def processAlgorithm(self, progress):
# Do the stuff
metric = self.m[self.getParameterValue(self.METRIC)]
envlayers = self.getParameterValue(self.ENV)
names = []
env = []
shape = None
# Load all arrays into an dictonary
for lay in envlayers.split(";"):
r = Processing.getObject(lay) # QgsRasterLayer object
name = str( r.name() )
names.append(name)
a = gdal.Open( lay )
array = a.GetRasterBand(1).ReadAsArray()
# Prepare by removing all no-data values from array
NA = a.GetRasterBand(1).GetNoDataValue()
if NA != None:
array[array==NA] = 0
env.append(array)
if shape == None: # Fast check if array are unequal
shape = array.shape
else:
if shape != array.shape:
raise GeoAlgorithmExecutionException("Input layers need to have the same extent and cellsize.")
a = r = None
if len( env ) == 1:
raise GeoAlgorithmExecutionException("You need at least two layers to calculate overlap statistics.")
progress.setConsoleInfo("Loaded %s arrays for calculation" % ( str( len( names) ) ) )
func.updateProcessing(progress,1,3)
results = []
func.updateProcessing(progress,2,3)
if len(env) > 2:
# Iterative Calculation of the metrics
for j in range(0,len(env)):
for k in range(j+1,len(env)):
progress.setConsoleInfo("Calculating Overlap of layers %s with %s" % (names[j],names[k]) )
r = self.Overlap(metric,env[j],env[k])
res = (names[j],names[k],metric,r)
results.append(res)
else:
# Only two input layers
r = self.Overlap(metric,env[0],env[1])
res = (names[0],names[1],metric,r)
results.append(res)
progress.setConsoleInfo("Saving results")
func.updateProcessing(progress,3,3)
output = self.getOutputValue(self.RESULTS)
titles = ['Layer1','Layer2','Metric','Overlap']
# Save Output
func.saveToCSV(results, titles, output )
def processAlgorithm(self, progress):
param = dict()
param["responsecurves"] = self.getParameterValue(self.RESP)
param["responsecurvesexponent"] = self.getParameterValue(self.RESP_EXP)
param["pictures"] = self.getParameterValue(self.PIC)
param["randomseed"] = self.getParameterValue(self.RANDOM)
param["logscale"] = self.getParameterValue(self.LOGSCALE)
param["writeclampgrid"] = self.getParameterValue(self.CLAMPGRID)
param["writemess"] = self.getParameterValue(self.MESS)
param["randomtestpoints"] = self.getParameterValue(self.RANDOM_POINTS)
param["betamultiplier"] = self.getParameterValue(self.BETA_MULT)
param["replicates"] = self.getParameterValue(self.REPLICATES)
param["replicatetype"] = self.R_TYPE[self.getParameterValue(self.REPLICATE_TYPE)]
param["linear"] = self.getParameterValue(self.LINEAR)
param["quadratic"] = self.getParameterValue(self.QUADRATIC)
param["product"] = self.getParameterValue(self.PRODUCT)
param["threshold"] = self.getParameterValue(self.THRESHOLD)
param["hinge"] = self.getParameterValue(self.HINGE)
param["fadebyclamping"] = self.getParameterValue(self.FADEBYCLAMPING)
param["extrapolate"] = self.getParameterValue(self.EXTRAPOLATE)
param["plots"] = self.getParameterValue(self.PLOTS)
param["maximumiterations"] = self.getParameterValue(self.MAXITERATIONS)
param["convergencethreshold"] = self.getParameterValue(self.CONVG_THRESH)
param["threads"] = self.getParameterValue(self.PROC)
param["defaultprevalence"] = self.getParameterValue(self.DEF_PREV)
param["perspeciesresults"] = self.getParameterValue(self.PERSPECRES)
# param["applythresholdrule"]= self.getParameterValue(self.APPLY_THRESH)
res = []
for option in param.iteritems():
res.append((option[0],str( option[1] ).lower()))
out = self.getOutputValue(self.OUT_PARAM)
species = func.saveToCSV(res,("command","value"),out)
def processAlgorithm(self, progress):
param = dict()
param["responsecurves"] = self.getParameterValue(self.RESP)
param["responsecurvesexponent"] = self.getParameterValue(self.RESP_EXP)
param["pictures"] = self.getParameterValue(self.PIC)
param["randomseed"] = self.getParameterValue(self.RANDOM)
param["logscale"] = self.getParameterValue(self.LOGSCALE)
param["writeclampgrid"] = self.getParameterValue(self.CLAMPGRID)
param["writemess"] = self.getParameterValue(self.MESS)
param["randomtestpoints"] = self.getParameterValue(self.RANDOM_POINTS)
param["betamultiplier"] = self.getParameterValue(self.BETA_MULT)
param["replicates"] = self.getParameterValue(self.REPLICATES)
param["replicatetype"] = self.R_TYPE[self.getParameterValue(
self.REPLICATE_TYPE)]
param["linear"] = self.getParameterValue(self.LINEAR)
param["quadratic"] = self.getParameterValue(self.QUADRATIC)
param["product"] = self.getParameterValue(self.PRODUCT)
param["threshold"] = self.getParameterValue(self.THRESHOLD)
param["hinge"] = self.getParameterValue(self.HINGE)
param["fadebyclamping"] = self.getParameterValue(self.FADEBYCLAMPING)
param["extrapolate"] = self.getParameterValue(self.EXTRAPOLATE)
param["plots"] = self.getParameterValue(self.PLOTS)
param["maximumiterations"] = self.getParameterValue(self.MAXITERATIONS)
param["convergencethreshold"] = self.getParameterValue(
self.CONVG_THRESH)
