class HotspotAnalysisDialogTest(unittest.TestCase):
"""Test dialog works."""
def setUp(self):
"""Runs before each test."""
self.dialog = HotspotAnalysisDialog(None)
def tearDown(self):
"""Runs after each test."""
self.dialog = None
def test_dialog_ok(self):
"""Test we can click OK."""
button = self.dialog.button_box.button(QDialogButtonBox.Ok)
button.click()
result = self.dialog.result()
self.assertEqual(result, QDialog.Accepted)
def test_dialog_cancel(self):
"""Test we can click cancel."""
button = self.dialog.button_box.button(QDialogButtonBox.Cancel)
button.click()
result = self.dialog.result()
self.assertEqual(result, QDialog.Rejected)
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',
'HotspotAnalysis_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
if qVersion() > '4.3.3':
QCoreApplication.installTranslator(self.translator)
# Create the dialog (after translation) and keep reference
self.dlg = HotspotAnalysisDialog()
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&Hotspot Analysis')
# TODO: We are going to let the user set this up in a future iteration
self.toolbar = self.iface.addToolBar(u'HotspotAnalysis')
self.toolbar.setObjectName(u'HotspotAnalysis')
# Load output directory path
self.dlg.lineEdit.clear()
self.dlg.pushButton.clicked.connect(self.select_output_file)
self.clear_ui()
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',
'HotspotAnalysis_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
if qVersion() > '4.3.3':
QCoreApplication.installTranslator(self.translator)
# Create the dialog (after translation) and keep reference
self.dlg = HotspotAnalysisDialog()
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&Hotspot Analysis')
# TODO: We are going to let the user set this up in a future iteration
self.toolbar = self.iface.addToolBar(u'HotspotAnalysis')
self.toolbar.setObjectName(u'HotspotAnalysis')
# Load output directory path
self.dlg.lineEdit.clear()
self.dlg.pushButton.clicked.connect(self.select_output_file)
self.clear_ui()
class HotspotAnalysis:
"""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',
'HotspotAnalysis_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
if qVersion() > '4.3.3':
QCoreApplication.installTranslator(self.translator)
# Create the dialog (after translation) and keep reference
self.dlg = HotspotAnalysisDialog()
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&Hotspot Analysis')
# TODO: We are going to let the user set this up in a future iteration
self.toolbar = self.iface.addToolBar(u'HotspotAnalysis')
self.toolbar.setObjectName(u'HotspotAnalysis')
# Load output directory path
self.dlg.lineEdit.clear()
self.dlg.pushButton.clicked.connect(self.select_output_file)
self.clear_ui()
# 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('HotspotAnalysis', 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:
self.toolbar.addAction(action)
if add_to_menu:
self.iface.addPluginToVectorMenu(
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/HotspotAnalysis/hotspot.png'
self.add_action(
icon_path,
text=self.tr(u'Hotspot Analysis'),
callback=self.run,
parent=self.iface.mainWindow())
def unload(self):
"""Removes the plugin menu item and icon from QGIS GUI."""
for action in self.actions:
self.iface.removePluginVectorMenu(
self.tr(u'&Hotspot Analysis'),
action)
self.iface.removeToolBarIcon(action)
# remove the toolbar
del self.toolbar
def select_output_file(self):
"""Selects the output file directory"""
filename = QFileDialog.getSaveFileName(self.dlg, "Select output path directory ")
self.dlg.lineEdit.setText(filename)
def optimizedThreshold(self, checked):
"""Settings for Optimized threshold"""
if checked == True:
self.dlg.lineEdit_minT.setEnabled(True)
self.dlg.lineEdit_maxT.setEnabled(True)
self.dlg.lineEdit_dist.setEnabled(True)
self.dlg.lineEditThreshold.setEnabled(False)
self.dlg.lineEditThreshold.clear()
self.dlg.label_threshold.setEnabled(False)
self.dlg.label_7.setEnabled(True)
self.dlg.label_8.setEnabled(True)
self.dlg.label_9.setEnabled(True)
else:
self.dlg.lineEdit_minT.setEnabled(False)
self.dlg.lineEdit_minT.clear()
self.dlg.lineEdit_maxT.clear()
self.dlg.lineEdit_dist.clear()
self.dlg.lineEdit_maxT.setEnabled(False)
self.dlg.lineEdit_dist.setEnabled(False)
self.dlg.lineEditThreshold.setEnabled(True)
self.dlg.label_threshold.setEnabled(True)
self.dlg.label_7.setEnabled(False)
self.dlg.label_8.setEnabled(False)
self.dlg.label_9.setEnabled(False)
def randomPermChecked(self, checked):
"""Settings for Random permutations"""
if checked == True:
self.dlg.lineEdit_random.setEnabled(True)
else:
self.dlg.lineEdit_random.setEnabled(False)
def moranBiChecked(self, checked):
if checked == True:
self.dlg.comboBox_C_2.setEnabled(True)
else:
self.dlg.comboBox_C_2.setEnabled(False)
def knnChecked(self, checked):
if checked == True:
self.dlg.lineEditThreshold.clear()
self.dlg.lineEditThreshold.setEnabled(False)
self.dlg.knn_number.setEnabled(True)
else:
self.dlg.lineEditThreshold.setEnabled(True)
def clear_ui(self):
"""Clearing the UI for new operations"""
self.dlg.comboBox.clear()
self.dlg.lineEdit.clear()
self.dlg.lineEditThreshold.clear()
self.dlg.comboBox_C.clear()
self.dlg.comboBox_C_2.clear()
self.dlg.comboBox_C_2.setEnabled(False)
self.dlg.lineEditThreshold.setEnabled(True)
self.dlg.checkBox_optimizeDistance.setChecked(False)
self.dlg.checkBox_rowStandard.setChecked(False)
self.dlg.checkBox_randomPerm.setChecked(False)
self.dlg.checkBox_queen.setChecked(False)
self.dlg.checkBox_queen.setEnabled(False)
self.dlg.lineEdit_minT.setEnabled(False)
self.dlg.lineEdit_maxT.setEnabled(False)
self.dlg.lineEdit_dist.setEnabled(False)
self.dlg.lineEdit_minT.clear()
self.dlg.lineEdit_maxT.clear()
self.dlg.lineEdit_dist.clear()
self.dlg.lineEditThreshold.clear()
self.dlg.label_7.setEnabled(False)
self.dlg.label_8.setEnabled(False)
self.dlg.label_9.setEnabled(False)
self.dlg.knn_number.setEnabled(False)
self.dlg.checkBox_knn.setChecked(False)
self.dlg.checkBox_knn.setEnabled(True)
self.load_comboBox()
def clear_fields(self):
"""Clearing the fields when layers are changed"""
self.dlg.comboBox_C.clear()
self.dlg.comboBox_C_2.clear()
def write_file(self, filename, statistics, layerName, inLayer, inDataSource, y, threshold1):
"""Writing the output shapefile into the mentioned directory"""
outDriver = ogr.GetDriverByName("ESRI Shapefile")
layerName = layerName.split('.')
layerName.pop()
# layerName = '.'.join(layerName)
outShapefile = filename + ".shp"
# Remove eventually alrady exisiting output
if os.path.exists(outShapefile):
outDriver.DeleteDataSource(outShapefile)
# Create the output shapefile
outDataSource = outDriver.CreateDataSource(outShapefile)
outLayer = outDataSource.CreateLayer("output", inLayer.GetSpatialRef(), inLayer.GetLayerDefn().GetGeomType())
# Add input Layer Fields to the output Layer
inLayerDefn = inLayer.GetLayerDefn()
for i in range(0, inLayerDefn.GetFieldCount()):
fieldDefn = inLayerDefn.GetFieldDefn(i)
outLayer.CreateField(fieldDefn)
##
# Add additional fields - for more types other than Strings take a look at http://pcjericks.github.io/py-gdalogr-cookbook/layers.html#create-a-new-shapefile-and-add-data
##
# Add empty field to store Pysal results
Z_field = ogr.FieldDefn("Z-score", ogr.OFTReal)
Z_field.SetWidth(15)
Z_field.SetPrecision(10)
outLayer.CreateField(Z_field)
p_field = ogr.FieldDefn("p-value", ogr.OFTReal)
p_field.SetWidth(15)
p_field.SetPrecision(10)
outLayer.CreateField(p_field)
# if not Gi*
if (self.dlg.checkBox_moran.isChecked() == 1 or self.dlg.checkBox_moranBi.isChecked() == 1):
intValue = int(ogr.OFTReal)
q_field = ogr.FieldDefn("q-value", intValue)
q_field.SetWidth(15)
q_field.SetPrecision(10)
outLayer.CreateField(q_field)
# Get the output Layer's Feature Definition
outLayerDefn = outLayer.GetLayerDefn()
# Get the input Layer's Feature Definition
inLayerDefn = inLayer.GetLayerDefn()
# Add features to the ouput Layer
for i in range(0, inLayer.GetFeatureCount()):
# Get the input Feature
inFeature = inLayer.GetFeature(i)
# Create output Feature
outFeature = ogr.Feature(outLayerDefn)
# Add field values from input Layer
for j in range(0, inLayerDefn.GetFieldCount()):
outFeature.SetField(outLayerDefn.GetFieldDefn(j).GetNameRef(), inFeature.GetField(j))
# Set geometry
geom = inFeature.GetGeometryRef()
outFeature.SetGeometry(geom)
if self.dlg.checkBox_gi.isChecked() == 1:
# Add Z-scores and p-values to their field column
if self.dlg.checkBox_randomPerm.isChecked() == 1: # to use permutation approach
if numpy.mean(y) <= 0 :
outFeature.SetField("Z-score", statistics.z_sim[i] * (-1))
outFeature.SetField("p-value", statistics.p_z_sim[i] * 2)
else:
outFeature.SetField("Z-score", statistics.z_sim[i])
outFeature.SetField("p-value", statistics.p_z_sim[i] * 2)
else: # to use normality hypothesis
if numpy.mean(y) <= 0 :
outFeature.SetField("Z-score", statistics.Zs[i] * (-1))
outFeature.SetField("p-value", statistics.p_norm[i] * 2)
else:
outFeature.SetField("Z-score", statistics.Zs[i])
outFeature.SetField("p-value", statistics.p_norm[i] * 2)
else:
if self.dlg.checkBox_randomPerm.isChecked() == 1: # to use permutation approach
if max(y) >= 0:
outFeature.SetField("Z-score", statistics.z_sim[i])
