def run_stats(self):
"""Main function which do the process."""
# Get the common fields.
self.admin_layer = self.cbx_aggregation_layer.currentLayer()
selected_indicators = self.indicators_list()
if not self.name_field:
self.name_field = self.le_new_column.placeholderText()
# Output.
self.output_file_path = self.le_output_filepath.text()
try:
self.button_box_ok.setDisabled(True)
# noinspection PyArgumentList
QApplication.setOverrideCursor(Qt.WaitCursor)
# noinspection PyArgumentList
QApplication.processEvents()
if not self.admin_layer:
raise NoLayerProvidedException
if not self.admin_layer and self.use_point_layer:
raise NoLayerProvidedException
crs_admin_layer = self.admin_layer.crs()
if not self.use_point_layer and not self.use_area:
if not self.cbx_list_indicators:
raise FieldException(
field_1='List Indicators should not empty')
# Output
if not self.output_file_path:
temp_file = NamedTemporaryFile(delete=False,
suffix='-geopublichealth.shp')
self.output_file_path = temp_file.name
temp_file.flush()
temp_file.close()
admin_layer_provider = self.admin_layer.dataProvider()
fields = self.admin_layer.fields()
if admin_layer_provider.fields().indexFromName(
self.name_field) != -1:
raise FieldExistingException(field=self.name_field)
for indicator_selected in selected_indicators:
fields.append(
QgsField("Z" + indicator_selected[0], QVariant.Double))
fields.append(QgsField(self.name_field, QVariant.Double))
file_writer = QgsVectorFileWriter(self.output_file_path, 'utf-8',
fields, QgsWkbTypes.Polygon,
self.admin_layer.crs(),
'ESRI Shapefile')
count = self.admin_layer.featureCount()
stats = {}
for indicator_selected in selected_indicators:
values = []
indicator_selected_name = str(indicator_selected[0])
for i, feature in enumerate(self.admin_layer.getFeatures()):
index = self.admin_layer.fields().indexFromName(
indicator_selected_name)
if feature[index]:
value = float(feature[index])
else:
value = 0.0
values.append(value)
stats[indicator_selected_name] = Stats(values)
for i, feature in enumerate(self.admin_layer.getFeatures()):
attributes = feature.attributes()
composite_index_value = 0.0
for indicator_selected in selected_indicators:
indicator_selected_name = str(indicator_selected[0])
index = self.admin_layer.fields().indexFromName(
indicator_selected_name)
if feature[index]:
value = float(feature[index])
else:
value = 0.0
zscore = (value - stats[indicator_selected_name].average(
)) / stats[indicator_selected_name].standard_deviation()
attributes.append(float(zscore))
if indicator_selected[1] == '+':
composite_index_value -= zscore
else:
composite_index_value += zscore
attributes.append(float(composite_index_value))
new_feature = QgsFeature()
new_geom = QgsGeometry(feature.geometry())
new_feature.setAttributes(attributes)
new_feature.setGeometry(new_geom)
file_writer.addFeature(new_feature)
del file_writer
self.output_layer = QgsVectorLayer(self.output_file_path,
self.name_field, 'ogr')
QgsProject.instance().addMapLayer(self.output_layer)
if self.symbology.isChecked():
self.add_symbology()
self.signalStatus.emit(3, tr('Successful process'))
except GeoPublicHealthException as e:
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
finally:
self.button_box_ok.setDisabled(False)
# noinspection PyArgumentList
QApplication.restoreOverrideCursor()
# noinspection PyArgumentList
QApplication.processEvents()
def run_stats(self):
"""Main function which do the process."""
# Get the common fields.
self.admin_layer = self.cbx_aggregation_layer.currentLayer()
if self.use_point_layer:
# If we use a point layer.
point_layer = self.cbx_case_layer.currentLayer()
else:
# If we use a column with number of case.
case_column = self.cbx_case_field.currentField()
index_case = self.admin_layer.fieldNameIndex(case_column)
if not self.use_area:
# If we don't use density.
population = self.cbx_population_field.currentField()
index_population = self.admin_layer.fieldNameIndex(population)
if not self.name_field:
self.name_field = self.le_new_column.placeholderText()
# Add new column.
add_nb_intersections = self.checkBox_addNbIntersections.isChecked()
# Ratio
ratio = self.cbx_ratio.currentText()
ratio = ratio.replace(' ', '')
