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vigour_maps.py
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vigour_maps.py
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# -*- coding: utf-8 -*-
"""
/***************************************************************************
VigourMaps
A QGIS plugin
This plugin creates vigour maps.
Generated by Plugin Builder: http://g-sherman.github.io/Qgis-Plugin-Builder/
-------------------
begin : 2020-11-04
git sha : $Format:%H$
copyright : (C) 2020 by FCUP_UTAD
email : liaduarte@fc.up.pt
***************************************************************************/
/***************************************************************************
* *
* 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 qgis.PyQt.QtCore import QSettings, QTranslator, QCoreApplication
from qgis.PyQt.QtGui import QIcon
from qgis.PyQt.QtWidgets import QAction, QFileDialog, QProgressBar, QTableWidgetItem
from qgis.PyQt.QtCore import *
from qgis.PyQt.QtGui import *
from qgis.PyQt.QtWidgets import *
from qgis.core import *
from qgis.gui import *
from .reclassify_dialog import Ui_Reclassify
# Initialize Qt resources from file resources.py
from .resources import *
# Import the code for the dialog
from .vigour_maps_dialog import VigourMapsDialog
from .vigour_maps_dialog import RectangleMapTool
import os.path
from processing.core.Processing import Processing
class VigourMaps:
"""QGIS Plugin Implementation."""
def __init__(self, iface):
"""Constructor.
:param iface: An interface instance that will be passed to this class
which provides the hook by which you can manipulate the QGIS
application at run time.
:type iface: QgsInterface
"""
# 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',
'VigourMaps_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
QCoreApplication.installTranslator(self.translator)
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&VigourMaps')
# Check if plugin was started the first time in current QGIS session
# Must be set in initGui() to survive plugin reloads
self.first_start = None
self.window = None
# noinspection PyMethodMayBeStatic
def tr(self, message):
"""Get the translation for a string using Qt translation API.
We implement this ourselves since we do not inherit QObject.
:param message: String for translation.
:type message: str, QString
:returns: Translated version of message.
:rtype: QString
"""
# noinspection PyTypeChecker,PyArgumentList,PyCallByClass
return QCoreApplication.translate('VigourMaps', 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):
"""Add a toolbar icon to the toolbar.
:param icon_path: Path to the icon for this action. Can be a resource
path (e.g. ':/plugins/foo/bar.png') or a normal file system path.
:type icon_path: str
:param text: Text that should be shown in menu items for this action.
:type text: str
:param callback: Function to be called when the action is triggered.
:type callback: function
:param enabled_flag: A flag indicating if the action should be enabled
by default. Defaults to True.
:type enabled_flag: bool
:param add_to_menu: Flag indicating whether the action should also
be added to the menu. Defaults to True.
:type add_to_menu: bool
:param add_to_toolbar: Flag indicating whether the action should also
be added to the toolbar. Defaults to True.
:type add_to_toolbar: bool
:param status_tip: Optional text to show in a popup when mouse pointer
hovers over the action.
:type status_tip: str
:param parent: Parent widget for the new action. Defaults None.
:type parent: QWidget
:param whats_this: Optional text to show in the status bar when the
mouse pointer hovers over the action.
:returns: The action that was created. Note that the action is also
added to self.actions list.
:rtype: QAction
"""
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:
# Adds plugin icon to Plugins toolbar
self.iface.addToolBarIcon(action)
if add_to_menu:
self.iface.addPluginToMenu(
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/vigour_maps/icon.png'
self.add_action(
icon_path,
text=self.tr(u'Creates Vigour Maps'),
callback=self.run,
parent=self.iface.mainWindow())
# will be set False in run()
self.first_start = True
def unload(self):
"""Removes the plugin menu item and icon from QGIS GUI."""
