def test_for_intermediate_core(workspace,lcpRas,corePairRas):
""" Test if there is an intermediate core by seeing if least-cost
path and remaining cores intersect
"""
try:
gp.workspace = workspace
gp.OverwriteOutput = True
if gp.exists("addRas"): #Can't use tif for getrasterproperties
gp.delete_management("addRas")
count = 0
if arcpy:
statement = ('outRas = Raster(lcpRas) + Raster(corePairRas); '
'outRas.save("addRas")')
else:
expression = (lcpRas + " + " + corePairRas)
statement = ('gp.SingleOutputMapAlgebra_sa(expression, "addRas")')
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec statement
else: break
#addRasPath = path.join(workspace,"addRas")
# make sure there is a raster, even if empty, and properties
# are obtainable
propertyType = "TOP"
topObject = gp.GetRasterProperties("addRas", propertyType)
# Test to see if raster has data
try:
propertyType = "MINIMUM"
# In Arc 10, next statement fails for empty rasters
minObject = gp.GetRasterProperties("addRas", propertyType)
# In Arc 9.3, next statement fails for empty rasters
minVal = int(minObject.getoutput(0))
return True # If there is data in raster, return True
except:
return False # Failure indicates empty raster and no overlap
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
# gprint('****Failed in step 3. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
# gprint('****Failed in step 3. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def test_for_intermediate_core(workspace,lcpRas,corePairRas):
""" Test if there is an intermediate core by seeing if least-cost
path and remaining cores intersect
"""
try:
gp.workspace = workspace
gp.OverwriteOutput = True
if gp.exists("addRas"): #Can't use tif for getrasterproperties
gp.delete_management("addRas")
count = 0
if arcpy:
statement = ('outRas = Raster(lcpRas) + Raster(corePairRas); '
'outRas.save("addRas")')
else:
expression = (lcpRas + " + " + corePairRas)
statement = ('gp.SingleOutputMapAlgebra_sa(expression, "addRas")')
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec statement
else: break
#addRasPath = path.join(workspace,"addRas")
# make sure there is a raster, even if empty, and properties
# are obtainable
propertyType = "TOP"
topObject = gp.GetRasterProperties("addRas", propertyType)
# Test to see if raster has data
try:
propertyType = "MINIMUM"
# In Arc 10, next statement fails for empty rasters
minObject = gp.GetRasterProperties("addRas", propertyType)
# In Arc 9.3, next statement fails for empty rasters
minVal = int(minObject.getoutput(0))
return True # If there is data in raster, return True
except:
return False # Failure indicates empty raster and no overlap
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
# gprint('****Failed in step 3. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
# gprint('****Failed in step 3. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def test_for_intermediate_core(workspace, lcpRas, corePairRas):
""" Test if there is an intermediate core by seeing if least-cost
path and remaining cores intersect
"""
try:
arcpy.env.workspace = workspace
if arcpy.Exists("addRas"): #Can't use tif for getrasterproperties
arcpy.Delete_management("addRas")
count = 0
statement = ('outRas = arcpy.sa.Raster(lcpRas) '
'+ arcpy.sa.Raster(corePairRas); '
'outRas.save("addRas")')
while True:
try:
exec(statement)
except Exception:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain: exec(statement)
else: break
# Test to see if raster has data
if (arcpy.GetRasterProperties_management(
"addRas", "ALLNODATA").getOutput(0) == "0"):
return True # Data present and therefore overlap
else:
return False # Empty and therefore no overlap
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except Exception:
lu.dashline(1)
lu.exit_with_python_error(_SCRIPT_NAME)
def calc_lccs(normalize):
try:
if normalize:
mosaicBaseName = "_corridors"
writeTruncRaster = cfg.WRITETRUNCRASTER
outputGDB = cfg.OUTPUTGDB
SAVENORMLCCS = cfg.SAVENORMLCCS
else:
mosaicBaseName = "_NON_NORMALIZED_corridors"
SAVENORMLCCS = False
outputGDB = cfg.EXTRAGDB
writeTruncRaster = False
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
linkTableFile = lu.get_prev_step_link_table(step=5)
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.compression = "NONE"
if cfg.MAXEUCDIST is not None:
gprint('Max Euclidean distance between cores')
gprint('for linkage mapping set to ' +
str(cfg.MAXEUCDIST))
if cfg.MAXCOSTDIST is not None:
gprint('Max cost-weighted distance between cores')
gprint('for linkage mapping set to ' +
str(cfg.MAXCOSTDIST))
# set the analysis extent and cell size to that of the resistance
# surface
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = arcpy.Describe(cfg.RESRAST).MeanCellHeight
arcpy.env.snapRaster = cfg.RESRAST
arcpy.env.mask = cfg.RESRAST
linkTable = lu.load_link_table(linkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg =('\nThere are no corridors to map. Bailing.')
lu.raise_error(msg)
if not cfg.STEP3 and not cfg.STEP4:
# re-check for links that are too long or in case script run out of
# sequence with more stringent settings
gprint('Double-checking for corridors that are too long to map.')
DISABLE_LEAST_COST_NO_VAL = True
linkTable,numDroppedLinks = lu.drop_links(
linkTable, cfg.MAXEUCDIST, cfg.MINEUCDIST, cfg.MAXCOSTDIST,
cfg.MINCOSTDIST, DISABLE_LEAST_COST_NO_VAL)
# Added to try to speed up:
arcpy.env.pyramid = "NONE"
arcpy.env.rasterStatistics = "NONE"
# set up directories for normalized lcc and mosaic grids
dirCount = 0
gprint("Creating output folder: " + cfg.LCCBASEDIR)
lu.delete_dir(cfg.LCCBASEDIR)
arcpy.CreateFolder_management(path.dirname(cfg.LCCBASEDIR),
path.basename(cfg.LCCBASEDIR))
arcpy.CreateFolder_management(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
clccdir = path.join(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
gprint("")
if normalize:
gprint('Normalized least-cost corridors will be written '
'to ' + clccdir + '\n')
PREFIX = cfg.PREFIX
# Add CWD layers for core area pairs to produce NORMALIZED LCC layers
numGridsWritten = 0
coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
coreList = npy.sort(coreList)
x = 0
linkCount = 0
endIndex = numLinks
while x < endIndex:
if (linkTable[x, cfg.LTB_LINKTYPE] < 1): # If not a valid link
x = x + 1
continue
linkCount = linkCount + 1
start_time = time.clock()
linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
# source and target cores
corex=int(coreList[x,0])
corey=int(coreList[x,1])
# Get cwd rasters for source and target cores
cwdRaster1 = lu.get_cwd_path(corex)
cwdRaster2 = lu.get_cwd_path(corey)
if not arcpy.Exists(cwdRaster1):
msg =('\nError: cannot find cwd raster:\n' + cwdRaster1)
if not arcpy.Exists(cwdRaster2):
msg =('\nError: cannot find cwd raster:\n' + cwdRaster2)
lu.raise_error(msg)
lccNormRaster = path.join(clccdir, str(corex) + "_" +
str(corey))# + ".tif")
arcpy.env.extent = "MINOF"
link = lu.get_links_from_core_pairs(linkTable, corex, corey)
offset = 10000
# Normalized lcc rasters are created by adding cwd rasters and
# subtracting the least cost distance between them.
lcDist = (float(linkTable[link,cfg.LTB_CWDIST]) - offset)
if normalize:
statement = ('outras = arcpy.sa.Raster(cwdRaster1) '
'+ arcpy.sa.Raster(cwdRaster2) - lcDist; '
'outras.save(lccNormRaster)')
else:
statement = ('outras = arcpy.sa.Raster(cwdRaster1) '
'+ arcpy.sa.Raster(cwdRaster2); '
'outras.save(lccNormRaster)')
count = 0
while True:
try:
exec(statement)
except Exception:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain:
exec(statement)
else: break
if normalize:
try:
minObject = arcpy.GetRasterProperties_management(lccNormRaster, "MINIMUM")
rasterMin = float(str(minObject.getOutput(0)))
except Exception:
lu.warn('\n------------------------------------------------')
lu.warn('WARNING: Raster minimum check failed in step 5. \n'
'This may mean the output rasters are corrupted. Please \n'
'be sure to check for valid rasters in '+ outputGDB)
rasterMin = 0
tolerance = (float(arcpy.env.cellSize) * -10)
if rasterMin < tolerance:
lu.dashline(1)
msg = ('WARNING: Minimum value of a corridor #' + str(x+1)
+ ' is much less than zero ('+str(rasterMin)+').'
'\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
'were too small and a corridor passed outside of a '
'bounding circle, or that a corridor passed outside of the '
'resistance map. \n')
lu.warn(msg)
arcpy.env.extent = cfg.RESRAST
mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1))
lu.create_dir(mosaicDir)
mosFN = 'mos'#.tif' change and move
mosaicRaster = path.join(mosaicDir,mosFN)
if numGridsWritten == 0 and dirCount == 0:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(lccNormRaster, mosaicRaster)
else:
statement = (
'arcpy.MosaicToNewRaster_management('
'input_rasters=";".join([lccNormRaster, '
'lastMosaicRaster]), output_location=mosaicDir, '
'raster_dataset_name_with_extension=mosFN, '
'pixel_type="32_BIT_FLOAT", cellsize=arcpy.env.cellSize, '
'number_of_bands="1", mosaic_method="MINIMUM")')
count = 0
while True:
try:
lu.write_log('Executing mosaic for link #'+str(linkId))
exec(statement)
lu.write_log('Done with mosaic.')
except Exception:
count,tryAgain = lu.retry_arc_error(count,statement)
lu.delete_data(mosaicRaster)
lu.delete_dir(mosaicDir)
# Try a new directory
mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1)+ '_' + str(count))
lu.create_dir(mosaicDir)
mosaicRaster = path.join(mosaicDir,mosFN)
if not tryAgain:
exec(statement)
else: break
endTime = time.clock()
processTime = round((endTime - start_time), 2)
if normalize == True:
printText = "Normalized and mosaicked "
else:
printText = "Mosaicked NON-normalized "
gprint(printText + "corridor for link ID #" + str(linkId) +
" connecting core areas " + str(corex) +
" and " + str(corey)+ " in " +
str(processTime) + " seconds. " + str(int(linkCount)) +
" out of " + str(int(numCorridorLinks)) + " links have been "
"processed.")
