed
plant.areaCovered = thePlantAreaTotal - thePlantAreaExposed
###now change the colour accordingly
plant.colourLeaf[2] = fractionExposed
if theGarden.showProgressBar:
i = i + 1
theProgressBar.update(i)
def main():
#why do only these need to be reminded they are global?
global simulationFile
global theWorldSize
global startPopulationSize
global seedPlacement
global sList
#Import Psyco if possible
try:
import psyco
psyco.log()
psyco.full()
except ImportError:
pass
CFDGtext=""
####################################
###experiments in importing events
import yaml
if os.path.exists(eventFile):
print "***Loading event file: %s***" % (eventFile)
theFile=open(eventFile)
eventData=yaml.load(theFile)
theFile.close
eventTimes=eventData.keys()
else:
eventTimes=[]
#####################################
if debug==1: print "***debug is on***"
theGarden= worldBasics.garden()
theGarden.platonicSeeds={}
theGarden.theRegions=[]
####
#########Check for multiple species. If none, use default
fileList=os.listdir("Species")
ymlList=[]
pythonList=[]
useDefaultYml=True
print "***Checking for species...***"
for file in fileList:
theExtension=os.path.splitext(file)[1]
if theExtension==".yml":
#add this file to the list of yaml files
ymlList.append(file)
useDefaultYml=False
elif theExtension==".py":
#this might be override info for a species
#add this file to the list of species python files
#this isn't implemented
pythonList.append(file)
fileList=[]
##########
if resumeSim==1 and not simulationFile=="":
simulationFile=open(simulationFile, 'r')
theGarden=pickle.load(simulationFile)
simulationFile.close()
theWorldSize=theGarden.theWorldSize
print "***Resuming Simulation: %s as %s***" % (theGarden.name, simulationName)
theGarden.name=simulationName
startPopulationSize=theGarden.numbPlants
##this should reload species data.
###Important if you want to compare runs
if reloadSpeciesData==1:
###fileLoc will be different for each species eventually
fileLoc="SERA_Data/Default_species.txt"
for item in theGarden.soil:
item.importPrefs(fileLoc)
else:
theGarden.makePlatonicSeedDict(ymlList, Species1)
print "***Species loaded.***"
theGarden.name=simulationName
theGarden.theWorldSize=theWorldSize
print "***Beginning Simulation: %s***" % (simulationName)
theGarden.showProgressBar=showProgressBar
print " World size: %ix%i" % (theWorldSize, theWorldSize)
print " Maximum population size will be: %i" % (maxPopulation)
print " and"
print " Running simulation for %i cycles" % (maxCycles)
print " (whichever comes first)"
print " Starting population size: %i" % (startPopulationSize)
if theGarden.carbonAllocationMethod==0:
print " Plants will allocate carbon to stem and leaf using methods defined by the species."
else:
print " All plants will allocate carbon to stem and leaf using method %i" % (theGarden.carbonAllocationMethod)
print ""
if produceGraphics==1:
print " Graphical output will be produced."
if theView==1:
print " Graphical output will be a bottom-up view."
elif theView==2:
print " Graphical output will be a top-down view."
elif theView==3:
print " Graphical output will be a side-view."
elif theView==12:
print " Graphical output will be a combination bottom-up and top-down view."
elif theView==21:
print " Graphical output will be a combination top-down and bottom-up view."
elif theView==23:
print " Graphical output will be a combined top-down and side view."
elif theView==13:
print " Graphical output will be a combined bottom-up and side view."
elif theView==123:
print " Graphical output will be a combination bottom-up, top-down and side view."
if produceVideo==1:
print " Graphical output will include a %s frame/second video." % (framesPerSecond)
###I think this is where to start the times to repeat bit
for x in range(timesToRepeat):
###make necessary directories
outputDirectory="Output-"+simulationName+"/"
outputDirectory=makeDirectory(outputDirectory)
if produceGraphics==1 or produceDXFGraphics==1:
outputGraphicsDirectory = outputDirectory +"Graphics/"
makeDirectory(outputGraphicsDirectory)
if produceDXFGraphics==1:
outputDXFGraphicsDirectory = outputGraphicsDirectory +"DXF/"
makeDirectory(outputDXFGraphicsDirectory)
####SUPER IMPORTANT!!!!
####DON'T USE SPACES IN DIR NAMES!
