def OnAddRangeSelection(self, event):
""" Select dissimilarity matrix cells meeting specified user criteria. """
if str(self.lblMatrixFilename.GetLabelText()) == '<No file loaded>':
wx.MessageBox("Please load dissimilarity matrix.", "Dissimilarity matrix not found")
return
# get user criteria
if isNumber(self.txtLessThanValue.GetValue()):
lessThanValue = float(self.txtLessThanValue.GetValue())
else:
wx.MessageBox("Selection criteria must be numeric.", "Invalid selection criteria")
return
if isNumber(self.txtGreaterThanValue.GetValue()):
greaterThanValue = float(self.txtGreaterThanValue.GetValue())
else:
wx.MessageBox("Selection criteria must be numeric.", "Invalid selection criteria")
return
bSelectUpper = self.chkSelectFromUpperTriangleByRange.IsChecked()
bSelectLower = self.chkSelectFromLowerTriangleByRange.IsChecked()
# select cells meeting user criteria
for i in xrange(0, len(self.index)):
for j in xrange(i+1, len(self.index)):
if bSelectUpper and self.matrix[i][j] <= lessThanValue and self.matrix[i][j] >= greaterThanValue:
self.dissMatrix.SelectBlock(i, j+1, i, j+1, True)
if bSelectLower and self.matrix[j][i] <= lessThanValue and self.matrix[j][i] >= greaterThanValue:
self.dissMatrix.SelectBlock(j, i+1, j, i+1, True)
def __init__(self, parent=None):
DerivedDataCalculatorLayout.__init__ ( self, parent )
self.SetIcon(wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico", wx.BITMAP_TYPE_ICO))
# check required data has been loaded
if GenGIS.layerTree.GetNumMapLayers() == 0 or GenGIS.layerTree.GetNumLocationSetLayers() == 0 or GenGIS.layerTree.GetNumSequenceLayers() == 0:
wx.MessageBox("This plugin requires map, location, and sequence data to be loaded.", "Additional data required.")
self.Close()
return
# populate unique sequence id combobox
for field in GenGIS.layerTree.GetSequenceLayer(0).GetController().GetMetadataFields():
self.cboUniqueSeqIdField.Append(field)
self.cboUniqueSeqIdField.SetSelection(0)
# populate sequence count comboxbox with 'likely' numeric fields
for field in GenGIS.layerTree.GetSequenceLayer(0).GetController().GetMetadataFields():
# check if field is numeric for first sequence
value = GenGIS.layerTree.GetSequenceLayer(0).GetController().GetData()[field]
if isNumber(value):
self.cboSeqCountField.Append(field)
if self.cboSeqCountField.GetCount() >= 1:
self.cboSeqCountField.SetSelection(0)
else:
self.cboSeqCountField.Append('<No numeric data>')
self.cboSeqCountField.SetStringSelection('<No numeric data>')
self.btnUniqueSeqs.Disable()
self.btnTotalSeqs.Disable()
self.btnNormalizeUniqueSeqs.Disable()
# resize frame to fit widgets
self.Fit()
def SortFields(self, layers, field):
values = []
self.locData = {}
for layer in layers:
if not layer.GetController().IsActive():
continue
data = layer.GetController().GetData()[field]
if self.isSequence:
id = layer.GetController().GetSiteId()
else:
id = layer.GetController().GetId()
layerNum = self.locationMap[id]
if layerNum in self.locData.keys():
self.locData[layerNum].append(data)
else:
self.locData[layerNum] = [data]
values.append(data)
# a flag for whether or not sorting should be descending or ascending
if self.sort:
ascend = True
else:
ascend = False
