def cc_copy_inputs():
"""Clip Climate Linkage Mapper inputs to smallest extent"""
lm_util.gprint("\nCOPYING LAYERS AND, IF NECESSARY, REDUCING EXTENT")
ext_poly = "ext_poly" # Extent polygon
climate_extent = arcpy.Raster(cc_env.climate_rast).extent
if cc_env.resist_rast is not None:
resist_extent = arcpy.Raster(cc_env.resist_rast).extent
xmin = max(climate_extent.XMin, resist_extent.XMin)
ymin = max(climate_extent.YMin, resist_extent.YMin)
xmax = min(climate_extent.XMax, resist_extent.XMax)
ymax = min(climate_extent.YMax, resist_extent.YMax)
# Set to minimum extent if resistance raster was given
arcpy.env.extent = arcpy.Extent(xmin, ymin, xmax, ymax)
# Want climate and resistance rasters in same spatial ref
# with same nodata cells
proj_resist_rast = sa.Con(sa.IsNull(cc_env.climate_rast),
sa.Int(cc_env.climate_rast),
cc_env.resist_rast)
proj_resist_rast.save(cc_env.prj_resist_rast)
else:
xmin = climate_extent.XMin
ymin = climate_extent.YMin
xmax = climate_extent.XMax
ymax = climate_extent.YMax
ones_resist_rast = sa.Con(sa.IsNull(cc_env.climate_rast),
sa.Int(cc_env.climate_rast), 1)
ones_resist_rast.save(cc_env.prj_resist_rast)
arcpy.CopyRaster_management(cc_env.climate_rast, cc_env.prj_climate_rast)
# Create core raster
arcpy.env.extent = arcpy.Extent(xmin, ymin, xmax, ymax)
lm_util.delete_data(cc_env.prj_core_rast)
arcpy.FeatureToRaster_conversion(
cc_env.core_fc, cc_env.core_fld, cc_env.prj_core_rast,
arcpy.Describe(cc_env.climate_rast).MeanCellHeight)
arcpy.env.extent = None
# Create array of boundary points
array = arcpy.Array()
pnt = arcpy.Point(xmin, ymin)
array.add(pnt)
pnt = arcpy.Point(xmax, ymin)
array.add(pnt)
pnt = arcpy.Point(xmax, ymax)
array.add(pnt)
pnt = arcpy.Point(xmin, ymax)
array.add(pnt)
# Add in the first point of the array again to close polygon boundary
array.add(array.getObject(0))
# Create a polygon geometry object using the array object
ext_feat = arcpy.Polygon(array)
arcpy.CopyFeatures_management(ext_feat, ext_poly)
# Clip core feature class
arcpy.Clip_analysis(cc_env.core_fc, ext_poly, cc_env.prj_core_fc)
patchIDs.append(row.VALUE)
row = rows.next()
del row, rows
# Loop through patches and and calculate least cost paths
streamFC = "in_memory/LCPlines"
first = True
for patchID in patchIDs:
msg("Working on patch %s of %s" % (patchID, len(patchIDs)))
# Idenfity the cost and back link rasters
cdRaster = os.path.join(CostDistWS, "CD_%s.img" % patchID)
blRaster = os.path.join(CostDistWS, "BL_%s.img" % patchID)
# Calculate least cost paths from all patches to the current patch
lcpRaster = sa.CostPath(patchFix, cdRaster, blRaster, "EACH_ZONE")
if first:
lcpOutput = sa.Con(sa.IsNull(lcpRaster), 0, 1)
first = False
else:
lcpTemp = sa.Con(sa.IsNull(lcpRaster), 0, 1) + lcpOutput
lcpOutput = sa.Con(lcpTemp, 1, 0, "VALUE > 0")
'''
# Convert the backlink to a flow direction raster
#fdRaster = sa.Int(sa.Exp2(blRaster) / 2)
# Convert the LCP raster to a vector
if first: # If the first patch, save the streamsFC to the output FC file
sa.StreamToFeature(lcpRaster,fdRaster,lcpFC,"NO_SIMPLIFY")
first = False
else: # Otherwise, create it and append it to the original
sa.StreamToFeature(lcpRaster,fdRaster,streamFC,"NO_SIMPLIFY")
arcpy.Append_management(streamFC,lcpFC)
'''
# f3: vegetation
f3t = os.path.join(scratch,"f3t")
f3 = os.path.join(scratch,"f3")
arcpy.AddMessage("Clipping vegetation to fishnet and joining parameter table...")
