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cloud_masking.py
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cloud_masking.py
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# -*- coding: utf-8 -*-
"""
/***************************************************************************
CloudMasking
A QGIS plugin
Cloud masking for landsat products using different process suck as fmask
-------------------
copyright : (C) 2016-2022 by Xavier Corredor Llano, SMByC
email : xcorredorl@ideam.gov.co
***************************************************************************/
/***************************************************************************
* *
* 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 3 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
"""
import os.path
import platform
import shutil
import tempfile
from datetime import datetime
from subprocess import call
from osgeo import gdal
from qgis.PyQt.QtCore import QSettings, QTranslator, qVersion, QCoreApplication, Qt, pyqtSlot, QLocale
from qgis.PyQt.QtWidgets import QAction, QMessageBox, QApplication, QFileDialog, QListWidgetItem, QSizePolicy
from qgis.PyQt.QtGui import QIcon
from qgis.PyQt.QtWidgets import QCheckBox, QGroupBox, QRadioButton
from qgis.core import QgsProject, QgsRasterLayer, QgsMapLayer, QgsCoordinateTransform, \
QgsMapLayerProxyModel, QgsVectorFileWriter, Qgis
from qgis.utils import iface
# Initialize Qt resources from file resources.py
from . import resources
from CloudMasking.core import cloud_filters, color_stack
from CloudMasking.core.utils import apply_symbology, get_prefer_name, update_process_bar, get_extent, \
load_and_select_filepath_in, get_file_path_of_layer, get_nodata_value_from_file, wait_process, error_handler
from CloudMasking.libs import gdal_calc, gdal_merge
from CloudMasking.gui.cloud_masking_dockwidget import CloudMaskingDockWidget
from CloudMasking.gui.about_dialog import AboutDialog
class CloudMasking:
"""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', QLocale().name())[0:2]
locale_path = os.path.join(
self.plugin_dir,
'i18n',
'CloudMasking_{}.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)
self.menu_name_plugin = self.tr("&Cloud masking for Landsat products")
self.pluginIsActive = False
self.dockwidget = None
# Obtaining the map canvas
self.canvas = iface.mapCanvas()
self.about_dialog = AboutDialog()
# 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('CloudMasking', message)
def initGui(self):
### Main dockwidget
# Create action that will start plugin configuration
icon_path = ':/plugins/CloudMasking/icons/cloud_masking.svg'
self.dockable_action = QAction(QIcon(icon_path), self.tr('&Cloud Masking'), self.iface.mainWindow())
# connect the action to the run method
self.dockable_action.triggered.connect(self.run)
# Add toolbar button and menu item
self.iface.addToolBarIcon(self.dockable_action)
self.iface.addPluginToMenu(self.menu_name_plugin, self.dockable_action)
### About dialog
# Create action that will start plugin configuration
icon_path = ':/plugins/CloudMasking/icons/about.svg'
self.about_action = QAction(QIcon(icon_path), self.tr('About'), self.iface.mainWindow())
# connect the action to the run method
self.about_action.triggered.connect(self.about)
# Add toolbar button and menu item
self.iface.addPluginToMenu(self.menu_name_plugin, self.about_action)
# --------------------------------------------------------------------------
def onClosePlugin(self):
"""Cleanup necessary items here when plugin dockwidget is closed"""
self.removes_temporary_files()
# disconnects
self.dockwidget.closingPlugin.disconnect(self.onClosePlugin)
QgsProject.instance().layersAdded.disconnect(self.updateLayersList_SingleLayerMask)
QgsProject.instance().layersRemoved.disconnect(self.updateLayersList_SingleLayerMask)
QgsProject.instance().layersAdded.disconnect(self.updateLayersList_MultipleLayerMask)
QgsProject.instance().layersRemoved.disconnect(self.updateLayersList_MultipleLayerMask)
# remove this statement if dockwidget is to remain
# for reuse if plugin is reopened
# Commented next statement since it causes QGIS crashe
# when closing the docked window:
self.dockwidget.deleteLater()
self.dockwidget = None
self.pluginIsActive = False
from qgis.utils import reloadPlugin
reloadPlugin("CloudMasking")
def about(self):
self.about_dialog.show()
def unload(self):
"""Removes the plugin menu item and icon from QGIS GUI."""