# temporarily disable links in linktable - don't want to mosaic
# them twice
for y in range (x+1,numLinks):
corex1 = int(coreList[y,0])
corey1 = int(coreList[y,1])
if corex1 == corex and corey1 == corey:
linkTable[y,cfg.LTB_LINKTYPE] = (
linkTable[y,cfg.LTB_LINKTYPE] + 1000)
elif corex1==corey and corey1==corex:
linkTable[y,cfg.LTB_LINKTYPE] = (
linkTable[y,cfg.LTB_LINKTYPE] + 1000)
numGridsWritten = numGridsWritten + 1
if not SAVENORMLCCS:
lu.delete_data(lccNormRaster)
lu.delete_dir(clccdir)
lu.create_dir(clccdir)
else:
if numGridsWritten == 100:
# We only write up to 100 grids to any one folder
# because otherwise Arc slows to a crawl
dirCount = dirCount + 1
numGridsWritten = 0
clccdir = path.join(cfg.LCCBASEDIR,
cfg.LCCNLCDIR_NM + str(dirCount))
gprint("Creating output folder: " + clccdir)
arcpy.CreateFolder_management(cfg.LCCBASEDIR,
path.basename(clccdir))
if numGridsWritten > 1 or dirCount > 0:
lu.delete_data(lastMosaicRaster)
lu.delete_dir(path.dirname(lastMosaicRaster))
lastMosaicRaster = mosaicRaster
x = x + 1
#rows that were temporarily disabled
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE]>1000)
linkTable[rows,cfg.LTB_LINKTYPE] = (
linkTable[rows,cfg.LTB_LINKTYPE] - 1000)
# ---------------------------------------------------------------------
# Create output geodatabase
if not arcpy.Exists(outputGDB):
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR, path.basename(outputGDB))
arcpy.env.workspace = outputGDB
arcpy.env.pyramid = "NONE"
arcpy.env.rasterStatistics = "NONE"
# ---------------------------------------------------------------------
# convert mosaic raster to integer
intRaster = path.join(outputGDB,PREFIX + mosaicBaseName)
statement = ('outras = arcpy.sa.Int(arcpy.sa.Raster(mosaicRaster) '
'- offset + 0.5); '
'outras.save(intRaster)')
count = 0
while True:
try:
exec(statement)
except Exception:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec(statement)
else: break
# ---------------------------------------------------------------------
if writeTruncRaster:
# -----------------------------------------------------------------
# Set anything beyond cfg.CWDTHRESH to NODATA.
truncRaster = (outputGDB + '\\' + PREFIX + mosaicBaseName +
'_truncated_at_' + lu.cwd_cutoff_str(cfg.CWDTHRESH))
statement = ('outRas = arcpy.sa.Raster(intRaster)'
'* (arcpy.sa.Con(arcpy.sa.Raster(intRaster) '
'<= cfg.CWDTHRESH, 1)); '
'outRas.save(truncRaster)')
count = 0
while True:
try:
exec(statement)
except Exception:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec(statement)
else: break
# ---------------------------------------------------------------------
# Check for unreasonably low minimum NLCC values
try:
mosaicGrid = path.join(cfg.LCCBASEDIR,'mos')
# Copy to grid to test
arcpy.CopyRaster_management(mosaicRaster, mosaicGrid)
minObject = arcpy.GetRasterProperties_management(mosaicGrid, "MINIMUM")
rasterMin = float(str(minObject.getOutput(0)))
except Exception:
lu.warn('\n------------------------------------------------')
lu.warn('WARNING: Raster minimum check failed in step 5. \n'
'This may mean the output rasters are corrupted. Please \n'
'be sure to check for valid rasters in '+ outputGDB)
rasterMin = 0
tolerance = (float(arcpy.env.cellSize) * -10)
if rasterMin < tolerance:
lu.dashline(1)
msg = ('WARNING: Minimum value of mosaicked corridor map is '
'much less than zero ('+str(rasterMin)+').'
'\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
'were too small and a corridor passed outside of a '
'bounding circle, or that a corridor passed outside of the '
'resistance map. \n')
lu.warn(msg)
gprint('\nWriting final LCP maps...')
if cfg.STEP4:
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=4,
thisStep=5)
elif cfg.STEP3:
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=3,
thisStep=5)
else:
# Don't know if step 4 was run, since this is started at step 5.
# Use presence of previous linktable files to figure this out.
# Linktable name includes step number.
prevLinkTableFile = lu.get_prev_step_link_table(step=5)
prevStepInd = len(prevLinkTableFile) - 5
lastStep = prevLinkTableFile[prevStepInd]
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep,
thisStep=5)
outlinkTableFile = lu.get_this_step_link_table(step=5)
gprint('Updating ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s5.csv")
lu.write_link_table(linkTable, linkTableLogFile)
linkTableFinalFile = path.join(cfg.OUTPUTDIR, PREFIX +
"_linkTable_s5.csv")
lu.write_link_table(finalLinkTable, linkTableFinalFile)
gprint('Copy of final linkTable written to '+
linkTableFinalFile)
gprint('Creating shapefiles with linework for links.')
try:
lu.write_link_maps(outlinkTableFile, step=5)
except Exception:
lu.write_link_maps(outlinkTableFile, step=5)
# Create final linkmap files in output directory, and remove files from
# scratch.
lu.copy_final_link_maps(step=5)
if not SAVENORMLCCS:
lu.delete_dir(cfg.LCCBASEDIR)
# Build statistics for corridor rasters
arcpy.AddMessage('\nBuilding output statistics and pyramids '
'for corridor raster')
lu.build_stats(intRaster)
if writeTruncRaster:
arcpy.AddMessage('Building output statistics '
'for truncated corridor raster')
lu.build_stats(truncRaster)
save_parameters()
if cfg.OUTPUTFORMODELBUILDER:
arcpy.CopyFeatures_management(cfg.COREFC, cfg.OUTPUTFORMODELBUILDER)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 5. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except Exception:
lu.dashline(1)
gprint('****Failed in step 5. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def STEP3_calc_cwds():
"""Calculates cost-weighted distances from each core area.
Uses bounding circles around source and target cores to limit
extent of cwd calculations and speed computation.
"""
try:
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
lu.dashline(0)
# Super secret setting to re-start failed run. Enter 'RESTART' as the
# Name of the pairwise distance table in step 2, and uncheck step 2.
# We can eventually place this in a .ini file.
rerun = False
if cfg.S2EUCDISTFILE != None:
if cfg.S2EUCDISTFILE.lower() == "restart":
rerun = True
# if cfg.TMAXCWDIST is None:
# gprint('NOT using a maximum cost-weighted distance.')
# else:
# gprint('Max cost-weighted distance for CWD calcs set '
# 'to ' + str(cfg.TMAXCWDIST) + '\n')
if (cfg.BUFFERDIST) is not None:
gprint('Bounding circles plus a buffer of ' +
str(float(cfg.BUFFERDIST)) + ' map units will '
'be used \n to limit extent of cost distance '
'calculations.')
elif cfg.TOOL <> cfg.TOOL_CC:
gprint('NOT using bounding circles in cost distance '
'calculations.')
# set the analysis extent and cell size
# So we don't extract rasters that go beyond extent of original raster
if arcpy:
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.extent="MINOF"
else:
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
gp.Extent = "MINOF"
gp.mask = cfg.RESRAST
if arcpy:
arcpy.env.overwriteOutput = True
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
else:
gp.OverwriteOutput = True
gp.workspace = cfg.SCRATCHDIR
gp.scratchWorkspace = cfg.ARCSCRATCHDIR
# Load linkTable (created in previous script)
linkTableFile = lu.get_prev_step_link_table(step=3)
linkTable = lu.load_link_table(linkTableFile)
lu.report_links(linkTable)
# Identify cores to map from LinkTable
coresToMap = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
numCoresToMap = len(coresToMap)
if numCoresToMap < 3:
# No need to check for intermediate cores, because there aren't any
cfg.S3DROPLCCSic = False
else:
cfg.S3DROPLCCSic = cfg.S3DROPLCCS
gprint('\nNumber of core areas to connect: ' +
str(numCoresToMap))
if rerun:
# If picking up a failed run, make sure needed files are there
lu.dashline(1)
gprint ('\n****** RESTART MODE ENABLED ******\n')
gprint ('**** NOTE: This mode picks up step 3 where a\n'
'previous run left off due to a crash or user\n'
'abort. It assumes you are using the same input\n'
'data used in the terminated run.\n\n')
lu.warn('IMPORTANT: Your LCP and stick feature classes\n'
'will LOSE LCPs that were already created, but\n'
'your final raster corridor map should be complete.\n')
lu.dashline(0)
lu.snooze(10)
savedLinkTableFile = path.join(cfg.DATAPASSDIR,
"temp_linkTable_s3_partial.csv")
coreListFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")
if not path.exists(savedLinkTableFile) or not path.exists(
coreListFile):
gprint('No partial results file found from previous '
'stopped run. Starting run from beginning.\n')
lu.dashline(0)
rerun = False
# If picking up a failed run, use old folders
if not rerun:
startIndex = 0
if cfg.TOOL <> cfg.TOOL_CC:
lu.make_cwd_paths(max(coresToMap)) # Set up cwd directories
# make a feature layer for input cores to select from
gp.MakeFeatureLayer(cfg.COREFC, cfg.FCORES)
# Drop links that are too long
gprint('\nChecking for corridors that are too long to map.')
