def __init__(self, host):
AnalysisModule.__init__(self, host)
if self.dataModel is None:
raise Exception("Photostim analysis module requires a data model, but none is loaded yet.")
self.dbIdentity = "Photostim" ## how we identify to the database; this determines which tables we own
self.selectedSpot = None
## setup analysis flowchart
modPath = os.path.abspath(os.path.split(__file__)[0])
flowchartDir = os.path.join(modPath, "analysis_fc")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput('events')
self.flowchart.addInput('regions')
self.flowchart.addInput('fileHandle')
self.flowchart.addOutput('dataOut')
self.analysisCtrl = self.flowchart.widget()
## color mapper
self.mapper = ColorMapper.ColorMapper(filePath=os.path.join(modPath, "colormaps"))
self.mapCtrl = QtGui.QWidget()
self.mapLayout = QtGui.QVBoxLayout()
self.mapCtrl.setLayout(self.mapLayout)
self.mapLayout.splitter = QtGui.QSplitter()
self.mapLayout.splitter.setOrientation(QtCore.Qt.Vertical)
self.mapLayout.splitter.setContentsMargins(0,0,0,0)
self.mapLayout.addWidget(self.mapLayout.splitter)
self.mapLayout.splitter.addWidget(self.analysisCtrl)
#self.mapLayout.splitter.addWidget(QtGui.QSplitter())
self.mapLayout.splitter.addWidget(self.mapper)
#self.mapLayout.splitter.addWidget(self.recolorBtn)
self.recolorLayout = QtGui.QHBoxLayout()
self.recolorWidget = QtGui.QWidget()
self.mapLayout.splitter.addWidget(self.recolorWidget)
self.recolorWidget.setLayout(self.recolorLayout)
self.recolorBtn = QtGui.QPushButton('Recolor')
self.recolorLayout.addWidget(self.recolorBtn)
self.recolorParallelCheck = QtGui.QCheckBox('Parallel')
self.recolorParallelCheck.setChecked(True)
self.recolorLayout.addWidget(self.recolorParallelCheck)
## scatter plot
self.scatterPlot = ScatterPlotter()
self.scatterPlot.sigClicked.connect(self.scatterPlotClicked)
## setup map DB ctrl
self.dbCtrl = DBCtrl(self, self.dbIdentity)
## storage for map data
#self.scanItems = {}
self.scans = []
#self.seriesScans = {}
self.maps = []
## create event detector
fcDir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), "detector_fc")
self.detector = EventDetector.EventDetector(host, flowchartDir=fcDir, dbIdentity=self.dbIdentity+'.events')
## override some of its elements
self.detector.setElement('File Loader', self)
self.detector.setElement('Database', self.dbCtrl)
## Create element list, importing some gui elements from event detector
elems = self.detector.listElements()
self._elements_ = OrderedDict([
('Database', {'type': 'ctrl', 'object': self.dbCtrl, 'size': (300, 600)}),
('Scatter Plot', {'type': 'ctrl', 'object': self.scatterPlot, 'pos': ('right',), 'size': (700,400)}),
('Canvas', {'type': 'canvas', 'pos': ('above', 'Scatter Plot'), 'size': (700,400), 'allowTransforms': False, 'hideCtrl': True, 'args': {'name': 'Photostim'}}),
#('Maps', {'type': 'ctrl', 'pos': ('bottom', 'Database'), 'size': (200,200), 'object': self.mapDBCtrl}),
('Map Opts', {'type': 'ctrl', 'object': self.mapCtrl, 'pos': ('above', 'Database'), 'size': (300,600)}),
('Detection Opts', elems['Detection Opts'].setParams(pos=('above', 'Map Opts'), size= (300,600))),
('File Loader', {'type': 'fileInput', 'size': (300, 300), 'pos': ('above', 'Detection Opts'), 'host': self, 'showFileTree': False}),
('Data Plot', elems['Data Plot'].setParams(pos=('bottom', 'Canvas'), size=(700,200))),
('Filter Plot', elems['Filter Plot'].setParams(pos=('bottom', 'Data Plot'), size=(700,200))),
('Event Table', elems['Output Table'].setParams(pos=('below', 'Filter Plot'), size=(700,200))),
('Stats', {'type': 'dataTree', 'size': (700,200), 'pos': ('below', 'Event Table')}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
self.detector.flowchart.sigOutputChanged.connect(self.detectorOutputChanged)
self.flowchart.sigOutputChanged.connect(self.analyzerOutputChanged)
self.detector.flowchart.sigStateChanged.connect(self.detectorStateChanged)
self.flowchart.sigStateChanged.connect(self.analyzerStateChanged)
self.recolorBtn.clicked.connect(self.recolor)
def __init__(self, host):
AnalysisModule.__init__(self, host)
if self.dataModel is None:
raise Exception(
"Photostim analysis module requires a data model, but none is loaded yet."
