def STEP7_calc_centrality():
""" Analyze network centrality using Circuitscape
given Linkage Mapper outputs
"""
try:
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
arcpy.env.workspace = cfg.SCRATCHDIR
# Check for valid LCP shapefile
prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep=7)
if not arcpy.Exists(prevLcpShapefile):
msg = ('Cannot find an LCP shapefile from step 5. Please '
'rerun that step and any previous ones if necessary.')
lu.raise_error(msg)
# Remove lcp shapefile from this step if run previously
lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s7.shp")
lu.delete_data(lcpShapefile)
invalidFNs = ['fid', 'id', 'oid', 'shape']
if cfg.COREFN.lower() in invalidFNs:
#if cfg.COREFN == 'FID' or cfg.COREFN == 'ID':
lu.dashline(1)
msg = ('ERROR: Core area field names ID, FID, SHAPE, and OID are'
' reserved for ArcGIS. \nPlease choose another field- must'
' be a positive integer.')
lu.raise_error(msg)
lu.dashline(1)
gprint('Mapping centrality of network cores and links'
'\nusing Circuitscape....')
lu.dashline(0)
# set the analysis extent and cell size to that of the resistance
# surface
coreCopy = path.join(cfg.SCRATCHDIR, 'cores.shp')
arcpy.CopyFeatures_management(cfg.COREFC, coreCopy)
if not arcpy.ListFields(coreCopy, "CF_Central"):
arcpy.AddField_management(coreCopy, "CF_Central", "DOUBLE")
inLinkTableFile = lu.get_prev_step_link_table(step=7)
linkTable = lu.load_link_table(inLinkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg = ('\nThere are no linkages. Bailing.')
lu.raise_error(msg)
if linkTable.shape[1] < 16: # If linktable has no entries from prior
# centrality or pinchpint analyses
extraCols = npy.zeros((numLinks, 6), dtype=npy.float64)
linkTable = linkTable[:, 0:10]
linkTable = npy.append(linkTable, extraCols, axis=1)
linkTable[:, cfg.LTB_LCPLEN] = -1
linkTable[:, cfg.LTB_CWDEUCR] = -1
linkTable[:, cfg.LTB_CWDPATHR] = -1
linkTable[:, cfg.LTB_EFFRESIST] = -1
linkTable[:, cfg.LTB_CWDTORR] = -1
del extraCols
linkTable[:, cfg.LTB_CURRENT] = -1
coresToProcess = npy.unique(linkTable[:,
cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
maxCoreNum = max(coresToProcess)
del coresToProcess
lu.dashline(0)
coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
coreList = npy.sort(coreList)
# set up directory for centrality
INCENTRALITYDIR = cfg.CENTRALITYBASEDIR
OUTCENTRALITYDIR = path.join(cfg.CENTRALITYBASEDIR,
cfg.CIRCUITOUTPUTDIR_NM)
CONFIGDIR = path.join(INCENTRALITYDIR, cfg.CIRCUITCONFIGDIR_NM)
# Set Circuitscape options and write config file
options = lu.set_cs_options()
options['data_type'] = 'network'
options['habitat_file'] = path.join(INCENTRALITYDIR,
'Circuitscape_graph.txt')
# Setting point file equal to graph to do all pairs in Circuitscape
options['point_file'] = path.join(INCENTRALITYDIR,
'Circuitscape_graph.txt')
outputFN = 'Circuitscape_network.out'
options['output_file'] = path.join(OUTCENTRALITYDIR, outputFN)
configFN = 'Circuitscape_network.ini'
outConfigFile = path.join(CONFIGDIR, configFN)
lu.write_cs_cfg_file(outConfigFile, options)
delRows = npy.asarray(npy.where(linkTable[:, cfg.LTB_LINKTYPE] < 1))
delRowsVector = npy.zeros((delRows.shape[1]), dtype="int32")
delRowsVector[:] = delRows[0, :]
LT = lu.delete_row(linkTable, delRowsVector)
del delRows
del delRowsVector
graphList = npy.zeros((LT.shape[0], 3), dtype=npy.float64)
graphList[:, 0] = LT[:, cfg.LTB_CORE1]
graphList[:, 1] = LT[:, cfg.LTB_CORE2]
graphList[:, 2] = LT[:, cfg.LTB_CWDIST]
write_graph(options['habitat_file'], graphList)
gprint('\nCalculating current flow centrality using Circuitscape...')
memFlag = lu.call_circuitscape(cfg.CSPATH, outConfigFile)
outputFN = 'Circuitscape_network_branch_currents_cum.txt'
currentList = path.join(OUTCENTRALITYDIR, outputFN)
if not arcpy.Exists(currentList):
write_graph(options['habitat_file'], graphList)
gprint('\nCalculating current flow centrality using Circuitscape '
'(2nd try)...')
memFlag = lu.call_circuitscape(cfg.CSPATH, outConfigFile)
if not arcpy.Exists(currentList):
lu.dashline(1)
msg = ('ERROR: No Circuitscape output found.\n'
'It looks like Circuitscape failed.')
arcpy.AddError(msg)
lu.write_log(msg)
exit(1)
currents = load_graph(currentList,
graphType='graph/network',
datatype=npy.float64)
numLinks = currents.shape[0]
for x in range(0, numLinks):
corex = currents[x, 0]
corey = currents[x, 1]
#linkId = LT[x,cfg.LTB_LINKID]
row = lu.get_links_from_core_pairs(linkTable, corex, corey)
#row = lu.get_linktable_row(linkId, linkTable)
linkTable[row, cfg.LTB_CURRENT] = currents[x, 2]
coreCurrentFN = 'Circuitscape_network_node_currents_cum.txt'
nodeCurrentList = path.join(OUTCENTRALITYDIR, coreCurrentFN)
nodeCurrents = load_graph(nodeCurrentList,
graphType='graph/network',
datatype=npy.float64)
numNodeCurrents = nodeCurrents.shape[0]
rows = arcpy.UpdateCursor(coreCopy)
row = rows.newRow()
for row in rows:
coreID = row.getValue(cfg.COREFN)
for i in range(0, numNodeCurrents):
if coreID == nodeCurrents[i, 0]:
row.setValue("CF_Central", nodeCurrents[i, 1])
break
rows.updateRow(row)
#row = rows.newRow()
del row, rows
gprint('Done with centrality calculations.')
finalLinkTable = lu.update_lcp_shapefile(linkTable,
lastStep=5,
thisStep=7)
linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
linkTableFinalFile = path.join(cfg.OUTPUTDIR,
cfg.PREFIX + "_linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable, linkTableFinalFile,
inLinkTableFile)
gprint('Copy of final linkTable written to ' + linkTableFinalFile)
finalCoreFile = path.join(cfg.CORECENTRALITYGDB, cfg.PREFIX + '_Cores')
#copy core area map to gdb.
if not arcpy.Exists(cfg.CORECENTRALITYGDB):
arcpy.CreateFileGDB_management(
cfg.OUTPUTDIR, path.basename(cfg.CORECENTRALITYGDB))
arcpy.CopyFeatures_management(coreCopy, finalCoreFile)
gprint('Creating shapefiles with linework for links.')
lu.write_link_maps(linkTableFinalFile, step=7)
# Copy final link maps to gdb and clean up.
lu.copy_final_link_maps(step=7)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 7. 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 7. 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 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 STEP6_calc_barriers():
"""Detects influential barriers given CWD calculations from
s3_calcCwds.py.
"""
try:
arcpy.CheckOutExtension("spatial")
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
if cfg.BARRIER_CWD_THRESH is not None:
lu.dashline(1)
gprint('Invoking CWD Threshold of ' + str(cfg.BARRIER_CWD_THRESH) +
' map units.')
if cfg.SUM_BARRIERS:
sumSuffix = '_Sum'
cfg.BARRIERBASEDIR = cfg.BARRIERBASEDIR + sumSuffix
baseName, extension = path.splitext(cfg.BARRIERGDB)
cfg.BARRIERGDB = baseName + sumSuffix + extension
gprint('\nBarrier scores will be SUMMED across core pairs.')
else:
sumSuffix = ''
# Delete contents of final ouptut geodatabase
# lu.clean_out_workspace(cfg.BARRIERGDB) #xxx try not doing this to allow multiple radii to be analyzed in separate runs
if not arcpy.Exists(cfg.BARRIERGDB):
# Create output geodatabase
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
path.basename(cfg.BARRIERGDB))
startRadius = int(cfg.STARTRADIUS)
endRadius = int(cfg.ENDRADIUS)
radiusStep = int(cfg.RADIUSSTEP)
if radiusStep == 0:
endRadius = startRadius # Calculate at just one radius value
radiusStep = 1
linkTableFile = lu.get_prev_step_link_table(step=6)
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.RefreshCatalog(cfg.PROJECTDIR)
PREFIX = path.basename(cfg.PROJECTDIR)
# For speed:
arcpy.env.pyramid = "NONE"
arcpy.env.rasterStatistics = "NONE"
# set the analysis extent and cell size to that of the resistance
# surface
arcpy.OverWriteOutput = True
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
spatialref = arcpy.Describe(cfg.RESRAST).spatialReference
mapUnits = (str(spatialref.linearUnitName)).lower()
if len(mapUnits) > 1 and mapUnits[-1] != 's':
mapUnits = mapUnits + 's'
if float(arcpy.env.cellSize) > startRadius or startRadius > endRadius:
msg = ('Error: minimum detection radius must be greater than '
'cell size (' + str(arcpy.env.cellSize) +
') \nand less than or equal to maximum detection radius.')
lu.raise_error(msg)
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 linkages. Bailing.')
lu.raise_error(msg)
# set up directories for barrier and barrier mosaic grids
dirCount = 0
gprint("Creating intermediate output folder: " + cfg.BARRIERBASEDIR)
lu.delete_dir(cfg.BARRIERBASEDIR)
lu.create_dir(cfg.BARRIERBASEDIR)
arcpy.CreateFolder_management(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
cbarrierdir = path.join(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
coresToProcess = npy.unique(linkTable[:,
cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
maxCoreNum = max(coresToProcess)
# Set up focal directories.
# To keep there from being > 100 grids in any one directory,
# outputs are written to:
# barrier\focalX_ for cores 1-99 at radius X
# barrier\focalX_1 for cores 100-199
# etc.
lu.dashline(0)
for radius in range(startRadius, endRadius + 1, radiusStep):
core1path = lu.get_focal_path(1, radius)
path1, dir1 = path.split(core1path)
path2, dir2 = path.split(path1)
arcpy.CreateFolder_management(path.dirname(path2),
path.basename(path2))
arcpy.CreateFolder_management(path.dirname(path1),
path.basename(path1))
if maxCoreNum > 99:
gprint('Creating subdirectories for ' + str(radius) + ' ' +
str(mapUnits) + ' radius analysis scale.')
maxDirCount = int(maxCoreNum / 100)
focalDirBaseName = dir2
cp100 = (coresToProcess.astype('int32')) / 100
ind = npy.where(cp100 > 0)
dirNums = npy.unique(cp100[ind])
for dirNum in dirNums:
focalDir = focalDirBaseName + str(dirNum)
gprint('...' + focalDir)
arcpy.CreateFolder_management(path2, focalDir)
# Create resistance raster with filled-in Nodata values for later use
arcpy.env.extent = cfg.RESRAST
resistFillRaster = path.join(cfg.SCRATCHDIR, "resist_fill")
output = arcpy.sa.Con(IsNull(cfg.RESRAST), 1000000000,
Raster(cfg.RESRAST) - 1)
output.save(resistFillRaster)
coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
coreList = npy.sort(coreList)
# Loop through each search radius to calculate barriers in each link
import time
radId = 0 #keep track of number of radii processed- used for temp dir naming
for radius in range(startRadius, endRadius + 1, radiusStep):
radId = radId + 1
linkTableTemp = linkTable.copy()
@retry(10)
#can't pass vars in and modify them.
def doRadiusLoop():
linkTable = linkTableTemp.copy()
startTime = time.clock()
randomerror()
linkLoop = 0
pctDone = 0
gprint('\nMapping barriers at a radius of ' + str(radius) +
' ' + str(mapUnits))
if cfg.SUM_BARRIERS:
gprint('using SUM method')
else:
gprint('using MAXIMUM method')
if numCorridorLinks > 1:
gprint('0 percent done')
lastMosaicRaster = None
lastMosaicRasterPct = None
for x in range(0, numLinks):
pctDone = lu.report_pct_done(linkLoop, numCorridorLinks,
pctDone)
linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
if ((linkTable[x, cfg.LTB_LINKTYPE] > 0)
and (linkTable[x, cfg.LTB_LINKTYPE] < 1000)):
linkLoop = linkLoop + 1
# 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)
# Mask out areas above CWD threshold
cwdTemp1 = None
cwdTemp2 = None
if cfg.BARRIER_CWD_THRESH is not None:
if x == 1:
lu.dashline(1)
gprint(' Using CWD threshold of ' +
str(cfg.BARRIER_CWD_THRESH) +
' map units.')
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
cwdTemp1 = path.join(cfg.SCRATCHDIR,
"tmp" + str(corex))
outCon = arcpy.sa.Con(
cwdRaster1 < float(cfg.BARRIER_CWD_THRESH),
cwdRaster1)
outCon.save(cwdTemp1)
cwdRaster1 = cwdTemp1
cwdTemp2 = path.join(cfg.SCRATCHDIR,
"tmp" + str(corey))
outCon = arcpy.sa.Con(
cwdRaster2 < float(cfg.BARRIER_CWD_THRESH),
cwdRaster2)
outCon.save(cwdTemp2)
cwdRaster2 = cwdTemp2
focalRaster1 = lu.get_focal_path(corex, radius)
focalRaster2 = lu.get_focal_path(corey, radius)
link = lu.get_links_from_core_pairs(
linkTable, corex, corey)
lcDist = float(linkTable[link, cfg.LTB_CWDIST])
# Detect barriers at radius using neighborhood stats
# Create the Neighborhood Object
innerRadius = radius - 1
outerRadius = radius
dia = 2 * radius
InNeighborhood = ("ANNULUS " + str(innerRadius) + " " +
str(outerRadius) + " MAP")
@retry(10)
def execFocal():
randomerror()
# Execute FocalStatistics
if not path.exists(focalRaster1):
arcpy.env.extent = cwdRaster1
outFocalStats = arcpy.sa.FocalStatistics(
cwdRaster1, InNeighborhood, "MINIMUM",
"DATA")
if setCoresToNull:
outFocalStats2 = arcpy.sa.Con(
outFocalStats > 0, outFocalStats
) # Set areas overlapping cores to NoData xxx
outFocalStats2.save(focalRaster1) #xxx
else:
outFocalStats.save(focalRaster1) #xxx
arcpy.env.extent = cfg.RESRAST
if not path.exists(focalRaster2):
arcpy.env.extent = cwdRaster2
outFocalStats = arcpy.sa.FocalStatistics(
cwdRaster2, InNeighborhood, "MINIMUM",
"DATA")
if setCoresToNull:
outFocalStats2 = arcpy.sa.Con(
outFocalStats > 0, outFocalStats
) # Set areas overlapping cores to NoData xxx
outFocalStats2.save(focalRaster2) #xxx
else:
outFocalStats.save(focalRaster2) #xxx
arcpy.env.extent = cfg.RESRAST
execFocal()
lu.delete_data(cwdTemp1)
lu.delete_data(cwdTemp2)
barrierRaster = path.join(
cbarrierdir, "b" + str(radius) + "_" + str(corex) +
"_" + str(corey) + '.tif')
if cfg.SUM_BARRIERS: # Need to set nulls to 0, also
# create trim rasters as we go
outRas = ((lcDist - Raster(focalRaster1) -
Raster(focalRaster2) - dia) / dia)
outCon = arcpy.sa.Con(IsNull(outRas), 0, outRas)
outCon2 = arcpy.sa.Con(outCon < 0, 0, outCon)
outCon2.save(barrierRaster)
# Execute FocalStatistics to fill out search radii
InNeighborhood = "CIRCLE " + str(
outerRadius) + " MAP"
fillRaster = path.join(
cbarrierdir, "b" + str(radius) + "_" +
str(corex) + "_" + str(corey) + "_fill.tif")
outFocalStats = arcpy.sa.FocalStatistics(
barrierRaster, InNeighborhood, "MAXIMUM",
"DATA")
outFocalStats.save(fillRaster)
if cfg.WRITE_TRIM_RASTERS:
trmRaster = path.join(
cbarrierdir,
"b" + str(radius) + "_" + str(corex) +
"_" + str(corey) + "_trim.tif")
rasterList = [fillRaster, resistFillRaster]
outCellStatistics = arcpy.sa.CellStatistics(
rasterList, "MINIMUM")
outCellStatistics.save(trmRaster)
else:
#Calculate potential benefit per map unit restored
@retry(10)
def calcBen():
randomerror()
outRas = ((lcDist - Raster(focalRaster1) -
Raster(focalRaster2) - dia) / dia)
outRas.save(barrierRaster)
calcBen()
if cfg.WRITE_PCT_RASTERS:
#Calculate PERCENT potential benefit per unit restored
barrierRasterPct = path.join(
cbarrierdir, "b" + str(radius) + "_" +
str(corex) + "_" + str(corey) + '_pct.tif')
@retry(10)
def calcBenPct():
randomerror()
outras = (100 *
(Raster(barrierRaster) / lcDist))
outras.save(barrierRasterPct)
calcBenPct()
# Mosaic barrier results across core area pairs
mosaicDir = path.join(
cfg.SCRATCHDIR,
'mos' + str(radId) + '_' + str(x + 1))
lu.create_dir(mosaicDir)
mosFN = 'mos_temp'
tempMosaicRaster = path.join(mosaicDir, mosFN)
tempMosaicRasterTrim = path.join(
mosaicDir, 'mos_temp_trm')
arcpy.env.workspace = mosaicDir
if linkLoop == 1:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(
barrierRaster, tempMosaicRaster)
if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
arcpy.CopyRaster_management(
trmRaster, tempMosaicRasterTrim)
else:
if cfg.SUM_BARRIERS:
outCon = arcpy.sa.Con(
Raster(barrierRaster) < 0,
lastMosaicRaster,
Raster(barrierRaster) +
Raster(lastMosaicRaster))
outCon.save(tempMosaicRaster)
if cfg.WRITE_TRIM_RASTERS:
outCon = arcpy.sa.Con(
Raster(trmRaster) < 0,
lastMosaicRasterTrim,
Raster(trmRaster) +
Raster(lastMosaicRasterTrim))
outCon.save(tempMosaicRasterTrim)
else:
rasterString = ('"' + barrierRaster + ";" +
lastMosaicRaster + '"')
@retry(10)
def mosaicToNew():
randomerror()
arcpy.MosaicToNewRaster_management(
rasterString, mosaicDir, mosFN, "",
"32_BIT_FLOAT", arcpy.env.cellSize,
"1", "MAXIMUM", "MATCH")
mosaicToNew()
# gprint(str(corex)+'0'+str(corey))
if linkLoop > 1: #Clean up from previous loop
lu.delete_data(lastMosaicRaster)
lastMosaicDir = path.dirname(lastMosaicRaster)
lu.clean_out_workspace(lastMosaicDir)
lu.delete_dir(lastMosaicDir)
lastMosaicRaster = tempMosaicRaster
if cfg.WRITE_TRIM_RASTERS:
lastMosaicRasterTrim = tempMosaicRasterTrim
if cfg.WRITE_PCT_RASTERS:
mosPctFN = 'mos_temp_pct'
mosaicDirPct = path.join(
cfg.SCRATCHDIR,
'mosP' + str(radId) + '_' + str(x + 1))
lu.create_dir(mosaicDirPct)
tempMosaicRasterPct = path.join(
mosaicDirPct, mosPctFN)
if linkLoop == 1:
# If this is the first grid then copy
# rather than mosaic
if cfg.SUM_BARRIERS:
outCon = arcpy.sa.Con(
Raster(barrierRasterPct) < 0, 0,
arcpy.sa.Con(IsNull(barrierRasterPct),
0, barrierRasterPct))
outCon.save(tempMosaicRasterPct)
else:
arcpy.CopyRaster_management(
barrierRasterPct, tempMosaicRasterPct)
else:
if cfg.SUM_BARRIERS:
@retry(10)
def sumBarriers():
randomerror()
outCon = arcpy.sa.Con(
Raster(barrierRasterPct) < 0,
lastMosaicRasterPct,
Raster(barrierRasterPct) +
Raster(lastMosaicRasterPct))
outCon.save(tempMosaicRasterPct)
sumBarriers()
else:
rasterString = ('"' + barrierRasterPct +
";" + lastMosaicRasterPct +
'"')
@retry(10)
def maxBarriers():
randomerror()
arcpy.MosaicToNewRaster_management(
rasterString, mosaicDirPct,
mosPctFN, "", "32_BIT_FLOAT",
arcpy.env.cellSize, "1", "MAXIMUM",
"MATCH")
maxBarriers()
if linkLoop > 1: #Clean up from previous loop
lu.delete_data(lastMosaicRasterPct)
lastMosaicDirPct = path.dirname(
lastMosaicRasterPct)
lu.clean_out_workspace(lastMosaicDirPct)
lu.delete_dir(lastMosaicDirPct)
# lu.delete_data(lastMosaicRasterPct)
lastMosaicRasterPct = tempMosaicRasterPct
if not cfg.SAVEBARRIERRASTERS:
lu.delete_data(barrierRaster)
if cfg.WRITE_PCT_RASTERS:
lu.delete_data(barrierRasterPct)
if cfg.WRITE_TRIM_RASTERS:
lu.delete_data(trmRaster)
# 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)
if numCorridorLinks > 1 and pctDone < 100:
gprint('100 percent done')
gprint('Summarizing barrier data for search radius.')
