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()
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(wx.NullColor)
# 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")
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, style=wx.CB_READONLY)
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, style=wx.CB_READONLY)
self.measurementsChoice.Select(0)
dataSourceSizer.Add(self.measurementsChoice)
dataSourceSizer.Add(wx.StaticText(self, label="Filter:"))
self.filterChoice = FilterComboBox(self)
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, style=wx.CB_READONLY)
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, style=wx.CB_READONLY)
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, style=wx.CB_READONLY)
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), style=wx.CB_READONLY)
if len(self.annotation_cols) > 0:
self.annotationCol.SetSelection(0)
annotationColSizer.Add(self.annotationCol)
annotationColSizer.AddSpacer((3, -1))
self.addAnnotationColBtn = wx.Button(self, -1, "Add", size=(44, -1))
annotationColSizer.Add(self.addAnnotationColBtn, 0, wx.TOP, 3)
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.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.OnShowAnotationValues)
self.filterChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectFilter)
self.AddPlateMap()
self.OnSelectMeasurement()
class PlateViewer(wx.Frame, CPATool):
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()
def AddPlateMap(self, plateIndex=0):
'''
Adds a new blank plateMap to the PlateMapSizer.
'''
data = np.ones(p.plate_shape)
# Try to get explicit labels for all wells.
res = db.execute('SELECT DISTINCT %s FROM %s WHERE %s != "" and %s IS NOT NULL'%
(dbconnect.UniqueWellClause(), p.image_table, p.well_id, p.well_id))
if p.plate_id:
self.plateMapChoices += [ComboBox(self, choices=db.GetPlateNames(), size=(400,-1))]
self.plateMapChoices[-1].Select(plateIndex)
self.plateMapChoices[-1].Bind(wx.EVT_COMBOBOX, self.OnSelectPlate)
#plate_col_type = db.GetColumnType(p.image_table, p.plate_id)
#plate_id = plate_col_type(self.plateMapChoices[-1].GetString(plateIndex))
plateMapChoiceSizer = wx.BoxSizer(wx.HORIZONTAL)
plateMapChoiceSizer.Add(wx.StaticText(self, label='Plate:'), flag=wx.ALIGN_CENTER_VERTICAL)
plateMapChoiceSizer.Add(self.plateMapChoices[-1], flag=wx.ALIGN_CENTER_VERTICAL)
well_keys = res
platemap = pmp.PlateMapPanel(self, data, well_keys, p.plate_shape,
colormap = self.colorMapsChoice.Value,
well_disp = self.wellDisplayChoice.Value)
platemap.add_well_selection_handler(self.OnSelectWell)
self.plateMaps += [platemap]
singlePlateMapSizer = wx.BoxSizer(wx.VERTICAL)
if p.plate_id:
singlePlateMapSizer.Add(plateMapChoiceSizer, 0, wx.ALIGN_CENTER)
singlePlateMapSizer.Add(platemap, 1, wx.EXPAND|wx.ALIGN_CENTER)
self.plateMapSizer.Add(singlePlateMapSizer, 1, wx.EXPAND|wx.ALIGN_CENTER)
def UpdatePlateMaps(self):
self.measurement = self.measurementsChoice.Value
measurement = self.measurement
table = self.sourceChoice.Value
self.aggMethod = self.aggregationMethodsChoice.Value
categorical = measurement not in get_numeric_columns_from_table(table)
fltr = self.filterChoice.Value
self.colorBar.ClearNotifyWindows()
q = sql.QueryBuilder()
well_key_cols = [sql.Column(p.image_table, col) for col in well_key_columns()]
select = list(well_key_cols)
if not categorical:
if self.aggMethod=='mean':
select += [sql.Column(table, measurement, 'AVG')]
elif self.aggMethod=='stdev':
select += [sql.Column(table, measurement, 'STDDEV')]
elif self.aggMethod=='cv%':
# stddev(col) / avg(col) * 100
select += [sql.Expression(
sql.Column(table, measurement, 'STDDEV'), ' / ',
sql.Column(table, measurement, 'AVG'), ' * 100')]
elif self.aggMethod=='sum':
select += [sql.Column(table, measurement, 'SUM')]
elif self.aggMethod=='min':
select += [sql.Column(table, measurement, 'MIN')]
elif self.aggMethod=='max':
select += [sql.Column(table, measurement, 'MAX')]
elif self.aggMethod=='median':
select += [sql.Column(table, measurement, 'MEDIAN')]
elif self.aggMethod=='none':
select += [sql.Column(table, measurement)]
else:
select += [sql.Column(table, measurement)]
q.set_select_clause(select)
q.set_group_columns(well_key_cols)
if fltr not in (FilterComboBox.NO_FILTER, FilterComboBox.NEW_FILTER, ''):
if fltr in p._filters:
q.add_filter(p._filters[fltr])
elif fltr in p.gates:
q.add_filter(p.gates[fltr].as_filter())
else:
raise Exception('Could not find filter "%s" in gates or filters'%(fltr))
wellkeys_and_values = db.execute(str(q))
wellkeys_and_values = np.array(wellkeys_and_values, dtype=object)
# Replace measurement None's with nan
for row in wellkeys_and_values:
if row[-1] is None:
row[-1] = np.nan
data = []
key_lists = []
dmax = -np.inf
dmin = np.inf
if p.plate_id:
for plateChoice, plateMap in zip(self.plateMapChoices, self.plateMaps):
plate = plateChoice.Value
plateMap.SetPlate(plate)
self.colorBar.AddNotifyWindow(plateMap)
self.keys_and_vals = [v for v in wellkeys_and_values if str(v[0])==plate]
platedata, wellkeys, ignore = FormatPlateMapData(self.keys_and_vals, categorical)
data += [platedata]
key_lists += [wellkeys]
if not categorical:
dmin = np.nanmin([float(kv[-1]) for kv in self.keys_and_vals]+[dmin])
dmax = np.nanmax([float(kv[-1]) for kv in self.keys_and_vals]+[dmax])
else:
self.colorBar.AddNotifyWindow(self.plateMaps[0])
platedata, wellkeys, ignore = FormatPlateMapData(wellkeys_and_values, categorical)
data += [platedata]
key_lists += [wellkeys]
if not categorical:
dmin = np.nanmin([float(kv[-1]) for kv in wellkeys_and_values])
dmax = np.nanmax([float(kv[-1]) for kv in wellkeys_and_values])
if not categorical:
if len(wellkeys_and_values) > 0:
# Compute the global extents if there is any data whatsoever
gmin = np.nanmin([float(vals[-1]) for vals in wellkeys_and_values])
gmax = np.nanmax([float(vals[-1]) for vals in wellkeys_and_values])
if np.isinf(dmin) or np.isinf(dmax):
gmin = gmax = dmin = dmax = 1.
# Warn if there was no data for this plate (and no filter was used)
if fltr == FilterComboBox.NO_FILTER:
wx.MessageBox('No numeric data was found in "%s.%s" for plate "%s"'
%(table, measurement, plate), 'Warning')
else:
gmin = gmax = 1.
if fltr == FilterComboBox.NO_FILTER:
wx.MessageBox('No numeric data was found in %s.%s'
%(table, measurement), 'Warning')
if categorical:
self.colorBar.Hide()
else:
self.colorBar.Show()
self.colorBar.SetLocalExtents([dmin,dmax])
self.colorBar.SetGlobalExtents([gmin,gmax])
self.rightSizer.Layout()
for keys, d, plateMap in zip(key_lists, data, self.plateMaps):
plateMap.SetWellKeys(keys)
if categorical:
plateMap.SetData(np.ones(d.shape) * np.nan)
plateMap.SetTextData(d)
else:
plateMap.SetData(d, data_range=self.colorBar.GetLocalExtents(),
clip_interval=self.colorBar.GetLocalInterval(),
clip_mode=self.colorBar.GetClipMode())
for keys, d, plateMap in zip(key_lists, data, self.plateMaps):
plateMap.SetWellKeys(keys)
if categorical:
plateMap.SetData(np.ones(d.shape) * np.nan)
plateMap.SetTextData(d)
else:
plateMap.SetData(d, data_range=self.colorBar.GetLocalExtents(),
clip_interval=self.colorBar.GetLocalInterval(),
clip_mode=self.colorBar.GetClipMode())
def UpdateMeasurementChoice(self, evt=None):
'''
Handles the selection of a source table (per-image or per-object) from
a choice box. The measurement choice box is populated with the names
of numeric columns from the selected table.
'''
table = self.sourceChoice.Value
if table == TableComboBox.OTHER_TABLE:
t = get_other_table_from_user(self)
if t is not None:
self.sourceChoice.Items = self.sourceChoice.Items[:-1] + [t] + self.sourceChoice.Items[-1:]
self.sourceChoice.Select(self.sourceChoice.Items.index(t))
table = t
else:
self.sourceChoice.Select(0)
return
self.measurementsChoice.SetItems(get_non_blob_types_from_table(table))
self.measurementsChoice.Select(0)
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def on_save_csv(self, evt):
defaultFileName = 'my_plate_table.csv'
saveDialog = wx.FileDialog(self, message="Save as:",
defaultDir=os.getcwd(),
defaultFile=defaultFileName,
wildcard='csv|*',
style=(wx.SAVE | wx.FD_OVERWRITE_PROMPT |
wx.FD_CHANGE_DIR))
if saveDialog.ShowModal() == wx.ID_OK:
filename = saveDialog.GetPath()
self.save_to_csv(filename)
self.Title = filename
saveDialog.Destroy()
def save_to_csv(self, filename):
with open(filename, 'wb') as f:
w = csv.writer(f)
w.writerow(['Plate', 'Well', self.measurement + ' ' + self.aggMethod])
w.writerows(self.keys_and_vals)
logging.info('Table saved to %s'%filename)
def OnSelectPlate(self, evt):
''' Handles the selection of a plate from the plate choice box. '''
self.UpdatePlateMaps()
def OnSelectMeasurement(self, evt=None):
''' Handles the selection of a measurement to plot from a choice box. '''
selected_measurement = self.measurementsChoice.Value
table = self.sourceChoice.Value
numeric_measurements = get_numeric_columns_from_table(table)
if (selected_measurement in numeric_measurements):
self.aggregationMethodsChoice.Enable()
self.colorMapsChoice.Enable()
else:
self.aggregationMethodsChoice.Disable()
self.colorMapsChoice.Disable()
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectAggregationMethod(self, evt=None):
''' Handles the selection of an aggregation method from the choice box. '''
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectColorMap(self, evt=None):