param["threads"] = self.getParameterValue(self.PROC)
param["defaultprevalence"] = self.getParameterValue(self.DEF_PREV)
param["perspeciesresults"] = self.getParameterValue(self.PERSPECRES)
# param["applythresholdrule"]= self.getParameterValue(self.APPLY_THRESH)
res = []
for option in param.iteritems():
res.append((option[0], str(option[1]).lower()))
out = self.getOutputValue(self.OUT_PARAM)
species = func.saveToCSV(res, ("command", "value"), out)
def processAlgorithm(self, progress):
# Get the location to the maxent jar file
maxent = qsdm_settings.maxent()
if os.path.basename(maxent) == 'maxent.jar':
pass
else:
maxent = os.path.join(qsdm_settings.maxent(), 'maxent.jar') # If the directory and not the file was chosen
# Get location of java, available memory and output path
if sys.platform == "win32" or "win64":
ex = "java.exe"
else:
ex = "java"
java = os.path.join(qsdm_settings.javaPath(),ex) # the path to java if basic execution fails
temp = qsdm_settings.getTEMP()+os.sep+"MAXENT" # folder where reprojected files and such are saved
mem = str( qsdm_settings.getMEM() ) # available memory for MAXENT
work = qsdm_settings.workPath() # get the name of the folder to save the Maxent model results to
env_dir = self.getParameterValue(self.ENV_DIR)
progress.setConsoleInfo("Starting Species Layer Preperation")
# Check if temp folder exists, otherwise create it
if os.path.exists(temp) == False:
os.mkdir(temp)
## Species layer preperation
# Get the species file to model. Take selected species column and coordinates
point = self.getParameterValue(self.SPECIES)
v = Processing.getObject(point)
scl = self.getParameterValue(self.SPEC_COL) # get names of species from input file
if v.source().find("type=csv") != -1 :
raise GeoAlgorithmExecutionException("Species point layer should be saved as ESRI Shapefile")
else:
crs = v.crs()
if crs.authid() != "EPSG:4326":
progress.setConsoleInfo("Species localities not in WGS84, reprojecting...")
# Reproject using ogr
func.reprojectLatLong(v,temp)
# Then open again as QgsVectorLayer
out = temp+os.sep+"localities.shp"
if (os.path.exists(out) and os.path.isfile(out)) == False:
raise GeoAlgorithmExecutionException("Species point layer data could not be reprojected to WGS84")
fileInfo = QFileInfo(out)
baseName = fileInfo.baseName()
v = QgsVectorLayer(out, baseName, "ogr")
if v.isValid() != True:
# If this didn't work, try to use the Processing way
v = Processing.getObject(out)
if v.isValid() != True:
# Otherwise return error
raise GeoAlgorithmExecutionException("No valid layer could be loaded from the reprojection.")
# Get Coordinates from point layer and add the species name
coord = func.point2table(v,scl)
if coord is None:
raise GeoAlgorithmExecutionException("Species point layer data could not be extracted")
# Convert coordinates and species name to csv, save in temporary Folder
# Get Systemwide temporary folder to save the species csv
speciesPath = temp + os.sep +"species.csv"
species = func.saveToCSV(coord,("Species","Long","Lat"),speciesPath)
specieslist = func.getUniqueAttributeList( v, scl, True)
progress.setConsoleInfo("Species data successfully prepared for MAXENT")
progress.setConsoleInfo("---")
## Maxent execution
# Try if JAVA can be executed like this, otherwise take the binary from the given path
try:
from subprocess import DEVNULL # python 3k
except ImportError:
DEVNULL = open(os.devnull, 'wb')
proc = subprocess.call(['java', '-version'],stdin=subprocess.PIPE, stdout=DEVNULL, stderr=subprocess.STDOUT)
if proc == 0:
start = "java -mx" + str(int(mem)) + "m -jar "
else:
progress.setConsoleInfo("JAVA could not be run by default. Using link to binary from set JAVA folder.")
start = java + " -mx" + str(int(mem)) + "m -jar "
# if Windows, encapsule jar file in "
if platform.system() == "Windows":
start += "\"" + maxent + "\""
else:
start += maxent
myCommand = start + " samplesfile=" + speciesPath
myCommand += " environmentallayers=" + env_dir
myCommand += " outputdirectory=" + work
# finish the command
myCommand += " redoifexists"
# add a message
progress.setConsoleInfo("#### Attempting to start MAXENT ####")
# execute the command
loglines = []
loglines.append('MAXENT execution console output')
# result = os.system(myCommand)
proc = subprocess.Popen(
myCommand,
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.STDOUT,
universal_newlines=True,
).stdout
for line in iter(proc.readline, ''):
loglines.append(line)
ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) # Print all loglines if delivered from MAXENT
err = False
for line in loglines:
progress.setConsoleInfo(line)
if line.find("Error") != -1:
err = True
if err:
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,"MAXENT calculations did not succed! Check the Processing Info output for possible error sources.")
print "Used command:" + myCommand
else:
ProcessingLog.addToLog(ProcessingLog.LOG_INFO,"MAXENT modelling finished.")