outFeature.SetField("p-value", statistics.p_sim[i] * 2)
else:
outFeature.SetField("Z-score", statistics.z_sim[i] * (-1))
outFeature.SetField("p-value", statistics.p_sim[i] * 2)
else: # to use normality hypothesis
if max(y) >= 0:
outFeature.SetField("Z-score", statistics.z_sim[i])
outFeature.SetField("p-value", statistics.p_z_sim[i] * 2)
else:
outFeature.SetField("Z-score", statistics.z_sim[i] * (-1))
outFeature.SetField("p-value", statistics.p_z_sim[i] * 2)
outFeature.SetField("q-value", statistics.q[i])
# Add new feature to output Layer
outLayer.CreateFeature(outFeature)
# Close DataSources
inDataSource.Destroy()
outDataSource.Destroy()
if threshold1:
self.success_msg(threshold1)
new_layer = self.iface.addVectorLayer(filename + ".shp", str(os.path.basename(os.path.normpath(filename))),
"ogr")
if not new_layer:
QMessageBox.information(self.dlg, self.tr("New Layer"), self.tr("Layer Cannot be Loaded"), QMessageBox.Ok)
self.clear_ui()
def load_comboBox(self):
"""Load the fields into combobox when layers are changed"""
layer_shp = []
layers = self.iface.legendInterface().layers()
if len(layers) != 0: # checklayers exist in the project
for layer in layers:
if hasattr(layer, "dataProvider"): # to not consider Openlayers basemaps in the layer list
myfilepath = layer.dataProvider().dataSourceUri() # directory including filename
(myDirectory, nameFile) = os.path.split(myfilepath) # splitting into directory and filename
if (".shp" in nameFile):
layer_shp.append(layer)
selectedLayerIndex = self.dlg.comboBox.currentIndex()
if selectedLayerIndex < 0 or selectedLayerIndex > len(layer_shp):
return
try:
selectedLayer = layer_shp[selectedLayerIndex]
except:
return
fieldnames = [field.name() for field in selectedLayer.pendingFields()]
self.clear_fields()
self.dlg.comboBox_C.addItems(fieldnames)
self.dlg.comboBox_C_2.addItems(fieldnames)
(path, layer_id) = selectedLayer.dataProvider().dataSourceUri().split('|')
inDriver = ogr.GetDriverByName("ESRI Shapefile")
inDataSource = inDriver.Open(path, 0)
inLayer = inDataSource.GetLayer()
global type
type = inLayer.GetLayerDefn().GetGeomType()
if type == 3: # is a polygon
self.dlg.checkBox_queen.setChecked(True)
self.dlg.lineEditThreshold.setEnabled(False)
self.dlg.checkBox_knn.setEnabled(False)
self.dlg.knn_number.setEnabled(False)
self.dlg.checkBox_optimizeDistance.setChecked(False)
self.dlg.checkBox_optimizeDistance.setEnabled(False)
self.dlg.lineEdit_minT.setEnabled(False)
self.dlg.lineEdit_maxT.setEnabled(False)
self.dlg.lineEdit_dist.setEnabled(False)
else:
self.dlg.checkBox_queen.setChecked(False)
self.dlg.checkBox_knn.setEnabled(True)
self.dlg.knn_number.setEnabled(True)
self.dlg.lineEditThreshold.setEnabled(True)
self.dlg.checkBox_optimizeDistance.setEnabled(True)
self.dlg.lineEdit_minT.setEnabled(True)
self.dlg.lineEdit_dist.setEnabled(True)
self.dlg.lineEdit_maxT.setEnabled(True)
thresh = pysal.min_threshold_dist_from_shapefile(path)
self.dlg.lineEditThreshold.setText(str(int(thresh)))
def error_msg(self):
"""Message to report missing fields"""
self.clear_ui()
self.loadLayerList()
QMessageBox.warning(self.dlg.show(), self.tr("HotspotAnalysis:Warning"),
self.tr("Please specify input fields properly"), QMessageBox.Ok)
def success_msg(self, distance):
"""Message to report succesful file creation"""
QMessageBox.information(self.dlg, self.tr("HotspotAnalysis:Success"),
self.tr("File is generated Succesfully (Distance used = " + str(distance) + ")"),
QMessageBox.Ok)
def validator(self):
"""Validator to Check whether the inputs are given properly"""
# Polygon case
if self.dlg.checkBox_queen.isChecked() == 1:
return 1
if ((self.dlg.checkBox_optimizeDistance.isChecked() == 0
and self.dlg.lineEditThreshold.text() != "")
or (self.dlg.checkBox_optimizeDistance.isChecked() == 1
and (self.dlg.lineEdit_dist.text() != ""
and self.dlg.lineEdit_maxT.text() != ""
and self.dlg.lineEdit_minT.text() != "")) or
(self.dlg.checkBox_knn.isChecked() == 1)) \
and self.dlg.lineEdit.text() != "":
return 1
else:
return 0
def loadLayerList(self):
layers_list = []
layers_shp = []
# Show the shapefiles in the ComboBox
layers = self.iface.legendInterface().layers()
if len(layers) != 0: # checklayers exist in the project
for layer in layers:
if hasattr(layer, "dataProvider"): # to not consider Openlayers basemaps in the layer list
myfilepath = layer.dataProvider().dataSourceUri() # directory including filename
(myDirectory, nameFile) = os.path.split(myfilepath) # splitting into directory and filename
if (".shp" in nameFile):
layers_list.append(layer.name())
layers_shp.append(layer)