DISABLE_LEAST_COST_NO_VAL = False
linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST, 0,
cfg.MAXCOSTDIST, 0,
DISABLE_LEAST_COST_NO_VAL)
# ------------------------------------------------------------------
# Bounding boxes
if (cfg.BUFFERDIST) is not None:
# create bounding boxes around cores
start_time = time.clock()
# lu.dashline(1)
gprint('Calculating bounding boxes for core areas.')
extentBoxList = npy.zeros((0,5), dtype='float32')
for x in range(len(coresToMap)):
core = coresToMap[x]
boxCoords = lu.get_extent_box_coords(core)
extentBoxList = npy.append(extentBoxList, boxCoords, axis=0)
gprint('\nDone calculating bounding boxes.')
start_time = lu.elapsed_time(start_time)
# lu.dashline()
# Bounding circle code
if cfg.BUFFERDIST is not None:
# Make a set of circles encompassing core areas we'll be connecting
start_time = time.clock()
gprint('Calculating bounding circles around potential'
' corridors.')
# x y corex corey radius- stores data for bounding circle centroids
boundingCirclePointArray = npy.zeros((0,5), dtype='float32')
circleList = npy.zeros((0,3), dtype='int32')
numLinks = linkTable.shape[0]
for x in range(0, numLinks):
if ((linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
(linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_KEEP)):
# if it's a valid corridor link
linkId = int(linkTable[x,cfg.LTB_LINKID])
# fixme- this code is clumsy- can trim down
cores = npy.zeros((1,3), dtype='int32')
cores[0,:] = npy.sort([0, linkTable[x,cfg.LTB_CORE1],
linkTable[x,cfg.LTB_CORE2]])
corex = cores[0,1]
corey = cores[0,2]
cores[0,0] = linkId
###################
foundFlag = False
for y in range(0,len(circleList)): # clumsy
if (circleList[y,1] == corex and
circleList[y,2] == corey):
foundFlag = True
if not foundFlag:
circlePointData = (
lu.get_bounding_circle_data(extentBoxList,
corex, corey, cfg.BUFFERDIST))
boundingCirclePointArray = (
npy.append(boundingCirclePointArray,
circlePointData, axis=0))
# keep track of which cores we draw bounding circles
# around
circleList = npy.append(circleList, cores, axis=0)
gprint('\nCreating bounding circles using buffer '
'analysis.')
dir, BNDCIRCENS = path.split(cfg.BNDCIRCENS)
lu.make_points(cfg.SCRATCHDIR, boundingCirclePointArray,
BNDCIRCENS)
lu.delete_data(cfg.BNDCIRS)
gp.buffer_analysis(cfg.BNDCIRCENS, cfg.BNDCIRS, "radius")
gp.deletefield (cfg.BNDCIRS, "BUFF_DIST")
gprint('Successfully created bounding circles around '
'potential corridors using \na buffer of ' +
str(float(cfg.BUFFERDIST)) + ' map units.')
start_time = lu.elapsed_time(start_time)
gprint('Reducing global processing area using bounding '
'circle plus buffer of ' +
str(float(cfg.BUFFERDIST)) + ' map units.\n')
extentBoxList = npy.zeros((0,5),dtype='float32')
boxCoords = lu.get_extent_box_coords()
extentBoxList = npy.append(extentBoxList,boxCoords,axis=0)
extentBoxList[0,0] = 0
boundingCirclePointArray = npy.zeros((0,5),dtype='float32')
circlePointData=lu.get_bounding_circle_data(extentBoxList, 0,
0, cfg.BUFFERDIST)
dir, BNDCIRCEN = path.split(cfg.BNDCIRCEN)
lu.make_points(cfg.SCRATCHDIR, circlePointData, BNDCIRCEN)
lu.delete_data(cfg.BNDCIR)
gp.buffer_analysis(cfg.BNDCIRCEN, cfg.BNDCIR, "radius")
gprint('Extracting raster....')
cfg.BOUNDRESIS = cfg.BOUNDRESIS + tif
lu.delete_data(cfg.BOUNDRESIS)
count = 0
statement = (
'gp.ExtractByMask_sa(cfg.RESRAST, cfg.BNDCIR, cfg.BOUNDRESIS)')
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec statement
else: break
gprint('\nReduced resistance raster extracted using '
'bounding circle.')
else: #if not using bounding circles, just go with resistance raster.
cfg.BOUNDRESIS = cfg.RESRAST
# ---------------------------------------------------------------------
# Rasterize core areas to speed cost distance calcs
# lu.dashline(1)
gprint("Creating core area raster.")
gp.SelectLayerByAttribute(cfg.FCORES, "CLEAR_SELECTION")
if arcpy:
arcpy.env.cellSize = cfg.BOUNDRESIS
arcpy.env.extent = cfg.BOUNDRESIS
else:
gp.cellSize = gp.Describe(cfg.BOUNDRESIS).MeanCellHeight
gp.extent = gp.Describe(cfg.BOUNDRESIS).extent
if rerun:
# saved linktable replaces the one now in memory
linkTable = lu.load_link_table(savedLinkTableFile)
coresToMapSaved = npy.loadtxt(coreListFile, dtype='Float64',
comments='#', delimiter=',')
startIndex = coresToMapSaved[0] # Index of core where we left off
del coresToMapSaved
gprint ('\n****** Re-starting run at core area number '
+ str(int(coresToMap[startIndex]))+ ' ******\n')
lu.dashline(0)
if arcpy:
arcpy.env.extent = "MINOF"
else:
gp.extent = "MINOF"
#----------------------------------------------------------------------
# Loop through cores, do cwd calcs for each
if cfg.TOOL == cfg.TOOL_CC:
gprint("\nMapping least-cost paths.\n")
else:
gprint("\nStarting cost distance calculations.\n")
lcpLoop = 0
failures = 0
x = startIndex
endIndex = len(coresToMap)
linkTableMod = linkTable.copy()
while x < endIndex:
startTime1 = time.clock()
# Modification of linkTable in function was causing problems. so
# make a copy:
linkTablePassed = linkTableMod.copy()
(linkTableReturned, failures, lcpLoop) = do_cwd_calcs(x,
linkTablePassed, coresToMap, lcpLoop, failures)
if failures == 0:
# If iteration was successful, continue with next core
linkTableMod = linkTableReturned
sourceCore = int(coresToMap[x])
gprint('Done with all calculations for core ID #' +
str(sourceCore) + '. ' + str(int(x + 1)) + ' of ' +
str(endIndex) + ' cores have been processed.')
start_time = lu.elapsed_time(startTime1)
outlinkTableFile = path.join(cfg.DATAPASSDIR,
"temp_linkTable_s3_partial.csv")
lu.write_link_table(linkTableMod, outlinkTableFile)
# Increment loop counter
x = x + 1
else:
# If iteration failed, try again after a wait period
delay_restart(failures)
#----------------------------------------------------------------------
linkTable = linkTableMod
# reinstate temporarily disabled links
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] > 1000)
linkTable[rows,cfg.LTB_LINKTYPE] = (linkTable[rows,cfg.LTB_LINKTYPE] -
1000)
# Drop links that are too long
DISABLE_LEAST_COST_NO_VAL = True
linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST,
cfg.MINEUCDIST, cfg.MAXCOSTDIST,
cfg.MINCOSTDIST,
DISABLE_LEAST_COST_NO_VAL)
# Write link table file
outlinkTableFile = lu.get_this_step_link_table(step=3)
gprint('Updating ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s3.csv")
lu.write_link_table(linkTable, linkTableLogFile)
start_time = time.clock()
gprint('Creating shapefiles with linework for links...')
try:
lu.write_link_maps(outlinkTableFile, step=3)
except:
lu.write_link_maps(outlinkTableFile, step=3)
start_time = lu.elapsed_time(start_time)
gprint('\nIndividual cost-weighted distance layers written '
'to "cwd" directory. \n')
gprint(outlinkTableFile +
'\n updated with cost-weighted distances between core areas.')
#Clean up temporary files for restart code
tempFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")
lu.delete_file(tempFile)
tempFile = path.join(cfg.DATAPASSDIR, "temp_linkTable_s3_partial.csv")
lu.delete_file(tempFile)
# Check if climate tool is calling linkage mapper
if cfg.TOOL == cfg.TOOL_CC:
coreList = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
for core in coreList:
cwdRaster = lu.get_cwd_path(int(core))
back_rast = cwdRaster.replace("cwd_", "back_")
lu.delete_data(back_rast)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 3. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 3. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def euadjacency():
"""Calculate Euclidean adjacency
Inputs: gp - geoprocessing object
"""
try:
ALLOC_RASFN = "Euc_alloc_ras"
lu.dashline()
gprint('Calculating Euclidean adjacency')
outcsvfile = cfg.EUCADJFILE
outcsvLogfile = path.join(cfg.LOGDIR, "eucAdj_STEP1.csv")
# ----------------------------------------------
# Euclidean allocation code
gp.workspace = cfg.ADJACENCYDIR
gprint('Starting Euclidean adjacency processing...')
