def import_file(self, in_file, out_file):
"""
Import Image and auxiliary information
Detailed description
Imports the image and all auxiliary information from a source file
to a newly created PCIDSK file
Parameters:
in_file -- Input file
out_file -- Output file
Return value:
Error statement if error occurs.
Limits and constraints:
"""
try:
logging.info(' Executing: OrthoMosaic.import_file')
dbiw = []
poption = "NEAR"
dblayout = "BAND"
fimport(in_file, out_file, dbiw, poption, dblayout)
logging.info(' Successfully completed OrthoMosaic.import_file: fimport')
except PCIException, e:
EGS_utility.EGSUtility().error('import_file(): {:s}'.format(e))
def readtopix(indir):
infiles = os.listdir(indir) # List input folders
for i in range(len(infiles)): # Add path for 10m S2 Bands
infiles[i] = "input/" + infiles[
i] + "/MTD_MSIL1C.xml?r=%3ABand+Resolution%3A10M"
pix = "pix/tile" + str(i) + ".pix" # Name converted pix output
pixfiles.append(pix) # Add to list of pix files
fili = infiles[i]
print "\tStarting pix conversion file %s" % str(i)
fimport(fili, pix) # Run import function
print "\tPix conversion completed for %s:" % infiles[i]
print "\tOutput to %s" % pix
def readtopix(inputdir):
infiles = os.listdir(inputdir) # List input folders
for i in range(len(infiles)): # Add paths for S2 band sets
fili_10 = "input/" + infiles[
i] + "/MTD_MSIL1C.xml?r=%3ABand+Resolution%3A10M"
fili_20 = "input/" + infiles[
i] + "/MTD_MSIL1C.xml?r=%3ABand+Resolution%3A20M"
fili_60 = "input/" + infiles[
i] + "/MTD_MSIL1C.xml?r=%3ABand+Resolution%3A60M"
name_fields = infiles[i].split("_") # Set up fields for filenames
mission = name_fields[0]
date = (name_fields[2])[:8]
if name_fields[
1] == "OPER": # Long-format naming scheme from 2015-2016
date = (name_fields[5])[:8]
findpath = os.path.join(indir, infiles[i])
find_xml = os.listdir(findpath)
for j in range(len(find_xml)):
if find_xml[j][-3:] == "xml" and find_xml[j] != "INSPIRE.xml":
xml_name = find_xml[j]
fili_10 = "input/" + infiles[
i] + "/" + xml_name + "?r=%3ABand+Resolution%3A10M"
fili_20 = "input/" + infiles[
i] + "/" + xml_name + "?r=%3ABand+Resolution%3A20M"
fili_60 = "input/" + infiles[
i] + "/" + xml_name + "?r=%3ABand+Resolution%3A60M"
pix10full = "pix/" + mission + "_" + date + "_10m_full.pix" # Set up paths for functions
pix20full = "pix/" + mission + "_" + date + "_20m_full.pix"
pix60full = "pix/" + mission + "_" + date + "_60m_full.pix"
pix10 = "pix/" + mission + "_" + date + "_10m_unmerged.pix"
pix20 = "pix/" + mission + "_" + date + "_20m_unmerged.pix"
pix_merged = "pix/" + mission + "_" + date + "_10m_merged.pix"
pix60 = "pix/" + mission + "_" + date + "_60m_atmospheric.pix"
start_time = time.time()
print "Starting pix conversion file %s_%s." % (mission, date)
fimport(fili_10, pix10full) # Import R,G,B,NIR bands
fimport(fili_20, pix20full) # Import RE,NIR,SWIR bands
fimport(fili_60, pix60full) # Import Coastal, Vapour, Cirrus
clip(
fili=pix10full, # Clip 10m bands
dbic=[1, 2, 3, 4],
dbsl=[],
sltype="",
filo=pix10,
ftype="PIX",
foptions="",
clipmeth="LAYERVEC",
clipfil=clipvec,
cliplay=[2])
clip(
fili=pix20full, # Clip 20m bands
dbic=[1, 2, 3, 4, 5, 6],
dbsl=[],
sltype="",
filo=pix20,
ftype="PIX",
foptions="",
clipmeth="LAYERVEC",
clipfil=clipvec,
cliplay=[2])
clip(
fili=pix60full, # Clip 60m bands
dbic=[1, 2, 3],
dbsl=[],
sltype="",
filo=pix60,
ftype="PIX",
foptions="",
clipmeth="LAYERVEC",
clipfil=clipvec,
cliplay=[2])
os.remove(pix10full) # Delete un-clipped images
os.remove(pix20full)
os.remove(pix60full)
