def main(argv=None):
"""Iterate over LM, BM, and restoration tasks."""
if argv is None:
argv = sys.argv # Get parameters from ArcGIS tool dialog
start_time = time.clock()
# USER SETTINGS ######################################################
# Restoration Settings
# ALL input data must be in the same projection
# Set to True to restore highest ROI. Set to False to restore strongest
# barrier
restore_max_roi = argv[1]
# Resistance value of restored habitat. Must be 1 or greater.
restored_resistance_val = argv[2]
# No spaces or special chars in paths or gdb names
restoration_data_gdb = argv[3]
# No spaces in path, avoid using dropbox or network drive
# Project directories will be created in this (iter1, iter2...) as will an
# output geodatabase
output_dir = argv[4]
# Resistance raster. Should be in input GDB
resistance_ras = argv[5]
# Core area feature class. Should be in input GDB 'URWA_HCAs_Doug_Grant'
core_fc = argv[6]
core_fn = argv[7] # Core area field name
radius = argv[8] # Restoration radius in meters
iterations = argv[9] # Number of restorations to perform
# If less than this proportion of ag in circle, don't consider restoring
# circle
min_ag_threshold = argv[10]
# Don't consider barriers below this improvement score (average improvement
# per meter diameter restored)
min_improvement_val = argv[11]
# Average per-m2 parcel cost per pixel. Snapped to resistance raster.
parcel_cost_ras = argv[12]
# Right now this is just a raster with all pixels set to 0.113174
restoration_cost_ras = argv[13]
ag_ras = argv[14] # 1=Ag, 0=Not Ag
# Some restorations benefit multiple corridors.
# 'Maximum' takes the greatest improvement across core area pairs
# 'Sum' adds improvement scores acreoss all pairs.
barrier_combine_method = argv[15]
# Use cwd_thresh = None for no threshold. Use cwd_thresh = X to not
# consider restorations more than X map units away from each core area.
cwd_thresh = argv[16]
# END USER SETTINGS ######################################################
try:
# Setup path and create directories
gprint('Hey! Make sure everything is in the same projection!\n')
gprint('Setting up paths and creating directories')
sys.path.append('..\\toolbox\\scripts')
res_ras = os.path.join(restoration_data_gdb, resistance_ras)
core_fc_path = os.path.join(restoration_data_gdb, core_fc)
# Set up a NEW output gdb (leave previous ones on drive)
i = None
for i in range(1, 200):
output_gdb = 'restorationOutput' + str(i) + '.gdb'
if not arcpy.Exists(os.path.join(output_dir, output_gdb)):
break
gprint('Previous output GDB ' + output_gdb + ' exists. '
'Delete to save disk space.')
arcpy.CreateFileGDB_management(output_dir, output_gdb)
output_gdb = os.path.join(output_dir, output_gdb)
log_file = os.path.join(output_gdb,
'Iterate Barriers' + str(i) + '.py')
# Write a copy of this file to output dir as a record of settings
shutil.copyfile(__file__, log_file)
arcpy.env.cellSize = res_ras
arcpy.env.extent = res_ras
arcpy.env.snapRaster = res_ras
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = output_gdb
arcpy.env.workspace = output_gdb
spatialref = arcpy.Describe(res_ras).spatialReference
mapunits = spatialref.linearUnitName
gprint('Cell size = ' + str(arcpy.env.cellSize) + ' ' + mapunits + 's')
# Calculate fraction of ag within radius of each pixel
gprint('Calculating purchase cost, fraction of ag, etc within radius '
'of each pixel.')
ag_ras = os.path.join(restoration_data_gdb, ag_ras)
in_neighborhood = arcpy.sa.NbrCircle(radius, "MAP")
arcpy.env.extent = ag_ras
out_focal_stats = arcpy.sa.FocalStatistics(ag_ras, in_neighborhood,
"MEAN", "NODATA")
proportion_ag_ras = os.path.join(output_gdb, 'proportionAgRas')
out_focal_stats.save(proportion_ag_ras)
arcpy.env.extent = res_ras
# Calculate purchase cost of circles
parcel_cost_ras = os.path.join(restoration_data_gdb, parcel_cost_ras)
arcpy.env.extent = parcel_cost_ras
out_focal_stats = arcpy.sa.FocalStatistics(parcel_cost_ras,
in_neighborhood, "MEAN",
"DATA")
cost_focal_stats_ras = os.path.join(output_gdb, 'cost_focal_stats_ras')
out_focal_stats.save(cost_focal_stats_ras)
arcpy.env.extent = res_ras
circle_area = float(npy.pi * radius * radius)
outras = arcpy.sa.Raster(cost_focal_stats_ras) * circle_area
purch_cost_ras = os.path.join(output_gdb, 'purchaseCostRaster')
outras.save(purch_cost_ras)
lu.delete_data(cost_focal_stats_ras)
restoration_cost_ras = os.path.join(restoration_data_gdb,
restoration_cost_ras)
outras = (
arcpy.sa.Raster(purch_cost_ras) +
(arcpy.sa.Raster(restoration_cost_ras) * radius * radius * npy.pi))
total_cost_ras = os.path.join(output_gdb, 'totalCostRaster')
outras.save(total_cost_ras)
# Create mask to remove areas without cost data
arcpy.env.extent = total_cost_ras
cost_mask_ras = os.path.join(output_gdb, 'costMaskRaster')
cost_thresh = 0
out_con = arcpy.sa.Con(
(arcpy.sa.Raster(total_cost_ras) > float(cost_thresh)), 1)
out_con.save(cost_mask_ras)
arcpy.env.extent = res_ras
# Create mask to remove areas below ag threshold
out_con = arcpy.sa.Con(
(arcpy.sa.Raster(proportion_ag_ras) > float(min_ag_threshold)), 1)
ag_mask_ras = os.path.join(output_gdb, 'agMaskRaster')
out_con.save(ag_mask_ras)
do_step_1 = 'true'
do_step_2 = 'true'
do_step_5 = 'false'
all_restored_areas_ras = ''
for cur_iter in range(1, iterations + 1):
start_time1 = time.clock()
# Some env settings get changed by linkage mapper and must be
# reset here
arcpy.env.cellSize = res_ras
arcpy.env.extent = res_ras
arcpy.env.snapRaster = res_ras
arcpy.env.scratchWorkspace = output_gdb
arcpy.env.workspace = output_gdb
lu.dashline(1)
gprint('Running iteration number ' + str(cur_iter))
proj_dir = os.path.join(output_dir,
'iter' + str(cur_iter) + 'Proj')
lu.create_dir(output_dir)
lu.delete_dir(proj_dir)
lu.create_dir(proj_dir)
if cur_iter > 1: # Copy previous s2 linktable to new project dir
datapass_dir = os.path.join(proj_dir, 'datapass')
lu.create_dir(datapass_dir)
proj_dir1 = os.path.join(output_dir, 'iter1Proj')
datapass_dir_iter1 = os.path.join(proj_dir1, 'datapass')
s2_link_tbl_iter1 = os.path.join(datapass_dir_iter1,
'linkTable_s2.csv')
s2_link_tbl = os.path.join(datapass_dir, 'linkTable_s2.csv')
shutil.copyfile(s2_link_tbl_iter1, s2_link_tbl)
# Run Linkage Mapper
# Copy distances text file from earlier LM run to the output
# directory- speeds things up!
dist_file = os.path.join(output_dir, core_fc + '_dists.txt')
if not os.path.exists(dist_file):
if cur_iter == 1:
gprint('Will calculate distance file.')
