def __init__(self, host):
AnalysisModule.__init__(self, host)
self.dbIdentity = 'Explorer'
self.dbCtrl = DBCtrl(host, self.dbIdentity)
self.ctrl = PlotCtrl(host, self.dbIdentity)
self._elements = OrderedDict([
('Database', {'type': 'ctrl', 'object':self.dbCtrl, 'size': (200, 300), 'host': self}),
('Scatter Plot', {'type': 'plot', 'pos':('right',), 'size': (800, 600)}),
('Plot Opts', {'type': 'ctrl', 'object': self.ctrl, 'pos':('bottom', 'Database'), 'size':(200,300)})
])
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.dbIdentity = 'Explorer'
self.dbCtrl = DBCtrl(host, self.dbIdentity)
self.ctrl = PlotCtrl(host, self.dbIdentity)
self._elements = OrderedDict([
('Database', {'type': 'ctrl', 'object':self.dbCtrl, 'size': (200, 300), 'host': self}),
('Scatter Plot', {'type': 'plot', 'pos':('right',), 'size': (800, 600)}),
('Plot Opts', {'type': 'ctrl', 'object': self.ctrl, 'pos':('bottom', 'Database'), 'size':(200,300)})
])
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.dbIdentity = 'MapImager' ## how we identify to the database; this determines which tables we own
modPath = os.path.abspath(os.path.split(__file__)[0])
self._elements_ = OrderedDict([
('Database Query', {'type':'ctrl', 'object': DatabaseQueryWidget(self.dataManager()), 'size':(300,200), 'host':self}),
('File Loader', {'type':'fileInput', 'pos':('below', 'Database Query'), 'host':self, 'showFileTree':False}),
('Color Mapper', {'type':'ctrl', 'object': MapImagerColorMapper(filePath=os.path.join(modPath, "colorMaps"), host=self), 'size': (200,300), 'pos':('right', 'Database Query')}),
('Contour Plotter', {'type':'ctrl', 'object':ContourPlotter(host=self), 'pos':('below', 'Color Mapper')}),
('Canvas', {'type': 'canvas', 'pos': ('bottom', 'Color Mapper'), 'size': (700,600), 'allowTransforms': False, 'hideCtrl': True, 'args': {'name': 'MapImager'}}),
('Map Convolver', {'type':'ctrl', 'object': MapConvolver(), 'size': (200, 200), 'pos':('bottom', 'File Loader')}),
('Spatial Correlator', {'type':'ctrl', 'object':SpatialCorrelator(), 'size':(100,100), 'pos': ('bottom', 'Map Convolver')})
#('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': True}}),
#('ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('bottom', 'File Loader'), 'size': (100, 100)}),
#('Rs Plot', {'type': 'plot', 'pos':('right', 'File Loader'), 'size':(200, 600), 'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
#('Rm Plot', {'type': 'plot', 'pos':('bottom', 'Rs Plot'), 'size':(200, 600),'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
#('Ih Plot', {'type': 'plot', 'pos':('bottom', 'Rm Plot'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None, 's')}}),
#('Traces Plot', {'type': 'plot', 'pos':('right', 'ctrl'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None,'s')}}),
])
self.initializeElements()
for el in self.getAllElements():
self.getElement(el, create=True)
## reserve variables that will get set later
self.imgItem = None
self.spacing = None
self.imgData = None
self.dbquery = self.getElement("Database Query")
self.canvas = self.getElement("Canvas")
self.mapConvolver = self.getElement("Map Convolver")
self.colorMapper = self.getElement("Color Mapper")
self.spatialCorrelator = self.getElement("Spatial Correlator")
self.contourPlotter = self.getElement("Contour Plotter")
self.contourPlotter.setCanvas(self.canvas)
#self.outline = self.spatialCorrelator.getOutline()
#self.canvas.addGraphicsItem(self.outline)
self.dbquery.sigTableChanged.connect(self.setData)
self.mapConvolver.sigOutputChanged.connect(self.convolverOutputChanged)
self.mapConvolver.sigFieldsChanged.connect(self.convolverFieldsChanged)
self.spatialCorrelator.sigOutputChanged.connect(self.correlatorOutputChanged)
self.colorMapper.sigChanged.connect(self.computeColors)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlWidget = QtGui.QWidget()
self.ctrl = ctrlTemplate.Ui_Form()
self.ctrl.setupUi(self.ctrlWidget)
## Setup basic GUI
self._elements_ = OrderedDict([
#('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self}),
#('IV Plot', {'type': 'plot', 'pos': ('right', 'File Loader'), 'size': (800, 300)}),
#('Data Plot', {'type': 'plot', 'pos': ('bottom',), 'size': (800, 300)}),
('Canvas', {'type': 'canvas', 'size': (600,600)}),
('Ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('left', 'Canvas'), 'size': (200,600)}),
])
self.initializeElements()
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlWidget = Qt.QWidget()
self.ctrl = ctrlTemplate.Ui_Form()
self.ctrl.setupUi(self.ctrlWidget)
## Setup basic GUI
self._elements_ = OrderedDict([
#('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self}),
#('IV Plot', {'type': 'plot', 'pos': ('right', 'File Loader'), 'size': (800, 300)}),
#('Data Plot', {'type': 'plot', 'pos': ('bottom',), 'size': (800, 300)}),
('Canvas', {'type': 'canvas', 'size': (600,600)}),
('Ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('left', 'Canvas'), 'size': (200,600)}),
])
self.initializeElements()
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrl = QtGui.QWidget()
l = QtGui.QVBoxLayout()
self.ctrl.setLayout(l)
self.analyzeBtn = QtGui.QPushButton('Analyze')
self.analyzeBtn.clicked.connect(self.updateProfiles)
self.saveBtn = QtGui.QPushButton('Save')
self.saveBtn.clicked.connect(self.save)
l.addWidget(self.analyzeBtn)
l.addWidget(self.saveBtn)
# Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': False}}),
('profiles', {'type': 'plot', 'pos': ('bottom', 'File Loader'), 'size': (300, 300)}),
('result table', {'type': 'table', 'pos': ('below', 'profiles')}),
('profile fits', {'type': 'plot', 'pos': ('below', 'result table'), 'size': (300, 300)}),
#('view', {'type': 'viewBox', 'pos': ('right', 'File Loader'), 'size': (300,300), 'args': {'lockAspect': True, 'invertY': True}}),
('view', {'type': 'imageView', 'pos': ('right', 'File Loader'), 'size': (300,300)}),
('normalized', {'type': 'imageView', 'pos': ('right', 'view'), 'size': (300,300)}),
('total', {'type': 'plot', 'pos': ('right', 'profiles'), 'size': (300, 100)}),
('peak', {'type': 'plot', 'pos': ('bottom', 'total'), 'size': (300, 100)}),
('width', {'type': 'plot', 'pos': ('bottom', 'peak'), 'size': (300, 100)}),
('ctrl', {'type': 'ctrl', 'object': self.ctrl, 'pos': ('bottom', 'File Loader'), 'size': (100, 20)}),
])
self.initializeElements()
self.image = None
#self.imageItem = pg.ImageItem()
self.view = self.getElement('view', create=True)
#view.addItem(self.imageItem)
self.dataRgn = pg.RectROI(pos=(120,0), size=(100,100), pen=(0,255,0))
self.dataRgn.addRotateHandle((1,0), (0.5, 0.5))
self.bgRgn = pg.ROI(pos=(0,0), size=(100,100), pen=(255, 0,0), parent=self.dataRgn)
self.bgRgn.addRotateHandle((1,0), (0.5, 0.5))
