def __init__(self, parent, size=(600, 600), **kwargs):
wx.Frame.__init__(self,
parent,
-1,
size=size,
title='Histogram',
**kwargs)
CPATool.__init__(self)
self.SetName(self.tool_name)
self.SetBackgroundColour("white")
points = []
figpanel = HistogramPanel(self, points)
configpanel = DataSourcePanel(self, figpanel)
figpanel.set_configpanel(configpanel)
self.SetToolBar(figpanel.get_toolbar())
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(figpanel, 1, wx.EXPAND)
sizer.Add(configpanel, 0, wx.EXPAND | wx.ALL, 5)
self.SetSizer(sizer)
#
# Forward save and load settings functionality to the configpanel
#
self.save_settings = configpanel.save_settings
self.load_settings = configpanel.load_settings
self.fig = figpanel
def __init__(self, parent, size=(600,600), **kwargs):
wx.Frame.__init__(self, parent, -1, size=size, title='Time Visual', **kwargs)
CPATool.__init__(self)
self.SetName(self.tool_name)
# Check for required properties fields.
#fail = False
#missing_fields = [field for field in required_fields if not props.field_defined(field)]
#if missing_fields:
#fail = True
#message = 'The following missing fields are required for TimeVisual: %s.'%(",".join(missing_fields))
#wx.MessageBox(message,'Required field(s) missing')
#logging.error(message)
#if fail:
#self.Destroy()
#return
self.configpanel = DataSourcePanel(self)
self.selected_dataset = self.configpanel.dataset_choice.GetStringSelection()
self.selected_colormap = self.configpanel.colormap_choice.GetStringSelection()
self.plot_updated = False
self.trajectory_selected = False
self.mayavi_view = MayaviView()
self.trajectory_info = None
self.selected_trajectories = None
self.selected_node = None
self.figpanel = self.mayavi_view.edit_traits(
parent=self,
kind='subpanel').control
self.generate_graph(True)
self.plot_trajectories(True)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.figpanel, 1, wx.EXPAND)
sizer.Add(self.configpanel, 0, wx.EXPAND|wx.ALL, 5)
self.SetSizer(sizer)
self.figpanel.Bind(wx.EVT_CONTEXT_MENU, self.on_show_popup_menu)
# Define events
wx.EVT_COMBOBOX(self.configpanel.dataset_choice, -1, self.on_dataset_selected)
wx.EVT_COMBOBOX(self.configpanel.feature_choice, -1, self.on_feature_selected)
wx.EVT_BUTTON(self.configpanel.trajectory_selection_button, -1, self.update_trajectory_selection)
wx.EVT_BUTTON(self.configpanel.colormap_choice, -1, self.on_colormap_selected)
wx.EVT_BUTTON(self.configpanel.update_plot_button, -1, self.update_plot)
def __init__(self, parent, size=(600,600), **kwargs):
wx.Frame.__init__(self, parent, -1, size=size, title='Density Plot', **kwargs)
CPATool.__init__(self)
self.SetName(self.tool_name)
self.SetBackgroundColour("white")
figpanel = DensityPanel(self)
configpanel = DataSourcePanel(self, figpanel)
figpanel.set_configpanel(configpanel)
self.SetToolBar(figpanel.get_toolbar())
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(figpanel, 1, wx.EXPAND)
sizer.Add(configpanel, 0, wx.EXPAND|wx.ALL, 5)
self.SetSizer(sizer)
#
# Forward save and load settings functionality to the configpanel
#
self.save_settings = configpanel.save_settings
self.load_settings = configpanel.load_settings
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()
def __init__(self,
parent,
id=-1,
title='Normalization Settings',
**kwargs):
kwargs['size'] = kwargs.get('size', (500, 500))
wx.Frame.__init__(self, parent, id, title=title, **kwargs)
CPATool.__init__(self)
wx.HelpProvider_Set(wx.SimpleHelpProvider())
self.n_steps = 1
self.SetBackgroundColour("white")
#
# Define the controls
#
tables = ([p.image_table]
or []) + ([p.object_table] if p.object_table else [])
self.table_choice = wx.Choice(self, -1, choices=tables)
select_all_btn = wx.Button(self, -1, 'Select all columns')
select_all_btn.SetHelpText("Click this button to check all columns.")
self.table_choice.Select(0)
self.table_choice.SetHelpText(
"Select the table containing the measurement columns to normalize."