####COMMAND LINES HATE THAT SHIT
if theView==1:
outputGraphicsDirectory = outputGraphicsDirectory +"bottom-up/"
makeDirectory(outputGraphicsDirectory)
elif theView==2:
outputGraphicsDirectory = outputGraphicsDirectory +"top-down/"
makeDirectory(outputGraphicsDirectory)
elif theView==3:
outputGraphicsDirectory = outputGraphicsDirectory +"side/"
makeDirectory(outputGraphicsDirectory)
elif theView==12:
outputGraphicsDirectory = outputGraphicsDirectory +"combined-bottom-top/"
makeDirectory(outputGraphicsDirectory)
elif theView==21:
outputGraphicsDirectory = outputGraphicsDirectory +"combined-top-bottom/"
makeDirectory(outputGraphicsDirectory)
elif theView==13:
outputGraphicsDirectory = outputGraphicsDirectory +"combined-bottom-side/"
makeDirectory(outputGraphicsDirectory)
elif theView==23:
outputGraphicsDirectory = outputGraphicsDirectory +"combined-top-side/"
makeDirectory(outputGraphicsDirectory)
elif theView==123:
outputGraphicsDirectory = outputGraphicsDirectory +"combined-bottom-top-side/"
makeDirectory(outputGraphicsDirectory)
if not archive=="n":
saveDirectory = outputDirectory+"Save_points/"
makeDirectory(saveDirectory)
if not saveData=="n":
dataDirectory = outputDirectory+"Simulation_data/"
makeDirectory(dataDirectory)
makeDirectory(dataDirectory+"Seeds/")
makeDirectory(dataDirectory+"Plants/")
makeDirectory(dataDirectory+"Corpses/")
if resumeSim==0:
#2008.11.06 Moved a huge block of code related to placing seeds to vworldr.py
theGarden.placeSeed(seedPlacement, sList, startPopulationSize, useDefaultYml, ymlList)
if produceGraphics and CFDGtext=="":
CFDGtext=outputGraphics.initCFDGText(theGarden, theView, percentTimeStamp, 50.0)
#######
cycleNumber=0
print "\n***Running simulation.***"
if not showProgressBar and not runningInNodeBox:
theProgressBar= progressBarClass.progressbarClass(maxCycles,"*") #why -1? because index 0. So if total=100, 0-99.
#print "Cycle, plant age, Mass Stem, Mass Leaf, # Seeds, Mass all Seeds, Radius Stem, Radius Leaf, Height Plant, areaPhoto, new mass"
while (theGarden.numbPlants<=maxPopulation and cycleNumber<=maxCycles) and (theGarden.numbPlants+theGarden.numbSeeds)>0:
###################################################################################
####Experimental scripting event stuff #
if cycleNumber in eventTimes: #
for aItem in eventData[cycleNumber]: #
for aKey in aItem.keys(): #
if aKey=="Garden": #
if debug==1: print "debug: A garden related event has been triggered." #
theDict=aItem[aKey][0] #
gardenAttrs=theDict.keys() #
for theGardenAttr in gardenAttrs: #
setattr(theGarden, theGardenAttr, theDict[theGardenAttr]) #
gardenAttrs=""
elif aKey=="Killzone" or aKey=="Safezone":
if debug==1: print "debug: generation of a zone event has been triggered."
