def setUp(self):
south = load_example('South')
db = libpysal.io.open(south.get_path("south.dbf"), 'r')
self.y_name = "HR90"
self.y = np.array(db.by_col(self.y_name))
self.y.shape = (len(self.y), 1)
self.x_names = ["RD90", "PS90", "UE90", "DV90"]
self.x = np.array([db.by_col(var) for var in self.x_names]).T
self.w = Queen.from_shapefile(south.get_path("south.shp"))
self.w.transform = 'r'
def _test():
import doctest
start_suppress = np.get_printoptions()['suppress']
np.set_printoptions(suppress=True)
doctest.testmod()
np.set_printoptions(suppress=start_suppress)
if __name__ == '__main__':
_test()
import numpy as np
import libpysal
from .sur_utils import sur_dictxy, sur_dictZ
from libpysal.examples import load_example
from libpysal.weights import Queen
nat = load_example('Natregimes')
db = libpysal.io.open(nat.get_path('natregimes.dbf'), 'r')
y_var = ['HR80', 'HR90']
x_var = [['PS80', 'UE80'], ['PS90', 'UE90']]
w = Queen.from_shapefile(nat.get_path("natregimes.shp"))
w.transform = 'r'
bigy0, bigX0, bigyvars0, bigXvars0 = sur_dictxy(db, y_var, x_var)
reg0 = SURerrorML(bigy0,bigX0,w,regimes=regimes,name_bigy=bigyvars0,name_bigX=bigXvars0,\
name_w="natqueen",name_ds="natregimes",vm=True,nonspat_diag=True,spat_diag=True)
# reg0 = SURerrorGM(bigy0,bigX0,w,regimes=regimes,name_bigy=bigyvars0,name_bigX=bigXvars0,\
# name_w="natqueen",name_ds="natregimes",vm=False,nonspat_diag=True,spat_diag=False)
print(reg0.summary)
import ols as OLS
from utils import optim_moments, RegressionPropsY, get_spFilter, spdot
# import user_output as USER
# import summary_output as SUMMARY
# import regimes as REGI
# First import libpysal to load the spatial analysis tools.
import libpysal
from libpysal.examples import load_example
from libpysal.weights import Queen
# Open data on NCOVR US County Homicides (3085 areas).
nat = load_example('Natregimes')
db = libpysal.io.open(nat.get_path('natregimes.dbf'),'r')
nat_shp = libpysal.examples.get_path("natregimes.shp")
w = Queen.from_shapefile(nat_shp)
w.transform = 'r'
name_y = ['HR70','HR80','HR90']
y = np.array([db.by_col(name) for name in name_y]).T
name_x = ['RD70','RD80','RD90','PS70','PS80','PS90']
x = np.array([db.by_col(name) for name in name_x]).T
full_weights = False
def _moments_kkp(ws, u, i, trace_w2=None):
'''
Compute G and g matrices for the KKP model.
...
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()