dist_file = '#'
else:
proj_dir1 = os.path.join(output_dir, 'iter1Proj')
dist_file1 = os.path.join(proj_dir1,
core_fc + '_dists.txt')
# Put a copy here for future runs
shutil.copyfile(dist_file1, dist_file)
arcpy.env.scratchWorkspace = output_gdb
arcpy.env.workspace = output_gdb
argv = ('lm_master.py', proj_dir, core_fc_path, core_fn, res_ras,
do_step_1, do_step_2, 'Cost-Weighted & Euclidean',
dist_file, 'true', 'true', 'false', '4', 'Cost-Weighted',
'true', do_step_5, 'true', '200000', '10000', '#', '#',
'#', '#')
gprint('Running ' + str(argv))
lm_master.lm_master(argv)
do_step_1 = 'false' # Can skip for future iterations
do_step_2 = 'false' # Can skip for future iterations
do_step_5 = 'false' # Skipping for future iterations
start_radius = str(radius)
end_radius = str(radius)
radius_step = '0'
save_radius_ras = 'false'
write_pct_ras = 'false'
argv = ('barrier_master.py', proj_dir, res_ras, start_radius,
end_radius, radius_step, barrier_combine_method,
save_radius_ras, write_pct_ras, cwd_thresh)
gprint('Running ' + str(argv))
barrier_master.bar_master(argv)
# Some env settings get changed by linkage mapper and must be
# reset here
arcpy.env.cellSize = res_ras
arcpy.env.extent = res_ras
arcpy.env.snapRaster = res_ras
arcpy.env.scratchWorkspace = output_gdb
arcpy.env.workspace = output_gdb
gprint('Finding restoration circles with max barrier score / ROI')
# Find points with max ROI
prefix = os.path.basename(proj_dir)
if barrier_combine_method == 'Sum':
sum_suffix = 'Sum'
else:
sum_suffix = ''
barrier_fn = (prefix + "_BarrierCenters" + sum_suffix + "_Rad" +
str(radius))
barrier_ras = os.path.join(proj_dir, 'output', 'barriers.gdb',
barrier_fn)
if not arcpy.Exists(barrier_ras):
msg = ('Error: cannot find barrier output: ' + barrier_ras)
lu.raise_error(msg)
if cur_iter > 1:
gprint('Creating mask for previously restored areas')
in_neighborhood = arcpy.sa.NbrCircle(radius, "MAP")
arcpy.env.extent = all_restored_areas_ras
out_focal_stats = arcpy.sa.FocalStatistics(
all_restored_areas_ras, in_neighborhood, "MEAN", "DATA")
all_restored_focal_ras = os.path.join(
output_gdb, 'allRestFocRas_iter' + str(cur_iter))
# Anything > 0 would include a restored area
out_focal_stats.save(all_restored_focal_ras)
arcpy.env.extent = res_ras
rest_mask_ras = os.path.join(
output_gdb, 'restMaskRaster_iter' + str(cur_iter))
minval = 0
out_con = arcpy.sa.Con(
(arcpy.sa.Raster(all_restored_focal_ras) == float(minval)),
1)
out_con.save(rest_mask_ras)
# Candidate areas have not been restored, have cost data, meet
# minimum improvement score criteria, and have enough ag in them
candidate_barrier_ras = os.path.join(
output_gdb, 'candidateBarrierRaster' + '_iter' + str(cur_iter))
if cur_iter > 1:
gprint('Creating candidate restoration raster using barrier '
'results, previous restorations, and selection '
'criteria')
# ROI scores will be in terms of total improvement
# (= score * diameter)
out_calc = (arcpy.sa.Raster(cost_mask_ras) *
arcpy.sa.Raster(ag_mask_ras) *
arcpy.sa.Raster(barrier_ras) *
arcpy.sa.Raster(rest_mask_ras) * (radius * 2))
else:
out_calc = (arcpy.sa.Raster(cost_mask_ras) *
arcpy.sa.Raster(ag_mask_ras) *
arcpy.sa.Raster(barrier_ras) * radius * 2)
min_barrier_score = min_improvement_val * radius * 2
if restored_resistance_val != 1:
out_calc_2 = (out_calc - (2 * radius *
(restored_resistance_val - 1)))
out_con = arcpy.sa.Con(
(out_calc_2 >= float(min_barrier_score)), out_calc_2)
else:
out_con = arcpy.sa.Con((out_calc >= float(min_barrier_score)),
out_calc)
out_con.save(candidate_barrier_ras)
lu.build_stats(candidate_barrier_ras)
purchase_roi_ras = os.path.join(
output_gdb, 'purchaseRoiRaster' + '_iter' + str(cur_iter))
out_calc = (arcpy.sa.Raster(candidate_barrier_ras) /
arcpy.sa.Raster(purch_cost_ras))
out_calc.save(purchase_roi_ras)
lu.build_stats(purchase_roi_ras)
total_roi_ras = os.path.join(
output_gdb, 'purchaseRestRoiRaster' + '_iter' + str(cur_iter))
out_calc = (arcpy.sa.Raster(candidate_barrier_ras) /
arcpy.sa.Raster(total_cost_ras))
out_calc.save(total_roi_ras)
lu.build_stats(total_roi_ras)
max_barrier = float(
arcpy.GetRasterProperties_management(candidate_barrier_ras,
"MAXIMUM").getOutput(0))
gprint('Maximum barrier improvement score: ' + str(max_barrier))
if max_barrier < 0:
arcpy.AddWarning("\nNo barriers found that meet CWD or Ag "
"threshold criteria.")
max_purch_roi = arcpy.GetRasterProperties_management(
purchase_roi_ras, "MAXIMUM")
gprint('Maximum purchase ROI score: ' +
str(max_purch_roi.getOutput(0)))
max_roi = arcpy.GetRasterProperties_management(
total_roi_ras, "MAXIMUM")
gprint('Maximum total ROI score: ' + str(max_roi.getOutput(0)))
if restore_max_roi:
out_point = os.path.join(
output_gdb, 'maxRoiPoint' + '_iter' + str(cur_iter))
gprint('Choosing circle with maximum ROI to restore')
out_con = arcpy.sa.Con(
(arcpy.sa.Raster(total_roi_ras) >= float(
max_roi.getOutput(0))), total_roi_ras)
max_roi_ras = os.path.join(output_gdb, 'max_roi_ras')
out_con.save(max_roi_ras)
# Save max ROI to point
try:
arcpy.RasterToPoint_conversion(max_roi_ras, out_point)
except Exception:
msg = ('Error: it looks like there are no viable '
'restoration candidates.')
lu.raise_error(msg)
else: # Restoring strongest barrier instead
out_point = os.path.join(
output_gdb, 'maxBarrierPoint' + '_iter' + str(cur_iter))
gprint('Choosing circle with maximum BARRIER IMPROVEMENT SCORE'
' to restore')
out_con = arcpy.sa.Con(
(arcpy.sa.Raster(candidate_barrier_ras) >= max_barrier),
candidate_barrier_ras)
max_barrier_ras = os.path.join(output_gdb, 'maxBarrierRaster')
out_con.save(max_barrier_ras)
# Save max barrier to point
try:
arcpy.RasterToPoint_conversion(max_barrier_ras, out_point)
except Exception:
msg = ('Error: it looks like there are no viable '
'restoration candidates.')