theDict=aItem[aKey][0] #
zoneAttrs=theDict.keys()
zoneX=float(theDict['x'])
zoneY=float(theDict['y'])
zoneSize=float(theDict['size'])
zoneShape=theDict['shape']
if zoneShape not in ['circle','square']:
print "***WARNING: improper zone shape defined. Defaulting to square.***"
zoneShape='square'
zoneTarget=theDict['target']
if zoneTarget not in ['all','plants','seeds']:
print "***WARNING: improper zone target defined. Defaulting to all.***"
zoneTarget='all'
if zoneShape=='circle':
killThese=[]
for theObject in theGarden.soil:
if theObject.isSeed:
r=theObject.radiusSeed
else:
r=theObject.radiusStem
theResult=geometry_utils.checkOverlap(theObject.x, theObject.y, r, zoneX, zoneY, zoneSize)
if theResult>0 and aKey=='Killzone':
if zoneTarget=='all' or (theObject.isSeed and zoneTarget=='seeds') or (not theObject.isSeed and zoneTarget=='plants'):
killThese.append(theObject)
elif aKey=='Safezone':
if theResult==0:
killThese.append(theObject)
elif theResult>0:
if (theObject.isSeed and zoneTarget=='plants') or (not theObject.isSeed and zoneTarget=='seeds'):
killThese.append(theObject)
for theObject in killThese:
theObject.causeOfDeath="zone"
theGarden.kill(theObject)
elif aKey=="Seed":
if debug==1: print "debug: A seeding related event has been triggered." #
theDict=aItem[aKey][0] #
seedingInfo=theDict.keys() #
for infoItem in seedingInfo:
if infoItem=="number" and not seedPlacement=="fromFile": startPopulationSize=theDict[infoItem]
if infoItem=="species":
sList=theDict[infoItem]
if sList=="random": sList=[]
if infoItem=="placement": seedPlacement=theDict[infoItem]
if seedPlacement=="hexagon": seedPlacement="hex" #just make sure it is consistant
if os.path.isfile(seedPlacement):
theFile=open(seedPlacement)
try:
sList=theFile.readlines()
finally:
theFile.close()
sList=checkSeedPlacementList(sList)
startPopulationSize=len(sList)
seedPlacement="fromFile"
if not seedPlacement=="fromFile" and not sList==[]:
newList=[]
for j in range(startPopulationSize):
newList.append(sList)
#print sList
sList=newList
newList=[]
#print sList
theGarden.placeSeed(seedPlacement, sList, startPopulationSize, useDefaultYml, ymlList)
elif aKey=="Region":
if debug: print "debug: Region event detected..."
theDict=aItem[aKey][0]
regionAttrs=theDict.keys()
theRegionName=str(theDict['name'])
if debug: print "debug: Region %s event detected." % (theRegionName)
regionNames=[]
for i in theGarden.theRegions:
regionNames.append(i.name)
if theRegionName in regionNames:
for j in theGarden.theRegions:
if j.name==theRegionName:
theRegion=j
break
for aAttr in regionAttrs:
if not getattr(theRegion,aAttr,"does not exist")==theDict[aAttr]:
if debug: print "debug: Region %s has had a change in one or more attributes." % (theRegionName)
updatePlants=True
break
#if (not theRegion.size==theDict["size"]) or (not theRegion.x==theDict["x"]) or (not theRegion.y==theDict["y"]) or (not theRegion.shape==theDict["shape"]):
# if debug:print "debug: a region has changed shape, size or location"
# updatePlants=True
##now just read in the values#
if debug: print "debug: Updating attributes for region %s." % (theRegionName)
for theRegionAttr in regionAttrs: #
setattr(theRegion, theRegionAttr, theDict[theRegionAttr]) #
if updatePlants:
if debug:print "debug: updating plants with changed region info"
for aPlant in theGarden.soil:
plantX=aPlant.x
plantY=aPlant.y
if theRegion.shape=='square':
inSubregion=geometry_utils.pointInsideSquare(theRegion.x, theRegion.y, theRegion.size, plantX, plantY)
elif theRegion.shape=='circle':
#size needs to be radius but region defines diameter
inSubregion=geometry_utils.pointInsideCircle(theRegion.x, theRegion.y, theRegion.size/2.0, plantX, plantY)
if inSubregion:
if not theRegion in aPlant.subregion:
aPlant.subregion.append(theRegion)
#print "\nX: %f Y: %f In region: %s" % (plantX, plantY, newRegion)
#print theRegion.size
else:
newRegion=worldBasics.garden()
newRegion.name=theRegionName
