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Port nearest neighbour analysis algorithm to new API
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@nyalldawson
nyalldawson committed Jul 15, 2017
1 parent 8af7318 commit b441a4f
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99 changes: 56 additions & 43 deletions python/plugins/processing/algs/qgis/NearestNeighbourAnalysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,21 +33,25 @@

from qgis.PyQt.QtGui import QIcon

from qgis.core import QgsFeatureRequest, QgsFeature, QgsDistanceArea, QgsProcessingUtils
from qgis.core import (QgsFeatureRequest,
QgsDistanceArea,
QgsProject,
QgsProcessing,
QgsProcessingParameterFeatureSource,
QgsProcessingParameterFileDestination,
QgsProcessingOutputHtml,
QgsProcessingOutputNumber,
QgsSpatialIndex)

from processing.algs.qgis.QgisAlgorithm import QgisAlgorithm
from processing.core.parameters import ParameterVector
from processing.core.outputs import OutputHTML
from processing.core.outputs import OutputNumber
from processing.tools import dataobjects

pluginPath = os.path.split(os.path.split(os.path.dirname(__file__))[0])[0]


class NearestNeighbourAnalysis(QgisAlgorithm):

POINTS = 'POINTS'
OUTPUT = 'OUTPUT'
INPUT = 'INPUT'
OUTPUT_HTML_FILE = 'OUTPUT_HTML_FILE'
OBSERVED_MD = 'OBSERVED_MD'
EXPECTED_MD = 'EXPECTED_MD'
NN_INDEX = 'NN_INDEX'
Expand All @@ -64,20 +68,21 @@ def __init__(self):
super().__init__()

def initAlgorithm(self, config=None):
self.addParameter(ParameterVector(self.POINTS,
self.tr('Points'), [dataobjects.TYPE_VECTOR_POINT]))

self.addOutput(OutputHTML(self.OUTPUT, self.tr('Nearest neighbour')))

self.addOutput(OutputNumber(self.OBSERVED_MD,
self.tr('Observed mean distance')))
self.addOutput(OutputNumber(self.EXPECTED_MD,
self.tr('Expected mean distance')))
self.addOutput(OutputNumber(self.NN_INDEX,
self.tr('Nearest neighbour index')))
self.addOutput(OutputNumber(self.POINT_COUNT,
self.tr('Number of points')))
self.addOutput(OutputNumber(self.Z_SCORE, self.tr('Z-Score')))
self.addParameter(QgsProcessingParameterFeatureSource(self.INPUT,
self.tr('Input layer'), [QgsProcessing.TypeVectorPoint]))

self.addParameter(QgsProcessingParameterFileDestination(self.OUTPUT_HTML_FILE, self.tr('Nearest neighbour'), self.tr('HTML files (*.html)'), None, True))
self.addOutput(QgsProcessingOutputHtml(self.OUTPUT_HTML_FILE, self.tr('Nearest neighbour')))

self.addOutput(QgsProcessingOutputNumber(self.OBSERVED_MD,
self.tr('Observed mean distance')))
self.addOutput(QgsProcessingOutputNumber(self.EXPECTED_MD,
self.tr('Expected mean distance')))
self.addOutput(QgsProcessingOutputNumber(self.NN_INDEX,
self.tr('Nearest neighbour index')))
self.addOutput(QgsProcessingOutputNumber(self.POINT_COUNT,
self.tr('Number of points')))
self.addOutput(QgsProcessingOutputNumber(self.Z_SCORE, self.tr('Z-Score')))

def name(self):
return 'nearestneighbouranalysis'
Expand All @@ -86,26 +91,30 @@ def displayName(self):
return self.tr('Nearest neighbour analysis')

def processAlgorithm(self, parameters, context, feedback):
layer = QgsProcessingUtils.mapLayerFromString(self.getParameterValue(self.POINTS), context)
output = self.getOutputValue(self.OUTPUT)
source = self.parameterAsSource(parameters, self.INPUT, context)
output_file = self.parameterAsFileOutput(parameters, self.OUTPUT_HTML_FILE, context)

spatialIndex = QgsProcessingUtils.createSpatialIndex(layer, context)
spatialIndex = QgsSpatialIndex(source)

