#print "Buffering all points for " + group + "\n"
#point_buffer = arcpy.sa.EucDistance(points_fc,buffer_dist,grid_resolution)
## get a list of the lineages in this group
lineage_list=[]
print "Lineages in " + group + ":"
for row in GroupLineageList:
if row[3] not in lineage_list:
if row[2] == group and "," not in row[3] and row[3] not in Lin_exclude_list: # exclude particular lineage names and those with dodgy punctuation (fix in data later)
lineage_list.append(row[3])
print " ", row[3]
maxent_extent = maxent_raster.extent
# get the extent of the points for the model group
yrange=LineageFunctions.getFieldMinMax(points_fc,"Lat")
ymin=yrange[0]
ymax=yrange[1]
xrange=LineageFunctions.getFieldMinMax(points_fc,"Long")
xmin=xrange[0]
xmax=xrange[1]
buffer_ratio = (1 + additional_buffer)
extent_buffer = buffer_dist * buffer_ratio
# new extent is the same as points layer + a buffer
# but where the extended buffer goes beyond the extent of the maxent model, limit to the model extent (determined by the buffered environemnt grids)
xmin=math.floor(max([xmin - extent_buffer,maxent_extent.XMin]))
ymin=math.floor(max([ymin - extent_buffer,maxent_extent.YMin]))
xmax=math.ceil(min([xmax + extent_buffer,maxent_extent.XMax]))
ymax=math.ceil(min([ymax + extent_buffer,maxent_extent.YMax]))
env.extent = Australia_extent
maxent_raster = arcpy.sa.Raster(maxent_model)
# start a list of layers to delete at the end
layers_to_delete = []
## Buffer the full set of sequenced locations STEPS 1 & 2
print "Buffering all points\n"
point_buffer = arcpy.sa.EucDistance(points, buffer_dist, grid_resolution)
point_buffer.save("all_points_buf") ## once the code is working, no need to save this layer
layers_to_delete.append("all_points_buf")
## from the points shapefile, get a list of the lineages
print "Lineage list\n"
lineage_list = LineageFunctions.getFieldValues(points, Lineage_field_name)
print "Lineages:"
for lineage in lineage_list:
print " ", lineage
# calculate the extent for weight grids
points_properties = arcpy.Describe(points)
points_extent = points_properties.extent
buffer_ratio = 1 + additional_buffer
extent_buffer = buffer_dist * buffer_ratio
# new extent is the same as points layer + a buffer
# but where the extended buffer goes beyond the extent of Australia, limit to Australia
xmin = math.floor(max([points_extent.xmin - extent_buffer, Australia_extent.XMin]))
ymin = math.floor(max([points_extent.ymin - extent_buffer, Australia_extent.YMin]))
xmax = math.ceil(min([points_extent.xmax + extent_buffer, Australia_extent.XMax]))
except:
print "\n" + outFeatureClass + " could not be created, or already exists."
points_fc = outLocation + "/" + outFeatureClass
# Loop through the list of Model Groups
for group in GroupList:
if group != 0 and group != "":
#if group == "Saproscincus challengeri": # this is a temp line to model just one group!!
print "\nStarting group " + group + "\n"
groupDefQuery = "[ModelGroup] = '" + group + "'"
points_layer_lin.definitionQuery = groupDefQuery
# get the extent of the points for the model group
xrange=LineageFunctions.getFieldMinMax(points_layer_lin,"long")
xmin=xrange[0]
xmax=xrange[1]
yrange=LineageFunctions.getFieldMinMax(points_layer_lin,"lat")
ymin=yrange[0]
ymax=yrange[1]
env.extent = arcpy.Extent(xmin,ymin,xmax,ymax)
# export a kml of the sites
group_nospaces = string.replace(group," ","_")
export_lyr = points_layer_lin
export_lyr.name = group_nospaces + "_lineages"
export_lyr.showLabels = True
lblClass = export_lyr.labelClasses[0]
lblClass.expression="[Lineage]"
kmz_name = export_lyr.name + ".kmz"