# Euclidean cell size
cellSizeEuclidean = gp.Describe(cfg.RESRAST).MeanCellHeight
oldextent = gp.extent
if cfg.BUFFERDIST is not None:
gp.extent = gp.Describe(cfg.BNDCIR).extent
start_time = time.clock()
gp.scratchworkspace = cfg.ARCSCRATCHDIR
outDistanceRaster = path.join(cfg.ADJACENCYDIR, "euc")
alloc_ras = path.join(cfg.ADJACENCYDIR, ALLOC_RASFN)
lu.delete_data(alloc_ras)
lu.delete_data(outDistanceRaster)
count = 0
statement = ('gp.EucAllocation_sa(cfg.CORERAS, alloc_ras, "","", '
'cellSizeEuclidean, "", outDistanceRaster, "")')
while True:
try:
exec statement
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain:
exec statement
else:
break
gp.scratchworkspace = cfg.ARCSCRATCHDIR
gprint('\nEuclidean distance allocation done.')
start_time = lu.elapsed_time(start_time)
gp.extent = oldextent
adjshiftwrite(alloc_ras, outcsvfile, outcsvLogfile)
# Clean up
lu.delete_data(outDistanceRaster)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def cwadjacency():
"""Calculate cost-weighted adjacency
Inputs: gp - geoprocessing object
"""
try:
ALLOC_RASFN = "CWD_alloc_ras"
gprint('\nCalculating cost-weighted distance adjacency')
outcsvfile = cfg.CWDADJFILE
outcsvLogfile = path.join(cfg.LOGDIR, "cwdAdj_STEP1.csv")
PREFIX = cfg.PREFIX
# May need to set extent prior to core poly to raster conversion...
# ----------------------------------------------
# Cost-weighted allocation code
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
gp.extent = gp.Describe(cfg.RESRAST).extent
if cfg.BUFFERDIST is not None:
# Clip resistance raster using bounding circle
start_time = time.clock()
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight#xxx
gp.extent = gp.Describe(cfg.RESRAST).Extent#xxx
bResistance = path.join(cfg.SCRATCHDIR, "bResistance")
gp.ExtractByMask_sa(cfg.RESRAST, cfg.BNDCIR,
bResistance)
gprint('\nReduced resistance raster extracted using '
'bounding circle.')
start_time = lu.elapsed_time(start_time)
else:
bResistance = cfg.RESRAST
start_time = time.clock()
gprint('Starting cost-weighted distance allocation...')
# core_rastmp = 'core_rastmp'
if cfg.TMAXCWDIST is not None:
gprint('Maximum cost-weighted distance set to ' +
str(cfg.TMAXCWDIST))
gp.CellSize = gp.Describe(bResistance).MeanCellHeight
gp.extent = "MAXOF"
gprint('Processing cell size: ' + gp.CellSize)
gp.workspace = cfg.ADJACENCYDIR
gp.scratchworkspace = cfg.ARCSCRATCHDIR
lu.delete_data(cfg.CWDGDB)
if not gp.exists(cfg.CWDGDB):
gp.createfilegdb(cfg.OUTPUTDIR, path.basename(cfg.CWDGDB))
outDistanceRaster = path.join(cfg.CWDGDB, PREFIX + "_cwd")
alloc_ras = path.join(cfg.ADJACENCYDIR, ALLOC_RASFN)
lu.delete_data(alloc_ras)
lu.delete_data(outDistanceRaster)
count = 0
if arcpy:
statement = ('costAllocOut = CostAllocation(cfg.CORERAS, '
'bResistance, cfg.TMAXCWDIST, cfg.CORERAS,"VALUE", '
'outDistanceRaster);'
'costAllocOut.save(alloc_ras)')
else:
statement = ('gp.Costallocation_sa(cfg.CORERAS, bResistance, '
'alloc_ras, cfg.TMAXCWDIST, cfg.CORERAS, "VALUE", '
'outDistanceRaster, "")')
while True:
try:
exec statement
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain:
exec statement
else:
break
gprint('\nBuilding output statistics and pyramids for CWD raster.')
lu.build_stats(outDistanceRaster)
gp.scratchworkspace = cfg.ARCSCRATCHDIR
gprint('Cost-weighted distance allocation done.')
start_time = lu.elapsed_time(start_time)
adjshiftwrite(alloc_ras, outcsvfile, outcsvLogfile)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def calc_lccs(normalize):
try:
if normalize:
mosaicBaseName = "_corridors"
writeTruncRaster = cfg.WRITETRUNCRASTER
outputGDB = cfg.OUTPUTGDB
if cfg.CALCNONNORMLCCS:
SAVENORMLCCS = False
else:
SAVENORMLCCS = cfg.SAVENORMLCCS
else:
mosaicBaseName = "_NON_NORMALIZED_corridors"
SAVENORMLCCS = False
outputGDB = cfg.EXTRAGDB
writeTruncRaster = False
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
linkTableFile = lu.get_prev_step_link_table(step=5)
if cfg.useArcpy:
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.overwriteOutput = True
arcpy.env.compression = "NONE"
else:
gp.workspace = cfg.SCRATCHDIR
gp.scratchWorkspace = cfg.ARCSCRATCHDIR
gp.OverwriteOutput = True
if cfg.MAXEUCDIST is not None:
gprint('Max Euclidean distance between cores')
gprint('for linkage mapping set to ' +
str(cfg.MAXEUCDIST))
if cfg.MAXCOSTDIST is not None:
gprint('Max cost-weighted distance between cores')
gprint('for linkage mapping set to ' +
str(cfg.MAXCOSTDIST))
# set the analysis extent and cell size to that of the resistance
# surface
if cfg.useArcpy:
arcpy.env.Extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
arcpy.env.mask = cfg.RESRAST
else:
gp.Extent = (gp.Describe(cfg.RESRAST)).Extent
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
gp.mask = cfg.RESRAST
gp.snapraster = cfg.RESRAST
linkTable = lu.load_link_table(linkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg =('\nThere are no corridors to map. Bailing.')
lu.raise_error(msg)
if not cfg.STEP3 and not cfg.STEP4:
# re-check for links that are too long or in case script run out of
# sequence with more stringent settings
gprint('Double-checking for corridors that are too long to map.')
DISABLE_LEAST_COST_NO_VAL = True
linkTable,numDroppedLinks = lu.drop_links(
linkTable, cfg.MAXEUCDIST, cfg.MINEUCDIST, cfg.MAXCOSTDIST,
cfg.MINCOSTDIST, DISABLE_LEAST_COST_NO_VAL)
# Added to try to speed up:
gp.pyramid = "NONE"
gp.rasterstatistics = "NONE"
# set up directories for normalized lcc and mosaic grids
dirCount = 0
gprint("Creating output folder: " + cfg.LCCBASEDIR)
lu.delete_dir(cfg.LCCBASEDIR)
gp.CreateFolder_management(path.dirname(cfg.LCCBASEDIR),
path.basename(cfg.LCCBASEDIR))
gp.CreateFolder_management(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
clccdir = path.join(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
# mosaicGDB = path.join(cfg.LCCBASEDIR, "mosaic.gdb")
# gp.createfilegdb(cfg.LCCBASEDIR, "mosaic.gdb")
#mosaicRaster = mosaicGDB + '\\' + "nlcc_mos" # Full path
gprint("")
if normalize:
gprint('Normalized least-cost corridors will be written '
'to ' + clccdir + '\n')
PREFIX = cfg.PREFIX
# Add CWD layers for core area pairs to produce NORMALIZED LCC layers
numGridsWritten = 0
coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
coreList = npy.sort(coreList)
x = 0
linkCount = 0
endIndex = numLinks
while x < endIndex:
if (linkTable[x, cfg.LTB_LINKTYPE] < 1): # If not a valid link
x = x + 1
continue
linkCount = linkCount + 1
start_time = time.clock()
linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
# source and target cores
corex=int(coreList[x,0])
corey=int(coreList[x,1])
# Get cwd rasters for source and target cores
cwdRaster1 = lu.get_cwd_path(corex)
cwdRaster2 = lu.get_cwd_path(corey)
if not gp.Exists(cwdRaster1):
msg =('\nError: cannot find cwd raster:\n' + cwdRaster1)
if not gp.Exists(cwdRaster2):
msg =('\nError: cannot find cwd raster:\n' + cwdRaster2)
lu.raise_error(msg)
lccNormRaster = path.join(clccdir, str(corex) + "_" +
str(corey))# + ".tif")
if cfg.useArcpy:
arcpy.env.Extent = "MINOF"
else:
gp.Extent = "MINOF"
# FIXME: need to check for this?:
# if exists already, don't re-create
#if not gp.Exists(lccRaster):
link = lu.get_links_from_core_pairs(linkTable, corex, corey)