# Output.
self.output_file_path = self.le_output_filepath.text()
try:
self.button_box_ok.setDisabled(True)
# noinspection PyArgumentList
QApplication.setOverrideCursor(Qt.WaitCursor)
# noinspection PyArgumentList
QApplication.processEvents()
if not self.admin_layer:
raise NoLayerProvidedException
if not self.admin_layer and self.use_point_layer:
raise NoLayerProvidedException
crs_admin_layer = self.admin_layer.crs()
if self.use_point_layer:
crs_point_layer = point_layer.crs()
if crs_admin_layer != crs_point_layer:
raise DifferentCrsException(
epsg1=crs_point_layer.authid(),
epsg2=crs_admin_layer.authid())
if not self.use_point_layer and not self.use_area:
if index_population == index_case:
raise FieldException(field_1='Population', field_2='Case')
try:
ratio = float(ratio)
except ValueError:
raise NotANumberException(suffix=ratio)
# Output
if not self.output_file_path:
temp_file = NamedTemporaryFile(
delete=False,
suffix='-geohealth.shp')
self.output_file_path = temp_file.name
temp_file.flush()
temp_file.close()
admin_layer_provider = self.admin_layer.dataProvider()
fields = self.admin_layer.pendingFields()
if admin_layer_provider.fieldNameIndex(self.name_field) != -1:
raise FieldExistingException(field=self.name_field)
fields.append(QgsField(self.name_field, QVariant.Double))
if add_nb_intersections:
fields.append(QgsField('nb_of_intersections', QVariant.Int))
data = []
file_writer = QgsVectorFileWriter(
self.output_file_path,
'utf-8',
fields,
QGis.WKBPolygon,
self.admin_layer.crs(),
'ESRI Shapefile')
if self.use_point_layer:
total_case = point_layer.featureCount()
else:
total_case = 0
for i, feature in enumerate(self.admin_layer.getFeatures()):
attributes = feature.attributes()
if self.use_point_layer:
count = 0
for f in point_layer.getFeatures():
if f.geometry().intersects(feature.geometry()):
count += 1
else:
count = int(attributes[index_case])
total_case += count
try:
if self.use_area:
area = feature.geometry().area()
value = float(count) / area * ratio
else:
try:
population = float(attributes[index_population])
except ValueError:
raise NotANumberException(
suffix=attributes[index_population])
value = float(count) / population * ratio
except ZeroDivisionError:
value = None
except TypeError:
value = None
data.append(value)
attributes.append(value)
if add_nb_intersections:
attributes.append(count)
new_feature = QgsFeature()
new_geom = QgsGeometry(feature.geometry())
new_feature.setAttributes(attributes)
new_feature.setGeometry(new_geom)
file_writer.addFeature(new_feature)
del file_writer
self.output_layer = QgsVectorLayer(
self.output_file_path,
self.name_field,
'ogr')
QgsMapLayerRegistry.instance().addMapLayer(self.output_layer)
if self.checkBox_incidence_runStats.isChecked():
stats = Stats(data)
items_stats = [
'Incidence null,%d' % stats.null_values(),
'Count(point),%d' % total_case,
'Count(polygon),%d' % self.admin_layer.featureCount(),
'Min,%d' % stats.min(),
'Average,%f' % stats.average(),
'Max,%d' % stats.max(),
'Median,%f' % stats.median(),
'Range,%d' % stats.range(),
'Variance,%f' % stats.variance(),
'Standard deviation,%f' % stats.standard_deviation()
]
self.tableWidget.clear()
self.tableWidget.setColumnCount(2)
labels = ['Parameters', 'Values']
self.tableWidget.setHorizontalHeaderLabels(labels)
self.tableWidget.setRowCount(len(items_stats))
for i, item in enumerate(items_stats):
s = item.split(',')
self.tableWidget.setItem(i, 0, QTableWidgetItem(s[0]))
self.tableWidget.setItem(i, 1, QTableWidgetItem(s[1]))
self.tableWidget.resizeRowsToContents()
self.draw_plot(data)
else:
self.hide()
if self.symbology.isChecked():
self.add_symbology()
self.signalStatus.emit(3, tr('Successful process'))
except GeoPublicHealthException, e:
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
def run_blur(self):
self.progressBar_blur.setValue(0)
self.label_progress.setText('')
# Get all the fields.
layer_to_blur = self.comboBox_layerToBlur.currentLayer()
radius = self.spinBox_radius.value()
display = self.checkBox_addToMap.isChecked()
selected_features_only = self.checkBox_selectedOnlyFeatures.isChecked()
file_name = self.lineEdit_outputFile.text()
export_radius = self.checkBox_exportRadius.isChecked()
export_centroid = self.checkBox_exportCentroid.isChecked()
if self.checkBox_envelope.isChecked():
layer_envelope = self.comboBox_envelope.currentLayer()
else:
layer_envelope = None
# Test values
try:
if not layer_to_blur:
raise NoLayerProvidedException
if not file_name and not display:
raise NoFileNoDisplayException
if layer_to_blur.crs().mapUnits() != 0:
msg = tr('The projection of the map or of the layer is not '
'in meters. These parameters should be in meters.')