for action in self.actions:
self.iface.removePluginMenu(
self.tr(u'&VigourMaps'),
action)
self.iface.removeToolBarIcon(action)
def close_window_main(self):
self.dlg.close()
def run(self):
"""Run method that performs all the real work"""
import time
# Create the dialog with elements (after translation) and keep reference
# Only create GUI ONCE in callback, so that it will only load when the plugin is started
if self.first_start == True:
self.first_start = False
self.dlg = VigourMapsDialog()
self.dlg.pushButton_13.clicked.connect(self.fillNDVI)
self.dlg.pushButton_21.clicked.connect(self.fillDSM)
self.dlg.pushButton_18.clicked.connect(self.fillDTM)
self.dlg.pushButton_17.clicked.connect(self.fillCSM)
self.dlg.pushButton_19.clicked.connect(self.fillOutput)
self.dlg.pushButton_20.clicked.connect(self.fillOutput_class)
self.dlg.pushButton_16.clicked.connect(self.vectorStudy)
self.dlg.pushButton.clicked.connect(self.reclassify)
self.dlg.pushButton_2.clicked.connect(self.conclude)
self.dlg.pushButton_3.clicked.connect(self.close_window_main)
# Get all loaded layers in the interface
layers = QgsProject.instance().mapLayers()
# Create an empty list which we can populate
list_names_layers = []
# list of layer names using list comprehension
l = [layer.name() for layer in QgsProject.instance().mapLayers().values()]
# dictionary with key = layer name and value = layer object
layers_list = {}
for l in QgsProject.instance().mapLayers().values():
layers_list[l.name()] = l
for name, value in layers_list.items():
list_names_layers.append(name)
self.dlg.comboBox_3.addItems(list_names_layers)
self.dlg.comboBox_9.addItems(list_names_layers)
self.dlg.comboBox_6.addItems(list_names_layers)
self.dlg.comboBox_8.addItems(list_names_layers)
self.dlg.comboBox_7.addItems(list_names_layers)
# show the dialog
canvas = self.dlg.widget
toolDraw = RectangleMapTool(canvas)
canvas.setMapTool(toolDraw)
# QLineEdit
line_bbox = QLineEdit()
line_bbox.hide()
# show the dialog
self.dlg.show()
# Run the dialog event loop
result = self.dlg.exec_()
def conclude(self):
import time
input_NDVI = self.dlg.comboBox_3.currentText()
input_DSM = self.dlg.comboBox_9.currentText()
input_DTM = self.dlg.comboBox_6.currentText()
input_CSM = self.dlg.comboBox_8.currentText()
study_zone = self.dlg.comboBox_7.currentText()
canvas = self.dlg.widget
toolDraw = RectangleMapTool(canvas)
canvas.setMapTool(toolDraw)
# QLineEdit
line_bbox = QLineEdit()
line_bbox.hide()
progressMessageBar = self.iface.messageBar().createMessage("Processing...")
progress = QProgressBar()
progress.setMaximum(10)
progress.setAlignment(Qt.AlignLeft | Qt.AlignVCenter)
progressMessageBar.layout().addWidget(progress)
self.iface.messageBar().pushWidget(progressMessageBar, Qgis.Info)
for i in range(10):
time.sleep(1)
progress.setValue(i + 1)
self.output = self.dlg.lineEdit_22.text()
#if csm is selected another output
self.output_class_map_csm = self.dlg.lineEdit_23.text()
#if there is study zone draw
if len(toolDraw.points) !=0:
poligono = QgsGeometry.fromPolygonXY([toolDraw.points])
vl = QgsVectorLayer("Polygon", "temp", "memory")
vl.setCrs(self.coord)
pr = vl.dataProvider()
f = QgsFeature()
f.setGeometry(poligono)
pr.addFeature(f)
vl.updateExtents()
QgsProject.instance().addMapLayer(vl)
Processing.initialize()
# input NDVI
# clip the layers
clip_ndvi1 = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(input_NDVI),
'MASK': vl,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('clip_ndvi1.tif')})
self.out_ndvi = clip_ndvi1['OUTPUT']
# mask for ndvi
value_ndvi = self.dlg.doubleSpinBox_3.value()
mask_ndvi = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.out_ndvi,
'b': None,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '((A>' + str(value_ndvi) + ')*1)/((A>' + str(
value_ndvi) + ')*1+(A<=' + str(value_ndvi) + ')*0)',
'output': QgsProcessingUtils.generateTempFilename('mask_ndvi.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.mask_for_ndvi = mask_ndvi['output']