self.bgRgn.addScaleHandle((1, 0.5), (0, 0.5))
#self.bgRgn.setParentItem(self.dataRgn)
self.view.addItem(self.bgRgn)
self.view.addItem(self.dataRgn)
self.dataRgn.sigRegionChanged.connect(self.updateImage)
self.bgRgn.sigRegionChanged.connect(self.updateImage)
def __init__(self, host):
AnalysisModule.__init__(self, host)
fcpath = os.path.join(os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
confpath = os.path.join(os.path.abspath(os.path.split(__file__)[0]), "configs")
self.confWidget = QtGui.QWidget()
self.confLoader = ConfLoader(self, confpath)
self.fileLoader = DataLoader(self, host.dataManager())
self.addPlotBtn = QtGui.QPushButton('Add Plot')
self.processWidget = QtGui.QWidget()
self.processLayout = QtGui.QHBoxLayout()
self.processWidget.setLayout(self.processLayout)
self.processBtn = QtGui.QPushButton('Process')
self.processCheck = QtGui.QCheckBox('Auto')
self.processLayout.addWidget(self.processBtn)
self.processLayout.addWidget(self.processCheck)
self.confLayout = QtGui.QGridLayout()
self.confWidget.setLayout(self.confLayout)
self.confLayout.addWidget(self.confLoader, 0, 0)
self.confLayout.addWidget(self.addPlotBtn, 1, 0)
self.confLayout.addWidget(self.processWidget, 2, 0)
self.plots = []
self.params = None
self.data = None
self.flowchart = fc.Flowchart(filePath=fcpath)
self.flowchart.addInput('Input')
self.flowchart.addOutput('Output')
#self.flowchart.sigChartLoaded.connect(self.connectPlots)
# Setup basic GUI
self._elements_ = OrderedDict([
('Configuration', {'type': 'ctrl', 'object': self.confWidget, 'size': (200,200)}),
('File Loader', {'type': 'ctrl', 'object': self.fileLoader, 'size': (200, 300), 'pos': ('bottom', 'Configuration')}),
('Flowchart', {'type': 'ctrl', 'object': self.flowchart.widget(), 'size': (300,500), 'pos': ('right',)}),
('Results', {'type': 'table', 'size': (500,200), 'pos': 'bottom'}),
])
self.initializeElements()
self.addPlotBtn.clicked.connect(self.addPlotClicked)
self.processBtn.clicked.connect(self.processClicked)
self.flowchart.sigOutputChanged.connect(self.outputChanged)
self.fileLoader.sigFileLoaded.connect(self.fileLoaded)
self.fileLoader.sigSelectedFileChanged.connect(self.fileSelected)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrl = QtGui.QWidget()
self.ui = Ui_Form()
self.ui.setupUi(self.ctrl)
self.atlas = None
self.canvas = None # grab canvas information when loading files
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self}),
('Mosaic', {'type': 'ctrl', 'object': self.ctrl, 'pos': ('right',), 'size': (600, 200)}),
('Canvas', {'type': 'canvas', 'pos': ('bottom', 'Mosaic'), 'size': (600, 800), 'args': {'name': 'MosaicEditor'}}),
])
self.initializeElements()
self.ui.canvas = self.getElement('Canvas', create=True)
self.items = weakref.WeakKeyDictionary()
self.files = weakref.WeakValueDictionary()
self.cells = {}
#addScanImagesBtn = QtGui.QPushButton()
#addScanImagesBtn.setText('Add Scan Image')
self.ui.fileLoader = self.getElement('File Loader', create=True)
self.ui.fileLoader.ui.fileTree.hide()
#self.ui.fileLoader.ui.verticalLayout_2.addWidget(addScanImagesBtn)
try:
self.ui.fileLoader.setBaseClicked() # get the currently selected directory in the DataManager
except:
pass
for a in atlas.listAtlases():
self.ui.atlasCombo.addItem(a)
self.ui.canvas.sigItemTransformChangeFinished.connect(self.itemMoved)
#self.ui.exportSvgBtn.clicked.connect(self.exportSvg)
self.ui.atlasCombo.currentIndexChanged.connect(self.atlasComboChanged)
self.ui.normalizeBtn.clicked.connect(self.normalizeImages)
self.ui.tileShadingBtn.clicked.connect(self.rescaleImages)
self.ui.mosaicApplyScaleBtn.clicked.connect(self.updateScaling)
self.ui.mosaicFlipLRBtn.clicked.connect(self.flipLR)
self.ui.mosaicFlipUDBtn.clicked.connect(self.flipUD)
self.imageMax = 0.0
def __init__(self, host, flowchartDir=None, dbIdentity="EventDetector", dbCtrl=None):
AnalysisModule.__init__(self, host)
if flowchartDir is None:
flowchartDir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
self.flowchart = Flowchart(filePath=flowchartDir)
self.dbIdentity = dbIdentity ## how we identify to the database; this determines which tables we own
#self.loader = FileLoader.FileLoader(host.dataManager())
#self.setCentralWidget(self.flowchart.widget())
#self.ui.chartDock1.setWidget(self.flowchart.widget())
self.flowchart.addInput("dataIn")
self.flowchart.addOutput('events')
#self.flowchart.addOutput('regions', multi=True)
self.flowchart.sigChartLoaded.connect(self.connectPlots)
if dbCtrl == None:
self.dbCtrl = DBCtrl(self, identity=self.dbIdentity)
self.dbCtrl.storeBtn.clicked.connect(self.storeClicked)
else:
self.dbCtrl = dbCtrl(self, identity=self.dbIdentity)
#self.ctrl = QtGui.QLabel('LABEL')
self.ctrl = self.flowchart.widget()
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self}),
('Database', {'type': 'ctrl', 'object': self.dbCtrl, 'size': (200,300), 'pos': ('bottom', 'File Loader')}),
('Data Plot', {'type': 'plot', 'pos': ('right',), 'size': (800, 300)}),
('Detection Opts', {'type': 'ctrl', 'object': self.ctrl, 'pos': ('bottom', 'Database'), 'size': (200, 500)}),
('Filter Plot', {'type': 'plot', 'pos': ('bottom', 'Data Plot'), 'size': (800, 300)}),
('Output Table', {'type': 'table', 'pos': ('bottom', 'Filter Plot'), 'optional': True, 'size': (800,200)}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
self.flowchart.sigOutputChanged.connect(self.outputChanged)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlWidget = Qt.QWidget()
self.ctrl = CellHealthCtrlTemplate.Ui_widget()
self.ctrl.setupUi(self.ctrlWidget)
self.ctrlStateGroup = pg.WidgetGroup(self.ctrlWidget)
self.ctrl.startSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.35, dec=False)
self.ctrl.stopSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.5, dec=False)
## Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': True}}),
('ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('bottom', 'File Loader'), 'size': (100, 100)}),
('Rs Plot', {'type': 'plot', 'pos':('right', 'File Loader'), 'size':(200, 600), 'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Rm Plot', {'type': 'plot', 'pos':('bottom', 'Rs Plot'), 'size':(200, 600),'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Ih Plot', {'type': 'plot', 'pos':('bottom', 'Rm Plot'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None, 's')}}),
('Traces Plot', {'type': 'plot', 'pos':('right', 'ctrl'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None,'s')}}),
])
self.initializeElements()
for el in self.getAllElements():
self.getElement(el, create=True)
self.tracesPlot = self.getElement('Traces Plot')
self.measurementArray = np.zeros(1000, dtype=[
('unixtime', float),