self.removes_temporary_files()
# Remove the plugin menu item and icon
self.iface.removePluginMenu(self.menu_name_plugin, self.dockable_action)
self.iface.removePluginMenu(self.menu_name_plugin, self.about_action)
self.iface.removeToolBarIcon(self.dockable_action)
# --------------------------------------------------------------------------
def run(self):
"""Run method that loads and starts the plugin"""
if not self.pluginIsActive:
self.pluginIsActive = True
# print "** STARTING CloudMasking"
# dockwidget may not exist if:
# first run of plugin
# removed on close (see self.onClosePlugin method)
if self.dockwidget == None:
# Create the dockwidget (after translation) and keep reference
self.dockwidget = CloudMaskingDockWidget()
# connect to provide cleanup on closing of dockwidget
self.dockwidget.closingPlugin.connect(self.onClosePlugin)
# show the dockwidget
self.iface.addDockWidget(Qt.RightDockWidgetArea, self.dockwidget)
self.dockwidget.tabWidget.setCurrentWidget(self.dockwidget.tab_OL) # focus first tab
self.dockwidget.show()
# initial masking and color stack instance
self.masking_result = None
self.color_stack_scene = None
# set properties to QgsMapLayerComboBox for mask list
self.dockwidget.select_SingleLayerMask.setCurrentIndex(-1)
self.dockwidget.select_SingleLayerMask.setFilters(QgsMapLayerProxyModel.RasterLayer)
self.dockwidget.OnlyMaskLayers_SingleMask.clicked.connect(self.updateLayersList_SingleLayerMask)
QgsProject.instance().layersAdded.connect(self.updateLayersList_SingleLayerMask)
QgsProject.instance().layersRemoved.connect(self.updateLayersList_SingleLayerMask)
self.updateLayersList_SingleLayerMask()
# tabwidget
self.update_tab_select_mask(0)
self.dockwidget.select_layer_mask.currentChanged.connect(self.update_tab_select_mask)
# set properties to list for select multiple layer mask
self.updateLayersList_MultipleLayerMask()
self.dockwidget.OnlyMaskLayers_MultipleMask.clicked.connect(self.updateLayersList_MultipleLayerMask)
QgsProject.instance().layersAdded.connect(self.updateLayersList_MultipleLayerMask)
QgsProject.instance().layersRemoved.connect(self.updateLayersList_MultipleLayerMask)
self.dockwidget.QPBtn_SelectAll.clicked.connect(self.selectAll_MultipleLayerMask)
self.dockwidget.QPBtn_DeselectAll.clicked.connect(self.deselectAll_MultipleLayerMask)
# set properties to QgsMapLayerComboBox for shape area
self.dockwidget.QCBox_MaskInShapeArea.setCurrentIndex(-1)
self.dockwidget.QCBox_MaskInShapeArea.setFilters(QgsMapLayerProxyModel.VectorLayer)
# call to browse the shape area for make mask inside it
self.dockwidget.button_BrowseShapeArea.clicked.connect(lambda: self.browser_dialog_to_load_file(
self.dockwidget.QCBox_MaskInShapeArea,
dialog_title=self.tr("Select the vector file"),
file_filters=self.tr("Vector files (*.gpkg *.shp);;All files (*.*)"),
suggested_path=os.path.dirname(self.dockwidget.mtl_path)))
# call to load MTL file
self.dockwidget.button_LoadMTL.clicked.connect(lambda: self.button_load_mtl())
# call to clear all
self.dockwidget.button_ClearAll.clicked.connect(lambda: self.button_clear_all())
# call to load natural color stack
self.dockwidget.button_NaturalColorStack.clicked.connect(lambda: self.set_color_stack("natural_color"))
# call to load false color stack
self.dockwidget.button_FalseColorStack.clicked.connect(lambda: self.set_color_stack("false_color"))
# call to load infrareds stack
self.dockwidget.button_InfraredsStack.clicked.connect(lambda: self.set_color_stack("infrareds"))
# call to process load stack
self.dockwidget.button_processLoadStack.clicked.connect(lambda: self.load_stack())
# call to process mask
self.dockwidget.button_processMask.clicked.connect(lambda: self.process_mask())
# save simple mask
self.dockwidget.button_SimpleSaveMask.clicked.connect(lambda: self.fileDialog_exportSimpleMask())
# save multi mask
self.dockwidget.button_MultiSaveMask.clicked.connect(lambda: self.fileDialog_exportMultiMask())
# select result
self.dockwidget.button_SelectResult.clicked.connect(self.fileDialog_SaveResult)
# select result
self.dockwidget.button_SelectPFile.clicked.connect(self.fileDialog_SelectPFile)
# button for Apply Mask
self.dockwidget.button_processApplyMask.clicked.connect(lambda: self.apply_mask())
def update_tab_select_mask(self, current_tab_idx):
"""Adjust the size tab based on the content"""
for tab_idx in range(self.dockwidget.select_layer_mask.count()):
if tab_idx != current_tab_idx:
self.dockwidget.select_layer_mask.widget(tab_idx).setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Ignored)
self.dockwidget.select_layer_mask.widget(current_tab_idx).setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Preferred)
self.dockwidget.select_layer_mask.widget(current_tab_idx).resize(
