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,Yield):
"""Create a PELvis frame
Keyword arguments:
Yield -- A function to give control back to the main event loop
"""
wx.Frame.__init__(self,None,wx.ID_ANY,"PEL Visualizer")
self.data = PelFile()
self.Yield = Yield
self.mask = np.ones((128,16),dtype=np.bool)
#Create items in the frame
self.yPanel = GraphPanel(self,(2,8),64,GraphPanel.VERTICAL)
self.xPanel = GraphPanel(self,(8,2),64,GraphPanel.INVERTED)
self.colorbar = ColorBarPanel(self,cm.jet)
self.opPanel = PelvisOptionPanel(self)
self.posPanel = PositionPanel(self)
self.imPanel = ImagePanel(self,self.posPanel.set,
self.opPanel.setPosMin,self.opPanel.setPosMax)
self.specDlg = SpectrumDialog(self)
self.cmp = None #color map
self.imageSaveDialog=wx.FileDialog(self,"Choose graphics file",wildcard="Portable Network Graphic (png)|*.PNG|Windows Bitmap (bmp)|*.BMP|Joint Photographic Experts Group (jpg)|*.JPG|Portable Network Monocrome (pnm)|*.PNM|Tagged Image File Format (tif)|*.TIF|Archaic, useless format (pcx)|*.PCX",style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
self.update = self.updateSingle#update the image
self.updateData = self.updateSingleData#update the data in the image
#Create the menu
menubar = wx.MenuBar()
filemenu = wx.Menu()
editmenu = wx.Menu()
scalemenu = wx.Menu()
analysismenu = wx.Menu()
noisemenu = wx.Menu()
#populate the menu
filemenu.Append(self.ID_OPEN,"&Open\tCtrl-O"," Open a PEL file")
filemenu.Append(self.ID_OPENTWO,"&Polarized Set"," Open two PEL files")
filemenu.Append(self.ID_SAVE,"&Save\tCtrl-S"," Save an image file")
filemenu.Append(self.ID_SPECTRUM,"Spectrum"," View the TOF spectrum")
filemenu.Append(self.ID_IMAGE_ARRAY,"&Export Images..."," Save a series of TOF snapshots")
filemenu.Append(self.ID_EXIT,"&Quit\tCtrl-Q"," Quit")
editmenu.Append(self.ID_COPY,"&Copy\tCtrl-c","Copy the current image to the clipboard")
scalemenu.Append(self.ID_GREY,"Greyscale\tCtrl-G","Monochrome images")
scalemenu.Append(self.ID_HUEVAL,"Hue and Value\tCtrl-H","Scaled Rainbow Images")
scalemenu.Append(self.ID_SPECTRAL,"spectral","Uses spectrum of light")
scalemenu.Append(self.ID_PICKER,"Map Picker..."," Select from the full list of colormaps")
analysismenu.Append(self.ID_POLAR,"Check Polarization\tCtrl-P","2d plot of polarization data")
analysismenu.Append(self.ID_FLIPPING,"Check Flipping Ratio\tCtrl-F","2d plot of spin up over spin down")
analysismenu.Append(self.ID_SPIN_UP,"View Spin Up State\tCtrl-U","2d plot of spin up")
analysismenu.Append(self.ID_SPIN_DOWN,"View Spin Down State\tCtrl-D","2d plot of spin down")
noisemenu.Append(self.ID_FLAT,"&Load Flat"," Load a blank run for background subtraction")
noisemenu.Append(self.ID_FAKEFLAT,"Si&mulate Flat"," Drop out background within the same image")
noisemenu.Append(self.ID_ROD,"Region of &Disinterest"," Drop out background within the same image")
noisemenu.Append(self.ID_EXPORT_ROI,"Export ROI"," Export a binary file corresponding to where the data is above the minimum intensity.")
noisemenu.Append(self.ID_IMPORT_ROI,"Import ROI"," Add another exclusion mask.")