('time', float),
('Rs', float),
('Rm', float),
('Ih', float)
])
self.files = {} ## keys are dhs, values are {'data': array of time/Rs/Rm/Ih, 'ctrlState': state, 'traces': clampData}
self.ctrl.processBtn.clicked.connect(self.processClicked)
self.ctrl.saveBtn.clicked.connect(self.saveClicked)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlWidget = QtGui.QWidget()
self.ctrl = CellHealthCtrlTemplate.Ui_widget()
self.ctrl.setupUi(self.ctrlWidget)
self.ctrlStateGroup = pg.WidgetGroup(self.ctrlWidget)
self.ctrl.startSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.35, dec=False)
self.ctrl.stopSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.5, dec=False)
## Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': True}}),
('ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('bottom', 'File Loader'), 'size': (100, 100)}),
('Rs Plot', {'type': 'plot', 'pos':('right', 'File Loader'), 'size':(200, 600), 'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Rm Plot', {'type': 'plot', 'pos':('bottom', 'Rs Plot'), 'size':(200, 600),'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Ih Plot', {'type': 'plot', 'pos':('bottom', 'Rm Plot'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None, 's')}}),
('Traces Plot', {'type': 'plot', 'pos':('right', 'ctrl'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None,'s')}}),
])
self.initializeElements()
for el in self.getAllElements():
self.getElement(el, create=True)
self.tracesPlot = self.getElement('Traces Plot')
self.measurementArray = np.zeros(1000, dtype=[
('unixtime', float),
('time', float),
('Rs', float),
('Rm', float),
('Ih', float)
])
self.files = {} ## keys are dhs, values are {'data': array of time/Rs/Rm/Ih, 'ctrlState': state, 'traces': clampData}
self.ctrl.processBtn.clicked.connect(self.processClicked)
self.ctrl.saveBtn.clicked.connect(self.saveClicked)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrl = QtGui.QWidget()
self.ui = Ui_Form()
self.ui.setupUi(self.ctrl)
self.atlas = None
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self}),
('Mosaic', {'type': 'ctrl', 'object': self.ctrl, 'pos': ('right',), 'size': (600, 200)}),
('Canvas', {'type': 'canvas', 'pos': ('bottom', 'Mosaic'), 'size': (600, 800), 'args': {'name': 'MosaicEditor'}}),
])
self.initializeElements()
self.ui.canvas = self.getElement('Canvas', create=True)
self.items = weakref.WeakKeyDictionary()
self.files = weakref.WeakValueDictionary()
self.cells = {}
#self.loaded = []
#addScanImagesBtn = QtGui.QPushButton()
#addScanImagesBtn.setText('Add Scan Image')
self.ui.fileLoader = self.getElement('File Loader', create=True)
self.ui.fileLoader.ui.fileTree.hide()
#self.ui.fileLoader.ui.verticalLayout_2.addWidget(addScanImagesBtn)
try:
self.ui.fileLoader.setBaseClicked() # get the currently selected directory in the DataManager
except:
pass
for a in atlas.listAtlases():
self.ui.atlasCombo.addItem(a)
self.ui.canvas.sigItemTransformChangeFinished.connect(self.itemMoved)
#self.ui.exportSvgBtn.clicked.connect(self.exportSvg)
self.ui.atlasCombo.currentIndexChanged.connect(self.atlasComboChanged)
def __init__(self, host, flowchartDir=None):
AnalysisModule.__init__(self, host)
self.dbIdentity = "IVCurveAnalyzer" ## how we identify to the database; this determines which tables we own
if flowchartDir is None:
flowchartDir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput("dataIn")
#self.flowchart.addOutput('events')
self.flowchart.addOutput('regions', multi=True)
#self.flowchart.sigChartLoaded.connect(self.connectPlots)
### DBCtrl class is from EventDetector -- need to make my own here
#self.dbCtrl = DBCtrl(self, identity=self.dbIdentity)
#self.dbCtrl.storeBtn.clicked.connect(self.storeClicked)
self.ctrl = self.flowchart.widget()
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self}),
#('Database', {'type': 'ctrl', 'object': self.dbCtrl, 'size': (200,300), 'pos': ('bottom', 'File Loader')}),
('Data Plot', {'type': 'plot', 'pos': ('right',), 'size': (800, 300)}),
('Detection Opts', {'type': 'ctrl', 'object': self.ctrl, 'pos': ('bottom', 'File Loader'), 'size': (200, 500)}),
('IV Plot', {'type': 'plot', 'pos': ('bottom', 'Data Plot'), 'size': (400, 300)}),
('Output Table', {'type': 'table', 'pos': ('bottom', 'IV Plot'), 'optional': True, 'size': (800,200)}),
('FI Plot', {'type': 'plot', 'pos': ('right', 'IV Plot'), 'size': (400, 300)}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrl = QtGui.QWidget()
l = QtGui.QVBoxLayout()
self.ctrl.setLayout(l)
self.analyzeBtn = QtGui.QPushButton('Analyze')
self.analyzeBtn.clicked.connect(self.updateProfiles)
self.saveBtn = QtGui.QPushButton('Save')
self.saveBtn.clicked.connect(self.save)
l.addWidget(self.analyzeBtn)
l.addWidget(self.saveBtn)
# Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {
'type': 'fileInput',
'size': (100, 300),
'host': self,
'args': {
'showFileTree': False
}
}),
('profiles', {
'type': 'plot',
'pos': ('bottom', 'File Loader'),
'size': (300, 300)
}),
('result table', {
'type': 'table',
'pos': ('below', 'profiles')
}),
('profile fits', {
'type': 'plot',
'pos': ('below', 'result table'),
'size': (300, 300)
}),
#('view', {'type': 'viewBox', 'pos': ('right', 'File Loader'), 'size': (300,300), 'args': {'lockAspect': True, 'invertY': True}}),
('view', {
'type': 'imageView',
'pos': ('right', 'File Loader'),
'size': (300, 300)
}),
('normalized', {
'type': 'imageView',
'pos': ('right', 'view'),
'size': (300, 300)
}),
('total', {
'type': 'plot',
'pos': ('right', 'profiles'),
'size': (300, 100)
}),
('peak', {
'type': 'plot',
'pos': ('bottom', 'total'),
'size': (300, 100)
}),
('width', {
'type': 'plot',
'pos': ('bottom', 'peak'),
'size': (300, 100)
}),
('ctrl', {
'type': 'ctrl',
'object': self.ctrl,
'pos': ('bottom', 'File Loader'),
'size': (100, 20)
}),
])
self.initializeElements()
self.image = None
#self.imageItem = pg.ImageItem()
self.view = self.getElement('view', create=True)
#view.addItem(self.imageItem)
self.dataRgn = pg.RectROI(pos=(120, 0),
size=(100, 100),
pen=(0, 255, 0))
self.dataRgn.addRotateHandle((1, 0), (0.5, 0.5))
self.bgRgn = pg.ROI(pos=(0, 0),
size=(100, 100),
pen=(255, 0, 0),
parent=self.dataRgn)
self.bgRgn.addRotateHandle((1, 0), (0.5, 0.5))
self.bgRgn.addScaleHandle((1, 0.5), (0, 0.5))
#self.bgRgn.setParentItem(self.dataRgn)
self.view.addItem(self.bgRgn)
self.view.addItem(self.dataRgn)
self.dataRgn.sigRegionChanged.connect(self.updateImage)
self.bgRgn.sigRegionChanged.connect(self.updateImage)
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 __init__(self, host):
AnalysisModule.__init__(self, host)
if self.dataModel is None:
raise Exception(
"MapAnalyzer module requires a data model, but none is loaded yet."