offset = 10000
# Normalized lcc rasters are created by adding cwd rasters and
# subtracting the least cost distance between them.
count = 0
if arcpyAvailable:
cfg.useArcpy = True # Fixes Canran Liu's bug with lcDist
if cfg.useArcpy:
lcDist = (float(linkTable[link,cfg.LTB_CWDIST]) - offset)
if normalize:
statement = ('outras = Raster(cwdRaster1) + Raster('
'cwdRaster2) - lcDist; outras.save(lccNormRaster)')
else:
statement = ('outras =Raster(cwdRaster1) + Raster('
'cwdRaster2); outras.save(lccNormRaster)')
else:
if normalize:
lcDist = str(linkTable[link,cfg.LTB_CWDIST] - offset)
expression = (cwdRaster1 + " + " + cwdRaster2 + " - "
+ lcDist)
else:
expression = (cwdRaster1 + " + " + cwdRaster2)
statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
'lccNormRaster)')
count = 0
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain:
exec statement
else: break
cfg.useArcpy = False # End fix for Conran Liu's bug with lcDist
if normalize and cfg.useArcpy:
try:
minObject = gp.GetRasterProperties(lccNormRaster, "MINIMUM")
rasterMin = float(str(minObject.getoutput(0)))
except:
gp.AddWarning('\n------------------------------------------------')
gp.AddWarning('WARNING: Raster minimum check failed in step 5. \n'
'This may mean the output rasters are corrupted. Please \n'
'be sure to check for valid rasters in '+ outputGDB)
rasterMin = 0
tolerance = (float(gp.cellSize) * -10) + offset
if rasterMin < tolerance:
lu.dashline(1)
msg = ('WARNING: Minimum value of a corridor #' + str(x+1)
+ ' is much less than zero ('+str(rasterMin)+').'
'\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
'were too small and a corridor passed outside of a '
'bounding circle, or that a corridor passed outside of the '
'resistance map. \n')
gp.AddWarning(msg)
if cfg.useArcpy:
arcpy.env.Extent = cfg.RESRAST
else:
gp.Extent = (gp.Describe(cfg.RESRAST)).Extent
mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1))
lu.create_dir(mosaicDir)
mosFN = 'mos'#.tif' change and move
mosaicRaster = path.join(mosaicDir,mosFN)
if numGridsWritten == 0 and dirCount == 0:
#If this is the first grid then copy rather than mosaic
arcObj.CopyRaster_management(lccNormRaster, mosaicRaster)
else:
rasterString = '"'+lccNormRaster+";"+lastMosaicRaster+'"'
statement = ('arcObj.MosaicToNewRaster_management('
'rasterString,mosaicDir,mosFN, "", '
'"32_BIT_FLOAT", gp.cellSize, "1", "MINIMUM", '
'"MATCH")')
# statement = ('arcpy.Mosaic_management(lccNormRaster, '
# 'mosaicRaster, "MINIMUM", "MATCH")')
count = 0
while True:
try:
lu.write_log('Executing mosaic for link #'+str(linkId))
exec statement
lu.write_log('Done with mosaic.')
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
lu.delete_data(mosaicRaster)
lu.delete_dir(mosaicDir)
# Try a new directory
mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1)+ '_' + str(count))
lu.create_dir(mosaicDir)
mosaicRaster = path.join(mosaicDir,mosFN)
if not tryAgain:
exec statement
else: break
endTime = time.clock()
processTime = round((endTime - start_time), 2)
if normalize == True:
printText = "Normalized and mosaicked "
else:
printText = "Mosaicked NON-normalized "
gprint(printText + "corridor for link ID #" + str(linkId) +
" connecting core areas " + str(corex) +
" and " + str(corey)+ " in " +
str(processTime) + " seconds. " + str(int(linkCount)) +
" out of " + str(int(numCorridorLinks)) + " links have been "
"processed.")
# temporarily disable links in linktable - don't want to mosaic
# them twice
for y in range (x+1,numLinks):
corex1 = int(coreList[y,0])
corey1 = int(coreList[y,1])
if corex1 == corex and corey1 == corey:
linkTable[y,cfg.LTB_LINKTYPE] = (
linkTable[y,cfg.LTB_LINKTYPE] + 1000)
elif corex1==corey and corey1==corex:
linkTable[y,cfg.LTB_LINKTYPE] = (
linkTable[y,cfg.LTB_LINKTYPE] + 1000)
numGridsWritten = numGridsWritten + 1
if not SAVENORMLCCS:
lu.delete_data(lccNormRaster)
lu.delete_dir(clccdir)
lu.create_dir(clccdir)
else:
if numGridsWritten == 100:
# We only write up to 100 grids to any one folder
# because otherwise Arc slows to a crawl
dirCount = dirCount + 1
numGridsWritten = 0
clccdir = path.join(cfg.LCCBASEDIR,
cfg.LCCNLCDIR_NM + str(dirCount))
gprint("Creating output folder: " + clccdir)
gp.CreateFolder_management(cfg.LCCBASEDIR,
path.basename(clccdir))
if numGridsWritten > 1 or dirCount > 0:
lu.delete_data(lastMosaicRaster)
lu.delete_dir(path.dirname(lastMosaicRaster))
lastMosaicRaster = mosaicRaster
x = x + 1
#rows that were temporarily disabled
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE]>1000)
linkTable[rows,cfg.LTB_LINKTYPE] = (
linkTable[rows,cfg.LTB_LINKTYPE] - 1000)
# ---------------------------------------------------------------------
# Create output geodatabase
if not gp.exists(outputGDB):
gp.createfilegdb(cfg.OUTPUTDIR, path.basename(outputGDB))
if cfg.useArcpy:
arcpy.env.workspace = outputGDB
else:
gp.workspace = outputGDB
gp.pyramid = "NONE"
gp.rasterstatistics = "NONE"
# Copy mosaic raster to output geodatabase
saveFloatRaster = False
if saveFloatRaster == True:
floatRaster = outputGDB + '\\' + PREFIX + mosaicBaseName + '_flt' # Full path
statement = 'arcObj.CopyRaster_management(mosaicRaster, floatRaster)'
try:
exec statement
except:
pass
# ---------------------------------------------------------------------
# convert mosaic raster to integer
intRaster = path.join(outputGDB,PREFIX + mosaicBaseName)
if cfg.useArcpy:
statement = ('outras = Int(Raster(mosaicRaster) - offset + 0.5); '
'outras.save(intRaster)')
else:
expression = "int(" + mosaicRaster + " - " + str(offset) + " + 0.5)"
statement = 'gp.SingleOutputMapAlgebra_sa(expression, intRaster)'
count = 0
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec statement
else: break
# ---------------------------------------------------------------------
if writeTruncRaster:
# -----------------------------------------------------------------
# Set anything beyond cfg.CWDTHRESH to NODATA.
if arcpyAvailable:
cfg.useArcpy = True # For Alissa Pump's error with 10.1
cutoffText = str(cfg.CWDTHRESH)
if cutoffText[-6:] == '000000':
cutoffText = cutoffText[0:-6]+'m'
elif cutoffText[-3:] == '000':
cutoffText = cutoffText[0:-3]+'k'
truncRaster = (outputGDB + '\\' + PREFIX + mosaicBaseName +
'_truncated_at_' + cutoffText)
count = 0
if cfg.useArcpy:
statement = ('outRas = Raster(intRaster) * '
'(Con(Raster(intRaster) <= cfg.CWDTHRESH,1)); '
'outRas.save(truncRaster)')
else:
expression = ("(" + intRaster + " * (con(" + intRaster + "<= "
+ str(cfg.CWDTHRESH) + ",1)))")
statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
'truncRaster)')
count = 0
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec statement
else: break
cfg.useArcpy = False # End fix for Alissa Pump's error with 10.1
# ---------------------------------------------------------------------
# Check for unreasonably low minimum NLCC values
try:
mosaicGrid = path.join(cfg.LCCBASEDIR,'mos')
# Copy to grid to test
arcObj.CopyRaster_management(mosaicRaster, mosaicGrid)
minObject = gp.GetRasterProperties(mosaicGrid, "MINIMUM")
rasterMin = float(str(minObject.getoutput(0)))
except:
gp.AddWarning('\n------------------------------------------------')
gp.AddWarning('WARNING: Raster minimum check failed in step 5. \n'
'This may mean the output rasters are corrupted. Please \n'
'be sure to check for valid rasters in '+ outputGDB)
rasterMin = 0
tolerance = (float(gp.cellSize) * -10)
if rasterMin < tolerance:
lu.dashline(1)
msg = ('WARNING: Minimum value of mosaicked corridor map is '
'much less than zero ('+str(rasterMin)+').'
'\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
'were too small and a corridor passed outside of a '
'bounding circle, or that a corridor passed outside of the '
'resistance map. \n')
gp.AddWarning(msg)
gprint('\nWriting final LCP maps...')
if cfg.STEP4:
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=4,
thisStep=5)
elif cfg.STEP3:
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=3,
thisStep=5)
else:
# Don't know if step 4 was run, since this is started at step 5.
# Use presence of previous linktable files to figure this out.
# Linktable name includes step number.
prevLinkTableFile = lu.get_prev_step_link_table(step=5)
prevStepInd = len(prevLinkTableFile) - 5
lastStep = prevLinkTableFile[prevStepInd]
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep,
thisStep=5)
outlinkTableFile = lu.get_this_step_link_table(step=5)
gprint('Updating ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s5.csv")
lu.write_link_table(linkTable, linkTableLogFile)
linkTableFinalFile = path.join(cfg.OUTPUTDIR, PREFIX +
"_linkTable_s5.csv")
lu.write_link_table(finalLinkTable, linkTableFinalFile)
gprint('Copy of final linkTable written to '+
linkTableFinalFile)
gprint('Creating shapefiles with linework for links.')
try:
lu.write_link_maps(outlinkTableFile, step=5)
except:
lu.write_link_maps(outlinkTableFile, step=5)
# Create final linkmap files in output directory, and remove files from
# scratch.
lu.copy_final_link_maps(step=5)
if not SAVENORMLCCS:
lu.delete_dir(cfg.LCCBASEDIR)
# Build statistics for corridor rasters
gp.addmessage('\nBuilding output statistics and pyramids '
'for corridor raster')
lu.build_stats(intRaster)
if writeTruncRaster:
gp.addmessage('Building output statistics '
'for truncated corridor raster')
lu.build_stats(truncRaster)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 5. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 5. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def STEP3_calc_cwds():
"""Calculates cost-weighted distances from each core area.
