def populateSegmentsMeanStdDev(inputImage, clumpsImg, colNamePrefix, bandlist, bandnames): """ A function to populate mean and standard deviation values as columns within the attribute table for a single band image. """ # Create an empty list bandStats = [] # Define the statistics to be calculated for the band and the field names # If the input image had mulitple image bands for which you wished to # calculate statistics you need to duplicate this line and change the # band number and field names. #colNamePrefix = 'h'+colNamePrefix for i in range(len(bandlist)): # bandStats.append(rastergis.BandAttStats(band=bandlist[i], minField = colNamePrefix+bandnames[i]+'_Min', maxField = colNamePrefix+bandnames[i]+'_Max', meanField=colNamePrefix+bandnames[i]+'_Mean', stdDevField=colNamePrefix+bandnames[i]+'_StdDev', medianField=colNamePrefix+bandnames[i]+'_Median')) bandStats.append(rastergis.BandAttStats(band=bandlist[i], minField = colNamePrefix+bandnames[i]+'_Min', maxField = colNamePrefix+bandnames[i]+'_Max', meanField=colNamePrefix+bandnames[i]+'_Mean', stdDevField=colNamePrefix+bandnames[i]+'_StdDev')) # Run the RSGISLib command with the input parameters. rastergis.populateRATWithStats(inputImage, clumpsImg, bandStats)
def segmentation(imagery_files, config):
dev_mode = config['dev_mode']
for element in imagery_files:
inputImage_difference = imagery_files[element][0]
inputImage_post = imagery_files[element][1]
inputImage_color = inputImage_post
nameFile = (element) + "_segmented"
clumpsFile = config['k_means_segmentation']['output'][
'segments'] + nameFile + '.kea'
# Run segmentation_file.py algorithm
segutils.runShepherdSegmentation(
inputImage_difference,
clumpsFile,
tmpath=config['k_means_segmentation']['temps']['shepherd'],
numClusters=config['k_means_segmentation']['params']
['numClusters'],
minPxls=config['k_means_segmentation']['params']['minPxls'],
distThres=config['k_means_segmentation']['params']['distThres'],
bands=[1],
sampling=config['k_means_segmentation']['params']['sampling'],
kmMaxIter=config['k_means_segmentation']['params']['kmMaxIter'])
# Features extraction and computation of statistical measures
# Feature from Image difference
bs = [rastergis.BandAttStats(band=1, meanField='ratio_rg_change')]
rastergis.populateRATWithStats(inputImage_difference, clumpsFile, bs)
bs = [rastergis.BandAttStats(band=2, meanField='ndvi_change')]
rastergis.populateRATWithStats(inputImage_difference, clumpsFile, bs)
bs = [rastergis.BandAttStats(band=3, meanField='brightness_change')]
rastergis.populateRATWithStats(inputImage_difference, clumpsFile, bs)
# Feature from post_image
bs = [
rastergis.BandAttStats(band=1, meanField='B4'),
rastergis.BandAttStats(band=2, meanField='B3'),
rastergis.BandAttStats(band=3, meanField='B2'),
rastergis.BandAttStats(band=4, meanField='B8'),
rastergis.BandAttStats(band=5, meanField='ndvi'),
rastergis.BandAttStats(band=6,
maxField='slope_max',
meanField='slope_mean'),
rastergis.BandAttStats(band=7,
meanField='mean_height',
minField='min_height',
maxField='max_height'),
rastergis.BandAttStats(band=8, meanField='nd_stdDev'),
rastergis.BandAttStats(band=12, meanField='gndvi'),
rastergis.BandAttStats(band=13, meanField='brightness')
]
rastergis.populateRATWithStats(inputImage_color, clumpsFile, bs)
add_Coordinates(clumpsFile)
if dev_mode:
input_training = imagery_files[element][2]
add_Training(clumpsFile, input_training, config)
reading_tables(clumpsFile, element, nameFile,
config['k_means_segmentation']['output']['tables'],
config)
outKEAFile = inSHPFile.replace('.shp', '_raster.' + outExt)
# Check if KEA file exists or needs creating - assume if it exists it has the attribute table already
if os.path.exists(outKEAFile) == False:
# Rasterize polygon using gdal
print('Creating raster')
rasterizeCommand = ['gdal_rasterize', '-of', outFormat,
'-ot', 'UInt32',
'-tr', outXRes, outYRes,
'-a', 'MUKEY',
inSHPFile, outKEAFile]
subprocess.call(rasterizeCommand)
# Convert to RAT and add entry 'mukey' using RSGISLib
rastergis.populateStats(outKEAFile, True, True)
stats2Calc = [rastergis.BandAttStats(band=1, minField='mukey')]
rastergis.populateRATWithStats(outKEAFile, outKEAFile, stats2Calc)
# Iterate through column names
for outColName in args.colname:
