def __init__(self, parent):
wx.Dialog.__init__(self, parent, wx.ID_ANY, 'Cluster Center Chooser', size=(550, 550))
self.CenterOnParent()
self.centers = []
# set up the plotting panel
self.dataPanel = CenterChooserPanel(self, self.OnClick)
(self.dataSelectors, self.selectorSizer) = customsizers.ChannelSelectorSizer(self)
if DataStore.getCurrentIndex() is not None:
self.dataPanel.addData(DataStore.getCurrentIndex())
# filter the list of labels to include only user-selected ones
selDims = DataStore.getCurrentDataSet().selDims
labels = [DataStore.getCurrentDataSet().labels[i] for i in selDims]
customsizers.populateSelectors(self.dataSelectors, labels, selDims)
self.dataPanel.updateAxes((selDims[0],selDims[1]))
# main sizer
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.sizer.Add(self.dataPanel, True, wx.EXPAND | wx.BOTTOM | wx.TOP, -20)
self.sizer.AddSpacer(20)
self.sizer.Add(self.selectorSizer, False, wx.EXPAND | wx.TOP, 20)
self.sizer.Add(self.CreateButtonSizer(wx.OK | wx.CANCEL), False, wx.EXPAND)
self.SetSizer(self.sizer)
self.SetBackgroundColour("white")
def OnCluster(self, event):
"""
Handles all clustering requests.
Clustering requests are handled in the following method:
1. Passes the requested clustering method to
L{cluster.dialogs.ClusterOptionsDialog.showDialog} method
2. Passes the data and the returned method options to L{cluster.methods.cluster}
3. Passes the returned cluster membership list to the FacsPlotPanel for display
"""
dlg = cDlgs.getClusterDialog(event.GetId(), self)
if dlg.ShowModal() == wx.ID_OK:
if (DataStore.getCurrentDataSet() is not None):
self.statusbar.SetStatusText('Running %s clustering...' % cMthds.methods[event.GetId()][1], 0)
fcs = DataStore.getCurrentDataSet()
data = fcs.data
# Remove columns from analysis as specified by the user
if len(fcs.selDims) > 0:
data = dh.filterData(data, fcs.selDims)
clusterIDs, msg = cMthds.cluster(event.GetId(), data, **dlg.getMethodArgs())
DataStore.addClustering(event.GetId(), clusterIDs, dlg.getMethodArgs())
clusteringIndex = DataStore.getCurrentDataSet().clustering.keys()[-1]
self.statusbar.SetStatusText(msg, 0)
if (dlg.isApplyChecked()):
if self.facsPlotPanel.SelectedSubplotIndex is not None:
self.facsPlotPanel.CurrentSubplot = dv.Subplot(self.facsPlotPanel.SelectedSubplotIndex,
DataStore.getCurrentIndex(), clusteringIndex)
self.facsPlotPanel.draw()
else:
self.facsPlotPanel.addSubplot(DataStore.getCurrentIndex(), clusteringIndex)
self.treeCtrlPanel.updateTree()
dlg.Destroy()
def AddChosenCenter(self, point):
cbxSelected = self._GetSelectedAxes()
dims = DataStore.getCurrentDataSet().labels
if (DataStore.getCurrentDataSet().selDims):
dims = DataStore.getCurrentDataSet().selDims
retPoint = [0 for i in dims]
for i in range(len(cbxSelected)):
retPoint[cbxSelected[i]] = point[i]
self.centers.append(retPoint)
self.dataPanel.addCenter(retPoint)
def isolateClusters(selection, datasetName):
"""
Create a new data set from a selection of clusters.
@type selection: list
@var selection: The indices of the clusters to be merged.
@type datasetName: str
@var datasetName: The display name for the new data set.