# Finished, Load all resulting layers in QGIS if successfully run
# In order to be compatible with processing copy or link them to the Processing output folder
#out_r = self.getOutputValue(self.OUT_PRED)
#out_t = self.getOutputValue(self.OUT_PRED_RES)
p = work + os.sep + "maxentResults.csv"
func.tableInQgis(p,",")
#load in only generated Prediction
for species in specieslist:
t = species.replace(" ","_")
p = work + os.sep + t + ".asc"
func.rasterInQgis(p)
def processAlgorithm(self, progress):
## Parameter preperation ##
# Get the location to the maxent jar file
maxent = qsdm_settings.maxent()
if os.path.basename(maxent) == 'maxent.jar':
pass
else:
maxent = os.path.join(qsdm_settings.maxent(), 'maxent.jar') # If the directory and not the file was chosen
# Get location of java, available memory and output path
if sys.platform == "win32" or "win64":
ex = "java.exe"
else:
ex = "java"
java = os.path.join(qsdm_settings.javaPath(),ex) # the path to java if basic execution fails
mem = str( qsdm_settings.getMEM() ) # available memory for MAXENT
work = qsdm_settings.workPath() # get the name of the folder to save the Maxent model results to
temp = qsdm_settings.getTEMP()+os.sep+"MAXENT" # folder where reprojected files and such are saved
progress.setConsoleInfo("Starting Parameter and File Preperation")
# Check if temp folder exists, otherwise create it
if os.path.exists(temp) == False:
os.mkdir(temp)
# Get optional parameters
param = self.getParameterValue(self.PARAM)
o = Processing.getObject(param)
if type(o)==QgsVectorLayer and o.isValid() and os.path.splitext(o.source())[1]==".csv":
progress.setConsoleInfo("Using optional parameter file for MAXENT")
param = dict()
# Format Parameters to dictionary
dp = o.dataProvider()
for feat in dp.getFeatures():
geom = feat.geometry()
com = feat["command"]
val = feat["value"]
param[com] = val
# and make maxent invisible to the modeller
param["visible"] = False
else:
progress.setConsoleInfo("No valid optional Parameter file detected")
# Use default parameters
param = dict()
# per default write a separate maxent results file for each species
param["perspeciesresults"] = False
# and make maxent invisible to the modeller
param["visible"] = False
# Progress updater:
n = len(self.getParameterValue(self.ENV).split(";"))+5
func.updateProcessing(progress,1,n,"Loaded Parameters.")
## Species layer
# Get the species file to model. Take selected species column and coordinates
point = self.getParameterValue(self.SPECIES)
v = Processing.getObject(point)
crs = v.crs()
if crs.authid() != "EPSG:4326":
progress.setConsoleInfo("Species localities not in WGS84, reprojecting...")
# Reproject using ogr
func.reprojectLatLong(v,temp)
# Then open again as QgsVectorLayer
out = temp+os.sep+"localities.shp"
if (os.path.exists(out) and os.path.isfile(out)) == False:
raise GeoAlgorithmExecutionException("Species point layer data could not be reprojected to WGS84")
fileInfo = QFileInfo(out)
baseName = fileInfo.baseName()
v = QgsVectorLayer(out, baseName, "ogr")
if v.isValid() != True:
# If this didn't work, try to use the Processing way
v = Processing.getObject(out)
if v.isValid() != True:
# Otherwise return error
raise GeoAlgorithmExecutionException("No valid layer could be loaded from the reprojection.")
# get names of species from input file
scl = self.getParameterValue(self.SPEC_COL)
# Get Coordinates from point layer and add the species name
coord = func.point2table(v,scl)
if coord is None:
raise GeoAlgorithmExecutionException("Species point layer data could not be extracted")
# Convert coordinates and species name to csv, save in temporary Folder
# Get Systemwide temporary folder to save the species csv
speciesPath = temp + os.sep +"species.csv"
species = func.saveToCSV(coord,("Species","Long","Lat"),speciesPath)
specieslist = func.getUniqueAttributeList( v, scl,True)
progress.setConsoleInfo("Species data successfully prepared for MAXENT")
progress.setConsoleInfo("---")
func.updateProcessing(progress,2,n,"Loaded Species data.")
## Environmental Layers
# get the selected environmental layers and prepare them for MAXENT
progress.setConsoleInfo("Starting preparing the environmental layers")
envlayers = self.getParameterValue(self.ENV)
env = dict()
layers = []
# Project to WGS84 if necessary
for lay in envlayers.split(";"):
r = Processing.getObject(lay) # QgsRasterLayer object
name = str( r.name() )
crs = r.crs()
if crs.authid() != "EPSG:4326":
# Reproject layer
progress.setConsoleInfo("Originial Layer %s not in WGS84, reprojecting..." % (name))
r = func.reprojectRasterLatLong(r,temp,True)
if r == False or r.isValid()==False :
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,"Projecting "+name+" to WGS84 failed!")
layers.append( r.source() )
if len(layers) == 0:
raise GeoAlgorithmExecutionException("Environmental Layers could not be reprojected!")
else:
func.updateProcessing(progress,3,n,"Reprojection finished.")