# Since the fields are unicode values, this sorts them numericaly if applicable, or alphabetically
if re.search(r"(\d+/\d+/\d+)", data):
values = self.SortDates(values, ascend)
elif dh.isNumber(data):
values = sorted(set(values), key=lambda val: float(val), reverse=ascend)
else:
values = sorted(set(values), reverse=ascend)
return values
def SortFields( self, layers, field):
values = []
self.locData = {}
for layer in layers:
if not layer.GetController().IsActive():
continue
data = layer.GetController().GetData()[field]
if self.isSequence:
id = layer.GetController().GetSiteId()
else:
id = layer.GetController().GetId()
layerNum = self.locationMap[id]
if layerNum in self.locData.keys():
self.locData[layerNum].append(data)
else:
self.locData[layerNum] = [data]
values.append(data)
# a flag for whether or not sorting should be descending or ascending
if self.sort:
ascend = True
else:
ascend = False
# Since the fields are unicode values, this sorts them numericaly if applicable, or alphabetically
if re.search(r'(\d+/\d+/\d+)',data):
values = self.SortDates( values , ascend)
elif( dh.isNumber(data) ):
values = sorted( set(values), key = lambda val: float(val), reverse= ascend )
else:
values = sorted( set(values), reverse = ascend )
return values
def __init__(self, parent=None):
BetaDiversityLayout.__init__(self, parent)
self.SetIcon(
wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico",
wx.BITMAP_TYPE_ICO))
self.graphicalElementIds = []
# check required data has been loaded
if GenGIS.layerTree.GetNumMapLayers(
) == 0 or GenGIS.layerTree.GetNumLocationSetLayers(
) == 0 or GenGIS.layerTree.GetNumSequenceLayers() == 0:
wx.MessageBox(
"This plugin requires map, location, and sequence data to be loaded.",
"Additional data required.")
self.Close()
return
# set measure combobox
self.betaDiversityMeasures = BetaDiversityMeasures()
for measure in self.betaDiversityMeasures.measures:
self.cboMeasure.Append(measure)
self.cboMeasure.SetSelection(0)
# set category field combobox
seqLayerController = GenGIS.layerTree.GetSequenceLayer(
0).GetController()
fields = seqLayerController.GetData().keys()
for field in fields:
if field.lower() != 'siteid' and field.lower() != 'site id':
self.cboCategoryField.Append(field)
self.cboCategoryField.SetSelection(0)
# set count field combobox
numericFields = ['<none>']
for field in sorted(fields):
bNumeric = True
for i in xrange(0, GenGIS.layerTree.GetNumSequenceLayers()):
if isNumber(
GenGIS.layerTree.GetSequenceLayer(
i).GetController().GetData()[field]) == False:
bNumeric = False
break
if bNumeric:
numericFields.append(field)
for field in numericFields:
self.cboCountField.Append(field)
self.cboCountField.SetSelection(0)
self.UpdateInfo()
self.results = None
self.newickStr = None
def __init__(self, parent=None):
BetaDiversityLayout.__init__(self, parent)
self.SetIcon(wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico", wx.BITMAP_TYPE_ICO))
self.graphicalElementIds = []
# check required data has been loaded
if (
GenGIS.layerTree.GetNumMapLayers() == 0
or GenGIS.layerTree.GetNumLocationSetLayers() == 0
or GenGIS.layerTree.GetNumSequenceLayers() == 0
):
wx.MessageBox(
"This plugin requires map, location, and sequence data to be loaded.", "Additional data required."