)
self.col_choices = wx.CheckListBox(self,
-1,
choices=[],
size=(-1, 100))
self.col_choices.SetHelpText(
"Select the measurement columns to normalize. More than one column may be selected. "
"The normalization steps below will be performed on all columns.")
add_norm_step_btn = wx.Button(self, -1, 'Add normalization step')
add_norm_step_btn.SetHelpText(
"Click this button to add another normalization to perform. "
"The normalizations are performed from top to bottom, with the "
"results from one step being used as input into the following step."
)
self.norm_meas_checkbox = wx.CheckBox(self, -1,
'Normalized measurements')
self.norm_meas_checkbox.Set3StateValue(True)
self.norm_meas_checkbox.SetHelpText(
"Write a column of normalized measurements to the output table. "
"This column ihas the same name as the input, with the suffix '_NmV'"
)
self.norm_factor_checkbox = wx.CheckBox(self, -1,
'Normalization factors')
self.norm_factor_checkbox.SetHelpText(
"Write a column of normalization factors to the output table. "
"This column ihas the same name as the input, with the suffix '_NmF' added."
)
self.output_table = wx.TextCtrl(self,
-1,
'normalized_measurements',
size=(200, -1))
self.output_table.SetHelpText(
"Enter the name of the output table which will contain "
"your normalized measurements and/or the normalization factors.\n "
"The text will appear orange if the table already exists "
"in the database. The output table will be linked to the existing "
"tables so it is usable immediately.")
self.help_btn = wx.ContextHelpButton(self)
self.do_norm_btn = wx.Button(self, wx.ID_OK, 'Perform Normalization')
self.do_norm_btn.SetHelpText(
"Once you have adjusted the settings, click this button to start normalization "
"and write the results to the output table. A progress bar will inform you "
"of the normalization status.")
self.boxes = []
self.SetSizer(wx.BoxSizer(wx.VERTICAL))
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, 'Select a table:'), 0,
wx.EXPAND | wx.RIGHT, 5)
sz.Add(self.table_choice, 0)
sz.Add(select_all_btn, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND | wx.TOP | wx.LEFT | wx.RIGHT, 15)
self.col_choices_desc = wx.StaticText(
self, -1, 'Select measurements to normalize:')
self.Sizer.Add(self.col_choices_desc, 0,
wx.EXPAND | wx.TOP | wx.LEFT | wx.RIGHT, 15)
self.Sizer.AddSpacer((-1, 5))
self.Sizer.Add(self.col_choices, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 15)