Uses bounding circles around source and target cores to limit
extent of cwd calculations and speed computation.
"""
try:
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
lu.dashline(0)
# Super secret setting to re-start failed run. Enter 'RESTART' as the
# Name of the pairwise distance table in step 2, and uncheck step 2.
# We can eventually place this in a .ini file.
rerun = False
if cfg.S2EUCDISTFILE != None:
if cfg.S2EUCDISTFILE.lower() == "restart":
rerun = True
# if cfg.TMAXCWDIST is None:
# gprint('NOT using a maximum cost-weighted distance.')
# else:
# gprint('Max cost-weighted distance for CWD calcs set '
# 'to ' + str(cfg.TMAXCWDIST) + '\n')
if (cfg.BUFFERDIST) is not None:
gprint('Bounding circles plus a buffer of ' +
str(float(cfg.BUFFERDIST)) + ' map units will '
'be used \n to limit extent of cost distance '
'calculations.')
elif cfg.TOOL <> cfg.TOOL_CC:
gprint('NOT using bounding circles in cost distance '
'calculations.')
# set the analysis extent and cell size
# So we don't extract rasters that go beyond extent of original raster
if arcpy:
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.extent="MINOF"
else:
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
gp.Extent = "MINOF"
gp.mask = cfg.RESRAST
if arcpy:
arcpy.env.overwriteOutput = True
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
else:
gp.OverwriteOutput = True
gp.workspace = cfg.SCRATCHDIR
gp.scratchWorkspace = cfg.ARCSCRATCHDIR
# Load linkTable (created in previous script)
linkTableFile = lu.get_prev_step_link_table(step=3)
linkTable = lu.load_link_table(linkTableFile)
lu.report_links(linkTable)
# Identify cores to map from LinkTable
coresToMap = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
numCoresToMap = len(coresToMap)
if numCoresToMap < 3:
# No need to check for intermediate cores, because there aren't any
cfg.S3DROPLCCSic = False
else:
cfg.S3DROPLCCSic = cfg.S3DROPLCCS
gprint('\nNumber of core areas to connect: ' +
str(numCoresToMap))
if rerun:
# If picking up a failed run, make sure needed files are there
lu.dashline(1)
gprint ('\n****** RESTART MODE ENABLED ******\n')
gprint ('**** NOTE: This mode picks up step 3 where a\n'
'previous run left off due to a crash or user\n'
'abort. It assumes you are using the same input\n'
'data used in the terminated run.****\n')
lu.dashline(0)
lu.snooze(10)
savedLinkTableFile = path.join(cfg.DATAPASSDIR,
"temp_linkTable_s3_partial.csv")
coreListFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")
if not path.exists(savedLinkTableFile) or not path.exists(
coreListFile):
gprint('No partial results file found from previous '
'stopped run. Starting run from beginning.\n')
lu.dashline(0)
rerun = False
# If picking up a failed run, use old folders
if not rerun:
startIndex = 0
if cfg.TOOL <> cfg.TOOL_CC:
lu.make_cwd_paths(max(coresToMap)) # Set up cwd directories
# make a feature layer for input cores to select from
gp.MakeFeatureLayer(cfg.COREFC, cfg.FCORES)
# Drop links that are too long
gprint('\nChecking for corridors that are too long to map.')
DISABLE_LEAST_COST_NO_VAL = False
linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST, 0,
cfg.MAXCOSTDIST, 0,
DISABLE_LEAST_COST_NO_VAL)
# ------------------------------------------------------------------
# Bounding boxes
if (cfg.BUFFERDIST) is not None:
# create bounding boxes around cores
start_time = time.clock()
# lu.dashline(1)
gprint('Calculating bounding boxes for core areas.')
extentBoxList = npy.zeros((0,5), dtype='float32')
for x in range(len(coresToMap)):
core = coresToMap[x]
boxCoords = lu.get_extent_box_coords(core)
extentBoxList = npy.append(extentBoxList, boxCoords, axis=0)
gprint('\nDone calculating bounding boxes.')
start_time = lu.elapsed_time(start_time)
# lu.dashline()
# Bounding circle code
if cfg.BUFFERDIST is not None:
# Make a set of circles encompassing core areas we'll be connecting
start_time = time.clock()
gprint('Calculating bounding circles around potential'
' corridors.')
# x y corex corey radius- stores data for bounding circle centroids
boundingCirclePointArray = npy.zeros((0,5), dtype='float32')
circleList = npy.zeros((0,3), dtype='int32')
numLinks = linkTable.shape[0]
for x in range(0, numLinks):
if ((linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
(linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_KEEP)):
# if it's a valid corridor link
linkId = int(linkTable[x,cfg.LTB_LINKID])
# fixme- this code is clumsy- can trim down
cores = npy.zeros((1,3), dtype='int32')
cores[0,:] = npy.sort([0, linkTable[x,cfg.LTB_CORE1],
linkTable[x,cfg.LTB_CORE2]])
corex = cores[0,1]
corey = cores[0,2]
cores[0,0] = linkId
###################
foundFlag = False
for y in range(0,len(circleList)): # clumsy
if (circleList[y,1] == corex and
circleList[y,2] == corey):
foundFlag = True
if not foundFlag:
circlePointData = (
lu.get_bounding_circle_data(extentBoxList,
corex, corey, cfg.BUFFERDIST))
boundingCirclePointArray = (
npy.append(boundingCirclePointArray,
circlePointData, axis=0))
# keep track of which cores we draw bounding circles
# around
circleList = npy.append(circleList, cores, axis=0)
gprint('\nCreating bounding circles using buffer '
'analysis.')
dir, BNDCIRCENS = path.split(cfg.BNDCIRCENS)
lu.make_points(cfg.SCRATCHDIR, boundingCirclePointArray,
BNDCIRCENS)
lu.delete_data(cfg.BNDCIRS)
gp.buffer_analysis(cfg.BNDCIRCENS, cfg.BNDCIRS, "radius")
gp.deletefield (cfg.BNDCIRS, "BUFF_DIST")
gprint('Successfully created bounding circles around '
'potential corridors using \na buffer of ' +
str(float(cfg.BUFFERDIST)) + ' map units.')
start_time = lu.elapsed_time(start_time)
gprint('Reducing global processing area using bounding '
'circle plus buffer of ' +
str(float(cfg.BUFFERDIST)) + ' map units.\n')
extentBoxList = npy.zeros((0,5),dtype='float32')
boxCoords = lu.get_extent_box_coords()
extentBoxList = npy.append(extentBoxList,boxCoords,axis=0)
extentBoxList[0,0] = 0
boundingCirclePointArray = npy.zeros((0,5),dtype='float32')
circlePointData=lu.get_bounding_circle_data(extentBoxList, 0,
0, cfg.BUFFERDIST)
dir, BNDCIRCEN = path.split(cfg.BNDCIRCEN)
lu.make_points(cfg.SCRATCHDIR, circlePointData, BNDCIRCEN)
lu.delete_data(cfg.BNDCIR)
gp.buffer_analysis(cfg.BNDCIRCEN, cfg.BNDCIR, "radius")
gprint('Extracting raster....')
cfg.BOUNDRESIS = cfg.BOUNDRESIS + tif
lu.delete_data(cfg.BOUNDRESIS)
count = 0
statement = (
'gp.ExtractByMask_sa(cfg.RESRAST, cfg.BNDCIR, cfg.BOUNDRESIS)')
while True:
try:
exec statement
randomerror()
except:
count,tryAgain = lu.retry_arc_error(count,statement)
if not tryAgain: exec statement
else: break
gprint('\nReduced resistance raster extracted using '
'bounding circle.')
else: #if not using bounding circles, just go with resistance raster.
cfg.BOUNDRESIS = cfg.RESRAST
# ---------------------------------------------------------------------
# Rasterize core areas to speed cost distance calcs
# lu.dashline(1)
gprint("Creating core area raster.")