lu.raise_error(msg)
gprint('Done evaluating candidate restorations')
result = int(arcpy.GetCount_management(out_point).getOutput(0))
if result > 1:
# Would be better to retain point with max barrier score when
# we have multiple points with same ROI
arcpy.AddWarning('Deleting points with identical '
'ROI/improvement score values')
arcpy.DeleteIdentical_management(out_point, "grid_code", 0.1,
0.1)
arcpy.sa.ExtractMultiValuesToPoints(
out_point,
[[candidate_barrier_ras, "barrierScore"],
[purch_cost_ras, "purchCost"], [total_cost_ras, "totalCost"],
[purchase_roi_ras, "purchaseROI"],
[total_roi_ras, "totalROI"]], "NONE")
arcpy.AddField_management(out_point, "restorationNumber", "SHORT")
arcpy.CalculateField_management(out_point, "restorationNumber",
cur_iter, "PYTHON_9.3")
arcpy.AddField_management(out_point, "radius", "DOUBLE")
arcpy.CalculateField_management(out_point, "radius", radius,
"PYTHON_9.3")
arcpy.AddField_management(out_point, "barrierScore_per_m",
"DOUBLE")
arcpy.CalculateField_management(
out_point, "barrierScore_per_m",
"(float(!barrierScore!) / (!radius! * 2))", "PYTHON_9.3")
gprint('\nCreating restoration circles')
if restore_max_roi:
circle_fc = os.path.join(
output_gdb, 'maxRoiCircle' + '_iter' + str(cur_iter))
else:
circle_fc = os.path.join(
output_gdb, 'maxBarrierCircle' + '_iter' + str(cur_iter))
arcpy.Buffer_analysis(out_point, circle_fc, radius)
gprint('Rasterizing restoration circles')
if restore_max_roi:
circle_ras = os.path.join(
output_gdb, 'maxRoicircle_ras' + '_iter' + str(cur_iter))
else:
circle_ras = os.path.join(
output_gdb,
'maxBarrierCircleRas' + '_iter' + str(cur_iter))
arcpy.FeatureToRaster_conversion(circle_fc, 'totalROI', circle_ras,
arcpy.env.cellSize)
# restore raster
gprint('Digitally restoring resistance raster')
res_ras_restored = os.path.join(
output_gdb, 'resRastRestored' + '_iter' + str(cur_iter))
out_con = arcpy.sa.Con(arcpy.sa.IsNull(circle_ras), res_ras,
restored_resistance_val)
out_con.save(res_ras_restored)
all_restored_areas_ras = os.path.join(
output_gdb, 'allRestoredAreas_iter' + str(cur_iter))
prev_restored_areas_ras = os.path.join(
output_gdb, 'allRestoredAreas_iter' + str(cur_iter - 1))
if cur_iter == 1:
out_con = arcpy.sa.Con(arcpy.sa.IsNull(circle_ras), 0, 1)
else:
# Add this restoration to areas restored
out_con = arcpy.sa.Con(arcpy.sa.IsNull(circle_ras),
prev_restored_areas_ras, 1)
out_con.save(all_restored_areas_ras)
lu.delete_data(circle_ras)
# Use for next iteration resistance raster
res_ras = res_ras_restored
# Add circle into feature class with all circles
if restore_max_roi:
all_circles_fc = os.path.join(output_gdb, "allCirclesMaxROI")
else:
all_circles_fc = os.path.join(output_gdb,
"allCirclesMaxBarriers")
if cur_iter == 1:
arcpy.CopyFeatures_management(circle_fc, all_circles_fc)
else:
arcpy.Append_management(circle_fc, all_circles_fc, "TEST")
gprint('Finished iteration #' + str(cur_iter))
start_time1 = lu.elapsed_time(start_time1)
gprint('\nDone with iterations.')
start_time = lu.elapsed_time(start_time)
gprint('Outputs saved in: ' + output_gdb)
gprint('Back up your project directories if you want to save '
'corridor/barrier results.')
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Iteration script failed. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except Exception:
lu.dashline(1)
gprint('****Iteration script failed. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def main():
"""Iterates over LM, BM, and restoration tasks"""
## USER SETTINGS ######################################################
## Restoration Settings
## ALL input data must be in the same projection
start_time = time.clock()
restoreMaxROI = False # Set to True to restore highest ROI
# Set to False to restore strongest barrier
restoredResistanceVal = 1 # Resistance value of restored habitat. Must be 1 or greater.
restorationDataGDB = (
"C:\\barrierClassAnalysis\\RestorationINPUTS_July2013.gdb"
) # No spaces or special chars in paths or gdb names
outputDir = "C:\\barrierClassAnalysis\\output" # No spaces in path, avoid using dropbox or network drive
# Project directories will be created in this (iter1, iter2...)
# as will an output geodatabase
resistanceRaster = "URWA_resis" # Resistance raster. Should be in input GDB
coreFC = "URWA_HCAs_Doug_Grant" # Core area feature class. Should be in input GDB 'URWA_HCAs_Doug_Grant'
coreFN = "HCA_ID" # Core area field name
radius = 450 # restoration radius in meters
iterations = 13 # number of restorations to perform
minAgThreshold = 0.75 # if less than this proportion of ag in circle, don't consider restoring circle
minImprovementVal = (
0
) # Don't consider barriers below this improvement score (average improvement per meter diameter restored)
parcelCostRaster = (
"DougGrantParcelCost_m2_projected_90m"
) # Average per-m2 parcel cost per pixel. Snapped to resistance raster.
restorationCostRaster = "restCostPer_m2" # Right now this is just a raster with all pixels set to 0.113174
agRaster = "ARESmaskp_projected" # 1=Ag, 0 = not Ag
barrierCombineMethod = "Maximum" # Some restorations benefit multiple corridors.
# 'Maximum' takes the greatest improvement across core area pairs
# 'Sum' adds improvement scores acreoss all pairs.
cwdThresh = None # Use cwdThresh = None for no threshold. Use cwdThresh = X to not consider
# restorations more than X map units away from each core area.
## END USER SETTINGS ######################################################
try:
# Setup path and create directories
gprint("Hey! Make sure everything is in the same projection!\n")
gprint("Setting up paths and creating directories")
sys.path.append("..\\toolbox\\scripts")
resRast = os.path.join(restorationDataGDB, resistanceRaster)
coreFCPath = os.path.join(restorationDataGDB, coreFC)
# Set up a NEW output gdb (leave previous ones on drive)
for i in range(1, 200):
outputGDB = "restorationOutput" + str(i) + ".gdb"
if not arcpy.Exists(os.path.join(outputDir, outputGDB)):
break
gprint("Previous output GDB " + outputGDB + " exists. Delete to save disk space.")
arcpy.CreateFileGDB_management(outputDir, outputGDB)
outputGDB = os.path.join(outputDir, outputGDB)
logFile = os.path.join(outputGDB, "Iterate Barriers" + str(i) + ".py")
shutil.copyfile(__file__, logFile) # write a copy of this file to output dir as a record of settings
arcpy.env.cellSize = resRast
arcpy.env.extent = resRast
arcpy.env.snapRaster = resRast
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
spatialref = arcpy.Describe(resRast).spatialReference
mapunits = spatialref.linearUnitName
gprint("Cell size = " + str(arcpy.env.cellSize) + " " + mapunits + "s")
# Calculate fraction of ag within radius of each pixel
gprint("Calculating purchase cost, fraction of ag, etc within radius of each pixel.")
agRaster = os.path.join(restorationDataGDB, agRaster)
inNeighborhood = NbrCircle(radius, "MAP")
arcpy.env.extent = agRaster
outFocalStats = arcpy.sa.FocalStatistics(agRaster, inNeighborhood, "MEAN", "NODATA")
proportionAgRaster = os.path.join(outputGDB, "proportionAgRas")
outFocalStats.save(proportionAgRaster)
arcpy.env.extent = resRast
# Calculate purchase cost of circles
parcelCostRaster = os.path.join(restorationDataGDB, parcelCostRaster)
arcpy.env.extent = parcelCostRaster
outFocalStats = arcpy.sa.FocalStatistics(parcelCostRaster, inNeighborhood, "MEAN", "DATA")
costFocalStatsRaster = os.path.join(outputGDB, "costFocalStatsRaster")
outFocalStats.save(costFocalStatsRaster)
arcpy.env.extent = resRast
circleArea = float(npy.pi * radius * radius)
outras = Raster(costFocalStatsRaster) * circleArea
purchCostRaster = os.path.join(outputGDB, "purchaseCostRaster")
outras.save(purchCostRaster)
lu.delete_data(costFocalStatsRaster)
# restCost = npy.pi * radius * radius * restCostPer_m2
restorationCostRaster = os.path.join(restorationDataGDB, restorationCostRaster)
outras = Raster(purchCostRaster) + (Raster(restorationCostRaster) * radius * radius * npy.pi)
totalCostRaster = os.path.join(outputGDB, "totalCostRaster")
outras.save(totalCostRaster)
# lu.build_stats(totalCostRaster)
# Create mask to remove areas without cost data
arcpy.env.extent = totalCostRaster
costMaskRaster = os.path.join(outputGDB, "costMaskRaster")
costThresh = 0
outCon = arcpy.sa.Con((Raster(totalCostRaster) > float(costThresh)), 1)
outCon.save(costMaskRaster)
arcpy.env.extent = resRast
# Create mask to remove areas below ag threshold
outCon = arcpy.sa.Con((Raster(proportionAgRaster) > float(minAgThreshold)), 1)
agMaskRaster = os.path.join(outputGDB, "agMaskRaster")
outCon.save(agMaskRaster)
doStep1 = "true"
doStep2 = "true"
doStep5 = "false"
for iter in range(1, iterations + 1): # xxx
start_time1 = time.clock()
arcpy.env.cellSize = resRast # Some env settings get changed by linkage mapper and must be reset here
arcpy.env.extent = resRast
arcpy.env.snapRaster = resRast
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
lu.dashline(1)
gprint("Running iteration number " + str(iter))
projDir = os.path.join(outputDir, "iter" + str(iter) + "Proj")
lu.create_dir(outputDir)
lu.delete_dir(projDir) # xxx
lu.create_dir(projDir)
if iter > 1: # Copy previous s2 linktable to new project directory
datapassDir = os.path.join(projDir, "datapass")
lu.create_dir(datapassDir)
projDir1 = os.path.join(outputDir, "iter1Proj")
datapassDirIter1 = os.path.join(projDir1, "datapass")
s2LinktableIter1 = os.path.join(datapassDirIter1, "linkTable_s2.csv")
s2LinkTable = os.path.join(datapassDir, "linkTable_s2.csv")
shutil.copyfile(s2LinktableIter1, s2LinkTable)
# Run Linkage Mapper
distFile = os.path.join(
outputDir, coreFC + "_dists.txt"
) # Copy distances text file from earlier LM run to the output directory- speeds things up!
