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 = 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, manager, name, config):
Module.__init__(self, manager, name, config)
self.recordDir = None
self.recordWritable = False
self.running = False
self.win = Qt.QSplitter()
self.ctrlWidget = pg.LayoutWidget()
self.win.addWidget(self.ctrlWidget)
self.newBtn = Qt.QPushButton('New Record')
self.loadBtn = Qt.QPushButton('Load Record')
self.startBtn = Qt.QPushButton('Start')
self.startBtn.setCheckable(True)
self.fileLabel = Qt.QLabel()
self.ctrlWidget.addWidget(self.newBtn, 0, 0)
self.ctrlWidget.addWidget(self.loadBtn, 1, 0)
self.ctrlWidget.addWidget(self.startBtn, 2, 0)
self.ctrlWidget.addWidget(self.fileLabel, 3, 0)
self.newBtn.clicked.connect(self.newRecord)
self.loadBtn.clicked.connect(self.loadClicked)
self.startBtn.toggled.connect(self.startToggled)
self.params = pg.parametertree.Parameter.create(
name='params',
type='group',
children=[
dict(name='interval',
type='float',
value=10,
suffix='s',
siPrefix=True,
limits=[0.001, None],
step=1.0),
dict(name='trace duration',
type='float',
value=1.0,
suffix='s',
siPrefix=True,
limits=[0.001, None],
step=0.1),
dict(name='sample rate',
type='int',
value=1e6,
suffix='Hz',
siPrefix=True,
limits=[100, None],
step=1e5),
])
self.ptree = pg.parametertree.ParameterTree()
self.ptree.setParameters(self.params)
self.ctrlWidget.addWidget(self.ptree, 4, 0)
self.channelLayout = Qt.QSplitter()
self.win.addWidget(self.channelLayout)
self.channels = collections.OrderedDict()
self.win.show()
self.timer = Qt.QTimer()
self.timer.timeout.connect(self.runOnce)
#db.update('Cell', {'type': typ}, rowid=i[0])
#print d, typ
global eventView, siteView, cells
eventView = 'events_view'
siteView = 'sites_view'
firstRun = False
if 'events' not in locals():
global events
events = {}
firstRun = True
win = Qt.QMainWindow()
#cw = Qt.QWidget()
layout = pg.LayoutWidget()
#layout = Qt.QGridLayout()
#layout.setContentsMargins(0,0,0,0)
#layout.setSpacing(0)
#cw.setLayout(layout)
win.setCentralWidget(layout)
cellCombo = Qt.QComboBox()
cellCombo.setSizeAdjustPolicy(cellCombo.AdjustToContents)
layout.addWidget(cellCombo)
reloadBtn = Qt.QPushButton('reload')
layout.addWidget(reloadBtn)
separateCheck = Qt.QCheckBox("color pre/post")
layout.addWidget(separateCheck)