display_message_bar(msg, level=Qgis.Warning, duration=5)
#https://github.com/qgis/QGIS/commit/9302613f28207910608fe538a03e0bff82ca5629
if not file_name:
file_name = getTempFilename('blurring.shp')
pass
if layer_envelope:
if layer_to_blur.crs() != layer_envelope.crs():
raise DifferentCrsException(
epsg1=layer_to_blur.crs().authid(),
epsg2=layer_envelope.crs().authid())
self.label_progress.setText('Creating index ...')
layer_envelope = LayerIndex(layer_envelope)
self.progressBar_blur.setValue(0)
self.label_progress.setText('Blurring ...')
if selected_features_only:
features = layer_to_blur.selectedFeatures()
nb_features = layer_to_blur.selectedFeatureCount()
else:
features = layer_to_blur.getFeatures()
nb_features = layer_to_blur.featureCount()
# Fields
fields = layer_to_blur.fields()
if export_radius:
fields.append(QgsField(u"Radius", QVariant.Int))
if export_centroid:
fields.append(QgsField(u"X centroid", QVariant.Int))
fields.append(QgsField(u"Y centroid", QVariant.Int))
# Creating the output shapefile
file_writer = QgsVectorFileWriter(file_name, 'utf-8', fields,
Qgis.WKBPolygon,
layer_to_blur.crs(),
'ESRI Shapefile')
if file_writer.hasError() != QgsVectorFileWriter.NoError:
raise CreatingShapeFileException(suffix=file_writer.hasError())
# Creating the algorithm with radius
algo = Blur(radius, layer_envelope, export_radius, export_centroid)
for j, feature in enumerate(features):
feature = algo.blur(feature)
file_writer.addFeature(feature)
# Update progress bar
percent = int((j + 1) * 100 / nb_features)
self.progressBar_blur.setValue(percent)
# Write all features in the file
del file_writer
if display:
old_default_projection = self.settings.value(
'/Projections/defaultBehaviour')
self.settings.setValue('/Projections/defaultBehaviour',
'useProject')
layer_name = basename(file_name)
new_layer = QgsVectorLayer(file_name, layer_name, 'ogr')
new_layer.commitChanges()
new_layer.clearCacheImage()
# noinspection PyArgumentList
QgsProject.instance().addMapLayers([new_layer])
self.settings.setValue('/Projections/defaultBehaviour',
old_default_projection)
msg = tr('Successful export in %s' % file_name)
iface.messageBar().pushMessage(msg, level=Qgis.Info, duration=5)
self.signalAskCloseWindow.emit()
except GeoPublicHealthException as e:
self.label_progress.setText('')
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
finally:
# noinspection PyArgumentList
QApplication.restoreOverrideCursor()
# noinspection PyArgumentList
QApplication.processEvents()
def run_stats(self):
"""Main function which do the process."""
# Get the common fields..currentField()
self.admin_layer = self.cbx_aggregation_layer.currentLayer()
input_name = self.admin_layer.name()
field = self.cbx_indicator_field.currentField()
self.layer = QgsProject.instance().mapLayersByName(input_name)[0]
# Output.
self.output_file_path = self.le_output_filepath.text()
try:
self.button_box_ok.setDisabled(True)
# noinspection PyArgumentList
QApplication.setOverrideCursor(Qt.WaitCursor)
# noinspection PyArgumentList
QApplication.processEvents()
if not self.admin_layer:
raise NoLayerProvidedException
if not self.admin_layer and self.use_point_layer:
raise NoLayerProvidedException
crs_admin_layer = self.admin_layer.crs()
# Output
if not self.output_file_path:
temp_file = NamedTemporaryFile(delete=False,
suffix='-geopublichealth.shp')
self.output_file_path = temp_file.name
temp_file.flush()
temp_file.close()
else:
with open(self.output_file_path, 'w') as document:
pass
admin_layer_provider = self.layer.dataProvider()
fields = admin_layer_provider.fields()
if admin_layer_provider.fields().indexFromName(
self.name_field) != -1:
raise FieldExistingException(field=self.name_field)
fields.append(QgsField('LISA_P', QVariant.Double))
fields.append(QgsField('LISA_Z', QVariant.Double))
fields.append(QgsField('LISA_Q', QVariant.Int))
fields.append(QgsField('LISA_I', QVariant.Double))
fields.append(QgsField('LISA_C', QVariant.Double))
# The QgsVectorFileWriter was Deprecated since 3.10 However,.......
#The create() function DOEST NOT Flush the feature unless QGIS close.
