def __init__(self, parent, size=(800,-1), **kwargs):
wx.Frame.__init__(self, parent, -1, size=size, title='Plate Viewer', **kwargs)
CPATool.__init__(self)
self.SetName(self.tool_name)
self.SetBackgroundColour("white") # Fixing the color
# Check for required properties fields.
fail = False
for field in required_fields:
if not p.field_defined(field):
fail = True
raise Exception('Properties field "%s" is required for PlateViewer.'%(field))
if fail:
self.Destroy()
return
self.chMap = p.image_channel_colors[:]
self.menuBar = wx.MenuBar()
self.SetMenuBar(self.menuBar)
self.fileMenu = wx.Menu()
self.exitMenuItem = self.fileMenu.Append(id=wx.ID_EXIT, text='Exit\tCtrl+Q', help='Close Plate Viewer')
self.GetMenuBar().Append(self.fileMenu, 'File')
self.menuBar.Append(cpa.helpmenu.make_help_menu(self), 'Help')
save_csv_menu_item = self.fileMenu.Append(-1, 'Save table to CSV\tCtrl+S')
self.Bind(wx.EVT_MENU, self.on_save_csv, save_csv_menu_item)
wx.EVT_MENU(self, wx.ID_EXIT, lambda _:self.Close())
dataSourceSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='Source:'), wx.VERTICAL)
dataSourceSizer.Add(wx.StaticText(self, label='Data source:'))
self.sourceChoice = TableComboBox(self, -1, size=fixed_width)
dataSourceSizer.Add(self.sourceChoice)
dataSourceSizer.AddSpacer((-1,3))
dataSourceSizer.Add(wx.StaticText(self, label='Measurement:'))
measurements = get_non_blob_types_from_table(p.image_table)
self.measurementsChoice = ComboBox(self, choices=measurements, size=fixed_width)
self.measurementsChoice.Select(0)
dataSourceSizer.Add(self.measurementsChoice)
dataSourceSizer.Add(wx.StaticText(self, label='Filter:'))
self.filterChoice = FilterComboBox(self, size=fixed_width)
dataSourceSizer.Add(self.filterChoice)
groupingSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='Data aggregation:'), wx.VERTICAL)
groupingSizer.Add(wx.StaticText(self, label='Aggregation method:'))
aggregation = ['mean', 'sum', 'median', 'stdev', 'cv%', 'min', 'max']
self.aggregationMethodsChoice = ComboBox(self, choices=aggregation, size=fixed_width)
self.aggregationMethodsChoice.Select(0)
groupingSizer.Add(self.aggregationMethodsChoice)
viewSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='View options:'), wx.VERTICAL)
viewSizer.Add(wx.StaticText(self, label='Color map:'))
maps = [m for m in matplotlib.cm.datad.keys() if not m.endswith("_r")]
maps.sort()
self.colorMapsChoice = ComboBox(self, choices=maps, size=fixed_width)
self.colorMapsChoice.SetSelection(maps.index('jet'))
viewSizer.Add(self.colorMapsChoice)
viewSizer.AddSpacer((-1,3))
viewSizer.Add(wx.StaticText(self, label='Well display:'))
if p.image_thumbnail_cols:
choices = pmp.all_well_shapes
else:
choices = list(pmp.all_well_shapes)
choices.remove(pmp.THUMBNAIL)
self.wellDisplayChoice = ComboBox(self, choices=choices, size=fixed_width)
self.wellDisplayChoice.Select(0)
viewSizer.Add(self.wellDisplayChoice)
viewSizer.AddSpacer((-1,3))
viewSizer.Add(wx.StaticText(self, label='Number of plates:'))
self.numberOfPlatesTE = wx.TextCtrl(self, -1, '1', style=wx.TE_PROCESS_ENTER)
viewSizer.Add(self.numberOfPlatesTE)
if not p.plate_id:
self.numberOfPlatesTE.Disable()
annotationSizer = wx.StaticBoxSizer(wx.StaticBox(self, label='Annotation:'), wx.VERTICAL)
annotationSizer.Add(wx.StaticText(self, label='Annotation column:'))