if not os.path.exists(distFile):
if iter == 1:
gprint("Will calculate distance file.")
distFile = "#"
else:
projDir1 = os.path.join(outputDir, "iter1Proj")
distFile1 = os.path.join(projDir1, coreFC + "_dists.txt")
shutil.copyfile(distFile1, distFile) # Put a copy here for future runs
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
argv = (
"lm_master.py",
projDir,
coreFCPath,
coreFN,
resRast,
doStep1,
doStep2,
"Cost-Weighted & Euclidean",
distFile,
"true",
"true",
"false",
"4",
"Cost-Weighted",
"true",
doStep5,
"10000",
"#",
"#",
)
gprint("Running " + str(argv))
import lm_master # xxx
lm_master.lm_master(argv) # xxx
doStep1 = "false" # Can skip for future iterations
doStep2 = "false" # Can skip for future iterations
doStep5 = "false" # Skipping for future iterations
startRadius = str(radius)
endRadius = str(radius)
radiusStep = "0"
saveRadiusRasters = "false"
writePctRasters = "false"
argv = (
"barrier_master.py",
projDir,
resRast,
startRadius,
endRadius,
radiusStep,
barrierCombineMethod,
saveRadiusRasters,
writePctRasters,
cwdThresh,
)
gprint("Running " + str(argv))
import barrier_master # xxx
barrier_master.bar_master(argv) # xxx
arcpy.env.cellSize = resRast # Some env settings get changed by linkage mapper and must be reset here
arcpy.env.extent = resRast
arcpy.env.snapRaster = resRast
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
gprint("Finding restoration circles with max barrier score / ROI")
# Find points with max ROI
PREFIX = os.path.basename(projDir)
if barrierCombineMethod == "Sum":
sumSuffix = "Sum"
else:
sumSuffix = ""
barrierFN = PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" + str(radius)
barrierRaster = os.path.join(projDir, "output", "barriers.gdb", barrierFN)
if not arcpy.Exists(barrierRaster):
msg = "Error: cannot find barrier output: " + barrierRaster
lu.raise_error(msg)
# arcpy.env.cellSize = agMaskRaster
# arcpy.env.extent = agMaskRaster
if iter > 1:
gprint("Creating mask for previously restored areas")
inNeighborhood = NbrCircle(radius, "MAP")
arcpy.env.extent = allRestoredAreasRaster
outFocalStats = arcpy.sa.FocalStatistics(allRestoredAreasRaster, inNeighborhood, "MEAN", "DATA")
allRestoredFocalRaster = os.path.join(outputGDB, "allRestFocRas_iter" + str(iter))
outFocalStats.save(allRestoredFocalRaster) # Anything > 0 would include a restored area and
arcpy.env.extent = resRast
restMaskRaster = os.path.join(outputGDB, "restMaskRaster_iter" + str(iter))
minval = 0
outCon = arcpy.sa.Con((Raster(allRestoredFocalRaster) == float(minval)), 1)
outCon.save(restMaskRaster)
# Candidate areas have not been restored, have cost data, meet
# minimum improvement score criteria, and have enough ag in them
candidateBarrierRaster = os.path.join(outputGDB, "candidateBarrierRaster" + "_iter" + str(iter))
if iter > 1:
gprint(
"Creating candidate restoration raster using barrier results, previous restorations, and selection criteria"
)
outCalc = (
Raster(costMaskRaster)
* Raster(agMaskRaster)
* Raster(barrierRaster)
* Raster(restMaskRaster)
* (radius * 2)
) # ROI scores will be in terms of total improvement (= score * diameter)
else:
outCalc = Raster(costMaskRaster) * Raster(agMaskRaster) * Raster(barrierRaster) * radius * 2
minBarrierScore = minImprovementVal * radius * 2
if restoredResistanceVal != 1:
outCalc2 = outCalc - (2 * radius * (restoredResistanceVal - 1))
outCon = arcpy.sa.Con((outCalc2 >= float(minBarrierScore)), outCalc2)
else:
outCon = arcpy.sa.Con((outCalc >= float(minBarrierScore)), outCalc)
outCon.save(candidateBarrierRaster)
lu.build_stats(candidateBarrierRaster)
purchaseRoiRaster = os.path.join(outputGDB, "purchaseRoiRaster" + "_iter" + str(iter))
outCalc = Raster(candidateBarrierRaster) / Raster(purchCostRaster)
outCalc.save(purchaseRoiRaster)
lu.build_stats(purchaseRoiRaster)
totalRoiRaster = os.path.join(outputGDB, "purchaseRestRoiRaster" + "_iter" + str(iter))
outCalc = Raster(candidateBarrierRaster) / Raster(totalCostRaster)
outCalc.save(totalRoiRaster)
lu.build_stats(totalRoiRaster)
maxBarrier = arcpy.GetRasterProperties_management(candidateBarrierRaster, "MAXIMUM")
gprint("Maximum barrier improvement score: " + str(maxBarrier.getOutput(0)))
if maxBarrier < 0:
arcpy.AddWarning("\nNo barriers found that meet CWD or Ag threshold criteria.")
maxPurchROI = arcpy.GetRasterProperties_management(purchaseRoiRaster, "MAXIMUM")
gprint("Maximum purchase ROI score: " + str(maxPurchROI.getOutput(0)))
maxROI = arcpy.GetRasterProperties_management(totalRoiRaster, "MAXIMUM")
gprint("Maximum total ROI score: " + str(maxROI.getOutput(0)))
if restoreMaxROI:
outPoint = os.path.join(outputGDB, "maxRoiPoint" + "_iter" + str(iter))
gprint("Choosing circle with maximum ROI to restore")
outCon = arcpy.sa.Con((Raster(totalRoiRaster) >= float(maxROI.getOutput(0))), totalRoiRaster)
maxRoiRaster = os.path.join(outputGDB, "maxRoiRaster")
outCon.save(maxRoiRaster)
# Save max ROI to point
try:
arcpy.RasterToPoint_conversion(maxRoiRaster, outPoint)
except:
msg = "Error: it looks like there are no viable restoration candidates."
lu.raise_error(msg)
else: # Restoring strongest barrier instead
outPoint = os.path.join(outputGDB, "maxBarrierPoint" + "_iter" + str(iter))
gprint("Choosing circle with maximum BARRIER IMPROVEMENT SCORE to restore")
outCon = arcpy.sa.Con(
(Raster(candidateBarrierRaster) >= float(maxBarrier.getOutput(0))), candidateBarrierRaster
)
maxBarrierRaster = os.path.join(outputGDB, "maxBarrierRaster")
outCon.save(maxBarrierRaster)
# Save max barrier to point
try:
arcpy.RasterToPoint_conversion(maxBarrierRaster, outPoint)
except:
msg = "Error: it looks like there are no viable restoration candidates."