''' Handles the selection of a color map from a choice box. '''
map = self.colorMapsChoice.Value
cm = matplotlib.cm.get_cmap(map)
self.colorBar.SetMap(map)
for plateMap in self.plateMaps:
plateMap.SetColorMap(map)
def OnSelectWellDisplay(self, evt=None):
''' Handles the selection of a well display choice from a choice box. '''
sel = self.wellDisplayChoice.Value
if sel.lower() == 'image':
dlg = wx.MessageDialog(self,
'This mode will render each well as a shrunken image loaded '
'from that well. This feature is currently VERY SLOW since it '
'requires loading hundreds of full sized images. Are you sure '
'you want to continue?',
'Load all images?', wx.OK|wx.CANCEL|wx.ICON_QUESTION)
if dlg.ShowModal() != wx.ID_OK:
self.wellDisplayChoice.SetSelection(0)
return
if sel.lower() in ['image', 'thumbnail']:
self.colorBar.Hide()
else:
self.colorBar.Show()
for platemap in self.plateMaps:
platemap.SetWellDisplay(sel)
def OnEnterNumberOfPlates(self, evt=None):
''' Handles the entry of a plates to view from a choice box. '''
try:
nPlates = int(self.numberOfPlatesTE.GetValue())
except:
logging.warn('Invalid # of plates! Please enter a number between 1 and 100')
return
if nPlates>100:
logging.warn('Too many plates! Please enter a number between 1 and 100')
return
if nPlates<1:
logging.warn('You must display at least 1 plate.')
self.numberOfPlatesTE.SetValue('1')
nPlates = 1
# Record the indices of the plates currently selected.
# Pad the list with sequential plate indices then crop to the new number of plates.
currentPlates = [plateChoice.GetSelection() for plateChoice in self.plateMapChoices]
currentPlates = (currentPlates+[(currentPlates[-1]+1+p) % len(db.GetPlateNames()) for p in range(nPlates)])[:nPlates]
# Remove all plateMaps
self.plateMapSizer.Clear(deleteWindows=True)
self.plateMaps = []
self.plateMapChoices = []
# Restructure the plateMapSizer appropriately
rows = cols = np.ceil(np.sqrt(nPlates))
self.plateMapSizer.SetRows(rows)
self.plateMapSizer.SetCols(cols)
# Add the plate maps
for plateIndex in currentPlates:
self.AddPlateMap(plateIndex)
self.UpdatePlateMaps()
self.plateMapSizer.Layout()
# Update outlines
self.OnOutlineMarked()
def OnSelectWell(self):
'''When wells are selected: display their annotation in the annotation
label control. If multiple annotations are found then make sure the
user knows.
'''
wellkeys = []
for pm in self.plateMaps:
wellkeys += pm.get_selected_well_keys()
if len(wellkeys) > 0 and self.annotationCol.Value != '':
self.annotationLabel.Enable()
self.annotationLabel.SetForegroundColour(wx.BLACK)
self.annotationLabel.SetBackgroundColour(wx.WHITE)
annotations = db.execute('SELECT %s FROM %s WHERE %s'%(
self.annotationCol.Value,
p.image_table,
GetWhereClauseForWells(wellkeys)))
annotations = list(set([a[0] for a in annotations]))
if len(annotations) == 1:
if annotations[0] == None:
self.annotationLabel.SetValue('')
else:
self.annotationLabel.SetValue(str(annotations[0]))
else:
self.annotationLabel.SetValue(','.join([str(a) for a in annotations if a is not None]))
else:
self.annotationLabel.Disable()
self.annotationLabel.SetForegroundColour(wx.Colour(80,80,80))
self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY)
self.annotationLabel.SetValue('Select wells')
def OnAddAnnotationCol(self, evt):
'''Add a new user annotation column to the database.
'''
dlg = wx.TextEntryDialog(self, 'New annotation column name: User_','Add Annotation Column')
if dlg.ShowModal() != wx.ID_OK:
return
new_column = 'User_'+dlg.GetValue()
# user-type ==> (sql-type, python-type)
coltypes = {'Text' : ('VARCHAR(255)', str),
'Number' : ('FLOAT', float)}
dlg = wx.SingleChoiceDialog(self,
'What type of annotation column would you like to add?\nThis can not be changed.',
'Add Annotation Column', coltypes.keys(), wx.CHOICEDLG_STYLE)
if dlg.ShowModal() != wx.ID_OK:
return
usertype = dlg.GetStringSelection()
db.AppendColumn(p.image_table, new_column, coltypes[usertype][0])
self.annotation_cols[new_column] = coltypes[usertype][1]
self.annotationCol.Items += [new_column]
self.annotationCol.SetSelection(len(self.annotation_cols) - 1)
current_selection = self.measurementsChoice.Selection
self.measurementsChoice.SetItems(self.measurementsChoice.Strings + [new_column])
if self.annotationShowVals.IsChecked():
column = self.annotationCol.Value
self.sourceChoice.SetStringSelection(p.image_table)
self.measurementsChoice.SetStringSelection(column)
self.UpdatePlateMaps()
else:
self.measurementsChoice.SetSelection(current_selection[0])
self.annotationShowVals.Enable()
self.outlineMarked.Enable()
self.OnSelectWell()
def OnSelectAnnotationCol(self, evt=None):
'''Handles selection of an annotation column.