# Check the extent of all those layers and unify if necessary
# Check if necessary -> Do the raster layer have differing extents
func.updateProcessing(progress,4,n)
uni = []
app = False # Which approach should be used?
if len(layers) > 1 and func.unificationNecessary(layers):
progress.setConsoleInfo("Input layers have different extents, intersecting...")
# The credits of the following approach go to Yury Ryabov - http://ssrebelious.blogspot.com
if app == False:
# get coordinates of corners for the final raster
fin_coordinates = func.finCoordinates(layers)
r = gdal.Open(str( layers[0] ) )
main_geo_transform = r.GetGeoTransform()
proj = r.GetProjection()
no_data = r.GetRasterBand(1).GetNoDataValue()
if not no_data:
no_data = -9999
for lay in layers:
raster = gdal.Open(str(lay))
name = os.path.splitext(os.path.basename(lay))[0]
out = temp + os.sep + name + 'warp.tif'
result = func.ExtendRaster(raster, fin_coordinates, out, main_geo_transform, proj, no_data)
if result:
raster = None
if os.path.exists(out):
# Add output to uni
uni.append(out)
else:
raise GeoAlgorithmExecutionException("Unified layer could not be saved.")
else:
raise GeoAlgorithmExecutionException("Layers could not be unified. Please set do this manually.")
else:
# FIXME: Faster Approach down below. Currently not yet working
# 1. Build largest extent and geotransform
# big_coord has left, top, right, bottom of dataset's bounds in geospatial coordinates.
fin_coordinates, main_geo_transform, interp = func.CreateMainGeotransform(layers) # get coordinates and geotransform of corners for the final raster
# set number of columns and rows for raster
main_cols = (fin_coordinates[2] - fin_coordinates[0]) / abs(main_geo_transform[1])
main_rows = (fin_coordinates[3] - fin_coordinates[1]) / abs(main_geo_transform[5])
progress.setConsoleInfo("Creating new raster based on greatest extent with %s columns and %s rows" % (str(main_cols),str(main_rows)))
#FIXME: Check coordinates
big_coord = [main_geo_transform[0], main_geo_transform[3], main_geo_transform[0] + (main_geo_transform[1] * main_rows), main_geo_transform[3] + (main_geo_transform[5] * main_cols)]
# 2. Loop through rasters and Intersect them export the biggest
for lay in layers:
name = os.path.splitext(os.path.basename(lay))[0]
r = gdal.Open(str( lay ) )
src_p = r.GetProjection()
if interp:
# Interpolate to biggest cellsize
progress.setConsoleInfo("Resolution of Environmental Layers is different. Bilinear interpolation to the coarsest cellsize = xy(%s,%s)" % (abs(main_geo_transform[1]),abs(main_geo_transform[5])))
#FIXME: Maybe interpolate to nearest neighbor if categorical
r = func.gridInterpolation(r,temp,main_geo_transform,main_cols,main_rows,src_p, 'Bilinear',False)
wide = abs( r.RasterXSize )
high = abs( r.RasterYSize )
geotransform = r.GetGeoTransform()
nodata = r.GetRasterBand(1).GetNoDataValue() # should be -9999 if projected correctly
if nodata == None:
nodata = -9999
# target has left, top, right, bottom of dataset's bounds in geospatial coordinates.
target = [geotransform[0], geotransform[3], geotransform[0] + (geotransform[1] * wide), geotransform[3] + (geotransform[5] * high)]
#Intersection
intersection = [max(big_coord[0], target[0]), min(big_coord[1], target[1]), min(big_coord[2], target[2]), max(big_coord[3], target[3])]
# Convert to pixels
p1 = func.world2Pixel(geotransform,intersection[0],intersection[1])
p2 = func.world2Pixel(geotransform,intersection[2],intersection[3])
band = r.GetRasterBand(1)
result = band.ReadAsArray(p1[0], p1[1], p2[0] - p1[0], p2[1] - p1[1], p2[0] - p1[0], p2[1] - p1[1])
# Write to new raster
output = temp + os.sep + name + 'warp.tif'
func.createRaster(output,abs(main_geo_transform[1]),abs(main_geo_transform[5]),result,nodata,main_geo_transform,src_p,'GTiff')
if os.path.exists(output):
# Add output to uni
uni.append(output)
else:
raise GeoAlgorithmExecutionException("Environmental Layers could not be prepared for MAXENT")
return None
else:
uni = layers
if len(uni) == 0 or len(uni) != len(layers):
raise GeoAlgorithmExecutionException("Environmental Layers with unified extent could not be generated!")
else:
progress.setConsoleInfo("Environmental Layer successfully unified.")
func.updateProcessing(progress,5,n,"Unified environmental Layers.")
# Format to asc if necessary
for lay in uni:
r = Processing.getObject(lay) # QgsRasterLayer object
name = os.path.basename(str( r.name() ))
out = temp + os.sep + name + '.asc'
progress.setConsoleInfo("Convert environmental layers to ESRI ASC format...")
# Format to asc
proc = func.raster2ASC(r,out)
if proc and os.path.isfile(out):
env[name] = out
else:
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,"Converting/Projecting "+name+" to ESRI asc format failed!")
func.updateProcessing(progress,6,n,"Formated to ASC.")