vegetation = os.path.join("in_memory","vegetation")
if debug == True: arcpy.AddMessage(str(time.strftime("Clip Vegetation: %m/%d/%Y %H:%M:%S", time.localtime())))
arcpy.Clip_analysis(inputVegetation,inputAOI,vegetation)
deleteme.append(vegetation)
arcpy.JoinField_management(vegetation,"f_code",inputVegetationConversionTable,"f_code")
# Convert vegetation to Raster using MIN or MAX field
if min_max == "MAX":
arcpy.PolygonToRaster_conversion(vegetation,"f3max",f3t)
else:
arcpy.PolygonToRaster_conversion(vegetation,"f3min",f3t)
# if F3T is null, make it 1.0 (from constNoEffect), otherwise keep F3T value
outF3T = sa.Con(sa.IsNull(f3t),constNoEffect,f3t)
outF3T.save(f3)
deleteme.append(f3t)
deleteme.append(f3)
#TODO: what about areas in the AOI but outside VEG? No effect (value = 1.0)?
ccmFactorList.append(f3)
if inputSoils != types.NoneType and arcpy.Exists(inputSoils) == True:
# f4: soils
f4t = os.path.join(scratch,"f4t")
f4 = os.path.join(scratch,"f4")
arcpy.AddMessage("Clipping soils to fishnet and joining parameter table...")
clipSoils = os.path.join("in_memory","clipSoils")
if debug == True: arcpy.AddMessage(str(time.strftime("Clip Soils: %m/%d/%Y %H:%M:%S", time.localtime())))
arcpy.Clip_analysis(inputSoils,inputAOI,clipSoils)
deleteme.append(clipSoils)
def preprocess(layerName):
"""
Source dir: resistances
Output dir: preprocessed
"""
paths.setEnv(env)
env.overwriteOutput = True
source = paths.join(paths.resistances, layerName)
output = paths.join(paths.preprocessed, layerName)
print "Preprocessing {}: {} ==> {}".format(layerName, source, output)
if arcpy.Exists(output) and not redoExistingOutput:
print "{} already exists, leaving it as is.".format(output)
return output
for tempras in ["projected", "clipped"]:
try:
arcpy.Raster(tempras)
print "Deleting temporary: {}".format(tempras)
arcpy.Delete_management(tempras)
except RuntimeError:
pass # tempfile doesn't exist, we're good
print "Projecting and resampling..."
arcpy.ProjectRaster_management(source,
"projected",
paths.alaskaAlbers,
cell_size=500)
source = arcpy.Raster(source)
print "Initial extent: {} {} {} {}".format(source.extent.XMin,
source.extent.YMin,
source.extent.XMax,
source.extent.YMax)
newExt = arcpy.Describe(paths.studyArea).extent
print "New intended extent: {} {} {} {}".format(newExt.XMin, newExt.YMin,
newExt.XMax, newExt.YMax)
print "Clipping..."
# TODO: despite specifying an extent, it refuses to clip to exactly that (except by filling in borders with NoData)
arcpy.Clip_management("projected", "", "clipped", paths.studyArea, "",
"ClippingGeometry", "NO_MAINTAIN_EXTENT")
clipped = arcpy.Raster("clipped")
print "New actual extent: {} {} {} {}".format(clipped.extent.XMin,
clipped.extent.YMin,
clipped.extent.XMax,
clipped.extent.YMax)
print "Normalizing..."
outRas = arcpy.Raster("clipped")
outRas = (outRas - outRas.minimum) / (outRas.maximum - outRas.minimum)
# de-null
outRas = sa.Con(sa.IsNull(outRas), 0, outRas)
env.overwriteOutput = True
outRas.save(output)
arcpy.Delete_management("projected")
arcpy.Delete_management("clipped")
return output
dict = {}
dict[1] = 3 #D
dict[2] = 2 #C
dict[3] = 1 #V
dict[4] = 2 #C/D
dict[5] = 0 #A
dict[6] = 1 #B/D
dict[7] = 0 #A/D
return dict
cnDict = createCNDict()
hgrpDict = createHgrpLookup()
# Plug NoData values in hgrpRasters with a class of D
hgrpFix = sa.Con(sa.IsNull(hgrpRaster), 1, hgrpRaster)
# combine the rasters
msg("Combining NLCD and Hydrologic group rasters")
comboRaster = sa.Combine([nlcdRaster, hgrpFix])
nlcdFld = arcpy.ListFields(comboRaster)[-2].name
hgrpFld = arcpy.ListFields(comboRaster)[-1].name
# add a new field to the comboRaster
msg("Adding curve number field to output raster")
arcpy.AddField_management(comboRaster, "CN", "LONG", 4)
# update values based on the dictionary
msg("Adding curve number values to output raster")
rows = arcpy.UpdateCursor(comboRaster)
row = rows.next()
# ---Functions---
def msg(txt, type="message"):
print txt
if type == "message":
arcpy.AddMessage(txt)
elif type == "warning":
arcpy.AddWarning(txt)
elif type == "error":
arcpy.AddError(txt)
# ---Processes---
## Create a raster of stream cells, with values set to elevation
msg("Creating a streams raster (inverting NHD FlowDirNull Raster)")
strmRaster = sa.IsNull(fdrnullRaster)
msg("Assigning elevation values to stream cells")
strmElevRaster1 = sa.Con(strmRaster, elevRaster)
#If the elevation values
strmElevRaster = sa.Con(strmElevRaster1, strmElevRaster1, 1, "VALUE >= 1")