if self.dlg.checkBox_3.isChecked() or self.dlg.checkBox_3.isChecked():
# input DSM and DTM
if self.dlg.checkBox_3.isChecked():
csm = Processing.runAlgorithm("grass7:r.mapcalc.simple", {'a': str(input_DSM),
'b': str(input_DTM),
'c': None, 'd': None, 'e': None, 'f': None,
'expression': 'A-B',
'output': QgsProcessingUtils.generateTempFilename('csm.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.out_csm1 = csm['output']
# clip the layers
clip_csm = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(self.dlg.out_csm1),
'MASK': vl,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('clip_csm.tif')})
self.out_csm = clip_csm['OUTPUT']
# input CSM
if self.dlg.checkBox_2.isChecked():
# clip the layers
clip_csm = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(input_CSM),
'MASK': vl,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('clip_csm.tif')})
self.out_csm = clip_csm['OUTPUT']
#mask for csm
value_csm = self.dlg.doubleSpinBox_4.value()
mask_csm = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.out_csm),
'b': None,
'c': None, 'd': None, 'e': None, 'f': None, 'expression': '((A>'+ str(value_csm) +')*1)/((A>' + str(value_csm) +')*1+(A<=' + str(value_csm) + ')*0)',
'output': QgsProcessingUtils.generateTempFilename('mask_csm.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.mask_for_csm = mask_csm['output']
# mask for extra output classification map with csm and ndvi
# class 2 - vegetation, class 1 = vegetation rasteira, class 0 =soil
value_csm = self.dlg.doubleSpinBox_4.value()
mask_csm = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.out_csm),
'b': str(self.out_ndvi),
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '(A>' + str(value_csm) + 'AND B>' + str(value_ndvi)+')*2 ' + '(A<=' + str(value_csm) + 'AND B>' + str(value_ndvi) + ')*1',
'output': str(self.output_class_map_csm),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
#ndvi values for pixels with 1 in ndvi and csm
ndvi_values_1 = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.mask_for_ndvi,
'b': self.mask_for_csm,
'c': self.out_ndvi, 'd': None, 'e': None, 'f': None,
'expression': '(A==1 & B==1)*C',
'output': QgsProcessingUtils.generateTempFilename('ndvi_values_1.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.ndvi_values_for_1 = ndvi_values_1['output']
resamp = Processing.runAlgorithm("saga:closegaps",
{'INPUT': self.ndvi_values_for_1,
'MASK': None,
'THRESHOLD': '0.1',
'RESULT': QgsProcessingUtils.generateTempFilename('resamp.sdat')
})
self.out_resampling = resamp['RESULT']
self.horizontal_filter = self.dlg.spinBox.value()
self.vertical_filter = self.dlg.spinBox_2.value()
resamp_filter = Processing.runAlgorithm("grass7:r.resamp.filter", {
'input': str(self.out_resampling),
'filter': [0], 'radius': '', 'x_radius': str(self.horizontal_filter),
'y_radius': str(self.vertical_filter), '-n': False,
'output': QgsProcessingUtils.generateTempFilename('resamp_filter.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.resamp_filter_to_result = resamp_filter['output']
clip_resamp = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(self.resamp_filter_to_result),
'MASK': vl,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': str(self.output)})
else:
# ndvi values for pixels with 1 in ndvi and csm
ndvi_values_1 = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.mask_for_ndvi,
'b': self.out_ndvi,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '(A==1)*B',
'output': QgsProcessingUtils.generateTempFilename(
'ndvi_values_1.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.ndvi_values_for_1 = ndvi_values_1['output']
resamp = Processing.runAlgorithm("saga:closegaps",
{'INPUT': self.ndvi_values_for_1,
'MASK': None,
'THRESHOLD':'0.1',
'RESULT': QgsProcessingUtils.generateTempFilename('resamp.sdat')
})
self.out_resampling = resamp['RESULT']
