def RastersToSqlitePoint(path,
vecteur,
field,
outname,
ram,
rtype,
rasters,
maskmer=None,
split=None):
timeinit = time.time()
# Rasters concatenation
if len(rasters) > 1:
concatApp = OtbAppBank.CreateConcatenateImagesApplication({
"il":
rasters,
"ram":
ram,
"pixType":
rtype
})
concatApp.Execute()
classif = OtbAppBank.CreateBandMathApplication({
"il": rasters[0],
"exp": "im1b1",
"ram": ram,
"pixType": rtype
})
classif.Execute()
else:
concatApp = OtbAppBank.CreateBandMathApplication({
"il": rasters,
"exp": "im1b1",
"ram": ram,
"pixType": rtype
})
concatApp.Execute()
timeconcat = time.time()
print " ".join([
" : ".join(["Raster concatenation",
str(timeconcat - timeinit)]), "seconds"
])
# Stats and sample selection
if len(rasters) == 1:
classif = concatApp
outsqlite = sampleSelection(path, classif, vecteur, field, ram, split,
maskmer)
# Stats extraction
outtmp = os.path.join(path, os.path.basename(outname))
sampleExtraction(concatApp, outsqlite, field, outtmp, split, ram)
shutil.copyfile(outtmp, outname)
def extractStats(vectorIn, pathConf, wD=None):
dataField = Config(open(pathConf)).chain.dataField
iota2Folder = Config(open(pathConf)).chain.outputPath
tileToCompute = vectorIn.split("/")[-1].split("_")[0]
modelToCompute = vectorIn.split("/")[-1].split("_")[2].split("f")[0]
seed = vectorIn.split("/")[-1].split("_")[3].replace("seed", "")
workingDirectory = iota2Folder + "/final/TMP"
shapeMode = vectorIn.split("/")[-1].split("_")[-1].split(".")[
0] #'learn' or 'val'
if wD:
workingDirectory = wD
try:
refImg = fut.FileSearch_AND(iota2Folder + "/final/TMP", True,
tileToCompute, ".tif")[0]
except:
raise Exception("reference image can not be found in " + iota2Folder +
"/final/TMP")
statsFile = workingDirectory + "/" + tileToCompute + "_stats_model_" + modelToCompute + ".xml"
stats = otbApp.CreatePolygonClassStatisticsApplication({"in":refImg, "vec":vectorIn,\
"out":statsFile, "field":dataField})
stats.ExecuteAndWriteOutput()
selVector = workingDirectory + "/" + tileToCompute + "_selection_model_" + modelToCompute + ".sqlite"
sampleS = otbApp.CreateSampleSelectionApplication({"in":refImg, "vec":vectorIn, "out":selVector,\
"instats":statsFile, "strategy":"all",\
"field":dataField})
sampleS.ExecuteAndWriteOutput()
classificationRaster = fut.FileSearch_AND(
iota2Folder + "/final/TMP", True,
tileToCompute + "_seed_" + seed + ".tif")[0]
validity = fut.FileSearch_AND(iota2Folder + "/final/TMP", True,
tileToCompute + "_Cloud.tif")[0]
confiance = fut.FileSearch_AND(
iota2Folder + "/final/TMP", True,
tileToCompute + "_GlobalConfidence_seed_" + seed + ".tif")[0]
stack = [classificationRaster, validity, confiance]
dataStack = otbApp.CreateConcatenateImagesApplication({
"il": stack,
"ram": '1000',
"pixType": "uint8",
"out": ""
})
dataStack.Execute()
outSampleExtraction = workingDirectory + "/" + tileToCompute + "_extraction_model_" + modelToCompute + "_" + shapeMode + ".sqlite"
extraction = otbApp.CreateSampleExtractionApplication({"in":dataStack, "vec":selVector,\
"field":dataField, " out":outSampleExtraction,\
"outfield":"list",\
"outfield.list.names":["predictedClass", "validity", "confidence"]})
extraction.ExecuteAndWriteOutput()
conn = lite.connect(outSampleExtraction)
cursor = conn.cursor()
SQL = "alter table output add column TILE TEXT"
cursor.execute(SQL)
SQL = "update output set TILE='" + tileToCompute + "'"
cursor.execute(SQL)