# Check if anything is in env, worked
if len(env) == 0:
raise GeoAlgorithmExecutionException("Environmental Layers could not be prepared for MAXENT")
# Check if the number of the original selected layers is equal to
if len(envlayers.split(";")) != len(env):
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,"Successfully prepared environmental layers "+str( env.keys() ) )
raise GeoAlgorithmExecutionException("Not all environmental Layers could be prepared for MAXENT. Check Processing Log.")
# Test if species csv exists
if os.path.exists(speciesPath) == False:
raise GeoAlgorithmExecutionException("Species point layer could not be prepared for MAXENT")
## create the maxent command
progress.setConsoleInfo("---")
progress.setConsoleInfo("All fine so far. Attempting to build MAXENT execution command...")
# Try if JAVA can be executed like this, otherwise take the binary from the given path
try:
from subprocess import DEVNULL # python 3k
except ImportError:
DEVNULL = open(os.devnull, 'wb')
proc = subprocess.call(['java', '-version'],stdin=subprocess.PIPE, stdout=DEVNULL, stderr=subprocess.STDOUT)
if proc == 0:
start = "java -mx" + str(int(mem)) + "m -jar "
else:
progress.setConsoleInfo("JAVA could not be run by default. Using link to binary from set JAVA folder.")
start = java + " -mx" + str(int(mem)) + "m -jar "
# if Windows, encapsule jar file in "
if platform.system() == "Windows":
start += "\"" + maxent + "\""
else:
start += maxent
myCommand = start + " samplesfile=" + speciesPath
myCommand += " environmentallayers=" + temp
# Toggle all selected Layers
myCommand += " togglelayertype="
for i in range(0,len(env.keys())):
myCommand += os.path.splitext( env.keys()[i] )[0]
if i is not len(env.keys())-1:
myCommand += ","
myCommand += " outputdirectory=" + work
# Parse parameters into command
for option in param.iteritems():
myCommand += " " + option[0] + "=" + str( option[1] ).lower()
# finish the command
myCommand += " redoifexists autorun"
# add a message
progress.setConsoleInfo("#### Attempting to start MAXENT ####")
func.updateProcessing(progress,7,n)
# execute the command
loglines = []
loglines.append('MAXENT execution console output')
# result = os.system(myCommand)
proc = subprocess.Popen(
myCommand,
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.STDOUT,
universal_newlines=True,
).stdout
for line in iter(proc.readline, ''):
loglines.append(line)
ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) # Print all loglines if delivered from MAXENT
err = False
for line in loglines:
progress.setConsoleInfo(line)
if line.find("Error") != -1:
err = True
if err:
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,"MAXENT calculations did not succed! Check the Processing Info output for possible error sources.")
print "Used command:" + myCommand
else:
ProcessingLog.addToLog(ProcessingLog.LOG_INFO,"MAXENT modelling finished.")
func.updateProcessing(progress,n,n)
# Finished, Load all resulting layers in QGIS if successfully run
# In order to be compatible with processing copy or link them to the Processing output folder
#out_r = self.getOutputValue(self.OUT_PRED)
#out_t = self.getOutputValue(self.OUT_PRED_RES)
p = work + os.sep + "maxentResults.csv"
func.tableInQgis(p,",")
#load in only generated Prediction
for species in specieslist:
t = species.replace(" ","_")
p = work + os.sep + t + ".asc"
func.rasterInQgis(p)
## Styling and grouping
# Freeze the canvas
canvas = QgsMapCanvas()
canvas.freeze(True)
#Add a new group and all new layers to it
groups = iface.legendInterface().groups()
if ('MAXENT' in groups ) == False:
idx = iface.legendInterface().addGroup( "MAXENT" )
groups = iface.legendInterface().groups()
layerMap = QgsMapLayerRegistry.instance().mapLayers()
for lyr in layerMap.itervalues():
if lyr.name() in specieslist:
# Move them to the maxent group
iface.legendInterface().moveLayer( lyr, groups.index("MAXENT") )
# Style the output
lyr.setDrawingStyle("SingleBandPseudoColor")
# The band of classLayer
classLyrBnd = 1
# Color list for ramp
clrLst = [ QgsColorRampShader.ColorRampItem(0, QColor(224,224,224),"0"), # Grey
QgsColorRampShader.ColorRampItem(0.01, QColor(0,0,153),"> 0.01"), # darkblue
QgsColorRampShader.ColorRampItem(0.2, QColor(153,204,255),"0.2"), # lightblue
QgsColorRampShader.ColorRampItem(0.35,QColor(153,255,153),"0.35"), # lightgreen
QgsColorRampShader.ColorRampItem(0.5, QColor(0,153,0),"0.5"), # green
QgsColorRampShader.ColorRampItem(0.65, QColor(255,255,0),"0.65"), # yellow