# Set up name for standard raster file
outRasterImage = inSHPFile.replace('.shp', '_raster_' + outColName + '.' + outExt)
# Get field from dictionary
outColNum = cHorizonFields[outColName.strip()]
# JOIN ATTRIBUTES FROM TEXT FILE
print('Adding ' + outColName + ' (column ' + str(outColNum) + ') to RAT')
# Open SSURGO text files
componentFileName = os.path.join(inDIRName, 'tabular', 'comp.txt')
chorizonFileName = os.path.join(inDIRName, 'tabular', 'chorizon.txt')
import rsgislib from rsgislib import rastergis ############################################################################################## write stats from texture image to RAT from clumps clumps='S1B_20170728_stack_lee_clip_clumps2.kea' texture='S1B_20170728_stack_lee_clip_txt9.kea' bs = [] bs.append(rastergis.BandAttStats(band=2, minField='VHtxtMin', maxField='VHtxtb1Max', meanField='VHtxtMean', sumField='VHtxtSum', stdDevField='VHtxtStdDev')) rastergis.populateRATWithStats(texture, clumps, bs)
def colour_SM_image(inimage, colourimage, max_value=0.5, band=1):
"""
Colour image
"""
try:
import rsgislib
from rsgislib import imagecalc
from rsgislib.imagecalc import BandDefn
from rsgislib import rastergis
except ImportError:
raise ImportError("Could not import RSGISLib, required"
" to colour image")
if max_value == 0.5:
# Add class field:
bandDefns = []
bandDefns.append(BandDefn('SM', inimage, band))
expression = []
expression.append('0.00')
expression.append('(SM > 0.00) && (SM <= 0.05)? 1 : 0')
expression.append('(SM > 0.05) && (SM <= 0.10)? 2 : 0')
expression.append('(SM > 0.10) && (SM <= 0.15)? 3 : 0')
expression.append('(SM > 0.15) && (SM <= 0.20)? 4 : 0')
expression.append('(SM > 0.20) && (SM <= 0.25)? 5 : 0')
expression.append('(SM > 0.25) && (SM <= 0.30)? 6 : 0')
expression.append('(SM > 0.30) && (SM <= 0.35)? 7 : 0')
expression.append('(SM > 0.35) && (SM <= 0.40)? 8 : 0')
expression.append('(SM > 0.40) && (SM <= 0.45)? 9 : 0')
expression.append('(SM > 0.45) && (SM <= 0.50)? 10 : 0')
gdalformat = get_gdal_format(colourimage)
datatype = rsgislib.TYPE_8INT
temp_dir = tempfile.mkdtemp(prefix='soilscape_upscaling')
colourbase = os.path.basename(colourimage)
colourbase, colourext = os.path.splitext(colourbase)
colour = []
for i in range(11):
colour.append(
os.path.join(temp_dir,
"{}_{}{}".format(colourbase, i + 1, colourext)))
imagecalc.bandMath(colour[i], expression[i], gdalformat, datatype,
bandDefns)
bandDefns = []
for i in range(11):
SMclass = 'SM' + str(i)
bandDefns.append(BandDefn(SMclass, colour[i], 1))
if i == 0:
expression = SMclass
else:
expression = expression + '+' + SMclass
imagecalc.bandMath(colourimage, expression, gdalformat, datatype,
bandDefns)
shutil.rmtree(temp_dir)
# Populate stats (converts to RAT):
rastergis.populateStats(colourimage, False, False, True, ratband=1)
# Add class field:
bandStats = []
bandStats.append(rastergis.BandAttStats(band=1, maxField="SMclass"))
rastergis.populateRATWithStats(colourimage,
colourimage,
bandStats,
ratband=1)
field = 'SMclass'
classcolours = {}
colourCat = collections.namedtuple('ColourCat',
['red', 'green', 'blue', 'alpha'])
for i in range(11):
classcolours[i] = colourCat(red=0, green=0, blue=0, alpha=255)
classcolours[0] = colourCat(red=0, green=0, blue=0, alpha=255)
classcolours[1] = colourCat(red=165, green=0, blue=38, alpha=255)
classcolours[2] = colourCat(red=215, green=48, blue=39, alpha=255)
classcolours[3] = colourCat(red=244, green=109, blue=67, alpha=255)
classcolours[4] = colourCat(red=253, green=174, blue=97, alpha=255)
classcolours[5] = colourCat(red=254, green=224, blue=144, alpha=255)
classcolours[6] = colourCat(red=224, green=243, blue=248, alpha=255)
classcolours[7] = colourCat(red=171, green=217, blue=233, alpha=255)
classcolours[8] = colourCat(red=116, green=173, blue=209, alpha=255)
classcolours[9] = colourCat(red=69, green=117, blue=180, alpha=255)
classcolours[10] = colourCat(red=49, green=54, blue=149, alpha=255)
rastergis.colourClasses(colourimage, field, classcolours)
else:
raise ValueError('Failed to find colours for specified max_value')
def createMinDataTiles(inputImage,
outshp,
outclumpsFile,
width,
height,
validDataThreshold,
maskIntersect=None,
offset=False,
force=True,
tmpdir='tilestemp',
inImgNoDataVal=0.0):
"""
A function to create a tiling for an input image where each tile has a minimum amount of valid data.
