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grassland_loss.py
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grassland_loss.py
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################################################################
# December 3, 2014
# grassland_loss.py
# email: [email protected]
#################################################################
# Google Python Style Guide
# function_name, local_var_name, ClassName, method_name, ExceptionName,
# GLOBAL_CONSTANT_NAME, global_var_name, module_name, package_name,
# instance_var_name, function_parameter_name
from constants import *
date = datetime.datetime.now().strftime("mon_%m_day_%d_%H_%M")#'mon_09_day_09_21_52'#
# Directories
cdl_dir = 'C:\\Users\\ritvik\\Desktop\\MyDocuments\\PhD\\Projects\\CropIntensity\\input\\' # Contains input CDL files
base_dir = 'C:\\Users\\ritvik\\Desktop\\MyDocuments\\PhD\\Projects\\Grassland_Loss_PNAS\\'
inp_dir = 'C:\\Users\\ritvik\\workspace\\GrasslandLoss_WimberlyPNAS2013\\'
jager_dir = base_dir+'Raw_Data\\'#'C:\\Users\\ritvik\\Documents\\PhD\\Projects\\EPIC\\ML\\Switchgrass_OakRidge\\'
county_dir = base_dir+'Raw_Data\\'
gelfand_dir = base_dir+'Raw_Data\\USNC\\'
out_dir = base_dir+'output'+os.sep+TAG+'_'+date+os.sep
shared_dir = base_dir+'shared'+os.sep+TAG+os.sep
lcc_dir = base_dir+'Land_Capability_Classes\\GIS_Files\\'
vec_dir = base_dir+'Raw_Data\\'
# GIS data
nlcd_ras = base_dir+'Raw_Data\\NLCD\\5State_NLCD_06.img'
county_shp = county_dir+'5StateCounties.shp'
###############################################################################
#
#
#
#
###############################################################################
def backup_source_code(out_dir):
if not os.path.exists(out_dir):
os.makedirs(out_dir)
try:
shutil.copy(os.path.realpath(__file__),out_dir)
except:
print "WARNING: could not save source code file"
###############################################################################
#
#
#
#
###############################################################################
def make_dir_if_missing(d):
if not os.path.exists(d):
os.makedirs(d)
###############################################################################
#
#
#
#
###############################################################################
def merge_csv_horizontal(list_csvs,replace):
out_file = shared_dir+os.sep+'ZonalAll.csv'
if arcpy.Exists(out_file) and not(replace):
pass
else:
data = [pandas.DataFrame.from_csv(f) for f in list_csvs]
df = pandas.DataFrame(columns=['VALUE'])
for d in data:
cols = [x for x in d.columns if x not in df.columns or x == 'VALUE']
df = pandas.merge(df, d[cols], on='VALUE', how='outer', suffixes=['',''])
df.to_csv(out_file)
logger.info('\tMerge csv files horizontally')
return out_file
###############################################################################
# merge_csv_files
#
# list_csv_files: List of csv files to merge together one below other
# Only header from topmost csv files is used
# fname: name of output file
###############################################################################
def merge_csv_files(list_csv_files,fname):
write_file = shared_dir+fname+'.csv'
with open(write_file,'w+b') as append_file:
need_headers = True
for input_file in list_csv_files:
with open(input_file,'rU') as read_file:
headers = read_file.readline()
if need_headers:
# Write the headers only if we need them
append_file.write(headers)