self.horizontal_filter = self.dlg.spinBox.value()
self.vertical_filter = self.dlg.spinBox_2.value()
resamp_filter = Processing.runAlgorithm("grass7:r.resamp.filter", {
'input': str(self.out_resampling),
'filter': [0], 'radius': '', 'x_radius': str(self.horizontal_filter), 'y_radius': str(self.vertical_filter), '-n': False,
'output': QgsProcessingUtils.generateTempFilename('resamp_filter.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.resamp_filter_to_result = resamp_filter['output']
clip_resamp = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(self.resamp_filter_to_result),
'MASK': vl,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': str(self.output)})
# if there is no study zone draw
if len(toolDraw.points) ==0:
# if study zone defined by shapefile
if self.dlg.checkBox.isChecked():
clip_ndvi1 = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(input_NDVI),
'MASK': study_zone,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('clip_ndvi1.tif')})
self.out_ndvi = clip_ndvi1['OUTPUT']
# mask for ndvi
value_ndvi = self.dlg.doubleSpinBox_3.value()
mask_ndvi = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.out_ndvi,
'b': None,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '((A>' + str(value_ndvi) + ')*1)/((A>' + str(
value_ndvi) + ')*1+(A<=' + str(value_ndvi) + ')*0)',
'output': QgsProcessingUtils.generateTempFilename(
'mask_ndvi.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.mask_for_ndvi = mask_ndvi['output']
if self.dlg.checkBox_3.isChecked() or self.dlg.checkBox_2.isChecked():
if self.dlg.checkBox_3.isChecked():
csm = Processing.runAlgorithm("grass7:r.mapcalc.simple", {'a': str(input_DSM),
'b': str(input_DTM),
'c': None, 'd': None, 'e': None,
'f': None,
'expression': 'A-B',
'output': QgsProcessingUtils.generateTempFilename('csm.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.out_csm1 = csm['output']
# clip the layers
clip_csm = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(self.dlg.out_csm1),
'MASK': study_zone,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('clip_csm.tif')})
self.out_csm = clip_csm['OUTPUT']
if self.dlg.checkBox_2.isChecked():
# clip the layers
clip_csm = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(input_CSM),
'MASK': study_zone,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('clip_csm.tif')})
self.out_csm = clip_csm['OUTPUT']
# mask for csm
value_csm = self.dlg.doubleSpinBox_4.value()
mask_csm = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.out_csm),
'b': None,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '((A>' + str(value_csm) + ')*1)/((A>' + str(
value_csm) + ')*1+(A<=' + str(value_csm) + ')*0)',
'output': QgsProcessingUtils.generateTempFilename(
'mask_csm.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.mask_for_csm = mask_csm['output']
# mask for extra output classification map with csm and ndvi
# class 2 - vegetation, class 1 = vegetation rasteira, class 0 =soil
value_csm = self.dlg.doubleSpinBox_4.value()
mask_csm = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.out_csm),
'b': str(self.out_ndvi),
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '(A>' + str(value_csm) + ' & B>' + str(
value_ndvi) + ')*2 + ' + '(A<=' + str(
value_csm) + ' & B>' + str(value_ndvi) + ')*1',
'output': str(self.output_class_map_csm),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
# ndvi values for pixels with 1 in ndvi and csm
ndvi_values_1 = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.mask_for_ndvi,
'b': self.mask_for_csm,
'c': self.out_ndvi, 'd': None, 'e': None, 'f': None,
'expression': '(A==1 & B==1)*C',
'output': QgsProcessingUtils.generateTempFilename(
'ndvi_values_1.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.ndvi_values_for_1 = ndvi_values_1['output']
resamp = Processing.runAlgorithm("saga:closegaps",
{'INPUT': self.ndvi_values_for_1,
'MASK': None,
'THRESHOLD':'0.1',
