class Bench(wx.Frame):
def __init__(self, parent, id=-1, title='Bench', **kwargs):
wx.Frame.__init__(self, parent, id, title=title, **kwargs)
# --- FRAME IS SPLIT INTO 2 PARTS (top, bottom) ---
self.splitter = wx.SplitterWindow(self, style=wx.NO_BORDER|wx.SP_3DSASH)
self.top_panel = wx.Panel(self.splitter)
self.bot_panel = wx.Panel(self.splitter)
self.splitter.SplitHorizontally(self.top_panel, self.bot_panel)
# --- CREATE WIDGETS ---
# TOP
self.tlabel1 = wx.StaticText(self.top_panel, -1, "Time:")
self.time_text_box = wx.TextCtrl(self.top_panel, -1, '0:00', size=(50, -1))
self.time_spin = wx.SpinButton(self.top_panel, -1, style=wx.SP_VERTICAL)
self.time_spin.Max = 1000000
self.time_slider = wx.Slider(self.top_panel, -1)
self.time_slider.SetRange(0, 1440)
self.add24_button = wx.Button(self.top_panel, -1, "Add 24h")
self.taglistctrl = TemporalTagListCtrl(self.top_panel)
# BOTTOM
self.group_checklist = VesselGroupSelector(self.bot_panel)
self.group_checklist.update_choices(self.bot_panel)
self.vesselscroller = VesselScroller(self.bot_panel)
self.vesselscroller.SetBackgroundColour('WHITE')
# --- BIND CONTROL EVENTS ---
self.time_slider.Bind(wx.EVT_SLIDER, self.on_adjust_timepoint)
self.time_spin.Bind(wx.EVT_SPIN_UP, self.on_increment_time)
self.time_spin.Bind(wx.EVT_SPIN_DOWN, self.on_decrement_time)
self.time_text_box.Bind(wx.EVT_TEXT, self.on_edit_time_text_box)
self.add24_button.Bind(wx.EVT_BUTTON, lambda(evt):self.set_time_interval(0, self.time_slider.GetMax()+1440))
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_SELECTED, self.on_instance_selected)
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.on_instance_selected)
self.group_checklist.GetCheckList().Bind(wx.EVT_CHECKLISTBOX, self.update_plate_groups)
# --- LAY OUT THE FRAME ---
time_sizer = wx.BoxSizer(wx.HORIZONTAL)
time_sizer.Add(self.tlabel1,0, wx.EXPAND|wx.ALL, 5)
time_sizer.Add(self.time_slider, 1, wx.EXPAND|wx.ALL, 5)
time_sizer.Add(self.time_text_box, 0, wx.ALL, 5)
time_sizer.Add(self.time_spin, 0, wx.ALL, 5)
time_sizer.Add(self.add24_button, 0, wx.ALL, 5)
stack_sizer = wx.BoxSizer(wx.HORIZONTAL)
stack_sizer.Add(wx.StaticText(self.bot_panel, -1, 'Select Vessel Stack(s)'), 0, wx.TOP, 3)
stack_sizer.Add(self.group_checklist, 1, wx.EXPAND)
self.top_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.top_panel.Sizer.Add(time_sizer, 0, wx.EXPAND|wx.LEFT|wx.RIGHT, 10)
self.top_panel.Sizer.Add(self.taglistctrl, 1, wx.EXPAND)
self.bot_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.bot_panel.Sizer.Add(stack_sizer, 0, wx.EXPAND|wx.ALL, 10)
self.bot_panel.Sizer.Add(self.vesselscroller, 1, wx.EXPAND)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.splitter, 1, wx.EXPAND)
def on_instance_selected(self, event):
'''when a protocol is selected from the taglistctrl
'''
for plate in self.vesselscroller.get_vessels():
plate.enable_selection(self.taglistctrl.get_selected_protocols() != [])
self.update_well_selections()
def update_plate_groups(self, event=None):
'''called when a vessel group is selected.
'''
meta = ExperimentSettings.getInstance()
selected_groups = self.group_checklist.GetCheckedStrings()
self.vesselscroller.clear()
group_tags = meta.get_matching_tags('ExptVessel|*|GroupName|*')
for tag in group_tags:
if meta.get_field(tag) in selected_groups:
group_name = meta.get_field(tag)
prefix = get_tag_stump(tag, 2)
vessel_type = tag.split('|')[1]
inst = get_tag_instance(tag)
plate_id = PlateDesign.get_plate_id(vessel_type, inst)
plate_shape = PlateDesign.get_plate_format(plate_id)
well_ids = PlateDesign.get_well_ids(plate_shape)
plate = VesselPanel(self.vesselscroller, plate_id)
self.vesselscroller.add_vessel_panel(plate, plate_id)
plate.add_well_selection_handler(self.on_update_well)
self.update_well_selections()
self.vesselscroller.FitInside()
def on_adjust_timepoint(self, evt):
self.set_timepoint(self.time_slider.Value)
def get_selected_timepoint(self):
return self.time_slider.GetValue()
def set_time_interval(self, tmin, tmax):
'''Sets the time slider interval.
tmin, tmax -- min and max timepoint values
'''
self.time_slider.SetRange(tmin, tmax)
def set_timepoint(self, timepoint):
'''Sets the slider timepoint and updates the plate display.
If a timepoint is set that is greater than time_slider's max, then the
time_slider interval is increased to include the timepoint.
'''
if timepoint > self.time_slider.Max:
self.time_slider.SetRange(0, timepoint)
self.time_slider.Value = timepoint
self.time_text_box.Value = format_time_string(timepoint)
self.update_well_selections()
def on_increment_time(self, evt):
self.set_timepoint(self.time_slider.Value + 1)
def on_decrement_time(self, evt):
self.set_timepoint(self.time_slider.Value - 1)
def on_edit_time_text_box(self, evt):
time_string = self.time_text_box.GetValue()
if not re.match('^\d*:\d\d$', time_string):
self.time_text_box.SetForegroundColour(wx.RED)
return
try:
hours, mins = map(int, time_string.split(':'))
minutes = hours * 60 + mins
self.set_timepoint(minutes)
self.time_text_box.SetForegroundColour(wx.BLACK)
except:
self.time_text_box.SetForegroundColour(wx.RED)
def update_well_selections(self):
'''Updates the selected vessels based on the currently selected
timepoint and protocols in the Bench.
Disables vessel selection if no protocol is selected.
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
for plate in self.vesselscroller.get_vessels():
plate.disable_selection()
plate.set_selected_well_ids([])
return
for protocol in protocols:
prefix, instance = protocol.rsplit('|', 1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
selected_ids = meta.get_field(wells_tag, [])
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_id in selected_ids if pw_id[0]==plate.get_plate_id()]
plate.set_selected_well_ids(selected_well_ids)
def on_update_well(self, platewell_id, selected):
'''Called when a well is clicked.
Populate all action tags with the set of wells that were effected.
eg: AddProcess|Spin|Wells|<instance>|<timepoint> = ['A01',...]
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
# SPECIAL CASE: For harvesting, we prompt the user to specify the
# destination well(s) for each harvested well.
if prefix == 'CellTransfer|Harvest':
if selected:
#
# TODO:
#
## dlg = TimepointSelectionPopup(self)
## if dlg.ShowModal() != wx.ID_OK:
## self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
## return
## new_timepoint = dlg.get_timepoint()
dlg = VesselSelectionPopup(self)
if dlg.ShowModal() == wx.ID_OK:
destination_wells = dlg.get_selected_platewell_ids()
assert destination_wells
new_id = meta.get_new_protocol_id('CellTransfer|Seed')
meta.set_field('CellTransfer|Seed|Wells|%s|%s'%
(new_id, self.get_selected_timepoint() + 1), # For now all reseeding instances are set 1 minute after harvesting
destination_wells)
meta.set_field('CellTransfer|Seed|HarvestInstance|%s'%(new_id), instance)
else:
self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
return
else:
# Harvesting event removed.
# Remove all Seeding events that were linked to it.
seed_harvest_tags = meta.get_field_tags('CellTransfer|Seed|HarvestInstance')
for t in seed_harvest_tags:
if meta.get_field(t) == instance:
# if this seed harvest instance is the same as the
# harvest instance that is being removed, then remove
# all seed tags of this instance
seed_tags = meta.get_field_tags('CellTransfer|Seed', get_tag_instance(t))
for seed_tag in seed_tags:
meta.remove_field(seed_tag)
# Update the Wells tag
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
platewell_ids = set(meta.get_field(wells_tag, []))
if selected:
platewell_ids.update([platewell_id])
meta.set_field(wells_tag, list(platewell_ids))
else:
platewell_ids.remove(platewell_id)
if len(platewell_ids) > 0:
meta.set_field(wells_tag, list(platewell_ids))
else:
meta.remove_field(wells_tag)
# Update the Images tags
if selected and prefix.startswith('DataAcquis'):
images_tag = '%s|Images|%s|%s|%s'%(prefix, instance, self.get_selected_timepoint(), repr(platewell_id))
if prefix == 'DataAcquis|HCS':
dlg = wx.FileDialog(self,message='Select the images for Plate %s, '
'Well %s'%(platewell_id[0], platewell_id[1]),
defaultDir=os.getcwd(), defaultFile='',
style=wx.OPEN|wx.MULTIPLE)
elif prefix == 'DataAcquis|FCS':
dlg = wx.FileDialog(self,message='Select the FCS files for flask %s'%(platewell_id[0]),
defaultDir=os.getcwd(), defaultFile='', wildcard = "Adobe PDF files (*.pdf)|*.pdf|",
style=wx.OPEN|wx.MULTIPLE)
elif prefix == 'DataAcquis|TLM':
dlg = wx.FileDialog(self,message='Select the images for Plate %s, '
'Well %s'%(platewell_id[0], platewell_id[1]),
defaultDir=os.getcwd(), defaultFile='',
style=wx.OPEN|wx.MULTIPLE)
else:
raise Exception('unrecognized tag prefix')
if dlg.ShowModal() == wx.ID_OK:
meta.set_field(images_tag, dlg.GetPaths())
os.chdir(os.path.split(dlg.GetPath())[0])
dlg.Destroy()
else:
dlg.Destroy()
meta.remove_field(images_tag)
vessel = self.vesselscroller.get_vessel(platewell_id[0])
if vessel:
vessel.deselect_well_at_pos(
PlateDesign.get_pos_for_wellid(
PlateDesign.get_plate_format(platewell_id[0]),
platewell_id[1]))
else:
raise Exception('Could not find vessel: %s'%(platewell_id[0]))
class Bench(wx.Frame):
def __init__(self, parent, id=-1, title='Bench', **kwargs):
wx.Frame.__init__(self, parent, id, title=title, **kwargs)
# --- FRAME IS SPLIT INTO 2 PARTS (top, bottom) ---
self.splitter = wx.SplitterWindow(self,
style=wx.NO_BORDER | wx.SP_3DSASH)
self.top_panel = wx.Panel(self.splitter)
self.bot_panel = wx.Panel(self.splitter)
self.splitter.SplitHorizontally(self.top_panel, self.bot_panel)
# --- CREATE WIDGETS ---
# TOP
self.tlabel1 = wx.StaticText(self.top_panel, -1, "Time:")
self.time_text_box = wx.TextCtrl(self.top_panel,
-1,
'0:00',
size=(50, -1))
self.time_spin = wx.SpinButton(self.top_panel,
-1,
style=wx.SP_VERTICAL)
self.time_spin.Max = 1000000
self.time_slider = wx.Slider(self.top_panel, -1)
self.time_slider.SetRange(0, 1440)
self.add24_button = wx.Button(self.top_panel, -1, "Add 24h")
self.taglistctrl = TemporalTagListCtrl(self.top_panel)
# BOTTOM
self.group_checklist = VesselGroupSelector(self.bot_panel)
self.group_checklist.update_choices(self.bot_panel)
self.vesselscroller = VesselScroller(self.bot_panel)
self.vesselscroller.SetBackgroundColour('WHITE')
# --- BIND CONTROL EVENTS ---
self.time_slider.Bind(wx.EVT_SLIDER, self.on_adjust_timepoint)
self.time_spin.Bind(wx.EVT_SPIN_UP, self.on_increment_time)
self.time_spin.Bind(wx.EVT_SPIN_DOWN, self.on_decrement_time)
self.time_text_box.Bind(wx.EVT_TEXT, self.on_edit_time_text_box)
self.add24_button.Bind(
wx.EVT_BUTTON, lambda
(evt): self.set_time_interval(0,
self.time_slider.GetMax() + 1440))
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_SELECTED,
self.on_instance_selected)
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_DESELECTED,
self.on_instance_selected)
self.group_checklist.GetCheckList().Bind(wx.EVT_CHECKLISTBOX,
self.update_plate_groups)
# --- LAY OUT THE FRAME ---
time_sizer = wx.BoxSizer(wx.HORIZONTAL)
time_sizer.Add(self.tlabel1, 0, wx.EXPAND | wx.ALL, 5)
time_sizer.Add(self.time_slider, 1, wx.EXPAND | wx.ALL, 5)
time_sizer.Add(self.time_text_box, 0, wx.ALL, 5)
time_sizer.Add(self.time_spin, 0, wx.ALL, 5)
time_sizer.Add(self.add24_button, 0, wx.ALL, 5)
stack_sizer = wx.BoxSizer(wx.HORIZONTAL)
stack_sizer.Add(
wx.StaticText(self.bot_panel, -1, 'Select Vessel Stack(s)'), 0,
wx.TOP, 3)
stack_sizer.Add(self.group_checklist, 1, wx.EXPAND)
self.top_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.top_panel.Sizer.Add(time_sizer, 0, wx.EXPAND | wx.LEFT | wx.RIGHT,
10)
self.top_panel.Sizer.Add(self.taglistctrl, 1, wx.EXPAND)
self.bot_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.bot_panel.Sizer.Add(stack_sizer, 0, wx.EXPAND | wx.ALL, 10)
self.bot_panel.Sizer.Add(self.vesselscroller, 1, wx.EXPAND)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.splitter, 1, wx.EXPAND)
def on_instance_selected(self, event):
'''when a protocol is selected from the taglistctrl
'''
for plate in self.vesselscroller.get_vessels():
plate.enable_selection(
self.taglistctrl.get_selected_protocols() != [])
self.update_well_selections()
def update_plate_groups(self, event=None):
'''called when a vessel group is selected.
'''
meta = ExperimentSettings.getInstance()
selected_groups = self.group_checklist.GetCheckedStrings()
self.vesselscroller.clear()
group_tags = meta.get_matching_tags('ExptVessel|*|GroupName|*')
for tag in group_tags:
if meta.get_field(tag) in selected_groups:
group_name = meta.get_field(tag)
prefix = get_tag_stump(tag, 2)
vessel_type = tag.split('|')[1]
inst = get_tag_instance(tag)
plate_id = PlateDesign.get_plate_id(vessel_type, inst)
plate_shape = PlateDesign.get_plate_format(plate_id)
well_ids = PlateDesign.get_well_ids(plate_shape)
plate = VesselPanel(self.vesselscroller, plate_id)
self.vesselscroller.add_vessel_panel(plate, plate_id)
plate.add_well_selection_handler(self.on_update_well)
self.update_well_selections()
self.vesselscroller.FitInside()
def on_adjust_timepoint(self, evt):
self.set_timepoint(self.time_slider.Value)
def get_selected_timepoint(self):
return self.time_slider.GetValue()
def set_time_interval(self, tmin, tmax):
'''Sets the time slider interval.
tmin, tmax -- min and max timepoint values
'''
self.time_slider.SetRange(tmin, tmax)
def set_timepoint(self, timepoint):
'''Sets the slider timepoint and updates the plate display.
If a timepoint is set that is greater than time_slider's max, then the
time_slider interval is increased to include the timepoint.
'''
if timepoint > self.time_slider.Max:
self.time_slider.SetRange(0, timepoint)
self.time_slider.Value = timepoint
self.time_text_box.Value = format_time_string(timepoint)
self.update_well_selections()
def on_increment_time(self, evt):
self.set_timepoint(self.time_slider.Value + 1)
def on_decrement_time(self, evt):
self.set_timepoint(self.time_slider.Value - 1)
def on_edit_time_text_box(self, evt):
time_string = self.time_text_box.GetValue()
if not re.match('^\d*:\d\d$', time_string):
self.time_text_box.SetForegroundColour(wx.RED)
return
try:
hours, mins = map(int, time_string.split(':'))
minutes = hours * 60 + mins
self.set_timepoint(minutes)
self.time_text_box.SetForegroundColour(wx.BLACK)
except:
self.time_text_box.SetForegroundColour(wx.RED)
def update_well_selections(self):
'''Updates the selected vessels based on the currently selected
timepoint and protocols in the Bench.
Disables vessel selection if no protocol is selected.