need_headers = False
# Now write the rest of the input file.
for line in read_file:
append_file.write(line)
logger.info('\tAppended CSV files')
return write_file
###############################################################################
#
#
#
#
###############################################################################
def dbf_to_csv(file_name):
if file_name.endswith('.dbf'):
logger.info("Converting %s to csv" % file_name)
csv_fn = file_name[:-4]+ ".csv"
with open(csv_fn,'wb') as csvfile:
in_db = dbf.Dbf(file_name)
out_csv = csv.writer(csvfile)
names = []
for field in in_db.header.fields:
names.append(field.name)
out_csv.writerow(names)
for rec in in_db:
out_csv.writerow(rec.fieldData)
in_db.close()
else:
logger.info("\tFilename does not end with .dbf")
return csv_fn
###############################################################################
#
#
#
#
###############################################################################
def filter_raster(state,ras,replace):
tmp_state = shared_dir+'t_'+state+'_'+str(START_YEAR)[2:]+'_'+str(END_YEAR)[2:]
filtered_state = shared_dir+'f_'+state+'_'+str(START_YEAR)[2:]+'_'+str(END_YEAR)[2:]
null_clause = "VALUE < 1"
if arcpy.Exists(tmp_state) and not(replace):
pass
else:
try:
arcpy.gp.FocalStatistics_sa(ras,tmp_state,"Rectangle 5 5 CELL","MAJORITY","DATA")
except:
logger.info(arcpy.GetMessages())
logger.info('\t Filtering small pixels from state '+state)
if arcpy.Exists(filtered_state) and not(replace):
pass
else:
try:
out_null = SetNull(tmp_state,tmp_state,null_clause)
out_null.save(filtered_state)
except:
logger.info(arcpy.GetMessages())
logger.info('\t Nulling the filtered raster from '+state)
return filtered_state
###############################################################################
# extract_luchange_ppr
#
#
#
###############################################################################
def extract_luchange_ppr(state,ras,replace):
clip_ppr = shared_dir+PPR+'_'+state
ppr_vec = base_dir+'geoDB.gdb\\PPR.shp'
if arcpy.Exists(clip_ppr) and not(replace):
pass
else:
try:
arcpy.gp.ExtractByMask_sa(ras,ppr_vec,clip_ppr)
except:
logger.info(arcpy.GetMessages())
logger.info('\t Clipping LU change ras by PPR...'+clip_ppr)
return clip_ppr
###############################################################################
# clip_lu_ras_by_nlcd
#
#
#
###############################################################################
def clip_lu_ras_by_nlcd(state,ras,wtld,replace):
clip_ras = shared_dir+CLIP+'_'+state
if arcpy.Exists(clip_ras) and not(replace):
pass
else:
try:
arcpy.gp.ExtractByMask_sa(ras,wtld, clip_ras)
except:
logger.info(arcpy.GetMessages())
logger.info('\t Clipping LU change ras by buffered wetlands...'+clip_ras)
return clip_ras
###############################################################################
# tabulate_area_ras
#
#
#
###############################################################################
def tabulate_area_ras(state,ras,tab_field,fname,replace):
out_dbf = shared_dir+os.sep+state+fname+'.dbf'
merg_ras = shared_dir+state+'_tab_area'
if arcpy.Exists(out_dbf[:-4]+'.csv') and not(replace):
pass
else:
try:
#TabulateArea(county_shp,'FIPS',ras,'VALUE',out_dbf)
