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()
def main():
from data.io import loadDataFile
f = loadDataFile('/data/537-Filter-Spin_MMC-Top.fcs')
data = f[1]
kinit(data, 200)
def main():
from data.io import loadDataFile
f = loadDataFile('/data/537-Filter-Spin_MMC-Top.fcs')
data = f[1]
c = bakker_kMeans(data, numClusters=3)
print c
