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377b181c4e
Also - simplify and add tests - remove large memory leak (persistant store of all non-project layers) - remove broken support for direct loading postgres/virtual layers by string (Python version was very broken and would never match a postgres/virtual layer)
279 lines
11 KiB
Python
279 lines
11 KiB
Python
# -*- coding: utf-8 -*-
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"""
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***************************************************************************
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ZonalStatistics.py
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---------------------
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Date : August 2013
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Copyright : (C) 2013 by Alexander Bruy
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Email : alexander dot bruy at gmail dot com
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***************************************************************************
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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***************************************************************************
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"""
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from builtins import str
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__author__ = 'Alexander Bruy'
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__date__ = 'August 2013'
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__copyright__ = '(C) 2013, Alexander Bruy'
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# This will get replaced with a git SHA1 when you do a git archive
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__revision__ = '$Format:%H$'
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import numpy
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try:
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from scipy.stats.mstats import mode
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hasSciPy = True
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except:
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hasSciPy = False
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from osgeo import gdal, ogr, osr
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from qgis.core import (QgsApplication,
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QgsRectangle,
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QgsGeometry,
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QgsFeature)
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from processing.core.GeoAlgorithm import GeoAlgorithm
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from processing.core.parameters import ParameterVector
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from processing.core.parameters import ParameterRaster
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from processing.core.parameters import ParameterString
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from processing.core.parameters import ParameterNumber
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from processing.core.parameters import ParameterBoolean
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from processing.core.outputs import OutputVector
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from processing.tools.raster import mapToPixel
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from processing.tools import dataobjects, vector
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class ZonalStatistics(GeoAlgorithm):
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INPUT_RASTER = 'INPUT_RASTER'
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RASTER_BAND = 'RASTER_BAND'
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INPUT_VECTOR = 'INPUT_VECTOR'
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COLUMN_PREFIX = 'COLUMN_PREFIX'
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GLOBAL_EXTENT = 'GLOBAL_EXTENT'
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OUTPUT_LAYER = 'OUTPUT_LAYER'
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def icon(self):
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return QgsApplication.getThemeIcon("/providerQgis.svg")
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def svgIconPath(self):
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return QgsApplication.iconPath("providerQgis.svg")
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def group(self):
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return self.tr('Raster tools')
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def name(self):
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return 'zonalstatistics'
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def displayName(self):
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return self.tr('Zonal Statistics')
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def defineCharacteristics(self):
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self.addParameter(ParameterRaster(self.INPUT_RASTER,
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self.tr('Raster layer')))
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self.addParameter(ParameterNumber(self.RASTER_BAND,
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self.tr('Raster band'), 1, 999, 1))
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self.addParameter(ParameterVector(self.INPUT_VECTOR,
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self.tr('Vector layer containing zones'),
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[dataobjects.TYPE_VECTOR_POLYGON]))
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self.addParameter(ParameterString(self.COLUMN_PREFIX,
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self.tr('Output column prefix'), '_'))
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self.addParameter(ParameterBoolean(self.GLOBAL_EXTENT,
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self.tr('Load whole raster in memory')))
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self.addOutput(OutputVector(self.OUTPUT_LAYER, self.tr('Zonal statistics'), datatype=[dataobjects.TYPE_VECTOR_POLYGON]))
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def processAlgorithm(self, feedback):
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""" Based on code by Matthew Perry
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https://gist.github.com/perrygeo/5667173
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"""
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layer = dataobjects.getLayerFromString(self.getParameterValue(self.INPUT_VECTOR))
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rasterPath = str(self.getParameterValue(self.INPUT_RASTER))
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bandNumber = self.getParameterValue(self.RASTER_BAND)
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columnPrefix = self.getParameterValue(self.COLUMN_PREFIX)
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useGlobalExtent = self.getParameterValue(self.GLOBAL_EXTENT)
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rasterDS = gdal.Open(rasterPath, gdal.GA_ReadOnly)
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geoTransform = rasterDS.GetGeoTransform()
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rasterBand = rasterDS.GetRasterBand(bandNumber)
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noData = rasterBand.GetNoDataValue()
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cellXSize = abs(geoTransform[1])
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cellYSize = abs(geoTransform[5])
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rasterXSize = rasterDS.RasterXSize
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rasterYSize = rasterDS.RasterYSize
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rasterBBox = QgsRectangle(geoTransform[0],
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geoTransform[3] - cellYSize * rasterYSize,
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geoTransform[0] + cellXSize * rasterXSize,
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geoTransform[3])
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rasterGeom = QgsGeometry.fromRect(rasterBBox)
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crs = osr.SpatialReference()
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crs.ImportFromProj4(str(layer.crs().toProj4()))
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if useGlobalExtent:
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xMin = rasterBBox.xMinimum()
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xMax = rasterBBox.xMaximum()
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yMin = rasterBBox.yMinimum()
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yMax = rasterBBox.yMaximum()
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(startColumn, startRow) = mapToPixel(xMin, yMax, geoTransform)
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(endColumn, endRow) = mapToPixel(xMax, yMin, geoTransform)
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width = endColumn - startColumn
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height = endRow - startRow
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srcOffset = (startColumn, startRow, width, height)
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srcArray = rasterBand.ReadAsArray(*srcOffset)