#dbf_to_csv(out_dbf)
# Execute Times
#out_times = Raster(ras) * 100.0
# Save the output
#out_times.save(shared_dir+state+'_mult')
# Execute Int
#out_int = Int(shared_dir+state+'_mult')
# Save the output
#out_int.save(shared_dir+state+'_int')
# Execute Lookup
out_ras = Lookup(ras,tab_field)
# Save the output
out_ras.save(merg_ras)
# Zonal stat
out_zsat = ZonalStatisticsAsTable(county_shp,'FIPS',merg_ras,out_dbf, "DATA", "SUM")
dbf_to_csv(out_dbf)
except:
logger.info(arcpy.GetMessages())
logger.info('\t Tabulating area for ...'+ras)
return out_dbf[:-4]+'.csv'
###############################################################################
# create_buffer_wtld
#
#
#
###############################################################################
def create_buffer_wtld(state,ras,replace):
poly_wtld = shared_dir+NLCD+'_poly_'+state+'.shp'
buff_wtld = shared_dir+NLCD+'_buf_'+state+'.shp'
if arcpy.Exists(buff_wtld) and not(replace):
pass
else:
try:
# Convert ras to vector
arcpy.RasterToPolygon_conversion(ras,poly_wtld,"NO_SIMPLIFY","VALUE")
# Buffer vector
arcpy.Buffer_analysis(poly_wtld,buff_wtld,"500 Meters","FULL","ROUND","NONE","")
except:
logger.info(arcpy.GetMessages())
logger.info('\tBuffering wetlands from nlcd ...'+buff_wtld)
return buff_wtld
###############################################################################
# extract_wetlands_nlcd
#
#
#
###############################################################################
def join_csv_to_ras(state,filtered_ras,ras2,False):
state_csv = shared_dir+os.sep+state+'_filt_luc.csv'
try:
out_CR = shared_dir+os.sep+state+'_CR'
arcpy.CopyRows_management(scsv,out_CR)
arcpy.BuildRasterAttributeTable_management(filtered_ras, "Overwrite")
arcpy.JoinField_management(filtered_ras,"VALUE",ras2,"VALUE","")
fields = ['VALUE','COUNT']
with arcpy.da.SearchCursor(filtered_ras,fields) as cursor:
for row in cursor:
with open(state_csv, 'wb') as csv_file:
csvw = csv.writer(csv_file, delimiter=',')
csvw.writerow(['State','To_Crop'])
csvw.writerow([state,row[1]])
except:
logger.info(arcpy.GetMessages())
logger.info('\tJoin csv to raster ...'+scsv)
return filtered_ras,state_csv
###############################################################################
# extract_wetlands_nlcd
#
#
#
###############################################################################
def extract_wetlands_nlcd(state,replace):
state_vec = vec_dir+state.upper()+'.shp'
tmp_ras = shared_dir+'tmp_'+state
nlcd_tmp = shared_dir+NLCD+'_tmp_'+state
nlcd_wtld = shared_dir+NLCD+'_'+state
nlcd_recl = shared_dir+NLCD+'_recl_'+state
wtld_clause = "\"Value\" = 90 OR \"Value\" = 95"
# Extract NLCD for state
if arcpy.Exists(tmp_ras) and not(replace):
pass
else:
try:
arcpy.gp.ExtractByMask_sa(nlcd_ras,state_vec,tmp_ras)
except:
logger.info(arcpy.GetMessages())
logger.info('\tExtracted for state ...'+state_vec)
# Extract only the wetlands
if arcpy.Exists(nlcd_wtld) and not(replace):
pass
else:
try:
# Execute ExtractByAttributes
nlcd_ext = ExtractByAttributes(tmp_ras, wtld_clause)
nlcd_ext.save(nlcd_tmp)
except:
logger.info(arcpy.GetMessages())
logger.info('\tExtracted wetlands from nlcd ...'+tmp_ras)