self.dlg.comboBox.addItems(layers_list) # adding layers to comboBox
selectedLayerIndex = self.dlg.comboBox.currentIndex()
if selectedLayerIndex < 0 or selectedLayerIndex > len(layers_shp):
return
selectedLayer = layers_shp[selectedLayerIndex]
fieldnames = [field.name() for field in selectedLayer.pendingFields()] # fetching fieldnames of layer
self.clear_fields()
self.dlg.comboBox_C.addItems(fieldnames)
self.dlg.comboBox_C_2.addItems(fieldnames)
try:
self.dlg.comboBox.activated.connect(lambda: self.load_comboBox())
self.dlg.comboBox.currentIndexChanged.connect(lambda: self.load_comboBox())
self.dlg.checkBox_optimizeDistance.toggled.connect(self.optimizedThreshold) # checkbox toggle event
self.dlg.checkBox_randomPerm.toggled.connect(self.randomPermChecked) # checkbox toggle event
self.dlg.checkBox_moranBi.toggled.connect(self.moranBiChecked) # checkbox toggle event
self.dlg.checkBox_knn.toggled.connect(self.knnChecked) # checkbox toggle event
except:
return False
return [layers, layers_shp]
else:
return [layers, False]
def run(self):
"""Run method that performs all the real work""" # show the dialog
self.clear_ui()
layers, layers_shp = self.loadLayerList()
if len(layers) == 0:
return
self.dlg.show()
self.load_comboBox()
# Run the dialog event loop
result = self.dlg.exec_()
# See if OK was pressed and fields are not empty
if result and (self.validator() == 1):
selectedLayerIndex = self.dlg.comboBox.currentIndex()
if selectedLayerIndex < 0 or selectedLayerIndex > len(layers):
return
selectedLayer = layers_shp[selectedLayerIndex]
layerName = selectedLayer.dataProvider().dataSourceUri()
C = selectedLayer.fieldNameIndex(self.dlg.comboBox_C.currentText())
C2 = selectedLayer.fieldNameIndex(self.dlg.comboBox_C_2.currentText())
filename = self.dlg.lineEdit.text()
(path, layer_id) = layerName.split('|')
inDriver = ogr.GetDriverByName("ESRI Shapefile")
inDataSource = inDriver.Open(path, 0)
inLayer = inDataSource.GetLayer()
type = inLayer.GetLayerDefn().GetGeomType()
u = []
for i in range(0, inLayer.GetFeatureCount()):
geometry = inLayer.GetFeature(i)
u.append(geometry.GetField(C))
y = numpy.array(u) # attributes vector
if self.dlg.checkBox_moranBi.isChecked() == 1:
v = []
for i in range(0, inLayer.GetFeatureCount()):
geometry = inLayer.GetFeature(i)
v.append(geometry.GetField(C2))
x = numpy.array(v)
if type == 1: # point
t = ()
for feature in inLayer:
geometry = feature.GetGeometryRef()
xy = (geometry.GetX(), geometry.GetY())
t = t + (xy,)
# t = get_points_array_from_shapefile(layerName.split("|")[0])
if self.dlg.lineEditThreshold.text() and self.dlg.lineEditThreshold.text() != "": # if threshold is given
threshold1 = int(self.dlg.lineEditThreshold.text())
elif self.dlg.checkBox_knn.isChecked() == 0: # if user needs to optimize threshold (no knn)
mx_moran = -1000.0
mx_i = -1000.0
minT = int(self.dlg.lineEdit_minT.text())
maxT = int(self.dlg.lineEdit_maxT.text())
dist = int(self.dlg.lineEdit_dist.text())
for i in range(minT, maxT + dist, dist):
w = DistanceBand(t, threshold=i, p=2, binary=False)
moran = pysal.Moran(y, w)
# print moran.z_norm
if moran.z_norm > mx_moran:
mx_i = i
mx_moran = moran.z_norm
threshold1 = int(mx_i)
if self.dlg.checkBox_knn.isChecked() == 1:
weightValue = int(self.dlg.knn_number.text())
w = pysal.knnW_from_shapefile(layerName.split("|")[0], k=weightValue, p=1)
threshold1 = "None/KNN used " + self.dlg.knn_number.text()
else:
w = DistanceBand(t, threshold1, p=2, binary=False)
else: # polygon
w = pysal.queen_from_shapefile(layerName.split("|")[0])
threshold1 = "None/Queen's Case used"
if self.dlg.checkBox_rowStandard.isChecked() == 1:
type_w = "R"
else:
type_w = "B"
if self.dlg.checkBox_randomPerm.isChecked() == 1:
permutationsValue = int(self.dlg.lineEdit_random.text())
else:
permutationsValue = 999
numpy.random.seed(12345)
if self.dlg.checkBox_gi.isChecked() == 1:
statistics = G_Local(y, w, star=True, transform=type_w, permutations=permutationsValue)
elif self.dlg.checkBox_moran.isChecked() == 1:
statistics = Moran_Local(y, w, transformation=type_w, permutations=permutationsValue)
else:
statistics = Moran_Local_BV(y, x, w, transformation=type_w, permutations=permutationsValue)
self.write_file(filename, statistics, layerName, inLayer,
inDataSource,
y, threshold1)
# assign the style to the output layer on QGIS
if self.dlg.checkBox_gi.isChecked() == 1:
if type == 1: # point
stylePath = "/layer_style/hotspots_class.qml"
else:
stylePath = "/layer_style/hotspots_class_poly.qml"
self.iface.activeLayer().loadNamedStyle(os.path.dirname(__file__) + stylePath)
else:
if type == 1: # point
stylePath = "/layer_style/moran_class.qml"