# The order of data in merge list file matters:
# 10m bands first results in resampling of 20m resolution
# to 10m resolution. Avoids data loss due to resampling of 10m to 20.
mergefile_name = mission + "_" + date + "_merge.txt"
mergefile_path = os.path.join(mergedir, mergefile_name)
path10 = os.path.join(workingdir, pix10)
path20 = os.path.join(workingdir, pix20)
mergefile = open(mergefile_path, "w")
mergefile.write('"' + path10 + '"' + "\n")
mergefile.write('"' + path20 + '"')
mergefile.close()
datamerge(
mfile=
mergefile_path, # Merge 10m bands and 20m bands into one pix file
dbic=[],
filo=pix_merged,
ftype="PIX",
foptions="",
extent="UNION",
nodatval=[],
resample="NEAR")
completion_time = time.time() - start_time
print "Pix conversion completed for image %s_%s in %i seconds." % (
mission, date, completion_time)
print "Wrote files to:\n\t%s\n\t%s\n\t%s\n\t%s\n" % (pix_merged, pix10,
pix20, pix60)
def merge_filter_export(self, in_file, in_file2, out_file, out_file2, out_file3, hole_size):
"""
Imports, merges, filters and exports flooded products.
Import flood products into PCIPIX format, merge products, filters to remove holes / areas.
Outputs resulting products as compressed geotif and shapefile.
Merges image value polygons smaller than a user-specified
threshold with the largest neighboring polygon
Parameters:
in_file -- Input file1
in_file2 -- Input file2
out_file -- Working PCIPIX file
out_file2 -- Resuling output geotif
hole_size -- threshold for filter (hectares)
Return value:
Error statement if error occurs.
"""
#import required PCI Geomatica modules
import pci
from pci.sieve import *
from pci.fimport import *
from pci.fexport import *
from pci.thmrovr import *
from pci.mosaic import *
from pci.thmrmer import *
from pci.model import *
from pci.nspio import Report, enableDefaultReport
from pci.exceptions import PCIException
from pci.ras2poly import *
import arcpy
from osgeo import gdal, ogr, osr
from gdalconst import GA_Update
try:
util = EGS_utility.EGSUtility()
#Import first image (flooded vegetation) into PCIPIX file
logging.info(' Executing: MergeProcess.merge_filter_export')
fili = in_file
filo = out_file
dbiw = []
poption = ""
dblayout = "" #Defaults to "BAND"
Report.clear()
fimport(fili, filo, dbiw, poption, dblayout)
enableDefaultReport('term')
logging.info(' Successfully completed MergeProcess.merge_filter_export: fimport')
#Import second image (open water) into PCIPIX file
new_chans = EGS_utility.EGSUtility().add_8_channel(out_file)
fili = in_file2
dbic = [1] # use channel 1
dbvs = [] # default, no cutline defined
dblut = [] # default, no lookup table
filo = out_file
dboc = [int(new_chans[0])] # overwrite channel 1
blend = [] # default, no blending
backval = [] # default, 0
mosaic( fili, dbic, dbvs, dblut, filo, dboc, blend, backval )
logging.info(' Successfully completed MergeProcess.merge_filter_export: mosaic')
# Convert values using MODEL so 255 = 0
file = out_file
source_model = """if (%2 = 255) then
%2 = 0
endif"""
model( file, source=source_model)
#Merge two image together, possible use thmrovr for one step instead of two
merge_chan = util.add_8_channel(out_file)
fili = out_file # input file
filo = out_file # output file will be created
dbic = [1,int(new_chans[0])] # input thematic raster channels
dbib = [] # no bitmap mask
dboc = [int(merge_chan[0])]
omethod = "UNION" # default, "UNION"
thmrovr( fili, filo, dbic, dbib, dboc, omethod )
