def arc_wksp_setup():
"""Setup ArcPy workspace"""
arcpy.env.overwriteOutput = True
arcpy.env.cellSize = "MAXOF" # Setting to default. For batch runs.
if arcpy.Exists(cc_env.out_dir):
cc_util.delete_features(cc_env.out_dir)
arcpy.env.workspace = cc_util.mk_proj_dir(cc_env.out_dir)
arcpy.env.scratchWorkspace = cc_util.mk_proj_dir(cc_env.tmp_dir)
def arc_wksp_setup():
"""Setup ArcPy workspace"""
arcpy.env.overwriteOutput = True
arcpy.env.cellSize = "MAXOF" # Setting to default. For batch runs.
if arcpy.Exists(cc_env.out_dir):
cc_util.delete_features(cc_env.out_dir)
arcpy.env.workspace = cc_util.mk_proj_dir(cc_env.out_dir)
arcpy.env.scratchWorkspace = cc_util.mk_proj_dir(cc_env.tmp_dir)
def grass_cwd(core_list):
"""Creating CWD and Back rasters using GRASS r.walk function"""
cur_path = subprocess.Popen("echo %PATH%",
stdout=subprocess.PIPE,
shell=True).stdout.read()
gisdbase = os.path.join(cc_env.proj_dir, "gwksp")
ccr_grassrc = os.path.join(cc_env.proj_dir, "ccr_grassrc")
climate_asc = os.path.join(cc_env.out_dir, "cc_climate.asc")
resist_asc = os.path.join(cc_env.out_dir, "cc_resist.asc")
core_asc = os.path.join(cc_env.out_dir, "cc_cores.asc")
climate_lyr = "climate"
resist_lyr = "resist"
core_lyr = "cores"
try:
lm_util.gprint("\nRUNNING GRASS TO CREATE COST-WEIGHTED DISTANCE "
"RASTERS")
# Convert input GRID rasters to ASCII
lm_util.gprint("Converting ARCINFO GRID rasters to ASCII")
# Note: consider moving these to main:
arcpy.RasterToASCII_conversion(cc_env.prj_climate_rast, climate_asc)
arcpy.RasterToASCII_conversion(cc_env.prj_resist_rast, resist_asc)
arcpy.RasterToASCII_conversion(cc_env.prj_core_rast, core_asc)
# Create resource file and setup workspace
write_grassrc(ccr_grassrc, gisdbase)
setup_wrkspace(gisdbase, ccr_grassrc, climate_asc)
# Make cwd folder for Linkage Mapper
lm_util.make_cwd_paths(max(core_list))
# Import files into GRASS
lm_util.gprint("Importing raster files into GRASS")
run_grass_cmd("r.in.arc", input=climate_asc, output=climate_lyr)
run_grass_cmd("r.in.arc", input=resist_asc, output=resist_lyr)
run_grass_cmd("r.in.arc", input=core_asc, output=core_lyr)
# Generate CWD and Back rasters
gen_cwd_back(core_list, climate_lyr, resist_lyr, core_lyr)
except Exception:
raise
finally:
os.environ['PATH'] = cur_path # Revert to original windows path
if not cc_util.remove_grass_wkspc(gisdbase):
arcpy.AddWarning("Unable to delete temporary GRASS folder. "
"Program will contine.")
cc_util.delete_features(
[climate_asc, resist_asc, core_asc, ccr_grassrc])
def delete_proj_files():
"""Delete project input files on ending of analysis
Keep prj_resist_rast, prj_core_fc and out_dir for reruns.