)
self.dbIdentity = "Photostim" ## how we identify to the database; this determines which tables we own
self.selectedSpot = None
## setup analysis flowchart
modPath = os.path.abspath(os.path.split(__file__)[0])
flowchartDir = os.path.join(modPath, "analysis_fc")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput('events')
self.flowchart.addInput('regions')
self.flowchart.addInput('fileHandle')
self.flowchart.addOutput('dataOut')
self.analysisCtrl = self.flowchart.widget()
## color mapper
self.mapper = ColorMapper.ColorMapper(
filePath=os.path.join(modPath, "colormaps"))
self.mapCtrl = QtGui.QWidget()
self.mapLayout = QtGui.QVBoxLayout()
self.mapCtrl.setLayout(self.mapLayout)
self.mapLayout.splitter = QtGui.QSplitter()
self.mapLayout.splitter.setOrientation(QtCore.Qt.Vertical)
self.mapLayout.splitter.setContentsMargins(0, 0, 0, 0)
self.mapLayout.addWidget(self.mapLayout.splitter)
self.mapLayout.splitter.addWidget(self.analysisCtrl)
#self.mapLayout.splitter.addWidget(QtGui.QSplitter())
self.mapLayout.splitter.addWidget(self.mapper)
#self.mapLayout.splitter.addWidget(self.recolorBtn)
self.recolorLayout = QtGui.QHBoxLayout()
self.recolorWidget = QtGui.QWidget()
self.mapLayout.splitter.addWidget(self.recolorWidget)
self.recolorWidget.setLayout(self.recolorLayout)
self.recolorBtn = QtGui.QPushButton('Recolor')
self.recolorLayout.addWidget(self.recolorBtn)
self.recolorParallelCheck = QtGui.QCheckBox('Parallel')
self.recolorParallelCheck.setChecked(True)
self.recolorLayout.addWidget(self.recolorParallelCheck)
## scatter plot
self.scatterPlot = ScatterPlotter()
self.scatterPlot.sigClicked.connect(self.scatterPlotClicked)
## setup map DB ctrl
self.dbCtrl = DBCtrl(self, self.dbIdentity)
## storage for map data
#self.scanItems = {}
self.scans = []
#self.seriesScans = {}
self.maps = []
## create event detector
fcDir = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"detector_fc")
self.detector = EventDetector.EventDetector(
host, flowchartDir=fcDir, dbIdentity=self.dbIdentity + '.events')
## override some of its elements
self.detector.setElement('File Loader', self)
self.detector.setElement('Database', self.dbCtrl)
## Create element list, importing some gui elements from event detector
elems = self.detector.listElements()
self._elements_ = OrderedDict([
('Database', {
'type': 'ctrl',
'object': self.dbCtrl,
'size': (300, 600)
}),
('Scatter Plot', {
'type': 'ctrl',
'object': self.scatterPlot,
'pos': ('right', ),
'size': (700, 400)
}),
('Canvas', {
'type': 'canvas',
'pos': ('above', 'Scatter Plot'),
'size': (700, 400),
'allowTransforms': False,
'hideCtrl': True,
'args': {
'name': 'Photostim'
}
}),
#('Maps', {'type': 'ctrl', 'pos': ('bottom', 'Database'), 'size': (200,200), 'object': self.mapDBCtrl}),
('Map Opts', {
'type': 'ctrl',
'object': self.mapCtrl,
'pos': ('above', 'Database'),
'size': (300, 600)
}),
('Detection Opts',
elems['Detection Opts'].setParams(pos=('above', 'Map Opts'),
size=(300, 600))),
('File Loader', {
'type': 'fileInput',
'size': (300, 300),
'pos': ('above', 'Detection Opts'),
'host': self,
'showFileTree': False
}),
('Data Plot', elems['Data Plot'].setParams(pos=('bottom',
'Canvas'),
size=(700, 200))),
('Filter Plot', elems['Filter Plot'].setParams(pos=('bottom',
'Data Plot'),
size=(700, 200))),
('Event Table',
elems['Output Table'].setParams(pos=('below', 'Filter Plot'),
size=(700, 200))),
('Stats', {
'type': 'dataTree',
'size': (700, 200),
'pos': ('below', 'Event Table')
}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
self.detector.flowchart.sigOutputChanged.connect(
self.detectorOutputChanged)
self.flowchart.sigOutputChanged.connect(self.analyzerOutputChanged)
self.detector.flowchart.sigStateChanged.connect(
self.detectorStateChanged)
self.flowchart.sigStateChanged.connect(self.analyzerStateChanged)
self.recolorBtn.clicked.connect(self.recolor)
class Photostim(AnalysisModule):
"""
This module analyzes raw data from photostimulation scanning protocols to produce colored maps of features detected in the data. This analysis consists of multiple components:
1) Data is (optionally) processed through an event detector to determine the time, amplitude, and other characteristics of the recroded events. The exact analysis in this stage is fully customizable by a flowchart. Results of this analysis are stored to a DB table (named 'photostim_events' by default) for use in further analysis.
2) Each photostimulation is analyzed to determine the strength of evoked events, probability of presynaptic connection, probability of direct stimulation, etc. The exact analysis in this stage is fully customizable by a flowchart and results are stored to a DB table (named 'photostim_sites' by default) for use in further analysis.
3) Multiple scans may (optionally) be combined to produce a single map with repeated measures and/or extended area.
4) The values generated in steps 2 and 3 are mapped to colors which are displayed in a canvas.
"""
def __init__(self, host):
AnalysisModule.__init__(self, host)
if self.dataModel is None:
raise Exception("Photostim analysis module requires a data model, but none is loaded yet.")
self.dbIdentity = "Photostim" ## how we identify to the database; this determines which tables we own
self.selectedSpot = None
## setup analysis flowchart
modPath = os.path.abspath(os.path.split(__file__)[0])
flowchartDir = os.path.join(modPath, "analysis_fc")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput('events')
self.flowchart.addInput('regions')
self.flowchart.addInput('fileHandle')
self.flowchart.addOutput('dataOut')
self.analysisCtrl = self.flowchart.widget()
## color mapper
self.mapper = ColorMapper.ColorMapper(filePath=os.path.join(modPath, "colormaps"))
self.mapCtrl = QtGui.QWidget()
self.mapLayout = QtGui.QVBoxLayout()
self.mapCtrl.setLayout(self.mapLayout)
self.mapLayout.splitter = QtGui.QSplitter()
self.mapLayout.splitter.setOrientation(QtCore.Qt.Vertical)
self.mapLayout.splitter.setContentsMargins(0,0,0,0)
self.mapLayout.addWidget(self.mapLayout.splitter)
self.mapLayout.splitter.addWidget(self.analysisCtrl)
#self.mapLayout.splitter.addWidget(QtGui.QSplitter())
self.mapLayout.splitter.addWidget(self.mapper)
#self.mapLayout.splitter.addWidget(self.recolorBtn)
self.recolorLayout = QtGui.QHBoxLayout()
self.recolorWidget = QtGui.QWidget()
self.mapLayout.splitter.addWidget(self.recolorWidget)
self.recolorWidget.setLayout(self.recolorLayout)
self.recolorBtn = QtGui.QPushButton('Recolor')