#options = QgsVectorFileWriter.SaveVectorOptions()
#options.driverName = "ESRI Shapefile"
#file_writer=QgsVectorFileWriter.create(self.output_file_path,fields,QgsWkbTypes.Polygon,self.admin_layer.crs(),QgsCoordinateTransformContext(),options)
#It's currently a bug https://github.com/qgis/QGIS/issues/35021
# So I will keep it for now
file_writer = QgsVectorFileWriter(self.output_file_path, 'utf-8',
fields, QgsWkbTypes.Polygon,
self.admin_layer.crs(),
'ESRI Shapefile')
if self.cbx_contiguity.currentIndex() == 0: # queen
# fix_print_with_import
print('Info: Local Moran\'s using queen contiguity')
#Pysal 2.0 change
#https://github.com/pysal/pysal/blob/master/MIGRATING.md
w = Queen.from_shapefile(self.admin_layer.source())
else: # 1 for rook
# fix_print_with_import
print('Info: Local Moran\'s using rook contiguity')
w = Rook.from_shapefile(self.admin_layer.source())
#Pysal 2.0
#https://stackoverflow.com/questions/59455383/pysal-does-not-have-attribute-open
import geopandas
f = geopandas.read_file(self.admin_layer.source().replace(
'.shp', '.dbf'))
y = f[str(field)]
lm = Moran_Local(y, w, transformation="r", permutations=999)
sig_q = lm.q * (lm.p_sim <= 0.05
) # could make significance level an option
outFeat = QgsFeature()
i = 0
count = self.admin_layer.featureCount()
for i, feature in enumerate(self.admin_layer.getFeatures()):
attributes = feature.attributes()
attributes.append(float(lm.p_sim[i]))
attributes.append(float(lm.z_sim[i]))
attributes.append(int(lm.q[i]))
attributes.append(float(lm.Is[i]))
attributes.append(int(sig_q[i]))
new_feature = QgsFeature()
new_geom = QgsGeometry(feature.geometry())
new_feature.setAttributes(attributes)
new_feature.setGeometry(new_geom)
file_writer.addFeature(new_feature)
del file_writer
self.output_layer = QgsVectorLayer(self.output_file_path,
"LISA Moran's I - " + field,
'ogr')
QgsProject.instance().addMapLayer(self.output_layer)
self.add_symbology()
self.signalStatus.emit(3, tr('Successful process'))
except GeoPublicHealthException as e:
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
finally:
self.button_box_ok.setDisabled(False)
# noinspection PyArgumentList
QApplication.restoreOverrideCursor()
# noinspection PyArgumentList
QApplication.processEvents()
def run_blur(self):
self.progressBar_blur.setValue(0)
self.label_progress.setText('')
# Get all the fields.
layer_to_blur = self.comboBox_layerToBlur.currentLayer()
radius = self.spinBox_radius.value()
display = self.checkBox_addToMap.isChecked()
selected_features_only = self.checkBox_selectedOnlyFeatures.isChecked()
file_name = self.lineEdit_outputFile.text()
export_radius = self.checkBox_exportRadius.isChecked()
export_centroid = self.checkBox_exportCentroid.isChecked()
if self.checkBox_envelope.isChecked():
layer_envelope = self.comboBox_envelope.currentLayer()
else:
layer_envelope = None
# Test values
try:
if not layer_to_blur:
raise NoLayerProvidedException
if not file_name and not display:
raise NoFileNoDisplayException
if layer_to_blur.crs().mapUnits() != 0:
msg = tr('The projection of the map or of the layer is not '
'in meters. These parameters should be in meters.')
display_message_bar(
msg, level=QgsMessageBar.WARNING, duration=5)
if not file_name:
file_name = getTempFilenameInTempFolder('blurring.shp')
pass
if layer_envelope:
if layer_to_blur.crs() != layer_envelope.crs():
raise DifferentCrsException(
epsg1=layer_to_blur.crs().authid(),
epsg2=layer_envelope.crs().authid())
self.label_progress.setText('Creating index ...')
layer_envelope = LayerIndex(layer_envelope)
self.progressBar_blur.setValue(0)
self.label_progress.setText('Blurring ...')