#rows that were temporarily disabled
rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] > 1000)
linkTable[rows, cfg.LTB_LINKTYPE] = (
linkTable[rows, cfg.LTB_LINKTYPE] - 1000)
# -----------------------------------------------------------------
# Set negative values to null or zero and write geodatabase.
mosaicFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" +
str(radius))
mosaicRaster = path.join(cfg.BARRIERGDB, mosaicFN)
arcpy.env.extent = cfg.RESRAST
# if setCoresToNull:
# outCon = arcpy.sa.Con(Raster(tempMosaicRaster) < 0, 0,
# tempMosaicRaster) #xxx
# outCon.save(mosaicRaster) #xxx
# else:
outSetNull = arcpy.sa.SetNull(tempMosaicRaster,
tempMosaicRaster,
"VALUE < 0") #xxx orig
outSetNull.save(mosaicRaster)
lu.delete_data(tempMosaicRaster)
if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
mosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
"_Rad" + str(radius))
mosaicRasterTrim = path.join(cfg.BARRIERGDB, mosaicFN)
arcpy.CopyRaster_management(tempMosaicRasterTrim,
mosaicRasterTrim)
lu.delete_data(tempMosaicRaster)
if cfg.WRITE_PCT_RASTERS:
# Do same for percent raster
mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
"_Rad" + str(radius))
arcpy.env.extent = cfg.RESRAST
outSetNull = arcpy.sa.SetNull(tempMosaicRasterPct,
tempMosaicRasterPct,
"VALUE < 0")
mosaicRasterPct = path.join(cfg.BARRIERGDB, mosaicPctFN)
outSetNull.save(mosaicRasterPct)
lu.delete_data(tempMosaicRasterPct)
# 'Grow out' maximum restoration gain to
# neighborhood size for display
InNeighborhood = "CIRCLE " + str(outerRadius) + " MAP"
# Execute FocalStatistics
fillRasterFN = "barriers_fill" + str(outerRadius) + tif
fillRaster = path.join(cfg.BARRIERBASEDIR, fillRasterFN)
outFocalStats = arcpy.sa.FocalStatistics(
mosaicRaster, InNeighborhood, "MAXIMUM", "DATA")
outFocalStats.save(fillRaster)
if cfg.WRITE_PCT_RASTERS:
# Do same for percent raster
fillRasterPctFN = "barriers_fill_pct" + str(
outerRadius) + tif
fillRasterPct = path.join(cfg.BARRIERBASEDIR,
fillRasterPctFN)
outFocalStats = arcpy.sa.FocalStatistics(
mosaicRasterPct, InNeighborhood, "MAXIMUM", "DATA")
outFocalStats.save(fillRasterPct)
#Place copies of filled rasters in output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
fillRasterFN = (PREFIX + "_BarrrierCircles" + sumSuffix +
"_Rad" + str(outerRadius))
arcpy.CopyRaster_management(fillRaster, fillRasterFN)
if cfg.WRITE_PCT_RASTERS:
fillRasterPctFN = (PREFIX + "_BarrrierCircles_Pct" +
sumSuffix + "_Rad" + str(outerRadius))
arcpy.CopyRaster_management(fillRasterPct, fillRasterPctFN)
if not cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
# Create pared-down version of filled raster- remove pixels
# that don't need restoring by allowing a pixel to only
# contribute its resistance value to restoration gain
outRasterFN = "barriers_trm" + str(outerRadius) + tif
outRaster = path.join(cfg.BARRIERBASEDIR, outRasterFN)
rasterList = [fillRaster, resistFillRaster]
outCellStatistics = arcpy.sa.CellStatistics(
rasterList, "MINIMUM")
outCellStatistics.save(outRaster)
#SECOND ROUND TO CLIP BY DATA VALUES IN BARRIER RASTER
outRaster2FN = ("barriers_trm" + sumSuffix +
str(outerRadius) + "_2" + tif)
outRaster2 = path.join(cfg.BARRIERBASEDIR, outRaster2FN)
output = arcpy.sa.Con(IsNull(fillRaster), fillRaster,
outRaster)
output.save(outRaster2)
outRasterFN = (PREFIX + "_BarrierCircles_RBMin" +
sumSuffix + "_Rad" + str(outerRadius))
outRasterPath = path.join(cfg.BARRIERGDB, outRasterFN)
arcpy.CopyRaster_management(outRaster2, outRasterFN)
randomerror()
startTime = lu.elapsed_time(startTime)
# Call the above function
doRadiusLoop()
# Combine rasters across radii
gprint('\nCreating summary rasters...')
if startRadius != endRadius:
radiiSuffix = ('_Rad' + str(int(startRadius)) + 'To' +
str(int(endRadius)) + 'Step' + str(int(radiusStep)))
mosaicFN = "bar_radii"
mosaicPctFN = "bar_radii_pct"
arcpy.env.workspace = cfg.BARRIERBASEDIR
for radius in range(startRadius, endRadius + 1, radiusStep):
#Fixme: run speed test with gdb mosaicking above and here
radiusFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" +
str(radius))
radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRaster, mosaicFN)
else:
mosaicRaster = path.join(cfg.BARRIERBASEDIR, mosaicFN)
arcpy.Mosaic_management(radiusRaster, mosaicRaster,
"MAXIMUM", "MATCH")
if cfg.WRITE_PCT_RASTERS:
radiusPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
"_Rad" + str(radius))
radiusRasterPct = path.join(cfg.BARRIERGDB, radiusPctFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRasterPct,
mosaicPctFN)
else:
mosaicRasterPct = path.join(cfg.BARRIERBASEDIR,
mosaicPctFN)
arcpy.Mosaic_management(radiusRasterPct,
mosaicRasterPct, "MAXIMUM",
"MATCH")
# Copy results to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
mosaicFN = PREFIX + "_BarrierCenters" + sumSuffix + radiiSuffix
arcpy.CopyRaster_management(mosaicRaster, mosaicFN)
if cfg.WRITE_PCT_RASTERS:
mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
radiiSuffix)
arcpy.CopyRaster_management(mosaicRasterPct, mosaicPctFN)
#GROWN OUT rasters
fillMosaicFN = "barriers_radii_fill" + tif
fillMosaicPctFN = "barriers_radii_fill_pct" + tif
fillMosaicRaster = path.join(cfg.BARRIERBASEDIR, fillMosaicFN)
fillMosaicRasterPct = path.join(cfg.BARRIERBASEDIR,
fillMosaicPctFN)
arcpy.env.workspace = cfg.BARRIERBASEDIR
for radius in range(startRadius, endRadius + 1, radiusStep):
radiusFN = "barriers_fill" + str(radius) + tif
#fixme- do this when only a single radius too
radiusRaster = path.join(cfg.BARRIERBASEDIR, radiusFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRaster, fillMosaicFN)
else:
arcpy.Mosaic_management(radiusRaster, fillMosaicRaster,
"MAXIMUM", "MATCH")
if cfg.WRITE_PCT_RASTERS:
radiusPctFN = "barriers_fill_pct" + str(radius) + tif
#fixme- do this when only a single radius too
radiusRasterPct = path.join(cfg.BARRIERBASEDIR,
radiusPctFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRasterPct,
fillMosaicPctFN)
else:
arcpy.Mosaic_management(radiusRasterPct,
fillMosaicRasterPct, "MAXIMUM",
"MATCH")
# Copy result to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
fillMosaicFN = PREFIX + "_BarrierCircles" + sumSuffix + radiiSuffix
arcpy.CopyRaster_management(fillMosaicRaster, fillMosaicFN)
if cfg.WRITE_PCT_RASTERS:
fillMosaicPctFN = (PREFIX + "_BarrierCircles_Pct" + sumSuffix +
radiiSuffix)
arcpy.CopyRaster_management(fillMosaicRasterPct,
fillMosaicPctFN)
# if not cfg.SUM_BARRIERS:
#GROWN OUT AND TRIMMED rasters (Can't do percent)
if cfg.WRITE_TRIM_RASTERS:
trimMosaicFN = "bar_radii_trm"
arcpy.env.workspace = cfg.BARRIERBASEDIR
trimMosaicRaster = path.join(cfg.BARRIERBASEDIR, trimMosaicFN)
for radius in range(startRadius, endRadius + 1, radiusStep):
radiusFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
"_Rad" + str(radius))
#fixme- do this when only a single radius too
radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRaster, trimMosaicFN)
else:
arcpy.Mosaic_management(radiusRaster, trimMosaicRaster,
"MAXIMUM", "MATCH")
# Copy result to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
trimMosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
radiiSuffix)
arcpy.CopyRaster_management(trimMosaicRaster, trimMosaicFN)
if not cfg.SAVE_RADIUS_RASTERS:
arcpy.env.workspace = cfg.BARRIERGDB
rasters = arcpy.ListRasters()
for raster in rasters:
if 'rad' in raster.lower() and not 'step' in raster.lower():
lu.delete_data(raster)
arcpy.env.workspace = cfg.BARRIERGDB
rasters = arcpy.ListRasters()
for raster in rasters:
gprint('\nBuilding output statistics and pyramids\n'
'for raster ' + raster)
lu.build_stats(raster)
#Clean up temporary files and directories
if not cfg.SAVEBARRIERRASTERS:
lu.delete_dir(cbarrierdir)
lu.delete_dir(cfg.BARRIERBASEDIR)
if not cfg.SAVEFOCALRASTERS:
for radius in range(startRadius, endRadius + 1, radiusStep):
core1path = lu.get_focal_path(1, radius)
path1, dir1 = path.split(core1path)
path2, dir2 = path.split(path1)
lu.delete_dir(path2)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 6. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 6. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def STEP8_calc_pinchpoints():
""" Maps pinch points in Linkage Mapper corridors using Circuitscape
given CWD calculations from s3_calcCwds.py.
"""
try:
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
restartFlag = False
if cfg.CWDCUTOFF < 0:
cfg.CWDCUTOFF = cfg.CWDCUTOFF * -1
restartFlag = True # Restart code in progress
CSPATH = lu.get_cs_path()
outputGDB = path.join(cfg.OUTPUTDIR, path.basename(cfg.PINCHGDB))
arcpy.OverWriteOutput = True
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.pyramid = "NONE"
arcpy.env.rasterstatistics = "NONE"
# set the analysis extent and cell size to that of the resistance
# surface
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.snapraster = cfg.RESRAST
resRaster = cfg.RESRAST
arcpy.env.extent = "MINOF"
minObject = arcpy.GetRasterProperties_management(resRaster, "MINIMUM")
rasterMin = float(str(minObject.getOutput(0)))
if rasterMin <= 0:
msg = ('Error: resistance raster cannot have 0 or negative values.')
lu.raise_error(msg)
if cfg.DO_ADJACENTPAIRS:
prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep = 8)
if not arcpy.Exists(prevLcpShapefile):
msg = ('Cannot find an LCP shapefile from step 5. Please '
'rerun that step and any previous ones if necessary.')
lu.raise_error(msg)
# Remove lcp shapefile
lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s8.shp")
lu.delete_data(lcpShapefile)
inLinkTableFile = lu.get_prev_step_link_table(step=8)
linkTable = lu.load_link_table(inLinkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg =('\nThere are no linkages. Bailing.')
lu.raise_error(msg)
if linkTable.shape[1] < 16: # If linktable has no entries from prior
# centrality or pinchpint analyses
extraCols = npy.zeros((numLinks, 6), dtype="float64")
linkTable = linkTable[:,0:10]
linkTable = npy.append(linkTable, extraCols, axis=1)
linkTable[:, cfg.LTB_LCPLEN] = -1
linkTable[:, cfg.LTB_CWDEUCR] = -1
linkTable[:, cfg.LTB_CWDPATHR] = -1
linkTable[:, cfg.LTB_EFFRESIST] = -1
linkTable[:, cfg.LTB_CWDTORR] = -1
linkTable[:, cfg.LTB_CURRENT] = -1
del extraCols
# set up directories for circuit and circuit mosaic grids
# Create output geodatabase
if not arcpy.Exists(cfg.PINCHGDB):
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
path.basename(cfg.PINCHGDB))
mosaicRaster = path.join(cfg.CIRCUITBASEDIR, "current_mos" + tif)
coresToProcess = npy.unique(
linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
maxCoreNum = max(coresToProcess)
del coresToProcess
lu.dashline(0)
coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
coreList = npy.sort(coreList)
#gprint('There are ' + str(len(npy.unique(coreList))) ' core areas.')
