def __init__(self, dataset, mainWindow, process, pipe):
"""
Initialize the controller for the main window.
:param dataset: Dataset model.
:param mainWindow: MainWindow view.
:param process: Worker subprocess.
:param pipe: Message pipe for the worker subprocess.
"""
self.spatialData = dataset.spatialData
self.temporalData = dataset.temporalData
self.auxiliaryData = dataset.auxiliaryData
self.selectedSpecies = dataset.selectedSpecies
self.map = LeafletMap(dataset, "Landscape")
self.plot = ScatterPlot(dataset)
spatial = SpatialAnalysisWidget(self.map.webView)
temporal = TemporalAnalysisWidget(self.plot.mplCanvas)
cooccurrence = CooccurrenceAnalysisWidget()
self.correlationTable = CorrelationTable(dataset, spatial, temporal)
self.cooccurrenceCalculation = CooccurrenceCalculation(
dataset, cooccurrence, process, pipe
)
self.mainWindow = mainWindow
self.mainWindow.setupWidgets(
spatial, temporal, cooccurrence, self, self.cooccurrenceCalculation
)
self.mainWindow.show()
class MainAction:
def __init__(self, dataset, mainWindow, process, pipe):
"""
Initialize the controller for the main window.
:param dataset: Dataset model.
:param mainWindow: MainWindow view.
:param process: Worker subprocess.
:param pipe: Message pipe for the worker subprocess.
"""
self.spatialData = dataset.spatialData
self.temporalData = dataset.temporalData
self.auxiliaryData = dataset.auxiliaryData
self.selectedSpecies = dataset.selectedSpecies
self.map = LeafletMap(dataset, "Landscape")
self.plot = ScatterPlot(dataset)
spatial = SpatialAnalysisWidget(self.map.webView)
temporal = TemporalAnalysisWidget(self.plot.mplCanvas)
cooccurrence = CooccurrenceAnalysisWidget()
self.correlationTable = CorrelationTable(dataset, spatial, temporal)
self.cooccurrenceCalculation = CooccurrenceCalculation(
dataset, cooccurrence, process, pipe
)
self.mainWindow = mainWindow
self.mainWindow.setupWidgets(
spatial, temporal, cooccurrence, self, self.cooccurrenceCalculation
)
self.mainWindow.show()
# noinspection PyCallByClass, PyTypeChecker, PyArgumentList, PyBroadException
def importData(self):
"""
Import data from a Darwin Core Archive (DwC-A) file. |br|
Store them in ``Dataset``.
:return: None.
"""
if self.spatialData:
title = "Dataset Already Imported"
content = "To import new data, please clear data first."
self.mainWindow.alert(title, content, 3)
return
title, extension = "Select a DwC-A File", "DwC-A File (*.zip)"
filename = self.mainWindow.openFile(title, extension)
if filename:
try:
archiveData, archiveMeta = DatasetProcessor.extractDarwinCoreArchive(filename)
if archiveMeta["coreType"] not in Dataset.supportedCores:
title = "Unsupported DwC Type"
content = (
"The provided file has core type of " + archiveMeta["coreType"] + ".\n"
"This program only support " + ", ".join(Dataset.supportedCores) + "."
)
self.mainWindow.alert(title, content, 3)
return
columns = [
("individualCount", True),
("eventDate", True),
("decimalLatitude", True),
("decimalLongitude", True),
("scientificName", True),
("vernacularName", False)
]
try:
dataList = DatasetProcessor.extractCsv(archiveData, archiveMeta, columns)
except ValueError as e:
title = "Invalid DwC-A File"
content = str(e) + "\nPlease select a DwC-A file with such field."
self.mainWindow.alert(title, content, 3)
return
except:
title = "Invalid DwC-A File"
content = (
"The provided file is either not in DwC-A format or corrupted.\n"
"Please select a valid one.\n\n"
)
self.mainWindow.alert(title, content + format_exc(), 3)
return
for r in dataList:
try:
r0int = int(r[0])
r1datetime = parse(r[1])
r2float = float(r[2])
r3float = float(r[3])
if not r[4]:
raise ValueError("Field \"scientificName\" is empty.")
except:
title = "Invalid Record Found"
content = "The following record is invalid and will be ignored:\n"
self.mainWindow.alert(title, content + pformat(r), 2)
else:
self.spatialData[r[4]] = ((r2float, r3float), r0int)
self.temporalData[r[4]] = (r1datetime, r0int)
self.auxiliaryData[r[4]] = r[5]
title = "Dataset Successfully Imported"
content = "{:,d} records have been loaded.".format(len(dataList))
self.mainWindow.alert(title, content, 0)
# noinspection PyTypeChecker
def setFilters(self):
"""
Only leave filtered data in ``Dataset``.
