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 __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 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 buildDataTree(self, parent, dataDict, visited):
for dIndex, fData in dataDict.iteritems():
# add tree node for the FACS data set
if fData.ID in visited:
return
child = self.tree.AppendItem(parent, fData.displayname)
if (DataStore.getCurrentIndex() == dIndex):
self.tree.SetItemBold(child, True)
self.tree.SetPyData(child, (DATA_SET_ITEM, dIndex))
self.tree.SetItemImage(child, self.fldridx, wx.TreeItemIcon_Normal)
self.tree.SetItemImage(child, self.fldropenidx, wx.TreeItemIcon_Expanded)
# add nodes for all the clusterings of the current data set
for cIndex in fData.clustering:
clust = self.tree.AppendItem(child,
cluster.methods.getStringRepr(fData.methodIDs[cIndex]) +
" " + str(cIndex+1))
if ((fData.selectedClustering == cIndex) and (fData.ID == DataStore.getCurrentIndex())):
self.tree.SetItemBold(clust, True)
toolTip = clusteringInfo(fData, cIndex)
self.tree.SetPyData(clust, (DATA_SET_ITEM, dIndex, cIndex, toolTip)) #(data index, cluster index, tooltip)
self.tree.SetItemImage(clust, self.fldridx, wx.TreeItemIcon_Normal)
self.tree.SetItemImage(clust, self.fldropenidx, wx.TreeItemIcon_Expanded)
# set clustering options
for line in toolTip.split('\n'):
if (line != ''):
info = self.tree.AppendItem(clust, line)
self.tree.SetPyData(info, None)
if (fData.infoExpanded[cIndex]):
self.tree.Expand(clust)
# recursive call to build the tree for any children
visited.append(fData.ID)
self.buildDataTree(child, dict([(i,DataStore.getData()[i]) for i in fData.children]), visited)
if (fData.nodeExpanded and self.tree.GetChildrenCount(child) > 0):
self.tree.Expand(child)
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 saveState(dir, filename):
"""
Save a representation of the system state: All the loaded data sets,
their clusterings, any transformations or analyses (future),
and all plots.
The state is saved in JSON format based on a dict of the following form:
data: list of IDs
binfile: the filename of the binary file used to store all the actual data
data-dID: dict of settings belonging to a FacsData instance
clust-dID-cID: a dict of attributes belonging to a clustering
figures: list of figureID strings
fig-ID: A dict for each figure keyed on the ID. The subplot attribute here
is replaced with a list of fig-ID-p-ID strings for locating subplot dicts
fig-ID-p-ID: A dict for each subplot in each figure keyed on fig ID and plot ID.
current-data: data ID
current-figure: figure ID
"""
store = shelve.open(os.path.join(dir, filename))
#store = dbopen(os.path.join(dir, filename), 'c', format='csv')
# The actual numeric data will be stored in a separate binary file using
# the numpy savez() method allowing for efficient storage/retrieval of data
binfile = '%s.npz' % filename
bindata = {}
store['data'] = DataStore.getData().keys()
store['binfile'] = binfile
for dID in DataStore.getData():
fdata = DataStore.get(dID)
dStr = 'data-%i' % dID
dfname = fdata.filename if (fdata.filename is not '') else binfile
bindata[dStr] = fdata.data
store[dStr] = {'filename': dfname,
'displayname': fdata.displayname,
'labels': fdata.labels,
'annotations': fdata.annotations,
'analysis': fdata.analysis,
'ID': fdata.ID,
'parent': fdata.parent,
'children': fdata.children,
'selDims': fdata.selDims,
'clustering': fdata.clustering.keys(),
'nodeExpanded': fdata.nodeExpanded,
'selectedClustering': fdata.selectedClustering}
# clusterings
for cID in fdata.clustering:
cStr = 'clust-%i-%i' % (dID, cID)
csett = {'method': fdata.methodIDs[cID],
'opts': fdata.clusteringOpts[cID],
'clusteringSelDims': fdata.clusteringSelDims[cID],
'infoExpanded': fdata.infoExpanded[cID]}
store[cStr] = csett
bindata[cStr] = fdata.clustering[cID]
# figures
sfigs = []
for figID in FigureStore.getFigures():
fig = FigureStore.get(figID)
fStr = 'fig-%i' % figID
d = dict(fig.__dict__)
splots = packSubplots(store, figID, fig.subplots)
d['subplots'] = splots
store[fStr] = d
sfigs.append(fStr)
store['figures'] = list(sfigs)
# other
store['current-data'] = DataStore.getCurrentIndex()
store['current-figure'] = FigureStore.getSelectedIndex()
# write out settings data
store.close()
# write out numeric data to binary file
np.savez(os.path.join(dir, binfile), **bindata)
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()