)
self.currentMap = None
self.analysisValid = False
self.colorsValid = False
self.ctrlLayout = pg.LayoutWidget()
self.ctrl = ptree.ParameterTree(showHeader=False)
self.ctrlLayout.addWidget(self.ctrl, row=0, col=0)
self.recalcBtn = QtGui.QPushButton('Recalculate')
self.ctrlLayout.addWidget(self.recalcBtn, row=1, col=0)
self.storeBtn = pg.FeedbackButton('Store to DB')
self.ctrlLayout.addWidget(self.storeBtn, row=2, col=0)
self.loader = Loader(host=self, dm=host.dataManager())
modPath = os.path.abspath(os.path.dirname(__file__))
self.colorMapper = ColorMapper(
filePath=os.path.join(modPath, "colorMaps"))
self._elements_ = OrderedDict([
('File Loader', {
'type': 'fileInput',
'size': (300, 300),
'host': self,
'showFileTree': False
}),
('Map Loader', {
'type': 'ctrl',
'object': self.loader,
'size': (300, 300),
'pos': ('below', 'File Loader')
}),
('Color Mapper', {
'type': 'ctrl',
'object': self.colorMapper,
'size': (800, 200),
'pos': ('right', 'Map Loader')
}),
('Canvas', {
'type': 'canvas',
'size': (800, 400),
'pos': ('right', 'Color Mapper'),
'args': {
'name': 'MapAnalyzer'
}
}),
('Options', {
'type': 'ctrl',
'object': self.ctrlLayout,
'size': (300, 500),
'pos': ('bottom', 'Map Loader')
}),
('Data Plot', {
'type': 'plot',
'pos': ('top', 'Color Mapper'),
'size': (800, 300)
}),
('Score Histogram', {
'type': 'plot',
'pos': ('bottom', 'Data Plot'),
'size': (800, 300)
}),
('Timeline', {
'type': 'plot',
'pos': ('bottom', 'Data Plot'),
'size': (800, 300)
}),
('Stats Table', {
'type': 'dataTree',
'pos': ('bottom', 'Canvas'),
'size': (800, 300)
}),
])
host.resize(1100, 800)
self.initializeElements()
self.filterStage = EventFilter()
self.spontRateStage = SpontRateAnalyzer(
plot=self.getElement('Timeline', create=True))
self.statsStage = EventStatisticsAnalyzer(
histogramPlot=self.getElement('Score Histogram', create=True))
self.regions = RegionMarker(self.getElement('Canvas', create=True))
self.stages = [
self.filterStage, self.spontRateStage, self.statsStage,
self.regions
]
params = [
dict(name='Time Ranges',
type='group',
children=[
dict(name='Direct Start',
type='float',
value=0.498,
suffix='s',
step=0.001,
siPrefix=True),
dict(name='Stimulus',
type='float',
value=0.5,
suffix='s',
step=0.001,
siPrefix=True),
dict(name='Post Start',
type='float',
value=0.502,
suffix='s',
step=0.001,
siPrefix=True),
dict(name='Post Stop',
type='float',
value=0.700,
suffix='s',
step=0.001,
siPrefix=True),
]),
]
## each processing stage comes with its own set of parameters
for stage in self.stages:
params.append(stage.parameters())
self.params = ptree.Parameter.create(name='options',
type='group',
children=params)
self.ctrl.setParameters(self.params, showTop=False)
canvas = self.getElement('Canvas', create=True)
#self.scalebar = pg.ScaleBar(100e-6)
#canvas.addGraphicsItem(self.scalebar, name="ScaleBar")
self.scalebar = pg.ScaleBar(size=500e-6)
self.scalebar.setParentItem(canvas.view)
self.scalebar.anchor((1, 1), (1, 1), offset=(-20, -20))