# Reclassify wetlands into 1 group
if arcpy.Exists(nlcd_wtld) and not(replace):
pass
else:
try:
out_reclass = ReclassByASCIIFile(nlcd_tmp,NLCD_REMAP,"NODATA")
out_reclass.save(nlcd_recl)
except:
logger.info(arcpy.GetMessages())
logger.info('\tReclassed wetlands from nlcd ...'+nlcd_recl)
# Extract wetlands in PPR
ppr_vec = base_dir+'geoDB.gdb\\PPR.shp'
if arcpy.Exists(nlcd_wtld) and not(replace):
pass
else:
try:
arcpy.gp.ExtractByMask_sa(nlcd_recl,ppr_vec,nlcd_wtld)
except:
logger.info(arcpy.GetMessages())
logger.info('\t Clipping LU change ras by PPR...'+nlcd_wtld)
return nlcd_wtld
###############################################################################
# reclassify_and_combine
#
#
#
###############################################################################
def reclassify_and_combine(state,state_cdl_files,replace):
tmp_comb = shared_dir+os.sep+'t_c_'+state+'_'+str(range_of_yrs[0])[2:]+'_'+str(range_of_yrs[len(range_of_yrs)-1])[2:]
comb_raster = shared_dir+os.sep+'comb_'+state+'_'+str(range_of_yrs[0])[2:]+'_'+str(range_of_yrs[len(range_of_yrs)-1])[2:]
null_raster = shared_dir+os.sep+'null_'+state+'_'+str(range_of_yrs[0])[2:]+'_'+str(range_of_yrs[len(range_of_yrs)-1])[2:]
state_csv = shared_dir+os.sep+state+'_UnFiltered_LUChange.csv'
to_comb_rasters = []
# Create output directory for each state
state_dir = out_dir+os.sep+state+os.sep
make_dir_if_missing(state_dir)
# Reclassify and then extract to get corn/soy and grassland separately
for j in range(len(range_of_yrs)):
recl_raster = shared_dir+RECL+'_'+state+'_'+str(range_of_yrs[j])
# Reclassify raster
if arcpy.Exists(recl_raster) and not(replace):
pass
else:
try:
out_reclass = ReclassByASCIIFile(state_cdl_files[j],REMAP_FILE,"NODATA")
out_reclass.save(recl_raster)
except:
logger.info(arcpy.GetMessages())
to_comb_rasters.append(recl_raster)
logger.info('\tReclassified ...'+recl_raster)
### End For loop
# Combine rasters
if arcpy.Exists(tmp_comb) and not(replace):
pass
else:
try:
out_combine = Combine(to_comb_rasters)
out_combine.save(tmp_comb)
except:
logger.info(arcpy.GetMessages())
logger.info('\tCombined...'+tmp_comb)
# Iterate through raster and output to csv those rows
# with LU change to/from grasslands/crops
if arcpy.Exists(state_csv) and not (replace):
pass
else:
fields = ['RECL_'+state.upper()+"_"+str(START_YEAR),'RECL_'+state.upper()+"_"+str(END_YEAR),'COUNT']
to_crop = 0.0
from_crop = 0.0
with arcpy.da.SearchCursor(tmp_comb,fields) as cursor:
for row in cursor:
# If row[0] <> row[1], then LU change has happened
if(row[0] <> row[1]):
if(row[0]==CROP):
from_crop = row[2]
else:
to_crop = row[2]
else:
continue
with open(state_csv, 'wb') as csv_file:
csvw = csv.writer(csv_file, delimiter=',')
csvw.writerow(['State','To_Crop','From_Crop'])
csvw.writerow([state,to_crop,from_crop])
if arcpy.Exists(null_raster) and not(replace):
pass
else:
try:
where_clause = "(\"RECL_"+state.upper()+"_"+str(START_YEAR)+"\" = "+str(CROP)+" AND \"RECL_"+\
state.upper()+"_"+str(END_YEAR)+"\" = "+str(CROP)+") OR ( \"RECL_"+state.upper()+\
"_"+str(START_YEAR)+"\" = "+str(OPEN)+" AND \"RECL_"+state.upper()+"_"+str(END_YEAR)+\
"\" = "+str(OPEN)+") OR ( \"RECL_"+state.upper()+"_"+str(START_YEAR)+"\" = "+str(OPEN)+\