###these are default values###
newRegion.x=0.0 #
newRegion.y=0.0 #
newRegion.worldSize=1.0 #
newRegion.shape='square' #
##############################
##now just read in the values#
if debug: print "debug: Making attributes for region"
for theRegionAttr in regionAttrs: #
setattr(newRegion, theRegionAttr, theDict[theRegionAttr]) #
theGarden.theRegions.append(newRegion)
for aPlant in theGarden.soil:
plantX=aPlant.x
plantY=aPlant.y
if newRegion.shape=='square':
inSubregion=geometry_utils.pointInsideSquare(newRegion.x, newRegion.y, newRegion.size, plantX, plantY)
elif newRegion.shape=='circle':
#size needs to be radius but region defines diameter
inSubregion=geometry_utils.pointInsideCircle(newRegion.x, newRegion.y, newRegion.size/2.0, plantX, plantY)
if inSubregion:
if not newRegion in aPlant.subregion:
aPlant.subregion.append(newRegion)
#print "\nX: %f Y: %f In region: %s" % (plantX, plantY, newRegion)
newRegion=""
theDict=[]#just clear this to free up the memory
###################################################################################
theGarden.cycleNumber=cycleNumber
if not showProgressBar and not runningInNodeBox:
theProgressBar.update(cycleNumber)
#print "%i, %i, %f, %f, %i, %f, %f, %f, %f, %f, %f" % (cycleNumber-1, theGarden.soil[0].age, theGarden.soil[0].massStem, theGarden.soil[0].massLeaf, len(theGarden.soil[0].seedList), theGarden.soil[0].massSeedsTotal, theGarden.soil[0].radiusStem, theGarden.soil[0].radiusLeaf, theGarden.soil[0].heightStem+theGarden.soil[0].heightLeafMax, theGarden.soil[0].areaPhotosynthesis, theGarden.soil[0].massFixed)
###START OF SEEING CHANGES TO SPECIES FOLDER
#########Check for multiple species. If none, use default
fileList=os.listdir("Species")
#print fileList
#ymlList=[]
#print "***Checking for species...***"
#for file in fileList:
# theExtension=os.path.splitext(file)[1]
# if theExtension==".yml":
# #add this file to the list of yaml files
# ymlList.append(file)
# useDefaultYml=False
#fileList=[]
##########
if debug==1: print "number of plants: "+str(theGarden.numbPlants)
if debug==1: print "number of seeds: "+str(theGarden.numbSeeds)
#generate graphics if requested
if produceDXFGraphics:
theData=vdxfGraphics.makeDXF(theGarden)
theFileName= simulationName+str(cycleNumber)
vdxfGraphics.writeDXF(outputDXFGraphicsDirectory, theFileName, theData)
if produceGraphics:
theData=outputGraphics.makeCFDG(theView, CFDGtext, theGarden, cycleNumber)
if webOutput==0:
if theView==1:
cfdgFileName= simulationName +"-bottom-"+str(cycleNumber)
elif theView==2:
cfdgFileName= simulationName +"-top-"+str(cycleNumber)
elif theView==3:
cfdgFileName= simulationName +"-side-"+str(cycleNumber)
elif theView==12:
cfdgFileName= simulationName +"-bottom-top-"+str(cycleNumber)
elif theView==21:
cfdgFileName= simulationName +"-top-bottom-"+str(cycleNumber)
elif theView==13:
cfdgFileName= simulationName +"-bottom-side-"+str(cycleNumber)
elif theView==23:
cfdgFileName= simulationName +"-top-side-"+str(cycleNumber)
elif theView==123:
cfdgFileName= simulationName +"-bottom-top-side"+str(cycleNumber)
outputGraphics.writeCFDG(outputGraphicsDirectory, cfdgFileName, theData)
else:
cfdgFileName= simulationName
outputGraphics.writeCFDG(outputGraphicsDirectory, cfdgFileName, theData)
outputGraphics.outputPNGs(outputGraphicsDirectory, webDirectory)
#outputGraphics.deleteCFDGFiles(outputGraphicsDirectory)
###go through the soil list and germinate seed or grow plant
if theGarden.showProgressBar:
print"***Allowing plants a turn to grow***"
theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*")
theBar=0
for obj in theGarden.soil[:]:
if obj.isSeed:
obj.germinate(theGarden)
else:
obj.growPlant(theGarden)
if theGarden.showProgressBar:
theBar=theBar+1
theProgressBar.update(theBar)
###deal with violaters of basic physics
theGarden.causeRandomDeath()
theGarden.checkSenescence()
theGarden.removeOffWorldViolaters()
theGarden.removeEulerGreenhillViolaters()
theGarden.removeOverlaps()