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
for plate in self.vesselscroller.get_vessels():
plate.disable_selection()
plate.set_selected_well_ids([])
return
for protocol in protocols:
prefix, instance = protocol.rsplit('|', 1)
wells_tag = '%s|Wells|%s|%s' % (prefix, instance,
self.get_selected_timepoint())
selected_ids = meta.get_field(wells_tag, [])
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [
pw_id for pw_id in selected_ids
if pw_id[0] == plate.get_plate_id()
]
plate.set_selected_well_ids(selected_well_ids)
def on_update_well(self, platewell_id, selected):
'''Called when a well is clicked.
Populate all action tags with the set of wells that were effected.
eg: AddProcess|Spin|Wells|<instance>|<timepoint> = ['A01',...]
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|', 1)
# SPECIAL CASE: For harvesting, we prompt the user to specify the
# destination well(s) for each harvested well.
if prefix == 'CellTransfer|Harvest':
if selected:
#
# TODO:
#
## dlg = TimepointSelectionPopup(self)
## if dlg.ShowModal() != wx.ID_OK:
## self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
## return
## new_timepoint = dlg.get_timepoint()
dlg = VesselSelectionPopup(self)
if dlg.ShowModal() == wx.ID_OK:
destination_wells = dlg.get_selected_platewell_ids()
assert destination_wells
new_id = meta.get_new_protocol_id('CellTransfer|Seed')
meta.set_field(
'CellTransfer|Seed|Wells|%s|%s' % (
new_id, self.get_selected_timepoint() + 1
), # For now all reseeding instances are set 1 minute after harvesting
destination_wells)
meta.set_field(
'CellTransfer|Seed|HarvestInstance|%s' % (new_id),
instance)
else:
self.vesselscroller.get_vessel(
platewell_id[0]).deselect_well_id(platewell_id)
return
else:
# Harvesting event removed.
# Remove all Seeding events that were linked to it.
seed_harvest_tags = meta.get_field_tags(
'CellTransfer|Seed|HarvestInstance')
for t in seed_harvest_tags:
if meta.get_field(t) == instance:
# if this seed harvest instance is the same as the
# harvest instance that is being removed, then remove
# all seed tags of this instance
seed_tags = meta.get_field_tags(
'CellTransfer|Seed', get_tag_instance(t))
for seed_tag in seed_tags:
meta.remove_field(seed_tag)
# Update the Wells tag
wells_tag = '%s|Wells|%s|%s' % (prefix, instance,
self.get_selected_timepoint())
platewell_ids = set(meta.get_field(wells_tag, []))
if selected:
platewell_ids.update([platewell_id])
meta.set_field(wells_tag, list(platewell_ids))
else:
platewell_ids.remove(platewell_id)
if len(platewell_ids) > 0:
meta.set_field(wells_tag, list(platewell_ids))
else:
meta.remove_field(wells_tag)
# Update the Images tags
if selected and prefix.startswith('DataAcquis'):
images_tag = '%s|Images|%s|%s|%s' % (prefix, instance,
self.get_selected_timepoint(),
repr(platewell_id))
if prefix == 'DataAcquis|HCS':
dlg = wx.FileDialog(self,
message='Select the images for Plate %s, '
'Well %s' %
(platewell_id[0], platewell_id[1]),
defaultDir=os.getcwd(),
defaultFile='',
style=wx.OPEN | wx.MULTIPLE)
elif prefix == 'DataAcquis|FCS':
dlg = wx.FileDialog(
self,
message='Select the FCS files for flask %s' %
(platewell_id[0]),
defaultDir=os.getcwd(),
defaultFile='',
wildcard="Adobe PDF files (*.pdf)|*.pdf|",
style=wx.OPEN | wx.MULTIPLE)
elif prefix == 'DataAcquis|TLM':
dlg = wx.FileDialog(self,
message='Select the images for Plate %s, '
'Well %s' %
(platewell_id[0], platewell_id[1]),
defaultDir=os.getcwd(),
defaultFile='',
style=wx.OPEN | wx.MULTIPLE)
else:
raise Exception('unrecognized tag prefix')
if dlg.ShowModal() == wx.ID_OK:
meta.set_field(images_tag, dlg.GetPaths())
os.chdir(os.path.split(dlg.GetPath())[0])
dlg.Destroy()
else:
dlg.Destroy()
meta.remove_field(images_tag)
vessel = self.vesselscroller.get_vessel(platewell_id[0])
if vessel:
vessel.deselect_well_at_pos(
PlateDesign.get_pos_for_wellid(
PlateDesign.get_plate_format(platewell_id[0]),
platewell_id[1]))
else:
raise Exception('Could not find vessel: %s' %
(platewell_id[0]))
class Bench(wx.Panel):
def __init__(self, protocol_navigator, parent, id=-1, **kwargs):
wx.Panel.__init__(self, parent, id, **kwargs)
self.protocol_navigator = protocol_navigator
# --- FRAME IS SPLIT INTO 2 PARTS (top, bottom) ---
self.splitter = wx.SplitterWindow(self, style=wx.NO_BORDER|wx.SP_3DSASH)
self.top_panel = wx.Panel(self.splitter)
self.bot_panel = wx.Panel(self.splitter)
self.splitter.SplitHorizontally(self.top_panel, self.bot_panel, -200)
# --- CREATE WIDGETS ---
# TOP
self.tlabel1 = wx.StaticText(self.top_panel, -1, "Time:")
self.time_text_box = wx.TextCtrl(self.top_panel, -1, '0:00', size=(50, -1))
self.time_spin = wx.SpinButton(self.top_panel, -1, style=wx.SP_VERTICAL)
self.time_spin.Max = 1000000
self.time_slider = wx.Slider(self.top_panel, -1)
self.time_slider.SetRange(0, 1440)
self.add24_button = wx.Button(self.top_panel, -1, "Add 24h")
self.taglistctrl = TemporalTagListCtrl(self.top_panel)
# BOTTOM
undo_bmp = icons.undo.Scale(24.0, 24.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.del_evt_button = wx.BitmapButton(self.bot_panel, -1, undo_bmp, style=0)
note_bmp = icons.note.Scale(24.0, 24.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.add_note_button = wx.BitmapButton(self.bot_panel, -1, note_bmp, style=0)
self.group_checklist = VesselGroupSelector(self.bot_panel)
self.group_checklist.update_choices(self.bot_panel)
self.vesselscroller = VesselScroller(self.bot_panel)
self.vesselscroller.SetBackgroundColour('WHITE')
# --- BIND CONTROL EVENTS ---
self.time_slider.Bind(wx.EVT_SLIDER, self.on_adjust_timepoint)
self.time_spin.Bind(wx.EVT_SPIN_UP, self.on_increment_time)
self.time_spin.Bind(wx.EVT_SPIN_DOWN, self.on_decrement_time)
self.time_text_box.Bind(wx.EVT_TEXT, self.on_edit_time_text_box)
self.add24_button.Bind(wx.EVT_BUTTON, lambda(evt):self.set_time_interval(0, self.time_slider.GetMax()+1440))
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_SELECTED, self.on_instance_selected)
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.on_instance_selected)
self.del_evt_button.Bind(wx.EVT_BUTTON, self.on_del_event)
self.del_evt_button.Disable()
self.add_note_button.Bind(wx.EVT_BUTTON, self.on_add_note)
self.group_checklist.GetCheckList().Bind(wx.EVT_CHECKLISTBOX, self.update_plate_groups)
# --- LAY OUT THE FRAME ---
time_sizer = wx.BoxSizer(wx.HORIZONTAL)
time_sizer.Add(self.tlabel1,0, wx.EXPAND|wx.ALL, 5)
time_sizer.Add(self.time_slider, 1, wx.EXPAND|wx.ALL, 5)
time_sizer.Add(self.time_text_box, 0, wx.ALL, 5)
time_sizer.Add(self.time_spin, 0, wx.ALL, 5)
time_sizer.Add(self.add24_button, 0, wx.ALL, 5)
#menu_sizer = wx.BoxSizer(wx.HORIZONTAL)
edit_staticbox = wx.StaticBox(self.bot_panel, -1, "Edit")
edit_flex = wx.FlexGridSizer(cols=2, hgap=5, vgap=5)
edit_flex.Add(wx.StaticText(self.bot_panel, -1, 'Undo Event'), 0, wx.CENTER)
edit_flex.Add(self.del_evt_button, 0)
edit_flex.Add(wx.StaticText(self.bot_panel, -1, 'Add Note'), 0, wx.CENTER)
edit_flex.Add(self.add_note_button, 0)
editSizer = wx.StaticBoxSizer(edit_staticbox, wx.VERTICAL)
editSizer.Add(edit_flex, 1, wx.EXPAND|wx.ALL, 2)
stack_sizer = wx.BoxSizer(wx.HORIZONTAL)
stack_sizer.Add(wx.StaticText(self.bot_panel, -1, 'Select Vessel Stack(s)'), 0, wx.LEFT|wx.CENTER, 3)
stack_sizer.Add(self.group_checklist, 1, wx.LEFT|wx.CENTER, 5)
stack_sizer.AddSpacer((10,-1))
stack_sizer.Add(editSizer, 0, wx.RIGHT|wx.CENTER)
self.top_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.top_panel.Sizer.Add(time_sizer, 0, wx.EXPAND|wx.LEFT|wx.RIGHT, 10)
self.top_panel.Sizer.Add(self.taglistctrl, 1, wx.EXPAND)
self.bot_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.bot_panel.Sizer.Add(stack_sizer, 0, wx.EXPAND|wx.ALL, 10)
self.bot_panel.Sizer.Add(self.vesselscroller, 1, wx.EXPAND)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.splitter, 1, wx.EXPAND)
def on_instance_selected(self, event):
'''when a protocol is selected from the taglistctrl
'''
for plate in self.vesselscroller.get_vessels():
plate.enable_selection(self.taglistctrl.get_selected_protocols() != [])
self.update_well_selections()
def update_plate_groups(self, event=None):
'''called when a vessel group is selected.