else:
stylePath = "/layer_style/moran_class_poly.qml"
self.iface.activeLayer().loadNamedStyle(os.path.dirname(__file__) + stylePath)
elif result and (self.validator() == 0):
self.error_msg()
else:
self.clear_ui()
pass
class HotspotAnalysis:
"""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',
'HotspotAnalysis_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
if qVersion() > '4.3.3':
QCoreApplication.installTranslator(self.translator)
# Create the dialog (after translation) and keep reference
self.dlg = HotspotAnalysisDialog()
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&Hotspot Analysis')
# TODO: We are going to let the user set this up in a future iteration
self.toolbar = self.iface.addToolBar(u'HotspotAnalysis')
self.toolbar.setObjectName(u'HotspotAnalysis')
# Load output directory path
self.dlg.lineEdit.clear()
self.dlg.pushButton.clicked.connect(self.select_output_file)
self.clear_ui()
# 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('HotspotAnalysis', 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:
self.toolbar.addAction(action)
if add_to_menu:
self.iface.addPluginToVectorMenu(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/HotspotAnalysis/hotspot.png'
self.add_action(icon_path,
text=self.tr(u'Hotspot Analysis'),
callback=self.run,
parent=self.iface.mainWindow())
def unload(self):
"""Removes the plugin menu item and icon from QGIS GUI."""
for action in self.actions:
self.iface.removePluginVectorMenu(self.tr(u'&Hotspot Analysis'),
action)
self.iface.removeToolBarIcon(action)
# remove the toolbar
del self.toolbar
def select_output_file(self):
"""Selects the output file directory"""
filename = QFileDialog.getSaveFileName(
self.dlg, "Select output path directory ")
self.dlg.lineEdit.setText(filename)
def optimizedThreshold(self, checked):
"""Settings for Optimized threshold"""
if checked == True:
self.dlg.lineEdit_minT.setEnabled(True)
self.dlg.lineEdit_maxT.setEnabled(True)
self.dlg.lineEdit_dist.setEnabled(True)
self.dlg.lineEditThreshold.setEnabled(False)
self.dlg.lineEditThreshold.clear()
self.dlg.label_threshold.setEnabled(False)
self.dlg.label_7.setEnabled(True)
self.dlg.label_8.setEnabled(True)
self.dlg.label_9.setEnabled(True)
else:
self.dlg.lineEdit_minT.setEnabled(False)
self.dlg.lineEdit_minT.clear()
self.dlg.lineEdit_maxT.clear()
self.dlg.lineEdit_dist.clear()
self.dlg.lineEdit_maxT.setEnabled(False)
self.dlg.lineEdit_dist.setEnabled(False)
self.dlg.lineEditThreshold.setEnabled(True)
self.dlg.label_threshold.setEnabled(True)
self.dlg.label_7.setEnabled(False)
self.dlg.label_8.setEnabled(False)
self.dlg.label_9.setEnabled(False)
def randomPermChecked(self, checked):
"""Settings for Random permutations"""
if checked == True:
self.dlg.lineEdit_random.setEnabled(True)
else:
self.dlg.lineEdit_random.setEnabled(False)
def moranBiChecked(self, checked):
if checked == True:
self.dlg.comboBox_C_2.setEnabled(True)
else:
self.dlg.comboBox_C_2.setEnabled(False)
def knnChecked(self, checked):
if checked == True:
self.dlg.lineEditThreshold.clear()
self.dlg.lineEditThreshold.setEnabled(False)
self.dlg.knn_number.setEnabled(True)
else:
self.dlg.lineEditThreshold.setEnabled(True)
def clear_ui(self):
"""Clearing the UI for new operations"""
self.dlg.comboBox.clear()
self.dlg.lineEdit.clear()
self.dlg.lineEditThreshold.clear()
self.dlg.comboBox_C.clear()
self.dlg.comboBox_C_2.clear()
self.dlg.comboBox_C_2.setEnabled(False)
self.dlg.lineEditThreshold.setEnabled(True)
self.dlg.checkBox_optimizeDistance.setChecked(False)
self.dlg.checkBox_rowStandard.setChecked(False)
self.dlg.checkBox_randomPerm.setChecked(False)
self.dlg.checkBox_queen.setChecked(False)
self.dlg.checkBox_queen.setEnabled(False)
self.dlg.lineEdit_minT.setEnabled(False)
self.dlg.lineEdit_maxT.setEnabled(False)
self.dlg.lineEdit_dist.setEnabled(False)
self.dlg.lineEdit_minT.clear()
self.dlg.lineEdit_maxT.clear()
self.dlg.lineEdit_dist.clear()
self.dlg.lineEditThreshold.clear()
self.dlg.label_7.setEnabled(False)
self.dlg.label_8.setEnabled(False)
self.dlg.label_9.setEnabled(False)
self.dlg.knn_number.setEnabled(False)
self.dlg.checkBox_knn.setChecked(False)
self.dlg.checkBox_knn.setEnabled(True)
self.load_comboBox()
def clear_fields(self):
"""Clearing the fields when layers are changed"""
self.dlg.comboBox_C.clear()
self.dlg.comboBox_C_2.clear()
def write_file(self, filename, statistics, layerName, inLayer,
inDataSource, y, threshold1):
"""Writing the output shapefile into the mentioned directory"""
outDriver = ogr.GetDriverByName("ESRI Shapefile")
layerName = layerName.split('.')