gp.SelectLayerByAttribute(cfg.FCORES, "CLEAR_SELECTION")
if arcpy:
arcpy.env.cellSize = cfg.BOUNDRESIS
arcpy.env.extent = cfg.BOUNDRESIS
else:
gp.cellSize = gp.Describe(cfg.BOUNDRESIS).MeanCellHeight
gp.extent = gp.Describe(cfg.BOUNDRESIS).extent
if rerun:
# saved linktable replaces the one now in memory
linkTable = lu.load_link_table(savedLinkTableFile)
coresToMapSaved = npy.loadtxt(coreListFile, dtype='Float64',
comments='#', delimiter=',')
startIndex = coresToMapSaved[0] # Index of core where we left off
del coresToMapSaved
gprint ('\n****** Re-starting run at core area number '
+ str(int(coresToMap[startIndex]))+ ' ******\n')
lu.dashline(0)
if arcpy:
arcpy.env.extent = "MINOF"
else:
gp.extent = "MINOF"
#----------------------------------------------------------------------
# Loop through cores, do cwd calcs for each
if cfg.TOOL == cfg.TOOL_CC:
gprint("\nMapping least-cost paths.\n")
else:
gprint("\nStarting cost distance calculations.\n")
lcpLoop = 0
failures = 0
x = startIndex
endIndex = len(coresToMap)
linkTableMod = linkTable.copy()
while x < endIndex:
startTime1 = time.clock()
# Modification of linkTable in function was causing problems. so
# make a copy:
linkTablePassed = linkTableMod.copy()
(linkTableReturned, failures, lcpLoop) = do_cwd_calcs(x,
linkTablePassed, coresToMap, lcpLoop, failures)
if failures == 0:
# If iteration was successful, continue with next core
linkTableMod = linkTableReturned
sourceCore = int(coresToMap[x])
gprint('Done with all calculations for core ID #' +
str(sourceCore) + '. ' + str(int(x + 1)) + ' of ' +
str(endIndex) + ' cores have been processed.')
start_time = lu.elapsed_time(startTime1)
outlinkTableFile = path.join(cfg.DATAPASSDIR,
"temp_linkTable_s3_partial.csv")
lu.write_link_table(linkTableMod, outlinkTableFile)
# Increment loop counter
x = x + 1
else:
# If iteration failed, try again after a wait period
delay_restart(failures)
#----------------------------------------------------------------------
linkTable = linkTableMod
# reinstate temporarily disabled links
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] > 1000)
linkTable[rows,cfg.LTB_LINKTYPE] = (linkTable[rows,cfg.LTB_LINKTYPE] -
1000)
# Drop links that are too long
DISABLE_LEAST_COST_NO_VAL = True
linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST,
cfg.MINEUCDIST, cfg.MAXCOSTDIST,
cfg.MINCOSTDIST,
DISABLE_LEAST_COST_NO_VAL)
# Write link table file
outlinkTableFile = lu.get_this_step_link_table(step=3)
gprint('Updating ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s3.csv")
lu.write_link_table(linkTable, linkTableLogFile)
start_time = time.clock()
gprint('Creating shapefiles with linework for links...')
try:
lu.write_link_maps(outlinkTableFile, step=3)
except:
lu.write_link_maps(outlinkTableFile, step=3)
start_time = lu.elapsed_time(start_time)
gprint('\nIndividual cost-weighted distance layers written '
'to "cwd" directory. \n')
gprint(outlinkTableFile +
'\n updated with cost-weighted distances between core areas.')
#Clean up temporary files for restart code
tempFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")
lu.delete_file(tempFile)
tempFile = path.join(cfg.DATAPASSDIR, "temp_linkTable_s3_partial.csv")
lu.delete_file(tempFile)
# Check if climate tool is calling linkage mapper
if cfg.TOOL == cfg.TOOL_CC:
coreList = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
for core in coreList:
cwdRaster = lu.get_cwd_path(int(core))
back_rast = cwdRaster.replace("cwd_", "back_")
lu.delete_data(back_rast)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 3. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 3. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def calc_lccs(normalize):
try:
if normalize:
mosaicBaseName = "_corridors"
writeTruncRaster = cfg.WRITETRUNCRASTER
outputGDB = cfg.OUTPUTGDB
if cfg.CALCNONNORMLCCS:
SAVENORMLCCS = False
else:
SAVENORMLCCS = cfg.SAVENORMLCCS
else:
mosaicBaseName = "_NON_NORMALIZED_corridors"
SAVENORMLCCS = False
outputGDB = cfg.EXTRAGDB
writeTruncRaster = False
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
linkTableFile = lu.get_prev_step_link_table(step=5)
if cfg.useArcpy:
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.overwriteOutput = True
arcpy.env.compression = "NONE"
else:
gp.workspace = cfg.SCRATCHDIR
gp.scratchWorkspace = cfg.ARCSCRATCHDIR
gp.OverwriteOutput = True
if cfg.MAXEUCDIST is not None:
gprint('Max Euclidean distance between cores')
gprint('for linkage mapping set to ' + str(cfg.MAXEUCDIST))
if cfg.MAXCOSTDIST is not None:
gprint('Max cost-weighted distance between cores')
gprint('for linkage mapping set to ' + str(cfg.MAXCOSTDIST))
# set the analysis extent and cell size to that of the resistance
# surface
if cfg.useArcpy:
arcpy.env.Extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
arcpy.env.mask = cfg.RESRAST
else:
gp.Extent = (gp.Describe(cfg.RESRAST)).Extent
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
gp.mask = cfg.RESRAST
gp.snapraster = cfg.RESRAST
linkTable = lu.load_link_table(linkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg = ('\nThere are no corridors to map. Bailing.')
lu.raise_error(msg)
if not cfg.STEP3 and not cfg.STEP4:
# re-check for links that are too long or in case script run out of
# sequence with more stringent settings
gprint('Double-checking for corridors that are too long to map.')
DISABLE_LEAST_COST_NO_VAL = True
linkTable, numDroppedLinks = lu.drop_links(
linkTable, cfg.MAXEUCDIST, cfg.MINEUCDIST, cfg.MAXCOSTDIST,
cfg.MINCOSTDIST, DISABLE_LEAST_COST_NO_VAL)
# Added to try to speed up:
gp.pyramid = "NONE"
gp.rasterstatistics = "NONE"
# set up directories for normalized lcc and mosaic grids
dirCount = 0
gprint("Creating output folder: " + cfg.LCCBASEDIR)
lu.delete_dir(cfg.LCCBASEDIR)
gp.CreateFolder_management(path.dirname(cfg.LCCBASEDIR),
path.basename(cfg.LCCBASEDIR))
gp.CreateFolder_management(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
clccdir = path.join(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
# mosaicGDB = path.join(cfg.LCCBASEDIR, "mosaic.gdb")
# gp.createfilegdb(cfg.LCCBASEDIR, "mosaic.gdb")
#mosaicRaster = mosaicGDB + '\\' + "nlcc_mos" # Full path
gprint("")
if normalize:
gprint('Normalized least-cost corridors will be written '
'to ' + clccdir + '\n')
PREFIX = cfg.PREFIX
# Add CWD layers for core area pairs to produce NORMALIZED LCC layers
numGridsWritten = 0
coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
coreList = npy.sort(coreList)
x = 0
linkCount = 0
endIndex = numLinks
while x < endIndex:
if (linkTable[x, cfg.LTB_LINKTYPE] < 1): # If not a valid link
x = x + 1
continue
linkCount = linkCount + 1
start_time = time.clock()
linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
# source and target cores
corex = int(coreList[x, 0])
corey = int(coreList[x, 1])
# Get cwd rasters for source and target cores
cwdRaster1 = lu.get_cwd_path(corex)
cwdRaster2 = lu.get_cwd_path(corey)
if not gp.Exists(cwdRaster1):
msg = ('\nError: cannot find cwd raster:\n' + cwdRaster1)
if not gp.Exists(cwdRaster2):
msg = ('\nError: cannot find cwd raster:\n' + cwdRaster2)
lu.raise_error(msg)
lccNormRaster = path.join(clccdir,
str(corex) + "_" +
str(corey)) # + ".tif")
if cfg.useArcpy:
arcpy.env.Extent = "MINOF"
else:
gp.Extent = "MINOF"
# FIXME: need to check for this?:
# if exists already, don't re-create
#if not gp.Exists(lccRaster):
link = lu.get_links_from_core_pairs(linkTable, corex, corey)
offset = 10000
# Normalized lcc rasters are created by adding cwd rasters and
# subtracting the least cost distance between them.
count = 0
if arcpyAvailable:
cfg.useArcpy = True # Fixes Canran Liu's bug with lcDist
if cfg.useArcpy:
lcDist = (float(linkTable[link, cfg.LTB_CWDIST]) - offset)
if normalize:
statement = (
'outras = Raster(cwdRaster1) + Raster('
'cwdRaster2) - lcDist; outras.save(lccNormRaster)')
else:
statement = ('outras =Raster(cwdRaster1) + Raster('
'cwdRaster2); outras.save(lccNormRaster)')
else:
if normalize:
lcDist = str(linkTable[link, cfg.LTB_CWDIST] - offset)
expression = (cwdRaster1 + " + " + cwdRaster2 + " - " +
lcDist)
else:
expression = (cwdRaster1 + " + " + cwdRaster2)
statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
'lccNormRaster)')
count = 0
while True:
try:
exec statement
randomerror()
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain:
exec statement
else:
break
cfg.useArcpy = False # End fix for Conran Liu's bug with lcDist
if normalize and cfg.useArcpy:
try:
minObject = gp.GetRasterProperties(lccNormRaster,
"MINIMUM")
rasterMin = float(str(minObject.getoutput(0)))
except:
gp.AddWarning(
'\n------------------------------------------------')
gp.AddWarning(
'WARNING: Raster minimum check failed in step 5. \n'
'This may mean the output rasters are corrupted. Please \n'
'be sure to check for valid rasters in ' + outputGDB)
rasterMin = 0
tolerance = (float(gp.cellSize) * -10) + offset
if rasterMin < tolerance:
lu.dashline(1)
msg = (
'WARNING: Minimum value of a corridor #' + str(x + 1) +
' is much less than zero (' + str(rasterMin) + ').'