INCIRCUITDIR = cfg.CIRCUITBASEDIR
OUTCIRCUITDIR = path.join(cfg.CIRCUITBASEDIR,
cfg.CIRCUITOUTPUTDIR_NM)
CONFIGDIR = path.join(INCIRCUITDIR, cfg.CIRCUITCONFIGDIR_NM)
# Cutoff value text to append to filenames
cutoffText = str(cfg.CWDCUTOFF)
if cutoffText[-6:] == '000000':
cutoffText = cutoffText[0:-6]+'m'
elif cutoffText[-3:] == '000':
cutoffText = cutoffText[0:-3]+'k'
if cfg.SQUARERESISTANCES:
# Square resistance values
squaredRaster = path.join(cfg.SCRATCHDIR,'res_sqr')
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
outRas = Raster(resRaster) * Raster(resRaster)
outRas.save(squaredRaster)
resRaster = squaredRaster
if cfg.DO_ADJACENTPAIRS:
linkLoop = 0
lu.dashline(1)
gprint('Mapping pinch points in individual corridors \n'
'using Circuitscape.')
lu.dashline(1)
gprint('If you try to cancel your run and the Arc dialog hangs, ')
gprint('you can kill Circuitscape by opening Windows Task Manager')
gprint('and ending the cs_run.exe process.')
lu.dashline(2)
for x in range(0,numLinks):
linkId = str(int(linkTable[x,cfg.LTB_LINKID]))
if not (linkTable[x,cfg.LTB_LINKTYPE] > 0):
continue
linkLoop = linkLoop + 1
linkDir = path.join(cfg.SCRATCHDIR, 'link' + linkId)
if restartFlag == True and path.exists(linkDir):
gprint('continuing')
continue
restartFlag = False
lu.create_dir(linkDir)
start_time1 = time.clock()
# 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)
lccNormRaster = path.join(linkDir, 'lcc_norm')
arcpy.env.extent = "MINOF"
link = lu.get_links_from_core_pairs(linkTable, corex,
corey)
lcDist = float(linkTable[link,cfg.LTB_CWDIST])
# Normalized lcc rasters are created by adding cwd rasters
# and subtracting the least cost distance between them.
outRas = Raster(cwdRaster1) + Raster(cwdRaster2) - lcDist
outRas.save(lccNormRaster)
#create raster mask
resMaskRaster = path.join(linkDir, 'res_mask'+tif)
#create raster mask
outCon = arcpy.sa.Con(Raster(lccNormRaster) <= cfg.CWDCUTOFF, 1)
outCon.save(resMaskRaster)
# Convert to poly. Use as mask to clip resistance raster.
resMaskPoly = path.join(linkDir,
'res_mask_poly.shp')
arcpy.RasterToPolygon_conversion(resMaskRaster, resMaskPoly,
"NO_SIMPLIFY")
arcpy.env.extent = resMaskPoly
# Includes 0 values in some cases with CP LI model if tif
# so using ESRI Grid format
resClipRasterMasked = path.join(linkDir,
'res_clip_m')
# Extract masked resistance raster.
# Needs to be float to get export to npy to work.
outRas = arcpy.sa.ExtractByMask(resRaster, resMaskPoly) + 0.0
outRas.save(resClipRasterMasked)
resNpyFN = 'resistances_link_' + linkId + '.npy'
resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
numElements, numResistanceNodes = export_ras_to_npy(resClipRasterMasked,
resNpyFile)
totMem, availMem = lu.get_mem()
# gprint('Total memory: str(totMem))
if numResistanceNodes / availMem > 2000000:
lu.dashline(1)
gwarn('Warning:')
gwarn('Circuitscape can only solve 2-3 million nodes')
gwarn('per gigabyte of available RAM. \nTotal physical RAM'
' on your machine is ~' + str(totMem)
+ ' GB. \nAvailable memory is ~'+ str(availMem)
+ ' GB. \nYour resistance raster has '
+ str(numResistanceNodes) + ' nodes.')
lu.dashline(2)
corePairRaster = path.join(linkDir, 'core_pairs'+tif)
arcpy.env.extent = resClipRasterMasked
# Next result needs to be floating pt for numpy export
outCon = arcpy.sa.Con(Raster(cwdRaster1) == 0, corex,
arcpy.sa.Con(Raster(cwdRaster2) == 0, corey + 0.0))
outCon.save(corePairRaster)
coreNpyFN = 'cores_link_' + linkId + '.npy'
coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
numElements, numNodes = export_ras_to_npy(corePairRaster,
coreNpyFile)
arcpy.env.extent = "MINOF"
# Set circuitscape options and call
options = lu.setCircuitscapeOptions()
if cfg.WRITE_VOLT_MAPS == True:
options['write_volt_maps']=True
options['habitat_file'] = resNpyFile
# if int(linkId) > 2:
# options['habitat_file'] = 'c:\\test.dummy'
options['point_file'] = coreNpyFile
options['set_focal_node_currents_to_zero']=True
outputFN = 'Circuitscape_link' + linkId + '.out'
options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
if numElements > 250000:
options['print_timings']=True
configFN = 'pinchpoint_config' + linkId + '.ini'
outConfigFile = path.join(CONFIGDIR, configFN)
lu.writeCircuitscapeConfigFile(outConfigFile, options)
gprint('Processing link ID #' + str(linkId) + '. Resistance map'
' has ' + str(int(numResistanceNodes)) + ' nodes.')
memFlag = call_circuitscape(CSPATH, outConfigFile)
currentFN = ('Circuitscape_link' + linkId
+ '_cum_curmap.npy')
currentMap = path.join(OUTCIRCUITDIR, currentFN)
if not arcpy.Exists(currentMap):
print_failure(numResistanceNodes, memFlag, 10)
numElements, numNodes = export_ras_to_npy(
resClipRasterMasked,resNpyFile)
memFlag = call_circuitscape(CSPATH, outConfigFile)
currentFN = ('Circuitscape_link' + linkId
+ '_cum_curmap.npy')
currentMap = path.join(OUTCIRCUITDIR, currentFN)
if not arcpy.Exists(currentMap):
msg = ('\nCircuitscape failed. See error information above.')
arcpy.AddError(msg)
lu.write_log(msg)
exit(1)
# Either set core areas to nodata in current map or
# divide each by its radius
currentRaster = path.join(linkDir, "current" + tif)
import_npy_to_ras(currentMap,corePairRaster,currentRaster)
if cfg.WRITE_VOLT_MAPS == True:
voltFN = ('Circuitscape_link' + linkId + '_voltmap_'
+ str(corex) + '_'+str(corey) + '.npy')
voltMap = path.join(OUTCIRCUITDIR, voltFN)
voltRaster = path.join(outputGDB,
cfg.PREFIX + "_voltMap_"+ str(corex) + '_'+str(corey))
import_npy_to_ras(voltMap,corePairRaster,voltRaster)
gprint('Building output statistics and pyramids '
'for voltage raster\n')
lu.build_stats(voltRaster)
arcpy.env.extent = currentRaster
if SETCORESTONULL:
# Set core areas to NoData in current map for color ramping
currentRaster2 = currentRaster + '2' + tif
outCon = arcpy.sa.Con(arcpy.sa.IsNull(Raster
(corePairRaster)), Raster(currentRaster))
outCon.save(currentRaster2)
currentRaster = currentRaster2
arcpy.env.extent = "MAXOF"
if linkLoop == 1:
lu.delete_data(mosaicRaster)
@retry(10)
def copyRas2():
arcpy.CopyRaster_management(currentRaster,
mosaicRaster)
copyRas2()
else:
@retry(10)
def mosaicRas():
arcpy.Mosaic_management(currentRaster,
mosaicRaster, "MAXIMUM", "MATCH")
mosaicRas()
resistancesFN = ('Circuitscape_link' + linkId
+ '_resistances_3columns.out')
resistancesFile = path.join(OUTCIRCUITDIR,resistancesFN)
resistances = npy.loadtxt(resistancesFile,
dtype = 'Float64', comments='#')
resistance = float(str(arcpy.env.cellSize)) * resistances[2]
linkTable[link,cfg.LTB_EFFRESIST] = resistance
# Ratio
if not cfg.SQUARERESISTANCES:
linkTable[link,cfg.LTB_CWDTORR] = (linkTable[link,
cfg.LTB_CWDIST] / linkTable[link,cfg.LTB_EFFRESIST])
# Clean up
if cfg.SAVE_TEMP_CIRCUIT_FILES == False:
lu.delete_file(coreNpyFile)
coreNpyBase, extension = path.splitext(coreNpyFile)
lu.delete_data(coreNpyBase + '.hdr')
lu.delete_file(resNpyFile)
resNpyBase, extension = path.splitext(resNpyFile)
lu.delete_data(resNpyBase + '.hdr')
lu.delete_file(currentMap)
curMapBase, extension = path.splitext(currentMap)
lu.delete_data(curMapBase + '.hdr')
lu.delete_data(currentRaster)
lu.clean_out_workspace(linkDir)
lu.delete_dir(linkDir)
gprint('Finished with link ID #' + str(linkId) + '. ' +
str(linkLoop) + ' out of ' + str(numCorridorLinks) +
' links have been processed.')
start_time1 = lu.elapsed_time(start_time1)
outputRaster = path.join(outputGDB, cfg.PREFIX +
"_current_adjacentPairs_" + cutoffText)
lu.delete_data(outputRaster)
@retry(10)
def copyRas():
arcpy.CopyRaster_management(mosaicRaster, outputRaster)
copyRas()
gprint('Building output statistics and pyramids '
'for corridor pinch point raster\n')
lu.build_stats(outputRaster)
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=5,
thisStep=8)
linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
linkTableFinalFile = path.join(cfg.OUTPUTDIR, cfg.PREFIX +
"_linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable,
linkTableFinalFile, inLinkTableFile)
gprint('Copy of linkTable written to '+
linkTableFinalFile)
#fixme: update sticks?
gprint('Creating shapefiles with linework for links.')
lu.write_link_maps(linkTableFinalFile, step=8)
# Copy final link maps to gdb.
lu.copy_final_link_maps(step=8)
lu.delete_data(mosaicRaster)
if not cfg.DO_ALLPAIRS:
# Clean up temporary files
if not cfg.SAVECURRENTMAPS:
lu.delete_dir(OUTCIRCUITDIR)
return
lu.dashline(1)
gprint('Mapping global pinch points among all\n'
'core area pairs using Circuitscape.')
if cfg.ALL_PAIR_SCENARIO=='pairwise':
gprint('Circuitscape will be run in PAIRWISE mode.')
else:
gprint('Circuitscape will be run in ALL-TO-ONE mode.')
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
S8CORE_RAS = "s8core_ras"
s8CoreRasPath = path.join(cfg.SCRATCHDIR,S8CORE_RAS)
arcpy.FeatureToRaster_conversion(cfg.COREFC, cfg.COREFN,
s8CoreRasPath, arcpy.env.cellSize)
binaryCoreRaster = path.join(cfg.SCRATCHDIR,"core_ras_bin")
# The following commands cause file lock problems on save. using gp
# instead.
# outCon = arcpy.sa.Con(S8CORE_RAS, 1, "#", "VALUE > 0")
# outCon.save(binaryCoreRaster)
# gp.Con_sa(s8CoreRasPath, 1, binaryCoreRaster, "#", "VALUE > 0")
outCon = arcpy.sa.Con(Raster(s8CoreRasPath) > 0, 1)
outCon.save(binaryCoreRaster)
s5corridorRas = path.join(cfg.OUTPUTGDB,cfg.PREFIX + "_corridors")
if not arcpy.Exists(s5corridorRas):
s5corridorRas = path.join(cfg.OUTPUTGDB,cfg.PREFIX +
"_lcc_mosaic_int")
outCon = arcpy.sa.Con(Raster(s5corridorRas) <= cfg.CWDCUTOFF, Raster(
resRaster), arcpy.sa.Con(Raster(
binaryCoreRaster) > 0, Raster(resRaster)))
resRasClipPath = path.join(cfg.SCRATCHDIR,'res_ras_clip')
outCon.save(resRasClipPath)
arcpy.env.cellSize = resRasClipPath
arcpy.env.extent = resRasClipPath
s8CoreRasClipped = s8CoreRasPath + '_c'
# Produce core raster with same extent as clipped resistance raster
# added to ensure correct data type- nodata values were positive for
# cores otherwise
outCon = arcpy.sa.Con(arcpy.sa.IsNull(Raster(s8CoreRasPath)),
-9999, Raster(s8CoreRasPath))
outCon.save(s8CoreRasClipped)
resNpyFN = 'resistances.npy'
resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
numElements, numResistanceNodes = export_ras_to_npy(resRasClipPath,resNpyFile)
totMem, availMem = lu.get_mem()
# gprint('Total memory: str(totMem))
if numResistanceNodes / availMem > 2000000:
lu.dashline(1)
gwarn('Warning:')
gwarn('Circuitscape can only solve 2-3 million nodes')
gwarn('per gigabyte of available RAM. \nTotal physical RAM '
'on your machine is ~' + str(totMem)
+ ' GB. \nAvailable memory is ~'+ str(availMem)
+ ' GB. \nYour resistance raster has '
+ str(numResistanceNodes) + ' nodes.')
lu.dashline(0)
coreNpyFN = 'cores.npy'
coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
numElements, numNodes = export_ras_to_npy(s8CoreRasClipped,coreNpyFile)
arcpy.env.extent = "MINOF"
options = lu.setCircuitscapeOptions()
options['scenario']=cfg.ALL_PAIR_SCENARIO
options['habitat_file'] = resNpyFile
options['point_file'] = coreNpyFile
options['set_focal_node_currents_to_zero']=True
outputFN = 'Circuitscape.out'
options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
options['print_timings']=True
configFN = 'pinchpoint_allpair_config.ini'
outConfigFile = path.join(CONFIGDIR, configFN)
lu.writeCircuitscapeConfigFile(outConfigFile, options)
gprint('\nResistance map has ' + str(int(numResistanceNodes)) + ' nodes.')
lu.dashline(1)
gprint('If you try to cancel your run and the Arc dialog hangs, ')
gprint('you can kill Circuitscape by opening Windows Task Manager')
gprint('and ending the cs_run.exe process.')
lu.dashline(0)
call_circuitscape(CSPATH, outConfigFile)
# test = subprocess.call([CSPATH, outConfigFile],
# creationflags = subprocess.CREATE_NEW_CONSOLE)
if options['scenario']=='pairwise':
rasterSuffix = "_current_allPairs_" + cutoffText
else:
rasterSuffix = "_current_allToOne_" + cutoffText
currentFN = 'Circuitscape_cum_curmap.npy'
currentMap = path.join(OUTCIRCUITDIR, currentFN)
outputRaster = path.join(outputGDB, cfg.PREFIX + rasterSuffix)
currentRaster = path.join(cfg.SCRATCHDIR, "current")
try:
import_npy_to_ras(currentMap,resRasClipPath,outputRaster)
except:
lu.dashline(1)
msg = ('ERROR: Circuitscape failed. \n'
'Note: Circuitscape can only solve 2-3 million nodes'
'\nper gigabyte of available RAM. The resistance '
'\nraster for the last corridor had '
+ str(numResistanceNodes) + ' nodes.\n\nResistance '
'raster values that vary by >6 orders of \nmagnitude'
' can also cause failures, as can a mismatch in '
'\ncore area and resistance raster extents.')
arcpy.AddError(msg)
lu.write_log(msg)
exit(1)
#set core areas to nodata
if SETCORESTONULL:
# Set core areas to NoData in current map for color ramping
outputRasterND = outputRaster + '_noDataCores'
outCon = arcpy.sa.SetNull(Raster(s8CoreRasClipped) > 0,
Raster(outputRaster))
outCon.save(outputRasterND)
gprint('\nBuilding output statistics and pyramids '
'for centrality raster.')
lu.build_stats(outputRaster)
lu.build_stats(outputRasterND)
# Clean up temporary files
if not cfg.SAVECURRENTMAPS:
lu.delete_dir(OUTCIRCUITDIR)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 8. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 8. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def STEP8_calc_pinchpoints():
""" Maps pinch points in Linkage Mapper corridors using Circuitscape
given CWD calculations from s3_calcCwds.py.
"""
try:
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
restartFlag = False
if cfg.CWDCUTOFF < 0:
cfg.CWDCUTOFF = cfg.CWDCUTOFF * -1
restartFlag = True # Restart code in progress
CSPATH = lu.get_cs_path()
outputGDB = path.join(cfg.OUTPUTDIR, path.basename(cfg.PINCHGDB))
arcpy.OverWriteOutput = True
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.pyramid = "NONE"
arcpy.env.rasterstatistics = "NONE"
# set the analysis extent and cell size to that of the resistance
# surface
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.snapraster = cfg.RESRAST
resRaster = cfg.RESRAST
arcpy.env.extent = "MINOF"
minObject = arcpy.GetRasterProperties_management(resRaster, "MINIMUM")
rasterMin = float(str(minObject.getOutput(0)))
if rasterMin <= 0:
msg = (
'Error: resistance raster cannot have 0 or negative values.')
lu.raise_error(msg)
if cfg.DO_ADJACENTPAIRS:
prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep=8)
if not arcpy.Exists(prevLcpShapefile):
msg = ('Cannot find an LCP shapefile from step 5. Please '
'rerun that step and any previous ones if necessary.')
lu.raise_error(msg)
# Remove lcp shapefile
lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s8.shp")
lu.delete_data(lcpShapefile)
inLinkTableFile = lu.get_prev_step_link_table(step=8)
linkTable = lu.load_link_table(inLinkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg = ('\nThere are no linkages. Bailing.')
lu.raise_error(msg)
if linkTable.shape[1] < 16: # If linktable has no entries from prior
# centrality or pinchpint analyses
extraCols = npy.zeros((numLinks, 6), dtype="float64")
linkTable = linkTable[:, 0:10]
linkTable = npy.append(linkTable, extraCols, axis=1)
linkTable[:, cfg.LTB_LCPLEN] = -1
linkTable[:, cfg.LTB_CWDEUCR] = -1
linkTable[:, cfg.LTB_CWDPATHR] = -1
linkTable[:, cfg.LTB_EFFRESIST] = -1
linkTable[:, cfg.LTB_CWDTORR] = -1
linkTable[:, cfg.LTB_CURRENT] = -1
del extraCols
# set up directories for circuit and circuit mosaic grids
# Create output geodatabase
if not arcpy.Exists(cfg.PINCHGDB):
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
path.basename(cfg.PINCHGDB))
mosaicRaster = path.join(cfg.CIRCUITBASEDIR, "current_mos" + tif)
coresToProcess = npy.unique(linkTable[:,
cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
maxCoreNum = max(coresToProcess)
del coresToProcess
lu.dashline(0)
coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
coreList = npy.sort(coreList)
#gprint('There are ' + str(len(npy.unique(coreList))) ' core areas.')