'RESULT': QgsProcessingUtils.generateTempFilename('resamp.sdat')
})
self.out_resampling = resamp['RESULT']
self.horizontal_filter = self.dlg.spinBox.value()
self.vertical_filter = self.dlg.spinBox_2.value()
gaps_clip = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(self.out_resampling),
'MASK': study_zone,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': QgsProcessingUtils.generateTempFilename('gaps_clip.tif')})
self.out_gaps_clip = gaps_clip['OUTPUT']
resamp_filter = Processing.runAlgorithm("grass7:r.resamp.filter", {
'input': str(self.out_gaps_clip),
'filter': [0], 'radius': '', 'x_radius': str(self.horizontal_filter), 'y_radius': str(self.vertical_filter), '-n': False,
'output': str(self.output), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
#
else:
# ndvi values for pixels with 1 in ndvi and csm
ndvi_values_1 = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.mask_for_ndvi,
'b': self.out_ndvi,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '(A==1)*B',
'output': QgsProcessingUtils.generateTempFilename(
'ndvi_values_1.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.ndvi_values_for_1 = ndvi_values_1['output']
resamp = Processing.runAlgorithm("saga:closegaps",
{'INPUT': self.ndvi_values_for_1,
'MASK': None,
'THRESHOLD':'0.1',
'RESULT': QgsProcessingUtils.generateTempFilename('resamp.sdat')
})
self.out_resampling = resamp['RESULT']
self.horizontal_filter = self.dlg.spinBox.value()
self.vertical_filter = self.dlg.spinBox_2.value()
resamp_filter = Processing.runAlgorithm("grass7:r.resamp.filter", {
'input': str(self.out_resampling),
'filter': [0], 'radius': '', 'x_radius': str(self.horizontal_filter), 'y_radius': str(self.vertical_filter), '-n': False,
'output': QgsProcessingUtils.generateTempFilename('resamp_filter.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.resamp_filter_to_result = resamp_filter['output']
clip_resamp = Processing.runAlgorithm("gdal:cliprasterbymasklayer", {
'INPUT': str(self.resamp_filter_to_result),
'MASK': study_zone,
'SOURCE_CRS': None,
'TARGET_CRS': None, 'NODATA': None,
'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'KEEP_RESOLUTION': False,
'SET_RESOLUTION': False, 'X_RESOLUTION': None, 'Y_RESOLUTION': None,
'MULTITHREADING': False, 'OPTIONS': '', 'DATA_TYPE': 0, 'EXTRA': '',
'OUTPUT': str(self.output)})
else:
# if it is all the area
self.out_ndvi = input_NDVI
# mask for ndvi
t4 = time.time()
value_ndvi = self.dlg.doubleSpinBox_3.value()
mask_ndvi = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': self.out_ndvi,
'b': None,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '((A>' + str(value_ndvi) + ')*1)/((A>' + str(
value_ndvi) + ')*1+(A<=' + str(value_ndvi) + ')*0)',
'output': QgsProcessingUtils.generateTempFilename('mask_ndvi.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.mask_for_ndvi = mask_ndvi['output']
t5 = time.time()
if self.dlg.checkBox_3.isChecked() or self.dlg.checkBox_3.isChecked():
if self.dlg.checkBox_3.isChecked():
csm = Processing.runAlgorithm("grass7:r.mapcalc.simple", {'a': str(input_DSM),
'b': str(input_DTM),
'c': None, 'd': None, 'e': None,
'f': None,
'expression': 'A-B',
'output': QgsProcessingUtils.generateTempFilename(
'csm.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.out_csm = csm['output']
if self.dlg.checkBox_2.isChecked():
self.out_csm = input_CSM
# mask for csm
t2 = time.time()
value_csm = self.dlg.doubleSpinBox_4.value()
mask_csm = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.out_csm),
'b': None,
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '((A>'+ str(value_csm) +')*1)/((A>' + str(value_csm) +')*1+(A<=' + str(value_csm) + ')*0)',
'output': QgsProcessingUtils.generateTempFilename('mask_csm.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.mask_for_csm = mask_csm['output']
t3 = time.time()
# ndvi values for pixels with 1 in ndvi and csm
t6 = time.time()