###sort the garden.soil by height of the plants.Ordered shortest to tallest
theGarden.soil= list_utils.sort_by_attr(theGarden.soil, "heightStem")
###flip the list so it's ordered tallest to shortest
theGarden.soil.reverse()
###work out shading
worldBasics.determineShade(theGarden)
###Calculate the amount of carbon each plant will have to start the next turn
if theGarden.showProgressBar:
print "***Calculating new mass from photosynthesis***"
theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*")
i=0
for plant in theGarden.soil[:]:
if plant.isSeed==False:
plant.massFixed=plant.calcNewMassFromLeaf(theGarden)
if plant.massFixed==-1.0:
plant.causeOfDeath="lack of light"
theGarden.kill(plant)
else:
plant.massFixedRecord.append(plant.massFixed)
while len(plant.massFixedRecord)>plant.numYearsGrowthMemory:
plant.massFixedRecord.pop(0)
if theGarden.showProgressBar:
i=i+1
theProgressBar.update(i)
if archive=="a":
fileName=simulationName+'-'+str(cycleNumber)+'.pickle'
saveSimulationPoint(saveDirectory, fileName, theGarden)
if saveData=="a":
fileName=simulationName+'-'+str(cycleNumber)+'.csv'
saveDataPoint(dataDirectory, fileName, theGarden)
#print theGarden.deathNote
theGarden.deathNote=[]
cycleNumber= cycleNumber+1
###pause if you're making web graphic
#if webOutput==1:
# time.sleep(5)
if archive=="e":
fileName=simulationName+'-'+str(cycleNumber)+'.pickle'
saveSimulationPoint(saveDirectory, fileName, theGarden)
if saveData=="e":
fileName=simulationName+'-'+str(cycleNumber)+'.csv'
saveDataPoint(dataDirectory, fileName, theGarden)
if produceStats:
#print dataDirectory
theArgument="-n '%s' -fs" % (dataDirectory+"Seeds/")
print "***sending to Extract: %s" % (theArgument)
os.system("python SERA_Data/vextract.py %s" % (theArgument))
theArgument="-n '%s' -fs" % (dataDirectory+"Plants/")
print "***sending to Extract: %s" % (theArgument)
os.system("python SERA_Data/vextract.py %s" % (theArgument))
theArgument="-n '%s' -fs" % (dataDirectory+"Corpses/")
print "***sending to Extract: %s" % (theArgument)
os.system("python SERA_Data/vextract.py %s" % (theArgument))
###final graphics calls
if produceGraphics==1 and webOutput==0:
print "Producing PNG files..."
outputGraphics.outputPNGs(outputGraphicsDirectory, outputGraphicsDirectory)
if produceGraphics==1 and deleteCfdgFiles==1 and webOutput==0:
print "Deleting .cfdg files..."
outputGraphics.deleteCFDGFiles(outputGraphicsDirectory)
###only try and make a video if it is wanted and if pngs were made
if produceVideo and produceGraphics and webOutput==0:
print "Producing MOV file..."
outputGraphics.outputMOV(outputGraphicsDirectory, simulationName, framesPerSecond)
print "*****Simulation Complete*****"
#print theGarden.deathNote
#clear the values
theGarden.soil=[]
theGarden.deathNote=[]
theGarden.cycleNumber=0
for aRegion in theGarden.theRegions:
aRegion.size=0.0
def determineShade(theGarden): if theGarden.showProgressBar: print "***Generating lists of overlapping plants. This could take a while...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 ###populate the overlap list theIndex=0 for plantOne in theGarden.soil: if plantOne.isSeed==0 or (plantOne.isSeed and plantOne.minimumLightForGermination>0.0): plantOne.overlapList=[] plantOne.areaCovered=0.0 plantOne.colourLeaf[2]= 1.0 ###the following might be able to be used to speed things up #for overlappingItem in plantOne.overlapList: # if not overlappingItem in theGarden.soil or not overlappingItem.z>plantOne.z: # ###make sure the overlapping item is still alive # ###and that overlapping item is still taller # plantOne.overlapList.remove(overlappingItem) ###need to insert something so tallest plant looks at all the other plants of exactly the same size ###if they are the same size and overlapping, they need to share shading for plantTwo in range(theIndex): plantTwo=theGarden.soil[plantTwo] ###is plant two overlapping