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[processing] add zonal statistics algorithm
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‎python/plugins/processing/algs/QGISAlgorithmProvider.py

+3-1
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@@ -87,6 +87,7 @@
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from processing.algs.PointsLayerFromTable import PointsLayerFromTable
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from processing.algs.PointsDisplacement import PointsDisplacement
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from sextante.algs.ZonalStatistics import ZonalStatistics
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#from processing.algs.VectorLayerHistogram import VectorLayerHistogram
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#from processing.algs.VectorLayerScatterplot import VectorLayerScatterplot
@@ -141,7 +142,8 @@ def __init__(self):
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#VectorLayerHistogram(), VectorLayerScatterplot(), RasterLayerHistogram(),
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#MeanAndStdDevPlot(), BarPlot(), PolarPlot()
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# ------ vector ------
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PointsDisplacement()
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PointsDisplacement(),
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ZonalStatistics()
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]
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def initializeSettings(self):

‎python/plugins/sextante/algs/QGISUtils.py

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# -*- coding: utf-8 -*-
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"""
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***************************************************************************
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QGISUtils.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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__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 math
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from PyQt4.QtCore import *
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from qgis.core import *
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def mapToPixel(mX, mY, geoTransform):
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'''Convert map coordinates to pixel coordinates.
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@param mX Input map X coordinate (double)
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@param mY Input map Y coordinate (double)
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@param geoTransform Input geotransform (six doubles)
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@return pX, pY Output coordinates (two doubles)
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'''
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if geoTransform[2] + geoTransform[4] == 0:
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pX = (mX - geoTransform[0]) / geoTransform[1]
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pY = (mY - geoTransform[3]) / geoTransform[5]
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else:
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pX, pY = applyGeoTransform(mX, mY, invertGeoTransform(geoTransform))
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return int(pX), int(pY)
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def pixelToMap(pX, pY, geoTransform):
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'''Convert pixel coordinates to map coordinates.
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@param pX Input pixel X coordinate (double)
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@param pY Input pixel Y coordinate (double)
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@param geoTransform Input geotransform (six doubles)
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@return mX, mY Output coordinates (two doubles)
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'''
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mX, mY = applyGeoTransform(pX + 0.5, pY + 0.5, geoTransform)
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return mX, mY
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def applyGeoTransform(inX, inY, geoTransform):
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'''Apply a geotransform to coordinates.
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@param inX Input coordinate (double)
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@param inY Input coordinate (double)
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@param geoTransform Input geotransform (six doubles)
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@return outX, outY Output coordinates (two doubles)
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'''
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outX = geoTransform[0] + inX * geoTransform[1] + inY * geoTransform[2]
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outY = geoTransform[3] + inX * geoTransform[4] + inY * geoTransform[5]
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return outX, outY
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def invertGeoTransform(geoTransform):
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'''Invert standard 3x2 set of geotransform coefficients.
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@param geoTransform Input GeoTransform (six doubles - unaltered)
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@return outGeoTransform Output GeoTransform (six doubles - updated)
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on success, None if the equation is uninvertable
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'''
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# we assume a 3rd row that is [1 0 0]
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# compute determinate
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det = geoTransform[1] * geoTransform[5] - geoTransform[2] * geoTransform[4]
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if abs(det) < 0.000000000000001:
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return
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invDet = 1.0 / det
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# compute adjoint and divide by determinate
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outGeoTransform = [0, 0, 0, 0, 0, 0]
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outGeoTransform[1] = geoTransform[5] * invDet
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outGeoTransform[4] = -geoTransform[4] * invDet
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outGeoTransform[2] = -geoTransform[2] * invDet
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outGeoTransfrom[5] = geoTransform[1] * invDet
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outGeoTransform[0] = (geoTransform[2] * geoTransform[3] - geoTransform[0] * geoTransform[5]) * invDet
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outGeoTransform[3] = (-geoTransform[1] * geoTransform[3] + geoTransform[0] * geoTransform[4]) * invDet
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return outGeoTransform

‎python/plugins/sextante/algs/ZonalStatistics.py

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# -*- 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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__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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from PyQt4.QtCore import *
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import numpy
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from osgeo import gdal, ogr, osr
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from qgis.core import *
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from sextante.core.GeoAlgorithm import GeoAlgorithm
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from sextante.core.QGisLayers import QGisLayers
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from sextante.parameters.ParameterVector import ParameterVector
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from sextante.parameters.ParameterRaster import ParameterRaster
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from sextante.parameters.ParameterString import ParameterString
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from sextante.parameters.ParameterNumber import ParameterNumber
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from sextante.parameters.ParameterBoolean import ParameterBoolean
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from sextante.outputs.OutputVector import OutputVector
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from sextante.algs.ftools import FToolsUtils as ftools_utils
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from sextante.algs import QGISUtils as utils
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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 defineCharacteristics(self):
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self.name = "Zonal Statistics"
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self.group = "Raster tools"
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self.addParameter(ParameterRaster(self.INPUT_RASTER, "Raster layer"))
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self.addParameter(ParameterNumber(self.RASTER_BAND, "Raster band", 1, 999, 1))
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self.addParameter(ParameterVector(self.INPUT_VECTOR, "Vector layer containing zones", [ParameterVector.VECTOR_TYPE_POLYGON]))
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self.addParameter(ParameterString(self.COLUMN_PREFIX, "Output column prefix", "_"))
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self.addParameter(ParameterBoolean(self.GLOBAL_EXTENT, "Load whole raster in memory"))
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self.addOutput(OutputVector(self.OUTPUT_LAYER, "Output layer"))
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def processAlgorithm(self, progress):
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layer = QGisLayers.getObjectFromUri(self.getParameterValue(self.INPUT_VECTOR))
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rasterPath = unicode(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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)
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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 = utils.mapToPixel(xMin, yMax, geoTransform)
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endColumn, endRow = utils.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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newGeoTransform = (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.pendingFields()
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idxMin, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "min", 21, 6)
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idxMax, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "max", 21, 6)
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idxSum, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "sum", 21, 6)
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idxCount, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "count", 21, 6)
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idxMean, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "mean", 21, 6)
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idxStd, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "std", 21, 6)
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idxUnique, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "unique", 21, 6)
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idxRange, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "range", 21, 6)
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idxCV, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "cv", 21, 6)
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#idxMedian, fields = ftools_utils.findOrCreateField(layer, fields, columnPrefix + "median", 21, 6)
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writer = self.getOutputFromName(self.OUTPUT_LAYER).getVectorWriter(fields.toList(),
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layer.dataProvider().geometryType(), 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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current = 0
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features = QGisLayers.features(layer)
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total = 100.0 / len(features)
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for f in 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 = utils.mapToPixel(xMin, yMax, geoTransform)
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endColumn, endRow = utils.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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newGeoTransform = (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], 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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)
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)
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outFeat.setGeometry(geom)
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attrs = f.attributes()
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attrs.insert(idxMin, float(masked.min()))
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attrs.insert(idxMax, float(masked.max()))
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attrs.insert(idxSum, float(masked.sum()))
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attrs.insert(idxCount, int(masked.count()))
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attrs.insert(idxMean, float(masked.mean()))
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attrs.insert(idxStd, float(masked.std()))
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attrs.insert(idxUnique, numpy.unique(masked.compressed()).size)
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attrs.insert(idxRange, float(masked.max()) - float(masked.min()))
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attrs.insert(idxCV, float(masked.var()))
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#attrs.insert(idxMedian, float(masked.median()))
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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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current += 1
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progress.setPercentage(int(current * total))
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rasterDS = None
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del writer

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