)
self.Close()
return
# set measure combobox
self.betaDiversityMeasures = BetaDiversityMeasures()
for measure in self.betaDiversityMeasures.measures:
self.cboMeasure.Append(measure)
self.cboMeasure.SetSelection(0)
# set category field combobox
seqLayerController = GenGIS.layerTree.GetSequenceLayer(0).GetController()
fields = seqLayerController.GetData().keys()
for field in fields:
if field.lower() != "siteid" and field.lower() != "site id":
self.cboCategoryField.Append(field)
self.cboCategoryField.SetSelection(0)
# set count field combobox
numericFields = ["<none>"]
for field in sorted(fields):
bNumeric = True
for i in xrange(0, GenGIS.layerTree.GetNumSequenceLayers()):
if isNumber(GenGIS.layerTree.GetSequenceLayer(i).GetController().GetData()[field]) == False:
bNumeric = False
break
if bNumeric:
numericFields.append(field)
for field in numericFields:
self.cboCountField.Append(field)
self.cboCountField.SetSelection(0)
self.UpdateInfo()
self.results = None
self.newickStr = None
def OnDataChange( self, event ): # isSequence self.m_StartChoice.Clear() self.m_StopChoice.Clear() field = self.m_DataChoice.GetStringSelection() #if there are sequence layers if GenGIS.layerTree.GetNumSequenceLayers() > 0: #if field is in sequences or locations if field in GenGIS.layerTree.GetSequenceLayer(0).GetController().GetData().keys(): self.isSequence = True # layers = GenGIS.layerTree.GetSequenceLayers() layers = dh.GetNonNullSequences( field ) else: self.isSequence = False # layers = GenGIS.layerTree.GetLocationLayers() layers = dh.GetNonNullLocations( field ) else: self.isSequence = False # layers = GenGIS.layerTree.GetLocationLayers() layers = dh.GetNonNullLocations( field ) values = self.SortFields( layers, field ) for value in values: self.m_StartChoice.Append(value) self.m_StopChoice.Append(value) self.m_StartChoice.SetSelection(0) self.m_StopChoice.SetSelection( len(values)-1 ) # Update the size of steps startData = self.m_StartChoice.GetStringSelection() stopData = self.m_StopChoice.GetStringSelection() steps = self.m_StepsCtrl.GetValue() #Compute Deltas to display to the user. For use with Binning if self.IsDate( startData,stopData ): startData = dateutil.parser.parse(startData) stopData = dateutil.parser.parse(stopData) if self.sort: Delta = ( startData - stopData ) /steps else: Delta = ( stopData - startData ) / steps elif dh.isNumber(startData): Delta = ( float(stopData) - float(startData) ) / float(steps) else: Delta = math.ceil( self.m_StartChoice.GetCount() / float(steps) ) self.m_StepSizeTextCtrl.SetValue( str(Delta) ) self.m_BinStartCtrl.SetValue( str( abs(Delta/2) ) ) self.m_BinEndCtrl.SetValue( str( abs(Delta/2) ) )
def OnDataChange(self, event):
# isSequence
self.m_StartChoice.Clear()
self.m_StopChoice.Clear()
field = self.m_DataChoice.GetStringSelection()
# if there are sequence layers
if GenGIS.layerTree.GetNumSequenceLayers() > 0:
# if field is in sequences or locations
if field in GenGIS.layerTree.GetSequenceLayer(0).GetController().GetData().keys():
self.isSequence = True
# layers = GenGIS.layerTree.GetSequenceLayers()
layers = dh.GetNonNullSequences(field)
else:
self.isSequence = False
# layers = GenGIS.layerTree.GetLocationLayers()
layers = dh.GetNonNullLocations(field)
else:
self.isSequence = False
# layers = GenGIS.layerTree.GetLocationLayers()
layers = dh.GetNonNullLocations(field)
values = self.SortFields(layers, field)
for value in values:
self.m_StartChoice.Append(value)
self.m_StopChoice.Append(value)
self.m_StartChoice.SetSelection(0)
self.m_StopChoice.SetSelection(len(values) - 1)
# Update the size of steps
startData = self.m_StartChoice.GetStringSelection()
stopData = self.m_StopChoice.GetStringSelection()
steps = self.m_StepsCtrl.GetValue()
# Compute Deltas to display to the user. For use with Binning
if self.IsDate(startData, stopData):