you? overlapStatus=geometry_utils.checkOverlap(plantOne.x, plantOne.y, plantOne.r, plantTwo.x, plantTwo.y, plantTwo.r) if overlapStatus>0: if not plantTwo in plantOne.overlapList: if not plantTwo==plantOne: plantOne.overlapList.append(plantTwo) ###sort the overlap list by height of the plants. Ordered shortest to tallest plantOne.overlapList = list_utils.sort_by_attr(plantOne.overlapList, "heightStem") ###flip the list so it's ordered tallest to shortest plantOne.overlapList.reverse() theIndex=theIndex+1 if theGarden.showProgressBar: i=i+1 theProgressBar.update(i) ###take the overlap list and start dropping photons onto it. if theGarden.showProgressBar: print "***Determining shading. This could take a while...***" theProgressBar= progressBarClass.progressbarClass(len(theGarden.soil),"*") i=0 for plant in theGarden.soil: if plant.isSeed==0 or (plant.isSeed and plant.minimumLightForGermination>0.0): fractionExposed=1.0 if len(plant.subregion)>0: theRegion=plant.subregion[-1] else: theRegion=theGarden if len(plant.overlapList)>0: thePlantAreaTotal=geometry_utils.areaCircle(plant.r) if thePlantAreaTotal==0.0: print "name:%s r:%f isSeed:%i massSeed:%f massTotal:%f"%(plant.name, plant.r, plant.isSeed, plant.massSeed, plant.massTotal) if len(plant.overlapList)==1: ###if you are covered by just 1 other, do a direct calc overPlant =plant.overlapList[0] areaCovered=geometry_utils.areaOverlappingCircles(plant.x, plant.y, plant.r, overPlant.x, overPlant.y, overPlant.r) areaCovered=areaCovered-(areaCovered*plantTwo.canopyTransmittance) thePlantAreaExposed=thePlantAreaTotal-areaCovered #plant.areaCovered=areaCovered fractionExposed= thePlantAreaExposed/thePlantAreaTotal #fractionExposed=fractionExposed*theGarden.lightIntensity #try and take into account overall world light intensity fractionExposed=fractionExposed*theRegion.lightIntensity #try and take into account overall world light intensity thePlantAreaExposed= thePlantAreaTotal*fractionExposed plant.areaCovered=thePlantAreaTotal-thePlantAreaExposed elif len(plant.overlapList)>1: ###if you are covered by 2, use monte-carlo numbPhotons=int(thePlantAreaTotal) if numbPhotons==0: numbPhotons=1 numbPhotons= numbPhotons*100 if numbPhotons>750: #we don't need monster numbers numbPhotons=750 hitCount=0 for photon in range(numbPhotons): #####consider moving this to geometry_utils ###pick uniformly distributed point in a circle randr=(random.random()*(plant.r-0))+0 #random between 0 and the radius twoPi=math.pi*2 randAngle=random.random()*twoPi #randr =math.sqrt(randr) #if you don't use sqrt, you get clustering in the center randr =randr**0.5 #if you don't use sqrt, you get clustering in the center photonX = (randr*math.cos(randAngle))+plant.x photonY = (randr*math.sin(randAngle))+plant.y ###### for overPlant in plant.overlapList: if not photonX=="gone": if geometry_utils.pointInsideCircle(overPlant.x, overPlant.y, overPlant.r, photonX, photonY): randomValue=random.random() if randomValue > overPlant.canopyTransmittance: ###these points are where the overlap is photonX="gone" break if not photonX=="gone": hitCount=hitCount+1 if numbPhotons ==0: fractionExposed=0.0 else: fractionExposed=float(hitCount)/float(numbPhotons) #fractionExposed=fractionExposed*theGarden.lightIntensity #try and take into account overall world light intensity fractionExposed=fractionExposed*theRegion.lightIntensity #try and take into account overall world light intensity thePlantAreaExposed= thePlantAreaTotal*fractionExposed plant.areaCovered=thePlantAreaTotal-thePlantAreaExposed else: #if you are not covered at all thePlantAreaTotal=geometry_utils.areaCircle(plant.r) fractionExposed=1.0 #fractionExposed=fractionExposed*theGarden.lightIntensity #try and take into account overall world light intensity fractionExposed=fractionExposed*theRegion.lightIntensity #try and take into account overall world light intensity thePlantAreaExposed= thePlantAreaTotal*fractionExposed plant.areaCovered=thePlantAreaTotal-thePlantAreaExposed ###now change the colour accordingly plant.colourLeaf[2]= fractionExposed if theGarden.showProgressBar: i=i+1 theProgressBar.update(i)
