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mahalanobis_distance.py
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mahalanobis_distance.py
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# -*- coding: utf-8 -*-
"""
/***************************************************************************
MahalanobisDistance
A QGIS plugin
Calculates Mahalanobis distance
-------------------
begin : 2016-07-10
git sha : $Format:%H$
copyright : (C) 2016 by Damian Michal Harasymczuk
email : d.harasymczuk@gmail.com
***************************************************************************/
/***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
"""
from PyQt4.QtCore import QSettings, QTranslator, qVersion, QCoreApplication, QFileInfo, Qt
from PyQt4.QtGui import QAction, QIcon, QDoubleSpinBox, QFileDialog, QMessageBox, QTableWidgetItem
from qgis.gui import QgsMapLayerComboBox, QgsMapLayerProxyModel
from qgis.core import QgsRasterLayer, QgsMapLayerRegistry
import resources_rc
from mahalanobis_distance_dialog import MahalanobisDistanceDialog
import os.path, gdal, numpy
from scipy.spatial.distance import cdist
class MahalanobisDistance:
"""QGIS Plugin Implementation."""
def __init__(self, iface):
# Save reference to the QGIS interface
self.iface = iface
# initialize plugin directory
self.plugin_dir = os.path.dirname(__file__)
# initialize locale
locale = QSettings().value('locale/userLocale')[0:2]
locale_path = os.path.join(
self.plugin_dir,
'i18n',
'MahalanobisDistance_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
if qVersion() > '4.3.3':
QCoreApplication.installTranslator(self.translator)
# Create the dialog (after translation) and keep reference
self.dlg = MahalanobisDistanceDialog()
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&Mahalanobis Distance')
# TODO: We are going to let the user set this up in a future iteration
self.toolbar = self.iface.addToolBar(u'Mahalanobis Distance')
self.toolbar.setObjectName(u'Mahalanobis Distance')
# signals and slots
self.dlg.addBtn.clicked.connect(self.add_layer)
self.dlg.removeBtn.clicked.connect(self.remove_layer)
self.dlg.outputBtn.clicked.connect(self.output)
self.dlg.buttonBox.accepted.connect(self.calculate)
self.dlg.buttonBox.rejected.connect(self.dlg.close)
# noinspection PyMethodMayBeStatic
def tr(self, message):
# noinspection PyTypeChecker,PyArgumentList,PyCallByClass
return QCoreApplication.translate('Mahalanobis Distance', message)
def add_action(
self,
icon_path,
text,
callback,
enabled_flag=True,
add_to_menu=True,
add_to_toolbar=True,
status_tip=None,
whats_this=None,
parent=None):
icon = QIcon(icon_path)
action = QAction(icon, text, parent)
action.triggered.connect(callback)
action.setEnabled(enabled_flag)
if status_tip is not None:
action.setStatusTip(status_tip)
if whats_this is not None:
action.setWhatsThis(whats_this)
if add_to_toolbar:
self.toolbar.addAction(action)
if add_to_menu:
self.iface.addPluginToRasterMenu(
self.menu,
action)
self.actions.append(action)
return action
def initGui(self):
"""Create the menu entries and toolbar icons inside the QGIS GUI."""
icon_path = ':/plugins/MahalanobisDistance/icon.png'
self.add_action(
icon_path,
text=self.tr(u'Calculate Mahalanobis distance'),
callback=self.run,
parent=self.iface.mainWindow())
def unload(self):
"""Removes the plugin menu item and icon from QGIS GUI."""
for action in self.actions:
self.iface.removePluginRasterMenu(
self.tr(u'&Mahalanobis Distance'),
action)
self.iface.removeToolBarIcon(action)
# remove the toolbar
del self.toolbar
def add_layer(self):
i = self.dlg.table.rowCount()
self.dlg.table.insertRow(i)
layer = QgsMapLayerComboBox()
layer.setFilters(QgsMapLayerProxyModel.RasterLayer)
band = QTableWidgetItem('1')
band.setFlags(Qt.ItemIsEnabled)
mean = QDoubleSpinBox()
mean.setRange(-10000.00,10000.00)
self.dlg.table.setCellWidget(i, 0, layer)
self.dlg.table.setItem(i, 1, band)
self.dlg.table.setCellWidget(i, 2, mean)
def remove_layer(self):
self.dlg.table.removeRow(self.dlg.table.currentRow())
def output(self):
self.dlg.outputPath.setText(QFileDialog.getSaveFileName())
def calculate(self):
self.dlg.progressBar.setValue(0)
rows = self.dlg.table.rowCount()
if rows == 0:
msg = QMessageBox()
msg.setWindowTitle("Error!")
msg.setText("Choose minimum one input layer!")
msg.exec_()
return
paths = []
means = []
for row in range(rows):
path = self.dlg.table.cellWidget(row, 0).currentLayer().source()
mean = self.dlg.table.cellWidget(row, 2).value()
paths.append(path)
means.append(mean)
rasters = []
# parameters of the first raster
f1 = gdal.Open(paths[0])
size_x = f1.RasterXSize
size_y = f1.RasterYSize
proj = f1.GetProjection ()
georef = f1.GetGeoTransform()
del f1
for path in paths:
f = gdal.Open(path)
raster = f.ReadAsArray()
rasters.append(raster)
# covariance matrix and inverted covariance matrix
covariance = numpy.cov([i.ravel() for i in rasters])
inv_covariance = numpy.linalg.inv(covariance)
means = numpy.array(means)
# calculate mahalanobis distances for each pixel
rasters = numpy.dstack(rasters).reshape(-1, len(rasters))
result = cdist(rasters, means[None, :], metric='mahalanobis', VI=inv_covariance)
result = result.reshape(size_y, size_x)
# new raster
driver = gdal.GetDriverByName('GTiff')
fileName = self.dlg.outputPath.text()
output = driver.Create(fileName, size_x, size_y, 1, gdal.GDT_Float32)
output.GetRasterBand(1).WriteArray(result)
output.SetProjection( proj )
output.SetGeoTransform( georef )
output.FlushCache()
output = None
self.dlg.progressBar.setValue(100)
# add result to canvas
if self.dlg.checkBox.isChecked():
fileInfo = QFileInfo(fileName)
baseName = fileInfo.baseName()
new_layer = QgsRasterLayer(fileName, baseName)
QgsMapLayerRegistry.instance().addMapLayer(new_layer)
def run(self):
self.dlg.show()
result = self.dlg.exec_()
if result:
pass