self.dockwidget.select_layer_mask.widget(current_tab_idx).minimumSizeHint())
self.dockwidget.select_layer_mask.widget(current_tab_idx).adjustSize()
def updateLayersList_SingleLayerMask(self):
# filtering
excepted = []
if self.dockwidget.OnlyMaskLayers_SingleMask.isChecked():
for layer in [l for l in QgsProject.instance().mapLayers().values() if l.type() == QgsMapLayer.RasterLayer]:
if not layer.name().startswith("Cloud Mask"):
excepted.append(layer)
# set excepted layers
self.dockwidget.select_SingleLayerMask.setExceptedLayerList(excepted)
def updateLayersList_MultipleLayerMask(self):
# delete items
self.dockwidget.select_MultipleLayerMask.clear()
# filtering
for layer in [l for l in QgsProject.instance().mapLayers().values() if l.type() == QgsMapLayer.RasterLayer]:
if self.dockwidget.OnlyMaskLayers_MultipleMask.isChecked() and not layer.name().startswith("Cloud Mask"):
continue
item = QListWidgetItem(layer.name())
item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
item.setCheckState(Qt.Unchecked)
self.dockwidget.select_MultipleLayerMask.addItem(item)
def selectAll_MultipleLayerMask(self):
for x in range(self.dockwidget.select_MultipleLayerMask.count()):
self.dockwidget.select_MultipleLayerMask.item(x).setCheckState(Qt.Checked)
def deselectAll_MultipleLayerMask(self):
for x in range(self.dockwidget.select_MultipleLayerMask.count()):
self.dockwidget.select_MultipleLayerMask.item(x).setCheckState(Qt.Unchecked)
def getLayerByName(self, layer_name):
for layer in QgsProject.instance().mapLayers().values():
if layer.name() == layer_name:
return layer
def set_color_stack(self, color_type):
# select the bands for color stack for Landsat 4, 5 y 7
if self.dockwidget.landsat_version in [4, 5, 7]:
if color_type == "natural_color":
bands = [3, 2, 1]
if color_type == "false_color":
bands = [4, 3, 2]
if color_type == "infrareds":
bands = [4, 5, 7]
# select the bands for color stack for Landsat 8
if self.dockwidget.landsat_version in [8, 9]:
if color_type == "natural_color":
bands = [4, 3, 2]
if color_type == "false_color":
bands = [5, 4, 3]
if color_type == "infrareds":
bands = [5, 6, 7]
self.dockwidget.SelectBand_R.setCurrentIndex(self.dockwidget.reflectance_bands.index(bands[0]))
self.dockwidget.SelectBand_G.setCurrentIndex(self.dockwidget.reflectance_bands.index(bands[1]))
self.dockwidget.SelectBand_B.setCurrentIndex(self.dockwidget.reflectance_bands.index(bands[2]))
@wait_process
def load_stack(self):
update_process_bar(self.dockwidget.bar_progressLoadStack, 40,
self.dockwidget.status_processLoadStack, self.tr("Loading stack..."))
bands = []
try:
bands.append(int(self.dockwidget.SelectBand_R.currentText()))
bands.append(int(self.dockwidget.SelectBand_G.currentText()))
bands.append(int(self.dockwidget.SelectBand_B.currentText()))
except:
update_process_bar(self.dockwidget.bar_progressLoadStack, 0,
self.dockwidget.status_processLoadStack, self.tr("Error: first choose a color stack"))
return
self.color_stack_scene = color_stack.ColorStack(self.dockwidget.mtl_path,
self.dockwidget.mtl_file,
bands,
self.dockwidget.tmp_dir)
self.color_stack_scene.do_color_stack()
self.color_stack_scene.load_color_stack()
update_process_bar(self.dockwidget.bar_progressLoadStack, 100,
self.dockwidget.status_processLoadStack, self.tr("DONE"))
@pyqtSlot()
def browser_dialog_to_load_file(self, combo_box, dialog_title, file_filters, suggested_path=""):
file_path, _ = QFileDialog.getOpenFileName(self.dockwidget, dialog_title, suggested_path, file_filters)
if file_path != '' and os.path.isfile(file_path):
# load to qgis and update combobox list
load_and_select_filepath_in(combo_box, file_path)
@wait_process
def process_mask(self):
"""Make the process
"""
# initialize the symbology
enable_symbology = [False, False, False, False, False, False, False, False, False]
# check if any filters has been enabled before process
if (not self.dockwidget.checkBox_FMask.isChecked() and
not self.dockwidget.checkBox_BlueBand.isChecked() and
not self.dockwidget.checkBox_CloudQA.isChecked() and
not self.dockwidget.checkBox_Aerosol.isChecked() and
not self.dockwidget.checkBox_PixelQA.isChecked() and
not self.dockwidget.checkBox_QABandC1L457.isChecked() and
not self.dockwidget.checkBox_QABandC1L89.isChecked() and
not self.dockwidget.checkBox_QABandC2.isChecked()):
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters enabled for apply"))
return
# create the masking result instance if not exist
if (not isinstance(self.masking_result, cloud_filters.CloudMaskingResult) or
not self.masking_result.landsat_scene == self.dockwidget.mtl_file['LANDSAT_SCENE_ID'] or
not self.masking_result.collection == int(self.dockwidget.mtl_file['COLLECTION_NUMBER'])):