def placeSeed(self, seedPlacement, sList, startPopulationSize, useDefaultYml, ymlList): theGarden=self #print sList #This block of code came from the main SERA.py. Moved and working on 2008.11.06 to allow for calling during simulation runs at #not just at the start. if theGarden.cycleNumber<1: print "***Generating and placing seeds.***" ###initialize progress bar### if theGarden.showProgressBar or theGarden.cycleNumber<1: theProgressBar= progressBarClass.progressbarClass(startPopulationSize-1,"*") #why -1? because index 0. So if total=100, 0-99. if seedPlacement=="square" or seedPlacement=="hex": seedDistance=geometry_utils.placePointsInGrid(startPopulationSize, theGarden.theWorldSize) prevX=-theGarden.theWorldSize/2.0 prevY= theGarden.theWorldSize/2.0 if seedPlacement=="hex": currentRow=0 prevX= prevX-(seedDistance/2.0) prevY= prevY+(seedDistance/2.0) if seedPlacement=="defined" or len(sList)>0: theIndex=0 #print sList for i in range(startPopulationSize): countToGerm=0 theSpeciesFile="" if debug1 and startPopulationSize==1: x=0 y=0 elif len(sList)>0: if seedPlacement=="fromFile": x=sList[i][1] y=sList[i][2] countToGerm=sList[i][3] #radius of canopy would be sList[i][4]. Unused, but in place to be built on if sList[i][0] in ymlList: theSpeciesFile=sList[i][0] else: print "\nWARNING: The desired species %s was not found. \nA random species will be used.\n" % (sList[i][0]) else: if sList[i] in ymlList: theSpeciesFile=sList[i] if seedPlacement=="fromFile": x=sList[i][1] y=sList[i][2] countToGerm=sList[i][3] #radius of canopy would be sList[i][4]. Unused, but in place to be built on elif seedPlacement=="random": x=random.randrange(-(theGarden.theWorldSize/2),(theGarden.theWorldSize/2))+random.random() y=random.randrange(-(theGarden.theWorldSize/2),(theGarden.theWorldSize/2))+random.random() elif seedPlacement=="square" or seedPlacement=="hex": x=prevX+seedDistance y=prevY-seedDistance if x+seedDistance>=(theGarden.theWorldSize/2.0): prevX=-theGarden.theWorldSize/2.0 if seedPlacement=="hex": if currentRow==0: currentRow=1 else: currentRow=0 prevX= prevX-(seedDistance/2.0) prevY= prevY-seedDistance else: prevX=x #print theSpeciesFile if useDefaultYml==False or theSpeciesFile=="": #print "not default species" if theSpeciesFile=="" or theSpeciesFile=="_random_": whichSpecies=random.randint(0,len(ymlList)-1)##pick from the species randomly fileLoc= "Species/"+ymlList[whichSpecies] theSpeciesFile=ymlList[whichSpecies] #print theSpeciesFile if theGarden.platonicSeeds.has_key(theSpeciesFile): platonicSeed=theGarden.platonicSeeds[theSpeciesFile] theSeed=copy.deepcopy(platonicSeed) #else: # print "something is very wrong." else: #if there are no species listed, use the default species. theSeed=Species1() theSeed=theGarden.plantSeed(theSeed) #print theSeed.subregion #now set some attributes theSeed.timeCreation=time.time() theSeed.countToGerm=countToGerm theSeed.x=x theSeed.y=y #this is just to get the properties calculated.Give the seed the max seed mass #bootstrap the seed theSeed.massSeed=theSeed.massSeedMax #convert mass to volume and the get the radius j= theSeed.massSeed/theSeed.densitySeed #this is volume in m^3 j=j/(4.0/3.0) j=j/(math.pi) j=math.pow(j, 1.0/3.0) theSeed.radiusSeed=j theSeed.z= theSeed.radiusSeed theSeed.r= theSeed.radiusSeed #theSeed.growSeedOnPlant(theSeed.massSeedMax) #print "#######" #print theSeed.__class__().name #print "#######" #update the progress meter if theGarden.showProgressBar or theGarden.cycleNumber<1: theProgressBar.update(i)
def placeSeed(self, seedPlacement, sList, startPopulationSize,
useDefaultYml, ymlList):
theGarden = self
#print sList
#This block of code came from the main SERA.py. Moved and working on 2008.11.06 to allow for calling during simulation runs at
#not just at the start.