'''
col = self.annotationCol.Value
if col == '':
return
coltype = self.annotation_cols[col]
self.OnSelectWell()
self.OnOutlineMarked()
if self.annotationShowVals.IsChecked():
if coltype != str:
self.colorMapsChoice.Enable()
else:
self.colorMapsChoice.Disable()
self.measurementsChoice.SetStringSelection(col)
self.UpdatePlateMaps()
def OnEnterAnnotation(self, evt=None):
'''Store the annotation value in the annotation column of the db.
'''
if evt.KeyCode < 32 or evt.KeyCode > 127:
return
column = self.annotationCol.Value
value = self.annotationLabel.Value
wellkeys = []
for pm in self.plateMaps:
wellkeys += pm.get_selected_well_keys()
if value == '':
value = None
elif self.annotation_cols[column] == float:
try:
value = float(value)
self.annotationLabel.SetForegroundColour(wx.BLACK)
except:
self.annotationLabel.SetForegroundColour(wx.Color(255,0,0))
return
db.UpdateWells(p.image_table, column, value, wellkeys)
if self.outlineMarked.IsChecked():
for pm in self.plateMaps:
if value is None:
pm.UnOutlineWells(wellkeys)
else:
pm.OutlineWells(wellkeys)
if (self.sourceChoice.Value == p.image_table and
self.measurementsChoice.Value == column):
self.UpdatePlateMaps()
def OnOutlineMarked(self, evt=None):
'''Outlines all non-NULL values of the current annotation
'''
# Disable filters when outlining marked wells
#if self.outlineMarked.IsChecked():
#self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER)
#self.filterChoice.Disable()
#else:
#if not self.annotationShowVals.IsChecked():
#self.filterChoice.Enable()
# Update outlined wells in PlateMapPanels
for pm in self.plateMaps:
if self.outlineMarked.IsChecked():
column = self.annotationCol.Value
if p.plate_id:
res = db.execute('SELECT %s, %s FROM %s WHERE %s="%s"'%(
dbconnect.UniqueWellClause(), column, p.image_table,
p.plate_id, pm.plate))
else:
# if there's no plate_id, we assume there is only 1 plate
# and fetch all the data
res = db.execute('SELECT %s, %s FROM %s'%(
dbconnect.UniqueWellClause(), column, p.image_table))
keys = [tuple(r[:-1]) for r in res if r[-1] is not None]
pm.SetOutlinedWells(keys)
else:
pm.SetOutlinedWells([])
self.UpdatePlateMaps()
def OnShowAnnotationValues(self, evt=None):
'''Handler for the show values checkbox.
'''
if self.annotationShowVals.IsChecked():
column = self.annotationCol.Value
self.sourceChoice.SetStringSelection(p.image_table)
self.measurementsChoice.SetItems(get_non_blob_types_from_table(p.image_table))
self.measurementsChoice.SetStringSelection(column)
self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER)
self.sourceChoice.Disable()
self.measurementsChoice.Disable()
self.filterChoice.Disable()
self.aggregationMethodsChoice.Disable()
self.aggregationMethodsChoice.SetValue('none')
else:
self.sourceChoice.Enable()
self.measurementsChoice.Enable()
if not self.outlineMarked.IsChecked():
self.filterChoice.Enable()
if db.GetColumnType(self.sourceChoice.Value, self.measurementsChoice.Value) != str:
self.aggregationMethodsChoice.Enable()
self.aggregationMethodsChoice.SetSelection(0)
self.UpdatePlateMaps()
def OnSelectFilter(self, evt):
self.filterChoice.on_select(evt)
self.UpdatePlateMaps()
self.colorBar.ResetInterval()
def save_settings(self):
'''save_settings is called when saving a workspace to file.
returns a dictionary mapping setting names to values encoded as strings
'''
settings = {'table' : self.sourceChoice.Value,
'measurement' : self.measurementsChoice.Value,
'aggregation' : self.aggregationMethodsChoice.Value,
'colormap' : self.colorMapsChoice.Value,
'well display' : self.wellDisplayChoice.Value,
'number of plates' : self.numberOfPlatesTE.GetValue(),
}
for i, choice in enumerate(self.plateMapChoices):
settings['plate %d'%(i+1)] = choice.Value
return settings
def load_settings(self, settings):
'''load_settings is called when loading a workspace from file.
settings - a dictionary mapping setting names to values encoded as
strings.