QgsColorRampShader.ColorRampItem(0.75, QColor(255,128,0),"0.75"), # orange
QgsColorRampShader.ColorRampItem(0.85, QColor(255,0,0),">0.85") ] # red
#Create the shader
lyrShdr = QgsRasterShader()
#Create the color ramp function
clrFnctn = QgsColorRampShader()
clrFnctn.setColorRampType(QgsColorRampShader.INTERPOLATED)
clrFnctn.setColorRampItemList(clrLst)
#Set the raster shader function
lyrShdr.setRasterShaderFunction(clrFnctn)
#Create the renderer
lyrRndr = QgsSingleBandPseudoColorRenderer(lyr.dataProvider(), classLyrBnd, lyrShdr)
#Apply the renderer to classLayer
lyr.setRenderer(lyrRndr)
#refresh legend
if hasattr(lyr, "setCacheImage"):
lyr.setCacheImage(None)
lyr.triggerRepaint()
iface.legendInterface().refreshLayerSymbology(lyr)
#Finally move the Maxent results to the group as well
lyr = func.getLayerByName( "MaxentResults" )
iface.legendInterface().moveLayer( lyr, groups.index("MAXENT") )
canvas.freeze(False)
canvas.refresh()
def processAlgorithm(self, progress):
# Do the stuff
metric = self.m[self.getParameterValue(self.METRIC)]
envlayers = self.getParameterValue(self.ENV)
names = []
env = []
shape = None
# Load all arrays into an dictonary
for lay in envlayers.split(";"):
r = Processing.getObject(lay) # QgsRasterLayer object
name = str(r.name())
names.append(name)
a = gdal.Open(lay)
array = a.GetRasterBand(1).ReadAsArray()
# Prepare by removing all no-data values from array
NA = a.GetRasterBand(1).GetNoDataValue()
if NA != None:
array[array == NA] = 0
env.append(array)
if shape == None: # Fast check if array are unequal
shape = array.shape
else:
if shape != array.shape:
raise GeoAlgorithmExecutionException(
"Input layers need to have the same extent and cellsize."
)
a = r = None
if len(env) == 1:
raise GeoAlgorithmExecutionException(
"You need at least two layers to calculate overlap statistics."
)
progress.setConsoleInfo("Loaded %s arrays for calculation" %
(str(len(names))))
func.updateProcessing(progress, 1, 3)
results = []
func.updateProcessing(progress, 2, 3)
if len(env) > 2:
# Iterative Calculation of the metrics
for j in range(0, len(env)):
for k in range(j + 1, len(env)):
progress.setConsoleInfo(
"Calculating Overlap of layers %s with %s" %
(names[j], names[k]))
r = self.Overlap(metric, env[j], env[k])
res = (names[j], names[k], metric, r)
results.append(res)
else:
# Only two input layers
r = self.Overlap(metric, env[0], env[1])
res = (names[0], names[1], metric, r)
results.append(res)
progress.setConsoleInfo("Saving results")
func.updateProcessing(progress, 3, 3)
output = self.getOutputValue(self.RESULTS)
titles = ['Layer1', 'Layer2', 'Metric', 'Overlap']
# Save Output
func.saveToCSV(results, titles, output)
def processAlgorithm(self, progress):
# Set up the data as sklearn bunch (basically just a dictionary with specific attributes)
data = Bunch()
# Vector layer
vector = self.getParameterValue(self.SPECIES)
v = Processing.getObject(vector)
v_crs = v.crs()
# Environmental layers
envlayers = self.getParameterValue(self.ENV)
if func.unificationNecessary(envlayers.split(";")):
raise GeoAlgorithmExecutionException(
"All input environmental layers need to have the same resolution and extent. Use the Unify tool beforehand"
)
#TODO: Enable option to do this automatically
progress.setConsoleInfo("Loading Coverage Data")
# Check Projection and Cellsize
for lay in envlayers.split(";"):
r = Processing.getObject(lay) # QgsRasterLayer object
if r.crs() != v_crs:
raise GeoAlgorithmExecutionException(
"All input layers need to have the same projection")
if round(r.rasterUnitsPerPixelX()) != round(
r.rasterUnitsPerPixelY()):
raise GeoAlgorithmExecutionException(
"Grid Cell size values are not equal. Please be sure that grid cells are squares."
)
# Set coverage parameters
r = Processing.getObject(
envlayers.split(";")[0]) # QgsRasterLayer object
ex = r.extent()
data["grid_size"] = r.rasterUnitsPerPixelX()
data["Nx"] = r.width()
data["Ny"] = r.height()
data["x_left_lower_corner"] = ex.xMinimum()
data["y_left_lower_corner"] = ex.yMinimum()
# Load in Coverage values
coverage = []
for lay in envlayers.split(";"):
raster = gdal.Open(str(lay))
if raster.RasterCount > 1:
progress.setConsoleInfo(
"Warning: Multiple bands for layer detected. Using only first band."
)
array = raster.GetRasterBand(1).ReadAsArray()
NA = raster.GetRasterBand(1).GetNoDataValue()
if NA == None:
raise GeoAlgorithmExecutionException(
"Warning: Raster layer has no no-data value. Please specify a no-data value for this dataset."