"""
cpath = os.getcwd() # For files left behind by arcpy
prj_files = (
[cc_env.prj_climate_rast, cc_env.prj_core_rast, cc_env.tmp_dir,
os.path.join(cpath, ".prj"), os.path.join(cpath, "info")])
if cc_env.simplify_cores:
prj_files.append(cc_env.core_simp)
cc_util.delete_features(prj_files)
def grass_cwd(core_list):
"""Creating CWD and Back rasters using GRASS r.walk function"""
cur_path = subprocess.Popen("echo %PATH%", stdout=subprocess.PIPE,
shell=True).stdout.read()
gisdbase = os.path.join(cc_env.proj_dir, "gwksp")
ccr_grassrc = os.path.join(cc_env.proj_dir, "ccr_grassrc")
climate_asc = os.path.join(cc_env.out_dir, "cc_climate.asc")
resist_asc = os.path.join(cc_env.out_dir, "cc_resist.asc")
core_asc = os.path.join(cc_env.out_dir, "cc_cores.asc")
climate_lyr = "climate"
resist_lyr = "resist"
core_lyr = "cores"
try:
lm_util.gprint("\nRUNNING GRASS TO CREATE COST-WEIGHTED DISTANCE "
"RASTERS")
# Convert input GRID rasters to ASCII
lm_util.gprint("Converting ARCINFO GRID rasters to ASCII")
# Note: consider moving these to main:
arcpy.RasterToASCII_conversion(cc_env.prj_climate_rast, climate_asc)
arcpy.RasterToASCII_conversion(cc_env.prj_resist_rast, resist_asc)
arcpy.RasterToASCII_conversion(cc_env.prj_core_rast, core_asc)
# Create resource file and setup workspace
write_grassrc(ccr_grassrc, gisdbase)
setup_wrkspace(gisdbase, ccr_grassrc, climate_asc)
# Make cwd folder for Linkage Mapper
lm_util.make_cwd_paths(max(core_list))
# Import files into GRASS
lm_util.gprint("Importing raster files into GRASS")
run_grass_cmd("r.in.arc", input=climate_asc, output=climate_lyr)
run_grass_cmd("r.in.arc", input=resist_asc, output=resist_lyr)
run_grass_cmd("r.in.arc", input=core_asc, output=core_lyr)
# Generate CWD and Back rasters
gen_cwd_back(core_list, climate_lyr, resist_lyr, core_lyr)
except Exception:
raise
finally:
os.environ['PATH'] = cur_path # Revert to original windows path
if not cc_util.remove_grass_wkspc(gisdbase):
arcpy.AddWarning("Unable to delete temporary GRASS folder. "
"Program will contine.")
cc_util.delete_features(
[climate_asc, resist_asc, core_asc, ccr_grassrc])
def grass_cwd(core_list):
"""Creating CWD and Back rasters using GRASS r.walk function"""
gisdbase = os.path.join(cc_env.proj_dir, "gwksp")
ccr_grassrc = os.path.join(cc_env.proj_dir, "ccr_grassrc")
climate_asc = os.path.join(cc_env.out_dir, "cc_climate.asc")
resist_asc = os.path.join(cc_env.out_dir, "cc_resist.asc")
core_asc = os.path.join(cc_env.out_dir, "cc_cores.asc")
climate_lyr = "climate"
resist_lyr = "resist"
core_lyr = "cores"
try:
lm_util.gprint("\nRUNNING GRASS TO CREATE COST-WEIGHTED DISTANCE "
"RASTERS")
# Convert input GRID rasters to ASCII
lm_util.gprint("Converting ARCINFO GRID rasters to ASCII")
arcpy.RasterToASCII_conversion(cc_env.prj_climate_rast, climate_asc)
arcpy.RasterToASCII_conversion(cc_env.prj_resist_rast, resist_asc)
arcpy.RasterToASCII_conversion(cc_env.prj_core_rast, core_asc)
# Create resource file and setup workspace
start_path = os.environ["PATH"]
os.environ["PATH"] = cc_env.gpath
write_grassrc(ccr_grassrc, gisdbase)
setup_wrkspace(gisdbase, ccr_grassrc, climate_asc)
# Make cwd folder for Linkage Mapper
lm_util.make_cwd_paths(max(core_list))
# Import files into GRASS
lm_util.gprint("Importing raster files into GRASS")
run_grass_cmd("r.in.gdal", input=climate_asc, output=climate_lyr)
run_grass_cmd("r.in.gdal", input=resist_asc, output=resist_lyr)
run_grass_cmd("r.in.gdal", input=core_asc, output=core_lyr)
# Generate CWD and Back rasters
gen_cwd_back(core_list, climate_lyr, resist_lyr, core_lyr)
except Exception:
raise
finally:
os.environ["PATH"] = start_path
if not cc_util.remove_grass_wkspc(gisdbase):
lm_util.warn("Unable to delete temporary GRASS folder. "
"Program will contine.")
cc_util.delete_features(
[climate_asc, resist_asc, core_asc, ccr_grassrc])
def delete_proj_files():
"""Delete project input files on ending of analysis
Keep prj_resist_rast, prj_core_fc and out_dir for reruns.