:return: None.
"""
if not self.spatialData:
title, content = "Empty Dataset", "Please import data first."
self.mainWindow.alert(title, content, 3)
else:
xCoordinates = [n[0][1] for m in self.spatialData.values() for n in m]
yCoordinates = [n[0][0] for m in self.spatialData.values() for n in m]
timestamps = [n[0] for m in self.temporalData.values() for n in m]
xCoordinateMinMax = (min(xCoordinates), max(xCoordinates))
yCoordinateMinMax = (min(yCoordinates), max(yCoordinates))
timestampMinMax = (min(timestamps), max(timestamps))
dialog = SetFiltersDialog(xCoordinateMinMax, yCoordinateMinMax, timestampMinMax)
dialog.exec_()
if not dialog.xCoordinateMinMax:
return
for k in list(self.spatialData.keys()):
for i, u in enumerate(self.spatialData[k]):
v = self.temporalData[k][i]
if (
dialog.xCoordinateMinMax[0] <= u[0][1] <= dialog.xCoordinateMinMax[1] and
dialog.yCoordinateMinMax[0] <= u[0][0] <= dialog.yCoordinateMinMax[1] and
dialog.timestampMinMax[0] <= v[0] <= dialog.timestampMinMax[1]
):
break
else:
if k in self.selectedSpecies:
self.removeSpecies(k + " " + self.auxiliaryData[k])
del self.spatialData[k]
del self.temporalData[k]
del self.auxiliaryData[k]
self.cooccurrenceCalculation.halt()
self.plot.resetCache()
length = len([n for m in self.spatialData.values() for n in m])
title = "Filter Result"
content = "{:,d} records matches the specified range.".format(length)
self.mainWindow.alert(title, content, 0)
# noinspection PyCallByClass, PyTypeChecker, PyArgumentList
def addSpecies(self):
"""
Select a species from ``Dataset.spatialData``, append it to ``Dataset.selectedSpecies``.
:return: None.
"""
if not self.spatialData:
title, content = "Empty Dataset", "Please import data first."
self.mainWindow.alert(title, content, 3)
elif not Species.available():
title = "Too Many Species"
content = ("Selecting more than " + str(Species.nColor) +
" species is not supported.")
self.mainWindow.alert(title, content, 3)
else:
species = [(k, self.auxiliaryData[k]) for k in self.spatialData.keys()
if k not in self.selectedSpecies]
dialog = AddSpeciesDialog(species)
dialog.exec_()
if dialog.newSpecies:
newSpecies, vernacularName = dialog.newSpecies
self.selectedSpecies[newSpecies] = Species()
newColor = self.selectedSpecies[newSpecies].color
self.mainWindow.addSpeciesToLayout(newSpecies, vernacularName, newColor)
self.map.add(newSpecies)
self.map.refresh()
self.plot.rebuild()
self.correlationTable.add(newSpecies)
def removeSpecies(self, oldSpecies):
"""
Remove the specified species from ``Dataset.selectedSpecies``.
:param oldSpecies: Name of the old species to be removed.
:return: None.
"""
oldSpeciesShort = oldSpecies
for k in self.selectedSpecies.keys():
if oldSpecies.startswith(k):
oldSpeciesShort = k
del self.selectedSpecies[k]
break
self.mainWindow.removeSpeciesFromLayout(oldSpecies)
self.map.remove()
self.map.refresh()
self.plot.rebuild()
self.correlationTable.remove(oldSpeciesShort)
def clearData(self):
"""
Clear ``Dataset``.
:return: None.
"""
if not self.spatialData:
title, content = "Empty Dataset", "Please import data first."
self.mainWindow.alert(title, content, 3)
else:
self.spatialData.clear()
self.temporalData.clear()
self.auxiliaryData.clear()
self.selectedSpecies.clear()
self.mainWindow.removeSpeciesFromLayout()
self.map.rebuild()
self.map.refresh()
self.plot.resetCache()
self.plot.rebuild()
self.correlationTable.remove()
self.cooccurrenceCalculation.halt()
# noinspection PyCallByClass, PyTypeChecker, PyArgumentList
def about(self):
"""
Show information about this program.
:return: None.
"""
title = "About Biodiversity Analysis"
content = Dataset.license()
self.mainWindow.alert(title, content, 4)