self.recolorLayout.addWidget(self.recolorBtn)
self.recolorParallelCheck = QtGui.QCheckBox('Parallel')
self.recolorParallelCheck.setChecked(True)
self.recolorLayout.addWidget(self.recolorParallelCheck)
## scatter plot
self.scatterPlot = ScatterPlotter()
self.scatterPlot.sigClicked.connect(self.scatterPlotClicked)
## setup map DB ctrl
self.dbCtrl = DBCtrl(self, self.dbIdentity)
## storage for map data
#self.scanItems = {}
self.scans = []
#self.seriesScans = {}
self.maps = []
## create event detector
fcDir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), "detector_fc")
self.detector = EventDetector.EventDetector(host, flowchartDir=fcDir, dbIdentity=self.dbIdentity+'.events')
## override some of its elements
self.detector.setElement('File Loader', self)
self.detector.setElement('Database', self.dbCtrl)
## Create element list, importing some gui elements from event detector
elems = self.detector.listElements()
self._elements_ = OrderedDict([
('Database', {'type': 'ctrl', 'object': self.dbCtrl, 'size': (300, 600)}),
('Scatter Plot', {'type': 'ctrl', 'object': self.scatterPlot, 'pos': ('right',), 'size': (700,400)}),
('Canvas', {'type': 'canvas', 'pos': ('above', 'Scatter Plot'), 'size': (700,400), 'allowTransforms': False, 'hideCtrl': True, 'args': {'name': 'Photostim'}}),
#('Maps', {'type': 'ctrl', 'pos': ('bottom', 'Database'), 'size': (200,200), 'object': self.mapDBCtrl}),
('Map Opts', {'type': 'ctrl', 'object': self.mapCtrl, 'pos': ('above', 'Database'), 'size': (300,600)}),
('Detection Opts', elems['Detection Opts'].setParams(pos=('above', 'Map Opts'), size= (300,600))),
('File Loader', {'type': 'fileInput', 'size': (300, 300), 'pos': ('above', 'Detection Opts'), 'host': self, 'showFileTree': False}),
('Data Plot', elems['Data Plot'].setParams(pos=('bottom', 'Canvas'), size=(700,200))),
('Filter Plot', elems['Filter Plot'].setParams(pos=('bottom', 'Data Plot'), size=(700,200))),
('Event Table', elems['Output Table'].setParams(pos=('below', 'Filter Plot'), size=(700,200))),
('Stats', {'type': 'dataTree', 'size': (700,200), 'pos': ('below', 'Event Table')}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
self.detector.flowchart.sigOutputChanged.connect(self.detectorOutputChanged)
self.flowchart.sigOutputChanged.connect(self.analyzerOutputChanged)
self.detector.flowchart.sigStateChanged.connect(self.detectorStateChanged)
self.flowchart.sigStateChanged.connect(self.analyzerStateChanged)
self.recolorBtn.clicked.connect(self.recolor)
def quit(self):
self.scans = []
self.maps = []
return AnalysisModule.quit(self)
def elementChanged(self, element, old, new):
name = element.name()
## connect plots to flowchart, link X axes
if name == 'File Loader':
new.sigBaseChanged.connect(self.baseDirChanged)
new.ui.dirTree.sigSelectionChanged.connect(self.fileSelected)
self.baseDirChanged(new.baseDir())
def fileSelected(self):
fhl = self.getElement('File Loader').ui.dirTree.selectedFiles()
if len(fhl) == 0:
return
fh = fhl[0]
if fh is not None and fh.isDir():
print Scan.describe(self.dataModel, fh)
def baseDirChanged(self, dh):
if dh is None:
return ## should clear out map list here?
if 'dirType' not in dh.info():
return
typ = dh.info()['dirType']
if typ == 'Slice':
cells = [dh[d] for d in dh.subDirs() if dh[d].info().get('dirType',None) == 'Cell']
elif typ == 'Cell':
cells = [dh]
else:
return
#print "cells:", cells
self.dbCtrl.listMaps(cells)
def loadFileRequested(self, fhList):
canvas = self.getElement('Canvas')
model = self.dataModel
with pg.ProgressDialog("Loading data..", 0, len(fhList)) as dlg:
for fh in fhList:
try:
## TODO: use more clever detection of Scan data here.
if fh.isFile() or model.dirType(fh) == 'Cell':
canvas.addFile(fh)
else:
self.loadScan(fh)
return True
except:
debug.printExc("Error loading file %s" % fh.name())
return False
dlg += 1
if dlg.wasCancelled():
return
def loadScan(self, fh):
ret = []
## first see if we've already loaded this file
for scan in self.scans:
if scan.source() is fh:
ret.append(scan) ## if so, return all scans sourced by this file
if len(ret) > 0:
return ret
## Load the file, possibly generating multiple scans.
canvas = self.getElement('Canvas')
ret = []
scans = loadScanSequence(fh, self)
if len(scans) > 1:
parent = canvas.addGroup(fh.shortName())
else:
parent = None
print parent
for scan in scans:
canvasItem = scan.canvasItem()
if parent is not None:
canvasItem.setParentItem(parent)
canvas.addItem(canvasItem)
canvasItem.graphicsItem().sigClicked.connect(self.scanPointClicked)
self.scans.append(scan)
ret.append(scan)
self.dbCtrl.scanLoaded(scan)
self.scatterPlot.addScan(scan)
#canvasItems = canvas.addFile(fh, separateParams=True) ## returns list when fh is a scan
#for citem in canvasItems:
#scan = Scan(self, fh, citem, name=citem.opts['name'])
#self.scans.append(scan)
#citem.item.sigPointClicked.connect(self.scanPointClicked)
#self.dbCtrl.scanLoaded(scan)
#ret.append(scan)
#self.scatterPlot.addScan(scan)
return ret
def registerMap(self, map):
#if map in self.maps:
#return
canvas = self.getElement('Canvas')
map.canvasItem = canvas.addGraphicsItem(map.sPlotItem, name=map.name())
self.maps.append(map)
map.sPlotItem.sigClicked.connect(self.mapPointClicked)
def unregisterMap(self, map):
if hasattr(map, 'canvasItem'):
canvas = self.getElement('Canvas')
canvas.removeItem(map.canvasItem)
if map in self.maps:
self.maps.remove(map)
try:
map.sPlotItem.sigClicked.disconnect(self.mapPointClicked)
except TypeError:
pass
def scanPointClicked(self, plotItem, points):
try:
point = points[0]
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.WaitCursor))
#print "clicked:", point.data()
plot = self.getElement("Data Plot")
plot.clear()
self.selectedSpot = point
self.selectedScan = plotItem.scan
fh = self.dataModel.getClampFile(point.data())
self.detector.loadFileRequested(fh)
#self.dbCtrl.scanSpotClicked(fh)
finally:
QtGui.QApplication.restoreOverrideCursor()
def mapPointClicked(self, scan, points):
data = []
for p in points:
for source in p.data()['sites']:
data.append([source[0], self.dataModel.getClampFile(source[1])])
#data.extend(p.data)
self.redisplayData(data)
##self.dbCtrl.mapSpotClicked(point.data) ## Did this method exist at some point?
def scatterPlotClicked(self, plot, points):
#scan, fh, time = point.data
self.redisplayData([p.data() for p in points])
#self.scatterLine =
def redisplayData(self, points): ## data must be [(scan, fh, <event time>), ...]