"""
cpath = os.getcwd() # For files left behind by arcpy
prj_files = ([
cc_env.prj_climate_rast, cc_env.prj_core_rast, cc_env.tmp_dir,
os.path.join(cpath, ".prj"),
os.path.join(cpath, "info")
])
if cc_env.simplify_cores:
prj_files.append(cc_env.core_simp)
cc_util.delete_features(prj_files)
def limit_cores(pair_tbl, stats_tbl):
"""Limit core pairs based upon climate threshold"""
pair_vw = "dist_tbvw"
stats_vw = "stats_tbvw"
core_id = cc_env.core_fld.upper()
try:
lm_util.gprint("\nLIMITING CORE PAIRS BASED UPON CLIMATE "
"THRESHOLD")
arcpy.MakeTableView_management(pair_tbl, pair_vw)
arcpy.MakeTableView_management(stats_tbl, stats_vw)
# Add basic stats to distance table
lm_util.gprint("Joining zonal statistics to pairings table")
add_stats(stats_vw, core_id, "fr", pair_vw, TO_COL)
add_stats(stats_vw, core_id, "to", pair_vw, FR_COL)
# Calculate difference of 2 std
lm_util.gprint("Calculating difference of 2 std")
diffu_2std = "diffu_2std"
arcpy.AddField_management(pair_vw, diffu_2std, "Float", "", "",
"", "", "NULLABLE")
arcpy.CalculateField_management(pair_vw, diffu_2std,
"abs(!frumin2std! - !toumin2std!)",
"PYTHON")
# Filter distance table based on inputed threshold and delete rows
lm_util.gprint("Filtering table based on threshold")
diffu2std_fld = arcpy.AddFieldDelimiters(pair_vw, diffu_2std)
expression = diffu2std_fld + " <= " + str(cc_env.climate_threshold)
arcpy.SelectLayerByAttribute_management(pair_vw, "NEW_SELECTION",
expression)
rows_del = int(arcpy.GetCount_management(pair_vw).getOutput(0))
if rows_del > 0:
arcpy.DeleteRows_management(pair_vw)
lm_util.gprint(str(rows_del) + " rows deleted")
except Exception:
raise
finally:
cc_util.delete_features([stats_vw, pair_vw])
def limit_cores(pair_tbl, stats_tbl):
"""Limit core pairs based upon climate threshold"""
pair_vw = "dist_tbvw"
stats_vw = "stats_tbvw"
core_id = cc_env.core_fld.upper()
try:
lm_util.gprint("\nLIMITING CORE PAIRS BASED UPON CLIMATE " "THRESHOLD")
arcpy.MakeTableView_management(pair_tbl, pair_vw)
arcpy.MakeTableView_management(stats_tbl, stats_vw)
# Add basic stats to distance table
lm_util.gprint("Joining zonal statistics to pairings table")
add_stats(stats_vw, core_id, "fr", pair_vw, TO_COL)
add_stats(stats_vw, core_id, "to", pair_vw, FR_COL)
# Calculate difference of 2 std
lm_util.gprint("Calculating difference of 2 std")
diffu_2std = "diffu_2std"
arcpy.AddField_management(pair_vw, diffu_2std, "Float", "", "", "", "",
"NULLABLE")
arcpy.CalculateField_management(pair_vw, diffu_2std,
"abs(!frumin2std! - !toumin2std!)",
"PYTHON_9.3")
# Filter distance table based on inputed threshold and delete rows
lm_util.gprint("Filtering table based on threshold")
diffu2std_fld = arcpy.AddFieldDelimiters(pair_vw, diffu_2std)
expression = diffu2std_fld + " <= " + str(cc_env.climate_threshold)
arcpy.SelectLayerByAttribute_management(pair_vw, "NEW_SELECTION",
expression)
rows_del = int(arcpy.GetCount_management(pair_vw).getOutput(0))
if rows_del > 0:
arcpy.DeleteRows_management(pair_vw)
lm_util.gprint(str(rows_del) + " rows deleted")
except Exception:
raise
finally:
cc_util.delete_features([stats_vw, pair_vw])
def create_lnk_tbl(corefc, core_pairs, frm_cores):