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srcArray = srcArray * rasterBand.GetScale() + rasterBand.GetOffset()
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newGeoTransform = (
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geoTransform[0] + srcOffset[0] * geoTransform[1],
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geoTransform[1],
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0.0,
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geoTransform[3] + srcOffset[1] * geoTransform[5],
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0.0,
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geoTransform[5],
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)
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memVectorDriver = ogr.GetDriverByName('Memory')
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memRasterDriver = gdal.GetDriverByName('MEM')
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fields = layer.fields()
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(idxMin, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'min', 21, 6)
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(idxMax, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'max', 21, 6)
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(idxSum, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'sum', 21, 6)
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(idxCount, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'count', 21, 6)
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(idxMean, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'mean', 21, 6)
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(idxStd, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'std', 21, 6)
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(idxUnique, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'unique', 21, 6)
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(idxRange, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'range', 21, 6)
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(idxVar, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'var', 21, 6)
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(idxMedian, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'median', 21, 6)
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if hasSciPy:
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(idxMode, fields) = vector.findOrCreateField(layer, fields,
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columnPrefix + 'mode', 21, 6)
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writer = self.getOutputFromName(self.OUTPUT_LAYER).getVectorWriter(
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fields.toList(), layer.wkbType(), layer.crs())
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outFeat = QgsFeature()
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outFeat.initAttributes(len(fields))
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outFeat.setFields(fields)
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features = vector.features(layer)
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total = 100.0 / len(features)
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for current, f in enumerate(features):
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geom = f.geometry()
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intersectedGeom = rasterGeom.intersection(geom)
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ogrGeom = ogr.CreateGeometryFromWkt(intersectedGeom.exportToWkt())
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if not useGlobalExtent:
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bbox = intersectedGeom.boundingBox()
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xMin = bbox.xMinimum()
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xMax = bbox.xMaximum()
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yMin = bbox.yMinimum()
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yMax = bbox.yMaximum()
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(startColumn, startRow) = mapToPixel(xMin, yMax, geoTransform)
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(endColumn, endRow) = mapToPixel(xMax, yMin, geoTransform)
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width = endColumn - startColumn
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height = endRow - startRow
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if width == 0 or height == 0:
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continue
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srcOffset = (startColumn, startRow, width, height)
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srcArray = rasterBand.ReadAsArray(*srcOffset)
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srcArray = srcArray * rasterBand.GetScale() + rasterBand.GetOffset()
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newGeoTransform = (
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geoTransform[0] + srcOffset[0] * geoTransform[1],
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geoTransform[1],
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0.0,
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geoTransform[3] + srcOffset[1] * geoTransform[5],
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0.0,
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geoTransform[5],
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)
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# Create a temporary vector layer in memory
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memVDS = memVectorDriver.CreateDataSource('out')
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memLayer = memVDS.CreateLayer('poly', crs, ogr.wkbPolygon)
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ft = ogr.Feature(memLayer.GetLayerDefn())
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ft.SetGeometry(ogrGeom)
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memLayer.CreateFeature(ft)
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ft.Destroy()
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# Rasterize it
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rasterizedDS = memRasterDriver.Create('', srcOffset[2],
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srcOffset[3], 1, gdal.GDT_Byte)
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rasterizedDS.SetGeoTransform(newGeoTransform)
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gdal.RasterizeLayer(rasterizedDS, [1], memLayer, burn_values=[1])
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rasterizedArray = rasterizedDS.ReadAsArray()
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srcArray = numpy.nan_to_num(srcArray)
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masked = numpy.ma.MaskedArray(srcArray,
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mask=numpy.logical_or(srcArray == noData,
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numpy.logical_not(rasterizedArray)))
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outFeat.setGeometry(geom)
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attrs = f.attributes()
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v = float(masked.min())
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attrs.insert(idxMin, None if numpy.isnan(v) else v)
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v = float(masked.max())
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attrs.insert(idxMax, None if numpy.isnan(v) else v)
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v = float(masked.sum())
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attrs.insert(idxSum, None if numpy.isnan(v) else v)
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attrs.insert(idxCount, int(masked.count()))
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v = float(masked.mean())
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attrs.insert(idxMean, None if numpy.isnan(v) else v)
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v = float(masked.std())
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attrs.insert(idxStd, None if numpy.isnan(v) else v)
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attrs.insert(idxUnique, numpy.unique(masked.compressed()).size)
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v = float(masked.max()) - float(masked.min())
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attrs.insert(idxRange, None if numpy.isnan(v) else v)
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v = float(masked.var())
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attrs.insert(idxVar, None if numpy.isnan(v) else v)
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v = float(numpy.ma.median(masked))
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attrs.insert(idxMedian, None if numpy.isnan(v) else v)
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if hasSciPy:
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attrs.insert(idxMode, float(mode(masked, axis=None)[0][0]))
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outFeat.setAttributes(attrs)
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writer.addFeature(outFeat)
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memVDS = None
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rasterizedDS = None
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feedback.setProgress(int(current * total))
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rasterDS = None
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del writer
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