def deleteSelection(self):
"""
Delete the data object referenced by the current tree selection.
"""
item = self.getSanitizedItemSelectionData()
if item is None:
return
if item[0] is DATA_SET_ITEM:
ids = (item[1], None) if len(item) < 3 else (item[1], item[2])
self.Parent.TopLevelParent.facsPlotPanel.deleteAssociatedSubplots(ids)
self.applyToSelection(DataStore.remove, FacsData.removeClustering)
# if all data deleted, clear axes selectors
if len(DataStore.getData()) == 0:
self.Parent.TopLevelParent.updateAxesList([])
if item[0] is FIGURE_SET_ITEM:
id = item[1]
#TODO: figure out if this is a good shortcut for clearing the figure of subplots
if id == FigureStore.getSelectedIndex():
wx.MessageBox('The currently selected Figure cannot be deleted.', 'Invalid Action', wx.OK | wx.ICON_WARNING)
else:
FigureStore.remove(id)
self.updateTree()
def updateTree(self):
"""
Rebuilds the tree from the current state of the DataStore.
"""
self.tree.DeleteAllItems()
self.root = self.tree.AddRoot("Project")
self.tree.SetPyData(self.root, None)
self.tree.SetItemImage(self.root, self.fldridx, wx.TreeItemIcon_Normal)
self.tree.SetItemImage(self.root, self.fldropenidx, wx.TreeItemIcon_Expanded)
dataTree = self.tree.AppendItem(self.root, "Data Sets")
self.tree.SetPyData(dataTree, DATA_SET_ITEM)
self.tree.SetItemImage(dataTree, self.fldridx, wx.TreeItemIcon_Normal)
self.tree.SetItemImage(dataTree, self.fldropenidx, wx.TreeItemIcon_Expanded)
figsTree = self.tree.AppendItem(self.root, "Figure Sets")
self.tree.SetPyData(figsTree, FIGURE_SET_ITEM)
self.tree.SetItemImage(figsTree, self.fldridx, wx.TreeItemIcon_Normal)
self.tree.SetItemImage(figsTree, self.fldropenidx, wx.TreeItemIcon_Expanded)
# create tree
self.buildDataTree(dataTree, DataStore.getData(), [])
self.buildFigureTree(figsTree, FigureStore.getFigures())
self.tree.Expand(self.root)
if self.dataTreeExpanded:
self.tree.Expand(dataTree)
if self.figureTreeExpanded:
self.tree.Expand(figsTree)
def buildFigureTree(self, root, figures):
for id, fig in figures.iteritems():
child = self.tree.AppendItem(root, fig.name)
if (FigureStore.getSelectedIndex() == id):
self.tree.SetItemBold(child, True)
self.tree.SetPyData(child, (FIGURE_SET_ITEM, id))
self.tree.SetItemImage(child, self.figureicn, wx.TreeItemIcon_Normal)
def renameItem(self):
"""
Give a new display name to the currently selected data item
"""
item = self.getSanitizedItemSelectionData()
if item is None:
return
if (item[0] is DATA_SET_ITEM):
data = DataStore.get(item[1])
dlg = EditNameDialog(self.Parent, data.displayname)
if dlg.ShowModal() == wx.ID_OK:
data.displayname = dlg.Text
dlg.Destroy()
if (item[0] is FIGURE_SET_ITEM):
figure = FigureStore.get(item[1])
dlg = EditNameDialog(self.Parent, figure.name)
if dlg.ShowModal() == wx.ID_OK:
figure.name = dlg.Text
dlg.Destroy()
item = self.tree.GetSelection()
item.SetText(dlg.Text)
self.tree.RefreshSelected()
item.SetHilight(False)
item.SetHilight(True)
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 selectItemTreeSelection(self, rightClick=False):
"""
Using the selected tree item, set the corresponding object
in the data store as the current selection.
"""
item = self.getSanitizedItemSelectionData()
if item is not None:
if item[0] is DATA_SET_ITEM:
self.applyToSelection(DataStore.selectDataSet, FacsData.selectClustering)
if item[0] is FIGURE_SET_ITEM and not rightClick:
if item[1] != FigureStore.getSelectedIndex():
currFig = FigureStore.getSelectedFigure()
newFig = FigureStore.get(item[1])
switchFigures(self.Parent.TopLevelParent.facsPlotPanel, currFig, newFig, True)
self.Parent.TopLevelParent.selectAxes(newFig.axes)
FigureStore.setSelectedFigure(item[1])
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 OnSaveState(self, event):
from data.io import saveState
dlg = wx.FileDialog(self, "Save project to file", "", "", "*.find", wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK and dlg.Filename:
if not '.find' in dlg.Filename:
dlg.Filename = dlg.Filename + '.find'
dlg.Path = dlg.Path + '.find'
dv.saveToFigure(self.facsPlotPanel, FigureStore.getSelectedFigure())
saveState(dlg.Directory, dlg.Filename)
self.statusbar.SetStatusText("Project saved to %s" % dlg.Path, 0)
dlg.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 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()