startData = dateutil.parser.parse(startData)
stopData = dateutil.parser.parse(stopData)
if self.sort:
Delta = (startData - stopData) / steps
else:
Delta = (stopData - startData) / steps
elif dh.isNumber(startData):
Delta = (float(stopData) - float(startData)) / float(steps)
else:
Delta = math.ceil(self.m_StartChoice.GetCount() / float(steps))
self.m_StepSizeTextCtrl.SetValue(str(Delta))
self.m_BinStartCtrl.SetValue(str(abs(Delta / 2)))
self.m_BinEndCtrl.SetValue(str(abs(Delta / 2)))
def OnAddRangeSelection(self, event):
""" Select dissimilarity matrix cells meeting specified user criteria. """
if str(self.lblMatrixFilename.GetLabelText()) == '<No file loaded>':
wx.MessageBox("Please load dissimilarity matrix.",
"Dissimilarity matrix not found")
return
# get user criteria
if isNumber(self.txtLessThanValue.GetValue()):
lessThanValue = float(self.txtLessThanValue.GetValue())
else:
wx.MessageBox("Selection criteria must be numeric.",
"Invalid selection criteria")
return
if isNumber(self.txtGreaterThanValue.GetValue()):
greaterThanValue = float(self.txtGreaterThanValue.GetValue())
else:
wx.MessageBox("Selection criteria must be numeric.",
"Invalid selection criteria")
return
bSelectUpper = self.chkSelectFromUpperTriangleByRange.IsChecked()
bSelectLower = self.chkSelectFromLowerTriangleByRange.IsChecked()
# select cells meeting user criteria
for i in xrange(0, len(self.index)):
for j in xrange(i + 1, len(self.index)):
if bSelectUpper and self.matrix[i][
j] <= lessThanValue and self.matrix[i][
j] >= greaterThanValue:
self.dissMatrix.SelectBlock(i, j + 1, i, j + 1, True)
if bSelectLower and self.matrix[j][
i] <= lessThanValue and self.matrix[j][
i] >= greaterThanValue:
self.dissMatrix.SelectBlock(j, i + 1, j, i + 1, True)
def ShowSpread( self, startData, stopData, field, isDate ): #returns all the location in a location set if( self.isSequence ): # locData = GenGIS.layerTree.GetSequenceLayers() locData = dh.GetNonNullSequences( field ) else: # locData = GenGIS.layerTree.GetLocationLayers() locData = dh.GetNonNullLocations( field ) GenGIS.viewport.Refresh() # set initial visual properties of all location sites for i in xrange(0, len(locData)): if self.isSequence: id = locData[i].GetController().GetSiteId() index = self.locationMap[id] loc = GenGIS.layerTree.GetLocationLayer(index) if self.ColourIntensity: loc.GetController().SetColour( GenGIS.Colour(1.0, 0.5, 0) ) loc.GetController().SetSize(4.0) # Set initial state self.StartingState[loc.GetName()] = loc.GetController().IsActive() else: if self.ColourIntensity: locData[i].GetController().SetColour(GenGIS.Colour(1.0, 0.5, 0)) locData[i].GetController().SetSize(4.0) # Set Initial State # print "ID: ",locData[i].GetName()," State: ",locData[i].GetController().IsActive() self.StartingState[locData[i].GetName()] = locData[i].GetController().IsActive() locData[i].GetController().SetActive(False) GenGIS.viewport.Refresh() # label for showing current date # Don't really like the labels anymore # self.label.SetScreenPosition(GenGIS.Point3D(40.0, 300.0, 1.0)) # self.label.SetRenderingStyle(GenGIS.LABEL_RENDERING_STYLE.PERSPECTIVE) # GenGIS.graphics.AddLabel(self.label) if isDate: self.DisplayTemporal( locData, field, startData, stopData ) elif dh.isNumber(startData): self.DisplayNumeric( locData, startData, stopData ) else: self.DisplayText( locData, startData, stopData )
def ShowSpread(self, startData, stopData, field, isDate):
# returns all the location in a location set
if self.isSequence:
# locData = GenGIS.layerTree.GetSequenceLayers()
locData = dh.GetNonNullSequences(field)
else:
# locData = GenGIS.layerTree.GetLocationLayers()
locData = dh.GetNonNullLocations(field)
GenGIS.viewport.Refresh()