lu.raise_error(msg)
gprint("Done evaluating candidate restorations")
result = int(arcpy.GetCount_management(outPoint).getOutput(0))
if result > 1:
arcpy.AddWarning(
"Deleting points with identical ROI/improvement score values"
) # Would be better to retain point with max barrier score when we have multiple points with same ROI
arcpy.DeleteIdentical_management(outPoint, "grid_code", 0.1, 0.1)
arcpy.sa.ExtractMultiValuesToPoints(
outPoint,
[
[candidateBarrierRaster, "barrierScore"],
[purchCostRaster, "purchCost"],
[totalCostRaster, "totalCost"],
[purchaseRoiRaster, "purchaseROI"],
[totalRoiRaster, "totalROI"],
],
"NONE",
)
arcpy.AddField_management(outPoint, "restorationNumber", "SHORT")
arcpy.CalculateField_management(outPoint, "restorationNumber", iter)
arcpy.AddField_management(outPoint, "radius", "DOUBLE")
arcpy.CalculateField_management(outPoint, "radius", radius)
arcpy.AddField_management(outPoint, "barrierScore_per_m", "DOUBLE")
arcpy.CalculateField_management(
outPoint, "barrierScore_per_m", "(float(!barrierScore!) / (!radius! * 2))", "PYTHON"
)
gprint("\nCreating restoration circles")
if restoreMaxROI:
circleFC = os.path.join(outputGDB, "maxRoiCircle" + "_iter" + str(iter))
else:
circleFC = os.path.join(outputGDB, "maxBarrierCircle" + "_iter" + str(iter))
arcpy.Buffer_analysis(outPoint, circleFC, radius)
gprint("Rasterizing restoration circles")
if restoreMaxROI:
circleRas = os.path.join(outputGDB, "maxRoiCircleRas" + "_iter" + str(iter))
else:
circleRas = os.path.join(outputGDB, "maxBarrierCircleRas" + "_iter" + str(iter))
arcpy.FeatureToRaster_conversion(circleFC, "totalROI", circleRas, arcpy.env.cellSize)
# restore raster
gprint("Digitally restoring resistance raster")
resRastRestored = os.path.join(outputGDB, "resRastRestored" + "_iter" + str(iter))
outCon = arcpy.sa.Con(IsNull(circleRas), resRast, restoredResistanceVal)
outCon.save(resRastRestored)
allRestoredAreasRaster = os.path.join(outputGDB, "allRestoredAreas_iter" + str(iter))
PrevRestoredAreasRaster = os.path.join(outputGDB, "allRestoredAreas_iter" + str(iter - 1))
if iter == 1:
outCon = arcpy.sa.Con(IsNull(circleRas), 0, 1)
else:
outCon = arcpy.sa.Con(
IsNull(circleRas), PrevRestoredAreasRaster, 1
) # Add this restoration to areas restored
outCon.save(allRestoredAreasRaster)
lu.delete_data(circleRas)
resRast = resRastRestored # Use for next iteration resistance raster
# Add circle into feature class with all circles
if restoreMaxROI:
allCirclesFC = os.path.join(outputGDB, "allCirclesMaxROI")
else:
allCirclesFC = os.path.join(outputGDB, "allCirclesMaxBarriers")
if iter == 1:
arcpy.CopyFeatures_management(circleFC, allCirclesFC)
else:
arcpy.Append_management(circleFC, allCirclesFC, "TEST")
gprint("Finished iteration #" + str(iter))
start_time1 = lu.elapsed_time(start_time1)
gprint("\nDone with iterations.")
start_time = lu.elapsed_time(start_time)
gprint("Outputs saved in: " + outputGDB)
gprint("Back up your project directories if you want to save corridor/barrier results.")
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint("****Iteration script failed. Details follow.****")
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint("****Iteration script failed. Details follow.****")
lu.exit_with_python_error(_SCRIPT_NAME)
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 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 generate_distance_file():
"""Use ArcGIS to create Conefor distance file
Requires ArcInfo license.
"""
try:
#gp.Extent = gp.Describe(cfg.COREFC).Extent
gp.CellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
S2COREFC = cfg.COREFC
if cfg.SIMPLIFY_CORES:
try:
gprint('Simplifying polygons for core pair distance calculations')
COREFC_SIMP = path.join(cfg.SCRATCHDIR, "CoreFC_Simp.shp")
tolerance = float(gp.CellSize) / 3
try:
import arcpy
import arcpy.cartography as CA
except:
arcpy = False
if arcpy:
CA.SimplifyPolygon(cfg.COREFC, COREFC_SIMP, "POINT_REMOVE",
tolerance, "#", "NO_CHECK")
else:
gp.SimplifyPolygon(cfg.COREFC, COREFC_SIMP, "POINT_REMOVE",
tolerance, "#", "NO_CHECK")
S2COREFC = COREFC_SIMP
except:
pass # In case point geometry is entered for core area FC
gp.workspace = cfg.SCRATCHDIR
FS2COREFC = "fcores"
FS2COREFC2 = "fcores2"
gp.MakeFeatureLayer(S2COREFC, FS2COREFC)
gp.MakeFeatureLayer(S2COREFC, FS2COREFC2)
output = []
csvseparator = "\t"
adjList = get_full_adj_list()
# sourceCores = npy.unique(adjList[:, 0])
gprint('\nFinding distances between cores using Generate Near Table.')
# gp.OutputCoordinateSystem = gp.describe(cfg.COREFC).SpatialReference
near_tbl = path.join(cfg.SCRATCHDIR, "neartbl.dbf")
# gprint('old method')
# start_time = time.clock()
# gp.generateneartable(S2COREFC, S2COREFC, near_tbl, "#",
# "NO_LOCATION", "NO_ANGLE", "ALL", "0")
# start_time = lu.elapsed_time(start_time)
gprint('There are ' + str(len(adjList)) + ' adjacent core pairs to '
'process.')
pctDone = 0
start_time = time.clock()
for x in range(0, len(adjList)):
pctDone = lu.report_pct_done(x, len(adjList), pctDone)
sourceCore = adjList[x, 0]
targetCore = adjList[x, 1]
expression = cfg.COREFN + " = " + str(sourceCore)
gp.selectlayerbyattribute(FS2COREFC, "NEW_SELECTION", expression)
expression = cfg.COREFN + " = " + str(targetCore)
gp.selectlayerbyattribute(FS2COREFC2, "NEW_SELECTION", expression)
gp.generateneartable(FS2COREFC, FS2COREFC2, near_tbl, "#",
"NO_LOCATION", "NO_ANGLE", "ALL", "0")
rows = gp.searchcursor(near_tbl)
row = rows.Next()
minDist = 1e20
if row: # May be running on selected core areas in step 2
while row:
dist = row.getvalue("NEAR_DIST")
if dist <= 0: # In case simplified polygons abut one another
dist = float(gp.CellSize)
if dist < minDist:
minDist = dist
outputrow = []
outputrow.append(str(sourceCore))
outputrow.append(str(targetCore))
outputrow.append(str(dist))
del row
row = rows.Next()
del rows
output.append(csvseparator.join(outputrow))
start_time = lu.elapsed_time(start_time)
# In case coreFC is grouped in TOC, get coreFN for non-Arc statement
group,coreFN = path.split(cfg.COREFC)
dist_fname = path.join(cfg.PROJECTDIR, (coreFN + "_dists.txt"))
dist_file = open(dist_fname, 'w')
dist_file.write('\n'.join(output))
dist_file.close()
gprint('Distance file ' + dist_fname + ' generated.\n')
return dist_fname
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 2. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 2. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def cwadjacency():
"""Calculate cost-weighted adjacency
Inputs: gp - geoprocessing object
"""
try:
ALLOC_RASFN = "CWD_alloc_ras"
gprint('\nCalculating cost-weighted distance adjacency')
outcsvfile = cfg.CWDADJFILE
outcsvLogfile = path.join(cfg.LOGDIR, "cwdAdj_STEP1.csv")
PREFIX = cfg.PREFIX
# May need to set extent prior to core poly to raster conversion...
# ----------------------------------------------
# Cost-weighted allocation code
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
gp.extent = gp.Describe(cfg.RESRAST).extent
if cfg.BUFFERDIST is not None:
# Clip resistance raster using bounding circle
start_time = time.clock()
gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight#xxx
gp.extent = gp.Describe(cfg.RESRAST).Extent#xxx
bResistance = path.join(cfg.SCRATCHDIR, "bResistance")
gp.ExtractByMask_sa(cfg.RESRAST, cfg.BNDCIR,
bResistance)
gprint('\nReduced resistance raster extracted using '
'bounding circle.')
start_time = lu.elapsed_time(start_time)
else:
bResistance = cfg.RESRAST
start_time = time.clock()
gprint('Starting cost-weighted distance allocation...')