#Bind events to the menu
self.Connect(self.ID_EXIT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExit)
self.Connect(self.ID_OPEN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpen)
self.Connect(self.ID_OPENTWO,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpenSet)
self.Connect(self.ID_SAVE,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSave)
self.Connect(self.ID_SPECTRUM,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectrum)
self.Connect(self.ID_IMAGE_ARRAY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImageArray)
self.Connect(self.ID_GREY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnGrey)
self.Connect(self.ID_HUEVAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnHueVal)
self.Connect(self.ID_SPECTRAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectral)
self.Connect(self.ID_PICKER,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPicker)
self.Connect(self.ID_POLAR,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPolar)
self.Connect(self.ID_FLIPPING,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlipping)
self.Connect(self.ID_SPIN_UP,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinUp)
self.Connect(self.ID_SPIN_DOWN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinDown)
self.Connect(self.ID_FLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlat)
self.Connect(self.ID_FAKEFLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFakeFlat)
self.Connect(self.ID_ROD,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnROD)
self.Connect(self.ID_EXPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExportROI)
self.Connect(self.ID_IMPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImportROI)
self.Connect(self.ID_COPY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnCopy)
menubar.Append(filemenu,"&File")
menubar.Append(editmenu,"&Edit")
menubar.Append(scalemenu,"&Color")
menubar.Append(analysismenu,"&Analysis")
menubar.Append(noisemenu,"&Noise")
self.SetMenuBar(menubar)
#arrange window
sizer = wx.GridBagSizer()
sizer.Add(self.colorbar,pos=wx.GBPosition(0,9),span=wx.GBSpan(9,1))
sizer.Add(self.imPanel,pos=wx.GBPosition(0,1),span=wx.GBSpan(8,8))
sizer.Add(self.yPanel,pos=wx.GBPosition(0,0),span=wx.GBSpan(8,1))
sizer.Add(self.xPanel,pos=wx.GBPosition(8,1),span=wx.GBSpan(1,8))
sizer.Add(self.opPanel,pos=wx.GBPosition(0,10),span=wx.GBSpan(8,1),flag=wx.EXPAND)
sizer.Add(self.posPanel,pos=wx.GBPosition(8,0),flag=wx.EXPAND)
self.progress = wx.Gauge(self,range=1000)
sizer.Add(self.progress,pos=wx.GBPosition(9,0),span=wx.GBSpan(1,11),flag=wx.EXPAND)
updateButton = wx.Button(self,-1,"Update")
updateButton.Bind(wx.EVT_BUTTON,self.OnUpdateButton)
sizer.Add(updateButton,flag=wx.EXPAND,pos=wx.GBPosition(8,10))
self.data = self.makePel()
self.flatrun = None#background data
sizer.SetSizeHints(self)
self.SetSizer(sizer)
self.Show(True)
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 PelvisFrame(wx.Frame):
"""The main application window for PELvis"""
#Menu ID constants
ID_OPEN = 100
ID_OPENTWO = 110
ID_SAVE = 130
ID_SPECTRUM=140
ID_IMAGE_ARRAY=160
ID_EXIT = 190
ID_GREY = 200
ID_HUEVAL = 220
ID_SPECTRAL = 230
ID_PICKER = 290
ID_POLAR = 300
ID_FLIPPING = 310