" AND \"RECL_"+state.upper()+"_"+str(END_YEAR)+"\" = "+str(CROP)+")"
arcpy.gp.Con_sa(tmp_comb,"0",null_raster,tmp_comb,where_clause)
except:
logger.info(arcpy.GetMessages())
logger.info('\tNulled...'+null_raster)
# Replace all NODATA values with 0
if arcpy.Exists(comb_raster) and not(replace):
pass
else:
try:
out_con = Con(IsNull(null_raster),0,null_raster)
out_con.save(comb_raster)
except:
logger.info(arcpy.GetMessages())
logger.info('\tCombined (Nulled NODATA)...'+comb_raster)
return comb_raster, state_csv
###############################################################################
#
#
#
#
###############################################################################
def compute_avg_epic_var(col_name,replace):
ras_gelfand = gelfand_dir+'usnc'
out_CR = shared_dir+os.sep+col_name+'_CR'
# Read in data from Gelfand et al., 2013
gelfand_df = pandas.read_csv(gelfand_dir+'All.csv')
gelfand_df[col_name] *= RAS_MULT
gelfand_df[col_name] = gelfand_df[col_name].astype(int)
gelfand_df = gelfand_df[['VALUE',col_name]]
gelfand_df.to_csv(shared_dir+os.sep+col_name+'.csv')
# Join Gelfand et al. 2013 data to raster
try:
arcpy.CopyRows_management(shared_dir+os.sep+col_name+'.csv',out_CR)
arcpy.BuildRasterAttributeTable_management(ras_gelfand,"Overwrite")
logger.info('\tCopy rows and build raster '+ras_gelfand)
arcpy.JoinField_management(ras_gelfand,"VALUE",out_CR,"VALUE","")
logger.info('\tJoined raster to Gelfand et al data '+ras_gelfand)
except:
logger.info(arcpy.GetMessages())
# Lookup
out_name = shared_dir+os.sep+'r_'+col_name
if arcpy.Exists(out_name) and not(replace):
pass
else:
try:
out_ras = Lookup(ras_gelfand,col_name)
out_ras.save(out_name)
except:
logger.info(arcpy.GetMessages())
logger.info('\tLookup '+out_name)
# Zonal statistics
dbf_file = shared_dir+os.sep+'dbf_'+col_name
if arcpy.Exists(dbf_file) and not(replace):
pass
else:
try:
out_zsat = ZonalStatistics(county_shp,'FIPS',out_name,"MEAN", "DATA")
out_zsat.save(dbf_file)
csv_fn = dbf_to_csv(dbf_file)
except:
logger.info(arcpy.GetMessages())
logger.info('\tZonal stat ' + dbf_file)
return csv_fn
###############################################################################
# main
#
#
#
###############################################################################
if __name__ == "__main__":
# make output dir
make_dir_if_missing(out_dir)
make_dir_if_missing(shared_dir)
# Read in all state names
lines = open(inp_dir+os.sep+list_states, 'rb').readlines()
range_of_yrs = [START_YEAR,END_YEAR]
for subdir, dir_list, files in os.walk(cdl_dir):
break
# Logger
LOG_FILENAME = out_dir+os.sep+'Log_'+TAG+'_'+date+'.txt'
logging.basicConfig(filename = LOG_FILENAME, level=logging.DEBUG,\
format='%(asctime)s %(levelname)s %(module)s - %(funcName)s: %(message)s',\
datefmt="%Y-%m-%d %H:%M:%S") # Logging levels are DEBUG, INFO, WARNING, ERROR, and CRITICAL
logger = logging
# Backup source code
backup_source_code(out_dir)
# N0_WD N0_WS N0_NS N0_NMN N0_WUEF N0_NUF N0_YLDF N68_YLDF N123_YLDF
# N68_WS N123_WS N68_NS N123_NS N68_NUF N123_NUF N68_WUEF N123_WUEF
# N0_DWOC N68_DWOC N123_DWOC N0_Q N68_Q N123_Q N0_DN N68_DN N123_DN
# N0_AVOL N68_AVOL N123_AVOL
# For each variable of interest:
# 1. Multiply by large number to make it integer
# 2. Join data to raster
# 3. Perform Lookup
# 4. Perform Zonal Statistics (Mean) and output to table
# 5. Read table and divide my multiplier used in step 1
list_csv_zonal = []