'''
if 'table' in settings:
self.sourceChoice.SetStringSelection(settings['table'])
self.UpdateMeasurementChoice()
if 'measurement' in settings:
self.measurementsChoice.SetStringSelection(settings['measurement'])
self.OnSelectMeasurement()
if 'aggregation' in settings:
self.aggregationMethodsChoice.SetStringSelection(settings['aggregation'])
self.OnSelectAggregationMethod()
if 'colormap' in settings:
self.colorMapsChoice.SetStringSelection(settings['colormap'])
self.OnSelectColorMap()
if 'number of plates' in settings:
self.numberOfPlatesTE.SetValue(settings['number of plates'])
self.OnEnterNumberOfPlates()
for s, v in settings.items():
if s.startswith('plate '):
self.plateMapChoices[int(s.strip('plate ')) - 1].SetValue(v)
# set well display last since each step currently causes a redraw and
# this could take a long time if they are displaying images
if 'well display' in settings:
self.wellDisplayChoice.SetStringSelection(settings['well display'])
self.OnSelectWellDisplay()
class PlateViewer(wx.Frame, CPATool):
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(wx.NullColor)
# 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")
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, style=wx.CB_READONLY)
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, style=wx.CB_READONLY)
self.measurementsChoice.Select(0)
dataSourceSizer.Add(self.measurementsChoice)
dataSourceSizer.Add(wx.StaticText(self, label="Filter:"))
self.filterChoice = FilterComboBox(self)
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, style=wx.CB_READONLY)
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, style=wx.CB_READONLY)
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, style=wx.CB_READONLY)
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), style=wx.CB_READONLY)
if len(self.annotation_cols) > 0:
self.annotationCol.SetSelection(0)
annotationColSizer.Add(self.annotationCol)
annotationColSizer.AddSpacer((3, -1))
self.addAnnotationColBtn = wx.Button(self, -1, "Add", size=(44, -1))
annotationColSizer.Add(self.addAnnotationColBtn, 0, wx.TOP, 3)
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.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.OnShowAnotationValues)
self.filterChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectFilter)
self.AddPlateMap()
self.OnSelectMeasurement()
def AddPlateMap(self, plateIndex=0):
"""
Adds a new blank plateMap to the PlateMapSizer.
"""
data = np.ones(p.plate_shape)
# Try to get explicit labels for all wells.
res = db.execute(
'SELECT DISTINCT %s FROM %s WHERE %s != "" and %s IS NOT NULL'
% (dbconnect.UniqueWellClause(), p.image_table, p.well_id, p.well_id)
)
if p.plate_id:
self.plateMapChoices += [ComboBox(self, choices=db.GetPlateNames(), style=wx.CB_READONLY, size=(100, -1))]
self.plateMapChoices[-1].Select(plateIndex)
self.plateMapChoices[-1].Bind(wx.EVT_COMBOBOX, self.OnSelectPlate)
plate_col_type = db.GetColumnType(p.image_table, p.plate_id)
plate_id = plate_col_type(self.plateMapChoices[-1].GetString(plateIndex))
plateMapChoiceSizer = wx.BoxSizer(wx.HORIZONTAL)
plateMapChoiceSizer.Add(wx.StaticText(self, label="Plate:"), 0, wx.EXPAND)
plateMapChoiceSizer.Add(self.plateMapChoices[-1])
well_keys = res
platemap = pmp.PlateMapPanel(
self,
data,
well_keys,
p.plate_shape,
colormap=self.colorMapsChoice.Value,
well_disp=self.wellDisplayChoice.Value,
)
platemap.add_well_selection_handler(self.OnSelectWell)
self.plateMaps += [platemap]
singlePlateMapSizer = wx.BoxSizer(wx.VERTICAL)
if p.plate_id:
singlePlateMapSizer.Add(plateMapChoiceSizer, 0, wx.ALIGN_CENTER)
singlePlateMapSizer.Add(platemap, 1, wx.EXPAND | wx.ALIGN_CENTER)
self.plateMapSizer.Add(singlePlateMapSizer, 1, wx.EXPAND | wx.ALIGN_CENTER)
def UpdatePlateMaps(self):
measurement = self.measurementsChoice.Value
table = self.sourceChoice.Value
aggMethod = self.aggregationMethodsChoice.Value
categorical = measurement not in get_numeric_columns_from_table(table)
fltr = self.filterChoice.Value
self.colorBar.ClearNotifyWindows()
q = sql.QueryBuilder()
well_key_cols = [sql.Column(p.image_table, col) for col in well_key_columns()]
select = list(well_key_cols)
if not categorical:
if aggMethod == "mean":
select += [sql.Column(table, measurement, "AVG")]
elif aggMethod == "stdev":
select += [sql.Column(table, measurement, "STDDEV")]
elif aggMethod == "cv%":
# stddev(col) / avg(col) * 100
select += [
sql.Expression(
sql.Column(table, measurement, "STDDEV"), " / ", sql.Column(table, measurement, "AVG"), " * 100"
)
]
elif aggMethod == "sum":
select += [sql.Column(table, measurement, "SUM")]
elif aggMethod == "min":
select += [sql.Column(table, measurement, "MIN")]
elif aggMethod == "max":
select += [sql.Column(table, measurement, "MAX")]
elif aggMethod == "median":
select += [sql.Column(table, measurement, "MEDIAN")]
elif aggMethod == "none":
select += [sql.Column(table, measurement)]
else:
select += [sql.Column(table, measurement)]
q.set_select_clause(select)
q.set_group_columns(well_key_cols)
if fltr not in (FilterComboBox.NO_FILTER, FilterComboBox.NEW_FILTER, ""):
if fltr in p._filters:
q.add_filter(p._filters[fltr])
elif fltr in p.gates:
q.add_filter(p.gates[fltr].as_filter())
else:
raise Exception('Could not find filter "%s" in gates or filters' % (fltr))
wellkeys_and_values = db.execute(str(q))
wellkeys_and_values = np.array(wellkeys_and_values, dtype=object)
# Replace measurement None's with nan
for row in wellkeys_and_values:
if row[-1] is None:
row[-1] = np.nan
data = []
key_lists = []
dmax = -np.inf
dmin = np.inf
if p.plate_id:
for plateChoice, plateMap in zip(self.plateMapChoices, self.plateMaps):
plate = plateChoice.Value
plateMap.SetPlate(plate)
self.colorBar.AddNotifyWindow(plateMap)
keys_and_vals = [v for v in wellkeys_and_values if str(v[0]) == plate]
platedata, wellkeys, ignore = FormatPlateMapData(keys_and_vals, categorical)
data += [platedata]
key_lists += [wellkeys]
if not categorical:
dmin = np.nanmin([float(kv[-1]) for kv in keys_and_vals] + [dmin])
dmax = np.nanmax([float(kv[-1]) for kv in keys_and_vals] + [dmax])
else:
self.colorBar.AddNotifyWindow(self.plateMaps[0])
platedata, wellkeys, ignore = FormatPlateMapData(wellkeys_and_values, categorical)
data += [platedata]
key_lists += [wellkeys]
if not categorical:
dmin = np.nanmin([float(kv[-1]) for kv in wellkeys_and_values])
dmax = np.nanmax([float(kv[-1]) for kv in wellkeys_and_values])
if not categorical:
if len(wellkeys_and_values) > 0:
# Compute the global extents if there is any data whatsoever
gmin = np.nanmin([float(vals[-1]) for vals in wellkeys_and_values])
gmax = np.nanmax([float(vals[-1]) for vals in wellkeys_and_values])
if np.isinf(dmin) or np.isinf(dmax):
gmin = gmax = dmin = dmax = 1.0
# Warn if there was no data for this plate (and no filter was used)
if fltr == FilterComboBox.NO_FILTER:
wx.MessageBox(
'No numeric data was found in "%s.%s" for plate "%s"' % (table, measurement, plate),
"Warning",
)
else:
gmin = gmax = 1.0
if fltr == FilterComboBox.NO_FILTER:
wx.MessageBox("No numeric data was found in %s.%s" % (table, measurement), "Warning")
if categorical:
self.colorBar.Hide()
else:
self.colorBar.Show()
self.colorBar.SetLocalExtents([dmin, dmax])
self.colorBar.SetGlobalExtents([gmin, gmax])
self.rightSizer.Layout()
for keys, d, plateMap in zip(key_lists, data, self.plateMaps):
plateMap.SetWellKeys(keys)
if categorical:
plateMap.SetData(np.ones(d.shape) * np.nan)
plateMap.SetTextData(d)
else:
plateMap.SetData(
d,
data_range=self.colorBar.GetLocalExtents(),
clip_interval=self.colorBar.GetLocalInterval(),
clip_mode=self.colorBar.GetClipMode(),
)
for keys, d, plateMap in zip(key_lists, data, self.plateMaps):
plateMap.SetWellKeys(keys)
if categorical:
plateMap.SetData(np.ones(d.shape) * np.nan)
plateMap.SetTextData(d)
else:
plateMap.SetData(
d,
data_range=self.colorBar.GetLocalExtents(),
clip_interval=self.colorBar.GetLocalInterval(),
clip_mode=self.colorBar.GetClipMode(),
)
def UpdateMeasurementChoice(self, evt=None):
"""
Handles the selection of a source table (per-image or per-object) from
a choice box. The measurement choice box is populated with the names
of numeric columns from the selected table.
"""
table = self.sourceChoice.Value
if table == TableComboBox.OTHER_TABLE:
t = get_other_table_from_user(self)
if t is not None:
self.sourceChoice.Items = self.sourceChoice.Items[:-1] + [t] + self.sourceChoice.Items[-1:]
self.sourceChoice.Select(self.sourceChoice.Items.index(t))
table = t
else:
self.sourceChoice.Select(0)
return
self.measurementsChoice.SetItems(get_non_blob_types_from_table(table))
self.measurementsChoice.Select(0)
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectPlate(self, evt):
""" Handles the selection of a plate from the plate choice box. """
self.UpdatePlateMaps()
def OnSelectMeasurement(self, evt=None):
""" Handles the selection of a measurement to plot from a choice box. """
selected_measurement = self.measurementsChoice.Value
table = self.sourceChoice.Value
numeric_measurements = get_numeric_columns_from_table(table)
if selected_measurement in numeric_measurements:
self.aggregationMethodsChoice.Enable()
self.colorMapsChoice.Enable()
else:
self.aggregationMethodsChoice.Disable()
self.colorMapsChoice.Disable()
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectAggregationMethod(self, evt=None):
""" Handles the selection of an aggregation method from the choice box. """
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectColorMap(self, evt=None):
""" Handles the selection of a color map from a choice box. """
map = self.colorMapsChoice.Value
cm = matplotlib.cm.get_cmap(map)
self.colorBar.SetMap(map)
for plateMap in self.plateMaps:
plateMap.SetColorMap(map)
def OnSelectWellDisplay(self, evt=None):
""" Handles the selection of a well display choice from a choice box. """
sel = self.wellDisplayChoice.Value
if sel.lower() == "image":
dlg = wx.MessageDialog(
self,
"This mode will render each well as a shrunken image loaded "
"from that well. This feature is currently VERY SLOW since it "
"requires loading hundreds of full sized images. Are you sure "
"you want to continue?",
"Load all images?",
wx.OK | wx.CANCEL | wx.ICON_QUESTION,
)
if dlg.ShowModal() != wx.ID_OK:
self.wellDisplayChoice.SetSelection(0)
return
if sel.lower() in ["image", "thumbnail"]:
self.colorBar.Hide()
else:
self.colorBar.Show()
for platemap in self.plateMaps:
platemap.SetWellDisplay(sel)
def OnEnterNumberOfPlates(self, evt=None):
""" Handles the entry of a plates to view from a choice box. """
try:
nPlates = int(self.numberOfPlatesTE.GetValue())
except:
logging.warn("Invalid # of plates! Please enter a number between 1 and 100")
return
if nPlates > 100:
logging.warn("Too many plates! Please enter a number between 1 and 100")
return
if nPlates < 1:
logging.warn("You must display at least 1 plate.")