ID_SPIN_UP = 320
ID_SPIN_DOWN = 330
ID_FLAT = 420
ID_FAKEFLAT = 430
ID_ROD = 440
ID_EXPORT_ROI = 450
ID_IMPORT_ROI = 460
ID_COPY = 500
def __init__(self,Yield):
"""Create a PELvis frame
Keyword arguments:
Yield -- A function to give control back to the main event loop
"""
wx.Frame.__init__(self,None,wx.ID_ANY,"PEL Visualizer")
self.data = PelFile()
self.Yield = Yield
self.mask = np.ones((128,16),dtype=np.bool)
#Create items in the frame
self.yPanel = GraphPanel(self,(2,8),64,GraphPanel.VERTICAL)
self.xPanel = GraphPanel(self,(8,2),64,GraphPanel.INVERTED)
self.colorbar = ColorBarPanel(self,cm.jet)
self.opPanel = PelvisOptionPanel(self)
self.posPanel = PositionPanel(self)
self.imPanel = ImagePanel(self,self.posPanel.set,
self.opPanel.setPosMin,self.opPanel.setPosMax)
self.specDlg = SpectrumDialog(self)
self.cmp = None #color map
self.imageSaveDialog=wx.FileDialog(self,"Choose graphics file",wildcard="Portable Network Graphic (png)|*.PNG|Windows Bitmap (bmp)|*.BMP|Joint Photographic Experts Group (jpg)|*.JPG|Portable Network Monocrome (pnm)|*.PNM|Tagged Image File Format (tif)|*.TIF|Archaic, useless format (pcx)|*.PCX",style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
self.update = self.updateSingle#update the image
self.updateData = self.updateSingleData#update the data in the image
#Create the menu
menubar = wx.MenuBar()
filemenu = wx.Menu()
editmenu = wx.Menu()
scalemenu = wx.Menu()
analysismenu = wx.Menu()
noisemenu = wx.Menu()
#populate the menu
filemenu.Append(self.ID_OPEN,"&Open\tCtrl-O"," Open a PEL file")
filemenu.Append(self.ID_OPENTWO,"&Polarized Set"," Open two PEL files")
filemenu.Append(self.ID_SAVE,"&Save\tCtrl-S"," Save an image file")
filemenu.Append(self.ID_SPECTRUM,"Spectrum"," View the TOF spectrum")
filemenu.Append(self.ID_IMAGE_ARRAY,"&Export Images..."," Save a series of TOF snapshots")
filemenu.Append(self.ID_EXIT,"&Quit\tCtrl-Q"," Quit")
editmenu.Append(self.ID_COPY,"&Copy\tCtrl-c","Copy the current image to the clipboard")
scalemenu.Append(self.ID_GREY,"Greyscale\tCtrl-G","Monochrome images")
scalemenu.Append(self.ID_HUEVAL,"Hue and Value\tCtrl-H","Scaled Rainbow Images")
scalemenu.Append(self.ID_SPECTRAL,"spectral","Uses spectrum of light")
scalemenu.Append(self.ID_PICKER,"Map Picker..."," Select from the full list of colormaps")
analysismenu.Append(self.ID_POLAR,"Check Polarization\tCtrl-P","2d plot of polarization data")
analysismenu.Append(self.ID_FLIPPING,"Check Flipping Ratio\tCtrl-F","2d plot of spin up over spin down")
analysismenu.Append(self.ID_SPIN_UP,"View Spin Up State\tCtrl-U","2d plot of spin up")
analysismenu.Append(self.ID_SPIN_DOWN,"View Spin Down State\tCtrl-D","2d plot of spin down")
noisemenu.Append(self.ID_FLAT,"&Load Flat"," Load a blank run for background subtraction")
noisemenu.Append(self.ID_FAKEFLAT,"Si&mulate Flat"," Drop out background within the same image")
noisemenu.Append(self.ID_ROD,"Region of &Disinterest"," Drop out background within the same image")
noisemenu.Append(self.ID_EXPORT_ROI,"Export ROI"," Export a binary file corresponding to where the data is above the minimum intensity.")
noisemenu.Append(self.ID_IMPORT_ROI,"Import ROI"," Add another exclusion mask.")