#raise Exception('blah')
#print points
try:
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.WaitCursor))
plot = self.getElement("Data Plot")
plot.clear()
eTable = self.getElement("Event Table")
sTable = self.getElement("Stats")
#num = len(point.data)
num = len(points)
statList = []
evList = []
for i in range(num):
color = pg.intColor(i, num)
#scan, fh = point.data[i]
try:
scan, fh = points[i][:2]
except:
print points[i]
raise
if len(points[i]) == 3:
evTime = points[i][2]
else:
evTime = None
scan.displayData(fh, plot, color, evTime)
## show stats
stats = scan.getStats(fh.parent())
statList.append(stats)
events = scan.getEvents(fh)['events']
if len(events) > 0:
evList.append(events)
sTable.setData(statList)
if len(evList) > 0:
try:
eTable.setData(np.concatenate(evList))
except:
for i in range(1,len(evList)):
if len(evList[i].dtype) != len(evList[i-1].dtype):
print "Cannot concatenate; event lists have different dtypes:"
print evList[i].dtype
print evList[i-1].dtype
else:
for j in range(len(evList[i].dtype)):
if evList[i-1].dtype[j] != evList[i].dtype[j]:
for l in evList:
print l
print "Warning: can not concatenate--field '%s' has inconsistent types %s, %s (data printed above)" % (evList[i].dtype.names[j], str(evList[i-1].dtype[j]), str(evList[i].dtype[j]))
raise
finally:
QtGui.QApplication.restoreOverrideCursor()
def detectorStateChanged(self):
#print "STATE CHANGE"
#print "Detector state changed"
for scan in self.scans:
scan.invalidateEvents()
def detectorOutputChanged(self):
if self.selectedSpot==None:
return
output = self.detector.flowchart.output()
output['fileHandle']=self.selectedSpot.data()
self.flowchart.setInput(**output)
#errs = output['events']['fitFractionalError']
#if len(errs) > 0:
#print "Detector events error mean / median / max:", errs.mean(), np.median(errs), errs.max()
def analyzerStateChanged(self):
#print "Analyzer state changed."
for scan in self.scans:
scan.invalidateStats()
def analyzerOutputChanged(self):
table = self.getElement('Stats')
stats = self.processStats() ## gets current stats
table.setData(stats)
if stats is None:
return
self.mapper.setArgList(stats.keys())
#def getCurrentStats(self):
#stats = self.flowchart.output()['dataOut']
#spot = self.selectedSpot
#pos = spot.scenePos()
#stats['xPos'] = pos.x()
#stats['yPos'] = pos.y()
#return stats
def recolor(self):
## Select only visible scans and maps for recoloring
try:
allScans = [s for s in self.scans if s.isVisible()]
allScans.extend([s for s in self.maps if s.isVisible()])
for i in range(len(allScans)):
allScans[i].recolor(i, len(allScans), parallel=self.recolorParallelCheck.isChecked())
except pg.multiprocess.CanceledError:
pass
#for i in range(len(self.scans)):
#self.scans[i].recolor(i, len(self.scans))
#for i in range(len(self.maps)):
#self.maps[i].recolor(self, i, len(self.maps))
def getColor(self, stats, data=None):
## Note: the data argument is used elsewhere (MapAnalyzer)
#print "STATS:", stats
return self.mapper.getColor(stats)
def processEvents(self, fh):
print "Process Events:", fh
ret = self.detector.process(fh)
return ret
def processStats(self, data=None, spot=None):
## Process output of stats flowchart for a single spot, add spot position fields.
## data is the input to the stats flowchart
## if data is omitted, then the stats for the currently selected spot are returned
## (this is just the pre-existing output of the stats flowchart)
## spot is used to determine the x,y coords of the spot
if data is None:
stats = self.flowchart.output()['dataOut']
spot = self.selectedSpot
if spot is None:
return
dh = spot.data()
else:
if 'regions' not in data:
data['regions'] = self.detector.flowchart.output()['regions']
dh = spot.data()
data['fileHandle'] = dh
#if dh is None:
#data['fileHandle'] = self.selectedSpot.data
#else:
#data['fileHandle'] = fh
stats = self.flowchart.process(**data)['dataOut']
if stats is None:
raise Exception('No data returned from analysis (check flowchart for errors).')
try:
pos = spot.viewPos()
stats['xPos'] = pos.x()
stats['yPos'] = pos.y()
except:
# just try substituting with spot.pos:
p = spot.pos()
stats['xPos'] = p[0]
stats['yPos'] = p[1]
#d = spot.data.parent()
#size = d.info().get('Scanner', {}).get('spotSize', 100e-6)
#stats['spotSize'] = size
#print "Process Stats:", spot.data
#stats['SourceFile'] = self.dataModel.getClampFile(dh)
stats['ProtocolDir'] = dh ## stats should be stored with the protocol dir, not the clamp file.
stats['ProtocolSequenceDir'] = self.dataModel.getParent(dh, 'ProtocolSequence')
#parent = dh.parent()
#if self.dataModel.dirType(parent) != 'ProtocolSequence':
#parent = None
#stats['ProtocolSequenceDir'] = parent
return stats
def storeDBSpot(self):
"""Stores data for selected spot immediately, using current flowchart outputs"""
dbui = self.getElement('Database')
db = dbui.getDb()
## get events and stats for selected spot
spot = self.selectedSpot
if spot is None:
raise Exception("No spot selected")
#print "Store spot:", spot.data
#parentDir = spot.data
#p2 = parentDir.parent()
#if self.dataModel.dirType(p2) == 'ProtocolSequence':
#parentDir = p2
## ask eventdetector to store events for us.
#print parentDir
with db.transaction():
self.detector.storeToDB()
events = self.detector.output()
## store stats
stats = self.processStats(spot=spot) ## gets current stats if no processing is requested
self.storeStats(stats)
## update data in Map
self.selectedScan.updateSpot(spot.data(), events, stats)
def storeDBScan(self, scan, storeEvents=True):
"""Store all data for a scan, using cached values if possible"""
p = debug.Profiler("Photostim.storeDBScan", disabled=True)
if storeEvents:
self.clearDBScan(scan)
with pg.BusyCursor():
#dh = scan.source()
#print "Store scan:", scan.source().name()
events = []
stats = []
spots = scan.spots()
with pg.ProgressDialog("Preparing data for %s" % scan.name(), 0, len(spots)+1) as dlg:
## collect events and stats from all spots in the scan
for i in xrange(len(spots)):
s = spots[i]
fh = self.dataModel.getClampFile(s.data())
try:
ev = scan.getEvents(fh)['events']
events.append(ev)
except:
print fh, scan.getEvents(fh)
raise
st = scan.getStats(s.data())
stats.append(st)
dlg.setValue(i)
if dlg.wasCanceled():
raise HelpfulException("Scan store canceled by user.", msgType='status')
p.mark("Prepared data")
dbui = self.getElement('Database')
db = dbui.getDb()
with db.transaction():
## Store all events for this scan
if storeEvents:
events = [x for x in events if len(x) > 0]
if len(events) > 0:
ev = np.concatenate(events)
p.mark("concatenate events")
self.detector.storeToDB(ev)
p.mark("stored all events")
## Store spot data
self.storeStats(stats)
p.mark("stored all stats")
p.finish()
#print " scan %s is now locked" % scan.source().name()
#scan.lock() ## handled by Scan now
def rewriteSpotPositions(self, scan):