'\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
'were too small and a corridor passed outside of a '
'bounding circle, or that a corridor passed outside of the '
'resistance map. \n')
gp.AddWarning(msg)
if cfg.useArcpy:
arcpy.env.Extent = cfg.RESRAST
else:
gp.Extent = (gp.Describe(cfg.RESRAST)).Extent
mosaicDir = path.join(cfg.LCCBASEDIR, 'mos' + str(x + 1))
lu.create_dir(mosaicDir)
mosFN = 'mos' #.tif' change and move
mosaicRaster = path.join(mosaicDir, mosFN)
if numGridsWritten == 0 and dirCount == 0:
#If this is the first grid then copy rather than mosaic
arcObj.CopyRaster_management(lccNormRaster, mosaicRaster)
else:
rasterString = '"' + lccNormRaster + ";" + lastMosaicRaster + '"'
statement = ('arcObj.MosaicToNewRaster_management('
'rasterString,mosaicDir,mosFN, "", '
'"32_BIT_FLOAT", gp.cellSize, "1", "MINIMUM", '
'"MATCH")')
# statement = ('arcpy.Mosaic_management(lccNormRaster, '
# 'mosaicRaster, "MINIMUM", "MATCH")')
count = 0
while True:
try:
lu.write_log('Executing mosaic for link #' +
str(linkId))
exec statement
lu.write_log('Done with mosaic.')
randomerror()
except:
count, tryAgain = lu.retry_arc_error(count, statement)
lu.delete_data(mosaicRaster)
lu.delete_dir(mosaicDir)
# Try a new directory
mosaicDir = path.join(
cfg.LCCBASEDIR,
'mos' + str(x + 1) + '_' + str(count))
lu.create_dir(mosaicDir)
mosaicRaster = path.join(mosaicDir, mosFN)
if not tryAgain:
exec statement
else:
break
endTime = time.clock()
processTime = round((endTime - start_time), 2)
if normalize == True:
printText = "Normalized and mosaicked "
else:
printText = "Mosaicked NON-normalized "
gprint(printText + "corridor for link ID #" + str(linkId) +
" connecting core areas " + str(corex) + " and " +
str(corey) + " in " + str(processTime) + " seconds. " +
str(int(linkCount)) + " out of " +
str(int(numCorridorLinks)) + " links have been "
"processed.")
# temporarily disable links in linktable - don't want to mosaic
# them twice
for y in range(x + 1, numLinks):
corex1 = int(coreList[y, 0])
corey1 = int(coreList[y, 1])
if corex1 == corex and corey1 == corey:
linkTable[y, cfg.LTB_LINKTYPE] = (
linkTable[y, cfg.LTB_LINKTYPE] + 1000)
elif corex1 == corey and corey1 == corex:
linkTable[y, cfg.LTB_LINKTYPE] = (
linkTable[y, cfg.LTB_LINKTYPE] + 1000)
numGridsWritten = numGridsWritten + 1
if not SAVENORMLCCS:
lu.delete_data(lccNormRaster)
lu.delete_dir(clccdir)
lu.create_dir(clccdir)
else:
if numGridsWritten == 100:
# We only write up to 100 grids to any one folder
# because otherwise Arc slows to a crawl
dirCount = dirCount + 1
numGridsWritten = 0
clccdir = path.join(cfg.LCCBASEDIR,
cfg.LCCNLCDIR_NM + str(dirCount))
gprint("Creating output folder: " + clccdir)
gp.CreateFolder_management(cfg.LCCBASEDIR,
path.basename(clccdir))
if numGridsWritten > 1 or dirCount > 0:
lu.delete_data(lastMosaicRaster)
lu.delete_dir(path.dirname(lastMosaicRaster))
lastMosaicRaster = mosaicRaster
x = x + 1
#rows that were temporarily disabled
rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] > 1000)
linkTable[rows,
cfg.LTB_LINKTYPE] = (linkTable[rows, cfg.LTB_LINKTYPE] -
1000)
# ---------------------------------------------------------------------
# Create output geodatabase
if not gp.exists(outputGDB):
gp.createfilegdb(cfg.OUTPUTDIR, path.basename(outputGDB))
if cfg.useArcpy:
arcpy.env.workspace = outputGDB
else:
gp.workspace = outputGDB
gp.pyramid = "NONE"
gp.rasterstatistics = "NONE"
# Copy mosaic raster to output geodatabase
saveFloatRaster = False
if saveFloatRaster == True:
floatRaster = outputGDB + '\\' + PREFIX + mosaicBaseName + '_flt' # Full path
statement = 'arcObj.CopyRaster_management(mosaicRaster, floatRaster)'
try:
exec statement
except:
pass
# ---------------------------------------------------------------------
# convert mosaic raster to integer
intRaster = path.join(outputGDB, PREFIX + mosaicBaseName)
if cfg.useArcpy:
statement = ('outras = Int(Raster(mosaicRaster) - offset + 0.5); '
'outras.save(intRaster)')
else:
expression = "int(" + mosaicRaster + " - " + str(
offset) + " + 0.5)"
statement = 'gp.SingleOutputMapAlgebra_sa(expression, intRaster)'
count = 0
while True:
try:
exec statement
randomerror()
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain: exec statement
else: break
# ---------------------------------------------------------------------
if writeTruncRaster:
# -----------------------------------------------------------------
# Set anything beyond cfg.CWDTHRESH to NODATA.
if arcpyAvailable:
cfg.useArcpy = True # For Alissa Pump's error with 10.1
cutoffText = str(cfg.CWDTHRESH)
if cutoffText[-6:] == '000000':
cutoffText = cutoffText[0:-6] + 'm'
elif cutoffText[-3:] == '000':
cutoffText = cutoffText[0:-3] + 'k'
truncRaster = (outputGDB + '\\' + PREFIX + mosaicBaseName +
'_truncated_at_' + cutoffText)
count = 0
if cfg.useArcpy:
statement = ('outRas = Raster(intRaster) * '
'(Con(Raster(intRaster) <= cfg.CWDTHRESH,1)); '
'outRas.save(truncRaster)')
else:
expression = ("(" + intRaster + " * (con(" + intRaster +
"<= " + str(cfg.CWDTHRESH) + ",1)))")
statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
'truncRaster)')
count = 0
while True:
try:
exec statement
randomerror()
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain: exec statement
else: break
cfg.useArcpy = False # End fix for Alissa Pump's error with 10.1
# ---------------------------------------------------------------------
# Check for unreasonably low minimum NLCC values
try:
mosaicGrid = path.join(cfg.LCCBASEDIR, 'mos')
# Copy to grid to test
arcObj.CopyRaster_management(mosaicRaster, mosaicGrid)
minObject = gp.GetRasterProperties(mosaicGrid, "MINIMUM")
rasterMin = float(str(minObject.getoutput(0)))
except:
gp.AddWarning('\n------------------------------------------------')
gp.AddWarning(
'WARNING: Raster minimum check failed in step 5. \n'
'This may mean the output rasters are corrupted. Please \n'
'be sure to check for valid rasters in ' + outputGDB)
rasterMin = 0
tolerance = (float(gp.cellSize) * -10)
if rasterMin < tolerance:
lu.dashline(1)
msg = ('WARNING: Minimum value of mosaicked corridor map is '
'much less than zero (' + str(rasterMin) + ').'
'\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
'were too small and a corridor passed outside of a '
'bounding circle, or that a corridor passed outside of the '
'resistance map. \n')
gp.AddWarning(msg)
gprint('\nWriting final LCP maps...')
if cfg.STEP4:
finalLinkTable = lu.update_lcp_shapefile(linkTable,
lastStep=4,
thisStep=5)
elif cfg.STEP3:
finalLinkTable = lu.update_lcp_shapefile(linkTable,
lastStep=3,
thisStep=5)
else:
# Don't know if step 4 was run, since this is started at step 5.
# Use presence of previous linktable files to figure this out.
# Linktable name includes step number.
prevLinkTableFile = lu.get_prev_step_link_table(step=5)
prevStepInd = len(prevLinkTableFile) - 5
lastStep = prevLinkTableFile[prevStepInd]
finalLinkTable = lu.update_lcp_shapefile(linkTable,
lastStep,
thisStep=5)
outlinkTableFile = lu.get_this_step_link_table(step=5)
gprint('Updating ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s5.csv")
lu.write_link_table(linkTable, linkTableLogFile)
linkTableFinalFile = path.join(cfg.OUTPUTDIR,
PREFIX + "_linkTable_s5.csv")
lu.write_link_table(finalLinkTable, linkTableFinalFile)
gprint('Copy of final linkTable written to ' + linkTableFinalFile)
gprint('Creating shapefiles with linework for links.')
try:
lu.write_link_maps(outlinkTableFile, step=5)
except:
lu.write_link_maps(outlinkTableFile, step=5)
# Create final linkmap files in output directory, and remove files from
# scratch.
lu.copy_final_link_maps(step=5)
if not SAVENORMLCCS:
lu.delete_dir(cfg.LCCBASEDIR)
# Build statistics for corridor rasters
gp.addmessage('\nBuilding output statistics and pyramids '
'for corridor raster')
lu.build_stats(intRaster)
if writeTruncRaster:
gp.addmessage('Building output statistics '
'for truncated corridor raster')
lu.build_stats(truncRaster)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 5. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 5. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
