def OnAddFigure(self, event):
if len(DataStore.getData()) == 0:
return
nameDlg = displayDialogs.EditNameDialog(self, '')
if (nameDlg.ShowModal() == wx.ID_OK):
newFig = Figure(nameDlg.Text, [dv.Subplot()], 1, (1,1), (0,1))
currFig = FigureStore.getSelectedFigure()
FigureStore.add(newFig)
dv.switchFigures(self.facsPlotPanel, currFig, newFig)
self.facsPlotPanel.subplots = []
self.addSubplot()
self.treeCtrlPanel.updateTree()
nameDlg.Destroy()
def loadState(dir, filename):
"""
Restore the system state as stored to disk.
@type dir: string
@param path: The directory under which the the saved system state is stored
@type filename: str
@param filename: The name of the saved project file (.find)
@rtype: tuple
@return: A list of subplot settings (dicts) retrieved from the file,
The index of the currently selected subplot,
The currently selected axes,
The number of rows and columns in the figure (grid size)
"""
store = shelve.open(os.path.join(dir, filename))
#store = dbopen(os.path.join(dir, filename))
datakeys = store['data']
try:
bindata = np.load(os.path.join(dir,store['binfile']))
except IOError:
bindata = None
except BadZipfile:
wx.MessageBox('The file \'%s\' may have become corrupted. Project loading has been cancelled' % store['binfile'],
'Data Loading Error',
wx.OK|wx.ICON_ERROR)
raise ProjectLoadingError('BadZipfile: %s' % os.path.join(dir,store['binfile']))
# Parse data sets
for dID in datakeys:
dStr = 'data-%s' % dID
dsett = store[dStr]
ann = dsett['annotations'] if 'annotations' in dsett else {}
ana = dsett['analysis'] if 'analysis' in dsett else {}
fdata = FacsData(dsett['filename'], dsett['labels'], bindata[dStr],
annotations=ann, analysis=ana,
parent=dsett['parent'])
fdata.displayname = dsett['displayname']
fdata.ID = dsett['ID']
fdata.children = dsett['children']
fdata.selDims = dsett['selDims']
fdata.nodeExpanded = dsett['nodeExpanded']
# Parse clusterings
for cID in dsett['clustering']:
cStr = 'clust-%i-%i' % (dID, cID)
csett = store[cStr]
clusterIDs = bindata[cStr]
fdata.addClustering(csett['method'], clusterIDs, csett['opts'], cID)
fdata.clusteringSelDims[cID] = csett['clusteringSelDims']
fdata.infoExpanded[cID] = csett['infoExpanded']
DataStore.add(fdata)
DataStore.selectDataSet(store['current-data'])
# Figures
if 'figures' in store:
for fStr in store['figures']:
fDict = store[fStr]
splots = []
for pStr in fDict['subplots']:
splots.append(store[pStr])
fDict['subplots'] = splots
f = Figure()
f.load(fDict)
FigureStore.add(f)
# handle older save files w/o Figure support
else:
# load the saved subplots into a new 'Default' Figure
plots = []
for pStr in store['plots']:
plots.append(store[pStr])
defFig = Figure('Default', plots, store['current-subplot'], store['grid'], store['selected-axes'])
FigureStore.add(defFig)
if 'current-figure' in store:
FigureStore.setSelectedFigure(store['current-figure'])
else:
FigureStore.setSelectedFigure(0)
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()