## for now, let's just rewrite everything.
#self.storeDBScan(scan)
## attempt to actually make this work
dbui = self.getElement('Database')
db = dbui.getDb()
identity = self.dbIdentity+'.sites'
table = dbui.getTableName(identity)
#dh = scan.source()
for spot in scan.spots():
protocolID = db('Select rowid from DirTable_Protocol where Dir="%s"'%(spot.data().name(relativeTo=db.baseDir())))
if len(protocolID) <1:
continue
protocolID = protocolID[0]['rowid']
pos = spot.viewPos()
db('UPDATE %s SET xPos=%f, yPos=%f WHERE ProtocolDir=%i' % (table, pos.x(), pos.y(), protocolID))
## Should look like this:
# pos = spot.viewPos()
# db.update(table, {'xPos': pos.x(), 'yPos': pos.y()}, where={'ProtocolDir': spot.data})
def clearDBScan(self, scan):
dbui = self.getElement('Database')
db = dbui.getDb()
#loader = self.getElement('File Loader')
#dh = loader.selectedFile()
#scan = self.scans[dh]
dh = scan.source()
#print "Clear scan", dh
#pRow = db.getDirRowID(dh)
colName = self.dataModel.dirType(dh)+'Dir'
identity = self.dbIdentity+'.sites'
table = dbui.getTableName(identity)
#db.delete(table, "SourceDir=%d" % pRow)
if table in db.listTables():
db.delete(table, where={colName: dh})
identity = self.dbIdentity+'.events'
table = dbui.getTableName(identity)
if table in db.listTables():
db.delete(table, where={colName: dh})
#db.delete(table, "SourceDir=%d" % pRow)
#scan.unlock()
#scan.forgetEvents()
def storeStats(self, data):
## Store a list of dict records, one per spot.
## data: {'SourceFile': clamp file handle, 'xPos':, 'yPos':, ...other fields from stats flowchart...}
## parentDir: protocolSequence dir handle (or protocol for single spots)
#print "Store stats:", fh
## If only one record was given, make it into a list of one record
if isinstance(data, dict):
data = [data]
dbui = self.getElement('Database')
identity = self.dbIdentity+'.sites'
table = dbui.getTableName(identity)
db = dbui.getDb()
if db is None:
raise Exception("No DB selected")
## determine the set of fields we expect to find in the table
fields = db.describeData(data)
## override directory fields since describeData can't guess these for us
fields['ProtocolDir'] = 'directory:Protocol'
fields['ProtocolSequenceDir'] = 'directory:ProtocolSequence'
with db.transaction():
## Make sure target table exists and has correct columns, links to input file
db.checkTable(table, owner=identity, columns=fields, create=True, addUnknownColumns=True, indexes=[['ProtocolDir'], ['ProtocolSequenceDir']])
# delete old
for source in set([d['ProtocolDir'] for d in data]):
#name = rec['SourceFile']
db.delete(table, where={'ProtocolDir': source})
# write new
with pg.ProgressDialog("Storing spot stats...", 0, 100) as dlg:
for n, nmax in db.iterInsert(table, data, chunkSize=30):
dlg.setMaximum(nmax)
dlg.setValue(n)
if dlg.wasCanceled():
raise HelpfulException("Scan store canceled by user.", msgType='status')
def loadSpotFromDB(self, dh):
dbui = self.getElement('Database')
db = dbui.getDb()
if db is None:
raise Exception("No DB selected")
fh = self.dataModel.getClampFile(dh)
parentDir = fh.parent()
identity = self.dbIdentity+'.sites'
table = dbui.getTableName(identity)
if not db.hasTable(table):
return None, None
stats = db.select(table, '*', where={'ProtocolDir': parentDir})
events = self.detector.readFromDb(sourceFile=fh)
return events, stats
def loadScanFromDB(self, sourceDir):
## sourceDir should be protocolsequence
dbui = self.getElement('Database')
db = dbui.getDb()
if db is None:
raise Exception("No DB selected")
identity = self.dbIdentity+'.sites'
table = dbui.getTableName(identity)
if not db.hasTable(table):
return None, None
stats = db.select(table, '*', where={'ProtocolSequenceDir': sourceDir})
events = self.detector.readFromDb(sequenceDir=sourceDir)
return events, stats
def getDb(self):
dbui = self.getElement('Database')
db = dbui.getDb()
return db
class Photostim(AnalysisModule):
"""
This module analyzes raw data from photostimulation scanning protocols to produce colored maps of features detected in the data. This analysis consists of multiple components:
1) Data is (optionally) processed through an event detector to determine the time, amplitude, and other characteristics of the recroded events. The exact analysis in this stage is fully customizable by a flowchart. Results of this analysis are stored to a DB table (named 'photostim_events' by default) for use in further analysis.
2) Each photostimulation is analyzed to determine the strength of evoked events, probability of presynaptic connection, probability of direct stimulation, etc. The exact analysis in this stage is fully customizable by a flowchart and results are stored to a DB table (named 'photostim_sites' by default) for use in further analysis.
3) Multiple scans may (optionally) be combined to produce a single map with repeated measures and/or extended area.
4) The values generated in steps 2 and 3 are mapped to colors which are displayed in a canvas.
"""
def __init__(self, host):
AnalysisModule.__init__(self, host)
if self.dataModel is None:
raise Exception(
"Photostim analysis module requires a data model, but none is loaded yet."