#Bind events to the menu
self.Connect(self.ID_EXIT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExit)
self.Connect(self.ID_OPEN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpen)
self.Connect(self.ID_OPENTWO,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnOpenSet)
self.Connect(self.ID_SAVE,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSave)
self.Connect(self.ID_SPECTRUM,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectrum)
self.Connect(self.ID_IMAGE_ARRAY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImageArray)
self.Connect(self.ID_GREY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnGrey)
self.Connect(self.ID_HUEVAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnHueVal)
self.Connect(self.ID_SPECTRAL,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnSpectral)
self.Connect(self.ID_PICKER,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPicker)
self.Connect(self.ID_POLAR,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnPolar)
self.Connect(self.ID_FLIPPING,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlipping)
self.Connect(self.ID_SPIN_UP,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinUp)
self.Connect(self.ID_SPIN_DOWN,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnAnalysisSpinDown)
self.Connect(self.ID_FLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFlat)
self.Connect(self.ID_FAKEFLAT,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnFakeFlat)
self.Connect(self.ID_ROD,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnROD)
self.Connect(self.ID_EXPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnExportROI)
self.Connect(self.ID_IMPORT_ROI,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnImportROI)
self.Connect(self.ID_COPY,-1,wx.wxEVT_COMMAND_MENU_SELECTED,self.OnCopy)
menubar.Append(filemenu,"&File")
menubar.Append(editmenu,"&Edit")
menubar.Append(scalemenu,"&Color")
menubar.Append(analysismenu,"&Analysis")
menubar.Append(noisemenu,"&Noise")
self.SetMenuBar(menubar)
#arrange window
sizer = wx.GridBagSizer()
sizer.Add(self.colorbar,pos=wx.GBPosition(0,9),span=wx.GBSpan(9,1))
sizer.Add(self.imPanel,pos=wx.GBPosition(0,1),span=wx.GBSpan(8,8))
sizer.Add(self.yPanel,pos=wx.GBPosition(0,0),span=wx.GBSpan(8,1))
sizer.Add(self.xPanel,pos=wx.GBPosition(8,1),span=wx.GBSpan(1,8))
sizer.Add(self.opPanel,pos=wx.GBPosition(0,10),span=wx.GBSpan(8,1),flag=wx.EXPAND)
sizer.Add(self.posPanel,pos=wx.GBPosition(8,0),flag=wx.EXPAND)
self.progress = wx.Gauge(self,range=1000)
sizer.Add(self.progress,pos=wx.GBPosition(9,0),span=wx.GBSpan(1,11),flag=wx.EXPAND)
updateButton = wx.Button(self,-1,"Update")
updateButton.Bind(wx.EVT_BUTTON,self.OnUpdateButton)
sizer.Add(updateButton,flag=wx.EXPAND,pos=wx.GBPosition(8,10))
self.data = self.makePel()
self.flatrun = None#background data
sizer.SetSizeHints(self)
self.SetSizer(sizer)
self.Show(True)
def makePel(self):
"""Create a blank Pel object for loading detector data"""
data = PelFile()
def statusfunc(x):
self.progress.SetValue(x)
self.Yield()
data.statusfunc = statusfunc
return data
def loadPel(self,message):
"""Load a .pel file and its monitor data.
Keyword arguments:
message -- The title for the load file dialog.
"""
dlg=wx.FileDialog(self,message,wildcard="He3 data|*neutron_event.dat|Preformatted Histograms|*.npy",style=wx.FD_OPEN)
if dlg.ShowModal()==wx.ID_OK:
# self.SetCursor(wx.CURSOR_WAIT)
path = dlg.GetPath()
if path[-3:] == "dat":
data = self.makePel()
data.readfileimage(path)
elif path[-3:] == "npy":
data = np.load(path)
# self.SetCursor(wx.CURSOR_ARROW)
else:
return (None,None)
mon = MonFile(path[:-17]+"bmon_histo.dat")
return (data,mon)
def OnImageArray(self,event):
"""Exports the 2d detector image by wavelength"""
dlg = self.imageSaveDialog
if dlg.ShowModal()==wx.ID_OK:
path=dlg.GetPath()
ext = path[-4:]
path = path[:-4]
(lmin,lmax) = self.opPanel.getLambdaRange()
for i in range(lmin,lmax):
file=path+("%03i"%i)+ext
self.opPanel.setLambdaRange(0.1*i,0.1*(i+1))
self.updateData()
self.update()
self.imPanel.saveImage(file)
self.progress.SetValue(1000*(i-lmin)/(lmax-lmin))