layerName.pop()
# layerName = '.'.join(layerName)
outShapefile = filename + ".shp"
# Remove eventually alrady exisiting output
if os.path.exists(outShapefile):
outDriver.DeleteDataSource(outShapefile)
# Create the output shapefile
outDataSource = outDriver.CreateDataSource(outShapefile)
outLayer = outDataSource.CreateLayer(
"output", inLayer.GetSpatialRef(),
inLayer.GetLayerDefn().GetGeomType())
# Add input Layer Fields to the output Layer
inLayerDefn = inLayer.GetLayerDefn()
for i in range(0, inLayerDefn.GetFieldCount()):
fieldDefn = inLayerDefn.GetFieldDefn(i)
outLayer.CreateField(fieldDefn)
##
# Add additional fields - for more types other than Strings take a look at http://pcjericks.github.io/py-gdalogr-cookbook/layers.html#create-a-new-shapefile-and-add-data
##
# Add empty field to store Pysal results
Z_field = ogr.FieldDefn("Z-score", ogr.OFTReal)
Z_field.SetWidth(15)
Z_field.SetPrecision(10)
outLayer.CreateField(Z_field)
p_field = ogr.FieldDefn("p-value", ogr.OFTReal)
p_field.SetWidth(15)
p_field.SetPrecision(10)
outLayer.CreateField(p_field)
# if not Gi*
if (self.dlg.checkBox_moran.isChecked() == 1
or self.dlg.checkBox_moranBi.isChecked() == 1):
intValue = int(ogr.OFTReal)
q_field = ogr.FieldDefn("q-value", intValue)
q_field.SetWidth(15)
q_field.SetPrecision(10)
outLayer.CreateField(q_field)
# Get the output Layer's Feature Definition
outLayerDefn = outLayer.GetLayerDefn()
# Get the input Layer's Feature Definition
inLayerDefn = inLayer.GetLayerDefn()
# Add features to the ouput Layer
for i in range(0, inLayer.GetFeatureCount()):
# Get the input Feature
inFeature = inLayer.GetFeature(i)
# Create output Feature
outFeature = ogr.Feature(outLayerDefn)
# Add field values from input Layer
for j in range(0, inLayerDefn.GetFieldCount()):
outFeature.SetField(
outLayerDefn.GetFieldDefn(j).GetNameRef(),
inFeature.GetField(j))
# Set geometry
geom = inFeature.GetGeometryRef()
outFeature.SetGeometry(geom)
if self.dlg.checkBox_gi.isChecked() == 1:
# Add Z-scores and p-values to their field column
if self.dlg.checkBox_randomPerm.isChecked(
) == 1: # to use permutation approach
if numpy.mean(y) <= 0:
outFeature.SetField("Z-score",
statistics.z_sim[i] * (-1))
outFeature.SetField("p-value",
statistics.p_z_sim[i] * 2)
else:
outFeature.SetField("Z-score", statistics.z_sim[i])
outFeature.SetField("p-value",
statistics.p_z_sim[i] * 2)
else: # to use normality hypothesis
if numpy.mean(y) <= 0:
outFeature.SetField("Z-score", statistics.Zs[i] * (-1))
outFeature.SetField("p-value",
statistics.p_norm[i] * 2)
else:
outFeature.SetField("Z-score", statistics.Zs[i])
outFeature.SetField("p-value",
statistics.p_norm[i] * 2)
else:
if self.dlg.checkBox_randomPerm.isChecked(
) == 1: # to use permutation approach
if max(y) >= 0:
outFeature.SetField("Z-score", statistics.z_sim[i])
outFeature.SetField("p-value", statistics.p_sim[i] * 2)
else:
outFeature.SetField("Z-score",
statistics.z_sim[i] * (-1))
outFeature.SetField("p-value", statistics.p_sim[i] * 2)
else: # to use normality hypothesis
if max(y) >= 0:
outFeature.SetField("Z-score", statistics.z_sim[i])
outFeature.SetField("p-value",
statistics.p_z_sim[i] * 2)
else:
outFeature.SetField("Z-score",
statistics.z_sim[i] * (-1))
outFeature.SetField("p-value",
statistics.p_z_sim[i] * 2)
outFeature.SetField("q-value", statistics.q[i])
# Add new feature to output Layer
outLayer.CreateFeature(outFeature)
# Close DataSources
inDataSource.Destroy()
outDataSource.Destroy()
if threshold1:
self.success_msg(threshold1)
new_layer = self.iface.addVectorLayer(
filename + ".shp",
str(os.path.basename(os.path.normpath(filename))), "ogr")
if not new_layer:
QMessageBox.information(self.dlg, self.tr("New Layer"),
self.tr("Layer Cannot be Loaded"),
QMessageBox.Ok)
self.clear_ui()
def load_comboBox(self):
"""Load the fields into combobox when layers are changed"""
layer_shp = []
layers = self.iface.legendInterface().layers()
if len(layers) != 0: # checklayers exist in the project
for layer in layers:
if hasattr(
layer, "dataProvider"
): # to not consider Openlayers basemaps in the layer list
myfilepath = layer.dataProvider().dataSourceUri(