)
self.dbIdentity = "Photostim" ## how we identify to the database; this determines which tables we own
self.selectedSpot = None
## setup analysis flowchart
modPath = os.path.abspath(os.path.split(__file__)[0])
flowchartDir = os.path.join(modPath, "analysis_fc")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput('events')
self.flowchart.addInput('regions')
self.flowchart.addInput('fileHandle')
self.flowchart.addOutput('dataOut')
self.analysisCtrl = self.flowchart.widget()
## color mapper
self.mapper = ColorMapper.ColorMapper(
filePath=os.path.join(modPath, "colormaps"))
self.mapCtrl = QtGui.QWidget()
self.mapLayout = QtGui.QVBoxLayout()
self.mapCtrl.setLayout(self.mapLayout)
self.mapLayout.splitter = QtGui.QSplitter()
self.mapLayout.splitter.setOrientation(QtCore.Qt.Vertical)
self.mapLayout.splitter.setContentsMargins(0, 0, 0, 0)
self.mapLayout.addWidget(self.mapLayout.splitter)
self.mapLayout.splitter.addWidget(self.analysisCtrl)
#self.mapLayout.splitter.addWidget(QtGui.QSplitter())
self.mapLayout.splitter.addWidget(self.mapper)
#self.mapLayout.splitter.addWidget(self.recolorBtn)
self.recolorLayout = QtGui.QHBoxLayout()
self.recolorWidget = QtGui.QWidget()
self.mapLayout.splitter.addWidget(self.recolorWidget)
self.recolorWidget.setLayout(self.recolorLayout)
self.recolorBtn = QtGui.QPushButton('Recolor')
self.recolorLayout.addWidget(self.recolorBtn)
self.recolorParallelCheck = QtGui.QCheckBox('Parallel')
self.recolorParallelCheck.setChecked(True)
self.recolorLayout.addWidget(self.recolorParallelCheck)
## scatter plot
self.scatterPlot = ScatterPlotter()
self.scatterPlot.sigClicked.connect(self.scatterPlotClicked)
## setup map DB ctrl
self.dbCtrl = DBCtrl(self, self.dbIdentity)
## storage for map data
#self.scanItems = {}
self.scans = []
#self.seriesScans = {}
self.maps = []
## create event detector
fcDir = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"detector_fc")
self.detector = EventDetector.EventDetector(
host, flowchartDir=fcDir, dbIdentity=self.dbIdentity + '.events')
## override some of its elements
self.detector.setElement('File Loader', self)
self.detector.setElement('Database', self.dbCtrl)
## Create element list, importing some gui elements from event detector
elems = self.detector.listElements()
self._elements_ = OrderedDict([
('Database', {
'type': 'ctrl',
'object': self.dbCtrl,
'size': (300, 600)
}),
('Scatter Plot', {
'type': 'ctrl',
'object': self.scatterPlot,
'pos': ('right', ),
'size': (700, 400)
}),
('Canvas', {
'type': 'canvas',
'pos': ('above', 'Scatter Plot'),
'size': (700, 400),
'allowTransforms': False,
'hideCtrl': True,
'args': {
'name': 'Photostim'
}
}),
#('Maps', {'type': 'ctrl', 'pos': ('bottom', 'Database'), 'size': (200,200), 'object': self.mapDBCtrl}),
('Map Opts', {
'type': 'ctrl',
'object': self.mapCtrl,
'pos': ('above', 'Database'),
'size': (300, 600)
}),
('Detection Opts',
elems['Detection Opts'].setParams(pos=('above', 'Map Opts'),
size=(300, 600))),
('File Loader', {
'type': 'fileInput',
'size': (300, 300),
'pos': ('above', 'Detection Opts'),
'host': self,
'showFileTree': False
}),
('Data Plot', elems['Data Plot'].setParams(pos=('bottom',
'Canvas'),
size=(700, 200))),
('Filter Plot', elems['Filter Plot'].setParams(pos=('bottom',
'Data Plot'),
size=(700, 200))),
('Event Table',
elems['Output Table'].setParams(pos=('below', 'Filter Plot'),
size=(700, 200))),
('Stats', {
'type': 'dataTree',
'size': (700, 200),
'pos': ('below', 'Event Table')
}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
self.detector.flowchart.sigOutputChanged.connect(
self.detectorOutputChanged)
self.flowchart.sigOutputChanged.connect(self.analyzerOutputChanged)
self.detector.flowchart.sigStateChanged.connect(
self.detectorStateChanged)
self.flowchart.sigStateChanged.connect(self.analyzerStateChanged)
self.recolorBtn.clicked.connect(self.recolor)
def quit(self):
self.scans = []
self.maps = []
return AnalysisModule.quit(self)
def elementChanged(self, element, old, new):
name = element.name()
## connect plots to flowchart, link X axes
if name == 'File Loader':
new.sigBaseChanged.connect(self.baseDirChanged)
new.ui.dirTree.sigSelectionChanged.connect(self.fileSelected)
self.baseDirChanged(new.baseDir())
def fileSelected(self):
fhl = self.getElement('File Loader').ui.dirTree.selectedFiles()
if len(fhl) == 0:
return
fh = fhl[0]
if fh is not None and fh.isDir():
print Scan.describe(self.dataModel, fh)
def baseDirChanged(self, dh):
if dh is None:
return ## should clear out map list here?
if 'dirType' not in dh.info():
return
typ = dh.info()['dirType']
if typ == 'Slice':
cells = [
dh[d] for d in dh.subDirs()
if dh[d].info().get('dirType', None) == 'Cell'
]
elif typ == 'Cell':
cells = [dh]
else:
return
#print "cells:", cells
self.dbCtrl.listMaps(cells)
def loadFileRequested(self, fhList):
canvas = self.getElement('Canvas')
model = self.dataModel
with pg.ProgressDialog("Loading data..", 0, len(fhList)) as dlg:
for fh in fhList:
try:
## TODO: use more clever detection of Scan data here.
if fh.isFile() or model.dirType(fh) == 'Cell':
canvas.addFile(fh)
else:
self.loadScan(fh)
return True
except:
debug.printExc("Error loading file %s" % fh.name())
return False
dlg += 1
if dlg.wasCanceled():
return
def loadScan(self, fh):
ret = []
## first see if we've already loaded this file
for scan in self.scans:
if scan.source() is fh:
ret.append(
scan) ## if so, return all scans sourced by this file
if len(ret) > 0:
return ret
## Load the file, possibly generating multiple scans.
canvas = self.getElement('Canvas')
ret = []
scans = loadScanSequence(fh, self)
if len(scans) > 1:
parent = canvas.addGroup(fh.shortName())
else:
parent = None
print parent
for scan in scans:
canvasItem = scan.canvasItem()
if parent is not None:
canvasItem.setParentItem(parent)
canvas.addItem(canvasItem)
canvasItem.graphicsItem().sigClicked.connect(self.scanPointClicked)
self.scans.append(scan)
ret.append(scan)
self.dbCtrl.scanLoaded(scan)
self.scatterPlot.addScan(scan)
#canvasItems = canvas.addFile(fh, separateParams=True) ## returns list when fh is a scan
#for citem in canvasItems:
#scan = Scan(self, fh, citem, name=citem.opts['name'])
#self.scans.append(scan)
#citem.item.sigPointClicked.connect(self.scanPointClicked)
#self.dbCtrl.scanLoaded(scan)
#ret.append(scan)
#self.scatterPlot.addScan(scan)
return ret
def registerMap(self, map):
#if map in self.maps:
#return
canvas = self.getElement('Canvas')
map.canvasItem = canvas.addGraphicsItem(map.sPlotItem, name=map.name())
self.maps.append(map)
map.sPlotItem.sigClicked.connect(self.mapPointClicked)
def unregisterMap(self, map):
if hasattr(map, 'canvasItem'):
canvas = self.getElement('Canvas')
canvas.removeItem(map.canvasItem)
if map in self.maps:
self.maps.remove(map)
try:
map.sPlotItem.sigClicked.disconnect(self.mapPointClicked)
except TypeError:
pass
def scanPointClicked(self, plotItem, points):
try:
point = points[0]
QtGui.QApplication.setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
#print "clicked:", point.data()
plot = self.getElement("Data Plot")
plot.clear()
self.selectedSpot = point
self.selectedScan = plotItem.scan
fh = self.dataModel.getClampFile(point.data())
self.detector.loadFileRequested(fh)
#self.dbCtrl.scanSpotClicked(fh)
finally:
QtGui.QApplication.restoreOverrideCursor()
def mapPointClicked(self, scan, points):
data = []
for p in points:
for source in p.data()['sites']:
data.append(
[source[0],
self.dataModel.getClampFile(source[1])])
#data.extend(p.data)
self.redisplayData(data)
##self.dbCtrl.mapSpotClicked(point.data) ## Did this method exist at some point?
def scatterPlotClicked(self, plot, points):
#scan, fh, time = point.data
self.redisplayData([p.data() for p in points])
#self.scatterLine =
def redisplayData(self,
points): ## data must be [(scan, fh, <event time>), ...]
#raise Exception('blah')
#print points
try:
QtGui.QApplication.setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
plot = self.getElement("Data Plot")
plot.clear()
eTable = self.getElement("Event Table")
sTable = self.getElement("Stats")
#num = len(point.data)
num = len(points)
statList = []
evList = []
for i in range(num):
color = pg.intColor(i, num)
#scan, fh = point.data[i]
try:
scan, fh = points[i][:2]
except:
print points[i]
raise
if len(points[i]) == 3:
evTime = points[i][2]
else:
evTime = None
scan.displayData(fh, plot, color, evTime)
## show stats
stats = scan.getStats(fh.parent())
statList.append(stats)
events = scan.getEvents(fh)['events']
if len(events) > 0:
evList.append(events)
sTable.setData(statList)
if len(evList) > 0:
try:
eTable.setData(np.concatenate(evList))
except:
for i in range(1, len(evList)):
if len(evList[i].dtype) != len(evList[i - 1].dtype):
print "Cannot concatenate; event lists have different dtypes:"
print evList[i].dtype
print evList[i - 1].dtype
else:
for j in range(len(evList[i].dtype)):
if evList[i -
1].dtype[j] != evList[i].dtype[j]:
for l in evList:
print l
print "Warning: can not concatenate--field '%s' has inconsistent types %s, %s (data printed above)" % (
evList[i].dtype.names[j],
str(evList[i - 1].dtype[j]),
str(evList[i].dtype[j]))
raise
finally:
QtGui.QApplication.restoreOverrideCursor()
def detectorStateChanged(self):
#print "STATE CHANGE"
#print "Detector state changed"
for scan in self.scans:
scan.invalidateEvents()
def detectorOutputChanged(self):
if self.selectedSpot == None:
return
output = self.detector.flowchart.output()
output['fileHandle'] = self.selectedSpot.data()
self.flowchart.setInput(**output)
#errs = output['events']['fitFractionalError']
#if len(errs) > 0:
#print "Detector events error mean / median / max:", errs.mean(), np.median(errs), errs.max()
def analyzerStateChanged(self):
#print "Analyzer state changed."
for scan in self.scans:
scan.invalidateStats()
def analyzerOutputChanged(self):
table = self.getElement('Stats')
stats = self.processStats() ## gets current stats
table.setData(stats)
if stats is None:
return
self.mapper.setArgList(stats.keys())
#def getCurrentStats(self):
#stats = self.flowchart.output()['dataOut']
#spot = self.selectedSpot
#pos = spot.scenePos()
#stats['xPos'] = pos.x()
#stats['yPos'] = pos.y()
#return stats
def recolor(self):
## Select only visible scans and maps for recoloring
try:
allScans = [s for s in self.scans if s.isVisible()]
allScans.extend([s for s in self.maps if s.isVisible()])
for i in range(len(allScans)):
allScans[i].recolor(
i,
len(allScans),
parallel=self.recolorParallelCheck.isChecked())
except pg.multiprocess.CanceledError:
pass
#for i in range(len(self.scans)):
#self.scans[i].recolor(i, len(self.scans))
#for i in range(len(self.maps)):
#self.maps[i].recolor(self, i, len(self.maps))
def getColor(self, stats, data=None):
## Note: the data argument is used elsewhere (MapAnalyzer)
#print "STATS:", stats
return self.mapper.getColor(stats)
def processEvents(self, fh):
print "Process Events:", fh
ret = self.detector.process(fh)
return ret
def processStats(self, data=None, spot=None):
## Process output of stats flowchart for a single spot, add spot position fields.
## data is the input to the stats flowchart
## if data is omitted, then the stats for the currently selected spot are returned
## (this is just the pre-existing output of the stats flowchart)
## spot is used to determine the x,y coords of the spot
if data is None:
stats = self.flowchart.output()['dataOut']
spot = self.selectedSpot
if spot is None:
return
dh = spot.data()
else:
if 'regions' not in data:
data['regions'] = self.detector.flowchart.output()['regions']
dh = spot.data()
data['fileHandle'] = dh
#if dh is None:
#data['fileHandle'] = self.selectedSpot.data
#else:
#data['fileHandle'] = fh
stats = self.flowchart.process(**data)['dataOut']
if stats is None:
raise Exception(
'No data returned from analysis (check flowchart for errors).')
try:
pos = spot.viewPos()
stats['xPos'] = pos.x()
stats['yPos'] = pos.y()
except:
# just try substituting with spot.pos:
p = spot.pos()
stats['xPos'] = p[0]
stats['yPos'] = p[1]
#d = spot.data.parent()
#size = d.info().get('Scanner', {}).get('spotSize', 100e-6)
#stats['spotSize'] = size
#print "Process Stats:", spot.data
#stats['SourceFile'] = self.dataModel.getClampFile(dh)
stats[
'ProtocolDir'] = dh ## stats should be stored with the protocol dir, not the clamp file.