'''
meta = ExperimentSettings.getInstance()
selected_groups = self.group_checklist.GetCheckedStrings()
self.vesselscroller.clear()
group_tags = meta.get_matching_tags('ExptVessel|*|StackName|*')
for tag in sorted(group_tags, key=meta.stringSplitByNumbers):
if meta.get_field(tag) in selected_groups:
stack_name = meta.get_field(tag)
prefix = get_tag_stump(tag, 2)
vessel_type = tag.split('|')[1]
inst = get_tag_instance(tag)
plate_id = PlateDesign.get_plate_id(vessel_type, inst)
plate_shape = PlateDesign.get_plate_format(plate_id)
well_ids = PlateDesign.get_well_ids(plate_shape)
plate = VesselPanel(self.vesselscroller, plate_id)
self.vesselscroller.add_vessel_panel(plate, plate_id)
plate.add_well_selection_handler(self.on_update_well)
self.update_well_selections()
self.vesselscroller.FitInside()
def on_adjust_timepoint(self, evt):
self.set_timepoint(self.time_slider.Value)
def get_selected_timepoint(self):
return self.time_slider.GetValue()
def set_time_interval(self, tmin, tmax):
'''Sets the time slider interval.
tmin, tmax -- min and max timepoint values
'''
self.time_slider.SetRange(tmin, tmax)
def set_timepoint(self, timepoint):
'''Sets the slider timepoint and updates the plate display.
If a timepoint is set that is greater than time_slider's max, then the
time_slider interval is increased to include the timepoint.
'''
if timepoint > self.time_slider.Max:
self.time_slider.SetRange(0, timepoint)
self.time_slider.Value = timepoint
self.time_text_box.Value = format_time_string(timepoint)
self.protocol_navigator.get_lineage().set_hover_timepoint(timepoint)
self.update_well_selections()
self.update_well_state_status()
def on_increment_time(self, evt):
self.set_timepoint(self.time_slider.Value + 1)
def on_decrement_time(self, evt):
self.set_timepoint(self.time_slider.Value - 1)
def on_edit_time_text_box(self, evt):
time_string = self.time_text_box.GetValue()
if not re.match('^\d*:\d\d$', time_string):
self.time_text_box.SetForegroundColour(wx.RED)
return
try:
hours, mins = map(int, time_string.split(':'))
minutes = hours * 60 + mins
self.set_timepoint(minutes)
self.time_text_box.SetForegroundColour(wx.BLACK)
except:
self.time_text_box.SetForegroundColour(wx.RED)
def on_add_note(self, evt):
# check whether any event occured at this timepoint
timeline = meta.get_timeline()
self.events_by_timepoint = timeline.get_events_by_timepoint()
prefixes = set([get_tag_stump(ev.get_welltag(), 2) for ev in self.events_by_timepoint[self.get_selected_timepoint()]])
if not prefixes:
dial = wx.MessageDialog(None, 'Notes need to be associated with events!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
try:
lineage_panel = wx.GetApp().get_lineage()
except:
return
self.page_counter = meta.get_new_protocol_id('Notes')
if int(self.page_counter) > 1:
lineage_panel.timeline_panel.on_note_icon_add()
note_dia = NotePad(self, None, None, None) # timepoint and instance number as none because users might click Cancel
if note_dia.ShowModal() == wx.ID_OK:
# Notes|<type>|<timepoint>|<instance> = value
meta.set_field('Notes|%s|%s|%s' %(note_dia.noteType, str(self.get_selected_timepoint()), str(self.page_counter)), note_dia.noteDescrip.GetValue())
lineage_panel.timeline_panel.on_note_icon_add()
def on_del_event(self, evt):
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
dial = wx.MessageDialog(None, 'No event was found for deletion\nor\nCan not undo cell transfer event', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
meta.remove_field(wells_tag)
self.update_well_selections()
self.del_evt_button.Disable()
def update_well_selections(self):
'''Updates the selected vessels based on the currently selected
timepoint and protocols in the Bench.
Disables vessel selection if no protocol is selected.
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
for plate in self.vesselscroller.get_vessels():
plate.disable_selection()
plate.set_selected_well_ids([])
return
for protocol in protocols:
prefix, instance = protocol.rsplit('|', 1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
selected_ids = meta.get_field(wells_tag, [])
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_id in selected_ids if pw_id[0]==plate.get_plate_id()]
plate.set_selected_well_ids(selected_well_ids)
def update_well_state_status(self):
timeline = meta.get_timeline()
selected_ids = [timeline.get_well_ids(utp) for utp in timeline.get_unique_timepoints() if utp <= self.get_selected_timepoint()]
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_ids in selected_ids for pw_id in pw_ids if pw_id[0]==plate.get_plate_id()]
plate.set_well_ids_state(selected_well_ids)
def on_update_well(self, platewell_id, selected):
'''Called when a well is clicked.
Populate all action tags with the set of wells that were effected.
eg: AddProcess|Spin|Wells|<instance>|<timepoint> = ['A01',...]
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
#platewell_ids = set(meta.get_field(wells_tag, []))
# SPECIAL CASE: For harvesting, we prompt the user to specify the
# destination well(s) for each harvested well.
if prefix == 'CellTransfer|Harvest':
if selected:
#
# TODO:
#
## dlg = TimepointSelectionPopup(self)
## if dlg.ShowModal() != wx.ID_OK:
## self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
## return
## new_timepoint = dlg.get_timepoint()
dlg = VesselSelectionPopup(self)
if dlg.ShowModal() == wx.ID_OK:
destination_wells = dlg.get_selected_platewell_ids()
assert destination_wells
new_id = meta.get_new_protocol_id('CellTransfer|Seed')
meta.set_field('CellTransfer|Seed|Wells|%s|%s'%
(new_id, self.get_selected_timepoint() + 1), # For now all reseeding instances are set 1 minute after harvesting
destination_wells)
meta.set_field('CellTransfer|Seed|HarvestInstance|%s'%(new_id), instance)
h_density = meta.get_field('CellTransfer|Harvest|HarvestingDensity|%s'%instance, [])
s_density = [0,'']
if len(h_density) > 0:
s_density[0]= h_density[0]
if len(h_density) > 1:
s_density[1]= h_density[1]
meta.set_field('CellTransfer|Seed|SeedingDensity|%s'%(new_id), s_density)
if meta.get_field('CellTransfer|Harvest|MediumAddatives|%s'%instance) is not None:
meta.set_field('CellTransfer|Seed|MediumAddatives|%s'%(new_id), meta.get_field('CellTransfer|Harvest|MediumAddatives|%s'%instance))
else:
self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
return
else:
# Harvesting event removed.
# Remove all Seeding events that were linked to it.
seed_harvest_tags = meta.get_field_tags('CellTransfer|Seed|HarvestInstance')
for t in seed_harvest_tags:
if meta.get_field(t) == instance:
# if this seed harvest instance is the same as the
# harvest instance that is being removed, then remove
# all seed tags of this instance
seed_tags = meta.get_field_tags('CellTransfer|Seed', get_tag_instance(t))
for seed_tag in seed_tags:
meta.remove_field(seed_tag)
# GENERIC CASE: Associate or dissociate event with selected wells
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
platewell_ids = set(meta.get_field(wells_tag, []))
if selected:
platewell_ids.update(platewell_id)
meta.set_field(wells_tag, list(platewell_ids))
#else:
#platewell_ids.discard(platewell_id)
#if len(platewell_ids) > 0:
#meta.set_field(wells_tag, list(platewell_ids))
#else:
#meta.remove_field(wells_tag)
# Update the Images tags
if selected and prefix.startswith('DataAcquis'):
images_tag = '%s|Images|%s|%s|%s'%(prefix, instance, self.get_selected_timepoint(), repr(platewell_id))
if prefix == 'DataAcquis|HCS':
dlg = wx.FileDialog(self,message='Select the images files',
defaultDir=os.getcwd(), defaultFile='', style=wx.OPEN|wx.MULTIPLE)
elif prefix == 'DataAcquis|FCS':
#dlg = wx.FileDialog(self,message='Select the FCS files for flask %s'%(platewell_id[0].strip('[]')),
dlg = wx.FileDialog(self,message='Select the FCS (pdf) files for flask',
defaultDir=os.getcwd(), defaultFile='', wildcard = "Adobe PDF files (*.pdf)|*.pdf|", style=wx.OPEN|wx.MULTIPLE)
elif prefix == 'DataAcquis|TLM':
dlg = wx.FileDialog(self,message='Select the images files',
defaultDir=os.getcwd(), defaultFile='', style=wx.OPEN|wx.MULTIPLE)
else:
raise Exception('unrecognized tag prefix')
if dlg.ShowModal() == wx.ID_OK:
meta.set_field(images_tag, dlg.GetPaths())
os.chdir(os.path.split(dlg.GetPath())[0])
dlg.Destroy()
else:
dlg.Destroy()
meta.remove_field(wells_tag)
vessel = self.vesselscroller.get_vessel(platewell_id[0])
if vessel:
vessel.deselect_well_at_pos(
PlateDesign.get_pos_for_wellid(
PlateDesign.get_plate_format(platewell_id[0]),
platewell_id[1]))
else:
raise Exception('Could not find vessel: %s'%(platewell_id[0]))
class Bench(wx.Panel):
def __init__(self, protocol_navigator, parent, id=-1, **kwargs):
wx.Panel.__init__(self, parent, id, **kwargs)
self.protocol_navigator = protocol_navigator
# --- FRAME IS SPLIT INTO 2 PARTS (top, bottom) ---
self.splitter = wx.SplitterWindow(self, style=wx.NO_BORDER|wx.SP_3DSASH)
self.top_panel = wx.Panel(self.splitter)
self.bot_panel = wx.Panel(self.splitter)
self.splitter.SplitHorizontally(self.top_panel, self.bot_panel)
self.splitter.SetSashGravity(0.6)
self.selected_harvest_inst = None
# --- CREATE WIDGETS ---
# TOP PANEL
self.time_text_box = wx.TextCtrl(self.top_panel, -1, '0:00', size=(50, -1))
self.time_spin = wx.SpinButton(self.top_panel, -1, style=wx.SP_VERTICAL)
self.time_spin.Max = 1000000
self.time_slider = wx.Slider(self.top_panel, -1)
self.time_slider.SetRange(0, 1440)
self.taglistctrl = TemporalTagListCtrl(self.top_panel)
clock_bmp = icons.clock.Scale(24.0, 24.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.add24_button = wx.BitmapButton(self.top_panel, -1, clock_bmp)
self.add24_button.SetToolTipString("Add 24 Hr.")
attach_bmp = icons.clip.Scale(20.0, 20.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.attach_button = wx.BitmapButton(self.top_panel, -1, attach_bmp)
self.attach_button.SetToolTipString("Attach any type of files with particular event.")
note_bmp = icons.note.Scale(20.0, 20.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.add_note_button = wx.BitmapButton(self.top_panel, -1, note_bmp)
self.add_note_button.SetToolTipString("Additional textual notes, URL or multimedia files about an event can be added.")
undo_bmp = icons.undo.Scale(20.0, 20.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.del_evt_button = wx.BitmapButton(self.top_panel, -1, undo_bmp)
self.del_evt_button.SetToolTipString("Undo event, select event first and then click this undo button.")
# BOTTOM PANEL
self.group_checklist = VesselGroupSelector(self.bot_panel)
self.group_checklist.update_choices(self.bot_panel)
self.vesselscroller = VesselScroller(self.bot_panel)
self.vesselscroller.SetBackgroundColour('WHITE')
# --- BIND CONTROL EVENTS ---
self.time_slider.Bind(wx.EVT_SLIDER, self.on_adjust_timepoint)
self.time_spin.Bind(wx.EVT_SPIN_UP, self.on_increment_time)
self.time_spin.Bind(wx.EVT_SPIN_DOWN, self.on_decrement_time)
self.time_text_box.Bind(wx.EVT_TEXT, self.on_edit_time_text_box)
self.add24_button.Bind(wx.EVT_BUTTON, lambda(evt):self.set_time_interval(0, self.time_slider.GetMax()+1440))
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_SELECTED, self.on_instance_selected)
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.on_instance_selected)
self.del_evt_button.Bind(wx.EVT_BUTTON, self.on_del_event)
self.del_evt_button.Disable()
self.attach_button.Bind(wx.EVT_BUTTON, self.OnAttachPropFile)
self.add_note_button.Bind(wx.EVT_BUTTON, self.on_add_note)
self.group_checklist.GetCheckList().Bind(wx.EVT_CHECKLISTBOX, self.update_plate_groups)
# --- LAY OUT THE FRAME ---
menu_sizer = wx.BoxSizer(wx.HORIZONTAL)
menu_sizer.Add(self.attach_button, 0)
menu_sizer.AddSpacer((5,-1))
#menu_sizer.Add(wx.StaticText(self.top_panel, -1, 'Add Note'), 0, wx.CENTER)
menu_sizer.Add(self.add_note_button, 0)
menu_sizer.AddSpacer((5,-1))
#menu_sizer.Add(wx.StaticText(self.top_panel, -1, 'Undo Event'), 0, wx.CENTER)
menu_sizer.Add(self.del_evt_button, 0)
time_sizer = wx.BoxSizer(wx.HORIZONTAL)
time_sizer.Add(self.time_slider, 1, wx.EXPAND|wx.TOP, 5)
time_sizer.Add(self.time_text_box, 0, wx.TOP, 5)
time_sizer.Add(self.time_spin, 0, wx.BOTTOM, 5)
time_sizer.Add(self.add24_button, 0, wx.LEFT|wx.TOP|wx.RIGHT, 5)
#tadd_sizer = wx.BoxSizer(wx.VERTICAL)
#tadd_sizer.Add(wx.StaticText(self.top_panel, -1, 'Add 24h'), 0, wx.ALIGN_CENTER_VERTICAL)
#tadd_sizer.Add(self.add24_button, 0, wx.ALIGN_BOTTOM)
time_staticbox = wx.StaticBox(self.top_panel, -1, "Time")
timeSizer = wx.StaticBoxSizer(time_staticbox, wx.HORIZONTAL)
timeSizer.Add(time_sizer, 1, wx.EXPAND|wx.ALL, 5)
#timeSizer.Add(tadd_sizer)
stack_sizer = wx.BoxSizer(wx.HORIZONTAL)
stack_sizer.Add(wx.StaticText(self.bot_panel, -1, 'Select Vessel Stack(s)'), 0, wx.LEFT|wx.CENTER, 3)
stack_sizer.Add(self.group_checklist, 1, wx.LEFT|wx.CENTER, 5)
self.top_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.top_panel.Sizer.Add((-1, 5))
self.top_panel.Sizer.Add(menu_sizer, 0, wx.ALIGN_RIGHT|wx.RIGHT, 10)
self.top_panel.Sizer.Add(timeSizer, 0, wx.EXPAND|wx.LEFT|wx.RIGHT, 10)
self.top_panel.Sizer.Add((-1, 5))
self.top_panel.Sizer.Add(self.taglistctrl, 1, wx.EXPAND)
self.bot_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.bot_panel.Sizer.Add(stack_sizer, 0, wx.EXPAND|wx.ALL, 10)
self.bot_panel.Sizer.Add(self.vesselscroller, 1, wx.EXPAND)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.splitter, 1, wx.EXPAND)
def on_instance_selected(self, event):
'''when a protocol is selected from the taglistctrl
'''
for plate in self.vesselscroller.get_vessels():
plate.enable_selection(self.taglistctrl.get_selected_protocols() != [])
self.update_well_selections()
def update_plate_groups(self, event=None):
'''called when a vessel group is selected.