INCIRCUITDIR = cfg.CIRCUITBASEDIR
OUTCIRCUITDIR = path.join(cfg.CIRCUITBASEDIR, cfg.CIRCUITOUTPUTDIR_NM)
CONFIGDIR = path.join(INCIRCUITDIR, cfg.CIRCUITCONFIGDIR_NM)
# Cutoff value text to append to filenames
cutoffText = str(cfg.CWDCUTOFF)
if cutoffText[-6:] == '000000':
cutoffText = cutoffText[0:-6] + 'm'
elif cutoffText[-3:] == '000':
cutoffText = cutoffText[0:-3] + 'k'
if cfg.SQUARERESISTANCES:
# Square resistance values
squaredRaster = path.join(cfg.SCRATCHDIR, 'res_sqr')
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
outRas = Raster(resRaster) * Raster(resRaster)
outRas.save(squaredRaster)
resRaster = squaredRaster
if cfg.DO_ADJACENTPAIRS:
linkLoop = 0
lu.dashline(1)
gprint('Mapping pinch points in individual corridors \n'
'using Circuitscape.')
lu.dashline(1)
gprint('If you try to cancel your run and the Arc dialog hangs, ')
gprint('you can kill Circuitscape by opening Windows Task Manager')
gprint('and ending the cs_run.exe process.')
lu.dashline(2)
for x in range(0, numLinks):
linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
if not (linkTable[x, cfg.LTB_LINKTYPE] > 0):
continue
linkLoop = linkLoop + 1
linkDir = path.join(cfg.SCRATCHDIR, 'link' + linkId)
if restartFlag == True and path.exists(linkDir):
gprint('continuing')
continue
restartFlag = False
lu.create_dir(linkDir)
start_time1 = time.clock()
# 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)
lccNormRaster = path.join(linkDir, 'lcc_norm')
arcpy.env.extent = "MINOF"
link = lu.get_links_from_core_pairs(linkTable, corex, corey)
lcDist = float(linkTable[link, cfg.LTB_CWDIST])
# Normalized lcc rasters are created by adding cwd rasters
# and subtracting the least cost distance between them.
outRas = Raster(cwdRaster1) + Raster(cwdRaster2) - lcDist
outRas.save(lccNormRaster)
#create raster mask
resMaskRaster = path.join(linkDir, 'res_mask' + tif)
#create raster mask
outCon = arcpy.sa.Con(
Raster(lccNormRaster) <= cfg.CWDCUTOFF, 1)
outCon.save(resMaskRaster)
# Convert to poly. Use as mask to clip resistance raster.
resMaskPoly = path.join(linkDir, 'res_mask_poly.shp')
arcpy.RasterToPolygon_conversion(resMaskRaster, resMaskPoly,
"NO_SIMPLIFY")
arcpy.env.extent = resMaskPoly
# Includes 0 values in some cases with CP LI model if tif
# so using ESRI Grid format
resClipRasterMasked = path.join(linkDir, 'res_clip_m')
# Extract masked resistance raster.
# Needs to be float to get export to npy to work.
outRas = arcpy.sa.ExtractByMask(resRaster, resMaskPoly) + 0.0
outRas.save(resClipRasterMasked)
resNpyFN = 'resistances_link_' + linkId + '.npy'
resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
numElements, numResistanceNodes = export_ras_to_npy(
resClipRasterMasked, resNpyFile)
totMem, availMem = lu.get_mem()
# gprint('Total memory: str(totMem))
if numResistanceNodes / availMem > 2000000:
lu.dashline(1)
lu.warn('Warning:')
lu.warn('Circuitscape can only solve 2-3 million nodes')
lu.warn(
'per gigabyte of available RAM. \nTotal physical RAM'
' on your machine is ~' + str(totMem) +
' GB. \nAvailable memory is ~' + str(availMem) +
' GB. \nYour resistance raster has ' +
str(numResistanceNodes) + ' nodes.')
lu.dashline(2)
corePairRaster = path.join(linkDir, 'core_pairs' + tif)
arcpy.env.extent = resClipRasterMasked
# Next result needs to be floating pt for numpy export
outCon = arcpy.sa.Con(
Raster(cwdRaster1) == 0, corex,
arcpy.sa.Con(Raster(cwdRaster2) == 0, corey + 0.0))
outCon.save(corePairRaster)
coreNpyFN = 'cores_link_' + linkId + '.npy'
coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
numElements, numNodes = export_ras_to_npy(
corePairRaster, coreNpyFile)
arcpy.env.extent = "MINOF"
# Set circuitscape options and call
options = lu.setCircuitscapeOptions()
if cfg.WRITE_VOLT_MAPS == True:
options['write_volt_maps'] = True
options['habitat_file'] = resNpyFile
# if int(linkId) > 2:
# options['habitat_file'] = 'c:\\test.dummy'
options['point_file'] = coreNpyFile
options['set_focal_node_currents_to_zero'] = True
outputFN = 'Circuitscape_link' + linkId + '.out'
options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
if numElements > 250000:
options['print_timings'] = True
configFN = 'pinchpoint_config' + linkId + '.ini'
outConfigFile = path.join(CONFIGDIR, configFN)
lu.writeCircuitscapeConfigFile(outConfigFile, options)
gprint('Processing link ID #' + str(linkId) +
'. Resistance map'
' has ' + str(int(numResistanceNodes)) + ' nodes.')
memFlag = call_circuitscape(CSPATH, outConfigFile)
currentFN = ('Circuitscape_link' + linkId + '_cum_curmap.npy')
currentMap = path.join(OUTCIRCUITDIR, currentFN)
if not arcpy.Exists(currentMap):
print_failure(numResistanceNodes, memFlag, 10)
numElements, numNodes = export_ras_to_npy(
resClipRasterMasked, resNpyFile)
memFlag = call_circuitscape(CSPATH, outConfigFile)
currentFN = ('Circuitscape_link' + linkId +
'_cum_curmap.npy')
currentMap = path.join(OUTCIRCUITDIR, currentFN)
if not arcpy.Exists(currentMap):
msg = (
'\nCircuitscape failed. See error information above.')
arcpy.AddError(msg)
lu.write_log(msg)
exit(1)
# Either set core areas to nodata in current map or
# divide each by its radius
currentRaster = path.join(linkDir, "current" + tif)
import_npy_to_ras(currentMap, corePairRaster, currentRaster)
if cfg.WRITE_VOLT_MAPS == True:
voltFN = ('Circuitscape_link' + linkId + '_voltmap_' +
str(corex) + '_' + str(corey) + '.npy')
voltMap = path.join(OUTCIRCUITDIR, voltFN)
voltRaster = path.join(
outputGDB, cfg.PREFIX + "_voltMap_" + str(corex) +
'_' + str(corey))
import_npy_to_ras(voltMap, corePairRaster, voltRaster)
gprint('Building output statistics and pyramids '
'for voltage raster\n')
lu.build_stats(voltRaster)
arcpy.env.extent = currentRaster
if SETCORESTONULL:
# Set core areas to NoData in current map for color ramping
currentRaster2 = currentRaster + '2' + tif
outCon = arcpy.sa.Con(
arcpy.sa.IsNull(Raster(corePairRaster)),
Raster(currentRaster))
outCon.save(currentRaster2)
currentRaster = currentRaster2
arcpy.env.extent = "MAXOF"
if linkLoop == 1:
lu.delete_data(mosaicRaster)
@retry(10)
def copyRas2():
arcpy.CopyRaster_management(currentRaster,
mosaicRaster)
copyRas2()
else:
@retry(10)
def mosaicRas():
arcpy.Mosaic_management(currentRaster, mosaicRaster,
"MAXIMUM", "MATCH")
mosaicRas()
resistancesFN = ('Circuitscape_link' + linkId +
'_resistances_3columns.out')
resistancesFile = path.join(OUTCIRCUITDIR, resistancesFN)
resistances = npy.loadtxt(resistancesFile,
dtype='Float64',
comments='#')
resistance = float(str(arcpy.env.cellSize)) * resistances[2]
linkTable[link, cfg.LTB_EFFRESIST] = resistance
# Ratio
if not cfg.SQUARERESISTANCES:
linkTable[link, cfg.LTB_CWDTORR] = (
linkTable[link, cfg.LTB_CWDIST] /
linkTable[link, cfg.LTB_EFFRESIST])
# Clean up
if cfg.SAVE_TEMP_CIRCUIT_FILES == False:
lu.delete_file(coreNpyFile)
coreNpyBase, extension = path.splitext(coreNpyFile)
lu.delete_data(coreNpyBase + '.hdr')
lu.delete_file(resNpyFile)
resNpyBase, extension = path.splitext(resNpyFile)
lu.delete_data(resNpyBase + '.hdr')
lu.delete_file(currentMap)
curMapBase, extension = path.splitext(currentMap)
lu.delete_data(curMapBase + '.hdr')
lu.delete_data(currentRaster)
lu.clean_out_workspace(linkDir)
lu.delete_dir(linkDir)
gprint('Finished with link ID #' + str(linkId) + '. ' +
str(linkLoop) + ' out of ' + str(numCorridorLinks) +
' links have been processed.')
start_time1 = lu.elapsed_time(start_time1)
outputRaster = path.join(
outputGDB, cfg.PREFIX + "_current_adjacentPairs_" + cutoffText)
lu.delete_data(outputRaster)
@retry(10)
def copyRas():
arcpy.CopyRaster_management(mosaicRaster, outputRaster)
copyRas()
gprint('Building output statistics and pyramids '
'for corridor pinch point raster\n')
lu.build_stats(outputRaster)
finalLinkTable = lu.update_lcp_shapefile(linkTable,
lastStep=5,
thisStep=8)
linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
linkTableFinalFile = path.join(
cfg.OUTPUTDIR, cfg.PREFIX + "_linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable, linkTableFinalFile,
inLinkTableFile)
gprint('Copy of linkTable written to ' + linkTableFinalFile)
#fixme: update sticks?
gprint('Creating shapefiles with linework for links.')
lu.write_link_maps(linkTableFinalFile, step=8)
# Copy final link maps to gdb.
lu.copy_final_link_maps(step=8)
lu.delete_data(mosaicRaster)
if not cfg.DO_ALLPAIRS:
# Clean up temporary files
if not cfg.SAVECURRENTMAPS:
lu.delete_dir(OUTCIRCUITDIR)
return
lu.dashline(1)
gprint('Mapping global pinch points among all\n'
'core area pairs using Circuitscape.')
if cfg.ALL_PAIR_SCENARIO == 'pairwise':
gprint('Circuitscape will be run in PAIRWISE mode.')
else:
gprint('Circuitscape will be run in ALL-TO-ONE mode.')
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
S8CORE_RAS = "s8core_ras"
s8CoreRasPath = path.join(cfg.SCRATCHDIR, S8CORE_RAS)
arcpy.FeatureToRaster_conversion(cfg.COREFC, cfg.COREFN, s8CoreRasPath,
arcpy.env.cellSize)
binaryCoreRaster = path.join(cfg.SCRATCHDIR, "core_ras_bin")
# The following commands cause file lock problems on save. using gp
# instead.
# outCon = arcpy.sa.Con(S8CORE_RAS, 1, "#", "VALUE > 0")
# outCon.save(binaryCoreRaster)
# gp.Con_sa(s8CoreRasPath, 1, binaryCoreRaster, "#", "VALUE > 0")
outCon = arcpy.sa.Con(Raster(s8CoreRasPath) > 0, 1)
outCon.save(binaryCoreRaster)
s5corridorRas = path.join(cfg.OUTPUTGDB, cfg.PREFIX + "_corridors")
if not arcpy.Exists(s5corridorRas):
s5corridorRas = path.join(cfg.OUTPUTGDB,
cfg.PREFIX + "_lcc_mosaic_int")
outCon = arcpy.sa.Con(
Raster(s5corridorRas) <= cfg.CWDCUTOFF, Raster(resRaster),
arcpy.sa.Con(Raster(binaryCoreRaster) > 0, Raster(resRaster)))
resRasClipPath = path.join(cfg.SCRATCHDIR, 'res_ras_clip')
outCon.save(resRasClipPath)
arcpy.env.cellSize = resRasClipPath
arcpy.env.extent = resRasClipPath
s8CoreRasClipped = s8CoreRasPath + '_c'
# Produce core raster with same extent as clipped resistance raster
# added to ensure correct data type- nodata values were positive for
# cores otherwise
outCon = arcpy.sa.Con(arcpy.sa.IsNull(Raster(s8CoreRasPath)), -9999,
Raster(s8CoreRasPath))
outCon.save(s8CoreRasClipped)
resNpyFN = 'resistances.npy'
resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
numElements, numResistanceNodes = export_ras_to_npy(
resRasClipPath, resNpyFile)
totMem, availMem = lu.get_mem()
# gprint('Total memory: str(totMem))
if numResistanceNodes / availMem > 2000000:
lu.dashline(1)
lu.warn('Warning:')
lu.warn('Circuitscape can only solve 2-3 million nodes')
lu.warn('per gigabyte of available RAM. \nTotal physical RAM '
'on your machine is ~' + str(totMem) +
' GB. \nAvailable memory is ~' + str(availMem) +
' GB. \nYour resistance raster has ' +
str(numResistanceNodes) + ' nodes.')
lu.dashline(0)
coreNpyFN = 'cores.npy'
coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
numElements, numNodes = export_ras_to_npy(s8CoreRasClipped,
coreNpyFile)
arcpy.env.extent = "MINOF"
options = lu.setCircuitscapeOptions()
options['scenario'] = cfg.ALL_PAIR_SCENARIO
options['habitat_file'] = resNpyFile
options['point_file'] = coreNpyFile
options['set_focal_node_currents_to_zero'] = True
outputFN = 'Circuitscape.out'
options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
options['print_timings'] = True
configFN = 'pinchpoint_allpair_config.ini'
outConfigFile = path.join(CONFIGDIR, configFN)
lu.writeCircuitscapeConfigFile(outConfigFile, options)
gprint('\nResistance map has ' + str(int(numResistanceNodes)) +
' nodes.')
lu.dashline(1)
gprint('If you try to cancel your run and the Arc dialog hangs, ')
gprint('you can kill Circuitscape by opening Windows Task Manager')
gprint('and ending the cs_run.exe process.')
lu.dashline(0)
call_circuitscape(CSPATH, outConfigFile)
# test = subprocess.call([CSPATH, outConfigFile],
# creationflags = subprocess.CREATE_NEW_CONSOLE)
if options['scenario'] == 'pairwise':
rasterSuffix = "_current_allPairs_" + cutoffText
else:
rasterSuffix = "_current_allToOne_" + cutoffText
currentFN = 'Circuitscape_cum_curmap.npy'
currentMap = path.join(OUTCIRCUITDIR, currentFN)
outputRaster = path.join(outputGDB, cfg.PREFIX + rasterSuffix)
currentRaster = path.join(cfg.SCRATCHDIR, "current")
try:
import_npy_to_ras(currentMap, resRasClipPath, outputRaster)
except:
lu.dashline(1)
msg = ('ERROR: Circuitscape failed. \n'
'Note: Circuitscape can only solve 2-3 million nodes'
'\nper gigabyte of available RAM. The resistance '
'\nraster for the last corridor had ' +
str(numResistanceNodes) + ' nodes.\n\nResistance '
'raster values that vary by >6 orders of \nmagnitude'
' can also cause failures, as can a mismatch in '
'\ncore area and resistance raster extents.')
arcpy.AddError(msg)
lu.write_log(msg)
exit(1)
#set core areas to nodata
if SETCORESTONULL:
# Set core areas to NoData in current map for color ramping
outputRasterND = outputRaster + '_noDataCores'
outCon = arcpy.sa.SetNull(
Raster(s8CoreRasClipped) > 0, Raster(outputRaster))
outCon.save(outputRasterND)
gprint('\nBuilding output statistics and pyramids '
'for centrality raster.')
lu.build_stats(outputRaster)
lu.build_stats(outputRasterND)
# Clean up temporary files
if not cfg.SAVECURRENTMAPS:
lu.delete_dir(OUTCIRCUITDIR)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 8. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 8. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def STEP6_calc_barriers():
"""Detects influential barriers given CWD calculations from
s3_calcCwds.py.