# set initial visual properties of all location sites
for i in xrange(0, len(locData)):
if self.isSequence:
id = locData[i].GetController().GetSiteId()
index = self.locationMap[id]
loc = GenGIS.layerTree.GetLocationLayer(index)
if self.ColourIntensity:
loc.GetController().SetColour(GenGIS.Colour(1.0, 0.5, 0))
loc.GetController().SetSize(4.0)
# Set initial state
self.StartingState[loc.GetName()] = loc.GetController().IsActive()
else:
if self.ColourIntensity:
locData[i].GetController().SetColour(GenGIS.Colour(1.0, 0.5, 0))
locData[i].GetController().SetSize(4.0)
# Set Initial State
# print "ID: ",locData[i].GetName()," State: ",locData[i].GetController().IsActive()
self.StartingState[locData[i].GetName()] = locData[i].GetController().IsActive()
locData[i].GetController().SetActive(False)
GenGIS.viewport.Refresh()
# label for showing current date
# Don't really like the labels anymore
# self.label.SetScreenPosition(GenGIS.Point3D(40.0, 300.0, 1.0))
# self.label.SetRenderingStyle(GenGIS.LABEL_RENDERING_STYLE.PERSPECTIVE)
# GenGIS.graphics.AddLabel(self.label)
if isDate:
self.DisplayTemporal(locData, field, startData, stopData)
elif dh.isNumber(startData):
self.DisplayNumeric(locData, startData, stopData)
else:
self.DisplayText(locData, startData, stopData)
def OnPlot(self, event):
if len(self.selectedCols) != 1:
wx.MessageBox("Select one (and only one) column to plot!")
return
if hasattr(self,'rca'):
metric=self.table.GetColLabelValue(self.selectedCols[0])
if isNumber(self.userScaleFactor.GetValue()):
userScaleFactor = float(self.userScaleFactor.GetValue())
else:
wx.MessageBox("Scale factor must be numeric.", "Invalid scale factor")
return
#Update the viewport using the metric selected by user
self.rca.ViewportPlot(metric,userScaleFactor)
else:
wx.MessageBox("Please 'Run' this plugin before attempting to update the plot!")
return
def __init__(self, parent=None):
DerivedDataCalculatorLayout.__init__(self, parent)
self.SetIcon(
wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico",
wx.BITMAP_TYPE_ICO))
# check required data has been loaded
if GenGIS.layerTree.GetNumMapLayers(
) == 0 or GenGIS.layerTree.GetNumLocationSetLayers(
) == 0 or GenGIS.layerTree.GetNumSequenceLayers() == 0:
wx.MessageBox(
"This plugin requires map, location, and sequence data to be loaded.",
"Additional data required.")
self.Close()
return
# populate unique sequence id combobox
for field in GenGIS.layerTree.GetSequenceLayer(
0).GetController().GetMetadataFields():
self.cboUniqueSeqIdField.Append(field)
self.cboUniqueSeqIdField.SetSelection(0)
# populate sequence count comboxbox with 'likely' numeric fields
for field in GenGIS.layerTree.GetSequenceLayer(
0).GetController().GetMetadataFields():
# check if field is numeric for first sequence
value = GenGIS.layerTree.GetSequenceLayer(
0).GetController().GetData()[field]
if isNumber(value):
self.cboSeqCountField.Append(field)
if self.cboSeqCountField.GetCount() >= 1:
self.cboSeqCountField.SetSelection(0)
else:
self.cboSeqCountField.Append('<No numeric data>')
self.cboSeqCountField.SetStringSelection('<No numeric data>')
self.btnUniqueSeqs.Disable()
self.btnTotalSeqs.Disable()
self.btnNormalizeUniqueSeqs.Disable()
# resize frame to fit widgets
self.Fit()
def OnPlot(self, event):
if len(self.selectedCols) != 1:
wx.MessageBox("Select one (and only one) column to plot!")
return
if hasattr(self, 'rca'):
metric = self.table.GetColLabelValue(self.selectedCols[0])
if isNumber(self.userScaleFactor.GetValue()):
userScaleFactor = float(self.userScaleFactor.GetValue())
else:
wx.MessageBox("Scale factor must be numeric.",
"Invalid scale factor")
return
#Update the viewport using the metric selected by user
self.rca.ViewportPlot(metric, userScaleFactor)
else:
wx.MessageBox(
"Please 'Run' this plugin before attempting to update the plot!"