'''
meta = ExperimentSettings.getInstance()
selected_groups = self.group_checklist.GetCheckedStrings()
self.vesselscroller.clear()
group_tags = meta.get_matching_tags('ExptVessel|*|StackName|*')
for tag in sorted(group_tags, key=meta.stringSplitByNumbers):
if meta.get_field(tag) in selected_groups:
stack_name = meta.get_field(tag)
prefix = get_tag_stump(tag, 2)
vessel_type = tag.split('|')[1]
inst = get_tag_instance(tag)
plate_id = PlateDesign.get_plate_id(vessel_type, inst)
plate_shape = PlateDesign.get_plate_format(plate_id)
well_ids = PlateDesign.get_well_ids(plate_shape)
plate = VesselPanel(self.vesselscroller, plate_id)
self.vesselscroller.add_vessel_panel(plate, plate_id)
plate.add_well_selection_handler(self.on_update_well)
self.update_well_selections()
self.vesselscroller.FitInside()
def on_adjust_timepoint(self, evt):
self.set_timepoint(self.time_slider.Value)
def get_selected_timepoint(self):
return self.time_slider.GetValue()
def set_time_interval(self, tmin, tmax):
'''Sets the time slider interval.
tmin, tmax -- min and max timepoint values
'''
self.time_slider.SetRange(tmin, tmax)
def set_timepoint(self, timepoint):
'''Sets the slider timepoint and updates the plate display.
If a timepoint is set that is greater than time_slider's max, then the
time_slider interval is increased to include the timepoint.
'''
if timepoint > self.time_slider.Max:
self.time_slider.SetRange(0, timepoint)
self.time_slider.Value = timepoint
self.time_text_box.Value = format_time_string(timepoint)
self.protocol_navigator.get_lineage().set_hover_timepoint(timepoint)
self.update_well_selections()
self.update_well_state_status()
def on_increment_time(self, evt):
self.set_timepoint(self.time_slider.Value + 1)
def on_decrement_time(self, evt):
self.set_timepoint(self.time_slider.Value - 1)
def on_edit_time_text_box(self, evt):
time_string = self.time_text_box.GetValue()
if not re.match('^\d*:\d\d$', time_string):
self.time_text_box.SetForegroundColour(wx.RED)
return
try:
hours, mins = map(int, time_string.split(':'))
minutes = hours * 60 + mins
self.set_timepoint(minutes)
self.time_text_box.SetForegroundColour(wx.BLACK)
except:
self.time_text_box.SetForegroundColour(wx.RED)
def on_add_note(self, evt):
# check whether any event occured at this timepoint
timeline = meta.get_timeline()
self.events_by_timepoint = timeline.get_events_by_timepoint()
if not self.events_by_timepoint:
dial = wx.MessageDialog(None, 'No Timeline found!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
prefixes = set([get_tag_stump(ev.get_welltag(), 2) for ev in self.events_by_timepoint[self.get_selected_timepoint()]])
if not prefixes:
dial = wx.MessageDialog(None, 'Notes need to be associated with events!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
try:
lineage_panel = wx.GetApp().get_lineage()
except:
return
self.page_counter = meta.get_new_protocol_id('Notes')
if int(self.page_counter) > 1:
lineage_panel.timeline_panel.on_note_icon_add()
note_dia = NotePad(self, None, None, None) # timepoint and instance number as none because users might click Cancel
if note_dia.ShowModal() == wx.ID_OK:
# Notes|<type>|<timepoint>|<instance> = description
if not hasattr(note_dia, 'noteDescrip'):
return
if not note_dia.noteDescrip.GetValue():
dial = wx.MessageDialog(None, 'Description required for the note!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
meta.set_field('Notes|%s|%s|%s' %(note_dia.noteType, str(self.get_selected_timepoint()), str(self.page_counter)), note_dia.noteDescrip.GetValue())
lineage_panel.timeline_panel.on_note_icon_add()
def OnAttachPropFile(self, event):
# check whether any event occured at this timepoint
timeline = meta.get_timeline()
self.events_by_timepoint = timeline.get_events_by_timepoint()
if not self.events_by_timepoint:
dial = wx.MessageDialog(None, 'No Timeline found!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
prefixes = set([get_tag_stump(ev.get_welltag(), 2) for ev in self.events_by_timepoint[self.get_selected_timepoint()]])
if not prefixes:
dial = wx.MessageDialog(None, 'Attachments need to be associated with events!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
try:
lineage_panel = wx.GetApp().get_lineage()
except:
return
self.page_counter = meta.get_new_protocol_id('Attachments')
if int(self.page_counter) > 1:
lineage_panel.timeline_panel.on_note_icon_add()
attfileTAG = 'Attachments|Files|%s|%s' %(str(self.get_selected_timepoint()), str(self.page_counter))
dia = FileListDialog(self, attfileTAG, meta.get_field(attfileTAG, []), None)
if dia.ShowModal()== wx.ID_OK:
f_list = dia.file_list
if f_list:
meta.set_field(attfileTAG, f_list)
lineage_panel.timeline_panel.on_note_icon_add()
def on_del_event(self, evt):
if self.selected_harvest_inst.startswith('Transfer|Harvest'):
#Make users aware that whole track will be deleted
try:
lineage_panel = wx.GetApp().get_lineage()
except:
return
lineage_panel.lineage_panel.remove_harvest_seed_track(self.selected_harvest_inst)
else:
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
dial = wx.MessageDialog(None, 'No event was found for deletion\nor\nCan not undo cell transfer event', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
meta.remove_field(wells_tag)
if prefix.startswith('DataAcquis'):
for images_tag in meta.get_matching_tags('%s|Images|%s|%s|*'%(prefix, instance, self.get_selected_timepoint())):
meta.remove_field(images_tag)
self.update_well_selections()
self.del_evt_button.Disable()
def update_well_selections(self):
'''Updates the selected vessels based on the currently selected
timepoint and protocols in the Bench.
Disables vessel selection if no protocol is selected.
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
for plate in self.vesselscroller.get_vessels():
plate.disable_selection()
plate.set_selected_well_ids([])
return
for protocol in protocols:
prefix, instance = protocol.rsplit('|', 1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
selected_ids = meta.get_field(wells_tag, [])
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_id in selected_ids if pw_id[0]==plate.get_plate_id()]
plate.set_selected_well_ids(selected_well_ids)
def update_well_state_status(self):
timeline = meta.get_timeline()
selected_ids = [timeline.get_well_ids(utp) for utp in timeline.get_unique_timepoints() if utp <= self.get_selected_timepoint()]
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_ids in selected_ids for pw_id in pw_ids if pw_id[0]==plate.get_plate_id()]
plate.set_well_ids_state(selected_well_ids)
def on_update_well(self, platewell_id, selected):
'''Called when a well is clicked.
Populate all action tags with the set of wells that were effected.
eg: AddProcess|Spin|Wells|<instance>|<timepoint> = ['A01',...]
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
err_dia = wx.MessageDialog(None, 'No instance selected, select an instance from the list', 'Error', wx.OK|wx.ICON_ERROR)
err_dia.ShowModal()
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
platewell_ids = set(meta.get_field(wells_tag, []))
selected_pw_id = list(set(platewell_id)-platewell_ids)
if selected_pw_id:
affected_pw_ids = []
for curr_tag in meta.get_matching_tags('*|*|Wells|*|%s'%self.get_selected_timepoint()):
affected_pw_ids.extend(meta.get_field(curr_tag))
if selected_pw_id[0] in affected_pw_ids:
err_dia = wx.MessageDialog(None, 'Multiple events at same time and location is not permissible', 'Error', wx.OK|wx.ICON_ERROR)
err_dia.ShowModal()
return
# SPECIAL CASE: For harvesting, we prompt the user to specify the
# destination well(s) for each harvested well.
if prefix == 'Transfer|Harvest':
if selected:
dlg = VesselSelectionPopup(self)
if dlg.ShowModal() == wx.ID_OK:
destination_wells = dlg.get_selected_platewell_ids()
assert destination_wells
new_id = meta.get_new_protocol_id('Transfer|Seed')
meta.set_field('Transfer|Seed|Wells|%s|%s'%
(new_id, self.get_selected_timepoint() + 1), # For now all reseeding instances are set 1 minute after harvesting
destination_wells)
meta.set_field('Transfer|Seed|HarvestInstance|%s'%(new_id), instance)
h_density = meta.get_field('Transfer|Harvest|HarvestingDensity|%s'%instance, [])
s_density = [0,'']
if len(h_density) > 0:
s_density[0]= h_density[0]
if len(h_density) > 1:
s_density[1]= h_density[1]
meta.set_field('Transfer|Seed|SeedingDensity|%s'%(new_id), s_density)
if meta.get_field('Transfer|Harvest|MediumAddatives|%s'%instance) is not None:
meta.set_field('Transfer|Seed|MediumAddatives|%s'%(new_id), meta.get_field('Transfer|Harvest|MediumAddatives|%s'%instance))
else:
self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
return
else:
# Harvesting event removed.
# Remove all Seeding events that were linked to it.
seed_harvest_tags = meta.get_field_tags('Transfer|Seed|HarvestInstance')
for t in seed_harvest_tags:
if meta.get_field(t) == instance:
# if this seed harvest instance is the same as the
# harvest instance that is being removed, then remove
# all seed tags of this instance
seed_tags = meta.get_field_tags('Transfer|Seed', get_tag_instance(t))
for seed_tag in seed_tags:
meta.remove_field(seed_tag)
# GENERIC CASE: Associate or dissociate event with selected wells
platewell_ids.update(platewell_id)
meta.set_field(wells_tag, list(platewell_ids))
# SPECIAL CASE: for data/image association or dissociation
if selected and prefix.startswith('DataAcquis'):
stack_name = PlateDesign.get_plate_group(selected_pw_id[0][0])
origin_location = '"'+stack_name+'_'+selected_pw_id[0][0]+'_'+selected_pw_id[0][1]+'"'
images_tag = '%s|Images|%s|%s|%s'%(prefix, instance, self.get_selected_timepoint(), selected_pw_id)
dia = FileListDialog(self, images_tag, meta.get_field(images_tag, []), origin_location)
if dia.ShowModal()== wx.ID_OK:
f_list = dia.file_list
if f_list:
meta_dia = ShowMetaDataLinkListDialog(self, f_list)
if meta_dia.ShowModal() == wx.ID_OK:
platewell_ids.update(platewell_id)
meta.set_field(wells_tag, list(platewell_ids))
meta.set_field(images_tag, meta_dia.data_metadata.items())
meta_dia.data_metadata.clear()
else:
meta.remove_field(wells_tag)
self.update_well_selections()
else:
meta.remove_field(wells_tag)
self.update_well_selections()
else:
meta.remove_field(wells_tag)
self.update_well_selections()
class Bench(wx.Frame):
def __init__(self, protocol_navigator, id=-1, title='Bench', **kwargs):
wx.Frame.__init__(self, None, id, title=title, **kwargs)
self.protocol_navigator = protocol_navigator
# --- FRAME IS SPLIT INTO 2 PARTS (top, bottom) ---
self.splitter = wx.SplitterWindow(self, style=wx.NO_BORDER|wx.SP_3DSASH)
self.top_panel = wx.Panel(self.splitter)
self.bot_panel = wx.Panel(self.splitter)
self.splitter.SplitHorizontally(self.top_panel, self.bot_panel)
# --- CREATE WIDGETS ---
# TOP
self.tlabel1 = wx.StaticText(self.top_panel, -1, "Time:")
self.time_text_box = wx.TextCtrl(self.top_panel, -1, '0:00', size=(50, -1))
self.time_spin = wx.SpinButton(self.top_panel, -1, style=wx.SP_VERTICAL)
self.time_spin.Max = 1000000
self.time_slider = wx.Slider(self.top_panel, -1)
self.time_slider.SetRange(0, 1440)
self.add24_button = wx.Button(self.top_panel, -1, "Add 24h")
self.taglistctrl = TemporalTagListCtrl(self.top_panel)
# BOTTOM
undo_bmp = icons.undo.Scale(24.0, 24.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.del_evt_button = wx.BitmapButton(self.bot_panel, -1, undo_bmp, style=0)
note_bmp = icons.note.Scale(24.0, 24.0, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
self.add_note_button = wx.BitmapButton(self.bot_panel, -1, note_bmp, style=0)
self.group_checklist = VesselGroupSelector(self.bot_panel)
self.group_checklist.update_choices(self.bot_panel)
self.vesselscroller = VesselScroller(self.bot_panel)
self.vesselscroller.SetBackgroundColour('WHITE')
# --- BIND CONTROL EVENTS ---
self.time_slider.Bind(wx.EVT_SLIDER, self.on_adjust_timepoint)
self.time_spin.Bind(wx.EVT_SPIN_UP, self.on_increment_time)
self.time_spin.Bind(wx.EVT_SPIN_DOWN, self.on_decrement_time)
self.time_text_box.Bind(wx.EVT_TEXT, self.on_edit_time_text_box)
self.add24_button.Bind(wx.EVT_BUTTON, lambda(evt):self.set_time_interval(0, self.time_slider.GetMax()+1440))
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_SELECTED, self.on_instance_selected)
self.taglistctrl.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.on_instance_selected)
self.del_evt_button.Bind(wx.EVT_BUTTON, self.on_del_event)
self.del_evt_button.Disable()
self.add_note_button.Bind(wx.EVT_BUTTON, self.on_add_note)
self.group_checklist.GetCheckList().Bind(wx.EVT_CHECKLISTBOX, self.update_plate_groups)
# --- LAY OUT THE FRAME ---
time_sizer = wx.BoxSizer(wx.HORIZONTAL)
time_sizer.Add(self.tlabel1,0, wx.EXPAND|wx.ALL, 5)
time_sizer.Add(self.time_slider, 1, wx.EXPAND|wx.ALL, 5)
time_sizer.Add(self.time_text_box, 0, wx.ALL, 5)
time_sizer.Add(self.time_spin, 0, wx.ALL, 5)
time_sizer.Add(self.add24_button, 0, wx.ALL, 5)
#menu_sizer = wx.BoxSizer(wx.HORIZONTAL)
edit_staticbox = wx.StaticBox(self.bot_panel, -1, "Edit")
edit_flex = wx.FlexGridSizer(cols=2, hgap=5, vgap=5)
edit_flex.Add(wx.StaticText(self.bot_panel, -1, 'Undo Event'), 0, wx.CENTER)
edit_flex.Add(self.del_evt_button, 0)
edit_flex.Add(wx.StaticText(self.bot_panel, -1, 'Add Note'), 0, wx.CENTER)
edit_flex.Add(self.add_note_button, 0)
editSizer = wx.StaticBoxSizer(edit_staticbox, wx.VERTICAL)
editSizer.Add(edit_flex, 1, wx.EXPAND|wx.ALL, 2)
stack_sizer = wx.BoxSizer(wx.HORIZONTAL)
stack_sizer.Add(wx.StaticText(self.bot_panel, -1, 'Select Vessel Stack(s)'), 0, wx.LEFT|wx.CENTER, 3)
stack_sizer.Add(self.group_checklist, 1, wx.LEFT|wx.CENTER, 5)
stack_sizer.AddSpacer((10,-1))
stack_sizer.Add(editSizer, 0, wx.RIGHT|wx.CENTER)
self.top_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.top_panel.Sizer.Add(time_sizer, 0, wx.EXPAND|wx.LEFT|wx.RIGHT, 10)
self.top_panel.Sizer.Add(self.taglistctrl, 1, wx.EXPAND)
self.bot_panel.Sizer = wx.BoxSizer(wx.VERTICAL)
self.bot_panel.Sizer.Add(stack_sizer, 0, wx.EXPAND|wx.ALL, 10)
self.bot_panel.Sizer.Add(self.vesselscroller, 1, wx.EXPAND)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.splitter, 1, wx.EXPAND)
def on_instance_selected(self, event):
'''when a protocol is selected from the taglistctrl
'''
for plate in self.vesselscroller.get_vessels():
plate.enable_selection(self.taglistctrl.get_selected_protocols() != [])
self.update_well_selections()
def update_plate_groups(self, event=None):
'''called when a vessel group is selected.
'''
meta = ExperimentSettings.getInstance()
selected_groups = self.group_checklist.GetCheckedStrings()
self.vesselscroller.clear()
group_tags = meta.get_matching_tags('ExptVessel|*|StackName|*')
for tag in sorted(group_tags, key=meta.stringSplitByNumbers):
if meta.get_field(tag) in selected_groups:
stack_name = meta.get_field(tag)
prefix = get_tag_stump(tag, 2)
vessel_type = tag.split('|')[1]
inst = get_tag_instance(tag)
plate_id = PlateDesign.get_plate_id(vessel_type, inst)
plate_shape = PlateDesign.get_plate_format(plate_id)
well_ids = PlateDesign.get_well_ids(plate_shape)
plate = VesselPanel(self.vesselscroller, plate_id)
self.vesselscroller.add_vessel_panel(plate, plate_id)
plate.add_well_selection_handler(self.on_update_well)
self.update_well_selections()
self.vesselscroller.FitInside()
def on_adjust_timepoint(self, evt):
self.set_timepoint(self.time_slider.Value)
def get_selected_timepoint(self):
return self.time_slider.GetValue()
def set_time_interval(self, tmin, tmax):
'''Sets the time slider interval.
tmin, tmax -- min and max timepoint values
'''
self.time_slider.SetRange(tmin, tmax)
def set_timepoint(self, timepoint):
'''Sets the slider timepoint and updates the plate display.