self.Yield()
self.opPanel.setLambdaRange(lmin*0.1,lmax*0.1)
self.updateData()
self.progress.SetValue(0)
def loadNormPel(self,message):
"""Load a .pel file, normalize it by monitor, and subtract background"""
(data,mon) = self.loadPel(message)
if isinstance(data,PelFile):
data = np.asarray(data.make3d(),np.float32)
if mon is None:
return (data,1)
if self.flatrun != None:
flatrun = np.load(self.flatrun)
self.flatrun.seek(0)
flatrun *= mon.time
data -= flatrun
spec = mon.spec
monsum = np.sum(spec)
print("Integrated monitor counts: " + str(monsum))
data /= monsum
return (data,np.sum(mon.spec))
# def getLambdaRange(self):
# try:
# lmin = int(float(self.lambdaMin.GetValue())*10)
# except ValueError:
# lmin = 0
# try:
# lmax = int(float(self.lambdaMax.GetValue())*10)
# except ValueError:
# lmax = 200
# return (lmin,lmax)
def updateSingleData(self,event=None):
"""Update changes in wavelength on a single file"""
print("Make 2d")
(lmin,lmax) = self.opPanel.getLambdaRange()
self.flatdata = np.sum(self.data[:,:,lmin:lmax],2)
self.update()
def updateDataFlip(self,event=None):
"""Update changes in wavelength for flipping ratios"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(u3d,d3d)=self.data
u = np.sum(u3d[:,:,lmin:lmax],2)
d = np.sum(d3d[:,:,lmin:lmax],2)
self.flatdata = u/(d+1e-6)
self.update()
def updateDataPolar(self,event=None):
"""Update changes in wavelength for polarizations"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(u3d,d3d)=self.data
u = np.sum(u3d[:,:,lmin:lmax],2)
d = np.sum(d3d[:,:,lmin:lmax],2)
self.flatdata = (u-d)/(u+d+1e-6)
self.update()
def updateDataUp(self,event=None):
"""Update changes in wavelength for the spin up state"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(u3d,_)=self.data
self.flatdata = np.sum(u3d[:,:,lmin:lmax],2)
self.update()
def updateDataDown(self,event=None):
"""Update changes in wavelength for the spin down state"""
(lmin,lmax) = self.opPanel.getLambdaRange()
(_,d3d)=self.data
self.flatdata = np.sum(d3d[:,:,lmin:lmax],2)
self.update()
def updateSingle(self,event=None):
"""Update the 2D data for the region of interest and intensity"""
(vMin,vMax) = self.opPanel.getIntensityRange()
(xMin,xMax,yMin,yMax) = self.opPanel.getRoi()
data = self.flatdata[:,:]
#Mask to zero during the summing parts
data[np.logical_not(self.mask)] = 0
self.posPanel.data = data
self.posPanel.setRange(xMin,yMin,xMax,yMax)
x=np.arange(128,0,-1)
y=np.sum(data[:,xMin:xMax],axis=1)
self.yPanel.SetPlot(x,y)
#handle the x-plot
x=np.arange(0,16,1)
y=np.sum(data[yMin:yMax,:],axis=0)
self.xPanel.SetPlot(x,y)
if vMin is None:
vMin = np.min(data)
if vMax is None:
vMax = np.max(data)
self.colorbar.setRange(vMin,vMax)
self.colorbar.update()
#mask to vmin for the plotting
data[np.logical_not(self.mask)] = vMin
self.imPanel.update(self.flatdata,vMin,vMax)
def OnUpdateButton(self,event):
"""Refresh the data when the user pushes the "Update" button"""
#This function is needed for wxWidgets to allow
#for dynamically changing the bound function
self.updateData(event)
def OnOpen(self,event):
"""Load a single .pel file for display"""
data,scale = self.loadNormPel("Choose the Pel File to Open")
if data is None:
return
self.data = data
self.scale = scale
self.progress.SetValue(0)
self.specDlg.setMode("up")
self.updateData = self.updateSingleData
self.update = self.updateSingle
self.updateData()
def OnOpenSet(self,event):
"""Load a spin flip measurement for display"""
if self.loadUpAndDown():
self.OnPolar(event)
def OnFlat(self,event):
"""Load a blank run for background subtraction"""
(data,mon) = self.loadPel("Choose a Blank Run")
if data == None:
return
if isinstance(data,PelFile):
flatrun = data.make3d()
elif isinstance(data,np.ndarray):
flatrun = data
flatrun = np.sum(flatrun,axis=2)
flatrun /= RESOLUTION
flatrun /= float(mon.time)
flatrun = np.expand_dims(flatrun,2)
self.flatrun = TemporaryFile()
np.save(self.flatrun,flatrun)
self.flatrun.seek(0)
self.progress.SetValue(0)
def OnFakeFlat(self,event):
"""Create a fake background run from outside the region of interest."""