)
return
def ViewportPlot(self):
terrainController = GenGIS.layerTree.GetMapLayer(0).GetController()
# remove previously plotted lines
for id in self.graphicalElementIds:
GenGIS.graphics.RemoveLine(id)
self.graphicalElementIds = []
# get data to plot
plotType = self.cboViewportPlot.GetStringSelection()
if plotType == 'x data':
data = self.x
elif plotType == 'y data':
data = self.y
# bail if data can't be plotted
if data == None:
GenGIS.viewport.Refresh()
return
# desired plot attributes
lineWidth = self.spinLineWidth.GetValue()
if isNumber(self.txtScaleFactor.GetValue()):
userScaleFactor = float(self.txtScaleFactor.GetValue())
else:
wx.MessageBox("Scale factor must be numeric.",
"Invalid scale factor")
return
# calculate scale factor
maxValue = max(max(data), abs(min(data)))
if maxValue != 0:
scaleFactor = (0.2 * terrainController.GetWidth()) / maxValue
else:
scaleFactor = 0
scaleFactor *= userScaleFactor
# get min and max values for mapping colours
if min(data) < 0 and max(data) > 0:
# have both negative and positive values so map negative values to
# first half of map and positive values to the second half of the map
maxValue = max(max(data), -min(data))
minValue = -maxValue
else:
# all data is either negative or positive so just map over the full colour map
minValue = min(data)
maxValue = max(data)
# plot data
activeLocLayers = GenGIS.layerTree.GetLocationSetLayer(
0).GetAllActiveLocationLayers()
for i in xrange(0, len(activeLocLayers)):
locLayer = activeLocLayers[i]
geoCoord = GenGIS.GeoCoord(locLayer.GetController().GetLongitude(),
locLayer.GetController().GetLatitude())
pos = GenGIS.Point3D()
terrainController.GeoToGrid(geoCoord, pos)
colour = self.colourMap.GetInterpolatedColour(
data[i], minValue, maxValue)
endPos = GenGIS.Point3D(pos.x, scaleFactor * abs(data[i]), pos.z)
line = GenGIS.VisualLine(colour, lineWidth,
GenGIS.LINE_STYLE.SOLID,
GenGIS.Line3D(pos, endPos))
lineId = GenGIS.graphics.AddLine(line)
self.graphicalElementIds.append(lineId)
GenGIS.viewport.Refresh()
def __init__(self, parent=None):
AlphaDiversityVisualizerLayout.__init__ ( self, parent )
self.SetIcon(wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico", wx.BITMAP_TYPE_ICO))
# initialize member variables
self.graphicalLines = []
self.graphicalMarkers = []
self.selectedRows = []
self.regressionResults = {}
# check required data has been loaded
if GenGIS.layerTree.GetNumMapLayers() == 0 or GenGIS.layerTree.GetNumLocationSetLayers() == 0 or GenGIS.layerTree.GetNumSequenceLayers() == 0:
wx.MessageBox("This plugin requires map and location data to be loaded.", "Additional data required.")