Where:
:param inputImage: is a string for the image to be tiled
:param outshp: is a string for the output shapefile the tiling will be written to (if None a shapefile won't be outputted).
:param outclumpsFile: is a string for the output image file containing the tiling
:param width: is an int for the width of the tiles
:param height: is an int for the height of the tiles
:param validDataThreshold: is a float (0-1) with the proportion of valid data needed within a tile.
:param force: is a boolean (default True) to delete the output shapefile if it already exists.
:param tmpdir: is a string with a temporary directory for temp outputs to be stored (they will be deleted).
if tmpdir doesn't exist it will be created and then deleted during the processing.
:param inImgNoDataVal: is a float for providing the input image no data value (Default: 0.0)
"""
tmpPresent = True
if not os.path.exists(tmpdir):
print("WARNING: tmpdir directory does not exist so creating it...")
os.makedirs(tmpdir)
tmpPresent = False
inImgBaseName = os.path.splitext(os.path.basename(inputImage))[0]
tileClumpsImage = os.path.join(tmpdir, inImgBaseName + '_tilesimg.kea')
segmentation.generateRegularGrid(inputImage, tileClumpsImage, 'KEA', width,
height, offset)
rastergis.populateStats(tileClumpsImage, True, True)
if not maskIntersect == None:
bs = []
bs.append(rastergis.BandAttStats(band=1, maxField='Mask'))
rastergis.populateRATWithStats(maskIntersect, tileClumpsImage, bs)
ratDS = gdal.Open(tileClumpsImage, gdal.GA_Update)
MaskField = rat.readColumn(ratDS, "Mask")
Selected = numpy.zeros_like(MaskField, dtype=int)
Selected[MaskField == inImgNoDataVal] = 1
rat.writeColumn(ratDS, "Selected", Selected)
ratDS = None
tileClumpsImageDropClumps = os.path.join(
tmpdir, inImgBaseName + '_tilesimgdropped.kea')
segmentation.dropSelectedClumps(tileClumpsImage,
tileClumpsImageDropClumps, 'KEA',
'Selected')
os.remove(tileClumpsImage)
tileClumpsImage = tileClumpsImageDropClumps
rastergis.populateRATWithPropValidPxls(inputImage, tileClumpsImage,
"ValidPxls", inImgNoDataVal)
ratDS = gdal.Open(tileClumpsImage, gdal.GA_Update)
ValidPxls = rat.readColumn(ratDS, "ValidPxls")
Selected = numpy.zeros_like(ValidPxls, dtype=int)
NoDataClumps = numpy.zeros_like(ValidPxls, dtype=int)
Selected[ValidPxls < validDataThreshold] = 1
NoDataClumps[ValidPxls == 0] = 1
Selected[ValidPxls == 0] = 0
rat.writeColumn(ratDS, "Selected", Selected)
rat.writeColumn(ratDS, "NoDataClumps", NoDataClumps)
ratDS = None
segmentation.mergeSegments2Neighbours(tileClumpsImage, inputImage,
outclumpsFile, 'KEA', "Selected",
"NoDataClumps")
if not outshp is None:
tilesDS = gdal.Open(outclumpsFile, gdal.GA_ReadOnly)
tilesDSBand = tilesDS.GetRasterBand(1)
dst_layername = os.path.splitext(os.path.basename(outshp))[0]
#print(dst_layername)
drv = ogr.GetDriverByName("ESRI Shapefile")
if force and os.path.exists(outshp):
drv.DeleteDataSource(outshp)
dst_ds = drv.CreateDataSource(outshp)
dst_layer = dst_ds.CreateLayer(dst_layername, srs=None)
gdal.Polygonize(tilesDSBand,
tilesDSBand,
dst_layer,
-1, [],
callback=None)
tilesDS = None
dst_ds = None
if not tmpPresent:
shutil.rmtree(tmpdir, ignore_errors=True)
else:
os.remove(tileClumpsImage)