## Note: need to reconnect this!!
#self.params.sigTreeStateChanged.connect(self.invalidate)
self.recalcBtn.clicked.connect(self.recalcClicked)
self.storeBtn.clicked.connect(self.storeToDB)
self.params.param('Time Ranges').sigTreeStateChanged.connect(
self.updateTimes)
self.getElement('Color Mapper',
create=True).sigChanged.connect(self.colorMapChanged)
self.regions.sigRegionChanged.connect(self.processRegions)
def __init__(self, host):
AnalysisModule.__init__(self, host)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ChR2 = ChR2.ChR2() # create instance of the analysis
fcpath = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"flowcharts")
confpath = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"configs")
self.dbIdentity = "ChR2TraceAnalysis" ## how we identify to the database; this determines which tables we own
self._sizeHint = (1024, 800) # try to establish size of window
self.confWidget = Qt.QWidget()
self.confLoader = ConfLoader(self, confpath)
self.fileLoader = DataLoader(self, host.dataManager())
self.addPlotBtn = Qt.QPushButton('Add Plot')
self.processWidget = Qt.QWidget()
self.processLayout = Qt.QGridLayout()
self.processWidget.setLayout(self.processLayout)
self.processProtocolBtn = Qt.QPushButton('Process Protocol')
self.processSliceBtn = Qt.QPushButton('Process Slice')
self.processCellBtn = Qt.QPushButton('Process Cell')
self.processCheck = Qt.QCheckBox('Auto')
self.processLayout.addWidget(self.processSliceBtn, 0, 0)
self.processLayout.addWidget(self.processCellBtn, 1, 0)
self.processLayout.addWidget(self.processProtocolBtn, 2, 0)
self.processLayout.addWidget(self.processCheck, 3, 0)
self.confWidget = Qt.QWidget()
self.confLayout = Qt.QGridLayout()
self.confWidget.setLayout(self.confLayout)
self.confLayout.addWidget(self.confLoader, 0, 0)
self.confLayout.addWidget(self.addPlotBtn, 1, 0)
self.confLayout.addWidget(self.processWidget, 2, 0)
self.plots = []
self.params = None
self.data = None
## setup map DB ctrl
#self.dbCtrl = DBCtrl(self, self.dbIdentity)
self.flowchart = fc.Flowchart(filePath=fcpath)
self.flowchart.addInput('Input')
self.flowchart.addOutput('Output')
#self.flowchart.sigChartLoaded.connect(self.connectPlots)
## 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')
self.flowchart.sigChartLoaded.connect(self.connectPlots)
#elems = self.detector.listElements()
#print elems
# Setup basic GUI
self._elements_ = OrderedDict([
('Configuration', {
'type': 'ctrl',
'object': self.confWidget,
'size': (200, 200)
}),
('File Loader', {
'type': 'ctrl',
'object': self.fileLoader,
'size': (200, 300),
'pos': ('above', 'Configuration')
}),
('Flowchart', {
'type': 'ctrl',
'object': self.flowchart.widget(),
'size': (400, 500),
'pos': ('right', 'Configuration')
}),
('Data Plot', {
'type': 'plot',
'pos': ('bottom', 'Flowchart'),
'size': (400, 300)
}),
('PSP Plot', {
'type': 'plot',
'pos': ('bottom', 'Data Plot'),
'size': (400, 300)
}),
('Scatter Plot1', {
'type': 'plot',
'pos': ('right', ),
'size': (300, 300)
}),
('Scatter Plot2', {
'type': 'plot',
'pos': ('bottom', 'Scatter Plot1'),
'size': (300, 300)
}),
('Scatter Plot3', {
'type': 'plot',
'pos': ('bottom', 'Scatter Plot2'),
'size': (300, 300)
}),
('Results', {
'type': 'table',
'size': (500, 200),
'pos': 'bottom'
}),
])
self.initializeElements()
self.addPlotBtn.clicked.connect(self.addPlotClicked)
self.processSliceBtn.clicked.connect(self.processSliceClicked)
self.processCellBtn.clicked.connect(self.processCellClicked)
self.processProtocolBtn.clicked.connect(self.processProtocolClicked)
self.flowchart.sigOutputChanged.connect(self.outputChanged)
self.fileLoader.sigFileLoaded.connect(self.fileLoaded)
self.fileLoader.sigSelectedFileChanged.connect(self.fileSelected)
def __init__(self, host):
AnalysisModule.__init__(self, host)
if self.dataModel is None:
raise Exception("MapAnalyzer module requires a data model, but none is loaded yet.")
self.currentMap = None
self.analysisValid = False
self.colorsValid = False
self.ctrlLayout = pg.LayoutWidget()
self.ctrl = ptree.ParameterTree(showHeader=False)
self.ctrlLayout.addWidget(self.ctrl, row=0, col=0)
self.recalcBtn = QtGui.QPushButton('Recalculate')
self.ctrlLayout.addWidget(self.recalcBtn, row=1, col=0)
self.storeBtn = pg.FeedbackButton('Store to DB')
self.ctrlLayout.addWidget(self.storeBtn, row=2, col=0)
self.loader = Loader(host=self, dm=host.dataManager())
modPath = os.path.abspath(os.path.dirname(__file__))
self.colorMapper = ColorMapper(filePath=os.path.join(modPath, "colorMaps"))
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (300, 300), 'host': self, 'showFileTree': False}),
('Map Loader', {'type': 'ctrl', 'object': self.loader, 'size': (300, 300), 'pos': ('below', 'File Loader')}),
('Color Mapper', {'type':'ctrl', 'object': self.colorMapper, 'size': (800,200), 'pos': ('right', 'Map Loader')}),
('Canvas', {'type': 'canvas', 'size': (800, 400), 'pos':('right', 'Color Mapper'), 'args': {'name': 'MapAnalyzer'}}),
('Options', {'type': 'ctrl', 'object': self.ctrlLayout, 'size': (300, 500), 'pos': ('bottom', 'Map Loader')}),
('Data Plot', {'type': 'plot', 'pos': ('top', 'Color Mapper'), 'size': (800, 300)}),
('Score Histogram', {'type': 'plot', 'pos': ('bottom', 'Data Plot'), 'size': (800, 300)}),
('Timeline', {'type': 'plot', 'pos': ('bottom', 'Data Plot'), 'size': (800, 300)}),
('Stats Table', {'type': 'dataTree', 'pos': ('bottom', 'Canvas'), 'size': (800,300)}),
])
host.resize(1100, 800)
self.initializeElements()
self.filterStage = EventFilter()
self.spontRateStage = SpontRateAnalyzer(plot=self.getElement('Timeline', create=True))
self.statsStage = EventStatisticsAnalyzer(histogramPlot=self.getElement('Score Histogram', create=True))
self.regions = RegionMarker(self.getElement('Canvas', create=True))
self.stages = [self.filterStage, self.spontRateStage, self.statsStage, self.regions]
params = [
dict(name='Time Ranges', type='group', children=[
dict(name='Direct Start', type='float', value=0.498, suffix='s', step=0.001, siPrefix=True),
dict(name='Stimulus', type='float', value=0.5, suffix='s', step=0.001, siPrefix=True),
dict(name='Post Start', type='float', value=0.502, suffix='s', step=0.001, siPrefix=True),
dict(name='Post Stop', type='float', value=0.700, suffix='s', step=0.001, siPrefix=True),
]),
]
## each processing stage comes with its own set of parameters
for stage in self.stages:
params.append(stage.parameters())
self.params = ptree.Parameter.create(name='options', type='group', children=params)
self.ctrl.setParameters(self.params, showTop=False)
canvas = self.getElement('Canvas', create=True)
#self.scalebar = pg.ScaleBar(100e-6)
#canvas.addGraphicsItem(self.scalebar, name="ScaleBar")
self.scalebar = pg.ScaleBar(size=500e-6)
self.scalebar.setParentItem(canvas.view)
self.scalebar.anchor((1, 1), (1, 1), offset=(-20, -20))