If a timepoint is set that is greater than time_slider's max, then the
time_slider interval is increased to include the timepoint.
'''
if timepoint > self.time_slider.Max:
self.time_slider.SetRange(0, timepoint)
self.time_slider.Value = timepoint
self.time_text_box.Value = format_time_string(timepoint)
self.protocol_navigator.get_lineage().set_hover_timepoint(timepoint)
self.update_well_selections()
self.update_well_state_status()
def on_increment_time(self, evt):
self.set_timepoint(self.time_slider.Value + 1)
def on_decrement_time(self, evt):
self.set_timepoint(self.time_slider.Value - 1)
def on_edit_time_text_box(self, evt):
time_string = self.time_text_box.GetValue()
if not re.match('^\d*:\d\d$', time_string):
self.time_text_box.SetForegroundColour(wx.RED)
return
try:
hours, mins = map(int, time_string.split(':'))
minutes = hours * 60 + mins
self.set_timepoint(minutes)
self.time_text_box.SetForegroundColour(wx.BLACK)
except:
self.time_text_box.SetForegroundColour(wx.RED)
def on_add_note(self, evt):
# check whether any event occured at this timepoint
timeline = meta.get_timeline()
self.events_by_timepoint = timeline.get_events_by_timepoint()
prefixes = set([get_tag_stump(ev.get_welltag(), 2) for ev in self.events_by_timepoint[self.get_selected_timepoint()]])
if not prefixes:
dial = wx.MessageDialog(None, 'Notes need to be associated with events!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
try:
lineage_panel = wx.GetApp().get_lineage()
except:
return
self.page_counter = meta.get_new_protocol_id('Notes')
if int(self.page_counter) > 1:
lineage_panel.timeline_panel.on_note_icon_add()
note_dia = NotePad(self, None, None, None) # timepoint and instance number as none because users might click Cancel
if note_dia.ShowModal() == wx.ID_OK:
# Notes|<type>|<timepoint>|<instance> = value
meta.set_field('Notes|%s|%s|%s' %(note_dia.noteType, str(self.get_selected_timepoint()), str(self.page_counter)), note_dia.noteDescrip.GetValue())
lineage_panel.timeline_panel.on_note_icon_add()
def on_del_event(self, evt):
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
dial = wx.MessageDialog(None, 'No event was found for deletion\nor\nCan not undo cell transfer event', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
meta.remove_field(wells_tag)
self.update_well_selections()
self.del_evt_button.Disable()
def update_well_selections(self):
'''Updates the selected vessels based on the currently selected
timepoint and protocols in the Bench.
Disables vessel selection if no protocol is selected.
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
for plate in self.vesselscroller.get_vessels():
plate.disable_selection()
plate.set_selected_well_ids([])
return
for protocol in protocols:
prefix, instance = protocol.rsplit('|', 1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
selected_ids = meta.get_field(wells_tag, [])
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_id in selected_ids if pw_id[0]==plate.get_plate_id()]
plate.set_selected_well_ids(selected_well_ids)
def update_well_state_status(self):
timeline = meta.get_timeline()
selected_ids = [timeline.get_well_ids(utp) for utp in timeline.get_unique_timepoints() if utp <= self.get_selected_timepoint()]
for plate in self.vesselscroller.get_vessels():
plate.enable_selection()
selected_well_ids = [pw_id for pw_ids in selected_ids for pw_id in pw_ids if pw_id[0]==plate.get_plate_id()]
plate.set_well_ids_state(selected_well_ids)
def on_update_well(self, platewell_id, selected):
'''Called when a well is clicked.
Populate all action tags with the set of wells that were effected.
eg: AddProcess|Spin|Wells|<instance>|<timepoint> = ['A01',...]
'''
protocols = self.taglistctrl.get_selected_protocols()
if protocols == []:
return
protocol = protocols[0]
prefix, instance = protocol.rsplit('|',1)
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
#platewell_ids = set(meta.get_field(wells_tag, []))
# SPECIAL CASE: For harvesting, we prompt the user to specify the
# destination well(s) for each harvested well.
if prefix == 'CellTransfer|Harvest':
if selected:
#
# TODO:
#
## dlg = TimepointSelectionPopup(self)
## if dlg.ShowModal() != wx.ID_OK:
## self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
## return
## new_timepoint = dlg.get_timepoint()
dlg = VesselSelectionPopup(self)
if dlg.ShowModal() == wx.ID_OK:
destination_wells = dlg.get_selected_platewell_ids()
assert destination_wells
new_id = meta.get_new_protocol_id('CellTransfer|Seed')
meta.set_field('CellTransfer|Seed|Wells|%s|%s'%
(new_id, self.get_selected_timepoint() + 1), # For now all reseeding instances are set 1 minute after harvesting
destination_wells)
meta.set_field('CellTransfer|Seed|HarvestInstance|%s'%(new_id), instance)
h_density = meta.get_field('CellTransfer|Harvest|HarvestingDensity|%s'%instance, [])
s_density = [0,'']
if len(h_density) > 0:
s_density[0]= h_density[0]
if len(h_density) > 1:
s_density[1]= h_density[1]
meta.set_field('CellTransfer|Seed|SeedingDensity|%s'%(new_id), s_density)
if meta.get_field('CellTransfer|Harvest|MediumAddatives|%s'%instance) is not None:
meta.set_field('CellTransfer|Seed|MediumAddatives|%s'%(new_id), meta.get_field('CellTransfer|Harvest|MediumAddatives|%s'%instance))
else:
self.vesselscroller.get_vessel(platewell_id[0]).deselect_well_id(platewell_id)
return
else:
# Harvesting event removed.
# Remove all Seeding events that were linked to it.
seed_harvest_tags = meta.get_field_tags('CellTransfer|Seed|HarvestInstance')
for t in seed_harvest_tags:
if meta.get_field(t) == instance:
# if this seed harvest instance is the same as the
# harvest instance that is being removed, then remove
# all seed tags of this instance
seed_tags = meta.get_field_tags('CellTransfer|Seed', get_tag_instance(t))
for seed_tag in seed_tags:
meta.remove_field(seed_tag)
# GENERIC CASE: Associate or dissociate event with selected wells
wells_tag = '%s|Wells|%s|%s'%(prefix, instance, self.get_selected_timepoint())
platewell_ids = set(meta.get_field(wells_tag, []))
if selected:
platewell_ids.update(platewell_id)
meta.set_field(wells_tag, list(platewell_ids))
#else:
#platewell_ids.discard(platewell_id)
#if len(platewell_ids) > 0:
#meta.set_field(wells_tag, list(platewell_ids))
#else:
#meta.remove_field(wells_tag)
# Update the Images tags
if selected and prefix.startswith('DataAcquis'):
images_tag = '%s|Images|%s|%s|%s'%(prefix, instance, self.get_selected_timepoint(), repr(platewell_id))
if prefix == 'DataAcquis|HCS':
dlg = wx.FileDialog(self,message='Select the images files',
defaultDir=os.getcwd(), defaultFile='', style=wx.OPEN|wx.MULTIPLE)
elif prefix == 'DataAcquis|FCS':
#dlg = wx.FileDialog(self,message='Select the FCS files for flask %s'%(platewell_id[0].strip('[]')),
dlg = wx.FileDialog(self,message='Select the FCS (pdf) files for flask',
defaultDir=os.getcwd(), defaultFile='', wildcard = "Adobe PDF files (*.pdf)|*.pdf|", style=wx.OPEN|wx.MULTIPLE)
elif prefix == 'DataAcquis|TLM':
dlg = wx.FileDialog(self,message='Select the images files',
defaultDir=os.getcwd(), defaultFile='', style=wx.OPEN|wx.MULTIPLE)
else:
raise Exception('unrecognized tag prefix')
if dlg.ShowModal() == wx.ID_OK:
meta.set_field(images_tag, dlg.GetPaths())
os.chdir(os.path.split(dlg.GetPath())[0])
dlg.Destroy()
else:
dlg.Destroy()
meta.remove_field(wells_tag)
vessel = self.vesselscroller.get_vessel(platewell_id[0])
if vessel:
vessel.deselect_well_at_pos(
PlateDesign.get_pos_for_wellid(
PlateDesign.get_plate_format(platewell_id[0]),
platewell_id[1]))
else:
raise Exception('Could not find vessel: %s'%(platewell_id[0]))