)
else:
array[array ==
NA] = -9999 # Replace nodata-values of array with -9999
coverage.append(array)
data["coverages"] = numpy.array(
coverage) # Load all the coverage values into the bunch
# Setup parameters for output prediction
a = gdal.Open(envlayers.split(";")[0])
columns = a.RasterXSize
rows = a.RasterYSize
driver = a.GetDriver()
NA = -9999
gt = a.GetGeoTransform()
proj = a.GetProjection()
output = self.getOutputValue(self.OUT_PRED)
# Set up the data grid
xgrid, ygrid = construct_grids(data)
# The grid in x,y coordinates
X, Y = numpy.meshgrid(xgrid, ygrid[::-1])
# background points (grid coordinates) for evaluation
numpy.random.seed(100)
background_points = numpy.c_[
numpy.random.randint(low=0, high=data.Ny, size=10000),
numpy.random.randint(low=0, high=data.Nx, size=10000)].T
# We'll make use of the fact that coverages[6] has measurements at all
# land points. This will help us decide between land and water.
# FIXME: Assuming that all predictors have a similar distribution. Might be violated
land_reference = data.coverages[0]
progress.setConsoleInfo("Loading Occurence Data and coverage")
# Creating response
train = []
for feature in v.getFeatures():
geom = feature.geometry().asPoint()
mx = geom.x()
my = geom.y()
train.append((mx, my))
data["train"] = numpy.array(train) # Add to bunch as training dataset
# create species bunch
sp_Bunch = Bunch(name="Species")
points = dict(train=data.train)
for label, pts in points.iteritems():
#determine coverage values for each of the training & testing points
ix = numpy.searchsorted(xgrid, pts[0])
iy = numpy.searchsorted(ygrid, pts[1])
bunch['cov_%s' % label] = data.coverages[:, -iy, ix].T
progress.setConsoleInfo(
"Finished loading coverage data of environmental layers")
# Starting modelling
progress.setConsoleInfo("Finished preparing the data for the analysis")
progress.setConsoleInfo("----")
progress.setConsoleInfo("Starting Modelling with support of sklearn")
# Standardize features
#TODO: Enable different or no Standardization methods
mean = sp_Bunch.cov.mean(axis=0)
std = sp_Bunch.cov.std(axis=0)
train_cover_std = (sp_Bunch.cov - mean) / std
# Fit OneClassSVM
progress.setConsoleInfo("Fitting Support Vector Machine")
# TODO: Allow the user to vary the input
clf = svm.OneClassSVM(nu=0.1, kernel="rbf", gamma=0.5)
clf.fit(train_cover_std)
progress.setConsoleInfo("Fitting done")
# Predict species distribution using the training data
Z = numpy.ones((data.Ny, data.Nx), dtype=numpy.float64)
# We'll predict only for the land points.
idx = numpy.where(land_reference > -9999)
coverages_land = data.coverages[:, idx[0], idx[1]].T
pred = clf.decision_function((coverages_land - mean) / std)[:, 0]
Z *= pred.min()
Z[idx[0], idx[1]] = pred
levels = numpy.linspace(Z.min(), Z.max(), 25)
Z[land_reference == -9999] = -9999
result = Z # save the final results scores
# Compute AUC w.r.t. background points
pred_background = Z[background_points[0], background_points[1]]
pred_test = clf.decision_function((species.cov_test - mean) / std)[:,
0]
scores = numpy.r_[pred_test, pred_background]
y = numpy.r_[numpy.ones(pred_test.shape),
numpy.zeros(pred_background.shape)]
fpr, tpr, thresholds = metrics.roc_curve(y, scores)
roc_auc = metrics.auc(fpr, tpr) # Area under the ROC curve
# TODO: Evaluate the availability of other metrics to compute on (average mean error, etc.. )
# Create Output Prediction File
output = self.getOutputValue(self.OUT_PRED_RES)
titles = ['AUC']
res_pred = [roc_auc]
# Save Output
func.saveToCSV(res_pred, titles, output)
# Create Output for resulting prediction
metadata = driver.GetMetadata()
if metadata.has_key(
gdal.DCAP_CREATE) and metadata[gdal.DCAP_CREATE] == "YES":
pass
else:
progress.setConsoleInfo(
"Output creation of input Fileformat is not supported by gdal. Create GTiff by default."
)
driver = gdal.GetDriverByName("GTiff")
data_type = result.dtype
try:
outData = driver.Create(output, columns, rows, 1, data_type)
except Exception, e:
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,
"Output file could not be created!")
def processAlgorithm(self, progress):
# Set up the data as sklearn bunch (basically just a dictionary with specific attributes)
data = Bunch()
# Vector layer
vector = self.getParameterValue(self.SPECIES)
v = Processing.getObject(vector)
v_crs = v.crs()
# Environmental layers
envlayers = self.getParameterValue(self.ENV)
if func.unificationNecessary(envlayers.split(";")):
raise GeoAlgorithmExecutionException("All input environmental layers need to have the same resolution and extent. Use the Unify tool beforehand")
#TODO: Enable option to do this automatically
progress.setConsoleInfo("Loading Coverage Data")
# Check Projection and Cellsize
for lay in envlayers.split(";"):
r = Processing.getObject(lay) # QgsRasterLayer object
if r.crs() != v_crs:
raise GeoAlgorithmExecutionException("All input layers need to have the same projection")
if round(r.rasterUnitsPerPixelX()) != round(r.rasterUnitsPerPixelY()):
raise GeoAlgorithmExecutionException("Grid Cell size values are not equal. Please be sure that grid cells are squares.")