#
# Lay out the first normalization step inside a scrolled window
# and a static box sizer.
#
self.Sizer.Add(
wx.StaticText(
self, -1,
'Specify the normalization steps you want to perform:'), 0,
wx.EXPAND | wx.TOP | wx.LEFT | wx.RIGHT, 15)
self.sw = wx.ScrolledWindow(self)
sbs = wx.StaticBoxSizer(wx.StaticBox(self.sw, label=''), wx.VERTICAL)
nsp = NormalizationStepPanel(self.sw, allow_delete=False)
self.norm_steps = [nsp]
self.boxes = [sbs]
sbs.Add(nsp, 0, wx.EXPAND)
self.sw.Sizer = wx.BoxSizer(wx.VERTICAL)
self.sw.Sizer.Add(sbs, 0, wx.EXPAND)
(w, h) = self.sw.Sizer.GetSize()
self.sw.SetScrollbars(20, 20, w / 20, h / 20, 0, 0)
self.Sizer.Add(self.sw, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.AddStretchSpacer()
sz.Add(add_norm_step_btn, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND | wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
self.output_table_desc = wx.StaticText(self, -1,
'Name your output table:')
sz.Add(self.output_table_desc, 0, wx.EXPAND | wx.RIGHT, 5)
sz.Add(self.output_table, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND | wx.TOP | wx.LEFT | wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
self.output_format_desc = wx.StaticText(self, -1, 'Output columns:')
sz.Add(self.output_format_desc, 0, wx.EXPAND | wx.RIGHT, 5)
sz.Add(self.norm_meas_checkbox, 0, wx.EXPAND | wx.RIGHT, 5)
sz.Add(self.norm_factor_checkbox, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND | wx.TOP | wx.LEFT | wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(self.help_btn)
sz.AddStretchSpacer()
sz.Add(self.do_norm_btn)
self.Sizer.Add(sz, 0, wx.EXPAND | wx.ALL, 15)
self.table_choice.Bind(wx.EVT_CHOICE, self.on_select_table)
select_all_btn.Bind(wx.EVT_BUTTON, self.on_select_all_columns)
add_norm_step_btn.Bind(wx.EVT_BUTTON, self.on_add_norm_step)
self.col_choices.Bind(wx.EVT_CHECKLISTBOX, lambda e: self.validate())
self.norm_meas_checkbox.Bind(wx.EVT_CHECKBOX,
lambda e: self.validate())
self.norm_factor_checkbox.Bind(wx.EVT_CHECKBOX,
lambda e: self.validate())
self.output_table.Bind(wx.EVT_TEXT, lambda e: self.validate())
self.do_norm_btn.Bind(wx.EVT_BUTTON, self.on_do_normalization)
self.update_measurement_choices()
self.validate()
def __init__(self, parent, id=-1, title='Normalization Settings', **kwargs):
kwargs['size'] = kwargs.get('size', (500,500))
wx.Frame.__init__(self, parent, id, title=title, **kwargs)
CPATool.__init__(self)
wx.HelpProvider_Set(wx.SimpleHelpProvider())
self.n_steps = 1
self.SetBackgroundColour("white")
#
# Define the controls
#
tables = ([p.image_table] or []) + ([p.object_table] if p.object_table else [])
self.table_choice = wx.Choice(self, -1, choices=tables)
select_all_btn = wx.Button(self, -1, 'Select all columns')
select_all_btn.SetHelpText("Click this button to check all columns.")
self.table_choice.Select(0)
self.table_choice.SetHelpText("Select the table containing the measurement columns to normalize.")
self.col_choices = wx.CheckListBox(self, -1, choices=[], size=(-1, 100))
self.col_choices.SetHelpText("Select the measurement columns to normalize. More than one column may be selected. "
"The normalization steps below will be performed on all columns.")
add_norm_step_btn = wx.Button(self, -1, 'Add normalization step')
add_norm_step_btn.SetHelpText("Click this button to add another normalization to perform. "
"The normalizations are performed from top to bottom, with the "
"results from one step being used as input into the following step.")
self.norm_meas_checkbox = wx.CheckBox(self, -1, 'Normalized measurements')
self.norm_meas_checkbox.Set3StateValue(True)
self.norm_meas_checkbox.SetHelpText("Write a column of normalized measurements to the output table. "
"This column ihas the same name as the input, with the suffix '_NmV'")
self.norm_factor_checkbox = wx.CheckBox(self, -1, 'Normalization factors')
self.norm_factor_checkbox.SetHelpText("Write a column of normalization factors to the output table. "
"This column ihas the same name as the input, with the suffix '_NmF' added.")