) # directory including filename
(myDirectory, nameFile) = os.path.split(
myfilepath) # splitting into directory and filename
if (".shp" in nameFile):
layer_shp.append(layer)
selectedLayerIndex = self.dlg.comboBox.currentIndex()
if selectedLayerIndex < 0 or selectedLayerIndex > len(layer_shp):
return
try:
selectedLayer = layer_shp[selectedLayerIndex]
except:
return
fieldnames = [field.name() for field in selectedLayer.pendingFields()]
self.clear_fields()
self.dlg.comboBox_C.addItems(fieldnames)
self.dlg.comboBox_C_2.addItems(fieldnames)
(path,
layer_id) = selectedLayer.dataProvider().dataSourceUri().split('|')
inDriver = ogr.GetDriverByName("ESRI Shapefile")
inDataSource = inDriver.Open(path, 0)
inLayer = inDataSource.GetLayer()
global type
type = inLayer.GetLayerDefn().GetGeomType()
if type == 3: # is a polygon
self.dlg.checkBox_queen.setChecked(True)
self.dlg.lineEditThreshold.setEnabled(False)
self.dlg.checkBox_knn.setEnabled(False)
self.dlg.knn_number.setEnabled(False)
self.dlg.checkBox_optimizeDistance.setChecked(False)
self.dlg.checkBox_optimizeDistance.setEnabled(False)
self.dlg.lineEdit_minT.setEnabled(False)
self.dlg.lineEdit_maxT.setEnabled(False)
self.dlg.lineEdit_dist.setEnabled(False)
else:
self.dlg.checkBox_queen.setChecked(False)
self.dlg.checkBox_knn.setEnabled(True)
self.dlg.knn_number.setEnabled(True)
self.dlg.lineEditThreshold.setEnabled(True)
self.dlg.checkBox_optimizeDistance.setEnabled(True)
self.dlg.lineEdit_minT.setEnabled(True)
self.dlg.lineEdit_dist.setEnabled(True)
self.dlg.lineEdit_maxT.setEnabled(True)
thresh = pysal.min_threshold_dist_from_shapefile(path)
self.dlg.lineEditThreshold.setText(str(int(thresh)))
def error_msg(self):
"""Message to report missing fields"""
self.clear_ui()
self.loadLayerList()
QMessageBox.warning(self.dlg.show(),
self.tr("HotspotAnalysis:Warning"),
self.tr("Please specify input fields properly"),
QMessageBox.Ok)
def success_msg(self, distance):
"""Message to report succesful file creation"""
QMessageBox.information(
self.dlg, self.tr("HotspotAnalysis:Success"),
self.tr("File is generated Succesfully (Distance used = " +
str(distance) + ")"), QMessageBox.Ok)
def validator(self):
"""Validator to Check whether the inputs are given properly"""
# Polygon case
if self.dlg.checkBox_queen.isChecked() == 1:
return 1
if ((self.dlg.checkBox_optimizeDistance.isChecked() == 0
and self.dlg.lineEditThreshold.text() != "")
or (self.dlg.checkBox_optimizeDistance.isChecked() == 1
and (self.dlg.lineEdit_dist.text() != ""
and self.dlg.lineEdit_maxT.text() != ""
and self.dlg.lineEdit_minT.text() != "")) or
(self.dlg.checkBox_knn.isChecked() == 1)) \
and self.dlg.lineEdit.text() != "":
return 1
else:
return 0
def loadLayerList(self):
layers_list = []
layers_shp = []
# Show the shapefiles in the ComboBox
layers = self.iface.legendInterface().layers()
if len(layers) != 0: # checklayers exist in the project
for layer in layers:
if hasattr(
layer, "dataProvider"
): # to not consider Openlayers basemaps in the layer list
myfilepath = layer.dataProvider().dataSourceUri(
) # directory including filename
(myDirectory, nameFile) = os.path.split(
myfilepath) # splitting into directory and filename
if (".shp" in nameFile):
layers_list.append(layer.name())
layers_shp.append(layer)
self.dlg.comboBox.addItems(
layers_list) # adding layers to comboBox
selectedLayerIndex = self.dlg.comboBox.currentIndex()
if selectedLayerIndex < 0 or selectedLayerIndex > len(layers_shp):
return
selectedLayer = layers_shp[selectedLayerIndex]
fieldnames = [
field.name() for field in selectedLayer.pendingFields()
] # fetching fieldnames of layer
self.clear_fields()
self.dlg.comboBox_C.addItems(fieldnames)
self.dlg.comboBox_C_2.addItems(fieldnames)
try:
self.dlg.comboBox.activated.connect(
lambda: self.load_comboBox())
self.dlg.comboBox.currentIndexChanged.connect(
lambda: self.load_comboBox())
self.dlg.checkBox_optimizeDistance.toggled.connect(
self.optimizedThreshold) # checkbox toggle event
self.dlg.checkBox_randomPerm.toggled.connect(
self.randomPermChecked) # checkbox toggle event
self.dlg.checkBox_moranBi.toggled.connect(