list_epic_vars = ['N0_YLDF','N68_YLDF','N123_YLDF','N0_DWOC',\
'N68_DWOC','N123_DWOC','N0_DN','N68_DN','N123_DN']
for var in list_epic_vars:
logger.info('\tAveraging EPIC var: '+var)
out_csv = compute_avg_epic_var(var,False)
list_csv_zonal.append(out_csv)
all_csv = merge_csv_horizontal(list_csv_zonal,False)
#tab_gelfand_csv = tabulate_area_ras('WCB',ras_gelfand,'YIELD_N_0','_gelfand_tabulate',True)
pdb.set_trace()
luchange_csvs = []
f_luc_csvs = []
tab_clip_csv = []
tab_jager_csv = []
tab_gelfand_csv = []
# Loop across all states
for line in lines:
state_cdl_files = []
# Find out state name
state = line.split()[0]
print state
logger.info(state)
# Collect all CDL files for state within given year range
for j in range(len(range_of_yrs)):
for position, item in enumerate(dir_list):
if (str(range_of_yrs[j]) in item):
cdl_file = glob.glob(cdl_dir+os.sep+dir_list[position]+os.sep+state+os.sep+'*_'+state+'_*'+str(range_of_yrs[j])+'*.tif')
if cdl_file:
state_cdl_files.append(''.join(cdl_file))
else:
logger.info(cdl_file + 'not found!')
sys.exit(0)
# Set snap extent
if(SET_SNAP):
arcpy.env.snapRaster = state_cdl_files[0]
SET_SNAP = False
logger.info('\tSet snap extent')
# 1. Combine CDL (START_YEAR ... END_YEAR)
comb_raster, scsv = reclassify_and_combine(state,state_cdl_files,False)
luchange_csvs.append(scsv)
# 2. Run majority filter
filtered_ras = filter_raster(state,comb_raster,False)
# 3. Join filtered raster with csv containing LU change info
filtered_ras,fcsv = join_csv_to_ras(state,filtered_ras,comb_raster,False)
f_luc_csvs.append(fcsv)
# 4. Extract wetlands from NLCD and create user-specified buffer
wtld_nlcd = extract_wetlands_nlcd(state,False)
# 5. Create buffer around wetlands
buff_wtld = create_buffer_wtld(state,wtld_nlcd,False)
# 6. Extract LU change in PPR
#ppr_ras = extract_luchange_ppr(state,filtered_ras,True)
# 7. Clip LU change raster by buffered NLCD wetlands
clip_lu_ras = clip_lu_ras_by_nlcd(state,filtered_ras,buff_wtld,False)
# 8. Tabulate area within FIPS zones
tab_clip_csv.append(tabulate_area_ras(state,clip_lu_ras,'VALUE','_clip_tabulate',False))
# 9. Tabulate area for Jager
#ras_jager = jager_dir+'Jager_Maxylds'
#dsc = arcpy.Describe(clip_lu_ras)
#coord_sys = dsc.spatialReference
#arcpy.DefineProjection_management(ras_jager,coord_sys)
#tab_jager_csv.append(tabulate_area_ras(state,ras_jager,'_jager_tabulate',False))
# 10. Tabulate area for Gelfand et al.
ras_gelfand = gelfand_dir+'usnc'
out_CR = shared_dir+os.sep+'Ylds_CR'
try:
arcpy.CopyRows_management(gelfand_dir+'Ylds.csv',out_CR)
arcpy.BuildRasterAttributeTable_management(ras_gelfand, "Overwrite")
arcpy.JoinField_management(ras_gelfand,"VALUE",out_CR,"VALUE","")
except:
print arcpy.GetMessages()
tab_gelfand_csv = tabulate_area_ras('WCB',ras_gelfand,'YIELD_N_0','_gelfand_tabulate',True)
# Output to-from land-use change information into csv
merge_csv_files(luchange_csvs,'WCB_UnFilt_LUC')
merge_csv_files(f_luc_csvs,'WCB_Filt_LUC')
merge_csv_files(tab_clip_csv,'WCB_Tabulate_LUC')