SQL = "alter table output add column MODEL TEXT"
cursor.execute(SQL)
SQL = "update output set MODEL='" + modelToCompute + "'"
cursor.execute(SQL)
conn.commit()
os.remove(statsFile)
os.remove(selVector)
if wD:
shutil.copy(outSampleExtraction, iota2Folder + "/final/TMP")
def clumpAndStackClassif(path,
raster,
outpath,
ram,
float64=False,
exe64="",
logger=logger):
begin_clump = time.time()
# split path and file name of outfilename
out = os.path.dirname(outpath)
outfilename = os.path.basename(outpath)
# Clump Classif with OTB segmentation algorithm
clumpAppli = OtbAppBank.CreateClumpApplication({
"in":
raster,
"filter.cc.expr":
'distance<1',
"ram":
str(0.2 * float(ram)),
"pixType":
'uint32',
"mode":
"raster",
"filter":
"cc",
"mode.raster.out":
os.path.join(path, 'clump.tif')
})
if not float64:
clumpAppli.Execute()
clumptime = time.time()
logger.info(" ".join([
" : ".join(
["Input raster well clumped : ",
str(clumptime - begin_clump)]), "seconds"
]))
# Add 300 to all clump ID
bandMathAppli = OtbAppBank.CreateBandMathApplication({
"il":
clumpAppli,
"exp":
'im1b1+300',
"ram":
str(0.2 * float(ram)),
"pixType":
'uint32',
"out":
os.path.join(path, 'clump300.tif')
})
bandMathAppli.Execute()
dataRamAppli = OtbAppBank.CreateBandMathApplication({
"il":
raster,
"exp":
'im1b1',
"ram":
str(0.2 * float(ram)),
"pixType":
'uint8'
})
dataRamAppli.Execute()
concatImages = OtbAppBank.CreateConcatenateImagesApplication({
"il": [dataRamAppli, bandMathAppli],
"ram":
str(0.2 * float(ram)),
"pixType":
'uint32',
"out":
os.path.join(path, outfilename)
})
concatImages.ExecuteAndWriteOutput()
concattime = time.time()
logger.info(" ".join([
" : ".join([
"Regularized and Clumped rasters concatenation : ",
str(concattime - clumptime)
]), "seconds"
]))
shutil.copyfile(os.path.join(path, outfilename),
os.path.join(out, outfilename))
else:
clumpAppli.ExecuteAndWriteOutput()
command = '%s/iota2BandMath %s "%s" %s %s'%(exe64, \
os.path.join(path, 'clump.tif'), \
"im1b1+300", \
os.path.join(path, 'clump300.tif'), \
10)
try:
Utils.run(command)
clumptime = time.time()
logger.info(" ".join([
" : ".join([
"Input raster well clumped : ",
str(clumptime - begin_clump)
]), "seconds"
]))
except:
logger.error(
"Application 'iota2BandMath' for 64 bits does not exist, please change 64 bits binaries path"
)
sys.exit()
command = '%s/iota2ConcatenateImages %s %s %s %s'%((exe64,
raster, \
os.path.join(path, 'clump300.tif'), \
os.path.join(path, outfilename),
10))
try:
Utils.run(command)
concattime = time.time()
logger.info(" ".join([" : ".join(["Regularized and Clumped rasters concatenation : ", \
str(concattime - clumptime)]), "seconds"]))
shutil.copyfile(os.path.join(path, outfilename),
os.path.join(out, outfilename))
os.remove(os.path.join(path, 'clump.tif'))
os.remove(os.path.join(path, 'clump300.tif'))
except:
logger.error(
"Application 'iota2ConcatenateImages' for 64 bits does not exist, please change 64 bits binaries path"
)
sys.exit()
command = "gdal_translate -q -b 2 -ot Uint32 %s %s" % (os.path.join(
path, outfilename), os.path.join(path, "clump32bits.tif"))
Utils.run(command)
shutil.copy(os.path.join(path, "clump32bits.tif"), out)
os.remove(os.path.join(path, "clump32bits.tif"))
if os.path.exists(os.path.join(path, outfilename)):
os.remove(os.path.join(path, outfilename))
clumptime = time.time()
logger.info(" ".join(
[" : ".join(["Clump : ", str(clumptime - begin_clump)]), "seconds"]))