self.moranBiChecked) # checkbox toggle event
self.dlg.checkBox_knn.toggled.connect(
self.knnChecked) # checkbox toggle event
except:
return False
return [layers, layers_shp]
else:
return [layers, False]
def run(self):
"""Run method that performs all the real work""" # show the dialog
self.clear_ui()
layers, layers_shp = self.loadLayerList()
if len(layers) == 0:
return
self.dlg.show()
self.load_comboBox()
# Run the dialog event loop
result = self.dlg.exec_()
# See if OK was pressed and fields are not empty
if result and (self.validator() == 1):
selectedLayerIndex = self.dlg.comboBox.currentIndex()
if selectedLayerIndex < 0 or selectedLayerIndex > len(layers):
return
selectedLayer = layers_shp[selectedLayerIndex]
layerName = selectedLayer.dataProvider().dataSourceUri()
C = selectedLayer.fieldNameIndex(self.dlg.comboBox_C.currentText())
C2 = selectedLayer.fieldNameIndex(
self.dlg.comboBox_C_2.currentText())
filename = self.dlg.lineEdit.text()
(path, layer_id) = layerName.split('|')
inDriver = ogr.GetDriverByName("ESRI Shapefile")
inDataSource = inDriver.Open(path, 0)
inLayer = inDataSource.GetLayer()
type = inLayer.GetLayerDefn().GetGeomType()
u = []
for i in range(0, inLayer.GetFeatureCount()):
geometry = inLayer.GetFeature(i)
u.append(geometry.GetField(C))
y = numpy.array(u) # attributes vector
if self.dlg.checkBox_moranBi.isChecked() == 1:
v = []
for i in range(0, inLayer.GetFeatureCount()):
geometry = inLayer.GetFeature(i)
v.append(geometry.GetField(C2))
x = numpy.array(v)
if type == 1: # point
t = ()
for feature in inLayer:
geometry = feature.GetGeometryRef()
xy = (geometry.GetX(), geometry.GetY())
t = t + (xy, )
# t = get_points_array_from_shapefile(layerName.split("|")[0])
if self.dlg.lineEditThreshold.text(
) and self.dlg.lineEditThreshold.text(
) != "": # if threshold is given
threshold1 = int(self.dlg.lineEditThreshold.text())
elif self.dlg.checkBox_knn.isChecked(
) == 0: # if user needs to optimize threshold (no knn)
mx_moran = -1000.0
mx_i = -1000.0
minT = int(self.dlg.lineEdit_minT.text())
maxT = int(self.dlg.lineEdit_maxT.text())
dist = int(self.dlg.lineEdit_dist.text())
for i in range(minT, maxT + dist, dist):
w = DistanceBand(t, threshold=i, p=2, binary=False)
moran = pysal.Moran(y, w)
# print moran.z_norm
if moran.z_norm > mx_moran:
mx_i = i
mx_moran = moran.z_norm
threshold1 = int(mx_i)
if self.dlg.checkBox_knn.isChecked() == 1:
weightValue = int(self.dlg.knn_number.text())
w = pysal.knnW_from_shapefile(layerName.split("|")[0],
k=weightValue,
p=1)
threshold1 = "None/KNN used " + self.dlg.knn_number.text()
else:
w = DistanceBand(t, threshold1, p=2, binary=False)
else: # polygon
w = pysal.queen_from_shapefile(layerName.split("|")[0])
threshold1 = "None/Queen's Case used"
if self.dlg.checkBox_rowStandard.isChecked() == 1:
type_w = "R"
else:
type_w = "B"
if self.dlg.checkBox_randomPerm.isChecked() == 1:
permutationsValue = int(self.dlg.lineEdit_random.text())
else:
permutationsValue = 999
numpy.random.seed(12345)
if self.dlg.checkBox_gi.isChecked() == 1:
statistics = G_Local(y,
w,
star=True,
transform=type_w,
permutations=permutationsValue)
elif self.dlg.checkBox_moran.isChecked() == 1:
statistics = Moran_Local(y,
w,
transformation=type_w,
permutations=permutationsValue)
else:
statistics = Moran_Local_BV(y,
x,
w,
transformation=type_w,
permutations=permutationsValue)
self.write_file(filename, statistics, layerName, inLayer,
inDataSource, y, threshold1)
# assign the style to the output layer on QGIS
if self.dlg.checkBox_gi.isChecked() == 1:
if type == 1: # point
stylePath = "/layer_style/hotspots_class.qml"
else:
stylePath = "/layer_style/hotspots_class_poly.qml"
self.iface.activeLayer().loadNamedStyle(
os.path.dirname(__file__) + stylePath)
else:
if type == 1: # point
stylePath = "/layer_style/moran_class.qml"
else:
stylePath = "/layer_style/moran_class_poly.qml"
self.iface.activeLayer().loadNamedStyle(
os.path.dirname(__file__) + stylePath)
elif result and (self.validator() == 0):
self.error_msg()
else:
self.clear_ui()
pass
def setUp(self):
"""Runs before each test."""
self.dialog = HotspotAnalysisDialog(None)