# Threshold type
gtorlt = p1.gtorlt
# Reclass loss year name
rclyname = p1.rclyname
# List loss year files
fl = os.listdir(p1.tld + p1.fcd)
fl = [i for i in fl if 'lossyear' in i and i.endswith('.tif')]
# Get file name to work on
fnamely = p1.tld + p1.fcd + '/' + fl[j]
# Loss year
lyear = hfu.raster2array(fnamely)
lya = lyear[0]
del lyear
if gtorlt == 'gt':
# Reclass loss year > 12 to 1, else 0
lya = np.where(lya > lyv, 1, 0)
lya = lya.astype('int8')
else:
# Reclass loss year <= 12 to 1, else 0
lya = np.where((lya > 0) & (lya <= lyv), 1, 0)
lya = lya.astype('int8')
# Output reclassed loss file name
ofn = os.path.dirname(fnamely) + os.sep + os.path.basename(fnamely).replace(
'lossyear', rclyname)
# Get flux extent
fluxext = hfu.raster_corners(flname)
# Get tree cover extent
tcext = hfu.raster_corners(tcname)
# Get tree cover loss extent
tclext = hfu.raster_corners(idir + emtd + '/' + tclosslayers[0])
# Get intersection of extents
minx = np.max([minx, fluxext[0], tcext[0], tclext[0]])
miny = np.max([miny, fluxext[1], tcext[1], tclext[1]])
maxx = np.min([maxx, fluxext[2], tcext[2], tclext[2]])
maxy = np.min([maxy, fluxext[3], tcext[3], tclext[3]])
#--------------------------------------------------
# Read in flux raster, subset by shape bounding box
dfr = hfu.raster2array(flname, clip=[minx, miny, maxx, maxy])
# If raster2array returns a valid output, keep processing
if dfr != False:
# Write clipped raster to file
hfu.array2raster(otiff1,
'#',
gdal.GDT_Float32,
'GTiff',
dfr[0],
geotrans=dfr[1],
rasterproj=rwkt)
# Use zone boundary to mask flux sum layer
with rasterio.open(otiff1) as src:
out_image1, out_transform = mask(src, geoms, crop=True)
out_meta = src.meta.copy()
# Delete rectangle cropped raster
bext[2] = newymin
bext[3] = newymax
# Save extent to a new Shapefile
boundingbox = box(bext[0], bext[2], bext[1], bext[3])
#%%
# Create resistance vrt tile
csrast = tdir + vrtp + str(gc1) + '_' + str(ptid1) + '_' + str(
gc2) + '_' + str(ptid2) + '.vrt'
subprocess.call([
"gdalbuildvrt", "-te",
str(bext[0]),
str(bext[2]),
str(bext[1]),
str(bext[3]), "-input_file_list", forfileindex, csrast
])
cso = hfu.raster2array(csrast)
cs = cso[0]
cs[cs == 255] = 1000 # set no go areas to higher value
# Give x and y coordinates. Returns row and column indices of coordinates
locs1 = hfu.coord2pixelOffset(csrast, [cx1], [cy1])
locs1 = [i[0] for i in locs1] # drop list level
locs1 = [(locs1[0], locs1[1])] # convert to a list of lists...
# Get distance from point in first layer
# Create graph object
go = graph.MCP_Geometric(cs,
offsets=None,
sampling=(xint, yint),
fully_connected=True)
cc1, tb = go.find_costs(locs1)
del tb # delete traceback
locs2 = hfu.coord2pixelOffset(csrast, [cx2], [cy2])
'_' + l + '.shp')
# Get shapefile extent in regional sinusoidal coordinates
minx, miny, maxx, maxy = cx.geometry.total_bounds
# Convert to bounding box
bboxcx = gpd.GeoDataFrame({
'id': [1],
'ucode': [l]
},
geometry=[box(minx, miny, maxx, maxy)])
# Get intersection between raster bounding box and shapefile bounding box in sinusoidal
ix = gpd.overlay(bbox, bboxcx, how='intersection', use_sindex=True)