# core_rastmp = 'core_rastmp'
if cfg.TMAXCWDIST is not None:
gprint('Maximum cost-weighted distance set to ' +
str(cfg.TMAXCWDIST))
gp.CellSize = gp.Describe(bResistance).MeanCellHeight
gp.extent = "MAXOF"
gprint('Processing cell size: ' + gp.CellSize)
gp.workspace = cfg.ADJACENCYDIR
gp.scratchworkspace = cfg.ARCSCRATCHDIR
lu.delete_data(cfg.CWDGDB)
if not gp.exists(cfg.CWDGDB):
gp.createfilegdb(cfg.OUTPUTDIR, path.basename(cfg.CWDGDB))
outDistanceRaster = path.join(cfg.CWDGDB, PREFIX + "_cwd")
alloc_ras = path.join(cfg.ADJACENCYDIR, ALLOC_RASFN)
lu.delete_data(alloc_ras)
lu.delete_data(outDistanceRaster)
count = 0
if arcpy:
statement = ('costAllocOut = CostAllocation(cfg.CORERAS, '
'bResistance, cfg.TMAXCWDIST, cfg.CORERAS,"VALUE", '
'outDistanceRaster);'
'costAllocOut.save(alloc_ras)')
else:
statement = ('gp.Costallocation_sa(cfg.CORERAS, bResistance, '
'alloc_ras, cfg.TMAXCWDIST, cfg.CORERAS, "VALUE", '
'outDistanceRaster, "")')
while True:
try:
exec statement
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain:
exec statement
else:
break
gprint('\nBuilding output statistics and pyramids for CWD raster.')
lu.build_stats(outDistanceRaster)
gp.scratchworkspace = cfg.ARCSCRATCHDIR
gprint('Cost-weighted distance allocation done.')
start_time = lu.elapsed_time(start_time)
adjshiftwrite(alloc_ras, outcsvfile, outcsvLogfile)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def euadjacency():
"""Calculate Euclidean adjacency
Inputs: gp - geoprocessing object
"""
try:
ALLOC_RASFN = "Euc_alloc_ras"
lu.dashline()
gprint('Calculating Euclidean adjacency')
outcsvfile = cfg.EUCADJFILE
outcsvLogfile = path.join(cfg.LOGDIR, "eucAdj_STEP1.csv")
# ----------------------------------------------
# Euclidean allocation code
gp.workspace = cfg.ADJACENCYDIR
gprint('Starting Euclidean adjacency processing...')
# Euclidean cell size
cellSizeEuclidean = gp.Describe(cfg.RESRAST).MeanCellHeight
oldextent = gp.extent
if cfg.BUFFERDIST is not None:
gp.extent = gp.Describe(cfg.BNDCIR).extent
start_time = time.clock()
gp.scratchworkspace = cfg.ARCSCRATCHDIR
outDistanceRaster = path.join(cfg.ADJACENCYDIR, "euc")
alloc_ras = path.join(cfg.ADJACENCYDIR, ALLOC_RASFN)
lu.delete_data(alloc_ras)
lu.delete_data(outDistanceRaster)
count = 0
statement = ('gp.EucAllocation_sa(cfg.CORERAS, alloc_ras, "","", '
'cellSizeEuclidean, "", outDistanceRaster, "")')
while True:
try:
exec statement
except:
count, tryAgain = lu.retry_arc_error(count, statement)
if not tryAgain:
exec statement
else:
break
gp.scratchworkspace = cfg.ARCSCRATCHDIR
gprint('\nEuclidean distance allocation done.')
start_time = lu.elapsed_time(start_time)
gp.extent = oldextent
adjshiftwrite(alloc_ras, outcsvfile, outcsvLogfile)
# Clean up
lu.delete_data(outDistanceRaster)
# Return GEOPROCESSING specific errors
except arcgisscripting.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Failed in step 1. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
def 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)
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)
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 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 main():
"""Iterates over LM, BM, and restoration tasks"""
## USER SETTINGS ######################################################
## Restoration Settings
## ALL input data must be in the same projection
start_time = time.clock()
restoreMaxROI = False # Set to True to restore highest ROI
# Set to False to restore strongest barrier
restoredResistanceVal = 1 # Resistance value of restored habitat. Must be 1 or greater.
restorationDataGDB = "C:\\barrierClassAnalysis\\RestorationINPUTS_July2013.gdb" # No spaces or special chars in paths or gdb names
outputDir = "C:\\barrierClassAnalysis\\output" # No spaces in path, avoid using dropbox or network drive
# Project directories will be created in this (iter1, iter2...)
# as will an output geodatabase
resistanceRaster = "URWA_resis"# Resistance raster. Should be in input GDB
coreFC = 'URWA_HCAs_Doug_Grant'# Core area feature class. Should be in input GDB 'URWA_HCAs_Doug_Grant'
coreFN = 'HCA_ID' # Core area field name
radius = 450 # restoration radius in meters
iterations = 13 # number of restorations to perform
minAgThreshold = 0.75 # if less than this proportion of ag in circle, don't consider restoring circle
minImprovementVal = 0 # Don't consider barriers below this improvement score (average improvement per meter diameter restored)
parcelCostRaster = 'DougGrantParcelCost_m2_projected_90m' # Average per-m2 parcel cost per pixel. Snapped to resistance raster.
restorationCostRaster = 'restCostPer_m2' # Right now this is just a raster with all pixels set to 0.113174
agRaster = "ARESmaskp_projected" # 1=Ag, 0 = not Ag
barrierCombineMethod = 'Maximum' # Some restorations benefit multiple corridors.
# 'Maximum' takes the greatest improvement across core area pairs
# 'Sum' adds improvement scores acreoss all pairs.
cwdThresh = None # Use cwdThresh = None for no threshold. Use cwdThresh = X to not consider
# restorations more than X map units away from each core area.
## END USER SETTINGS ######################################################
try:
# Setup path and create directories
gprint('Hey! Make sure everything is in the same projection!\n')
gprint('Setting up paths and creating directories')
sys.path.append('..\\toolbox\\scripts')
resRast = os.path.join(restorationDataGDB, resistanceRaster)
coreFCPath = os.path.join(restorationDataGDB, coreFC)
# Set up a NEW output gdb (leave previous ones on drive)
for i in range (1,200):
outputGDB = 'restorationOutput'+str(i)+'.gdb'
if not arcpy.Exists(os.path.join(outputDir,outputGDB)):
break
gprint('Previous output GDB '+ outputGDB +' exists. Delete to save disk space.')
arcpy.CreateFileGDB_management(outputDir,outputGDB)
outputGDB = os.path.join(outputDir,outputGDB)
logFile = os.path.join(outputGDB,'Iterate Barriers'+str(i)+'.py')
shutil.copyfile(__file__, logFile) #write a copy of this file to output dir as a record of settings
arcpy.env.cellSize = resRast
arcpy.env.extent = resRast
arcpy.env.snapRaster = resRast
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
spatialref = arcpy.Describe(resRast).spatialReference
mapunits = spatialref.linearUnitName
gprint('Cell size = ' + str(arcpy.env.cellSize) + ' ' + mapunits +'s')
# Calculate fraction of ag within radius of each pixel
gprint('Calculating purchase cost, fraction of ag, etc within radius of each pixel.')