# create a new instance of cloud masking result
self.masking_result = cloud_filters.CloudMaskingResult(self.dockwidget.mtl_path,
self.dockwidget.mtl_file,
self.dockwidget.tmp_dir)
self.masking_result.process_status = self.dockwidget.status_processMask
self.masking_result.process_bar = self.dockwidget.bar_processMask
# re-init the result masking files
self.masking_result.cloud_masking_files = []
########################################
## Set the extent selector
# set for rectangular region
if self.dockwidget.checkBox_AOISelector.isChecked():
self.masking_result.clipping_with_aoi = True
self.masking_result.aoi_features = self.dockwidget.aoi_features
else:
self.masking_result.clipping_with_aoi = False
# set for the shape selector
if self.dockwidget.checkBox_ShapeSelector.isChecked():
self.masking_result.clipping_with_shape = True
self.masking_result.shape_layer = self.dockwidget.QCBox_MaskInShapeArea.currentLayer()
# get and save trim extent of shapefile for clip
canvas_crs = self.canvas.mapSettings().destinationCrs()
shape_crs = self.masking_result.shape_layer.crs()
shape_canvas_transform = QgsCoordinateTransform(shape_crs, canvas_crs, QgsProject.instance())
self.masking_result.shape_extent = shape_canvas_transform.transform(
self.masking_result.shape_layer.extent())
self.masking_result.shape_path = get_file_path_of_layer(
self.dockwidget.QCBox_MaskInShapeArea.currentLayer())
# check if the shape is a memory layer, then save and used it
if not os.path.isfile(self.masking_result.shape_path):
mem_layer = self.dockwidget.QCBox_MaskInShapeArea.currentLayer()
tmp_memory_fd, tmp_memory_file = tempfile.mkstemp(prefix='memory_layer_', suffix='.gpkg', dir=self.dockwidget.tmp_dir)
QgsVectorFileWriter.writeAsVectorFormat(mem_layer, tmp_memory_file, "UTF-8", mem_layer.crs(), "GPKG")
os.close(tmp_memory_fd)
self.masking_result.shape_path = tmp_memory_file
if self.dockwidget.shapeSelector_CutWithShape.isChecked():
self.masking_result.crop_to_cutline = True
else:
self.masking_result.crop_to_cutline = False
else:
self.masking_result.clipping_with_shape = False
# check extent area selector and shape file
if self.dockwidget.checkBox_AOISelector.isChecked() and (self.dockwidget.aoi_features is None \
or not self.dockwidget.aoi_features.hasFeatures()):
self.dockwidget.status_processMask.setText(
self.tr("Error: no AOI drawn in canvas"))
return
if self.dockwidget.checkBox_ShapeSelector.isChecked():
if not self.masking_result.shape_path:
self.dockwidget.status_processMask.setText(
self.tr("Error: not shape file defined"))
return
if not os.path.isfile(self.masking_result.shape_path):
self.dockwidget.status_processMask.setText(
self.tr("Error: shape file not exists"))
return
########################################
# FMask filter
if self.dockwidget.checkBox_FMask.isChecked():
# get enabled Fmask filters from UI and set symbology
enable_symbology[0:4] = [False, False, False, False]
filters_enabled = {"Fmask Cloud": False, "Fmask Shadow": False, "Fmask Snow": False, "Fmask Water": False, }
# Cloud
if self.dockwidget.checkBox_FMask_Cloud.isChecked():
enable_symbology[0] = True
filters_enabled["Fmask Cloud"] = True
# Shadow
if self.dockwidget.checkBox_FMask_Shadow.isChecked():
enable_symbology[1] = True
filters_enabled["Fmask Shadow"] = True
# Snow
if self.dockwidget.checkBox_FMask_Snow.isChecked():
enable_symbology[2] = True
filters_enabled["Fmask Snow"] = True
# Water
if self.dockwidget.checkBox_FMask_Water.isChecked():
enable_symbology[3] = True
filters_enabled["Fmask Water"] = True
# fmask filter
self.masking_result.do_fmask(
filters_enabled=filters_enabled,
cloud_prob_thresh=float(self.dockwidget.doubleSpinBox_CPT.value()),
cirrus_prob_ratio=float(self.dockwidget.doubleSpinBox_CPR.value()),
cloud_buffer_size=float(self.dockwidget.doubleSpinBox_CB.value()),
shadow_buffer_size=float(self.dockwidget.doubleSpinBox_SB.value()),
nir_fill_thresh=float(self.dockwidget.doubleSpinBox_NFT.value()),
swir2_thresh=float(self.dockwidget.doubleSpinBox_S2T.value()),
whiteness_thresh=float(self.dockwidget.doubleSpinBox_WT.value()),
swir2_water_test=float(self.dockwidget.doubleSpinBox_S2WT.value()),
nir_snow_thresh=float(self.dockwidget.doubleSpinBox_NST.value()),
green_snow_thresh=float(self.dockwidget.doubleSpinBox_GST.value()),
)
########################################
# Blue Band filter
if self.dockwidget.checkBox_BlueBand.isChecked():
self.masking_result.do_blue_band(int(self.dockwidget.doubleSpinBox_BB.value()))
enable_symbology[4] = True
########################################
# Cloud QA L457 filter
if self.dockwidget.checkBox_CloudQA.isChecked():
if self.dockwidget.landsat_version in [4, 5, 7]:
checked_items = {}