"""Create link table file and limit based on near table results"""
fcore_vw = "fcore_vw"
tcore_vw = "tcore_vw"
jtocore_fn = cc_env.core_fld[:8] + "_1" # dbf field length
near_tbl = os.path.join(cc_env.out_dir, "neartbl.dbf")
link_file = os.path.join(lm_env.DATAPASSDIR, "linkTable_s2.csv")
link_tbl, srow, srows = None, None, None
try:
link_tbl = open(link_file, 'wb')
writer = csv.writer(link_tbl, delimiter=',')
headings = [
"# link", "coreId1", "coreId2", "cluster1", "cluster2", "linkType",
"eucDist", "lcDist", "eucAdj", "cwdAdj"
]
writer.writerow(headings)
core_list = set()
no_cores = str(len(frm_cores))
i = 1
coreid_fld = arcpy.AddFieldDelimiters(corefc, cc_env.core_fld)
for core_no, frm_core in enumerate(frm_cores):
# From cores
expression = coreid_fld + " = " + frm_core
arcpy.MakeFeatureLayer_management(corefc, fcore_vw, expression)
# To cores
to_cores_lst = [x[1] for x in core_pairs if frm_core == x[0]]
to_cores = ', '.join(to_cores_lst)
expression = coreid_fld + " in (" + to_cores + ")"
arcpy.MakeFeatureLayer_management(corefc, tcore_vw, expression)
lm_util.gprint("Calculating Euclidean distance/s from Core " +
frm_core + " to " + str(len(to_cores_lst)) +
" other cores" + " (" + str(core_no + 1) + "/" +
no_cores + ")")
# Generate near table for these core pairings
arcpy.GenerateNearTable_analysis(fcore_vw, tcore_vw, near_tbl,
cc_env.max_euc_dist,
"NO_LOCATION", "NO_ANGLE", "ALL")
# Join near table to core table
arcpy.JoinField_management(near_tbl, "IN_FID", corefc, "FID",
cc_env.core_fld)
arcpy.JoinField_management(near_tbl, "NEAR_FID", corefc, "FID",
cc_env.core_fld)
# Limit pairings based on inputed Euclidean distances
srow, srows = None, None
euc_dist_fld = arcpy.AddFieldDelimiters(near_tbl, "NEAR_DIST")
expression = (euc_dist_fld + " > " + str(cc_env.min_euc_dist))
srows = arcpy.SearchCursor(near_tbl, expression, "",
jtocore_fn + "; NEAR_DIST",
jtocore_fn + " A; NEAR_DIST A")
# Process near table and output into a link table
srow = srows.next()
if srow:
core_list.add(int(frm_core))
while srow:
to_coreid = srow.getValue(jtocore_fn)
dist_value = srow.getValue("NEAR_DIST")
writer.writerow([
i, frm_core, to_coreid, -1, -1, 1, dist_value, -1, -1,
-1
])
core_list.add(to_coreid)
srow = srows.next()
i += 1
except Exception:
raise
finally:
cc_util.delete_features(
[near_tbl, os.path.splitext(corefc)[0] + "_Pnt.shp"])
if link_tbl:
link_tbl.close()
if srow:
del srow
if srows:
del srows
return core_list
def cc_copy_inputs():
"""Clip Climate Linkage Mapper inputs to smallest extent"""
ext_poly = os.path.join(cc_env.out_dir, "ext_poly.shp") # Extent polygon
try:
lm_util.gprint("\nCOPYING LAYERS AND, IF NECESSARY, REDUCING EXTENT")
if not arcpy.Exists(cc_env.inputs_gdb):
arcpy.CreateFileGDB_management(os.path.dirname(cc_env.inputs_gdb),
os.path.basename(cc_env.inputs_gdb))
climate_extent = arcpy.Raster(cc_env.climate_rast).extent
if cc_env.resist_rast is not None:
resist_extent = arcpy.Raster(cc_env.resist_rast).extent
xmin = max(climate_extent.XMin, resist_extent.XMin)
ymin = max(climate_extent.YMin, resist_extent.YMin)
xmax = min(climate_extent.XMax, resist_extent.XMax)
ymax = min(climate_extent.YMax, resist_extent.YMax)
# Set to minimum extent if resistance raster was given
arcpy.env.extent = arcpy.Extent(xmin, ymin, xmax, ymax)