## Create a watershed, using the stream elevation raster as the pour points.
'''Cell values in this output are the elevation at the point where the given
cell's location flows into the stream. This, in turn, can be compared to
the actual elevation at the cell's location to compute the vertical drop
between the cell and where it drains into the stream'''
msg("Calculating watersheds labeled with elevation")
try:
elevSheds = sa.Watershed(fldrRaster, strmElevRaster, "VALUE")
except:
#Output variables
dist2edgeRaster = sys.argv[
6] #r'C:\WorkSpace\GBAT2012\GHAT_V011\scratch\dist2edge'
corePatches = sys.argv[
7] #r'C:\WorkSpace\GBAT2012\GHAT_V011\scratch\corePatches'
dist2habRaster = sys.argv[
8] #r'C:\WorkSpace\GBAT2012\GHAT_V011\scratch\dist2hab'
subnetRaster = sys.argv[9] #r'C:\WorkSpace\GBAT2012\GHAT_V011\scratch\subnet'
dist2protRaster = sys.argv[
10] #r'C:\WorkSpace\GBAT2012\GHAT_V011\scratch\dist2prot'
##--Process 1: Calculate distance to patch edge--
arcpy.AddMessage("Calculating distance to patch edge")
arcpy.AddMessage("...inverting habitat raster")
nonHabitatBinary = sa.Con(sa.IsNull(patchRaster), 1)
arcpy.AddMessage("...calculating distances from edge into patch")
eucDist = sa.EucDistance(nonHabitatBinary)
eucDist.save(dist2edgeRaster)
##--Process 2: Extract core areas (using distance to edge)
arcpy.AddMessage("Extracting core areas")
core = sa.SetNull(eucDist, patchRaster, "VALUE <= %s" % edgeWidth)
core.save(corePatches)
##--Process 3: Calculate cost distance away from patch
arcpy.AddMessage("Calculating cost distance from patches")
costDist2H = sa.CostDistance(patchRaster, costRaster)
costDist2H.save(dist2habRaster)
##-Process 4: Extract patch subnetwork areas (from distance to habitat)
# Message function
def msg(txt): print txt; arcpy.AddMessage(txt); return
##-PROCESSES-
# 1. Convert curve number to a weight: Int((100 - cn) / 10). Higher CN values
# reflect increased runoff across the cell. This equation inverts the
# CN value and scales it to values from 0 to 10. The resulting value reflects
# a proxy for infiltration: higher values suggest more runoff stays in the cell
# meaning less pollutants will leave the cell to downstream neighbors.
msg("Calculating flow length weight from %s" %cnRaster)
weightRaster = sa.Int(sa.Divide(sa.Minus(100.0,cnRaster), 10.0) + 1)
# 2. Create a flow direction where streams are NoData. This enables calculation
# of flow length to the stream vs to the stream outlet.
msg("Creating modified flow direction to calculate distance to streams")
fdRaster = sa.Con(sa.IsNull(streamsRaster),flowdirRaster)
# 3. Calculate cost-weighted flowlength. Cell values represent the infiltrated-
# weighted distance along the flow path to a stream. Two paths may be the same
# length, but if one goes through cells with high curve numbers (low weights)
# it's path will be effectively shorter whereas a path going through cells with
# low curve numbers (high weights) will be effectively longer - in terms of
# suspended/dissolved pollutants reaching the stream.
msg("Calculating weighted flow length")
wtdflRaster1 = sa.FlowLength(fdRaster,"DOWNSTREAM",weightRaster) + 30
#Set stream pixels to 0
wtdflRaster = sa.Con(sa.IsNull(streamsRaster), wtdflRaster1, 0)
# 4. Apply a decay coefficient to weighted flow lengths to create distance decay raster
# k = math.log(0.01) / d, where d is obtained from the unweighted flow length(?)
msg("Calculating distance decayed rasters")