ndvi_values_1 = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.mask_for_ndvi),
'b': str(self.mask_for_csm),
'c': str(self.out_ndvi), 'd': None, 'e': None, 'f': None,
'expression': '(A==1 & B==1)*C',
'output': QgsProcessingUtils.generateTempFilename('ndvi_values_1.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.ndvi_values_for_1 = ndvi_values_1['output']
t7 = time.time()
t8 = time.time()
resamp = Processing.runAlgorithm("saga:closegaps",
{
'INPUT': str(self.ndvi_values_for_1),
'MASK': None,
'THRESHOLD':'0.1',
'RESULT': QgsProcessingUtils.generateTempFilename('resamp.sdat'),
})
self.out_resampling = resamp['RESULT']
t9 = time.time()
t10 = time.time()
self.horizontal_filter = self.dlg.spinBox.value()
self.vertical_filter = self.dlg.spinBox_2.value()
resamp_filter = Processing.runAlgorithm("grass7:r.resamp.filter", {
'input': str(self.out_resampling),
'filter': [0], 'radius': '', 'x_radius': str(self.horizontal_filter), 'y_radius': str(self.vertical_filter), '-n': False,
'output': QgsProcessingUtils.generateTempFilename('resamp_filter.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.out_resampling_filter = resamp_filter['output']
t11 = time.time()
# convert from .sdat to .tif
Processing.runAlgorithm("gdal:translate",
{'INPUT': str(self.out_resampling_filter), 'TARGET_CRS': None, 'NODATA': None,
'COPY_SUBDATASETS': False, 'OPTIONS': '', 'EXTRA': '', 'DATA_TYPE': 0,
'OUTPUT': str(self.output)})
else:
# ndvi values for pixels with 1 in ndvi and csm
t6 = time.time()
ndvi_values_1 = Processing.runAlgorithm("grass7:r.mapcalc.simple",
{'a': str(self.mask_for_ndvi),
'b': str(self.out_ndvi),
'c': None, 'd': None, 'e': None, 'f': None,
'expression': '(A==1)*B',
'output': QgsProcessingUtils.generateTempFilename(
'ndvi_values_1.tif'), 'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0,
'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.ndvi_values_for_1 = ndvi_values_1['output']
t7 = time.time()
t8 = time.time()
resamp = Processing.runAlgorithm("saga:closegaps",
{
'INPUT': str(self.ndvi_values_for_1),
'MASK': None,
'THRESHOLD':'0.1',
'RESULT': QgsProcessingUtils.generateTempFilename(
'resamp.sdat'),
})
self.out_resampling = resamp['RESULT']
t9 = time.time()
t10 = time.time()
self.horizontal_filter = self.dlg.spinBox.value()
self.vertical_filter = self.dlg.spinBox_2.value()
resamp_filter = Processing.runAlgorithm("grass7:r.resamp.filter", {
'input': str(self.out_resampling),
'filter': [0], 'radius': '', 'x_radius': str(self.horizontal_filter), 'y_radius': str(self.vertical_filter), '-n': False,
'output': QgsProcessingUtils.generateTempFilename('resamp_filter.tif'),
'GRASS_REGION_PARAMETER': None,
'GRASS_REGION_CELLSIZE_PARAMETER': 0, 'GRASS_RASTER_FORMAT_OPT': '',
'GRASS_RASTER_FORMAT_META': ''})
self.out_resampling_filter = resamp_filter['LOPASS']
t11 = time.time()
# convert from .sdat to .tif
Processing.runAlgorithm("gdal:translate",
{'INPUT': str(self.out_resampling_filter), 'TARGET_CRS': None,
'NODATA': None,
'COPY_SUBDATASETS': False, 'OPTIONS': '', 'EXTRA': '', 'DATA_TYPE': 0,
'OUTPUT': str(self.output)})
# add result into canvas
vigour_map = QFileInfo(str(self.output))
rlayer_vigour = QgsRasterLayer(self.output, vigour_map.fileName(), 'gdal')
QgsProject.instance().addMapLayer(rlayer_vigour)
self.dlg.widget.setExtent(rlayer_vigour.extent())
# set the map canvas layer set
self.dlg.widget.setLayers([rlayer_vigour])
if self.output_class_map_csm!=None:
# add result into canvas
dist_map = QFileInfo(str(self.output_class_map_csm))
rlayer_dist = QgsRasterLayer(self.output_class_map_csm, dist_map.fileName(), 'gdal')
QgsProject.instance().addMapLayer(rlayer_dist)
self.dlg.widget.setExtent(rlayer_dist.extent())
# set the map canvas layer set
self.dlg.widget.setLayers([rlayer_dist])
QMessageBox.about(self.dlg,"Message", "Vigour map and Vegetation Distribution Map are created!")
else:
QMessageBox.about(self.dlg, "Message", "Vigour map is created!")