# one bit items selected
cloud_qa_items_1b = ["Dark Dense Vegetation (bit 0)", "Cloud (bit 1)", "Cloud Shadow (bit 2)",
"Adjacent to cloud (bit 3)", "Snow (bit 4)", "Water (bit 5)"]
for checkbox in self.dockwidget.widget_CloudQA_L457_bits.findChildren(QCheckBox):
item = checkbox.text().replace("&", "")
if item in cloud_qa_items_1b:
checked_items[item] = checkbox.isChecked()
# set and check the specific decimal values
try:
cloud_qa_svalues = self.dockwidget.CloudQA_L457_svalues.text()
if cloud_qa_svalues:
cloud_qa_svalues = [int(sv) for sv in cloud_qa_svalues.split(",")]
else:
cloud_qa_svalues = []
except:
self.dockwidget.status_processMask.setText(
self.tr("Error: setting the specific values in Cloud QA"))
return
# check is not selected any Cloud QA filter
if not any(checked_items.values()) and not cloud_qa_svalues:
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters selected in Cloud QA"))
return
self.masking_result.do_cloud_qa_l457(self.dockwidget.cloud_qa_file, checked_items, cloud_qa_svalues)
enable_symbology[5] = True
########################################
# Aerosol L89 filter
if self.dockwidget.checkBox_Aerosol.isChecked():
if self.dockwidget.landsat_version in [8, 9]:
checked_items = {}
# one bit items selected
aerosol_items_1b = ["Aerosol Retrieval - Valid (bit 1)", "Aerosol Retrieval - Interpolated (bit 2)",
"Water Pixel (bit 3)"]
for checkbox in self.dockwidget.widget_Aerosol_bits.findChildren(QCheckBox):
item = checkbox.text().replace("&", "")
if item in aerosol_items_1b:
checked_items[item] = checkbox.isChecked()
# two bits items selected
aerosol_items_2b = ["Aerosol Content (bits 6-7)"]
levels = ["Climatology content", "Low content", "Average content", "High content"]
for groupbox in self.dockwidget.widget_Aerosol_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in aerosol_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# set and check the specific decimal values
try:
aerosol_svalues = self.dockwidget.Aerosol_L89_svalues.text()
if aerosol_svalues:
aerosol_svalues = [int(sv) for sv in aerosol_svalues.split(",")]
else:
aerosol_svalues = []
except:
self.dockwidget.status_processMask.setText(
self.tr("Error: setting the specific values in Aerosol"))
return
# check is not selected any Aerosol filter
if not any(checked_items.values()) and not aerosol_svalues:
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters selected in Aerosol"))
return
self.masking_result.do_aerosol_l89(self.dockwidget.aerosol_file, checked_items, aerosol_svalues)
enable_symbology[6] = True
########################################
# Pixel QA filter
if self.dockwidget.checkBox_PixelQA.isChecked():
checked_items = {}
# one bit items selected
if self.dockwidget.landsat_version in [4, 5, 7]:
pixel_qa_items_1b = ["Fill-nodata (bit 0)", "Water (bit 2)", "Cloud Shadow (bit 3)",
"Snow (bit 4)", "Cloud (bit 5)"]
if self.dockwidget.landsat_version in [8, 9]:
pixel_qa_items_1b = ["Fill-nodata (bit 0)", "Water (bit 2)", "Cloud Shadow (bit 3)",
"Snow (bit 4)", "Cloud (bit 5)", "Terrain Occlusion (bit 10)"]
for checkbox in self.dockwidget.widget_PixelQA_bits.findChildren(QCheckBox):
item = checkbox.text().replace("&", "")
if item in pixel_qa_items_1b:
checked_items[item] = checkbox.isChecked()
# two bits items selected
if self.dockwidget.landsat_version in [4, 5, 7]:
pixel_qa_items_2b = ["Cloud Confidence (bits 6-7)"]
if self.dockwidget.landsat_version in [8, 9]:
pixel_qa_items_2b = ["Cloud Confidence (bits 6-7)", "Cirrus Confidence (bits 8-9)"]
levels = ["0% None", "0-33% Low", "34-66% Medium", "67-100% High"]
for groupbox in self.dockwidget.widget_PixelQA_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in pixel_qa_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# set and check the specific decimal values
try:
pixel_qa_svalues = self.dockwidget.PixelQA_svalues.text()
if pixel_qa_svalues:
pixel_qa_svalues = [int(sv) for sv in pixel_qa_svalues.split(",")]
else:
pixel_qa_svalues = []
except:
self.dockwidget.status_processMask.setText(
self.tr("Error: setting the specific values in Pixel QA"))
return
# check is not selected any Pixel QA filter
if not any(checked_items.values()) and not pixel_qa_svalues:
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters selected in Pixel QA"))
return
self.masking_result.do_pixel_qa(self.dockwidget.pixel_qa_file, checked_items, pixel_qa_svalues)
enable_symbology[7] = True
########################################
# QA Band C1 filter L457
if self.dockwidget.checkBox_QABandC1L457.isChecked():
if self.dockwidget.landsat_version in [4, 5, 7]:
checked_items = {}
# one bit items selected
qaband_items_1b = ["Dropped Pixel (bit 1)", "Cloud (bit 4)"]
for checkbox in self.dockwidget.widget_QABandC1L457_bits.findChildren(QCheckBox):