"""
try:
arcpy.CheckOutExtension("spatial")
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
if cfg.BARRIER_CWD_THRESH is not None:
lu.dashline(1)
gprint('Invoking CWD Threshold of ' + str(cfg.BARRIER_CWD_THRESH) + ' map units.')
if cfg.SUM_BARRIERS:
sumSuffix = '_Sum'
cfg.BARRIERBASEDIR = cfg.BARRIERBASEDIR + sumSuffix
baseName, extension = path.splitext(cfg.BARRIERGDB)
cfg.BARRIERGDB = baseName + sumSuffix + extension
gprint('\nBarrier scores will be SUMMED across core pairs.')
else:
sumSuffix = ''
# Delete contents of final ouptut geodatabase
# lu.clean_out_workspace(cfg.BARRIERGDB) #xxx try not doing this to allow multiple radii to be analyzed in separate runs
if not arcpy.Exists(cfg.BARRIERGDB):
# Create output geodatabase
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
path.basename(cfg.BARRIERGDB))
startRadius = int(cfg.STARTRADIUS)
endRadius = int(cfg.ENDRADIUS)
radiusStep = int(cfg.RADIUSSTEP)
if radiusStep == 0:
endRadius = startRadius # Calculate at just one radius value
radiusStep = 1
linkTableFile = lu.get_prev_step_link_table(step=6)
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
arcpy.RefreshCatalog(cfg.PROJECTDIR)
PREFIX = path.basename(cfg.PROJECTDIR)
# For speed:
arcpy.env.pyramid = "NONE"
arcpy.env.rasterStatistics = "NONE"
# set the analysis extent and cell size to that of the resistance
# surface
arcpy.OverWriteOutput = True
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
spatialref = arcpy.Describe(cfg.RESRAST).spatialReference
mapUnits = (str(spatialref.linearUnitName)).lower()
if len(mapUnits) > 1 and mapUnits[-1] != 's':
mapUnits = mapUnits + 's'
if float(arcpy.env.cellSize) > startRadius or startRadius > endRadius:
msg = ('Error: minimum detection radius must be greater than '
'cell size (' + str(arcpy.env.cellSize) +
') \nand less than or equal to maximum detection radius.')
lu.raise_error(msg)
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 linkages. Bailing.')
lu.raise_error(msg)
# set up directories for barrier and barrier mosaic grids
dirCount = 0
gprint("Creating intermediate output folder: " + cfg.BARRIERBASEDIR)
lu.delete_dir(cfg.BARRIERBASEDIR)
lu.create_dir(cfg.BARRIERBASEDIR)
arcpy.CreateFolder_management(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
cbarrierdir = path.join(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
coresToProcess = npy.unique(linkTable
[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
maxCoreNum = max(coresToProcess)
# Set up focal directories.
# To keep there from being > 100 grids in any one directory,
# outputs are written to:
# barrier\focalX_ for cores 1-99 at radius X
# barrier\focalX_1 for cores 100-199
# etc.
lu.dashline(0)
for radius in range(startRadius, endRadius + 1, radiusStep):
core1path = lu.get_focal_path(1,radius)
path1, dir1 = path.split(core1path)
path2, dir2 = path.split(path1)
arcpy.CreateFolder_management(path.dirname(path2),
path.basename(path2))
arcpy.CreateFolder_management(path.dirname(path1),
path.basename(path1))
if maxCoreNum > 99:
gprint('Creating subdirectories for ' + str(radius) + ' ' +
str(mapUnits) + ' radius analysis scale.')
maxDirCount = int(maxCoreNum/100)
focalDirBaseName = dir2
cp100 = (coresToProcess.astype('int32'))/100
ind = npy.where(cp100 > 0)
dirNums = npy.unique(cp100[ind])
for dirNum in dirNums:
focalDir = focalDirBaseName + str(dirNum)
gprint('...' + focalDir)
arcpy.CreateFolder_management(path2, focalDir)
# Create resistance raster with filled-in Nodata values for later use
arcpy.env.extent = cfg.RESRAST
resistFillRaster = path.join(cfg.SCRATCHDIR, "resist_fill")
output = arcpy.sa.Con(IsNull(cfg.RESRAST), 1000000000,
Raster(cfg.RESRAST) - 1)
output.save(resistFillRaster)
coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
coreList = npy.sort(coreList)
# Loop through each search radius to calculate barriers in each link
import time
radId = 0 #keep track of number of radii processed- used for temp dir naming
for radius in range (startRadius, endRadius + 1, radiusStep):
radId = radId + 1
linkTableTemp = linkTable.copy()
@retry(10)
#can't pass vars in and modify them.
def doRadiusLoop():
linkTable = linkTableTemp.copy()
startTime = time.clock()
randomerror()
linkLoop = 0
pctDone = 0
gprint('\nMapping barriers at a radius of ' + str(radius) +
' ' + str(mapUnits))
if cfg.SUM_BARRIERS:
gprint('using SUM method')
else:
gprint('using MAXIMUM method')
if numCorridorLinks > 1:
gprint('0 percent done')
lastMosaicRaster = None
lastMosaicRasterPct = None
for x in range(0,numLinks):
pctDone = lu.report_pct_done(linkLoop, numCorridorLinks,
pctDone)
linkId = str(int(linkTable[x,cfg.LTB_LINKID]))
if ((linkTable[x,cfg.LTB_LINKTYPE] > 0) and
(linkTable[x,cfg.LTB_LINKTYPE] < 1000)):
linkLoop = linkLoop + 1
# 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)
# Mask out areas above CWD threshold
cwdTemp1 = None
cwdTemp2 = None
if cfg.BARRIER_CWD_THRESH is not None:
if x == 1:
lu.dashline(1)
gprint(' Using CWD threshold of ' + str(cfg.BARRIER_CWD_THRESH) + ' map units.')
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
cwdTemp1 = path.join(cfg.SCRATCHDIR, "tmp"+str(corex))
outCon = arcpy.sa.Con(cwdRaster1 < float(cfg.BARRIER_CWD_THRESH),cwdRaster1)
outCon.save(cwdTemp1)
cwdRaster1 = cwdTemp1
cwdTemp2 = path.join(cfg.SCRATCHDIR, "tmp"+str(corey))
outCon = arcpy.sa.Con(cwdRaster2 < float(cfg.BARRIER_CWD_THRESH),cwdRaster2)
outCon.save(cwdTemp2)
cwdRaster2 = cwdTemp2
focalRaster1 = lu.get_focal_path(corex,radius)
focalRaster2 = lu.get_focal_path(corey,radius)
link = lu.get_links_from_core_pairs(linkTable,
corex, corey)
lcDist = float(linkTable[link,cfg.LTB_CWDIST])
# Detect barriers at radius using neighborhood stats
# Create the Neighborhood Object
innerRadius = radius - 1
outerRadius = radius
dia = 2 * radius
InNeighborhood = ("ANNULUS " + str(innerRadius) + " " +
str(outerRadius) + " MAP")
@retry(10)
def execFocal():
randomerror()
# Execute FocalStatistics
if not path.exists(focalRaster1):
arcpy.env.extent = cwdRaster1
outFocalStats = arcpy.sa.FocalStatistics(cwdRaster1,
InNeighborhood, "MINIMUM","DATA")
if setCoresToNull:
outFocalStats2 = arcpy.sa.Con(outFocalStats > 0, outFocalStats) # Set areas overlapping cores to NoData xxx
outFocalStats2.save(focalRaster1) #xxx
else:
outFocalStats.save(focalRaster1) #xxx
arcpy.env.extent = cfg.RESRAST
if not path.exists(focalRaster2):
arcpy.env.extent = cwdRaster2
outFocalStats = arcpy.sa.FocalStatistics(cwdRaster2,
InNeighborhood, "MINIMUM","DATA")
if setCoresToNull:
outFocalStats2 = arcpy.sa.Con(outFocalStats > 0, outFocalStats) # Set areas overlapping cores to NoData xxx
outFocalStats2.save(focalRaster2)#xxx
else:
outFocalStats.save(focalRaster2) #xxx
arcpy.env.extent = cfg.RESRAST
execFocal()
lu.delete_data(cwdTemp1)
lu.delete_data(cwdTemp2)
barrierRaster = path.join(cbarrierdir, "b" + str(radius)
+ "_" + str(corex) + "_" +
str(corey)+'.tif')
if cfg.SUM_BARRIERS: # Need to set nulls to 0, also
# create trim rasters as we go
outRas = ((lcDist - Raster(focalRaster1) -
Raster(focalRaster2) - dia) / dia)
outCon = arcpy.sa.Con(IsNull(outRas),0,outRas)
outCon2 = arcpy.sa.Con(outCon<0,0,outCon)
outCon2.save(barrierRaster)
# Execute FocalStatistics to fill out search radii
InNeighborhood = "CIRCLE " + str(outerRadius) + " MAP"
fillRaster = path.join(cbarrierdir, "b" + str(radius)
+ "_" + str(corex) + "_" + str(corey) +"_fill.tif")
outFocalStats = arcpy.sa.FocalStatistics(barrierRaster,
InNeighborhood, "MAXIMUM","DATA")
outFocalStats.save(fillRaster)
if cfg.WRITE_TRIM_RASTERS:
trmRaster = path.join(cbarrierdir, "b" +
str(radius)
+ "_" + str(corex) + "_" + str(corey) +"_trim.tif")
rasterList = [fillRaster, resistFillRaster]
outCellStatistics = arcpy.sa.CellStatistics(
rasterList, "MINIMUM")
outCellStatistics.save(trmRaster)
else:
#Calculate potential benefit per map unit restored
@retry(10)
def calcBen():
randomerror()
outRas = ((lcDist - Raster(focalRaster1)
- Raster(focalRaster2) - dia) / dia)
outRas.save(barrierRaster)
calcBen()
if cfg.WRITE_PCT_RASTERS:
#Calculate PERCENT potential benefit per unit restored
barrierRasterPct = path.join(cbarrierdir, "b" +
str(radius)
+ "_" + str(corex) + "_" +
str(corey)+'_pct.tif')
@retry(10)
def calcBenPct():
randomerror()
outras = (100 * (Raster(barrierRaster) / lcDist))
outras.save(barrierRasterPct)
calcBenPct()
# Mosaic barrier results across core area pairs
mosaicDir = path.join(cfg.SCRATCHDIR,'mos'+str(radId)+'_'+str(x+1))
lu.create_dir(mosaicDir)
mosFN = 'mos_temp'
tempMosaicRaster = path.join(mosaicDir,mosFN)
tempMosaicRasterTrim = path.join(mosaicDir,'mos_temp_trm')
arcpy.env.workspace = mosaicDir
if linkLoop == 1:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(barrierRaster,
tempMosaicRaster)
if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
arcpy.CopyRaster_management(trmRaster,
tempMosaicRasterTrim)
else:
if cfg.SUM_BARRIERS:
outCon = arcpy.sa.Con(Raster (barrierRaster) < 0, lastMosaicRaster,
Raster(barrierRaster) + Raster(lastMosaicRaster))
outCon.save(tempMosaicRaster)
if cfg.WRITE_TRIM_RASTERS:
outCon = arcpy.sa.Con(Raster
(trmRaster) < 0, lastMosaicRasterTrim,
Raster(trmRaster) + Raster(
lastMosaicRasterTrim))
outCon.save(tempMosaicRasterTrim)
else:
rasterString = ('"'+barrierRaster+";" +
lastMosaicRaster+'"')
@retry(10)
def mosaicToNew():
randomerror()
arcpy.MosaicToNewRaster_management(
rasterString,mosaicDir,mosFN, "",
"32_BIT_FLOAT", arcpy.env.cellSize, "1",
"MAXIMUM", "MATCH")
mosaicToNew()
# gprint(str(corex)+'0'+str(corey))
if linkLoop>1: #Clean up from previous loop
lu.delete_data(lastMosaicRaster)
lastMosaicDir =path.dirname(lastMosaicRaster)
lu.clean_out_workspace(lastMosaicDir)
lu.delete_dir(lastMosaicDir)
lastMosaicRaster = tempMosaicRaster
if cfg.WRITE_TRIM_RASTERS:
lastMosaicRasterTrim = tempMosaicRasterTrim
if cfg.WRITE_PCT_RASTERS:
mosPctFN = 'mos_temp_pct'
mosaicDirPct = path.join(cfg.SCRATCHDIR,'mosP'+str(radId)+'_'+str(x+1))
lu.create_dir(mosaicDirPct)
tempMosaicRasterPct = path.join(mosaicDirPct,mosPctFN)
if linkLoop == 1:
# If this is the first grid then copy
# rather than mosaic
if cfg.SUM_BARRIERS:
outCon = arcpy.sa.Con(Raster(barrierRasterPct)
< 0, 0, arcpy.sa.Con(IsNull(
barrierRasterPct), 0, barrierRasterPct))
outCon.save(tempMosaicRasterPct)
else:
arcpy.CopyRaster_management(barrierRasterPct,
tempMosaicRasterPct)
else:
if cfg.SUM_BARRIERS:
@retry(10)
def sumBarriers():
randomerror()
outCon = arcpy.sa.Con(Raster(barrierRasterPct) < 0,
lastMosaicRasterPct, Raster(barrierRasterPct) + Raster(
lastMosaicRasterPct))
outCon.save(tempMosaicRasterPct)
sumBarriers()
else:
rasterString = ('"' + barrierRasterPct + ";" +
lastMosaicRasterPct + '"')
@retry(10)
def maxBarriers():
randomerror()
arcpy.MosaicToNewRaster_management(
rasterString,mosaicDirPct,mosPctFN, "",
"32_BIT_FLOAT", arcpy.env.cellSize, "1",
"MAXIMUM", "MATCH")
maxBarriers()
if linkLoop>1: #Clean up from previous loop
lu.delete_data(lastMosaicRasterPct)
lastMosaicDirPct =path.dirname(lastMosaicRasterPct)
lu.clean_out_workspace(lastMosaicDirPct)
lu.delete_dir(lastMosaicDirPct)
# lu.delete_data(lastMosaicRasterPct)
lastMosaicRasterPct = tempMosaicRasterPct
if not cfg.SAVEBARRIERRASTERS:
lu.delete_data(barrierRaster)
if cfg.WRITE_PCT_RASTERS:
lu.delete_data(barrierRasterPct)
if cfg.WRITE_TRIM_RASTERS:
lu.delete_data(trmRaster)
# 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)
if numCorridorLinks > 1 and pctDone < 100:
gprint('100 percent done')
gprint('Summarizing barrier data for search radius.')
#rows that were temporarily disabled
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE]>1000)
linkTable[rows,cfg.LTB_LINKTYPE] = (
linkTable[rows,cfg.LTB_LINKTYPE] - 1000)
# -----------------------------------------------------------------
# Set negative values to null or zero and write geodatabase.
mosaicFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" +
str(radius))
mosaicRaster = path.join(cfg.BARRIERGDB, mosaicFN)
arcpy.env.extent = cfg.RESRAST
# if setCoresToNull:
# outCon = arcpy.sa.Con(Raster(tempMosaicRaster) < 0, 0,
# tempMosaicRaster) #xxx
# outCon.save(mosaicRaster) #xxx
# else:
outSetNull = arcpy.sa.SetNull(tempMosaicRaster, tempMosaicRaster,
"VALUE < 0") #xxx orig
outSetNull.save(mosaicRaster)
lu.delete_data(tempMosaicRaster)
if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
mosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
"_Rad" + str(radius))
mosaicRasterTrim = path.join(cfg.BARRIERGDB, mosaicFN)
arcpy.CopyRaster_management(tempMosaicRasterTrim,
mosaicRasterTrim)
lu.delete_data(tempMosaicRaster)
if cfg.WRITE_PCT_RASTERS:
# Do same for percent raster
mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
"_Rad" + str(radius))
arcpy.env.extent = cfg.RESRAST
outSetNull = arcpy.sa.SetNull(tempMosaicRasterPct,
tempMosaicRasterPct, "VALUE < 0")
mosaicRasterPct = path.join(cfg.BARRIERGDB, mosaicPctFN)
outSetNull.save(mosaicRasterPct)
lu.delete_data(tempMosaicRasterPct)
# 'Grow out' maximum restoration gain to
# neighborhood size for display
InNeighborhood = "CIRCLE " + str(outerRadius) + " MAP"
# Execute FocalStatistics
fillRasterFN = "barriers_fill" + str(outerRadius) + tif
fillRaster = path.join(cfg.BARRIERBASEDIR, fillRasterFN)
outFocalStats = arcpy.sa.FocalStatistics(mosaicRaster,
InNeighborhood, "MAXIMUM","DATA")
outFocalStats.save(fillRaster)
if cfg.WRITE_PCT_RASTERS:
# Do same for percent raster
fillRasterPctFN = "barriers_fill_pct" + str(outerRadius) + tif
fillRasterPct = path.join(cfg.BARRIERBASEDIR, fillRasterPctFN)
outFocalStats = arcpy.sa.FocalStatistics(mosaicRasterPct,
InNeighborhood, "MAXIMUM","DATA")
outFocalStats.save(fillRasterPct)
#Place copies of filled rasters in output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
fillRasterFN = (PREFIX + "_BarrrierCircles" + sumSuffix + "_Rad" +
str(outerRadius))
arcpy.CopyRaster_management(fillRaster, fillRasterFN)
if cfg.WRITE_PCT_RASTERS:
fillRasterPctFN = (PREFIX + "_BarrrierCircles_Pct" + sumSuffix +
"_Rad" + str(outerRadius))
arcpy.CopyRaster_management(fillRasterPct, fillRasterPctFN)
if not cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
# Create pared-down version of filled raster- remove pixels
# that don't need restoring by allowing a pixel to only
# contribute its resistance value to restoration gain
outRasterFN = "barriers_trm" + str(outerRadius) + tif
outRaster = path.join(cfg.BARRIERBASEDIR,outRasterFN)
rasterList = [fillRaster, resistFillRaster]
outCellStatistics = arcpy.sa.CellStatistics(rasterList,
"MINIMUM")
outCellStatistics.save(outRaster)
#SECOND ROUND TO CLIP BY DATA VALUES IN BARRIER RASTER
outRaster2FN = ("barriers_trm" + sumSuffix + str(outerRadius)
+ "_2" + tif)
outRaster2 = path.join(cfg.BARRIERBASEDIR,outRaster2FN)
output = arcpy.sa.Con(IsNull(fillRaster),fillRaster,outRaster)
output.save(outRaster2)
outRasterFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
"_Rad" + str(outerRadius))
outRasterPath= path.join(cfg.BARRIERGDB, outRasterFN)
arcpy.CopyRaster_management(outRaster2, outRasterFN)
randomerror()
startTime=lu.elapsed_time(startTime)
# Call the above function
doRadiusLoop()
# Combine rasters across radii
gprint('\nCreating summary rasters...')