## Note: need to reconnect this!!
#self.params.sigTreeStateChanged.connect(self.invalidate)
self.recalcBtn.clicked.connect(self.recalcClicked)
self.storeBtn.clicked.connect(self.storeToDB)
self.params.param('Time Ranges').sigTreeStateChanged.connect(self.updateTimes)
self.getElement('Color Mapper', create=True).sigChanged.connect(self.colorMapChanged)
self.regions.sigRegionChanged.connect(self.processRegions)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlLayout = pg.LayoutWidget()
self.reloadBtn = QtGui.QPushButton('Reload Data')
self.ctrlLayout.addWidget(self.reloadBtn)
self.ctrl = ptree.ParameterTree(showHeader=False)
self.ctrlLayout.addWidget(self.ctrl, row='next', col=0)
self.filterBtn = QtGui.QPushButton('Filter')
self.ctrlLayout.addWidget(self.filterBtn, row='next', col=0)
self.cellList = QtGui.QListWidget()
self.cellList.setSelectionMode(self.cellList.ExtendedSelection)
self.filterText = QtGui.QTextEdit("selected = data")
self.ctrlLayout.addWidget(self.filterText, row='next', col=0)
self.ctrlLayout.addWidget(self.cellList, row='next', col=0)
## 3D atlas
self.atlas = CN.CNAtlasDisplayWidget()
self.stimPoints = gl.GLScatterPlotItem()
self.atlas.addItem(self.stimPoints)
self.cellPoints = gl.GLScatterPlotItem()
self.atlas.addItem(self.cellPoints)
modPath = os.path.abspath(os.path.dirname(__file__))
self.colorMapper = ColorMapper(filePath=os.path.join(modPath, "colorMaps"))
self._elements_ = OrderedDict([
#('Database Query', {'type':'ctrl', 'object': DatabaseQueryWidget(self.dataManager()), 'size':(300,200), 'pos': 'left'}),
('Options', {'type': 'ctrl', 'object': self.ctrlLayout, 'size': (300, 500), 'pos': 'left'}),
('Atlas', {'type': 'ctrl', 'object': self.atlas, 'size': (600,500), 'pos': 'right'}),
('Color Mapper', {'type': 'ctrl', 'object': self.colorMapper, 'size': (600,200), 'pos': ('bottom', 'Atlas')}),
])
host.resize(1100, 800)
self.initializeElements()
params = [
dict(name='Transform', type='group', children=[
dict(name='Mirror RL', type='bool', value=True),
dict(name='Cell-centered', type='bool', value=False),
]),
dict(name='Display', type='group', children=[
dict(name='Cells', type='bool', value=True),
dict(name='Color by type', type='bool', value=True),
dict(name='Stimulus Sites', type='bool', value=True),
dict(name='Atlas', type='bool', value=False),
dict(name='Grid', type='bool', value=True),
]),
FilterList(name='Filter'),
]
self.params = ptree.Parameter.create(name='options', type='group', children=params)
self.ctrl.setParameters(self.params, showTop=False)
#self.params.sigTreeStateChanged.connect(self.invalidate)
#dbq = self.getElement('Database Query', create=True)
#dbq.sigChanged.connect(self.dbDataChanged)
#db = dbq.currentDatabase()
db = self.dataManager().currentDatabase()
self.tableName = 'map_site_view'
if not db.hasTable(self.tableName):
print "Creating DB views."
db.createView(self.tableName, ['map_sites', 'photostim_maps', 'dirtable_cell', 'cochlearnucleus_protocol', 'cochlearnucleus_cell'])
## view creation SQL:
## select * from map_sites
## inner join photostim_maps on "photostim_maps"."rowid"="map_sites"."map"
## inner join dirtable_cell on "dirtable_cell"."rowid"="photostim_maps"."cell"
## inner join cochlearnucleus_protocol on cochlearnucleus_protocol.protocoldir=map_sites.firstsite
## inner join cochlearnucleus_cell on cochlearnucleus_cell.celldir=dirtable_cell.rowid;
self.reloadData()
self.reloadBtn.clicked.connect(self.reloadData)
self.filterBtn.clicked.connect(self.refilter)
self.cellList.itemSelectionChanged.connect(self.selectCells)
self.colorMapper.sigChanged.connect(self.recolor)
self.params.param('Display').sigTreeStateChanged.connect(self.updateDisplay)
self.params.param('Transform').sigTreeStateChanged.connect(self.transform)
self.transform()
self.refilter()
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.background = None
#self.view = pg.GraphicsView()
self.ctrl = Qt.QWidget()
l = Qt.QGridLayout()
self.ctrl.setLayout(l)
self.ctrl.layout = l
#self.loadBgBtn = Qt.QPushButton('load reference')
#l.addWidget(self.loadBgBtn, 0, 0)
self.addRoiBtn = Qt.QPushButton('add ROI')
l.addWidget(self.addRoiBtn, 0, 0)
s = Qt.QSpinBox()
s.setMaximum(10)
s.setMinimum(1)
self.nsegSpin = s
l.addWidget(s, 1, 0)
self.rois = []
self.data = []
## Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {
'type': 'fileInput',
'size': (200, 300),
'host': self,
'showFileTree': False
}),
('Image', {
'type': 'imageView',
'pos': ('right', 'File Loader'),
'size': (800, 300)
}),
('Time Plot', {
'type': 'plot',
'pos': ('bottom', ),
'size': (800, 300)
}),
('Trial Plot', {
'type': 'plot',
'pos': ('bottom', 'Time Plot'),
'size': (800, 300)
}),
('Line Scan', {
'type': 'imageView',
'pos': ('right', 'Time Plot'),
'size': (800, 300)
}),
#('Data Table', {'type': 'table', 'pos': ('below', 'Time Plot')}),
('Ctrl', {
'type': 'ctrl',
'pos': ('bottom', 'File Loader'),
'size': (200, 30),
'object': self.ctrl
}),
])
self.initializeElements()
#self.traces = None
self.plot = self.getElement('Time Plot', create=True)
self.plot2 = self.getElement('Trial Plot', create=True)
self.lr = pg.LinearRegionItem([0, 1])
self.plot.addItem(self.lr)
self.view = self.getElement('Image', create=True)
## Add a color scale
## removed for now--seems to be causing crashes :(
#self.colorScale = pg.GradientLegend(self.plot1, (20, 150), (-10, -10))
#self.plot1.scene().addItem(self.colorScale)
## Plots are updated when the selected region changes
self.lr.sigRegionChanged.connect(self.updateAnalysis)
self.addRoiBtn.clicked.connect(self.addRoi)
self.view.sigProcessingChanged.connect(self.processData)
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 __init__(self, host):
AnalysisModule.__init__(self, host)
flowchartDir = os.path.join(
os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput('dataIn')
self.flowchart.addOutput('results')
self.flowchart.outputNode._allowAddInput = False ## make sure all data is coming out of output['results']
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
tables = OrderedDict([(self.dbIdentity + '.traces',
'TimecourseAnalyzer_traces')])
self.dbGui = DatabaseGui(dm=host.dataManager(), tables=tables)
self.ctrl = Qt.QWidget()
self.ctrl.setLayout(Qt.QVBoxLayout())
self.analyzeBtn = Qt.QPushButton('Analyze')
self.storeToDBBtn = Qt.QPushButton('Store to DB')
self.ctrl.layout().addWidget(self.analyzeBtn)
self.ctrl.layout().addWidget(self.storeToDBBtn)
self._elements_ = OrderedDict([('Database', {