if theGarden.cycleNumber < 1:
print "***Generating and placing seeds.***"
###initialize progress bar###
if theGarden.showProgressBar or theGarden.cycleNumber < 1:
theProgressBar = progressBarClass.progressbarClass(
startPopulationSize - 1,
"*") #why -1? because index 0. So if total=100, 0-99.
if seedPlacement == "square" or seedPlacement == "hex":
seedDistance = geometry_utils.placePointsInGrid(
startPopulationSize, theGarden.theWorldSize)
prevX = -theGarden.theWorldSize / 2.0
prevY = theGarden.theWorldSize / 2.0
if seedPlacement == "hex":
currentRow = 0
prevX = prevX - (seedDistance / 2.0)
prevY = prevY + (seedDistance / 2.0)
if seedPlacement == "defined" or len(sList) > 0:
theIndex = 0
#print sList
for i in range(startPopulationSize):
countToGerm = 0
theSpeciesFile = ""
if debug1 and startPopulationSize == 1:
x = 0
y = 0
elif len(sList) > 0:
if seedPlacement == "fromFile":
x = sList[i][1]
y = sList[i][2]
countToGerm = sList[i][3]
#radius of canopy would be sList[i][4]. Unused, but in place to be built on
if sList[i][0] in ymlList:
theSpeciesFile = sList[i][0]
else:
print "\nWARNING: The desired species %s was not found. \nA random species will be used.\n" % (
sList[i][0])
else:
if sList[i] in ymlList:
theSpeciesFile = sList[i]
if seedPlacement == "fromFile":
x = sList[i][1]
y = sList[i][2]
countToGerm = sList[i][3]
#radius of canopy would be sList[i][4]. Unused, but in place to be built on
elif seedPlacement == "random":
x = random.randrange(
-(theGarden.theWorldSize / 2),
(theGarden.theWorldSize / 2)) + random.random()
y = random.randrange(
-(theGarden.theWorldSize / 2),
(theGarden.theWorldSize / 2)) + random.random()
elif seedPlacement == "square" or seedPlacement == "hex":
x = prevX + seedDistance
y = prevY - seedDistance
if x + seedDistance >= (theGarden.theWorldSize / 2.0):
prevX = -theGarden.theWorldSize / 2.0
if seedPlacement == "hex":
if currentRow == 0:
currentRow = 1
else:
currentRow = 0
prevX = prevX - (seedDistance / 2.0)
prevY = prevY - seedDistance
else:
prevX = x
#print theSpeciesFile
if useDefaultYml == False or theSpeciesFile == "":
#print "not default species"
if theSpeciesFile == "" or theSpeciesFile == "_random_":
whichSpecies = random.randint(
0,
len(ymlList) - 1) ##pick from the species randomly
fileLoc = "Species/" + ymlList[whichSpecies]
theSpeciesFile = ymlList[whichSpecies]
#print theSpeciesFile
if theGarden.platonicSeeds.has_key(theSpeciesFile):
platonicSeed = theGarden.platonicSeeds[theSpeciesFile]
theSeed = copy.deepcopy(platonicSeed)
#else:
# print "something is very wrong."
else:
#if there are no species listed, use the default species.
theSeed = Species1()
theSeed = theGarden.plantSeed(theSeed)
#print theSeed.subregion
#now set some attributes
theSeed.timeCreation = time.time()
theSeed.countToGerm = countToGerm
theSeed.x = x
theSeed.y = y
#this is just to get the properties calculated.Give the seed the max seed mass
#bootstrap the seed
theSeed.massSeed = theSeed.massSeedMax
#convert mass to volume and the get the radius
j = theSeed.massSeed / theSeed.densitySeed #this is volume in m^3
j = j / (4.0 / 3.0)
j = j / (math.pi)
j = math.pow(j, 1.0 / 3.0)
theSeed.radiusSeed = j
theSeed.z = theSeed.radiusSeed
theSeed.r = theSeed.radiusSeed
#theSeed.growSeedOnPlant(theSeed.massSeedMax)
#print "#######"
#print theSeed.__class__().name
#print "#######"
#update the progress meter
if theGarden.showProgressBar or theGarden.cycleNumber < 1:
theProgressBar.update(i)
#!/usr/bin/env python