if startRadius != endRadius:
radiiSuffix = ('_Rad' + str(int(startRadius)) + 'To' + str(int(
endRadius)) + 'Step' + str(int(radiusStep)))
mosaicFN = "bar_radii"
mosaicPctFN = "bar_radii_pct"
arcpy.env.workspace = cfg.BARRIERBASEDIR
for radius in range (startRadius, endRadius + 1, radiusStep):
#Fixme: run speed test with gdb mosaicking above and here
radiusFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad"
+ str(radius))
radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRaster, mosaicFN)
else:
mosaicRaster = path.join(cfg.BARRIERBASEDIR,mosaicFN)
arcpy.Mosaic_management(radiusRaster, mosaicRaster,
"MAXIMUM", "MATCH")
if cfg.WRITE_PCT_RASTERS:
radiusPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
"_Rad" + str(radius))
radiusRasterPct = path.join(cfg.BARRIERGDB, radiusPctFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRasterPct,
mosaicPctFN)
else:
mosaicRasterPct = path.join(cfg.BARRIERBASEDIR,
mosaicPctFN)
arcpy.Mosaic_management(radiusRasterPct,
mosaicRasterPct,
"MAXIMUM", "MATCH")
# Copy results to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
mosaicFN = PREFIX + "_BarrierCenters" + sumSuffix + radiiSuffix
arcpy.CopyRaster_management(mosaicRaster, mosaicFN)
if cfg.WRITE_PCT_RASTERS:
mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
radiiSuffix)
arcpy.CopyRaster_management(mosaicRasterPct, mosaicPctFN)
#GROWN OUT rasters
fillMosaicFN = "barriers_radii_fill" + tif
fillMosaicPctFN = "barriers_radii_fill_pct" + tif
fillMosaicRaster = path.join(cfg.BARRIERBASEDIR,fillMosaicFN)
fillMosaicRasterPct = path.join(cfg.BARRIERBASEDIR,fillMosaicPctFN)
arcpy.env.workspace = cfg.BARRIERBASEDIR
for radius in range (startRadius, endRadius + 1, radiusStep):
radiusFN = "barriers_fill" + str(radius) + tif
#fixme- do this when only a single radius too
radiusRaster = path.join(cfg.BARRIERBASEDIR, radiusFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRaster, fillMosaicFN)
else:
arcpy.Mosaic_management(radiusRaster, fillMosaicRaster,
"MAXIMUM", "MATCH")
if cfg.WRITE_PCT_RASTERS:
radiusPctFN = "barriers_fill_pct" + str(radius) + tif
#fixme- do this when only a single radius too
radiusRasterPct = path.join(cfg.BARRIERBASEDIR,
radiusPctFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRasterPct,
fillMosaicPctFN)
else:
arcpy.Mosaic_management(radiusRasterPct,
fillMosaicRasterPct,
"MAXIMUM", "MATCH")
# Copy result to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
fillMosaicFN = PREFIX + "_BarrierCircles" + sumSuffix + radiiSuffix
arcpy.CopyRaster_management(fillMosaicRaster, fillMosaicFN)
if cfg.WRITE_PCT_RASTERS:
fillMosaicPctFN = (PREFIX + "_BarrierCircles_Pct" + sumSuffix
+ radiiSuffix)
arcpy.CopyRaster_management(fillMosaicRasterPct,
fillMosaicPctFN)
# if not cfg.SUM_BARRIERS:
#GROWN OUT AND TRIMMED rasters (Can't do percent)
if cfg.WRITE_TRIM_RASTERS:
trimMosaicFN = "bar_radii_trm"
arcpy.env.workspace = cfg.BARRIERBASEDIR
trimMosaicRaster = path.join(cfg.BARRIERBASEDIR,trimMosaicFN)
for radius in range (startRadius, endRadius + 1, radiusStep):
radiusFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix
+ "_Rad" + str(radius))
#fixme- do this when only a single radius too
radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)
if radius == startRadius:
#If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radiusRaster, trimMosaicFN)
else:
arcpy.Mosaic_management(radiusRaster, trimMosaicRaster,
"MAXIMUM", "MATCH")
# Copy result to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
trimMosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix
+ radiiSuffix)
arcpy.CopyRaster_management(trimMosaicRaster, trimMosaicFN)
if not cfg.SAVE_RADIUS_RASTERS:
arcpy.env.workspace = cfg.BARRIERGDB
rasters = arcpy.ListRasters()
for raster in rasters:
if 'rad' in raster.lower() and not 'step' in raster.lower():
lu.delete_data(raster)
arcpy.env.workspace = cfg.BARRIERGDB
rasters = arcpy.ListRasters()
for raster in rasters:
gprint('\nBuilding output statistics and pyramids\n'
'for raster ' + raster)
lu.build_stats(raster)
#Clean up temporary files and directories
if not cfg.SAVEBARRIERRASTERS:
lu.delete_dir(cbarrierdir)
lu.delete_dir(cfg.BARRIERBASEDIR)
if not cfg.SAVEFOCALRASTERS:
for radius in range(startRadius, endRadius + 1, radiusStep):
core1path = lu.get_focal_path(1,radius)
path1, dir1 = path.split(core1path)
path2, dir2 = path.split(path1)
lu.delete_dir(path2)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 6. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 6. 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
def STEP4_refine_network():
"""Allows user to only connect each core area to its N
nearest neighbors, then connect any disjunct clusters ('constellations')
of core areas to their nearest neighboring cluster
"""
try:
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
cfg.gp.Workspace = cfg.OUTPUTDIR
linkTableFile = lu.get_prev_step_link_table(step=4)
linkTable = lu.load_link_table(linkTableFile)
numLinks = linkTable.shape[0]
lu.report_links(linkTable)
if not cfg.STEP3:
# re-check for links that are too long in case script run out of
# sequence with more stringent settings
gprint('Double-checking for corridors that are too long'
' or too short to map.')
DISABLE_LEAST_COST_NO_VAL = True
linkTable,numDroppedLinks = lu.drop_links(
linkTable, cfg.MAXEUCDIST, 0, cfg.MAXCOSTDIST, 0,
DISABLE_LEAST_COST_NO_VAL)
rows, cols = npy.where(
linkTable[:,cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] > 0)
# == cfg.LT_CORR
# or
# linkTable[:,cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] == cfg.LT_KEEP)
corridorLinks = linkTable[rows,:]
coresToProcess = npy.unique(
corridorLinks[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
if cfg.S4DISTTYPE_EU:
distCol = cfg.LTB_EUCDIST
else:
distCol = cfg.LTB_CWDIST
# Flag links that do not connect any core areas to their nearest
# N neighbors. (N = cfg.S4MAXNN)
lu.dashline(1)
gprint('Connecting each core area to its nearest ' +
str(cfg.S4MAXNN) + ' nearest neighbors.')
# Code written assuming NO duplicate core pairs
for core in coresToProcess:
rows,cols = npy.where(
corridorLinks[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1] == core)
distsFromCore = corridorLinks[rows,:]
# Sort by distance from target core
ind = npy.argsort(distsFromCore[:,distCol])
distsFromCore = distsFromCore[ind]
# Set N nearest neighbor connections to Nearest Neighbor (NNCT)
maxRange = min(len(rows), cfg.S4MAXNN)
for link in range (0, maxRange):
linkId = distsFromCore[link, cfg.LTB_LINKID]
# assumes linktable sequentially numbered with no gaps
linkTable[linkId - 1, cfg.LTB_LINKTYPE] = cfg.LT_NNCT
# Connect constellations (aka compoments or clusters)
# Fixme: needs testing. Move to function.
if cfg.S4CONNECT:
lu.dashline(1)
gprint('Connecting constellations')
# linkTableComp has 4 extra cols to track COMPONENTS
numLinks = linkTable.shape[0]
# g1' g2' THEN c1 c2
compCols = npy.zeros((numLinks, 4), dtype="int32")
linkTableComp = npy.append(linkTable, compCols, axis=1)
del compCols
# renumber cores to save memory for this next step. Place in
# columns 10 and 11
for coreInd in range(0, len(coresToProcess)):
# here, cols are 0 for cfg.LTB_CORE1 and 1 for cfg.LTB_CORE2
rows, cols = npy.where(
linkTableComp[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1] ==
coresToProcess[coreInd])
# want results in cols 10 and 11- These are NEW core numbers
# (0 - numcores)
linkTableComp[rows, cols + 10] = coreInd
rows, cols = npy.where(
linkTableComp[:, cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] ==
cfg.LT_NNCT)
# The new, improved corridorLinks- only NN links
corridorLinksComp = linkTableComp[rows, :]
# These are NEW core numbers (range from 0 to numcores)
coresToProcess = npy.unique(linkTableComp[:, 10:12])
#Create graph describing connected cores.
Graph = npy.zeros((len(coresToProcess), len(coresToProcess)),
dtype="int32")
rows = corridorLinksComp[:,10].astype('int32')
cols = corridorLinksComp[:,11].astype('int32')
vals = npy.where(corridorLinksComp[:,cfg.LTB_LINKTYPE] ==
cfg.LT_NNCT, cfg.LT_CORR, 0)
Graph[rows,cols] = vals
Graph = Graph + Graph.T
# Use graph to identify components (disconnected sub-groups) in
# core area network
components = lu.components_no_sparse(Graph)
for coreInd in range(0,len(coresToProcess)):
# In resulting cols, cols are 0 for LTB_CORE1 and 1 for
# LTB_CORE2
rows, cols = (npy.where(linkTableComp[:,10:12] ==
coresToProcess[coreInd]))
# want results in cols 12 and 13 Note: we've replaced new core
# numbers with COMPONENT numbers.
linkTableComp[rows,cols+12] = components[coreInd]
# Additional column indexes for linkTableComp
component1Col = 12
component2Col = 13
linkTableComp[:,cfg.LTB_CLUST1] = linkTableComp[:,component1Col]
linkTableComp[:,cfg.LTB_CLUST2] = linkTableComp[:,component2Col]
# Sort by distance
ind = npy.argsort(linkTableComp[:,distCol])
linkTableComp = linkTableComp[ind]
# Connect constellations via shortest inter-constellation links,
# until all constellations connected.
for row in range(0,numLinks):
if ((linkTableComp[row,distCol] > 0) and
((linkTableComp[row,cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
(linkTableComp[row,cfg.LTB_LINKTYPE] == cfg.LT_KEEP)) and
(linkTableComp[row,component1Col] !=
linkTableComp[row,component2Col])):
# Make this an inter-component link
linkTableComp[row,cfg.LTB_LINKTYPE] = cfg.LT_CLU
newComp = min(linkTableComp
[row,component1Col:component2Col + 1])
oldComp = max(linkTableComp
[row,component1Col:component2Col + 1])
# cols are 0 and 1
rows, cols = npy.where(linkTableComp
[:,component1Col:component2Col + 1]
== oldComp)
# want results in cols 12 and 13
linkTableComp[rows,cols + 12] = newComp
# Remove extra columns from link table
linkTable = lu.delete_col(linkTableComp,[10, 11, 12, 13])
# Re-sort link table by link ID
ind = npy.argsort(linkTable[:,cfg.LTB_LINKID])
linkTable = linkTable[ind]
# At end, any non-constellation links that are not NN's get dropped
# (too long to be in cfg.S4MAXNN, not a component link)
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] == cfg.LT_CORR)
linkTable[rows,cfg.LTB_LINKTYPE] = cfg.LT_CPLK
# set NNCT links to NN corridor links (NNC), get rid
# of extra columns, re-sort linktable
rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] == cfg.LT_NNCT)
linkTable[rows,cfg.LTB_LINKTYPE] = cfg.LT_NNC
# Write linkTable to disk
outlinkTableFile = lu.get_this_step_link_table(step=4)
# lu.dashline(1)
gprint('\nWriting ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s4.csv")
lu.write_link_table(linkTable, linkTableLogFile)
start_time = time.clock()
lu.update_lcp_shapefile(linkTable, lastStep=3, thisStep=4)
start_time = lu.elapsed_time(start_time)
# lu.dashline()
gprint('Creating shapefiles with linework for links.')
try:
lu.write_link_maps(outlinkTableFile, step=4)
except:
lu.write_link_maps(outlinkTableFile, step=4)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
gprint('****Failed in step 4. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
gprint('****Failed in step 4. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def STEP4_refine_network():
"""Allows user to only connect each core area to its N
nearest neighbors, then connect any disjunct clusters ('constellations')
of core areas to their nearest neighboring cluster
"""
try:
lu.dashline(1)
gprint('Running script ' + _SCRIPT_NAME)
cfg.gp.Workspace = cfg.OUTPUTDIR
linkTableFile = lu.get_prev_step_link_table(step=4)
linkTable = lu.load_link_table(linkTableFile)
numLinks = linkTable.shape[0]
lu.report_links(linkTable)
if not cfg.STEP3:
# re-check for links that are too long in case script run out of
# sequence with more stringent settings
gprint('Double-checking for corridors that are too long'
' or too short to map.')
DISABLE_LEAST_COST_NO_VAL = True
linkTable, numDroppedLinks = lu.drop_links(
linkTable, cfg.MAXEUCDIST, 0, cfg.MAXCOSTDIST, 0,
DISABLE_LEAST_COST_NO_VAL)
rows, cols = npy.where(
linkTable[:, cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] > 0)
# == cfg.LT_CORR
# or
# linkTable[:,cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] == cfg.LT_KEEP)
corridorLinks = linkTable[rows, :]
coresToProcess = npy.unique(
corridorLinks[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
if cfg.S4DISTTYPE_EU:
distCol = cfg.LTB_EUCDIST
else:
distCol = cfg.LTB_CWDIST
# Flag links that do not connect any core areas to their nearest
# N neighbors. (N = cfg.S4MAXNN)
lu.dashline(1)
# optionally ignore max nearest neighbor setting
if cfg.IGNORES4MAXNN:
gprint('Connecting each core area to all its neighbors.')
else:
gprint('Connecting each core area to its nearest ' +
str(cfg.S4MAXNN) + ' nearest neighbors.')
# Code written assuming NO duplicate core pairs
for core in coresToProcess:
rows, cols = npy.where(corridorLinks[:,
cfg.LTB_CORE1:cfg.LTB_CORE2 +
1] == core)
distsFromCore = corridorLinks[rows, :]
# Sort by distance from target core
ind = npy.argsort(distsFromCore[:, distCol])
distsFromCore = distsFromCore[ind]
# Set N nearest neighbor connections to Nearest Neighbor (NNCT)
# optionally ignore max nearest neighbor setting
if cfg.IGNORES4MAXNN:
maxRange = len(rows)
else:
maxRange = min(len(rows), cfg.S4MAXNN)
for link in range(0, maxRange):
linkId = distsFromCore[link, cfg.LTB_LINKID]
# assumes linktable sequentially numbered with no gaps
linkTable[linkId - 1, cfg.LTB_LINKTYPE] = cfg.LT_NNCT
# Connect constellations (aka components or clusters)
# Fixme: needs testing. Move to function.
if cfg.S4CONNECT:
lu.dashline(1)
gprint('Connecting constellations')
# linkTableComp has 4 extra cols to track COMPONENTS
numLinks = linkTable.shape[0]
# g1' g2' THEN c1 c2
compCols = npy.zeros((numLinks, 4), dtype="int32")
linkTableComp = npy.append(linkTable, compCols, axis=1)
del compCols
# renumber cores to save memory for this next step. Place in
# columns 10 and 11
for coreInd in range(0, len(coresToProcess)):
# here, cols are 0 for cfg.LTB_CORE1 and 1 for cfg.LTB_CORE2
rows, cols = npy.where(
linkTableComp[:, cfg.LTB_CORE1:cfg.LTB_CORE2 +
1] == coresToProcess[coreInd])
# want results in cols 10 and 11- These are NEW core numbers
# (0 - numcores)
linkTableComp[rows, cols + 10] = coreInd
rows, cols = npy.where(
linkTableComp[:, cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE +
1] == cfg.LT_NNCT)
# The new, improved corridorLinks- only NN links
corridorLinksComp = linkTableComp[rows, :]
# These are NEW core numbers (range from 0 to numcores)
coresToProcess = npy.unique(linkTableComp[:, 10:12])
#Create graph describing connected cores.