self.Close()
return
# initialize table
self.table.Freeze()
self.table.SetSelectionMode(wx.grid.Grid.wxGridSelectRows)
self.table.EnableScrolling(True, True)
self.table.EnableDragRowSize(True)
self.table.SetRowLabelSize(0)
# set field (column) labels
locationSetLayer = GenGIS.layerTree.GetLocationSetLayer(0)
self.table.DeleteCols(0, self.table.GetNumberCols());
self.table.AppendCols(6)
self.table.SetColLabelValue(0, 'Field')
self.table.SetColLabelValue(1, 'R-Squared Value')
self.table.SetColLabelValue(2, 'P-Value')
self.table.SetColLabelValue(3, 'Standard Error')
self.table.SetColLabelValue(4, 'Slope')
self.table.SetColLabelValue(5, 'Intercept')
# set site ids in first column
locationSetLayer = GenGIS.layerTree.GetLocationSetLayer(0)
numericFields = locationSetLayer.GetController().GetNumericMetadataFields(True)
self.table.DeleteRows(0, self.table.GetNumberRows());
self.table.AppendRows(len(numericFields))
for i in xrange(0, len(numericFields)):
self.table.SetCellValue(i, 0, numericFields[i])
self.table.AutoSizeColumns()
self.table.Update()
self.table.Thaw()
# set measure combobox
self.AlphaDiversityMeasures = AlphaDiversityMeasures()
for measure in self.AlphaDiversityMeasures.measures:
self.cboMeasure.Append(measure)
self.cboMeasure.SetSelection(0)
# set category field combobox
seqLayerController = GenGIS.layerTree.GetSequenceLayer(0).GetController()
fields = seqLayerController.GetData().keys()
for field in fields:
if field.lower() != 'siteid' and field.lower() != 'site id':
self.cboCategoryField.Append(field)
self.cboCategoryField.SetSelection(0)
# set count field combobox
numericFields = ['<none>']
for field in sorted(fields):
bNumeric = True
for i in xrange(0, GenGIS.layerTree.GetNumSequenceLayers()):
if isNumber(GenGIS.layerTree.GetSequenceLayer(i).GetController().GetData()[field]) == False:
bNumeric = False
break
if bNumeric:
numericFields.append(field)
for field in numericFields:
self.cboCountField.Append(field)
self.cboCountField.SetSelection(0)
# set colour map combobox
continuousColourMapNames = GenGIS.colourMapManager.GetColourMapContinuousNames()
for name in continuousColourMapNames:
self.cboColourMap.Append(name)
self.cboColourMap.SetSelection(self.cboColourMap.FindString('Diverging (Blue-White-Red)'))
# Set colour map comboboxes (dots)
for name in continuousColourMapNames:
self.cboColourMapDot.Append(name)
self.cboColourMapDot.SetSelection(self.cboColourMapDot.FindString('Diverging (Blue-White-Red)'))
# initialize plot
self.plot = ScatterPlot(self.pnlPlot)
self.plot.DrawEmptyPlot()
self.UpdateInfo()
def ViewportPlot(self):
terrainController = GenGIS.layerTree.GetMapLayer(0).GetController()
# remove previously plotted lines
for id in self.graphicalElementIds:
GenGIS.graphics.RemoveLine(id)
self.graphicalElementIds = []
# get data to plot
plotType = self.cboViewportPlot.GetStringSelection()
if plotType == 'x data':
data = self.x
elif plotType == 'y data':
data = self.y
# bail if data can't be plotted
if data == None:
GenGIS.viewport.Refresh()
return
# desired plot attributes
lineWidth = self.spinLineWidth.GetValue()
if isNumber(self.txtScaleFactor.GetValue()):
userScaleFactor = float(self.txtScaleFactor.GetValue())
else:
wx.MessageBox("Scale factor must be numeric.", "Invalid scale factor")
return
# calculate scale factor
maxValue = max(max(data), abs(min(data)))
if maxValue != 0:
scaleFactor = (0.2 * terrainController.GetWidth()) / maxValue
else:
scaleFactor = 0
scaleFactor *= userScaleFactor
# get min and max values for mapping colours
if min(data) < 0 and max(data) > 0:
# have both negative and positive values so map negative values to
# first half of map and positive values to the second half of the map
maxValue = max(max(data), -min(data))
minValue = -maxValue
else:
# all data is either negative or positive so just map over the full colour map
minValue = min(data)
maxValue = max(data)
# plot data
activeLocLayers = GenGIS.layerTree.GetLocationSetLayer(0).GetAllActiveLocationLayers()
for i in xrange(0, len(activeLocLayers)):
locLayer = activeLocLayers[i]
geoCoord = GenGIS.GeoCoord(locLayer.GetController().GetLongitude(), locLayer.GetController().GetLatitude())
pos = GenGIS.Point3D()
terrainController.GeoToGrid(geoCoord, pos)
colour = self.colourMap.GetInterpolatedColour(data[i], minValue, maxValue)
endPos = GenGIS.Point3D(pos.x, scaleFactor * abs(data[i]), pos.z)
line = GenGIS.VisualLine(colour, lineWidth, GenGIS.LINE_STYLE.SOLID, GenGIS.Line3D(pos, endPos))
lineId = GenGIS.graphics.AddLine(line)
self.graphicalElementIds.append(lineId)
GenGIS.viewport.Refresh()
def __init__(self, parent=None):
AlphaDiversityVisualizerLayout.__init__(self, parent)
self.SetIcon(
wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico",
wx.BITMAP_TYPE_ICO))
# initialize member variables
self.graphicalLines = []
self.graphicalMarkers = []
self.selectedRows = []
self.regressionResults = {}
# check required data has been loaded
if GenGIS.layerTree.GetNumMapLayers(
) == 0 or GenGIS.layerTree.GetNumLocationSetLayers(
) == 0 or GenGIS.layerTree.GetNumSequenceLayers() == 0:
wx.MessageBox(
"This plugin requires map, location and sequence data to be loaded.",
"Additional data required.")