annotationColSizer = wx.BoxSizer(wx.HORIZONTAL)
self.annotation_cols = dict([(col, db.GetColumnType(p.image_table, col))
for col in db.GetUserColumnNames(p.image_table)])
self.annotationCol = ComboBox(self, choices=self.annotation_cols.keys(), size=(120,-1))
if len(self.annotation_cols) > 0:
self.annotationCol.SetSelection(0)
annotationColSizer.Add(self.annotationCol, flag=wx.ALIGN_CENTER_VERTICAL)
annotationColSizer.AddSpacer((3,-1))
self.addAnnotationColBtn = wx.Button(self, -1, 'Add', size=(44,-1))
annotationColSizer.Add(self.addAnnotationColBtn, flag=wx.ALIGN_CENTER_VERTICAL)
annotationSizer.Add(annotationColSizer)
annotationSizer.AddSpacer((-1,3))
annotationSizer.Add(wx.StaticText(self, label='Label:'))
self.annotationLabel = wx.TextCtrl(self, -1, 'Select wells')#, style=wx.TE_PROCESS_ENTER)
self.annotationLabel.Disable()
self.annotationLabel.SetForegroundColour(wx.Colour(80,80,80))
self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY)
annotationSizer.Add(self.annotationLabel)
annotationSizer.AddSpacer((-1,3))
self.outlineMarked = wx.CheckBox(self, -1, label='Outline annotated wells')
annotationSizer.Add(self.outlineMarked)
annotationSizer.AddSpacer((-1,3))
self.annotationShowVals = wx.CheckBox(self, -1, label='Show values on plate')
annotationSizer.Add(self.annotationShowVals)
if len(db.GetUserColumnNames(p.image_table)) == 0:
self.outlineMarked.Disable()
self.annotationShowVals.Disable()
controlSizer = wx.BoxSizer(wx.VERTICAL)
controlSizer.Add(dataSourceSizer, 0, wx.EXPAND)
controlSizer.AddSpacer((-1,3))
controlSizer.Add(groupingSizer, 0, wx.EXPAND)
controlSizer.AddSpacer((-1,3))
controlSizer.Add(viewSizer, 0, wx.EXPAND)
controlSizer.AddSpacer((-1,3))
controlSizer.Add(annotationSizer, 0 , wx.EXPAND)
self.plateMapSizer = wx.GridSizer(1,1,5,5)
self.plateMaps = []
self.plateMapChoices = []
self.rightSizer = wx.BoxSizer(wx.VERTICAL)
self.rightSizer.Add(self.plateMapSizer, 1, wx.EXPAND|wx.BOTTOM, 10)
self.colorBar = ColorBarPanel(self, 'jet', size=(-1,25))
self.rightSizer.Add(self.colorBar, 0, wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL)
mainSizer = wx.BoxSizer(wx.HORIZONTAL)
mainSizer.Add(controlSizer, 0, wx.LEFT|wx.TOP|wx.BOTTOM, 10)
mainSizer.Add(self.rightSizer, 1, wx.EXPAND|wx.ALL, 10)
self.SetSizer(mainSizer)
self.SetClientSize((self.Size[0],self.Sizer.CalcMin()[1]))
self.sourceChoice.Bind(wx.EVT_COMBOBOX, self.UpdateMeasurementChoice)
self.measurementsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectMeasurement)
self.measurementsChoice.Select(0)
self.aggregationMethodsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectAggregationMethod)
self.colorMapsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectColorMap)
self.numberOfPlatesTE.Bind(wx.EVT_TEXT_ENTER, self.OnEnterNumberOfPlates)
self.wellDisplayChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectWellDisplay)
self.annotationCol.Bind(wx.EVT_COMBOBOX, self.OnSelectAnnotationCol)
self.addAnnotationColBtn.Bind(wx.EVT_BUTTON, self.OnAddAnnotationCol)
self.annotationLabel.Bind(wx.EVT_KEY_UP, self.OnEnterAnnotation)
self.outlineMarked.Bind(wx.EVT_CHECKBOX, self.OnOutlineMarked)
self.annotationShowVals.Bind(wx.EVT_CHECKBOX, self.OnShowAnnotationValues)
self.filterChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectFilter)
self.AddPlateMap()
self.OnSelectMeasurement()