Graph = npy.zeros((len(coresToProcess), len(coresToProcess)),
dtype="int32")
rows = corridorLinksComp[:, 10].astype('int32')
cols = corridorLinksComp[:, 11].astype('int32')
vals = npy.where(
corridorLinksComp[:, cfg.LTB_LINKTYPE] == cfg.LT_NNCT,
cfg.LT_CORR, 0)
Graph[rows, cols] = vals
Graph = Graph + Graph.T
# Use graph to identify components (disconnected sub-groups) in
# core area network
components = lu.components_no_sparse(Graph)
for coreInd in range(0, len(coresToProcess)):
# In resulting cols, cols are 0 for LTB_CORE1 and 1 for
# LTB_CORE2
rows, cols = (npy.where(
linkTableComp[:, 10:12] == coresToProcess[coreInd]))
# want results in cols 12 and 13 Note: we've replaced new core
# numbers with COMPONENT numbers.
linkTableComp[rows, cols + 12] = components[coreInd]
# Additional column indexes for linkTableComp
component1Col = 12
component2Col = 13
linkTableComp[:, cfg.LTB_CLUST1] = linkTableComp[:, component1Col]
linkTableComp[:, cfg.LTB_CLUST2] = linkTableComp[:, component2Col]
# Sort by distance
ind = npy.argsort(linkTableComp[:, distCol])
linkTableComp = linkTableComp[ind]
# Connect constellations via shortest inter-constellation links,
# until all constellations connected.
for row in range(0, numLinks):
if ((linkTableComp[row, distCol] > 0) and
((linkTableComp[row, cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
(linkTableComp[row, cfg.LTB_LINKTYPE] == cfg.LT_KEEP))
and (linkTableComp[row, component1Col] !=
linkTableComp[row, component2Col])):
# Make this an inter-component link
linkTableComp[row, cfg.LTB_LINKTYPE] = cfg.LT_CLU
newComp = min(
linkTableComp[row, component1Col:component2Col + 1])
oldComp = max(
linkTableComp[row, component1Col:component2Col + 1])
# cols are 0 and 1
rows, cols = npy.where(
linkTableComp[:, component1Col:component2Col +
1] == oldComp)
# want results in cols 12 and 13
linkTableComp[rows, cols + 12] = newComp
# Remove extra columns from link table
linkTable = lu.delete_col(linkTableComp, [10, 11, 12, 13])
# Re-sort link table by link ID
ind = npy.argsort(linkTable[:, cfg.LTB_LINKID])
linkTable = linkTable[ind]
# At end, any non-constellation links that are not NN's get dropped
# (too long to be in cfg.S4MAXNN, not a component link)
rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] == cfg.LT_CORR)
linkTable[rows, cfg.LTB_LINKTYPE] = cfg.LT_CPLK
# set NNCT links to NN corridor links (NNC), get rid
# of extra columns, re-sort linktable
rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] == cfg.LT_NNCT)
linkTable[rows, cfg.LTB_LINKTYPE] = cfg.LT_NNC
# Write linkTable to disk
outlinkTableFile = lu.get_this_step_link_table(step=4)
# lu.dashline(1)
gprint('\nWriting ' + outlinkTableFile)
lu.write_link_table(linkTable, outlinkTableFile)
linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s4.csv")
lu.write_link_table(linkTable, linkTableLogFile)
start_time = time.clock()
lu.update_lcp_shapefile(linkTable, lastStep=3, thisStep=4)
start_time = lu.elapsed_time(start_time)
# lu.dashline()
gprint('Creating shapefiles with linework for links.')
try:
lu.write_link_maps(outlinkTableFile, step=4)
except:
lu.write_link_maps(outlinkTableFile, step=4)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
gprint('****Failed in step 4. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
gprint('****Failed in step 4. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return
def STEP7_calc_centrality():
""" Analyze network centrality using Circuitscape
given Linkage Mapper outputs
"""
try:
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
arcpy.env.workspace = cfg.SCRATCHDIR
# Check for valid LCP shapefile
prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep = 7)
if not arcpy.Exists(prevLcpShapefile):
msg = ('Cannot find an LCP shapefile from step 5. Please '
'rerun that step and any previous ones if necessary.')
lu.raise_error(msg)
# Remove lcp shapefile from this step if run previously
lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s7.shp")
lu.delete_data(lcpShapefile)
csPath = lu.get_cs_path()
invalidFNs = ['fid','id','oid','shape']
if cfg.COREFN.lower() in invalidFNs:
#if cfg.COREFN == 'FID' or cfg.COREFN == 'ID':
lu.dashline(1)
msg = ('ERROR: Core area field names ID, FID, SHAPE, and OID are'
' reserved for ArcGIS. \nPlease choose another field- must'
' be a positive integer.')
lu.raise_error(msg)
lu.dashline(1)
gprint('Mapping centrality of network cores and links'
'\nusing Circuitscape....')
lu.dashline(0)
# set the analysis extent and cell size to that of the resistance
# surface
coreCopy = path.join(cfg.SCRATCHDIR, 'cores.shp')
arcpy.CopyFeatures_management(cfg.COREFC, coreCopy)
arcpy.AddField_management(coreCopy, "CF_Central", "DOUBLE", "10", "2")
inLinkTableFile = lu.get_prev_step_link_table(step=7)
linkTable = lu.load_link_table(inLinkTableFile)
numLinks = linkTable.shape[0]
numCorridorLinks = lu.report_links(linkTable)
if numCorridorLinks == 0:
lu.dashline(1)
msg =('\nThere are no linkages. Bailing.')
lu.raise_error(msg)
if linkTable.shape[1] < 16: # If linktable has no entries from prior
# centrality or pinchpint analyses
extraCols = npy.zeros((numLinks, 6), dtype="float64")
linkTable = linkTable[:,0:10]
linkTable = npy.append(linkTable, extraCols, axis=1)
linkTable[:, cfg.LTB_LCPLEN] = -1
linkTable[:, cfg.LTB_CWDEUCR] = -1
linkTable[:, cfg.LTB_CWDPATHR] = -1
linkTable[:, cfg.LTB_EFFRESIST] = -1
linkTable[:, cfg.LTB_CWDTORR] = -1
del extraCols
linkTable[:, cfg.LTB_CURRENT] = -1
coresToProcess = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
maxCoreNum = max(coresToProcess)
del coresToProcess
lu.dashline(0)
coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
coreList = npy.sort(coreList)
#gprint('There are ' + str(len(npy.unique(coreList))) ' core areas.')
# set up directory for centrality
INCENTRALITYDIR = cfg.CENTRALITYBASEDIR
OUTCENTRALITYDIR = path.join(cfg.CENTRALITYBASEDIR,
cfg.CIRCUITOUTPUTDIR_NM)
CONFIGDIR = path.join(INCENTRALITYDIR, cfg.CIRCUITCONFIGDIR_NM)
# Set Circuitscape options and write config file
options = lu.setCircuitscapeOptions()
options['data_type']='network'
options['habitat_file'] = path.join(INCENTRALITYDIR,
'Circuitscape_graph.txt')
# Setting point file equal to graph to do all pairs in Circuitscape
options['point_file'] = path.join(INCENTRALITYDIR,
'Circuitscape_graph.txt')
outputFN = 'Circuitscape_network.out'
options['output_file'] = path.join(OUTCENTRALITYDIR, outputFN)
configFN = 'Circuitscape_network.ini'
outConfigFile = path.join(CONFIGDIR, configFN)
lu.writeCircuitscapeConfigFile(outConfigFile, options)
delRows = npy.asarray(npy.where(linkTable[:,cfg.LTB_LINKTYPE] < 1))
delRowsVector = npy.zeros((delRows.shape[1]), dtype="int32")
delRowsVector[:] = delRows[0, :]
LT = lu.delete_row(linkTable, delRowsVector)
del delRows
del delRowsVector
graphList = npy.zeros((LT.shape[0],3), dtype="float64")
graphList[:,0] = LT[:,cfg.LTB_CORE1]
graphList[:,1] = LT[:,cfg.LTB_CORE2]
graphList[:,2] = LT[:,cfg.LTB_CWDIST]
write_graph(options['habitat_file'] ,graphList)
gprint('\nCalculating current flow centrality using Circuitscape...')
#subprocess.call([csPath, outConfigFile], shell=True)
memFlag = call_circuitscape(csPath, outConfigFile)
outputFN = 'Circuitscape_network_branch_currents_cum.txt'
currentList = path.join(OUTCENTRALITYDIR, outputFN)
if not arcpy.Exists(currentList):
write_graph(options['habitat_file'] ,graphList)
gprint('\nCalculating current flow centrality using Circuitscape '
'(2nd try)...')
# subprocess.call([csPath, outConfigFile], shell=True)
memFlag = call_circuitscape(csPath, outConfigFile)
if not arcpy.Exists(currentList):
lu.dashline(1)
msg = ('ERROR: No Circuitscape output found.\n'
'It looks like Circuitscape failed.')
arcpy.AddError(msg)
lu.write_log(msg)
exit(1)
currents = load_graph(currentList,graphType='graph/network',
datatype='float64')
numLinks = currents.shape[0]
for x in range(0,numLinks):
corex = currents[x,0]
corey = currents[x,1]
#linkId = LT[x,cfg.LTB_LINKID]
row = lu.get_links_from_core_pairs(linkTable, corex, corey)
#row = lu.get_linktable_row(linkId, linkTable)
linkTable[row,cfg.LTB_CURRENT] = currents[x,2]
coreCurrentFN = 'Circuitscape_network_node_currents_cum.txt'
nodeCurrentList = path.join(OUTCENTRALITYDIR, coreCurrentFN)
nodeCurrents = load_graph(nodeCurrentList,graphType='graph/network',
datatype='float64')
numNodeCurrents = nodeCurrents.shape[0]
rows = arcpy.UpdateCursor(coreCopy)
row = rows.newRow()
for row in rows:
coreID = row.getValue(cfg.COREFN)
for i in range (0, numNodeCurrents):
if coreID == nodeCurrents[i,0]:
row.setValue("CF_Central", nodeCurrents[i,1])
break
rows.updateRow(row)
#row = rows.newRow()
del row, rows
gprint('Done with centrality calculations.')
finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=5,
thisStep=7)
linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
linkTableFinalFile = path.join(cfg.OUTPUTDIR,
cfg.PREFIX + "_linkTable_s5_plus.csv")
lu.write_link_table(finalLinkTable,
linkTableFinalFile, inLinkTableFile)
gprint('Copy of final linkTable written to '+
linkTableFinalFile)
finalCoreFile = path.join(cfg.CORECENTRALITYGDB,
cfg.PREFIX + '_Cores')
#copy core area map to gdb.
if not arcpy.Exists(cfg.CORECENTRALITYGDB):
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
path.basename(cfg.CORECENTRALITYGDB))
arcpy.CopyFeatures_management(coreCopy, finalCoreFile)
gprint('Creating shapefiles with linework for links.')
lu.write_link_maps(linkTableFinalFile, step=7)
# Copy final link maps to gdb and clean up.
lu.copy_final_link_maps(step=7)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 7. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 7. 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
def step6_calc_barriers():
"""Detect influential barriers given CWD calculations from Step 3."""
try:
arcpy.CheckOutExtension("spatial")
lu.dashline(0)
gprint('Running script ' + _SCRIPT_NAME)
if cfg.BARRIER_CWD_THRESH is not None:
lu.dashline(1)
gprint('Invoking CWD Threshold of ' + str(cfg.BARRIER_CWD_THRESH)
+ ' map units.')
if cfg.SUM_BARRIERS:
sum_suffix = '_Sum'
cfg.BARRIERBASEDIR = cfg.BARRIERBASEDIR + sum_suffix
base_name, extension = path.splitext(cfg.BARRIERGDB)
cfg.BARRIERGDB = base_name + sum_suffix + extension
gprint('\nBarrier scores will be SUMMED across core pairs.')
else:
sum_suffix = ''
if not arcpy.Exists(cfg.BARRIERGDB):
# Create output geodatabase
arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
path.basename(cfg.BARRIERGDB))
start_radius = int(cfg.STARTRADIUS)
end_radius = int(cfg.ENDRADIUS)
radius_step = int(cfg.RADIUSSTEP)
if radius_step == 0:
end_radius = start_radius # Calculate at just one radius value
radius_step = 1
link_table_file = lu.get_prev_step_link_table(step=6)
arcpy.env.workspace = cfg.SCRATCHDIR
arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
prefix = path.basename(cfg.PROJECTDIR)
# For speed:
arcpy.env.pyramid = "NONE"
arcpy.env.rasterStatistics = "NONE"
# 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
spatialref = arcpy.Describe(cfg.RESRAST).spatialReference
map_units = (str(spatialref.linearUnitName)).lower()
if len(map_units) > 1 and map_units[-1] != 's':
map_units = map_units + 's'
if (float(arcpy.env.cellSize) > start_radius
or start_radius > end_radius):
msg = ('Error: minimum detection radius must be greater than '
'cell size (' + arcpy.env.cellSize +
') \nand less than or equal to maximum detection radius.')
lu.raise_error(msg)
link_table = lu.load_link_table(link_table_file)
num_links = link_table.shape[0]
num_corridor_links = lu.report_links(link_table)
if num_corridor_links == 0:
lu.dashline(1)
msg = '\nThere are no linkages. Bailing.'
lu.raise_error(msg)
# set up directories for barrier and barrier mosaic grids
gprint("Creating intermediate output folder: " + cfg.BARRIERBASEDIR)
lu.delete_dir(cfg.BARRIERBASEDIR)
lu.create_dir(cfg.BARRIERBASEDIR)
arcpy.CreateFolder_management(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
cbarrierdir = path.join(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
cores_to_process = npy.unique(
link_table[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
max_core_num = max(cores_to_process)
# Set up focal directories.
# To keep there from being > 100 grids in any one directory,
# outputs are written to:
# barrier\focalX_ for cores 1-99 at radius X
# barrier\focalX_1 for cores 100-199
# etc.
lu.dashline(0)
for radius in range(start_radius, end_radius + 1, radius_step):
core1path = lu.get_focal_path(1, radius)
path1 = path.split(core1path)[0]
path2, dir2 = path.split(path1)
arcpy.CreateFolder_management(path.dirname(path2),
path.basename(path2))
arcpy.CreateFolder_management(path.dirname(path1),
path.basename(path1))
if max_core_num > 99:
gprint('Creating subdirectories for ' + str(radius) + ' ' +
str(map_units) + ' radius analysis scale.')
focal_dir_base_name = dir2
cp100 = cores_to_process.astype('int32') // 100
ind = npy.where(cp100 > 0)
dir_nums = npy.unique(cp100[ind])
for dir_num in dir_nums:
focal_dir = focal_dir_base_name + str(dir_num)
gprint('...' + focal_dir)
arcpy.CreateFolder_management(path2, focal_dir)
# Create resistance raster with filled-in Nodata values for later use
arcpy.env.extent = cfg.RESRAST
resist_fill_ras = path.join(cfg.SCRATCHDIR, "resist_fill")
output = arcpy.sa.Con(arcpy.sa.IsNull(cfg.RESRAST), 1000000000,
arcpy.sa.Raster(cfg.RESRAST) - 1)
output.save(resist_fill_ras)
core_list = link_table[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
core_list = npy.sort(core_list)
# Loop through each search radius to calculate barriers in each link
rad_id = 0 # Keep track of no of radii processed - used for temp dir
for radius in range(start_radius, end_radius + 1, radius_step):
rad_id = rad_id + 1
link_table_tmp = link_table.copy()
@Retry(10)
# Can't pass vars in and modify them.
def do_radius_loop():
"""Do radius loop."""
link_table = link_table_tmp.copy()
start_time = time.clock()
link_loop = 0
pct_done = 0
gprint('\nMapping barriers at a radius of ' + str(radius) +
' ' + str(map_units))
if cfg.SUM_BARRIERS:
gprint('using SUM method')
else:
gprint('using MAXIMUM method')
if num_corridor_links > 1:
gprint('0 percent done')
last_mosaic_ras = None
last_mosaic_ras_pct = None
for x in range(0, num_links):
pct_done = lu.report_pct_done(
link_loop, num_corridor_links, pct_done)
if ((link_table[x, cfg.LTB_LINKTYPE] > 0) and
(link_table[x, cfg.LTB_LINKTYPE] < 1000)):
link_loop = link_loop + 1
# source and target cores
corex = int(core_list[x, 0])
corey = int(core_list[x, 1])
# Get cwd rasters for source and target cores
cwd_ras1 = lu.get_cwd_path(corex)
cwd_ras2 = lu.get_cwd_path(corey)
# Mask out areas above CWD threshold
cwd_tmp1 = None
cwd_tmp2 = None
if cfg.BARRIER_CWD_THRESH is not None:
if x == 1:
lu.dashline(1)
gprint(' Using CWD threshold of '
+ str(cfg.BARRIER_CWD_THRESH)
+ ' map units.')
arcpy.env.extent = cfg.RESRAST
arcpy.env.cellSize = cfg.RESRAST
arcpy.env.snapRaster = cfg.RESRAST
cwd_tmp1 = path.join(cfg.SCRATCHDIR,
"tmp" + str(corex))
out_con = arcpy.sa.Con(
cwd_ras1 < float(cfg.BARRIER_CWD_THRESH),
cwd_ras1)
out_con.save(cwd_tmp1)
cwd_ras1 = cwd_tmp1
cwd_tmp2 = path.join(cfg.SCRATCHDIR,
"tmp" + str(corey))
out_con = arcpy.sa.Con(
cwd_ras2 < float(cfg.BARRIER_CWD_THRESH),
cwd_ras2)
out_con.save(cwd_tmp2)
cwd_ras2 = cwd_tmp2
focal_ras1 = lu.get_focal_path(corex, radius)
focal_ras2 = lu.get_focal_path(corey, radius)
link = lu.get_links_from_core_pairs(link_table,
corex, corey)
lc_dist = float(link_table[link, cfg.LTB_CWDIST])
# Detect barriers at radius using neighborhood stats
# Create the Neighborhood Object
inner_radius = radius - 1
outer_radius = radius
dia = 2 * radius
in_neighborhood = ("ANNULUS " + str(inner_radius)
+ " " + str(outer_radius) + " MAP")
@Retry(10)
def exec_focal():
"""Execute focal statistics."""
if not path.exists(focal_ras1):
arcpy.env.extent = cwd_ras1
out_focal_stats = arcpy.sa.FocalStatistics(
cwd_ras1, in_neighborhood,
"MINIMUM", "DATA")
if SET_CORES_TO_NULL:
# Set areas overlapping cores to NoData xxx
out_focal_stats2 = arcpy.sa.Con(
out_focal_stats > 0, out_focal_stats)
out_focal_stats2.save(focal_ras1)
else:
out_focal_stats.save(focal_ras1)
arcpy.env.extent = cfg.RESRAST
if not path.exists(focal_ras2):
arcpy.env.extent = cwd_ras2
out_focal_stats = arcpy.sa.FocalStatistics(
cwd_ras2, in_neighborhood,
"MINIMUM", "DATA")
if SET_CORES_TO_NULL:
# Set areas overlapping cores to NoData xxx
out_focal_stats2 = arcpy.sa.Con(
out_focal_stats > 0, out_focal_stats)
out_focal_stats2.save(focal_ras2)
else:
out_focal_stats.save(focal_ras2)
arcpy.env.extent = cfg.RESRAST
exec_focal()
lu.delete_data(cwd_tmp1)
lu.delete_data(cwd_tmp2)
barrier_ras = path.join(
cbarrierdir, "b" + str(radius) + "_" + str(corex)
+ "_" + str(corey)+'.tif')
# Need to set nulls to 0,
# also create trim rasters as we go
if cfg.SUM_BARRIERS:
out_ras = ((lc_dist - arcpy.sa.Raster(focal_ras1) -
arcpy.sa.Raster(focal_ras2) - dia)
/ dia)
out_con = arcpy.sa.Con(arcpy.sa.IsNull(out_ras),
0, out_ras)
out_con2 = arcpy.sa.Con(out_con < 0, 0, out_con)
out_con2.save(barrier_ras)
# Execute FocalStatistics to fill out search radii
in_neighborhood = ("CIRCLE " + str(outer_radius)
+ " MAP")
fill_ras = path.join(
cbarrierdir, "b" + str(radius) + "_"
+ str(corex) + "_" + str(corey) + "_fill.tif")
out_focal_stats = arcpy.sa.FocalStatistics(
barrier_ras, in_neighborhood,
"MAXIMUM", "DATA")
out_focal_stats.save(fill_ras)
if cfg.WRITE_TRIM_RASTERS:
trm_ras = path.join(
cbarrierdir, "b" + str(radius) + "_"
+ str(corex) + "_" + str(corey)
+ "_trim.tif")
ras_list = [fill_ras, resist_fill_ras]
out_cell_statistics = arcpy.sa.CellStatistics(
ras_list, "MINIMUM")
out_cell_statistics.save(trm_ras)
else:
@Retry(10)
def clac_ben():
"""Calculate potential benefit.