# Set coverage parameters
r = Processing.getObject(envlayers.split(";")[0]) # QgsRasterLayer object
ex = r.extent()
data["grid_size"] = r.rasterUnitsPerPixelX()
data["Nx"] = r.width()
data["Ny"] = r.height()
data["x_left_lower_corner"] = ex.xMinimum()
data["y_left_lower_corner"] = ex.yMinimum()
# Load in Coverage values
coverage = []
for lay in envlayers.split(";"):
raster = gdal.Open(str(lay))
if raster.RasterCount > 1:
progress.setConsoleInfo("Warning: Multiple bands for layer detected. Using only first band.")
array = raster.GetRasterBand(1).ReadAsArray()
NA = raster.GetRasterBand(1).GetNoDataValue()
if NA == None:
raise GeoAlgorithmExecutionException("Warning: Raster layer has no no-data value. Please specify a no-data value for this dataset.")
else:
array[array==NA] = -9999 # Replace nodata-values of array with -9999
coverage.append(array)
data["coverages"] = numpy.array( coverage ) # Load all the coverage values into the bunch
# Setup parameters for output prediction
a = gdal.Open(envlayers.split(";")[0])
columns = a.RasterXSize
rows = a.RasterYSize
driver = a.GetDriver()
NA = -9999
gt = a.GetGeoTransform()
proj = a.GetProjection()
output = self.getOutputValue(self.OUT_PRED)
# Set up the data grid
xgrid, ygrid = construct_grids(data)
# The grid in x,y coordinates
X, Y = numpy.meshgrid(xgrid, ygrid[::-1])
# background points (grid coordinates) for evaluation
numpy.random.seed(100)
background_points = numpy.c_[numpy.random.randint(low=0, high=data.Ny,
size=10000),
numpy.random.randint(low=0, high=data.Nx,
size=10000)].T
# We'll make use of the fact that coverages[6] has measurements at all
# land points. This will help us decide between land and water.
# FIXME: Assuming that all predictors have a similar distribution. Might be violated
land_reference = data.coverages[0]
progress.setConsoleInfo("Loading Occurence Data and coverage")
# Creating response
train = []
for feature in v.getFeatures():
geom = feature.geometry().asPoint()
mx = geom.x()
my = geom.y()
train.append((mx,my))
data["train"] = numpy.array(train) # Add to bunch as training dataset
# create species bunch
sp_Bunch = Bunch(name="Species")
points = dict(train=data.train)
for label, pts in points.iteritems():
#determine coverage values for each of the training & testing points
ix = numpy.searchsorted(xgrid, pts[0])
iy = numpy.searchsorted(ygrid, pts[1])
bunch['cov_%s' % label] = data.coverages[:, -iy, ix].T
progress.setConsoleInfo("Finished loading coverage data of environmental layers")
# Starting modelling
progress.setConsoleInfo("Finished preparing the data for the analysis")
progress.setConsoleInfo("----")
progress.setConsoleInfo("Starting Modelling with support of sklearn")
# Standardize features
#TODO: Enable different or no Standardization methods
mean = sp_Bunch.cov.mean(axis=0)
std = sp_Bunch.cov.std(axis=0)
train_cover_std = (sp_Bunch.cov - mean) / std
# Fit OneClassSVM
progress.setConsoleInfo("Fitting Support Vector Machine")
# TODO: Allow the user to vary the input
clf = svm.OneClassSVM(nu=0.1, kernel="rbf", gamma=0.5)
clf.fit(train_cover_std)
progress.setConsoleInfo("Fitting done")
# Predict species distribution using the training data
Z = numpy.ones((data.Ny, data.Nx), dtype=numpy.float64)
# We'll predict only for the land points.
idx = numpy.where(land_reference > -9999)
coverages_land = data.coverages[:, idx[0], idx[1]].T
pred = clf.decision_function((coverages_land - mean) / std)[:, 0]
Z *= pred.min()
Z[idx[0], idx[1]] = pred
levels = numpy.linspace(Z.min(), Z.max(), 25)
Z[land_reference == -9999] = -9999
result = Z # save the final results scores
# Compute AUC w.r.t. background points
pred_background = Z[background_points[0], background_points[1]]
pred_test = clf.decision_function((species.cov_test - mean)
/ std)[:, 0]
scores = numpy.r_[pred_test, pred_background]
y = numpy.r_[numpy.ones(pred_test.shape), numpy.zeros(pred_background.shape)]
fpr, tpr, thresholds = metrics.roc_curve(y, scores)
roc_auc = metrics.auc(fpr, tpr) # Area under the ROC curve
# TODO: Evaluate the availability of other metrics to compute on (average mean error, etc.. )
# Create Output Prediction File
output = self.getOutputValue(self.OUT_PRED_RES)
titles = ['AUC']
res_pred = [roc_auc]
# Save Output
func.saveToCSV(res_pred, titles, output)
# Create Output for resulting prediction
metadata = driver.GetMetadata()
if metadata.has_key( gdal.DCAP_CREATE ) and metadata[ gdal.DCAP_CREATE ] == "YES":
pass
else:
progress.setConsoleInfo("Output creation of input Fileformat is not supported by gdal. Create GTiff by default.")
driver = gdal.GetDriverByName("GTiff")
data_type = result.dtype
try:
outData = driver.Create(output, columns, rows, 1, data_type)
except Exception, e:
ProcessingLog.addToLog(ProcessingLog.LOG_ERROR,"Output file could not be created!")