agRaster = os.path.join(restorationDataGDB, agRaster)
inNeighborhood = NbrCircle(radius, "MAP")
arcpy.env.extent = agRaster
outFocalStats = arcpy.sa.FocalStatistics(agRaster,
inNeighborhood, "MEAN","NODATA")
proportionAgRaster = os.path.join(outputGDB,'proportionAgRas')
outFocalStats.save(proportionAgRaster)
arcpy.env.extent = resRast
# Calculate purchase cost of circles
parcelCostRaster = os.path.join(restorationDataGDB, parcelCostRaster)
arcpy.env.extent = parcelCostRaster
outFocalStats = arcpy.sa.FocalStatistics(parcelCostRaster,inNeighborhood, "MEAN","DATA")
costFocalStatsRaster = os.path.join(outputGDB,'costFocalStatsRaster')
outFocalStats.save(costFocalStatsRaster)
arcpy.env.extent = resRast
circleArea = float(npy.pi * radius * radius)
outras = (Raster(costFocalStatsRaster) * circleArea)
purchCostRaster = os.path.join(outputGDB,'purchaseCostRaster')
outras.save(purchCostRaster)
lu.delete_data(costFocalStatsRaster)
# restCost = npy.pi * radius * radius * restCostPer_m2
restorationCostRaster = os.path.join(restorationDataGDB, restorationCostRaster)
outras = Raster(purchCostRaster) + (Raster(restorationCostRaster) * radius * radius * npy.pi)
totalCostRaster = os.path.join(outputGDB,'totalCostRaster')
outras.save(totalCostRaster)
# lu.build_stats(totalCostRaster)
# Create mask to remove areas without cost data
arcpy.env.extent = totalCostRaster
costMaskRaster = os.path.join(outputGDB,'costMaskRaster')
costThresh = 0
outCon = arcpy.sa.Con((Raster(totalCostRaster) > float(costThresh)), 1)
outCon.save(costMaskRaster)
arcpy.env.extent = resRast
# Create mask to remove areas below ag threshold
outCon = arcpy.sa.Con((Raster(proportionAgRaster) > float(minAgThreshold)), 1)
agMaskRaster = os.path.join(outputGDB, 'agMaskRaster')
outCon.save(agMaskRaster)
doStep1 = 'true'
doStep2 = 'true'
doStep5 = 'false'
for iter in range(1,iterations+1): #xxx
start_time1 = time.clock()
arcpy.env.cellSize = resRast # Some env settings get changed by linkage mapper and must be reset here
arcpy.env.extent = resRast
arcpy.env.snapRaster = resRast
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
lu.dashline(1)
gprint('Running iteration number '+str(iter))
projDir = os.path.join(outputDir,'iter' + str(iter)+'Proj')
lu.create_dir(outputDir)
lu.delete_dir(projDir) #xxx
lu.create_dir(projDir)
if iter > 1: # Copy previous s2 linktable to new project directory
datapassDir = os.path.join(projDir,'datapass')
lu.create_dir(datapassDir)
projDir1 = os.path.join(outputDir,'iter1Proj')
datapassDirIter1 = os.path.join(projDir1,'datapass')
s2LinktableIter1 = os.path.join(datapassDirIter1 ,'linkTable_s2.csv')
s2LinkTable = os.path.join(datapassDir ,'linkTable_s2.csv')
shutil.copyfile(s2LinktableIter1, s2LinkTable)
# Run Linkage Mapper
distFile = os.path.join(outputDir, coreFC + '_dists.txt') # Copy distances text file from earlier LM run to the output directory- speeds things up!
if not os.path.exists(distFile):
if iter == 1:
gprint('Will calculate distance file.')
distFile = '#'
else:
projDir1 = os.path.join(outputDir,'iter1Proj')
distFile1 = os.path.join(projDir1, coreFC + '_dists.txt')
shutil.copyfile(distFile1,distFile) # Put a copy here for future runs
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
argv = ('lm_master.py', projDir, coreFCPath, coreFN, resRast,
doStep1, doStep2, 'Cost-Weighted & Euclidean', distFile,
'true', 'true', 'false', '4', 'Cost-Weighted', 'true',
doStep5, 'true', '200000', '10000', '#', '#', '#', '#')
gprint('Running ' + str(argv))
cfg.lm_configured = False # Insures lm_master uses current argv
lm_master.lm_master(argv) #xxx
doStep1 = 'false' # Can skip for future iterations
doStep2 = 'false' # Can skip for future iterations
doStep5 = 'false' # Skipping for future iterations
startRadius = str(radius)
endRadius = str(radius)
radiusStep = '0'
saveRadiusRasters= 'false'
writePctRasters = 'false'
argv = ('barrier_master.py', projDir, resRast, startRadius, endRadius, radiusStep, barrierCombineMethod,
saveRadiusRasters, writePctRasters, cwdThresh)
gprint('Running ' + str(argv))
barrier_master.bar_master(argv) #xxx
arcpy.env.cellSize = resRast # Some env settings get changed by linkage mapper and must be reset here
arcpy.env.extent = resRast
arcpy.env.snapRaster = resRast
arcpy.env.overwriteOutput = True
arcpy.env.scratchWorkspace = outputGDB
arcpy.env.workspace = outputGDB
gprint('Finding restoration circles with max barrier score / ROI')
# Find points with max ROI
PREFIX = os.path.basename(projDir)
if barrierCombineMethod == 'Sum':
sumSuffix = 'Sum'
else:
sumSuffix = ''
barrierFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" + str(radius))
barrierRaster = os.path.join(projDir,'output','barriers.gdb',barrierFN)
if not arcpy.Exists(barrierRaster):
msg = ('Error: cannot find barrier output: '+barrierRaster)
lu.raise_error(msg)
# arcpy.env.cellSize = agMaskRaster
# arcpy.env.extent = agMaskRaster
if iter > 1:
gprint('Creating mask for previously restored areas')
inNeighborhood = NbrCircle(radius, "MAP")
arcpy.env.extent = allRestoredAreasRaster
outFocalStats = arcpy.sa.FocalStatistics(allRestoredAreasRaster,inNeighborhood, "MEAN","DATA")
allRestoredFocalRaster = os.path.join(outputGDB,'allRestFocRas_iter'+str(iter))
outFocalStats.save(allRestoredFocalRaster) # Anything > 0 would include a restored area and
arcpy.env.extent = resRast
restMaskRaster = os.path.join(outputGDB,'restMaskRaster_iter'+str(iter))
minval = 0
outCon = arcpy.sa.Con((Raster(allRestoredFocalRaster) == float(minval)), 1)
outCon.save(restMaskRaster)
# Candidate areas have not been restored, have cost data, meet
# minimum improvement score criteria, and have enough ag in them
candidateBarrierRaster = os.path.join(outputGDB, 'candidateBarrierRaster' + '_iter'+str(iter))
if iter > 1:
gprint('Creating candidate restoration raster using barrier results, previous restorations, and selection criteria')
outCalc = (Raster(costMaskRaster) * Raster(agMaskRaster) * Raster(barrierRaster) * Raster(restMaskRaster) * (radius * 2)) # ROI scores will be in terms of total improvement (= score * diameter)
else:
outCalc = (Raster(costMaskRaster) * Raster(agMaskRaster) * Raster(barrierRaster) * radius * 2)
minBarrierScore = minImprovementVal * radius * 2
if restoredResistanceVal != 1:
outCalc2 = (outCalc - (2 * radius * (restoredResistanceVal - 1)))
outCon = arcpy.sa.Con((outCalc2 >= float(minBarrierScore)), outCalc2)
else:
outCon = arcpy.sa.Con((outCalc >= float(minBarrierScore)), outCalc)
outCon.save(candidateBarrierRaster)
lu.build_stats(candidateBarrierRaster)
purchaseRoiRaster = os.path.join(outputGDB, 'purchaseRoiRaster' + '_iter'+str(iter))
outCalc = Raster(candidateBarrierRaster) / Raster(purchCostRaster)
outCalc.save(purchaseRoiRaster)
lu.build_stats(purchaseRoiRaster)
totalRoiRaster = os.path.join(outputGDB, 'purchaseRestRoiRaster' + '_iter'+str(iter))
outCalc = Raster(candidateBarrierRaster) / Raster(totalCostRaster)
outCalc.save(totalRoiRaster)
lu.build_stats(totalRoiRaster)
maxBarrier = arcpy.GetRasterProperties_management(candidateBarrierRaster,"MAXIMUM")
gprint('Maximum barrier improvement score: '+str(maxBarrier.getOutput(0)))
if maxBarrier < 0:
arcpy.AddWarning("\nNo barriers found that meet CWD or Ag threshold criteria.")
maxPurchROI = arcpy.GetRasterProperties_management(purchaseRoiRaster,"MAXIMUM")
gprint('Maximum purchase ROI score: '+str(maxPurchROI.getOutput(0)))
maxROI = arcpy.GetRasterProperties_management(totalRoiRaster,"MAXIMUM")
gprint('Maximum total ROI score: '+str(maxROI.getOutput(0)))
if restoreMaxROI:
outPoint = os.path.join(outputGDB, 'maxRoiPoint'+'_iter'+str(iter))
gprint('Choosing circle with maximum ROI to restore')
outCon = arcpy.sa.Con((Raster(totalRoiRaster) >= float(maxROI.getOutput(0))), totalRoiRaster)
maxRoiRaster = os.path.join(outputGDB, 'maxRoiRaster')
outCon.save(maxRoiRaster)
# Save max ROI to point
try:
arcpy.RasterToPoint_conversion(maxRoiRaster, outPoint)
except:
msg = ('Error: it looks like there are no viable restoration candidates.')