# Want climate and resistance rasters in same spatial ref
# with same nodata cells
proj_resist_rast = sa.Con(sa.IsNull(cc_env.climate_rast),
sa.Int(cc_env.climate_rast),
cc_env.resist_rast)
proj_resist_rast.save(cc_env.prj_resist_rast)
else:
xmin = climate_extent.XMin
ymin = climate_extent.YMin
xmax = climate_extent.XMax
ymax = climate_extent.YMax
ones_resist_rast = sa.Con(sa.IsNull(cc_env.climate_rast),
sa.Int(cc_env.climate_rast), 1)
ones_resist_rast.save(cc_env.prj_resist_rast)
arcpy.CopyRaster_management(cc_env.climate_rast,
cc_env.prj_climate_rast)
# Create core raster
arcpy.env.extent = arcpy.Extent(xmin, ymin, xmax, ymax)
lm_util.delete_data(cc_env.prj_core_rast)
arcpy.FeatureToRaster_conversion(
cc_env.core_fc, cc_env.core_fld, cc_env.prj_core_rast,
arcpy.Describe(cc_env.climate_rast).MeanCellHeight)
arcpy.env.extent = None
# Create array of boundary points
array = arcpy.Array()
pnt = arcpy.Point(xmin, ymin)
array.add(pnt)
pnt = arcpy.Point(xmax, ymin)
array.add(pnt)
pnt = arcpy.Point(xmax, ymax)
array.add(pnt)
pnt = arcpy.Point(xmin, ymax)
array.add(pnt)
# Add in the first point of the array again to close polygon boundary
array.add(array.getObject(0))
# Create a polygon geometry object using the array object
ext_feat = arcpy.Polygon(array)
arcpy.CopyFeatures_management(ext_feat, ext_poly)
# Clip core feature class
arcpy.Clip_analysis(cc_env.core_fc, ext_poly, cc_env.prj_core_fc)
except Exception:
raise
finally:
cc_util.delete_features(ext_poly)
def create_lnk_tbl(corefc, core_pairs, frm_cores):
"""Create link table file and limit based on near table results"""
fcore_vw = "fcore_vw"
tcore_vw = "tcore_vw"
jtocore_fn = cc_env.core_fld[:8] + "_1" # dbf field length
near_tbl = os.path.join(cc_env.out_dir, "neartbl.dbf")
link_file = os.path.join(lm_env.DATAPASSDIR, "linkTable_s2.csv")
link_tbl, srow, srows = None, None, None
try:
link_tbl = open(link_file, 'wb')
writer = csv.writer(link_tbl, delimiter=',')
headings = ["# link", "coreId1", "coreId2", "cluster1", "cluster2",
"linkType", "eucDist", "lcDist", "eucAdj", "cwdAdj"]
writer.writerow(headings)
core_list = set()
no_cores = str(len(frm_cores))
i = 1
coreid_fld = arcpy.AddFieldDelimiters(corefc, cc_env.core_fld)
for core_no, frm_core in enumerate(frm_cores):
# From cores
expression = coreid_fld + " = " + frm_core
arcpy.MakeFeatureLayer_management(corefc, fcore_vw, expression)
# To cores
to_cores_lst = [x[1] for x in core_pairs if frm_core == x[0]]
to_cores = ', '.join(to_cores_lst)
expression = coreid_fld + " in (" + to_cores + ")"
arcpy.MakeFeatureLayer_management(corefc, tcore_vw, expression)
lm_util.gprint("Calculating Euclidean distance/s from Core "
+ frm_core + " to " + str(len(to_cores_lst))
+ " other cores" + " (" + str(core_no + 1) + "/"
+ no_cores + ")")
# Generate near table for these core pairings
arcpy.GenerateNearTable_analysis(
fcore_vw, tcore_vw, near_tbl,
cc_env.max_euc_dist, "NO_LOCATION", "NO_ANGLE", "ALL")
# Join near table to core table
arcpy.JoinField_management(near_tbl, "IN_FID", corefc,
"FID", cc_env.core_fld)
arcpy.JoinField_management(near_tbl, "NEAR_FID", corefc,
"FID", cc_env.core_fld)