item = checkbox.text().replace("&", "")
if item in qaband_items_1b:
checked_items[item] = checkbox.isChecked()
# two bits items selected
qaband_items_2b = ["Radiometric Saturation (bits 2-3)"]
levels = ["No bands saturated", "1 to 2 bands saturated", "3 to 4 bands saturated", "> 4 bands saturated"]
for groupbox in self.dockwidget.widget_QABandC1L457_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in qaband_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# two bits items selected
qaband_items_2b = ["Cloud Confidence (bits 5-6)", "Cloud Shadow (bits 7-8)",
"Snow/Ice (bits 9-10)"]
levels = ["0% None", "0-33% Low", "34-66% Medium", "67-100% High"]
for groupbox in self.dockwidget.widget_QABandC1L457_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in qaband_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# set and check the specific decimal values
try:
qaband_svalues = self.dockwidget.QABandC1L457_svalues.text()
if qaband_svalues:
qaband_svalues = [int(sv) for sv in qaband_svalues.split(",")]
else:
qaband_svalues = []
except:
self.dockwidget.status_processMask.setText(
self.tr("Error: setting the specific values in QA Band"))
return
# check is not selected any QA Band filter
if not any(checked_items.values()) and not qaband_svalues:
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters selected in QA Band"))
return
self.masking_result.do_qaband_c1_l457(self.dockwidget.qabandc1_file_l457, checked_items, qaband_svalues)
enable_symbology[8] = True
########################################
# QA Band C1 filter L89
if self.dockwidget.checkBox_QABandC1L89.isChecked():
if self.dockwidget.landsat_version in [8, 9]:
checked_items = {}
# one bit items selected
qaband_items_1b = ["Terrain Occlusion (bit 1)", "Cloud (bit 4)"]
for checkbox in self.dockwidget.widget_QABandC1L89_bits.findChildren(QCheckBox):
item = checkbox.text().replace("&", "")
if item in qaband_items_1b:
checked_items[item] = checkbox.isChecked()
# two bits items selected
qaband_items_2b = ["Radiometric Saturation (bits 2-3)"]
levels = ["No bands saturated", "1 to 2 bands saturated", "3 to 4 bands saturated", "> 4 bands saturated"]
for groupbox in self.dockwidget.widget_QABandC1L89_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in qaband_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# two bits items selected
qaband_items_2b = ["Cloud Confidence (bits 5-6)", "Cloud Shadow (bits 7-8)",
"Snow/Ice (bits 9-10)", "Cirrus Confidence (bits 11-12)"]
levels = ["0% None", "0-33% Low", "34-66% Medium", "67-100% High"]
for groupbox in self.dockwidget.widget_QABandC1L89_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in qaband_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# set and check the specific decimal values
try:
qaband_svalues = self.dockwidget.QABandC1L89_svalues.text()
if qaband_svalues:
qaband_svalues = [int(sv) for sv in qaband_svalues.split(",")]
else:
qaband_svalues = []
except:
self.dockwidget.status_processMask.setText(
self.tr("Error: setting the specific values in QA Band"))
return
# check is not selected any QA Band filter
if not any(checked_items.values()) and not qaband_svalues:
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters selected in QA Band"))
return
self.masking_result.do_qaband_c1_l89(self.dockwidget.qabandc1_file_l89, checked_items, qaband_svalues)
enable_symbology[8] = True
########################################
# QA Band C2 filter
if self.dockwidget.checkBox_QABandC2.isChecked():
if self.dockwidget.landsat_version in [4, 5, 7, 8, 9]:
checked_items = {}
# one bit items selected
qaband_items_1b = ["Dilated Cloud (bit 1)", "Cirrus (bit 2)", "Cloud (bit 3)",
"Cloud Shadow (bit 4)", "Snow (bit 5)", "Water (bit 7)"]
for checkbox in self.dockwidget.widget_QABandC2_bits.findChildren(QCheckBox):
item = checkbox.text().replace("&", "")
if item in qaband_items_1b:
checked_items[item] = checkbox.isChecked()
# two bits items selected
qaband_items_2b = ["Cloud Confidence (bits 8-9)", "Cloud Shadow Confidence (bits 10-11)",
"Snow/Ice Confidence (bits 12-13)", "Cirrus Confidence (bits 14-15)"]
levels = ["Low", "Medium", "High"]
for groupbox in self.dockwidget.widget_QABandC2_bits.findChildren(QGroupBox):
group_item = groupbox.title().replace("&", "")
if group_item in qaband_items_2b and groupbox.isChecked():
levels_selected = []
for radiobutton in groupbox.findChildren(QRadioButton):
check_item = radiobutton.text().replace("&", "")
if check_item in levels and radiobutton.isChecked():
levels_selected.append(check_item)
if levels_selected:
checked_items[group_item] = levels_selected
# set and check the specific decimal values
try:
qaband_svalues = self.dockwidget.QABandC2_svalues.text()
if qaband_svalues:
qaband_svalues = [int(sv) for sv in qaband_svalues.split(",")]
else:
qaband_svalues = []
except:
self.dockwidget.status_processMask.setText(
self.tr("Error: setting the specific values in QA Band"))
return
# check is not selected any QA Band filter
if not any(checked_items.values()) and not qaband_svalues:
self.dockwidget.status_processMask.setText(
self.tr("Error: no filters selected in QA Band"))
return
self.masking_result.do_qaband_c2(self.dockwidget.qabandc2_file, checked_items, qaband_svalues)
enable_symbology[8] = True
########################################
# Blended cloud masking files
# only one filter is activated
if len(self.masking_result.cloud_masking_files) == 1:
self.final_cloud_mask_file = self.masking_result.cloud_masking_files[0]
# two filters are activated
if len(self.masking_result.cloud_masking_files) == 2:
self.final_cloud_mask_file = os.path.join(self.dockwidget.tmp_dir,
"cloud_blended_{}.tif".format(datetime.now().strftime('%H%M%S')))
gdal_calc.Calc(calc="A*(A>1)+B*(A==1)", outfile=self.final_cloud_mask_file,
A=self.masking_result.cloud_masking_files[0], B=self.masking_result.cloud_masking_files[1])
# three filters are activated
if len(self.masking_result.cloud_masking_files) == 3:
self.final_cloud_mask_file = os.path.join(self.dockwidget.tmp_dir,
"cloud_blended_{}.tif".format(datetime.now().strftime('%H%M%S')))
gdal_calc.Calc(calc="A*(A>1)+B*logical_and(A==1,B>1)+C*logical_and(A==1,B==1)",
outfile=self.final_cloud_mask_file,
A=self.masking_result.cloud_masking_files[0], B=self.masking_result.cloud_masking_files[1],
C=self.masking_result.cloud_masking_files[2])
# four filters are activated
if len(self.masking_result.cloud_masking_files) == 4:
self.final_cloud_mask_file = os.path.join(self.dockwidget.tmp_dir,
"cloud_blended_{}.tif".format(datetime.now().strftime('%H%M%S')))
gdal_calc.Calc(calc="A*(A>1)+B*logical_and(A==1,B>1)+C*logical_and(logical_and(A==1,B==1),C>1)"
"+D*logical_and(logical_and(A==1,B==1),C==1)",
outfile=self.final_cloud_mask_file,
A=self.masking_result.cloud_masking_files[0], B=self.masking_result.cloud_masking_files[1],
C=self.masking_result.cloud_masking_files[2], D=self.masking_result.cloud_masking_files[3])
# five filters are activated
if len(self.masking_result.cloud_masking_files) == 5:
self.final_cloud_mask_file = os.path.join(self.dockwidget.tmp_dir,
"cloud_blended_{}.tif".format(datetime.now().strftime('%H%M%S')))
gdal_calc.Calc(calc="A*(A>1)+B*logical_and(A==1,B>1)+C*logical_and(logical_and(A==1,B==1),C>1)"
"+D*logical_and(logical_and(A==1,B==1,C==1),D>1)+E*logical_and(logical_and(A==1,B==1,C==1),D==1)",
outfile=self.final_cloud_mask_file,
A=self.masking_result.cloud_masking_files[0], B=self.masking_result.cloud_masking_files[1],
C=self.masking_result.cloud_masking_files[2], D=self.masking_result.cloud_masking_files[3],
E=self.masking_result.cloud_masking_files[4])
########################################
# keep the data outside the shape area as valid data (=1), important for apply several mask
if (self.dockwidget.checkBox_ShapeSelector.isChecked() and not self.dockwidget.shapeSelector_CutWithShape.isChecked()) or \
self.dockwidget.checkBox_AOISelector.isChecked():
self.masking_result.clip(self.final_cloud_mask_file, self.final_cloud_mask_file.replace(".tif", "1.tif"),
nodata=1, process_bar=False)
os.remove(self.final_cloud_mask_file)
# expand to original extent
img_path = get_prefer_name(os.path.join(os.path.dirname(self.dockwidget.mtl_path),
self.dockwidget.mtl_file['FILE_NAME_BAND_1']))
if not os.path.exists(img_path):
img_path = get_prefer_name(os.path.join(os.path.dirname(self.dockwidget.mtl_path),
self.dockwidget.mtl_file['FILE_NAME_BAND_SR_1']))
extent = get_extent(img_path)
gdal.Translate(self.final_cloud_mask_file,
self.final_cloud_mask_file.replace(".tif", "1.tif"),
projWin=extent, noData=1)
os.remove(self.final_cloud_mask_file.replace(".tif", "1.tif"))
# unset nodata
cmd = ['gdal_edit' if platform.system() == 'Windows' else 'gdal_edit.py',
'"{}"'.format(self.final_cloud_mask_file), '-unsetnodata']
call(" ".join(cmd), shell=True)
else:
# mask the nodata value as 255 value
self.masking_result.do_nodata_mask(self.final_cloud_mask_file)
########################################
# Delete data outside the shapefile or selected area, as 255 value
if self.dockwidget.checkBox_ShapeSelector.isChecked() and self.dockwidget.shapeSelector_CutWithShape.isChecked():
# expand to original extent
img_path = get_prefer_name(os.path.join(os.path.dirname(self.dockwidget.mtl_path),
self.dockwidget.mtl_file['FILE_NAME_BAND_1']))
if not os.path.exists(img_path):
img_path = get_prefer_name(os.path.join(os.path.dirname(self.dockwidget.mtl_path),
self.dockwidget.mtl_file['FILE_NAME_BAND_SR_1']))