'type': 'ctrl',
'object': self.dbGui,
'size': (100, 100)
}),
('Analysis Options', {
'type': 'ctrl',
'object': self.flowchart.widget(),
'pos': ('above', 'Database'),
'size': (100, 400)
}),
('File Loader', {
'type': 'fileInput',
'size': (100, 100),
'pos':
('above', 'Analysis Options'),
'host': self
}),
('Experiment Plot', {
'type': 'plot',
'pos': ('right', 'File Loader'),
'size': (400, 100)
}),
('Traces Plot', {
'type': 'plot',
'pos':
('bottom', 'Experiment Plot'),
'size': (400, 200)
}),
('Results Plot', {
'type': 'plot',
'pos': ('bottom', 'Traces Plot'),
'size': (400, 200)
}),
('Results Table', {
'type': 'table',
'pos': ('bottom', 'Traces Plot'),
'size': (400, 200)
}),
('Store Ctrl', {
'type': 'ctrl',
'object': self.ctrl,
'size': (100, 100),
'pos': ('bottom', 'File Loader')
})])
self.initializeElements()
self.fileLoader = self.getElement('File Loader', create=True)
self.exptPlot = self.getElement('Experiment Plot', create=True)
self.tracesPlot = self.getElement('Traces Plot', create=True)
self.resultsTable = self.getElement('Results Table', create=True)
self.resultsTable.setSortingEnabled(False)
self.resultsPlot = self.getElement('Results Plot', create=True)
self.resultsPlot.getViewBox().setXLink(self.exptPlot.getViewBox(
)) ## link the x-axes of the exptPlot and the resultsPlot
### initialize variables
self.expStart = 0
self.traces = np.array([],
dtype=[('timestamp', float), ('data', object),
('fileHandle', object),
('results', object)])
self.files = []
self.traceSelectRgn = pg.LinearRegionItem()
self.traceSelectRgn.setRegion([0, 60])
self.exptPlot.addItem(self.traceSelectRgn)
self.traceSelectRgn.sigRegionChanged.connect(self.updateTracesPlot)
#self.traceSelectRgn.sigRegionChangeFinished.connect(self.updateAnalysis)
#self.flowchart.sigOutputChanged.connect(self.flowchartOutputChanged)
#self.addRegionParam = pg.parametertree.Parameter.create(name="Add Region", type='action')
#self.paramTree.addParameters(self.addRegionParam)
#self.addRegionParam.sigActivated.connect(self.newRegionRequested)
self.analyzeBtn.clicked.connect(self.analyzeBtnClicked)
self.storeToDBBtn.clicked.connect(self.storeToDBBtnClicked)
self.flowchart.sigChartLoaded.connect(self.connectPlots)
self.fileLoader.sigClearRequested.connect(self.clearFilesRequested)
def __init__(self,
host,
flowchartDir=None,
dbIdentity="EventDetector",
dbCtrl=None):
AnalysisModule.__init__(self, host)
if flowchartDir is None:
flowchartDir = os.path.join(
os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
self.flowchart = Flowchart(filePath=flowchartDir)
self.dbIdentity = dbIdentity ## how we identify to the database; this determines which tables we own
#self.loader = FileLoader.FileLoader(host.dataManager())
#self.setCentralWidget(self.flowchart.widget())
#self.ui.chartDock1.setWidget(self.flowchart.widget())
self.flowchart.addInput("dataIn")
self.flowchart.addOutput('events')
#self.flowchart.addOutput('regions', multi=True)
self.flowchart.sigChartLoaded.connect(self.connectPlots)
if dbCtrl == None:
self.dbCtrl = DBCtrl(self, identity=self.dbIdentity)
self.dbCtrl.storeBtn.clicked.connect(self.storeClicked)
else:
self.dbCtrl = dbCtrl(self, identity=self.dbIdentity)
#self.ctrl = QtGui.QLabel('LABEL')
self.ctrl = self.flowchart.widget()
self._elements_ = OrderedDict([
('File Loader', {
'type': 'fileInput',
'size': (200, 300),
'host': self
}),
('Database', {
'type': 'ctrl',
'object': self.dbCtrl,
'size': (200, 300),
'pos': ('bottom', 'File Loader')
}),
('Data Plot', {
'type': 'plot',
'pos': ('right', ),
'size': (800, 300)
}),
('Detection Opts', {
'type': 'ctrl',
'object': self.ctrl,
'pos': ('bottom', 'Database'),
'size': (200, 500)
}),
('Filter Plot', {
'type': 'plot',
'pos': ('bottom', 'Data Plot'),
'size': (800, 300)
}),
('Output Table', {
'type': 'table',
'pos': ('bottom', 'Filter Plot'),
'optional': True,
'size': (800, 200)
}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
self.flowchart.sigOutputChanged.connect(self.outputChanged)
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlLayout = pg.LayoutWidget()
self.reloadBtn = Qt.QPushButton('Reload Data')
self.ctrlLayout.addWidget(self.reloadBtn)
self.ctrl = ptree.ParameterTree(showHeader=False)
self.ctrlLayout.addWidget(self.ctrl, row='next', col=0)
self.filterBtn = Qt.QPushButton('Filter')
self.ctrlLayout.addWidget(self.filterBtn, row='next', col=0)
self.cellList = Qt.QListWidget()
self.cellList.setSelectionMode(self.cellList.ExtendedSelection)
self.filterText = Qt.QTextEdit("selected = data")
self.ctrlLayout.addWidget(self.filterText, row='next', col=0)
self.ctrlLayout.addWidget(self.cellList, row='next', col=0)
## 3D atlas
self.atlas = CN.CNAtlasDisplayWidget()
self.stimPoints = gl.GLScatterPlotItem()
self.atlas.addItem(self.stimPoints)
self.cellPoints = gl.GLScatterPlotItem()
self.atlas.addItem(self.cellPoints)
modPath = os.path.abspath(os.path.dirname(__file__))
self.colorMapper = ColorMapper(
filePath=os.path.join(modPath, "colorMaps"))
self._elements_ = OrderedDict([
#('Database Query', {'type':'ctrl', 'object': DatabaseQueryWidget(self.dataManager()), 'size':(300,200), 'pos': 'left'}),
('Options', {
'type': 'ctrl',
'object': self.ctrlLayout,
'size': (300, 500),
'pos': 'left'
}),
('Atlas', {
'type': 'ctrl',
'object': self.atlas,
'size': (600, 500),
'pos': 'right'
}),
('Color Mapper', {
'type': 'ctrl',
'object': self.colorMapper,
'size': (600, 200),
'pos': ('bottom', 'Atlas')
}),
])
host.resize(1100, 800)
self.initializeElements()
params = [
dict(name='Transform',
type='group',
children=[
dict(name='Mirror RL', type='bool', value=True),
dict(name='Cell-centered', type='bool', value=False),
]),
dict(name='Display',
type='group',
children=[
dict(name='Cells', type='bool', value=True),
dict(name='Color by type', type='bool', value=True),
dict(name='Stimulus Sites', type='bool', value=True),
dict(name='Atlas', type='bool', value=False),
dict(name='Grid', type='bool', value=True),
]),
FilterList(name='Filter'),
]
self.params = ptree.Parameter.create(name='options',
type='group',
children=params)
self.ctrl.setParameters(self.params, showTop=False)
#self.params.sigTreeStateChanged.connect(self.invalidate)
#dbq = self.getElement('Database Query', create=True)
#dbq.sigChanged.connect(self.dbDataChanged)
#db = dbq.currentDatabase()
db = self.dataManager().currentDatabase()
self.tableName = 'map_site_view'
if not db.hasTable(self.tableName):
print("Creating DB views.")