(xMin,xMax,yMin,yMax)=self.opPanel.getRoi()
totarea = 512*512
centarea = (yMax-yMin)*(xMax-xMin)
backgroundarea = totarea-centarea
if type(self.data) is tuple:
(u,d)=self.data
totu = np.sum(u)
totd = np.sum(d)
centu = np.sum(u[yMin:yMax,xMin:xMax,:])
centd = np.sum(d[yMin:yMax,xMin:xMax,:])
backgroundu = totu-centu
backgroundd = totd-centd
backgroundrateu = backgroundu/backgroundarea
backgroundrated = backgroundd/backgroundarea
backgroundrateu /= (RESOLUTION + 1) #normalize against the wavelengths
backgroundrated /= (RESOLUTION + 1) #normalize against the wavelengths
###Stupid Memory Errors
del self.data
u -= backgroundrateu
d -= backgroundrated
###
self.data=(u,d)
else:
d=self.data
tot = np.sum(d)
cent = np.sum(d[yMin:yMax,xMin:xMax,:])
background = tot-cent
backgroundrate = background/backgroundarea
backgroundrate /= (RESOLUTION + 1) #normalize against the wavelengths
self.data-=backgroundrate
self.updateData()
#Subtract out the region of disinterest
def OnROD(self,event):
"""Take the region of interest as background noise"""
(xMin,xMax,yMin,yMax)=self.opPanel.getRoi()
area = (yMax-yMin)*(xMax-xMin)
if type(self.data) is tuple:
u,d=self.data
del self.data
totu = np.sum(np.sum(u[yMin:yMax,xMin:xMax,:],axis=0),axis=0)
totd = np.sum(np.sum(d[yMin:yMax,xMin:xMax,:],axis=0),axis=0)
totu /= area
totd /= area
u -= totu
d -= totd
self.data=(u,d)
else:
d=self.data
totd = np.sum(np.sum(d[yMin:yMax,xMin:xMax,:],axis=0),axis=0)
#totd = np.atleast_3d(totd)
totd /= area
#print(totd.shape)
#print(self.data.shape)
self.data -= totd
self.updateData()
def OnExportROI(self,event):
"""Save a file containing a map of where the current data
image is greater than vmin"""
vMin,_ = self.opPanel.getIntensityRange()
mask = self.flatdata > vMin
# (vMin,vMax) = self.opPanel.getIntensityRange()#
# (xMin,xMax,yMin,yMax) = self.opPanel.getRoi()#
# (lMin,lMax) = self.opPanel.getLambdaRange()#
# (lMin,lMax) = (lMin/10,lMax/10)#
# mask = [["xMin",xMin], ["xMax",xMax], ["yMin",yMin], ["yMax",yMax], \
# ["lMin",lMin], ["lMax",lMax], ["vMin",vMin], ["vMax",vMax]]#
dlg = wx.FileDialog(self,
"Where to save the mask file?",
wildcard="Numpy dump (npy)|*.npy|Text (dat)|*.dat",
style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal()==wx.ID_OK:
path=dlg.GetPath()
ext = path[-4:]
if ext == ".dat":
np.savetxt(path,mask,fmt="%d")
else:
np.save(path,mask)
def OnImportROI(self,event):
"""Adds another mask to the current system mask"""
dlg = wx.FileDialog(self,
"Which Mask File?",
wildcard="Numpy dump (npy)|*.npy|Text (dat)|*.dat",
style=wx.FD_OPEN)
time.sleep(.1)
if dlg.ShowModal()==wx.ID_OK:
path = dlg.GetPath()
ext = path[-4:]
if ext == ".dat":
newmask = np.loadtxt(path,dtype=np.bool)
newmask=dict(newmask)#
else:
newmask = np.load(path)
self.mask = np.logical_and(self.mask,newmask)
#self.opPanel.setPosMin(newmask["xMin"],newmask["yMin"])#
#self.opPanel.setPosMax(newmask["xMax"],newmask["yMax"])#
#self.opPanel.setLambdaRange(newmask["lMin"],newmask["lMax"])#
#self.opPanel.setIntensityRange(newmask["vMin"],newmask["vMax"])#
self.updateData()
def OnSave(self,event):
"""Save the current 2D image to a file"""