self.numberOfPlatesTE.SetValue("1")
nPlates = 1
# Record the indices of the plates currently selected.
# Pad the list with sequential plate indices then crop to the new number of plates.
currentPlates = [plateChoice.GetSelection() for plateChoice in self.plateMapChoices]
currentPlates = (
currentPlates + [(currentPlates[-1] + 1 + p) % len(db.GetPlateNames()) for p in range(nPlates)]
)[:nPlates]
# Remove all plateMaps
self.plateMapSizer.Clear(deleteWindows=True)
self.plateMaps = []
self.plateMapChoices = []
# Restructure the plateMapSizer appropriately
rows = cols = np.ceil(np.sqrt(nPlates))
self.plateMapSizer.SetRows(rows)
self.plateMapSizer.SetCols(cols)
# Add the plate maps
for plateIndex in currentPlates:
self.AddPlateMap(plateIndex)
self.UpdatePlateMaps()
self.plateMapSizer.Layout()
# Update outlines
self.OnOutlineMarked()
def OnSelectWell(self):
"""When wells are selected: display their annotation in the annotation
label control. If multiple annotations are found then make sure the
user knows.
"""
wellkeys = []
for pm in self.plateMaps:
wellkeys += pm.get_selected_well_keys()
if len(wellkeys) > 0 and self.annotationCol.Value != "":
self.annotationLabel.Enable()
self.annotationLabel.SetForegroundColour(wx.BLACK)
self.annotationLabel.SetBackgroundColour(wx.WHITE)
annotations = db.execute(
"SELECT %s FROM %s WHERE %s"
% (self.annotationCol.Value, p.image_table, GetWhereClauseForWells(wellkeys))
)
annotations = list(set([a[0] for a in annotations]))
if len(annotations) == 1:
if annotations[0] == None:
self.annotationLabel.SetValue("")
else:
self.annotationLabel.SetValue(str(annotations[0]))
else:
self.annotationLabel.SetValue(",".join([str(a) for a in annotations if a is not None]))
else:
self.annotationLabel.Disable()
self.annotationLabel.SetForegroundColour(wx.Colour(80, 80, 80))
self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY)
self.annotationLabel.SetValue("Select wells")
def OnAddAnnotationCol(self, evt):
"""Add a new user annotation column to the database.
"""
dlg = wx.TextEntryDialog(self, "New annotation column name: User_", "Add Annotation Column")
if dlg.ShowModal() != wx.ID_OK:
return
new_column = "User_" + dlg.GetValue()
# user-type ==> (sql-type, python-type)
coltypes = {"Text": ("VARCHAR(255)", str), "Number": ("FLOAT", float)}
dlg = wx.SingleChoiceDialog(
self,
"What type of annotation column would you like to add?\nThis can not be changed.",
"Add Annotation Column",
coltypes.keys(),
wx.CHOICEDLG_STYLE,
)
if dlg.ShowModal() != wx.ID_OK:
return
usertype = dlg.GetStringSelection()
db.AppendColumn(p.image_table, new_column, coltypes[usertype][0])
self.annotation_cols[new_column] = coltypes[usertype][1]
self.annotationCol.Items += [new_column]
self.annotationCol.SetSelection(len(self.annotation_cols) - 1)
current_selection = self.measurementsChoice.Selection
self.measurementsChoice.SetItems(self.measurementsChoice.Strings + [new_column])
if self.annotationShowVals.IsChecked():
column = self.annotationCol.Value
self.sourceChoice.SetStringSelection(p.image_table)
self.measurementsChoice.SetStringSelection(column)
self.UpdatePlateMaps()
else:
self.measurementsChoice.SetSelection(current_selection)
self.annotationShowVals.Enable()
self.outlineMarked.Enable()
self.OnSelectWell()
def OnSelectAnnotationCol(self, evt=None):
"""Handles selection of an annotation column.
