Sunday 29 October 2017

raster - How to speed up this script in PyQGIS?


I am a new in PyQGIS, I want to create a Point layer from a raster layer. In table of point layer created, there is 3 fields by name of "X_coord", "Y_coord" and "Azimuth", each point in Point layer shows x ("X_coord" field), y ("Y_coord") center coordinate of each pixel from raster layer and "Azimuth" field shows azimuth from another single point layer to each center pixels. When I run this script for raster layer with 67*52 pixels in 30 meter resolution time for running is 5 seconds, for 133*105 pixels time is 15 seconds and for 291*220 pixels time is 22 minutes! I think this is unusual.How can I decrease time for run this script for large data?


My script is:


from qgis.core import *
from osgeo import gdal

from PyQt4.QtCore import *
import time

startTime = time.clock()

pnt = QgsVectorLayer(r'E:/Sample_Dataset_Lorestan/Point.shp', 'POINT','ogr')
for feat in pnt.getFeatures():
geom = feat.geometry()
pntxy=geom.asPoint()


# Open tif file
ds = gdal.Open(r'E:\Sample_Dataset_Lorestan\subset_a1.tif')

numpy_array = ds.ReadAsArray()
# GDAL affine transform parameters

geotransform = ds.GetGeoTransform()
originX = geotransform[0]
originY = geotransform[3]
rotationX = geotransform[2]

rotationY = geotransform[4]
pixelWidth = geotransform[1]
pixelHeight = geotransform[5]

cols=ds.RasterXSize
rows=ds.RasterYSize

def pixel2coord(x, y):
xp = (pixelWidth * x) + originX + (pixelWidth/2)
yp = (pixelHeight * y) + originY + (pixelHeight /2)

return(xp, yp)

#Create temporary vector layer and add to map
vl = QgsVectorLayer("Point?crs=", "temporary_points", "memory")
pr = vl.dataProvider()
QgsMapLayerRegistry.instance().addMapLayer(vl)
# Add points:
pr = vl.dataProvider()
# Enter editing mode
vl.startEditing()

# add fields
pr.addAttributes( [ QgsField("X_coord", QVariant.Int), QgsField("Y_coord", QVariant.Int), QgsField("Azimuth", QVariant.Int) ] )

# add a feature
fet = QgsFeature()

# get columns and rows of your image from gdalinfo

for row in range(0,rows):
for col in range(0,cols):

rspnt = pixel2coord(col,row)
rspnt2 = QgsPoint(rspnt[0], rspnt[1])
fet.setGeometry(QgsGeometry.fromPoint(rspnt2))
fet.initAttributes(3)
fet.setAttribute(0, rspnt[0] )
fet.setAttribute(1, rspnt[1])

az = pntxy.azimuth(rspnt2)
if az < 0.0:
azim = 360 + az

else:
azim = az

fet.setAttribute(2, azim)
pr.addFeatures( [fet] )

# Commit changes
vl.commitChanges()
print "completed within:", time.clock() - startTime, "seconds", "\n"

Answer




Try this version (modified from gene's response):


vl = QgsVectorLayer("Point?crs=", "temporary_points2", "memory")
vl.dataProvider().addAttributes([ QgsField("X_coord", QVariant.Int), QgsField("Y_coord", QVariant.Int), QgsField("Azimuth", QVariant.Int) ])

new_features = []
for row in range(0,rows):
for col in range(0,cols):
rspnt = pixel2coord(col,row)
fet = QgsFeature()
fet.setGeometry(QgsGeometry.fromPoint(QgsPoint(rspnt[0], rspnt[1])))

fet.initAttributes(3)
fet.setAttribute(0, rspnt[0] )
fet.setAttribute(1, rspnt[1])
az = pntxy.azimuth(QgsPoint(rspnt[0], rspnt[1]))
if az < 0.0:
azim = 360 + az
else:
azim = az
fet.setAttribute(2, azim)
new_features.append(fet)


vl.dataProvider().addFeatures( new_features )
vl.updateExtents()
vl.updateFields()
QgsMapLayerRegistry.instance().addMapLayers([vl])

This version only calls addFeatures once, rather than once per pixel in the loop.


Update: Here's a version to try to avoid the memory errors from storing everything in a single list. Now, the features are added once per row. It's not as fast as the above method, but less memory hungry:


vl = QgsVectorLayer("Point?crs=", "temporary_points2", "memory")
vl.dataProvider().addAttributes([ QgsField("X_coord", QVariant.Int), QgsField("Y_coord", QVariant.Int), QgsField("Azimuth", QVariant.Int) ])


for row in range(0,rows):
new_features = []
for col in range(0,cols):
rspnt = pixel2coord(col,row)
fet = QgsFeature()
fet.setGeometry(QgsGeometry.fromPoint(QgsPoint(rspnt[0], rspnt[1])))
fet.initAttributes(3)
fet.setAttribute(0, rspnt[0] )
fet.setAttribute(1, rspnt[1])

az = pntxy.azimuth(QgsPoint(rspnt[0], rspnt[1]))
if az < 0.0:
azim = 360 + az
else:
azim = az
fet.setAttribute(2, azim)
new_features.append(fet)

vl.dataProvider().addFeatures( new_features )
vl.updateExtents()

vl.updateFields()
QgsMapLayerRegistry.instance().addMapLayers([vl])

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