def generateTrueRelProbDistMapsForAllSpp (self, guppy):
"""
#--------------------------------------------------------------------
# Here, we now want to have the option to create the true relative
# probability maps in a different way.
# 1) Generate a very small number of presence locations.
# 2) Hand these to maxent with the environment layers and
# have it fit a distribution from them (no bootstrapping).
# 3) Return that as the true relative probability map.
#--------------------------------------------------------------------
# NOTE: This function is defined in computeSppDistributions.R
"""
print "\n\nGenerate true rel prob map using MAXENT.\n\n"
combinedSppPresTable = \
self.genCombinedSppPresTable (guppy) ### guppy.imgNumRows, guppy.imgNumCols)
print "\n\ncombinedSppPresTable = \n"
print combinedSppPresTable
combinedSppPresencesFilename = guppy.curFullMaxentSamplesDirName + \
CONST.dirSlash + \
"maxentGenSppPresCombined" + ".csv"
combinedSppPresTable.to_csv (combinedSppPresencesFilename, index=False)
# writeCsv (combinedSppPresTable,
# file = combinedSppPresencesFilename,
# rowNames = False,
# quote=False)
# Now have to make whatever changes and initializations are necessary to
# call maxent and have it generate new layers in the proper subdirectory
# and not do any bootstrapping.
# OUTPUTS FROM THIS GENERATOR NEED TO GO INTO THE MaxentProbDistLayers
# directory, just like the outputs of the arithmetic generator.
# Need to see where it builds its directory name and writes to it.
# Also, when maxent is finished generating these layers, there will probably
# be tons of crap left in there by maxent that needs to be deleted.
# This suggests it might be better to just make a scratch area for maxent
# to dump into and then just copy the species distribution files I need
# out of there and into the MaxentProbDistLayers directory.
# Call it MaxentProbDistGenOutputs.
#----------------------------------------------------------------
# Run maxent to generate a true relative probability map.
#----------------------------------------------------------------
runMaxentCmd (combinedSppPresencesFilename,
# guppy.maxentGenOutputDir, \
guppy.sppGenOutputDir, \
guppy.doMaxentReplicates,
guppy.maxentReplicateType, \
guppy.numMaxentReplicates, \
guppy.maxentFullPathName, \
guppy.curFullMaxentEnvLayersDirName, \
guppy.numProcessors, \
guppy.verboseMaxent \
)
def run(self):
# --------------------------------
# Generate environment layers.
# --------------------------------
self.loadEnvLayers()
# --------------------------------------------
# Generate true relative probability maps.
# --------------------------------------------
self.getTrueRelProbDistMapsForAllSpp()
# ----------------------------
# Generate true presences.
# ----------------------------
# Currently, this also generates the Sampled presences inside
# the same call to pyper genPresences().
# Need to separate that behavior out and make a new method
# for Guppy to genSampledPresences() and apply a SampleBias class
# to the data and the true presences to generate the
# sampled presences.
# ----------------------------
print "\n\n+++++\tBefore getNumTruePresencesForEachSpp()\n"
sys.stdout.flush()
# moved from up above.
numTruePresences = self.getNumTruePresencesForEachSpp()
print "\n\n+++++\tBefore genTruePresencesForAllSpp\n"
sys.stdout.flush()
listOfTruePresencesAndXYlocs = self.genTruePresencesForAllSpp(numTruePresences)
print "\n\n+++++\tJust after self.genTruePresencesForAllSpp (numTruePresences), listOfTruePresencesAndXYlocs = "
pprint(listOfTruePresencesAndXYlocs)
sys.stdout.flush()
# print "\n\n\n--------------- EXITING NOW ---------------\n\n\n"
# exit()
# combinedSppTruePresencesTable = \
# listOfTruePresencesAndXYlocs ["combined.spp.true.presences.table"]
# allSppTruePresenceLocsXY = \
# listOfTruePresencesAndXYlocs ["all.spp.true.presence.locs.x.y"]
# ----------------------------------------------------------------
# Run maxent to generate a predicted relative probability map.
# ----------------------------------------------------------------
maxentSamplesFileName = self.combinedPresSamplesFileName
print "\n\n+++++\tBefore", "runMaxentCmd", "\n"
sys.stdout.flush()
runMaxentCmd(
maxentSamplesFileName,
self.maxentOutputDir,
self.doMaxentReplicates,
self.maxentReplicateType,
self.numMaxentReplicates,
self.maxentFullPathName,
self.curFullMaxentEnvLayersDirName,
self.numProcessors,
self.verboseMaxent,
)
# ----------------------------------------------------------------
# Evaluate the results of maxent by comparing its output maps
# to the true relative probability maps.
# ----------------------------------------------------------------
print "\n\n+++++\tBefore" + "evaluateMaxentResults" + "\n"
### evaluateMaxentResults ()
###rinterface.set_flushconsole()
self.Rcaller.assign("rNumSppToCreate", self.numSppToCreate)
self.Rcaller.assign("rDoMaxentReplicates", self.doMaxentReplicates)
self.Rcaller.assign("rTrueProbDistFilePrefix", self.trueProbDistFilePrefix)
self.Rcaller.assign("rShowRawErrorInDist", self.showRawErrorInDist)
self.Rcaller.assign("rShowAbsErrorInDist", self.showAbsErrorInDist)
self.Rcaller.assign("rShowPercentErrorInDist", self.showPercentErrorInDist)
self.Rcaller.assign("rShowAbsPercentErrorInDist", self.showAbsPercentErrorInDist)
self.Rcaller.assign("rShowTruncatedPercentErrImg", self.showTruncatedPercentErrImg)
self.Rcaller.assign("rShowHeatmap", self.showHeatmap)
self.Rcaller.assign("rMaxentOutputDirWithSlash", self.maxentOutputDirWithSlash)
# self.Rcaller.assign('rProbDistLayersDirWithSlash', self.probDistLayersDirWithSlash)
self.Rcaller.assign("rSppGenOutputDirWithSlash", self.sppGenOutputDirWithSlash)
self.Rcaller.assign("rAnalysisDirWithSlash", self.analysisDirWithSlash)
self.Rcaller.assign("rUseOldMaxentOutputForInput", self.PARuseOldMaxentOutputForInput)
self.Rcaller.assign("rWriteToFile", self.writeToFile)
self.Rcaller.assign("rUseDrawImage", self.useDrawImage)
self.Rcaller("source ('/Users/Bill/D/rdv-framework/projects/guppy/evaluateMaxentResultsPyper.R')")
self.Rcaller(
"evaluateMaxentResults (rNumSppToCreate, rDoMaxentReplicates, \
rTrueProbDistFilePrefix, rShowRawErrorInDist, rShowAbsErrorInDist, \
rShowPercentErrorInDist, rShowAbsPercentErrorInDist, \
rShowTruncatedPercentErrImg, rShowHeatmap, rMaxentOutputDirWithSlash, \
rSppGenOutputDirWithSlash, rAnalysisDirWithSlash, \
rUseOldMaxentOutputForInput, rWriteToFile, rUseDrawImage)"
)