# Get clip coordinates from intersection
minx, miny, maxx, maxy = ix.geometry.total_bounds
# Read in forest cover raster, subset by intersection between polygon
# bounding box and raster.
dfr = hfu.raster2array(fcname, clip=[minx, miny, maxx, maxy])
# If raster2array returns a valid output, keep processing
if dfr != False:
# Rasterized ifl name
rifl = '/scratch/pj276/ifl_corridors/ifl/ifl_2000_tropics_ssu_' + i + '_' + j + '.tif'
# Read in rasterized ifl, subset by shape bounding box
rifl = hfu.raster2array(rifl, clip=[minx, miny, maxx, maxy])[0]
# Mask out forest cover that overlaps ifls
dfr[0][rifl >= 1] = ndval
dfra = dfr[0]
# Write to file
rwkt = gdal.Open(fcname)
rwkt = rwkt.GetProjectionRef()
hfu.array2raster(otiff1,
'#',
gdal.GDT_Float32,
# Get tree cover extent
tcext = hfu.raster_corners(tcname)
# Get tree cover loss extent
tclext = hfu.raster_corners(idir + emtd + '/' + tclosslayers[0])
# Get ifl extent
riflext = hfu.raster_corners(riflname)
# Get intersection of extents
minx = np.max([minx, fluxext[0], tcext[0], tclext[0], riflext[0]])
miny = np.max([miny, fluxext[1], tcext[1], tclext[1], riflext[1]])
maxx = np.min([maxx, fluxext[2], tcext[2], tclext[2], riflext[2]])
maxy = np.min([maxy, fluxext[3], tcext[3], tclext[3], riflext[3]])
#--------------------------------------------------
# Read in flux raster, subset by shape bounding box
dfr = hfu.raster2array(flname, clip=[minx, miny, maxx, maxy])
# If raster2array returns a valid output, keep processing
if dfr != False:
# Write clipped raster to file
hfu.array2raster(otiff1,'#',gdal.GDT_Float32,'GTiff',dfr[0],geotrans=dfr[1],rasterproj=rwkt)
# Use zone boundary to mask flux sum layer
with rasterio.open(otiff1) as src:
out_image1, out_transform = mask(src, geoms, crop=True)
out_meta = src.meta.copy()
# Delete rectangle cropped raster
os.remove(otiff1)
# Sum flux values to get total for the zone
fluxsum = np.sum(out_image1)
# Break out of script if there's no flux
if fluxsum == 0:
print('no flux, exiting script')
# Get flux extent
fluxext = hfu.raster_corners(flname)
# Get tree cover extent
tcext = hfu.raster_corners(tcname)
# Get tree cover loss extent
tclext = hfu.raster_corners(idir + emtd + '/' + tclosslayers[0])
# Get intersection of extents
minx = np.max([minx, fluxext[0], tcext[0], tclext[0]])
miny = np.max([miny, fluxext[1], tcext[1], tclext[1]])
maxx = np.min([maxx, fluxext[2], tcext[2], tclext[2]])
maxy = np.min([maxy, fluxext[3], tcext[3], tclext[3]])
# Read in zone raster subset
zrast = hfu.raster2array(zr, clip=[minx, miny, maxx, maxy])
# Read in euclidean zone raster subset
ezrast = hfu.raster2array(ezr, clip=[minx, miny, maxx, maxy])
# Read in flux raster, subset by zone bounding box
frast = hfu.raster2array(flname, clip=[minx, miny, maxx, maxy])
# If raster2array returns a valid output, keep processing
if frast != False:
zrast = zrast[0]
frast = frast[0]
# Sum flux values to get total for the zone
fluxsum = np.sum(frast[(zrast == lorig) & (ezrast > 0)])
# Break out of script if there's no flux
if fluxsum == 0:
print('no flux, exiting script')
# Job array index
j = int(sys.argv[1]) - 1 # subtract for python zero indexing
# Loss year by tree cover 2000 name
lybytc2000name = p1.lybytc2000name
# List loss year files
fl = os.listdir(p1.tld + p1.pfdd)
fl = [i for i in fl if 'lossyear' in i and i.endswith('.tif')]
fl.sort()
# Get file name to work on
fnamely = p1.tld + p1.pfdd + '/' + fl[j]
# Loss year
lyear = hfu.raster2array(fnamely)
lya = lyear[0]
del lyear
# List tree cover files
y2k = os.listdir(p1.tld + p1.pfdd)
y2k = [i for i in y2k if 'treecover2000' in i and i.endswith('.tif')]
y2k.sort()
# Get file name to work on
y2knamely = p1.tld + p1.pfdd + '/' + y2k[j]
# Year 2000 tree cover
y2k = hfu.raster2array(y2knamely)[0]
# Loop through years
for lyv in range(0, 19, 1):
# Reclass loss year
# Build a vrt from a file list
acmd = [
"gdalbuildvrt", "-te",
str(newbb[0]),
str(newbb[1]),
str(newbb[2]),
str(newbb[3]), ovrt
]
for myfile in flist:
acmd.append(myfile)
subprocess.call(acmd)
# If aggregating datamask files, reclassify water values (2) to 0
if 'datamask' in p:
# Read vrt to array
dm = hfu.raster2array(ovrt)[0]