# Limit pairings based on inputed Euclidean distances
srow, srows = None, None
euc_dist_fld = arcpy.AddFieldDelimiters(near_tbl, "NEAR_DIST")
expression = (euc_dist_fld + " > " + str(cc_env.min_euc_dist))
srows = arcpy.SearchCursor(near_tbl, expression, "",
jtocore_fn + "; NEAR_DIST",
jtocore_fn + " A; NEAR_DIST A")
# Process near table and output into a link table
srow = srows.next()
if srow:
core_list.add(int(frm_core))
while srow:
to_coreid = srow.getValue(jtocore_fn)
dist_value = srow.getValue("NEAR_DIST")
writer.writerow([i, frm_core, to_coreid, -1, -1, 1,
dist_value, -1, -1, -1])
core_list.add(to_coreid)
srow = srows.next()
i += 1
except Exception:
raise
finally:
cc_util.delete_features(
[near_tbl, os.path.splitext(corefc)[0] + "_Pnt.shp"])
if link_tbl:
link_tbl.close()
if srow:
del srow
if srows:
del srows
return core_list
def cc_copy_inputs():
"""Clip Climate Linkage Mapper inputs to smallest extent"""
ext_poly = os.path.join(cc_env.out_dir, "ext_poly.shp") # Extent polygon
try:
lm_util.gprint("\nCOPYING LAYERS AND, IF NECESSARY, REDUCING EXTENT")
if not arcpy.Exists(cc_env.inputs_gdb):
arcpy.CreateFileGDB_management(os.path.dirname(cc_env.inputs_gdb),
os.path.basename(cc_env.inputs_gdb))
climate_extent = arcpy.Raster(cc_env.climate_rast).extent
if cc_env.resist_rast is not None:
resist_extent = arcpy.Raster(cc_env.resist_rast).extent
xmin = max(climate_extent.XMin, resist_extent.XMin)
ymin = max(climate_extent.YMin, resist_extent.YMin)
xmax = min(climate_extent.XMax, resist_extent.XMax)
ymax = min(climate_extent.YMax, resist_extent.YMax)
# Set to minimum extent if resistance raster was given
arcpy.env.extent = arcpy.Extent(xmin, ymin, xmax, ymax)
# Want climate and resistance rasters in same spatial ref
# with same nodata cells
proj_resist_rast = sa.Con(
sa.IsNull(cc_env.climate_rast),
sa.Int(cc_env.climate_rast), cc_env.resist_rast)
proj_resist_rast.save(cc_env.prj_resist_rast)
else:
xmin = climate_extent.XMin
ymin = climate_extent.YMin
xmax = climate_extent.XMax
ymax = climate_extent.YMax
# Copying to gdb avoids gdal conflict later with ascii conversion
ones_resist_rast = sa.Con(
sa.IsNull(cc_env.climate_rast),
sa.Int(cc_env.climate_rast), 1)
ones_resist_rast.save(cc_env.prj_resist_rast)
arcpy.CopyRaster_management(cc_env.climate_rast,
cc_env.prj_climate_rast)
# Create core raster
arcpy.env.extent = arcpy.Extent(xmin, ymin, xmax, ymax)
lm_util.delete_data(cc_env.prj_core_rast)
arcpy.FeatureToRaster_conversion(
cc_env.core_fc, cc_env.core_fld,
cc_env.prj_core_rast,
arcpy.Describe(cc_env.climate_rast).MeanCellHeight)
arcpy.env.extent = None
# Create array of boundary points
array = arcpy.Array()
pnt = arcpy.Point(xmin, ymin)
array.add(pnt)
pnt = arcpy.Point(xmax, ymin)
array.add(pnt)
pnt = arcpy.Point(xmax, ymax)
array.add(pnt)
pnt = arcpy.Point(xmin, ymax)
array.add(pnt)
# Add in the first point of the array again to close polygon boundary
array.add(array.getObject(0))
# Create a polygon geometry object using the array object
ext_feat = arcpy.Polygon(array)
arcpy.CopyFeatures_management(ext_feat, ext_poly)
# Clip core feature class
arcpy.Clip_analysis(cc_env.core_fc, ext_poly, cc_env.prj_core_fc)
except Exception:
raise
finally:
cc_util.delete_features(ext_poly)