extent = get_extent(img_path)
gdal.Translate(self.final_cloud_mask_file.replace(".tif", "1.tif"), self.final_cloud_mask_file,
projWin=extent, noData=255)
os.remove(self.final_cloud_mask_file)
os.rename(self.final_cloud_mask_file.replace(".tif", "1.tif"), self.final_cloud_mask_file)
# unset nodata
cmd = ['gdal_edit' if platform.system() == 'Windows' else 'gdal_edit.py',
'"{}"'.format(self.final_cloud_mask_file), '-unsetnodata']
call(" ".join(cmd), shell=True)
########################################
# Post process mask
# delete unused output
# if memory/scratch layer was used
if self.dockwidget.checkBox_ShapeSelector.isChecked() and \
not os.path.isfile(get_file_path_of_layer(self.dockwidget.QCBox_MaskInShapeArea.currentLayer())):
if os.path.isfile(tmp_memory_file):
os.remove(tmp_memory_file)
# from fmask
if self.dockwidget.checkBox_FMask.isChecked():
os.remove(self.masking_result.angles_file)
os.remove(self.masking_result.saturationmask_file)
os.remove(self.masking_result.toa_file)
if os.path.isfile(self.masking_result.reflective_stack_clip_file):
os.remove(self.masking_result.reflective_stack_clip_file)
if os.path.isfile(self.masking_result.thermal_stack_clip_file):
os.remove(self.masking_result.thermal_stack_clip_file)
# from blue band
if self.dockwidget.checkBox_BlueBand.isChecked():
if os.path.isfile(self.masking_result.blue_band_clip_file):
os.remove(self.masking_result.blue_band_clip_file)
# from cloud QA
if self.dockwidget.checkBox_CloudQA.isChecked():
if os.path.isfile(self.masking_result.cloud_qa_clip_file):
os.remove(self.masking_result.cloud_qa_clip_file)
# from aerosol
if self.dockwidget.checkBox_Aerosol.isChecked():
if os.path.isfile(self.masking_result.aerosol_clip_file):
os.remove(self.masking_result.aerosol_clip_file)
# from Pixel QA
if self.dockwidget.checkBox_PixelQA.isChecked():
if os.path.isfile(self.masking_result.pixel_qa_clip_file):
os.remove(self.masking_result.pixel_qa_clip_file)
# from QA Band
if self.dockwidget.checkBox_QABandC1L457.isChecked() or \
self.dockwidget.checkBox_QABandC1L89.isChecked() or \
self.dockwidget.checkBox_QABandC2.isChecked():
if os.path.isfile(self.masking_result.qaband_clip_file):
os.remove(self.masking_result.qaband_clip_file)
# from original blended files
for cloud_masking_file in self.masking_result.cloud_masking_files:
if cloud_masking_file != self.final_cloud_mask_file:
os.remove(cloud_masking_file)
# Add to QGIS the reflectance stack file and cloud file
if self.masking_result.clipping_with_aoi:
masking_result_name = self.tr("Cloud Mask in area ({})".format(datetime.now().strftime('%H:%M:%S')))
elif self.dockwidget.checkBox_ShapeSelector.isChecked():
masking_result_name = self.tr("Cloud Mask in shape ({})".format(datetime.now().strftime('%H:%M:%S')))
else:
masking_result_name = self.tr("Cloud Mask ({})".format(datetime.now().strftime('%H:%M:%S')))
self.cloud_mask_rlayer = QgsRasterLayer(self.final_cloud_mask_file, masking_result_name)
QgsProject.instance().addMapLayer(self.cloud_mask_rlayer)
# Set symbology (thematic color and name) for new raster layer
symbology = {
'Fmask Cloud': (255, 0, 255, 255),
'Fmask Shadow': (255, 255, 0, 255),
'Fmask Snow': (85, 255, 255, 255),
'Fmask Water': (0, 0, 200, 255),
'Blue Band': (120, 212, 245, 255),
'Cloud QA': (255, 170, 0, 255),
'Aerosol': (255, 170, 0, 255),
'Pixel QA': (20, 180, 140, 255),
'QA Band': (170, 85, 255, 255),
}
# apply
apply_symbology(self.cloud_mask_rlayer,
symbology,
enable_symbology,
transparent=[])
# Refresh layer symbology
layer_node = QgsProject.instance().layerTreeRoot().findLayer(self.cloud_mask_rlayer)
self.iface.layerTreeView().layerTreeModel().refreshLayerLegend(layer_node)
# unselect AOI
self.dockwidget.checkBox_AOISelector.setChecked(False)
@wait_process
def fileDialog_exportSimpleMask(self):
"""Open QFileDialog for save mask file
"""
suggested_filename_mask = self.dockwidget.mtl_file['LANDSAT_SCENE_ID'] + "_Mask.tif"
mask_outpath, _ = QFileDialog.getSaveFileName(self.dockwidget, self.tr("Export the mask file"),
os.path.join(os.path.dirname(self.dockwidget.mtl_path),
suggested_filename_mask),
self.tr("GeoTiff files (*.tif);;All files (*.*)"))
mask_inpath = get_file_path_of_layer(self.getLayerByName(self.dockwidget.select_SingleLayerMask.currentText()))
if mask_outpath != '' and mask_inpath != '':
# unset nodata
cmd = ['gdal_edit' if platform.system() == 'Windows' else 'gdal_edit.py',
'"{}"'.format(mask_inpath), '-unsetnodata']
call(" ".join(cmd), shell=True)
cmd = ['gdal_calc' if platform.system() == 'Windows' else 'gdal_calc.py', '--quiet', '--overwrite',
'--calc "1*(A==1)+0*(A!=1)"', '-A "{}"'.format(mask_inpath), '--outfile "{}"'.format(mask_outpath),
'--type="Byte"', '--co COMPRESS=PACKBITS']