logging.info(' Successfully completed MergeProcess.merge_filter_export: thmrovr')
# Combine values using MODEL so zero = not flooded, 255 = flooded
file = out_file
source_model = """if (%3 >= 1) then
%3 = 255
endif"""
model( file, source=source_model)
#Determine filter size as pixel number
filtered_chan = util.add_8_channel(out_file)
pixelwidth = util.gdal_geotransform(out_file)[1]
pixelheight = util.gdal_geotransform(out_file)[5]
logging.info(' pixelwidth: ' + str(pixelwidth))
logging.info(' pixelheight: ' + str(pixelheight))
num_pixel = int((hole_size * 10000)/abs(pixelwidth * pixelheight)) # hole_size is in hectares
logging.info(' Number of pixels for threshold hole size: ' + str(num_pixel))
#Filter in order to remove holes
file = out_file
dbic = [int(merge_chan[0])]
dboc = [int(filtered_chan[0])]
sthresh = [num_pixel] # polygon size threshold in
keepvalu = [] # no keep value
connect = [] # default, 4-connection
sieve( file, dbic, dboc, sthresh, keepvalu, connect )
logging.info(' Successfully completed MergeProcess.merge_filter_export: sieve')
#EGS_utility.EGSUtility().raster_his(out_file,int(filtered_chan[0]))
#Export resulting product as a geotif
fili = out_file
filo = out_file2
dbiw = []
dbic = [int(filtered_chan[0])]
dbib = []
dbvs = []
dblut = []
dbpct = []
ftype = "tif"
foptions = "LZW"
fexport( fili, filo, dbiw, dbic, dbib, dbvs, dblut, dbpct, ftype, foptions )
logging.info(' Successfully completed MergeProcess.merge_filter_export: fexport')
fili = out_file # input raster file
dbic = [int(filtered_chan[0])] # using channel 6 from irvine.pix
filo = out_file # output file to be created
smoothv = "" # default, YES vectors are smoothed
dbsd = "" # defaults to "Created from Raster"
ftype = "" # default, PIX
foptions = "" # output format options
ras2poly(fili, dbic, filo, smoothv, dbsd, ftype, foptions)
logging.info(' Successfully completed MergeProcess.merge_filter_export: ras2poly')
# Export resulting product as a shapefile
# PCI creates shapefile with projection 'UTM 18 S E008 ', compared to 'UTM 18 T D122'
# These projections are the same projection, as E008 is the ellipsoid used by NAD 1983.
# but opted for arcpy export
fili = out_file
filo = out_file3
dbiw = []
dbic = []
dbib = []
dbvs = [3]
dblut = []
dbpct = []
ftype = "shp"
foptions = ""
#fexport( fili, filo, dbiw, dbic, dbib, dbvs, dblut, dbpct, ftype, foptions )
arcpy.RasterToPolygon_conversion(out_file2, out_file3, "NO_SIMPLIFY", "")
logging.info(' Successfully completed MergeProcess.merge_filter_export: arcpy.RasterToPolygon_conversion')
except PCIException, e:
EGS_utility.EGSUtility().error('merge_filter_export(): {:s}'.format(e))
folderz(report_dir)
folderz(final_dir)
print(' ...Part 1 completed')
#------------------------------------------
# Part2: Clip Imagery with SHP file
#------------------------------------------
print("... Part 2: Clipping Scene")
#make a list for shp file of clipping area
input_shp = (makelist(rootdir =working_dir, suffix = '.shp'))
#import shp file as pix with one vector layer
for shp in input_shp:
try:
fili = shp
filo = working_dir + "/" + "clip_pix" + "/" +"clip.pix"
fimport(fili, filo)
except PCIException as e:
print (e)
except Exception as e:
print (e)
# clip scene using pix file with the vector layer
input_meta = (makelist(rootdir = working_dir, suffix = 'MTL.txt'))
for image in input_meta:
try:
fili ='-'.join([image, 'MS'])
dbic = [1,2,3,4,5,6]
dbsl = []
sltype = ""
filo = clip_scene + '/' + "scene_clipped.pix"
ftype = "PIX"