print("OnSave")
# dlg=wx.FileDialog(self,"Choose graphics file",wildcard="Windows Bitmap (bmp)|*.BMP|Portable Network Graphic (png)|*.PNG|Joint Photographic Experts Group (jpg)|*.JPG|Portable Network Monocrome (pnm)|*.PNM|Tagged Image File Format (tif)|*.TIF|Archaic, useless format (pcx)|*.PCX",style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
dlg = self.imageSaveDialog
if dlg.ShowModal()==wx.ID_OK:
self.imPanel.saveImage(dlg.GetPath())
def OnSpectrum(self,event):
"""Display a plot of the region of interest versus wavelength"""
print("OnSpectrum")
(xMin,xMax,yMin,yMax)=self.opPanel.getRoi()
if type(self.data) is tuple:
u3d,d3d = self.data
u3d = u3d[:,:,:]
d3d = d3d[:,:,:]
u3d[np.logical_not(self.mask)] = 0
d3d[np.logical_not(self.mask)] = 0
u = np.sum(np.sum(u3d[yMin:yMax,xMin:xMax],0),0)
d = np.sum(np.sum(d3d[yMin:yMax,xMin:xMax],0),0)
uscale,dscale = self.scale
self.specDlg.setScale(uscale,dscale)
self.specDlg.setData(u,d)
else:
copy = self.data[:,:,:]
copy[np.logical_not(self.mask)] = 0
u = np.sum(np.sum(copy[yMin:yMax,xMin:xMax],0),0)
# u *= self.scale
self.specDlg.setScale(self.scale)
self.specDlg.setData(u)
self.specDlg.setIntensityRange(self.opPanel.getIntensityRange())
self.specDlg.Show()
def OnGrey(self,event):
"""Set the colormap to gray"""
self.imPanel.cmap = cm.gray
self.colorbar.setCmap(cm.gray)
self.update()
def OnHueVal(self,event):
"""Set the colormap to a rainbow"""
self.imPanel.cmap = cm.jet
self.colorbar.setCmap(cm.jet)
self.update()
def OnSpectral(self,event):
"""Set the colormap to the spectral map"""
self.imPanel.cmap = cm.spectral
self.colorbar.setCmap(cm.spectral)
self.update()
def OnPicker(self,event):
"""Let the user pick a color map from a list"""
if self.cmp is None:
self.cmp = ColorMapPicker(self,self.setColorMap)
self.cmp.Show()
def setColorMap(self,cmap):
"""Changes to the given colormap"""
self.imPanel.cmap = cmap
self.colorbar.setCmap(cmap)
self.update()
def OnExit(self,event):
"""Quit the program"""
self.Close()
def loadUpAndDown(self):
"""Read in spin flip data"""
u3d,uscale = self.loadNormPel("Spin Up State")
if u3d is None:
return False
del self.data
d3d,dscale = self.loadNormPel("Spin Down State")
self.data = (u3d,d3d)
self.scale = (uscale,dscale)
return True
def OnPolar(self,event):
"""Display neutron polarization"""
print("OnPolar")
self.specDlg.setMode("polar")
self.updateData = self.updateDataPolar
self.update = self.updateSingle
self.updateData()
def OnFlipping(self,event):
"""Display the flipping ratio"""
print("OnFlip")
self.specDlg.setMode("flipping")
self.updateData = self.updateDataFlip
self.update = self.updateSingle
self.updateData()
def OnAnalysisSpinUp(self,event):
"""Display the Spin Up data"""
print("OnSpinUp")
self.specDlg.setMode("up")
self.updateData = self.updateDataUp
self.update = self.updateSingle
self.updateData()
def OnAnalysisSpinDown(self,event):
"""Display the Spin Down data"""
print("OnSpinDown")
self.specDlg.setMode("down")
self.updateData = self.updateDataDown
self.update = self.updateSingle
self.updateData()
def OnCopy(self,event):
"""Copy the image to a clipboard"""
self.imPanel.copyToClipboard()