"""
if (len(selection) > 0):
currFCData = DataStore.getCurrentDataSet()
if (datasetName == ""):
datasetName = currFCData.displayname
clusters = separate(currFCData.data, currFCData.getCurrentClustering())
# merge selected clusters
newData = dh.mergeData(selection, clusters)
# assign new data set to the store
newFCData = FacsData('', currFCData.labels, newData, parent=currFCData.ID)
newFCData.displayname = datasetName
newFCData.selDims = currFCData.selDims
# add basic text annotations
textAnn = {'parent': currFCData.displayname}
textAnn['events'] = len(newFCData.data)
newFCData.annotations['text'] = textAnn
DataStore.add(newFCData)
def addSubplot(self):
cds = DataStore.getCurrentDataSet()
if cds is None:
return
try:
clusteringIndex = cds.clustering.keys()[-1]
except IndexError:
self.facsPlotPanel.addSubplot(DataStore.getCurrentIndex())
else:
self.facsPlotPanel.addSubplot(DataStore.getCurrentIndex(), clusteringIndex)
def OnLoadState(self, event):
from data.io import loadState
if len(DataStore.getData()) > 0:
dlgWarn = wx.MessageDialog(self, 'This action may overwrite currently loaded datasets and/or plots.\n\nContinue anyway?', 'Warning',
wx.YES_NO | wx.NO_DEFAULT | wx.ICON_WARNING)
if dlgWarn.ShowModal() == wx.ID_NO:
dlgWarn.Destroy()
return
dlgWarn.Destroy()
formats = "FIND Project File (*.find)|*.find"
dlg = wx.FileDialog(self, "Select saved project", self.dirname, "", formats, wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
try:
loadState(dlg.Directory, dlg.Filename)
except error.ProjectLoadingError:
return
# Load all Figures with Subplot instances from the stored dicts
for fID in FigureStore.getFigures():
fig = FigureStore.get(fID)
splots = []
for plot in fig.subplots:
s = dv.Subplot()
s.load(plot)
s.parent = self.facsPlotPanel.figure
splots.append(s)
fig.subplots = splots
currFigure = FigureStore.getSelectedFigure()
self.facsPlotPanel.subplots = currFigure.subplots
self.facsPlotPanel.SelectedSubplotIndex = currFigure.selectedSubplot
self.facsPlotPanel.updateAxes(currFigure.axes, False)
self.facsPlotPanel.updateSubplotGrid(currFigure.grid[0], currFigure.grid[1], True)
self.chkLinked.Value = self.facsPlotPanel.CurrentSubplotLinked
labels = DataStore.getCurrentDataSet().labels if DataStore.getCurrentDataSet() is not None else []
self.updateAxesList(labels, currFigure.axes)
self.treeCtrlPanel.updateTree()
self.statusbar.SetStatusText("Project loaded from %s" % dlg.Path, 0)
dlg.Destroy()
def OnAnalyze(self, event):
"""
Handles all requests for analysis methods; built-in and plugins.
Currently, analysis methods expect data, a list of dimensions
available to use in analysis, and a window ref in order to
display a subwindow/dialog with results or options.
Analysis methods are expected to return data and/or a status
message. Currently returned data is only used when called from
code, not from the menu; which this method represents.
"""
if (DataStore.getCurrentDataSet() is not None):
strID = aMthds.strID(event.GetId())
self.statusbar.SetStatusText('Running %s...' % aMthds.AvailableMethods()[strID][2], 0)
fcs = DataStore.getCurrentDataSet()
data = fcs.data
# Remove columns from analysis as specified by the user
if len(fcs.selDims) > 0:
data = dh.filterData(data, fcs.selDims)
args = {'parentWindow': self}
_, msg = aMthds.getMethod(strID)(data, **args)
self.statusbar.SetStatusText(msg, 0)
def OnExport(self, event):
if DataStore.getCurrentIndex() is None:
wx.MessageBox("Please load a dataset before attempting to export",
"Data Missing", wx.OK | wx.ICON_ERROR)
return
format = io.getMethod(event.GetId())().FileType
dlg = wx.FileDialog(self, "Save File", "", "",
format,
wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT|wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
io.exportDataFile(event.GetId(), dlg.Path, DataStore.getCurrentDataSet(), window=self)
dlg.Destroy()
def OnEditChannelNames(self, event):
"""
Allow users to modify the descriptors for each channel (dimension)
"""
fcData = DataStore.getCurrentDataSet()
if fcData is not None:
dgridDlg = displayDialogs.SampleDataDisplayDialog(self, fcData.data[0:10,:],
fcData.labels, 'Edit Channel Labels',
False, False)
if (dgridDlg.ShowModal() == wx.ID_OK):
# reassign FacsData instance labels
for fcd in DataStore.getData().values():
labels = [item[1] for item in sorted(dgridDlg.ColumnLabels.iteritems(), key=itemgetter(0))]
fcd.labels = labels
# update channel selection cbxs
self.updateAxesList(labels, self.facsPlotPanel.SelectedAxes)
# refresh plot window
self.facsPlotPanel.draw()
dgridDlg.Destroy()
else:
wx.MessageBox("There are no data currently loaded.", "Error", wx.OK | wx.ICON_ERROR)
def OnOpen(self, event):
"""
Opens a FACS data file, parses it, and updates the FacsPlotPanel instance.