self.Close()
return
# initialize table
self.table.Freeze()
self.table.SetSelectionMode(wx.grid.Grid.wxGridSelectRows)
self.table.EnableScrolling(True, True)
self.table.EnableDragRowSize(True)
self.table.SetRowLabelSize(0)
# set field (column) labels
locationSetLayer = GenGIS.layerTree.GetLocationSetLayer(0)
self.table.DeleteCols(0, self.table.GetNumberCols())
self.table.AppendCols(6)
self.table.SetColLabelValue(0, 'Field')
self.table.SetColLabelValue(1, 'R-Squared Value')
self.table.SetColLabelValue(2, 'P-Value')
self.table.SetColLabelValue(3, 'Standard Error')
self.table.SetColLabelValue(4, 'Slope')
self.table.SetColLabelValue(5, 'Intercept')
# set site ids in first column
locationSetLayer = GenGIS.layerTree.GetLocationSetLayer(0)
numericFields = locationSetLayer.GetController(
).GetNumericMetadataFields(True)
self.table.DeleteRows(0, self.table.GetNumberRows())
self.table.AppendRows(len(numericFields))
for i in xrange(0, len(numericFields)):
self.table.SetCellValue(i, 0, numericFields[i])
self.table.AutoSizeColumns()
self.table.Update()
self.table.Thaw()
# set measure combobox
self.AlphaDiversityMeasures = AlphaDiversityMeasures()
for measure in self.AlphaDiversityMeasures.measures:
self.cboMeasure.Append(measure)
self.cboMeasure.SetSelection(0)
# set category field combobox
seqLayerController = GenGIS.layerTree.GetSequenceLayer(
0).GetController()
fields = seqLayerController.GetData().keys()
for field in fields:
if field.lower() != 'siteid' and field.lower() != 'site id':
self.cboCategoryField.Append(field)
self.cboCategoryField.SetSelection(0)
# set count field combobox
numericFields = ['<none>']
for field in sorted(fields):
bNumeric = True
for i in xrange(0, GenGIS.layerTree.GetNumSequenceLayers()):
if isNumber(
GenGIS.layerTree.GetSequenceLayer(
i).GetController().GetData()[field]) == False:
bNumeric = False
break
if bNumeric:
numericFields.append(field)
for field in numericFields:
self.cboCountField.Append(field)
self.cboCountField.SetSelection(0)
# set colour map combobox
continuousColourMapNames = GenGIS.colourMapManager.GetColourMapContinuousNames(
)
for name in continuousColourMapNames:
self.cboColourMap.Append(name)
self.cboColourMap.SetSelection(
self.cboColourMap.FindString('Diverging (Blue-White-Red)'))
# Set colour map comboboxes (dots)
for name in continuousColourMapNames:
self.cboColourMapDot.Append(name)
self.cboColourMapDot.SetSelection(
self.cboColourMapDot.FindString('Diverging (Blue-White-Red)'))
# initialize plot
self.plot = ScatterPlot(self.pnlPlot)
self.plot.DrawEmptyPlot()
self.UpdateInfo()