self.output_table = wx.TextCtrl(self, -1, 'normalized_measurements', size=(200,-1))
self.output_table.SetHelpText("Enter the name of the output table which will contain "
"your normalized measurements and/or the normalization factors.\n "
"The text will appear orange if the table already exists "
"in the database. The output table will be linked to the existing "
"tables so it is usable immediately.")
self.help_btn = wx.ContextHelpButton(self)
self.do_norm_btn = wx.Button(self, wx.ID_OK, 'Perform Normalization')
self.do_norm_btn.SetHelpText("Once you have adjusted the settings, click this button to start normalization "
"and write the results to the output table. A progress bar will inform you "
"of the normalization status.")
self.boxes = [ ]
self.SetSizer(wx.BoxSizer(wx.VERTICAL))
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, 'Select a table:'), 0, wx.EXPAND|wx.RIGHT, 5)
sz.Add(self.table_choice, 0)
sz.Add(select_all_btn, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT, 15)
self.col_choices_desc = wx.StaticText(self, -1, 'Select measurements to normalize:')
self.Sizer.Add(self.col_choices_desc, 0, wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT, 15)
self.Sizer.AddSpacer((-1,5))
self.Sizer.Add(self.col_choices, 0, wx.EXPAND|wx.LEFT|wx.RIGHT, 15)
#
# Lay out the first normalization step inside a scrolled window
# and a static box sizer.
#
self.Sizer.Add(wx.StaticText(self, -1, 'Specify the normalization steps you want to perform:'), 0, wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT, 15)
self.sw = wx.ScrolledWindow(self)
sbs = wx.StaticBoxSizer(wx.StaticBox(self.sw, label=''), wx.VERTICAL)
nsp = NormalizationStepPanel(self.sw, allow_delete=False)
self.norm_steps = [ nsp ]
self.boxes = [ sbs ]
sbs.Add(nsp, 0, wx.EXPAND)
self.sw.Sizer = wx.BoxSizer(wx.VERTICAL)
self.sw.Sizer.Add(sbs, 0, wx.EXPAND)
(w,h) = self.sw.Sizer.GetSize()
self.sw.SetScrollbars(20,20,w/20,h/20,0,0)
self.Sizer.Add(self.sw, 1, wx.EXPAND|wx.LEFT|wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.AddStretchSpacer()
sz.Add(add_norm_step_btn, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND|wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
self.output_table_desc = wx.StaticText(self, -1, 'Name your output table:')
sz.Add(self.output_table_desc, 0, wx.EXPAND|wx.RIGHT, 5)
sz.Add(self.output_table, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
self.output_format_desc = wx.StaticText(self, -1, 'Output columns:')
sz.Add(self.output_format_desc, 0, wx.EXPAND|wx.RIGHT, 5)
sz.Add(self.norm_meas_checkbox, 0, wx.EXPAND|wx.RIGHT, 5)
sz.Add(self.norm_factor_checkbox, 0, wx.EXPAND)
self.Sizer.Add(sz, 0, wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT, 15)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(self.help_btn)
sz.AddStretchSpacer()
sz.Add(self.do_norm_btn)
self.Sizer.Add(sz, 0, wx.EXPAND|wx.ALL, 15)
self.table_choice.Bind(wx.EVT_CHOICE, self.on_select_table)
select_all_btn.Bind(wx.EVT_BUTTON, self.on_select_all_columns)
add_norm_step_btn.Bind(wx.EVT_BUTTON, self.on_add_norm_step)
self.col_choices.Bind(wx.EVT_CHECKLISTBOX, lambda e: self.validate())
self.norm_meas_checkbox.Bind(wx.EVT_CHECKBOX, lambda e: self.validate())
self.norm_factor_checkbox.Bind(wx.EVT_CHECKBOX, lambda e: self.validate())
self.output_table.Bind(wx.EVT_TEXT, lambda e: self.validate())
self.do_norm_btn.Bind(wx.EVT_BUTTON, self.on_do_normalization)
self.update_measurement_choices()
self.validate()