stats['ProtocolSequenceDir'] = self.dataModel.getParent(
dh, 'ProtocolSequence')
#parent = dh.parent()
#if self.dataModel.dirType(parent) != 'ProtocolSequence':
#parent = None
#stats['ProtocolSequenceDir'] = parent
return stats
def storeDBSpot(self):
"""Stores data for selected spot immediately, using current flowchart outputs"""
dbui = self.getElement('Database')
db = dbui.getDb()
## get events and stats for selected spot
spot = self.selectedSpot
if spot is None:
raise Exception("No spot selected")
#print "Store spot:", spot.data
#parentDir = spot.data
#p2 = parentDir.parent()
#if self.dataModel.dirType(p2) == 'ProtocolSequence':
#parentDir = p2
## ask eventdetector to store events for us.
#print parentDir
with db.transaction():
self.detector.storeToDB()
events = self.detector.output()
## store stats
stats = self.processStats(
spot=spot) ## gets current stats if no processing is requested
self.storeStats(stats)
## update data in Map
self.selectedScan.updateSpot(spot.data(), events, stats)
def storeDBScan(self, scan, storeEvents=True):
"""Store all data for a scan, using cached values if possible"""
p = debug.Profiler("Photostim.storeDBScan", disabled=True)
if storeEvents:
self.clearDBScan(scan)
with pg.BusyCursor():
#dh = scan.source()
#print "Store scan:", scan.source().name()
events = []
stats = []
spots = scan.spots()
with pg.ProgressDialog("Preparing data for %s" % scan.name(), 0,
len(spots) + 1) as dlg:
## collect events and stats from all spots in the scan
for i in xrange(len(spots)):
s = spots[i]
fh = self.dataModel.getClampFile(s.data())
try:
ev = scan.getEvents(fh)['events']
events.append(ev)
except:
print fh, scan.getEvents(fh)
raise
st = scan.getStats(s.data())
stats.append(st)
dlg.setValue(i)
if dlg.wasCanceled():
raise HelpfulException("Scan store canceled by user.",
msgType='status')
p.mark("Prepared data")
dbui = self.getElement('Database')
db = dbui.getDb()
with db.transaction():
## Store all events for this scan
if storeEvents:
events = [x for x in events if len(x) > 0]
if len(events) > 0:
ev = np.concatenate(events)
p.mark("concatenate events")
self.detector.storeToDB(ev)
p.mark("stored all events")
## Store spot data
self.storeStats(stats)
p.mark("stored all stats")
p.finish()
#print " scan %s is now locked" % scan.source().name()
#scan.lock() ## handled by Scan now
def rewriteSpotPositions(self, scan):
## for now, let's just rewrite everything.
#self.storeDBScan(scan)
## attempt to actually make this work
dbui = self.getElement('Database')
db = dbui.getDb()
identity = self.dbIdentity + '.sites'
table = dbui.getTableName(identity)
#dh = scan.source()
for spot in scan.spots():
protocolID = db(
'Select rowid from DirTable_Protocol where Dir="%s"' %
(spot.data().name(relativeTo=db.baseDir())))
if len(protocolID) < 1:
continue
protocolID = protocolID[0]['rowid']
pos = spot.viewPos()
db('UPDATE %s SET xPos=%f, yPos=%f WHERE ProtocolDir=%i' %
(table, pos.x(), pos.y(), protocolID))
## Should look like this:
# pos = spot.viewPos()
# db.update(table, {'xPos': pos.x(), 'yPos': pos.y()}, where={'ProtocolDir': spot.data})
def clearDBScan(self, scan):
dbui = self.getElement('Database')
db = dbui.getDb()
#loader = self.getElement('File Loader')
#dh = loader.selectedFile()
#scan = self.scans[dh]
dh = scan.source()
#print "Clear scan", dh
#pRow = db.getDirRowID(dh)
colName = self.dataModel.dirType(dh) + 'Dir'
identity = self.dbIdentity + '.sites'
table = dbui.getTableName(identity)
#db.delete(table, "SourceDir=%d" % pRow)
if table in db.listTables():
db.delete(table, where={colName: dh})
identity = self.dbIdentity + '.events'
table = dbui.getTableName(identity)
if table in db.listTables():
db.delete(table, where={colName: dh})
#db.delete(table, "SourceDir=%d" % pRow)
#scan.unlock()
#scan.forgetEvents()
def storeStats(self, data):
## Store a list of dict records, one per spot.
## data: {'SourceFile': clamp file handle, 'xPos':, 'yPos':, ...other fields from stats flowchart...}
## parentDir: protocolSequence dir handle (or protocol for single spots)
#print "Store stats:", fh
## If only one record was given, make it into a list of one record
if isinstance(data, dict):
data = [data]
dbui = self.getElement('Database')
identity = self.dbIdentity + '.sites'
table = dbui.getTableName(identity)
db = dbui.getDb()
if db is None:
raise Exception("No DB selected")
## determine the set of fields we expect to find in the table
fields = db.describeData(data)
## override directory fields since describeData can't guess these for us
fields['ProtocolDir'] = 'directory:Protocol'
fields['ProtocolSequenceDir'] = 'directory:ProtocolSequence'
with db.transaction():
## Make sure target table exists and has correct columns, links to input file
db.checkTable(table,
owner=identity,
columns=fields,
create=True,
addUnknownColumns=True,
indexes=[['ProtocolDir'], ['ProtocolSequenceDir']])
# delete old
for source in set([d['ProtocolDir'] for d in data]):
#name = rec['SourceFile']
db.delete(table, where={'ProtocolDir': source})
# write new
with pg.ProgressDialog("Storing spot stats...", 0, 100) as dlg:
for n, nmax in db.iterInsert(table, data, chunkSize=30):
dlg.setMaximum(nmax)
dlg.setValue(n)
if dlg.wasCanceled():
raise HelpfulException("Scan store canceled by user.",
msgType='status')
def loadSpotFromDB(self, dh):
dbui = self.getElement('Database')
db = dbui.getDb()
if db is None:
raise Exception("No DB selected")
fh = self.dataModel.getClampFile(dh)
parentDir = fh.parent()
identity = self.dbIdentity + '.sites'
table = dbui.getTableName(identity)
if not db.hasTable(table):
return None, None
stats = db.select(table, '*', where={'ProtocolDir': parentDir})
events = self.detector.readFromDb(sourceFile=fh)
return events, stats
def loadScanFromDB(self, sourceDir):
## sourceDir should be protocolsequence
dbui = self.getElement('Database')
db = dbui.getDb()
if db is None:
raise Exception("No DB selected")
identity = self.dbIdentity + '.sites'
table = dbui.getTableName(identity)
if not db.hasTable(table):
return None, None
stats = db.select(table, '*', where={'ProtocolSequenceDir': sourceDir})
events = self.detector.readFromDb(sequenceDir=sourceDir)
return events, stats
def getDb(self):
dbui = self.getElement('Database')
db = dbui.getDb()
return db