neighbour = QgsFeature()
distance = QgsDistanceArea()
distance.setSourceCrs(source.sourceCrs())
distance.setEllipsoid(QgsProject.instance().ellipsoid())

sumDist = 0.00
A = layer.extent()
A = source.sourceExtent()
A = float(A.width() * A.height())

features = QgsProcessingUtils.getFeatures(layer, context)
count = QgsProcessingUtils.featureCount(layer, context)
features = source.getFeatures()
count = source.featureCount()
total = 100.0 / count if count else 1
for current, feat in enumerate(features):
if feedback.isCanceled():
break

neighbourID = spatialIndex.nearestNeighbor(
feat.geometry().asPoint(), 2)[1]
request = QgsFeatureRequest().setFilterFid(neighbourID).setSubsetOfAttributes([])
neighbour = next(layer.getFeatures(request))
neighbour = next(source.getFeatures(request))
sumDist += distance.measureLine(neighbour.geometry().asPoint(),
feat.geometry().asPoint())

Expand All @@ -117,20 +126,24 @@ def processAlgorithm(self, parameters, context, feedback):
SE = float(0.26136 / math.sqrt(count ** 2 / A))
zscore = float((do - de) / SE)

data = []
data.append('Observed mean distance: ' + str(do))
data.append('Expected mean distance: ' + str(de))
data.append('Nearest neighbour index: ' + str(d))
data.append('Number of points: ' + str(count))
data.append('Z-Score: ' + str(zscore))

self.createHTML(output, data)

self.setOutputValue(self.OBSERVED_MD, float(data[0].split(': ')[1]))
self.setOutputValue(self.EXPECTED_MD, float(data[1].split(': ')[1]))
self.setOutputValue(self.NN_INDEX, float(data[2].split(': ')[1]))
self.setOutputValue(self.POINT_COUNT, float(data[3].split(': ')[1]))
self.setOutputValue(self.Z_SCORE, float(data[4].split(': ')[1]))
results = {}
results[self.OBSERVED_MD] = do
results[self.EXPECTED_MD] = de
results[self.NN_INDEX] = d
results[self.POINT_COUNT] = count
results[self.Z_SCORE] = zscore

if output_file:
data = []
data.append('Observed mean distance: ' + str(do))
data.append('Expected mean distance: ' + str(de))
data.append('Nearest neighbour index: ' + str(d))
data.append('Number of points: ' + str(count))
data.append('Z-Score: ' + str(zscore))
self.createHTML(output_file, data)
results[self.OUTPUT_HTML_FILE] = output_file

return results

def createHTML(self, outputFile, algData):
with codecs.open(outputFile, 'w', encoding='utf-8') as f:
Expand Down
5 changes: 3 additions & 2 deletions python/plugins/processing/algs/qgis/QGISAlgorithmProvider.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@
from .Intersection import Intersection
from .LinesToPolygons import LinesToPolygons
from .Merge import Merge
from .NearestNeighbourAnalysis import NearestNeighbourAnalysis
from .PointsInPolygon import PointsInPolygon
from .PointsLayerFromTable import PointsLayerFromTable
from .PolygonsToLines import PolygonsToLines
Expand All @@ -87,7 +88,6 @@
from .ZonalStatistics import ZonalStatistics

# from .ExtractByLocation import ExtractByLocation
# from .NearestNeighbourAnalysis import NearestNeighbourAnalysis
# from .LinesIntersection import LinesIntersection
# from .MeanCoords import MeanCoords
# from .PointDistance import PointDistance
Expand Down Expand Up @@ -183,7 +183,7 @@ def __init__(self):
self.externalAlgs = []

def getAlgs(self):
# algs = [NearestNeighbourAnalysis(), MeanCoords(),
# algs = [MeanCoords(),
# LinesIntersection(), UniqueValues(), PointDistance(),
# ExportGeometryInfo(),
# SinglePartsToMultiparts(),
Expand Down Expand Up @@ -259,6 +259,7 @@ def getAlgs(self):
Intersection(),
LinesToPolygons(),
Merge(),
NearestNeighbourAnalysis(),
PointsInPolygon(),
PointsLayerFromTable(),
PolygonsToLines(),
Expand Down

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