lu.raise_error(msg)
else: #Restoring strongest barrier instead
outPoint = os.path.join(outputGDB, 'maxBarrierPoint'+'_iter'+str(iter))
gprint('Choosing circle with maximum BARRIER IMPROVEMENT SCORE to restore')
outCon = arcpy.sa.Con((Raster(candidateBarrierRaster) >= float(maxBarrier.getOutput(0))), candidateBarrierRaster)
maxBarrierRaster = os.path.join(outputGDB, 'maxBarrierRaster')
outCon.save(maxBarrierRaster)
# Save max barrier to point
try:
arcpy.RasterToPoint_conversion(maxBarrierRaster, outPoint)
except:
msg = ('Error: it looks like there are no viable restoration candidates.')
lu.raise_error(msg)
gprint('Done evaluating candidate restorations')
result = int(arcpy.GetCount_management(outPoint).getOutput(0))
if result > 1:
arcpy.AddWarning('Deleting points with identical ROI/improvement score values') # Would be better to retain point with max barrier score when we have multiple points with same ROI
arcpy.DeleteIdentical_management(outPoint, "grid_code", 0.1, 0.1)
arcpy.sa.ExtractMultiValuesToPoints(outPoint,
[[candidateBarrierRaster, "barrierScore"],[purchCostRaster, "purchCost"],
[totalCostRaster, "totalCost"],[purchaseRoiRaster, "purchaseROI"],
[totalRoiRaster, "totalROI"]], "NONE")
arcpy.AddField_management(outPoint, "restorationNumber", "SHORT")
arcpy.CalculateField_management(outPoint, "restorationNumber", iter)
arcpy.AddField_management(outPoint, "radius", "DOUBLE")
arcpy.CalculateField_management(outPoint, "radius", radius)
arcpy.AddField_management(outPoint, "barrierScore_per_m", "DOUBLE")
arcpy.CalculateField_management(outPoint, "barrierScore_per_m", "(float(!barrierScore!) / (!radius! * 2))", "PYTHON")
gprint('\nCreating restoration circles')
if restoreMaxROI:
circleFC = os.path.join(outputGDB, 'maxRoiCircle'+'_iter'+str(iter))
else:
circleFC = os.path.join(outputGDB, 'maxBarrierCircle'+'_iter'+str(iter))
arcpy.Buffer_analysis(outPoint, circleFC, radius)
gprint('Rasterizing restoration circles')
if restoreMaxROI:
circleRas = os.path.join(outputGDB, 'maxRoiCircleRas'+'_iter'+str(iter))
else:
circleRas = os.path.join(outputGDB, 'maxBarrierCircleRas'+'_iter'+str(iter))
arcpy.FeatureToRaster_conversion(circleFC, 'totalROI', circleRas, arcpy.env.cellSize)
# restore raster
gprint('Digitally restoring resistance raster')
resRastRestored = os.path.join(outputGDB, 'resRastRestored'+'_iter'+str(iter))
outCon = arcpy.sa.Con(IsNull(circleRas), resRast, restoredResistanceVal)
outCon.save(resRastRestored)
allRestoredAreasRaster = os.path.join(outputGDB, 'allRestoredAreas_iter'+str(iter))
PrevRestoredAreasRaster= os.path.join(outputGDB, 'allRestoredAreas_iter'+str(iter-1))
if iter == 1:
outCon = arcpy.sa.Con(IsNull(circleRas), 0, 1)
else:
outCon = arcpy.sa.Con(IsNull(circleRas), PrevRestoredAreasRaster, 1) # Add this restoration to areas restored
outCon.save(allRestoredAreasRaster)
lu.delete_data(circleRas)
resRast = resRastRestored # Use for next iteration resistance raster
#Add circle into feature class with all circles
if restoreMaxROI:
allCirclesFC = os.path.join(outputGDB,"allCirclesMaxROI")
else:
allCirclesFC = os.path.join(outputGDB,"allCirclesMaxBarriers")
if iter == 1:
arcpy.CopyFeatures_management(circleFC, allCirclesFC)
else:
arcpy.Append_management(circleFC, allCirclesFC, "TEST")
gprint('Finished iteration #'+str(iter))
start_time1 = lu.elapsed_time(start_time1)
gprint('\nDone with iterations.')
start_time = lu.elapsed_time(start_time)
gprint('Outputs saved in: '+outputGDB)
gprint('Back up your project directories if you want to save corridor/barrier results.')
# Return GEOPROCESSING specific errors
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Iteration script failed. Details follow.****')
lu.exit_with_geoproc_error(_SCRIPT_NAME)
# Return any PYTHON or system specific errors
except:
lu.dashline(1)
gprint('****Iteration script failed. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
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 generate_distance_file():
"""Use ArcGIS to create Conefor distance file
For ArcGIS Desktop users an Advanced license is required.
"""
try:
arcpy.env.cellSize = arcpy.Raster(cfg.RESRAST).meanCellHeight
S2COREFC = cfg.COREFC
if cfg.SIMPLIFY_CORES:
try:
gprint(
'Simplifying polygons for core pair distance calculations')
COREFC_SIMP = path.join(cfg.SCRATCHDIR, "CoreFC_Simp.shp")
tolerance = float(arcpy.env.cellSize) / 3
arcpy.cartography.SimplifyPolygon(cfg.COREFC, COREFC_SIMP,
"POINT_REMOVE", tolerance,
"#", "NO_CHECK")
S2COREFC = COREFC_SIMP
except Exception:
pass # In case point geometry is entered for core area FC
arcpy.env.workspace = cfg.SCRATCHDIR
FS2COREFC = "fscores"
FS2COREFC2 = "fscores2"
arcpy.MakeFeatureLayer_management(S2COREFC, FS2COREFC)
arcpy.MakeFeatureLayer_management(S2COREFC, FS2COREFC2)
output = []
csvseparator = "\t"
adjList = get_full_adj_list()
gprint('\nFinding distances between cores using Generate Near Table.')
near_tbl = path.join(cfg.SCRATCHDIR, "neartbl.dbf")
gprint('There are ' + str(len(adjList)) + ' adjacent core pairs to '
'process.')
pctDone = 0
start_time = time.clock()
for x in range(0, len(adjList)):
pctDone = lu.report_pct_done(x, len(adjList), pctDone)
sourceCore = adjList[x, 0]
targetCore = adjList[x, 1]
expression = cfg.COREFN + " = " + str(sourceCore)
arcpy.SelectLayerByAttribute_management(FS2COREFC, "NEW_SELECTION",
expression)
expression = cfg.COREFN + " = " + str(targetCore)
arcpy.SelectLayerByAttribute_management(FS2COREFC2,
"NEW_SELECTION",
expression)
arcpy.GenerateNearTable_analysis(FS2COREFC, FS2COREFC2, near_tbl,
"#", "NO_LOCATION", "NO_ANGLE",
"ALL", "0")
rows = arcpy.SearchCursor(near_tbl)
row = next(rows)
minDist = 1e20
if row: # May be running on selected core areas in step 2
while row:
dist = row.getValue("NEAR_DIST")
if dist <= 0: # In case simplified polygons abut one another
dist = float(arcpy.env.cellSize)
if dist < minDist:
minDist = dist
outputrow = []
outputrow.append(str(sourceCore))
outputrow.append(str(targetCore))
outputrow.append(str(dist))
del row
row = next(rows)
del rows
output.append(csvseparator.join(outputrow))
start_time = lu.elapsed_time(start_time)
# In case coreFC is grouped in TOC, get coreFN for non-Arc statement
group, coreFN = path.split(cfg.COREFC)
dist_fname = path.join(cfg.PROJECTDIR, (coreFN + "_dists.txt"))
dist_file = open(dist_fname, 'w')
dist_file.write('\n'.join(output))
dist_file.close()
gprint('Distance file ' + dist_fname + ' generated.\n')
return dist_fname
except arcpy.ExecuteError:
lu.dashline(1)
gprint('****Failed in step 2. 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 2. Details follow.****')
lu.exit_with_python_error(_SCRIPT_NAME)
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 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)