self.iface.messageBar().clearWidgets()
def fillOutput(self):
filename, filter_string = QFileDialog.getSaveFileName(self.dlg, "Select output file ", "", '*.tif')
self.dlg.lineEdit_22.setText(filename)
def fillOutput_class(self):
filename, filter_string = QFileDialog.getSaveFileName(self.dlg, "Select output file ", "", '*.tif')
self.dlg.lineEdit_23.setText(filename)
def fillNDVI(self):
filename, filter_string = QFileDialog.getOpenFileName(self.dlg, "Select NDVI map ", "", '*.tif')
fileCI = str(filename)
fileInfo = QFileInfo(fileCI)
path = fileInfo.filePath()
basename = fileInfo.baseName()
# add the raster
vlayer = QgsRasterLayer(path, basename)
self.dlg.comboBox_3.addItem(filename)
crs_raster = vlayer.crs()
self.coord = self.crs(crs_raster)
# add layer to the registry
QgsProject.instance().addMapLayer(vlayer)
# set extent to the extent of our layer
self.dlg.widget.setExtent(vlayer.extent())
# set the map canvas layer set
self.dlg.widget.setLayers([vlayer])
def fillDSM(self):
filename, filter_string = QFileDialog.getOpenFileName(self.dlg, "Select DSM map ", "", '*.tif')
fileCI = str(filename)
fileInfo = QFileInfo(fileCI)
path = fileInfo.filePath()
basename = fileInfo.baseName()
# add the raster
vlayer = QgsRasterLayer(path, basename)
self.dlg.comboBox_9.addItem(filename)
crs_raster = vlayer.crs()
self.coord = self.crs(crs_raster)
# add layer to the registry
QgsProject.instance().addMapLayer(vlayer)
# set extent to the extent of our layer
self.dlg.widget.setExtent(vlayer.extent())
# set the map canvas layer set
self.dlg.widget.setLayers([vlayer])
def fillDTM(self):
filename, filter_string = QFileDialog.getOpenFileName(self.dlg, "Select DTM map ", "", '*.tif')
fileCI = str(filename)
fileInfo = QFileInfo(fileCI)
path = fileInfo.filePath()
basename = fileInfo.baseName()
# add the raster
vlayer = QgsRasterLayer(path, basename)
self.dlg.comboBox_6.addItem(filename)
crs_raster = vlayer.crs()
self.coord = self.crs(crs_raster)
# add layer to the registry
QgsProject.instance().addMapLayer(vlayer)
# set extent to the extent of our layer
self.dlg.widget.setExtent(vlayer.extent())
# set the map canvas layer set
self.dlg.widget.setLayers([vlayer])
def fillCSM(self):
filename, filter_string = QFileDialog.getOpenFileName(self.dlg, "Select CSM map ", "", '*.tif')
fileCI = str(filename)
fileInfo = QFileInfo(fileCI)
path = fileInfo.filePath()
basename = fileInfo.baseName()
# add the raster
vlayer = QgsRasterLayer(path, basename)
self.dlg.comboBox_8.addItem(filename)
crs_raster = vlayer.crs()
self.coord = self.crs(crs_raster)
# add layer to the registry
QgsProject.instance().addMapLayer(vlayer)
# set extent to the extent of our layer
self.dlg.widget.setExtent(vlayer.extent())
# set the map canvas layer set
self.dlg.widget.setLayers([vlayer])
def vectorStudy(self):
filename, filter_string = QFileDialog.getOpenFileName(self.dlg, "Select Study zone ", "", '*.shp')
fileCI = str(filename)
fileInfo = QFileInfo(fileCI)
path = fileInfo.filePath()
basename = fileInfo.baseName()
vlayer = QgsVectorLayer(path, basename)
self.dlg.comboBox_7.addItem(filename)
def bbox(self):
r = tool.rectangle()
line_bbox.setText(str(r.xMinimum()))
line_bbox.show()
def foo(self,rect):
print(rect)
def crs(self, crs):
return crs
def output_reclassify(self):
filename, filter_string = QFileDialog.getSaveFileName(self.window, "Select output file ", "", '*.tif')
self.window.lineEdit.setText(filename)
def output_prescription(self):
filename, filter_string = QFileDialog.getSaveFileName(self.window, "Select output file ", "", '*.shp')
self.window.lineEdit_2.setText(filename)
def quantile(self):
input_raster = self.dlg.lineEdit_22.text()
import numpy as np
from osgeo import gdal, gdal_array
dataset = gdal.Open(input_raster)
band = dataset.GetRasterBand(1)
nodata = band.GetNoDataValue()
array = dataset.ReadAsArray()
#number of rows
nrows = int(self.window.tableWidget.rowCount())
new_array = array
nan_array = array
nan_array[array == nodata] = np.nan
# routine to obtain quantiles
lista_quantile = [0]
j = 0
percentile_list = []
value = 100/(int(nrows)-1)
while j < int(nrows) - 1:
lista_quantile.append(round(int(lista_quantile[j]) + value, 3))
j = j + 1
for ii in lista_quantile:
percentile = np.nanpercentile(nan_array, int(ii))
percentile_list.append(round(percentile,3))
# values repeated in first column
percentile_ = []
for iii in range(0,nrows-1):