"""
# retrieve the I/O methods for inputting files
inputMethods = [m[2]() for m in io.AvailableMethods().values()]
formats = '|'.join([m.FileType for m in inputMethods if io.FILE_INPUT in m.register()])
allLabels = []
allColArr = []
allDims = []
fColsMoved = False
numLoaded = 0
# keep track of the common number of dimensions for datasets
numDims = DataStore.getCurrentDataSet()
if numDims is not None:
numDims = len(numDims.labels)
dlg = wx.FileDialog(self, "Choose a file", self.dirname, "", formats,
wx.FD_OPEN|wx.FD_MULTIPLE|wx.FD_CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
#TODO: move to data.io module?
# process each file selected
for n, path in enumerate(dlg.Paths):
self.statusbar.SetStatusText('loading: ' + path, 0)
try:
(labels, data, annotations) = io.loadDataFile(path, window=self)
except TypeError:
# if there was an error loading the file,
# loadDataFile should return None, so skip this file
continue
# make sure the new file matches dimensions of loaded files
if numDims is None:
numDims = len(labels)
elif len(labels) != numDims:
wx.MessageBox("Error loading file: %s\n\nThe number of channels does not match those in currently loaded datasets. \n\nThis file will not be loaded." % dlg.Filenames[n],
"File Error", wx.OK | wx.ICON_ERROR)
continue
# Give the user a brief preview of the data (10 rows) and allow
# column rearrangement and renaming
if (not allLabels):
dgridDlg = displayDialogs.SampleDataDisplayDialog(self, data[0:10,:], labels)
if (dgridDlg.ShowModal() == wx.ID_OK):
ca = dgridDlg.ColumnArrangement
lbls = dgridDlg.ColumnLabels
# Reassign the column labels
labels = [lbls[i] for i in ca]
if dgridDlg.ApplyToAll:
allLabels = list(labels)
allColArr = list(ca)
# Rearrange the data columns
if (dgridDlg.ColumnsMoved):
fColsMoved = True
data = dh.reorderColumns(data, ca)
else:
dgridDlg.Destroy()
continue
dgridDlg.Destroy()
else:
labels = list(allLabels)
if fColsMoved:
data = dh.reorderColumns(data, allColArr)
# update the DataStore
DataStore.add(FacsData(dlg.Filenames[n], labels, data, annotations=annotations))
numLoaded += 1
if n == 0:
self.updateAxesList(labels)
if (not allDims):
# Allow the user to choose columns for use in analysis
dimDlg = displayDialogs.DimensionExclusionDialog(self, labels)
dimDlg.Size=(dimDlg.Size[0]*.75, dimDlg.Size[1]*.8)
if (dimDlg.ShowModal() == wx.ID_OK):
DataStore.getCurrentDataSet().selDims = dimDlg.SelectedDimensions
if (dimDlg.ApplyToAll):
allDims = list(dimDlg.SelectedDimensions)
dimDlg.Destroy()
else:
DataStore.getCurrentDataSet().selDims = list(allDims)
# update the panel
self.facsPlotPanel.updateAxes([0,1])
if (len(self.facsPlotPanel.subplots) == 0 or len(dlg.Paths) > 1):
self.facsPlotPanel.addSubplot(DataStore.getCurrentIndex())
# Create an n/2 x 2 grid for the n selected data files
if (numLoaded > 1):
self.facsPlotPanel.updateSubplotGrid(int(math.ceil(numLoaded/2.0)), 2)
self.statusbar.SetStatusText('All data files loaded.')
if FigureStore.isEmpty():
fig = Figure('Default', self.facsPlotPanel.subplots, 1,
self.facsPlotPanel.Grid,
self.facsPlotPanel.SelectedAxes)
FigureStore.add(fig)
self.treeCtrlPanel.updateTree()
dlg.Destroy()