db.createView(self.tableName, [
'map_sites', 'photostim_maps', 'dirtable_cell',
'cochlearnucleus_protocol', 'cochlearnucleus_cell'
])
## view creation SQL:
## select * from map_sites
## inner join photostim_maps on "photostim_maps"."rowid"="map_sites"."map"
## inner join dirtable_cell on "dirtable_cell"."rowid"="photostim_maps"."cell"
## inner join cochlearnucleus_protocol on cochlearnucleus_protocol.protocoldir=map_sites.firstsite
## inner join cochlearnucleus_cell on cochlearnucleus_cell.celldir=dirtable_cell.rowid;
self.reloadData()
self.reloadBtn.clicked.connect(self.reloadData)
self.filterBtn.clicked.connect(self.refilter)
self.cellList.itemSelectionChanged.connect(self.selectCells)
self.colorMapper.sigChanged.connect(self.recolor)
self.params.param('Display').sigTreeStateChanged.connect(
self.updateDisplay)
self.params.param('Transform').sigTreeStateChanged.connect(
self.transform)
self.transform()
self.refilter()
def __init__(self, host):
AnalysisModule.__init__(self, host=host)
self.items = weakref.WeakKeyDictionary()
self.files = weakref.WeakValueDictionary()
self.ctrl = QtGui.QWidget()
self.ui = Ui_Form()
self.ui.setupUi(self.ctrl)
self.atlas = None
self.canvas = Canvas(name='MosaicEditor')
self._elements_ = OrderedDict([
('File Loader', {
'type': 'fileInput',
'size': (200, 300),
'host': self
}),
('Mosaic', {
'type': 'ctrl',
'object': self.ctrl,
'pos': ('right', ),
'size': (600, 100)
}),
('Canvas', {
'type': 'ctrl',
'object': self.canvas.ui.view,
'pos': ('bottom', 'Mosaic'),
'size': (600, 800)
}),
('ItemList', {
'type': 'ctrl',
'object': self.canvas.ui.canvasCtrlWidget,
'pos': ('right', 'Canvas'),
'size': (200, 400)
}),
('ItemCtrl', {
'type': 'ctrl',
'object': self.canvas.ui.canvasItemCtrl,
'pos': ('bottom', 'ItemList'),
'size': (200, 400)
}),
])
for name, spec in self._extensions.items():
builder = spec.pop('builder', None)
if builder is not None:
spec['object'] = builder(self)
self._elements_[name] = spec
self.initializeElements()
self.clear(ask=False)
self.ui.fileLoader = self.getElement('File Loader', create=True)
self.ui.fileLoader.ui.fileTree.hide()
try:
self.ui.fileLoader.setBaseClicked(
) # get the currently selected directory in the DataManager
except:
pass
for a in atlas.listAtlases():
self.ui.atlasCombo.addItem(a)
# Add buttons to the canvas control panel
self.btnBox = QtGui.QWidget()
self.btnLayout = QtGui.QGridLayout()
self.btnLayout.setContentsMargins(0, 0, 0, 0)
self.btnBox.setLayout(self.btnLayout)
l = self.canvas.ui.gridLayout
l.addWidget(self.btnBox, l.rowCount(), 0, 1, l.columnCount())
self.addCombo = QtGui.QComboBox()
self.addCombo.currentIndexChanged.connect(self._addItemChanged)
self.btnLayout.addWidget(self.addCombo, 0, 0, 1, 2)
self.addCombo.addItem('Add item..')
self.saveBtn = QtGui.QPushButton("Save ...")
self.saveBtn.clicked.connect(self.saveClicked)
self.btnLayout.addWidget(self.saveBtn, 1, 0)
self.clearBtn = QtGui.QPushButton("Clear All")
self.clearBtn.clicked.connect(lambda: self.clear(ask=True))
self.btnLayout.addWidget(self.clearBtn, 1, 1)
self.canvas.sigItemTransformChangeFinished.connect(self.itemMoved)
self.ui.atlasCombo.currentIndexChanged.connect(self.atlasComboChanged)
self.ui.normalizeBtn.clicked.connect(self.normalizeImages)
self.ui.tileShadingBtn.clicked.connect(self.rescaleImages)
self.ui.mosaicApplyScaleBtn.clicked.connect(self.updateScaling)
self.ui.mosaicFlipLRBtn.clicked.connect(self.flipLR)
self.ui.mosaicFlipUDBtn.clicked.connect(self.flipUD)
self.imageMax = 0.0
for menuString in self._addTypes:
self.addCombo.addItem(menuString)
def __init__(self, host, flowchartDir=None):
AnalysisModule.__init__(self, host)
self.dbIdentity = "IVCurveAnalyzer" ## how we identify to the database; this determines which tables we own
if flowchartDir is None:
flowchartDir = os.path.join(
os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput("dataIn")
#self.flowchart.addOutput('events')
self.flowchart.addOutput('regions', multi=True)
#self.flowchart.sigChartLoaded.connect(self.connectPlots)
### DBCtrl class is from EventDetector -- need to make my own here
#self.dbCtrl = DBCtrl(self, identity=self.dbIdentity)
#self.dbCtrl.storeBtn.clicked.connect(self.storeClicked)
self.ctrl = self.flowchart.widget()
self._elements_ = OrderedDict([
('File Loader', {
'type': 'fileInput',
'size': (200, 300),
'host': self
}),
#('Database', {'type': 'ctrl', 'object': self.dbCtrl, 'size': (200,300), 'pos': ('bottom', 'File Loader')}),
('Data Plot', {
'type': 'plot',
'pos': ('right', ),
'size': (800, 300)
}),
('Detection Opts', {
'type': 'ctrl',
'object': self.ctrl,
'pos': ('bottom', 'File Loader'),
'size': (200, 500)
}),
('IV Plot', {
'type': 'plot',
'pos': ('bottom', 'Data Plot'),
'size': (400, 300)
}),
('Output Table', {
'type': 'table',
'pos': ('bottom', 'IV Plot'),
'optional': True,
'size': (800, 200)
}),
('FI Plot', {
'type': 'plot',
'pos': ('right', 'IV Plot'),
'size': (400, 300)
}),
])
self.initializeElements()
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