if selected_features_only:
features = layer_to_blur.selectedFeatures()
nb_features = layer_to_blur.selectedFeatureCount()
else:
features = layer_to_blur.getFeatures()
nb_features = layer_to_blur.featureCount()
# Fields
fields = layer_to_blur.pendingFields()
if export_radius:
fields.append(QgsField(u"Radius", QVariant.Int))
if export_centroid:
fields.append(QgsField(u"X centroid", QVariant.Int))
fields.append(QgsField(u"Y centroid", QVariant.Int))
# Creating the output shapefile
file_writer = QgsVectorFileWriter(
file_name,
'utf-8',
fields,
QGis.WKBPolygon,
layer_to_blur.crs(),
'ESRI Shapefile')
if file_writer.hasError() != QgsVectorFileWriter.NoError:
raise CreatingShapeFileException(suffix=file_writer.hasError())
# Creating the algorithm with radius
algo = Blur(radius, layer_envelope, export_radius, export_centroid)
for j, feature in enumerate(features):
feature = algo.blur(feature)
file_writer.addFeature(feature)
# Update progress bar
percent = int((j + 1) * 100 / nb_features)
self.progressBar_blur.setValue(percent)
# Write all features in the file
del file_writer
if display:
old_default_projection = self.settings.value(
'/Projections/defaultBehaviour')
self.settings.setValue(
'/Projections/defaultBehaviour', 'useProject')
layer_name = basename(file_name)
new_layer = QgsVectorLayer(file_name, layer_name, 'ogr')
new_layer.commitChanges()
new_layer.clearCacheImage()
# noinspection PyArgumentList
QgsMapLayerRegistry.instance().addMapLayers([new_layer])
self.settings.setValue(
'/Projections/defaultBehaviour', old_default_projection)
msg = tr('Successful export in %s' % file_name)
iface.messageBar().pushMessage(
msg, level=QgsMessageBar.INFO, duration=5)
self.signalAskCloseWindow.emit()
except GeoPublicHealthException, e:
self.label_progress.setText('')
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
def run_stats(self):
"""Main function which do the process."""
# Get the common fields.
self.admin_layer = self.cbx_aggregation_layer.currentLayer()
if self.use_point_layer:
# If we use a point layer.
point_layer = self.cbx_case_layer.currentLayer()
else:
# If we use a column with number of case.
case_column = self.cbx_case_field.currentField()
index_case = self.admin_layer.fields().indexFromName(case_column)
#Replace laer.fieldNameIndex(name) to layer.fields().lookup\Field(name)
#http://learn.openwaterfoundation.org/owf-app-geoprocessor-python-doc-dev/resources/migrate-qgis2-qgis3/
if not self.use_area:
# If we don't use density.
population = self.cbx_population_field.currentField()
index_population = self.admin_layer.fields().indexFromName(population)
self.name_field=self.le_new_column.text()
if not self.name_field:
self.name_field = self.le_new_column.placeholderText()
# Add new column.
add_nb_intersections = self.checkBox_addNbIntersections.isChecked()
# Ratio
ratio = self.cbx_ratio.currentText()
ratio = ratio.replace(' ', '')
# Output.
self.output_file_path = self.le_output_filepath.text()
try:
self.button_box_ok.setDisabled(True)
# noinspection PyArgumentList
QApplication.setOverrideCursor(Qt.WaitCursor)
# noinspection PyArgumentList
QApplication.processEvents()
if not self.admin_layer:
QMessageBox.information(None, "DEBUG:", str("There is no layer"))
raise NoLayerProvidedException
if not self.admin_layer and self.use_point_layer:
QMessageBox.information(None, "DEBUG:", str("There is no layer"))
raise NoLayerProvidedException
crs_admin_layer = self.admin_layer.crs()
if self.use_point_layer:
crs_point_layer = point_layer.crs()
if crs_admin_layer != crs_point_layer:
QMessageBox.information(None, "DEBUG:", str("CRS of two layers are not the same. Please set CRS."))
raise DifferentCrsException(
epsg1=crs_point_layer.authid(),
epsg2=crs_admin_layer.authid())
if not self.use_point_layer and not self.use_area:
if index_population == index_case:
QMessageBox.information(None, "DEBUG:", str("You are using the same variable for case and population. Please change."))
raise FieldException(field_1='Population', field_2='Case')
try:
ratio = float(ratio)
except ValueError:
QMessageBox.information(None, "DEBUG:", str("The variable is not number."))
raise NotANumberException(suffix=ratio)
# Output
if not self.output_file_path:
temp_file = NamedTemporaryFile(
delete=False,
suffix='-geohealth.shp')
self.output_file_path = temp_file.name
temp_file.flush()
temp_file.close()
else:
with open(self.output_file_path, 'w') as document: pass
admin_layer_provider = self.admin_layer.dataProvider()
fields = self.admin_layer.fields()
if admin_layer_provider.fields().indexFromName(self.name_field) != -1:
QMessageBox.information(None, "DEBUG:", str("The field name already exist."))
raise FieldExistingException(field=self.name_field)
fields.append(QgsField(self.name_field, QVariant.Double))
if add_nb_intersections:
fields.append(QgsField('nb_of_intersections', QVariant.Int))
data = []
file_writer = QgsVectorFileWriter(
self.output_file_path,
'utf-8',
fields,
QgsWkbTypes.Polygon,
self.admin_layer.crs(),
'ESRI Shapefile')
if self.use_point_layer:
total_case = point_layer.featureCount()
else:
total_case = 0
for i, feature in enumerate(self.admin_layer.getFeatures()):
attributes = feature.attributes()
if self.use_point_layer:
count = 0
for f in point_layer.getFeatures():
if f.geometry().intersects(feature.geometry()):
count += 1
else:
count = int(attributes[index_case])
total_case += count
try:
if self.use_area:
area = feature.geometry().area()
value = float(count) / area * ratio
else:
try:
population = float(attributes[index_population])
except ValueError:
QMessageBox.information(None, "DEBUG:", str("This is not a number."))