# Reclassify
dm = np.where(dm == 2, 0, dm)
# Name for temporary tiff
ttiff = aggodir + '/ttiff_' + p + '_' + str(k) + '.tif'
# Write to tiff
hfu.array2raster(ttiff, ovrt, gdal.GDT_Byte, 'GTiff', dm)
# Aggregate to new resolution using average operator
ofile = aggodir + '/temp_90m_' + p + '_' + str(k) + '.tif'
subprocess.call([
"gdalwarp", "-multi", "-wo", "NUM_THREADS=ALL_CPUS", "-tr",
aggdim, aggdim, "-r", "average", "-srcnodata", ndval,
"-ot", "Float32", ttiff, ofile
])
# Create vrt from aggregated file, clipping off the collar
aggvrt = aggodir + '/agg_temp_' + p + str(k) + '.vrt'
d = {'id': [1], 'ucode': [l]}
dd = pd.DataFrame(data=d)
bboxcx = gpd.GeoDataFrame(dd, geometry=b)
bboxcx.crs = cx.crs
ix = gpd.overlay(bboxgeog, bboxcx, how='intersection', use_sindex=True)
if ix.shape[0] >= 1:
# Repro shapefile
cx = cx.to_crs(rproj4)
# Save shapefile if needed
if not os.path.exists(idir + '/rp5k130k90m_' + j + '_' + i + '_' + kk + '_ifl/cfinal/' + fluxdir + '/' + j + '_' + i + '_' + k + '_' + l + '.shp'):
cx.to_file(idir + '/rp5k130k90m_' + j + '_' + i + '_' + kk + '_ifl/cfinal/' + fluxdir + '/' + j + '_' + i + '_' + k + '_' + l + '.shp')
sflist.append(idir + '/rp5k130k90m_' + j + '_' + i + '_' + kk + '_ifl/cfinal/' + fluxdir + '/' + j + '_' + i + '_' + k + '_' + l + '.shp')
# Get shapefile extent in regional sinusoidal coordinates
minx, miny, maxx, maxy = cx.geometry.total_bounds
# Read in direct flux raster, subset by shape bounding box
dfr = hfu.raster2array(dfrname, clip=[minx, miny, maxx, maxy])
# If raster2array returns a valid output, keep processing
if dfr != False:
# Write to file
rwkt = gdal.Open(dfrname)
rwkt = rwkt.GetProjectionRef()
hfu.array2raster(otiff1,'#',gdal.GDT_Float32,'GTiff',dfr[0],geotrans=dfr[1],rasterproj=rwkt)
# Get geometry from zone shapefile
with fiona.open(idir + '/rp5k130k90m_' + j + '_' + i + '_' + kk + '_ifl/cfinal/' + fluxdir + '/' + j + '_' + i + '_' + k + '_' + l + '.shp', "r") as shapefile:
geoms = [feature["geometry"] for feature in shapefile]
# Use zone boundary to mask flux sum layer
with rasterio.open(otiff1) as src:
out_image, out_transform = mask(src, geoms, crop=True)
out_meta = src.meta.copy()
# Delete rectangle cropped raster
os.remove(otiff1)
else:
fpat = '_'
# Switch for using morphology or not
usemorph = p1.usemorph #'no'
#----
if usemorph == 'yes':
# Check for forest cover tile and make sure output doesn't exist
if (os.path.exists(idir + '/' + reg + '_rtile_treecover' + str(y) + fpat +
str(j) + '.tif')
) and not os.path.exists(odir + '/' + reg + '_rtile_cs' + str(y) +
spname + '_' + str(j) + '.tif'):
# Get forest cover tile
fortile = idir + '/' + reg + '_rtile_treecover' + str(y) + fpat + str(
j) + '.tif'
fco = hfu.raster2array(fortile)
fc = fco[0]
# Burn in MSPA classes
mspatile = mdir + '/mspa_' + str(y) + '_' + mnbo + '_' + str(
j) + '.tif'
mspa = hfu.raster2array(mspatile)[0]
# Codes: core-17; perforation-5,37,69; edge-3,35,67; bridge-33; loop-65; branch-1, patch-9
minusarray = np.zeros(mspa.shape)
minusarray[(mspa == 5) | (mspa == 37) | (mspa == 69)] = 5
minusarray[(mspa == 3) | (mspa == 35) | (mspa == 67)] = 10
minusarray[(mspa == 33) | (mspa == 65) | (mspa == 1)] = 15
minusarray[mspa == 9] = 20
fc = fc - minusarray
fc[fc < 0] == 0 # Recode any negative values
mspa = None
minusarray = None
# Update year
uyear = p1.uyear #'2012'
# Loss year value
lyv = p1.lyv #12
# List year 2000 tree cover files
fl = os.listdir(p1.tld + p1.fcd)
fl = [i for i in fl if 'treecover2000' in i and i.endswith('.tif')]
# Get file name to work on
fname2000 = p1.tld + p1.fcd + '/' + fl[j]
# Use to build file names for forest operations and read to array
# Tree cover in 2000
treecov = hfu.raster2array(fname2000)
tca = treecov[0]
# Build loss year file name from year 2000 forest cover name
fnameloss = os.path.dirname(fname2000) + '/' + os.path.basename(
fname2000).replace('treecover2000', 'lossyear')
# Loss year
lyear = hfu.raster2array(fnameloss)
lya = lyear[0]
del lyear
if usegain == True:
# Build gain file name from year 2000 forest cover name
fnamegain = os.path.dirname(fname2000) + '/' + os.path.basename(
fname2000).replace('treecover2000', 'gain')