Calculate potential benefit per map unit
restored.
"""
out_ras = (
(lc_dist - arcpy.sa.Raster(focal_ras1)
- arcpy.sa.Raster(focal_ras2) - dia)
/ dia)
out_ras.save(barrier_ras)
clac_ben()
if cfg.WRITE_PCT_RASTERS:
# Calculate % potential benefit per unit restored
barrier_ras_pct = path.join(
cbarrierdir, "b" + str(radius) + "_"
+ str(corex) + "_" + str(corey)
+ '_pct.tif')
@Retry(10)
def calc_ben_pct():
"""Calc benefit percentage."""
outras = (100 * (arcpy.sa.Raster(barrier_ras)
/ lc_dist))
outras.save(barrier_ras_pct)
calc_ben_pct()
# Mosaic barrier results across core area pairs
mosaic_dir = path.join(cfg.SCRATCHDIR, 'mos'
+ str(rad_id) + '_'
+ str(x + 1))
lu.create_dir(mosaic_dir)
mos_fn = 'mos_temp'
tmp_mosaic_ras = path.join(mosaic_dir, mos_fn)
tmp_mosaic_ras_trim = path.join(mosaic_dir,
'mos_temp_trm')
arcpy.env.workspace = mosaic_dir
if link_loop == 1:
last_mosaic_ras_trim = None
# For first grid copy rather than mosaic
arcpy.CopyRaster_management(barrier_ras,
tmp_mosaic_ras)
if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
arcpy.CopyRaster_management(
trm_ras, tmp_mosaic_ras_trim)
else:
if cfg.SUM_BARRIERS:
out_con = arcpy.sa.Con(
arcpy.sa.Raster(barrier_ras) < 0,
last_mosaic_ras,
arcpy.sa.Raster(barrier_ras)
+ arcpy.sa.Raster(last_mosaic_ras))
out_con.save(tmp_mosaic_ras)
if cfg.WRITE_TRIM_RASTERS:
out_con = arcpy.sa.Con(
arcpy.sa.Raster(trm_ras) < 0,
last_mosaic_ras_trim,
arcpy.sa.Raster(trm_ras)
+ arcpy.sa.Raster(last_mosaic_ras_trim)
)
out_con.save(tmp_mosaic_ras_trim)
else:
in_rasters = (";".join([barrier_ras,
last_mosaic_ras]))
@Retry(10)
def mosaic_to_new():
"""Mosaic to new raster."""
arcpy.MosaicToNewRaster_management(
input_rasters=in_rasters,
output_location=mosaic_dir,
raster_dataset_name_with_extension\
=mos_fn,
pixel_type="32_BIT_FLOAT",
cellsize=arcpy.env.cellSize,
number_of_bands="1",
mosaic_method="MAXIMUM")
mosaic_to_new()
if link_loop > 1: # Clean up from previous loop
lu.delete_data(last_mosaic_ras)
last_mosaic_dir = path.dirname(last_mosaic_ras)
lu.clean_out_workspace(last_mosaic_dir)
lu.delete_dir(last_mosaic_dir)
last_mosaic_ras = tmp_mosaic_ras
if cfg.WRITE_TRIM_RASTERS:
last_mosaic_ras_trim = tmp_mosaic_ras_trim
if cfg.WRITE_PCT_RASTERS:
mos_pct_fn = 'mos_temp_pct'
mosaic_dir_pct = path.join(cfg.SCRATCHDIR, 'mosP'
+ str(rad_id) + '_'
+ str(x+1))
lu.create_dir(mosaic_dir_pct)
tmp_mosaic_ras_pct = path.join(mosaic_dir_pct,
mos_pct_fn)
if link_loop == 1:
# If this is the first grid then copy
# rather than mosaic
if cfg.SUM_BARRIERS:
out_con = arcpy.sa.Con(
arcpy.sa.Raster(barrier_ras_pct)
< 0, 0,
arcpy.sa.Con(arcpy.sa.IsNull
(barrier_ras_pct),
0, barrier_ras_pct))
out_con.save(tmp_mosaic_ras_pct)
else:
arcpy.CopyRaster_management(
barrier_ras_pct, tmp_mosaic_ras_pct)
else:
if cfg.SUM_BARRIERS:
@Retry(10)
def sum_barriers():
"""Sum barriers."""
out_con = arcpy.sa.Con(
arcpy.sa.Raster(barrier_ras_pct)
< 0,
last_mosaic_ras_pct,
arcpy.sa.Raster(barrier_ras_pct)
+ arcpy.sa.Raster(
last_mosaic_ras_pct))
out_con.save(tmp_mosaic_ras_pct)
sum_barriers()
else:
in_rasters = (";".join([barrier_ras_pct,
last_mosaic_ras_pct]))
@Retry(10)
def max_barriers():
"""Get max barriers."""
arcpy.MosaicToNewRaster_management(
input_rasters=in_rasters,
output_location=mosaic_dir_pct,
raster_dataset_name_with_extension
=mos_pct_fn,
pixel_type="32_BIT_FLOAT",
cellsize=arcpy.env.cellSize,
number_of_bands="1",
mosaic_method="MAXIMUM")
max_barriers()
if link_loop > 1: # Clean up from previous loop
lu.delete_data(last_mosaic_ras_pct)
last_mosaic_dir_pct = path.dirname(
last_mosaic_ras_pct)
lu.clean_out_workspace(last_mosaic_dir_pct)
lu.delete_dir(last_mosaic_dir_pct)
last_mosaic_ras_pct = tmp_mosaic_ras_pct
if not cfg.SAVEBARRIERRASTERS:
lu.delete_data(barrier_ras)
if cfg.WRITE_PCT_RASTERS:
lu.delete_data(barrier_ras_pct)
if cfg.WRITE_TRIM_RASTERS:
lu.delete_data(trm_ras)
# Temporarily disable links in linktable -
# don't want to mosaic them twice
for y in range(x + 1, num_links):
corex1 = int(core_list[y, 0])
corey1 = int(core_list[y, 1])
if corex1 == corex and corey1 == corey:
link_table[y, cfg.LTB_LINKTYPE] = (
link_table[y, cfg.LTB_LINKTYPE] + 1000)
elif corex1 == corey and corey1 == corex:
link_table[y, cfg.LTB_LINKTYPE] = (
link_table[y, cfg.LTB_LINKTYPE] + 1000)
if num_corridor_links > 1 and pct_done < 100:
gprint('100 percent done')
gprint('Summarizing barrier data for search radius.')
# Rows that were temporarily disabled
rows = npy.where(link_table[:, cfg.LTB_LINKTYPE] > 1000)
link_table[rows, cfg.LTB_LINKTYPE] = (
link_table[rows, cfg.LTB_LINKTYPE] - 1000)
# -----------------------------------------------------------------
# Set negative values to null or zero and write geodatabase.
mosaic_fn = (prefix + "_BarrierCenters" + sum_suffix + "_Rad" +
str(radius))
mosaic_ras = path.join(cfg.BARRIERGDB, mosaic_fn)
arcpy.env.extent = cfg.RESRAST
out_set_null = arcpy.sa.SetNull(tmp_mosaic_ras,
tmp_mosaic_ras,
"VALUE < 0") # xxx orig
out_set_null.save(mosaic_ras)
lu.delete_data(tmp_mosaic_ras)
if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
mosaic_fn = (prefix + "_BarrierCircles_RBMin" + sum_suffix
+ "_Rad" + str(radius))
mosaic_ras_trim = path.join(cfg.BARRIERGDB, mosaic_fn)
arcpy.CopyRaster_management(tmp_mosaic_ras_trim,
mosaic_ras_trim)
lu.delete_data(tmp_mosaic_ras)
if cfg.WRITE_PCT_RASTERS:
# Do same for percent raster
mosaic_pct_fn = (prefix + "_BarrierCenters_Pct"
+ sum_suffix + "_Rad" + str(radius))
arcpy.env.extent = cfg.RESRAST
out_set_null = arcpy.sa.SetNull(tmp_mosaic_ras_pct,
tmp_mosaic_ras_pct,
"VALUE < 0")
mosaic_ras_pct = path.join(cfg.BARRIERGDB, mosaic_pct_fn)
out_set_null.save(mosaic_ras_pct)
lu.delete_data(tmp_mosaic_ras_pct)
# 'Grow out' maximum restoration gain to
# neighborhood size for display
in_neighborhood = "CIRCLE " + str(outer_radius) + " MAP"
# Execute FocalStatistics
fill_ras_fn = "barriers_fill" + str(outer_radius) + TIF
fill_ras = path.join(cfg.BARRIERBASEDIR, fill_ras_fn)
out_focal_stats = arcpy.sa.FocalStatistics(
mosaic_ras, in_neighborhood, "MAXIMUM", "DATA")
out_focal_stats.save(fill_ras)
if cfg.WRITE_PCT_RASTERS:
# Do same for percent raster
fill_ras_pct_fn = (
"barriers_fill_pct" + str(outer_radius) + TIF)
fill_ras_pct = path.join(cfg.BARRIERBASEDIR,
fill_ras_pct_fn)
out_focal_stats = arcpy.sa.FocalStatistics(
mosaic_ras_pct, in_neighborhood, "MAXIMUM", "DATA")
out_focal_stats.save(fill_ras_pct)
# Place copies of filled rasters in output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
fill_ras_fn = (prefix + "_BarrrierCircles" + sum_suffix
+ "_Rad" + str(outer_radius))
arcpy.CopyRaster_management(fill_ras, fill_ras_fn)
if cfg.WRITE_PCT_RASTERS:
fill_ras_pct_fn = (prefix + "_BarrrierCircles_Pct"
+ sum_suffix + "_Rad"
+ str(outer_radius))
arcpy.CopyRaster_management(fill_ras_pct,
fill_ras_pct_fn)
if not cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
# Create pared-down version of filled raster- remove pixels
# that don't need restoring by allowing a pixel to only
# contribute its resistance value to restoration gain
out_ras_fn = "barriers_trm" + str(outer_radius) + TIF
out_ras = path.join(cfg.BARRIERBASEDIR, out_ras_fn)
ras_list = [fill_ras, resist_fill_ras]
out_cell_statistics = arcpy.sa.CellStatistics(ras_list,
"MINIMUM")
out_cell_statistics.save(out_ras)
# SECOND ROUND TO CLIP BY DATA VALUES IN BARRIER RASTER
out_ras_2fn = ("barriers_trm" + sum_suffix
+ str(outer_radius) + "_2" + TIF)
out_ras2 = path.join(cfg.BARRIERBASEDIR, out_ras_2fn)
output = arcpy.sa.Con(arcpy.sa.IsNull(fill_ras),
fill_ras, out_ras)
output.save(out_ras2)
out_ras_fn = (prefix + "_BarrierCircles_RBMin"
+ sum_suffix + "_Rad"
+ str(outer_radius))
arcpy.CopyRaster_management(out_ras2, out_ras_fn)
start_time = lu.elapsed_time(start_time)
# Call the above function
do_radius_loop()
# Combine rasters across radii
gprint('\nCreating summary rasters...')
if start_radius != end_radius:
radii_suffix = ('_Rad' + str(int(start_radius)) + 'To'
+ str(int(end_radius)) + 'Step'
+ str(int(radius_step)))
mosaic_fn = "bar_radii"
mosaic_pct_fn = "bar_radii_pct"
arcpy.env.workspace = cfg.BARRIERBASEDIR
for radius in range(start_radius, end_radius + 1, radius_step):
# Fixme: run speed test with gdb mosaicking above and here
radius_fn = (prefix + "_BarrierCenters" + sum_suffix + "_Rad"
+ str(radius))
radius_ras = path.join(cfg.BARRIERGDB, radius_fn)
if radius == start_radius:
# If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radius_ras, mosaic_fn)
else:
mosaic_ras = path.join(cfg.BARRIERBASEDIR, mosaic_fn)
arcpy.Mosaic_management(radius_ras, mosaic_ras,
"MAXIMUM", "MATCH")
if cfg.WRITE_PCT_RASTERS:
radius_pct_fn = (prefix + "_BarrierCenters_Pct"
+ sum_suffix + "_Rad" + str(radius))
radius_ras_pct = path.join(cfg.BARRIERGDB, radius_pct_fn)
if radius == start_radius:
# If this is the first grid then copy rather than
# mosaic
arcpy.CopyRaster_management(radius_ras_pct,
mosaic_pct_fn)
else:
mosaic_ras_pct = path.join(cfg.BARRIERBASEDIR,
mosaic_pct_fn)
arcpy.Mosaic_management(radius_ras_pct,
mosaic_ras_pct,
"MAXIMUM", "MATCH")
# Copy results to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
mosaic_fn = prefix + "_BarrierCenters" + sum_suffix + radii_suffix
arcpy.CopyRaster_management(mosaic_ras, mosaic_fn)
if cfg.WRITE_PCT_RASTERS:
mosaic_pct_fn = (prefix + "_BarrierCenters_Pct" + sum_suffix +
radii_suffix)
arcpy.CopyRaster_management(mosaic_ras_pct, mosaic_pct_fn)
# GROWN OUT rasters
fill_mosaic_fn = "barriers_radii_fill" + TIF
fill_mosaic_pct_fn = "barriers_radii_fill_pct" + TIF
fill_mosaic_ras = path.join(cfg.BARRIERBASEDIR, fill_mosaic_fn)
trim_mosaic_ras_pct = path.join(cfg.BARRIERBASEDIR,
fill_mosaic_pct_fn)
arcpy.env.workspace = cfg.BARRIERBASEDIR
for radius in range(start_radius, end_radius + 1, radius_step):
radius_fn = "barriers_fill" + str(radius) + TIF
# fixme- do this when only a single radius too
radius_ras = path.join(cfg.BARRIERBASEDIR, radius_fn)
if radius == start_radius:
# If this is the first grid then copy rather than mosaic
arcpy.CopyRaster_management(radius_ras, fill_mosaic_fn)
else:
arcpy.Mosaic_management(radius_ras, fill_mosaic_ras,
"MAXIMUM", "MATCH")
if cfg.WRITE_PCT_RASTERS:
radius_pct_fn = "barriers_fill_pct" + str(radius) + TIF
# fixme- do this when only a single radius too
radius_ras_pct = path.join(cfg.BARRIERBASEDIR,
radius_pct_fn)
if radius == start_radius:
# For first grid copy rather than mosaic
arcpy.CopyRaster_management(radius_ras_pct,
fill_mosaic_pct_fn)
else:
arcpy.Mosaic_management(radius_ras_pct,
trim_mosaic_ras_pct,
"MAXIMUM", "MATCH")
# Copy result to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
fill_mosaic_fn = (prefix + "_BarrierCircles" + sum_suffix
+ radii_suffix)
arcpy.CopyRaster_management(fill_mosaic_ras, fill_mosaic_fn)
if cfg.WRITE_PCT_RASTERS:
fill_mosaic_pct_fn = (prefix + "_BarrierCircles_Pct"
+ sum_suffix + radii_suffix)
arcpy.CopyRaster_management(trim_mosaic_ras_pct,
fill_mosaic_pct_fn)
# GROWN OUT AND TRIMMED rasters (Can't do percent)
if cfg.WRITE_TRIM_RASTERS:
trim_mosaic_fn = "bar_radii_trm"
arcpy.env.workspace = cfg.BARRIERBASEDIR
trim_mosaic_ras = path.join(cfg.BARRIERBASEDIR, trim_mosaic_fn)
for radius in range(start_radius, end_radius + 1, radius_step):
radius_fn = (prefix + "_BarrierCircles_RBMin" + sum_suffix
+ "_Rad" + str(radius))
# fixme- do this when only a single radius too
radius_ras = path.join(cfg.BARRIERGDB, radius_fn)
if radius == start_radius:
# For first grid copy rather than mosaic
arcpy.CopyRaster_management(radius_ras, trim_mosaic_fn)
else:
arcpy.Mosaic_management(radius_ras, trim_mosaic_ras,
"MAXIMUM", "MATCH")
# Copy result to output geodatabase
arcpy.env.workspace = cfg.BARRIERGDB
trim_mosaic_fn = (prefix + "_BarrierCircles_RBMin" + sum_suffix
+ radii_suffix)
arcpy.CopyRaster_management(trim_mosaic_ras, trim_mosaic_fn)
if not cfg.SAVE_RADIUS_RASTERS:
arcpy.env.workspace = cfg.BARRIERGDB
rasters = arcpy.ListRasters()
for raster in rasters:
if 'rad' in raster.lower() and 'step' not in raster.lower():
lu.delete_data(raster)
arcpy.env.workspace = cfg.BARRIERGDB
rasters = arcpy.ListRasters()
for raster in rasters:
gprint('\nBuilding output statistics and pyramids\n'
'for raster ' + raster)
lu.build_stats(raster)
# Clean up temporary files and directories
if not cfg.SAVEBARRIERRASTERS:
lu.delete_dir(cbarrierdir)
lu.delete_dir(cfg.BARRIERBASEDIR)
if not cfg.SAVEFOCALRASTERS:
for radius in range(start_radius, end_radius + 1, radius_step):
core1path = lu.get_focal_path(1, radius)
path1 = path.split(core1path)[0]
path2 = path.split(path1)[0]
lu.delete_dir(path2)
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 6. 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 6. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
return