raise NotANumberException(
suffix=attributes[index_population])
value = float(count) / population * ratio
except ZeroDivisionError:
value = None
except TypeError:
value = None
data.append(value)
attributes.append(value)
if add_nb_intersections:
attributes.append(count)
new_feature = QgsFeature()
new_geom = QgsGeometry(feature.geometry())
new_feature.setAttributes(attributes)
new_feature.setGeometry(new_geom)
file_writer.addFeature(new_feature)
del file_writer
self.output_layer = QgsVectorLayer(
self.output_file_path,
self.name_field,
'ogr')
QgsProject.instance().addMapLayer(self.output_layer)
if self.checkBox_incidence_runStats.isChecked():
stats = Stats(data)
items_stats = [
'Incidence null,%d' % stats.null_values(),
'Count(point),%d' % total_case,
'Count(polygon),%d' % self.admin_layer.featureCount(),
'Min,%d' % stats.min(),
'Average,%f' % stats.average(),
'Max,%d' % stats.max(),
'Median,%f' % stats.median(),
'Range,%d' % stats.range(),
'Variance,%f' % stats.variance(),
'Standard deviation,%f' % stats.standard_deviation()
]
self.tableWidget.clear()
self.tableWidget.setColumnCount(2)
labels = ['Parameters', 'Values']
self.tableWidget.setHorizontalHeaderLabels(labels)
self.tableWidget.setRowCount(len(items_stats))
for i, item in enumerate(items_stats):
s = item.split(',')
self.tableWidget.setItem(i, 0, QTableWidgetItem(s[0]))
self.tableWidget.setItem(i, 1, QTableWidgetItem(s[1]))
self.tableWidget.resizeRowsToContents()
self.draw_plot(data)
else:
self.hide()
if self.symbology.isChecked():
self.add_symbology()
self.signalStatus.emit(3, tr('Successful process'))
except GeoPublicHealthException as e:
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
finally:
self.button_box_ok.setDisabled(False)
# noinspection PyArgumentList
QApplication.restoreOverrideCursor()
# noinspection PyArgumentList
QApplication.processEvents()
def run_stats(self):
self.progressBar_stats.setValue(0)
self.label_progressStats.setText('')
# noinspection PyArgumentList
QApplication.processEvents()
blurred_layer = self.comboBox_blurredLayer.currentLayer()
stats_layer = self.comboBox_statsLayer.currentLayer()
try:
if not blurred_layer or not stats_layer:
raise NoLayerProvidedException
crs_blurred_layer = blurred_layer.crs()
crs_stats_layer = stats_layer.crs()
if crs_blurred_layer != crs_stats_layer:
raise DifferentCrsException(
epsg1=crs_blurred_layer.authid(),
epsg2=crs_stats_layer.authid())
if blurred_layer == stats_layer:
raise NoLayerProvidedException
if not blurred_layer or not stats_layer:
raise NoLayerProvidedException
nb_feature_stats = stats_layer.featureCount()
nb_feature_blurred = blurred_layer.featureCount()
features_stats = {}
label_preparing = tr('Preparing index on the stats layer')
label_creating = tr('Creating index on the stats layer')
label_calculating = tr('Calculating')
if Qgis.QGIS_VERSION_INT < 20700:
self.label_progressStats.setText('%s 1/3' % label_preparing)
for i, feature in enumerate(stats_layer.getFeatures()):
features_stats[feature.id()] = feature
percent = int((i + 1) * 100 / nb_feature_stats)
self.progressBar_stats.setValue(percent)
# noinspection PyArgumentList
QApplication.processEvents()
self.label_progressStats.setText('%s 2/3' % label_creating)
# noinspection PyArgumentList
QApplication.processEvents()
index = QgsSpatialIndex()
for i, f in enumerate(stats_layer.getFeatures()):
index.insertFeature(f)
percent = int((i + 1) * 100 / nb_feature_stats)
self.progressBar_stats.setValue(percent)
# noinspection PyArgumentList
QApplication.processEvents()
self.label_progressStats.setText('%s 3/3' % label_calculating)
else:
# If QGIS >= 2.7, we can speed up the spatial index.
# From 1 min 15 to 7 seconds on my PC.
self.label_progressStats.setText('%s 1/2' % label_creating)
# noinspection PyArgumentList
QApplication.processEvents()
index = QgsSpatialIndex(stats_layer.getFeatures())
self.label_progressStats.setText('%s 2/2' % label_calculating)
# noinspection PyArgumentList
QApplication.processEvents()
self.tab = []
for i, feature in enumerate(blurred_layer.getFeatures()):
count = 0
ids = index.intersects(feature.geometry().boundingBox())
for unique_id in ids:
request = QgsFeatureRequest().setFilterFid(unique_id)
f = next(stats_layer.getFeatures(request))
if f.geometry().intersects(feature.geometry()):
count += 1
self.tab.append(count)
percent = int((i + 1) * 100 / nb_feature_blurred)
self.progressBar_stats.setValue(percent)
# noinspection PyArgumentList
QApplication.processEvents()
stats = Stats(self.tab)
items_stats = [
'Count(blurred),%d' % nb_feature_blurred,
'Count(stats),%d' % nb_feature_stats,
'Min,%d' % stats.min(),
'Average,%f' % stats.average(),
'Max,%d' % stats.max(), 'Median,%f' % stats.median(),
'Range,%d' % stats.range(),
'Variance,%f' % stats.variance(),
'Standard deviation,%f' % stats.standard_deviation()
]
self.tableWidget.clear()
self.tableWidget.setColumnCount(2)
labels = ['Parameters', 'Values']
self.tableWidget.setHorizontalHeaderLabels(labels)
self.tableWidget.setRowCount(len(items_stats))
for i, item in enumerate(items_stats):
s = item.split(',')
self.tableWidget.setItem(i, 0, QTableWidgetItem(s[0]))
self.tableWidget.setItem(i, 1, QTableWidgetItem(s[1]))
self.tableWidget.resizeRowsToContents()
self.draw_plot(self.tab)
except GeoPublicHealthException as e:
self.label_progressStats.setText('')
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
def run_stats(self):
self.progressBar_stats.setValue(0)
self.label_progressStats.setText('')
# noinspection PyArgumentList
QApplication.processEvents()
blurred_layer = self.comboBox_blurredLayer.currentLayer()
stats_layer = self.comboBox_statsLayer.currentLayer()
try:
if not blurred_layer or not stats_layer:
raise NoLayerProvidedException
crs_blurred_layer = blurred_layer.crs()
crs_stats_layer = stats_layer.crs()
if crs_blurred_layer != crs_stats_layer:
raise DifferentCrsException(
epsg1=crs_blurred_layer.authid(),
epsg2=crs_stats_layer.authid())
if blurred_layer == stats_layer:
raise NoLayerProvidedException
if not blurred_layer or not stats_layer:
raise NoLayerProvidedException
nb_feature_stats = stats_layer.featureCount()
nb_feature_blurred = blurred_layer.featureCount()
features_stats = {}
label_preparing = tr('Preparing index on the stats layer')
label_creating = tr('Creating index on the stats layer')
label_calculating = tr('Calculating')
if QGis.QGIS_VERSION_INT < 20700:
self.label_progressStats.setText('%s 1/3' % label_preparing)
for i, feature in enumerate(stats_layer.getFeatures()):
features_stats[feature.id()] = feature
percent = int((i + 1) * 100 / nb_feature_stats)
self.progressBar_stats.setValue(percent)
# noinspection PyArgumentList
QApplication.processEvents()
self.label_progressStats.setText('%s 2/3' % label_creating)
# noinspection PyArgumentList
QApplication.processEvents()
index = QgsSpatialIndex()
for i, f in enumerate(stats_layer.getFeatures()):
index.insertFeature(f)
percent = int((i + 1) * 100 / nb_feature_stats)
self.progressBar_stats.setValue(percent)
# noinspection PyArgumentList
QApplication.processEvents()
self.label_progressStats.setText('%s 3/3' % label_calculating)
else:
# If QGIS >= 2.7, we can speed up the spatial index.
# From 1 min 15 to 7 seconds on my PC.
self.label_progressStats.setText('%s 1/2' % label_creating)
# noinspection PyArgumentList
QApplication.processEvents()
index = QgsSpatialIndex(stats_layer.getFeatures())
self.label_progressStats.setText('%s 2/2' % label_calculating)
# noinspection PyArgumentList
QApplication.processEvents()
self.tab = []
for i, feature in enumerate(blurred_layer.getFeatures()):
count = 0
ids = index.intersects(feature.geometry().boundingBox())
for unique_id in ids:
request = QgsFeatureRequest().setFilterFid(unique_id)
f = stats_layer.getFeatures(request).next()
if f.geometry().intersects(feature.geometry()):
count += 1
self.tab.append(count)
percent = int((i + 1) * 100 / nb_feature_blurred)
self.progressBar_stats.setValue(percent)
# noinspection PyArgumentList
QApplication.processEvents()
stats = Stats(self.tab)
items_stats = [
'Count(blurred),%d' % nb_feature_blurred,
'Count(stats),%d' % nb_feature_stats,
'Min,%d' % stats.min(),
'Average,%f' % stats.average(),
'Max,%d' % stats.max(), 'Median,%f' % stats.median(),
'Range,%d' % stats.range(),
'Variance,%f' % stats.variance(),
'Standard deviation,%f' % stats.standard_deviation()
]
self.tableWidget.clear()
self.tableWidget.setColumnCount(2)
labels = ['Parameters', 'Values']
self.tableWidget.setHorizontalHeaderLabels(labels)
self.tableWidget.setRowCount(len(items_stats))
for i, item in enumerate(items_stats):
s = item.split(',')
self.tableWidget.setItem(i, 0, QTableWidgetItem(s[0]))
self.tableWidget.setItem(i, 1, QTableWidgetItem(s[1]))
self.tableWidget.resizeRowsToContents()
self.draw_plot(self.tab)
except GeoPublicHealthException, e:
self.label_progressStats.setText('')
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)
def run_stats(self):
"""Main function which do the process."""
# Get the common fields.
self.admin_layer = self.cbx_aggregation_layer.currentLayer()
selected_indicators = self.indicators_list()
if not self.name_field:
self.name_field = self.le_new_column.placeholderText()
# Output.
self.output_file_path = self.le_output_filepath.text()
try:
self.button_box_ok.setDisabled(True)
# noinspection PyArgumentList
QApplication.setOverrideCursor(Qt.WaitCursor)
# noinspection PyArgumentList
QApplication.processEvents()
if not self.admin_layer:
raise NoLayerProvidedException
if not self.admin_layer and self.use_point_layer:
raise NoLayerProvidedException
crs_admin_layer = self.admin_layer.crs()
if not self.use_point_layer and not self.use_area:
if not self.cbx_list_indicators:
raise FieldException(field_1='List Indicators should not empty')
# Output
if not self.output_file_path:
temp_file = NamedTemporaryFile(
delete=False,
suffix='-geopublichealth.shp')
self.output_file_path = temp_file.name
temp_file.flush()
temp_file.close()
admin_layer_provider = self.admin_layer.dataProvider()
fields = self.admin_layer.pendingFields()
if admin_layer_provider.fieldNameIndex(self.name_field) != -1:
raise FieldExistingException(field=self.name_field)
for indicator_selected in selected_indicators:
fields.append(QgsField("Z" + indicator_selected[0], QVariant.Double))
fields.append(QgsField(self.name_field, QVariant.Double))
file_writer = QgsVectorFileWriter(
self.output_file_path,
'utf-8',
fields,
QGis.WKBPolygon,
self.admin_layer.crs(),
'ESRI Shapefile')
count = self.admin_layer.featureCount()
stats = {}
for indicator_selected in selected_indicators:
values = []
indicator_selected_name = str(indicator_selected[0])
for i, feature in enumerate(self.admin_layer.getFeatures()):
index = self.admin_layer.fieldNameIndex(indicator_selected_name)
if feature[index]:
value = float(feature[index])
else:
value = 0.0
values.append(value)
stats[indicator_selected_name] = Stats(values)
for i, feature in enumerate(self.admin_layer.getFeatures()):
attributes = feature.attributes()
composite_index_value = 0.0
for indicator_selected in selected_indicators:
indicator_selected_name = str(indicator_selected[0])
index = self.admin_layer.fieldNameIndex(indicator_selected_name)
if feature[index]:
value = float(feature[index])
else:
value = 0.0
zscore = (value - stats[indicator_selected_name].average()) / stats[indicator_selected_name].standard_deviation()
attributes.append(float(zscore))
#msgBox = QMessageBox()
#msgBox.setText("indicator_selected: " + str(indicator_selected) + " value: " + str(value) + " stats[indicator_selected_name].average(): " + str(stats[indicator_selected_name].average()) + " zscore: " + str(zscore))
#msgBox.exec_()
if indicator_selected[1] == '+':
composite_index_value -= zscore
else:
composite_index_value += zscore
attributes.append(float(composite_index_value))
new_feature = QgsFeature()
new_geom = QgsGeometry(feature.geometry())
new_feature.setAttributes(attributes)
new_feature.setGeometry(new_geom)
file_writer.addFeature(new_feature)
del file_writer
self.output_layer = QgsVectorLayer(
self.output_file_path,
self.name_field,
'ogr')
QgsMapLayerRegistry.instance().addMapLayer(self.output_layer)
if self.symbology.isChecked():
self.add_symbology()
self.signalStatus.emit(3, tr('Successful process'))
except GeoPublicHealthException, e:
display_message_bar(msg=e.msg, level=e.level, duration=e.duration)