"""
col = self.annotationCol.Value
if col == "":
return
coltype = self.annotation_cols[col]
self.OnSelectWell()
self.OnOutlineMarked()
if self.annotationShowVals.IsChecked():
if coltype != str:
self.colorMapsChoice.Enable()
else:
self.colorMapsChoice.Disable()
self.measurementsChoice.SetStringSelection(col)
self.UpdatePlateMaps()
def OnEnterAnnotation(self, evt=None):
"""Store the annotation value in the annotation column of the db.
"""
if evt.KeyCode < 32 or evt.KeyCode > 127:
return
column = self.annotationCol.Value
value = self.annotationLabel.Value
wellkeys = []
for pm in self.plateMaps:
wellkeys += pm.get_selected_well_keys()
if value == "":
value = None
elif self.annotation_cols[column] == float:
try:
value = float(value)
self.annotationLabel.SetForegroundColour(wx.BLACK)
except:
self.annotationLabel.SetForegroundColour(wx.Color(255, 0, 0))
return
db.UpdateWells(p.image_table, column, value, wellkeys)
if self.outlineMarked.IsChecked():
for pm in self.plateMaps:
if value is None:
pm.UnOutlineWells(wellkeys)
else:
pm.OutlineWells(wellkeys)
if self.sourceChoice.Value == p.image_table and self.measurementsChoice.Value == column:
self.UpdatePlateMaps()
def OnOutlineMarked(self, evt=None):
"""Outlines all non-NULL values of the current annotation
"""
# Disable filters when outlining marked wells
# if self.outlineMarked.IsChecked():
# self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER)
# self.filterChoice.Disable()
# else:
# if not self.annotationShowVals.IsChecked():
# self.filterChoice.Enable()
# Update outlined wells in PlateMapPanels
for pm in self.plateMaps:
if self.outlineMarked.IsChecked():
column = self.annotationCol.Value
if p.plate_id:
res = db.execute(
'SELECT %s, %s FROM %s WHERE %s="%s"'
% (dbconnect.UniqueWellClause(), column, p.image_table, p.plate_id, pm.plate)
)
else:
# if there's no plate_id, we assume there is only 1 plate
# and fetch all the data
res = db.execute("SELECT %s, %s FROM %s" % (dbconnect.UniqueWellClause(), column, p.image_table))
keys = [tuple(r[:-1]) for r in res if r[-1] is not None]
pm.SetOutlinedWells(keys)
else:
pm.SetOutlinedWells([])
self.UpdatePlateMaps()
def OnShowAnotationValues(self, evt=None):
"""Handler for the show values checkbox.
"""
if self.annotationShowVals.IsChecked():
column = self.annotationCol.Value
self.sourceChoice.SetStringSelection(p.image_table)
self.measurementsChoice.SetItems(get_non_blob_types_from_table(p.image_table))
self.measurementsChoice.SetStringSelection(column)
self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER)
self.sourceChoice.Disable()
self.measurementsChoice.Disable()
self.filterChoice.Disable()
self.aggregationMethodsChoice.Disable()
self.aggregationMethodsChoice.SetValue("none")
else:
self.sourceChoice.Enable()
self.measurementsChoice.Enable()
if not self.outlineMarked.IsChecked():
self.filterChoice.Enable()
if db.GetColumnType(self.sourceChoice.Value, self.measurementsChoice.Value) != str:
self.aggregationMethodsChoice.Enable()
self.aggregationMethodsChoice.SetSelection(0)
self.UpdatePlateMaps()
def OnSelectFilter(self, evt):
self.filterChoice.on_select(evt)
self.UpdatePlateMaps()
self.colorBar.ResetInterval()
def save_settings(self):
"""save_settings is called when saving a workspace to file.
returns a dictionary mapping setting names to values encoded as strings
"""
settings = {
"table": self.sourceChoice.Value,
"measurement": self.measurementsChoice.Value,
"aggregation": self.aggregationMethodsChoice.Value,
"colormap": self.colorMapsChoice.Value,
"well display": self.wellDisplayChoice.Value,
"number of plates": self.numberOfPlatesTE.GetValue(),
}
for i, choice in enumerate(self.plateMapChoices):
settings["plate %d" % (i + 1)] = choice.Value
return settings
def load_settings(self, settings):
"""load_settings is called when loading a workspace from file.
settings - a dictionary mapping setting names to values encoded as
strings.
"""
if "table" in settings:
self.sourceChoice.SetStringSelection(settings["table"])
self.UpdateMeasurementChoice()
if "measurement" in settings:
self.measurementsChoice.SetStringSelection(settings["measurement"])
self.OnSelectMeasurement()
if "aggregation" in settings:
self.aggregationMethodsChoice.SetStringSelection(settings["aggregation"])
self.OnSelectAggregationMethod()
if "colormap" in settings:
self.colorMapsChoice.SetStringSelection(settings["colormap"])
self.OnSelectColorMap()
if "number of plates" in settings:
self.numberOfPlatesTE.SetValue(settings["number of plates"])
self.OnEnterNumberOfPlates()
for s, v in settings.items():
if s.startswith("plate "):
self.plateMapChoices[int(s.strip("plate ")) - 1].SetValue(v)
# set well display last since each step currently causes a redraw and
# this could take a long time if they are displaying images
if "well display" in settings:
self.wellDisplayChoice.SetStringSelection(settings["well display"])
self.OnSelectWellDisplay()
