class ExperimentSettings(Singleton):
global_settings = {}
timeline = Timeline('TEST_STOCK')
subscribers = {}
def __init__(self):
pass
def set_field(self, tag, value, notify_subscribers=True):
self.global_settings[tag] = value
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'SET FIELD: %s = %s' % (tag, value)
def get_field(self, tag, default=None):
return self.global_settings.get(tag, default)
def remove_field(self, tag, notify_subscribers=True):
'''completely removes the specified tag from the metadata (if it exists)
'''
#if self.get_field(tag) is not None:
self.global_settings.pop(tag)
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'DEL FIELD: %s' % (tag)
def get_action_tags(self):
'''returns all existing TEMPORAL tags as list'''
return [
tag for tag in self.global_settings
if tag.split('|')[0] in ('CellTransfer', 'Perturbation',
'Labeling', 'AddProcess', 'DataAcquis')
]
def get_field_instances(self, tag_prefix):
'''returns a list of unique instance ids for each tag beginning with
tag_prefix'''
ids = set([
get_tag_instance(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_attribute_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([
get_tag_attribute(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_attribute_dict(self, protocol):
'''returns a dict mapping attribute names to their values for a given
protocol.
eg: get_attribute_dict('CellTransfer|Seed|1') -->
{'SeedingDensity': 12, 'MediumUsed': 'agar',
'MediumAddatives': 'None', 'Trypsinization': True}
'''
d = {}
for tag in self.get_matching_tags('|*|'.join(protocol.rsplit('|', 1))):
if (get_tag_attribute(tag) not in ('Wells', 'EventTimepoint',
'Images', 'OriginWells')):
d[get_tag_attribute(tag)] = self.global_settings[tag]
return d
def get_eventtype_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([
tag.split('|')[1] for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_eventclass_list(self, tag_prefix):
'''returns a list of event class name for each tag beginning with
tag_prefix'''
ids = set([
tag.split('|')[0] for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_field_tags(self, tag_prefix=None, instance=None):
'''returns a list of all tags beginning with tag_prefix. If instance
is passed in, only tags of the given instance will be returned'''
tags = []
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
tags += [tag]
return tags
def get_matching_tags(self, matchstring):
'''returns a list of all tags matching matchstring
matchstring -- a string that matches the tags you want
eg: CellTransfer|*
'''
tags = []
for tag in self.global_settings:
match = True
for m, subtag in map(None, matchstring.split('|'), tag.split('|')):
if m != subtag and m not in ('*', None):
match = False
break
if match:
tags += [tag]
return tags
def get_protocol_instances(self, prefix):
'''returns a list of protocol instance names for tags
matching the given prefix.
'''
return list(
set([get_tag_instance(tag)
for tag in self.get_field_tags(prefix)]))
def get_new_protocol_id(self, prefix):
'''returns an id string that hasn't been used for the given tag prefix
prefix -- eg: CellTransfer|Seed
'''
instances = self.get_protocol_instances(prefix)
for i in xrange(1, 100000):
if str(i) not in instances:
return str(i)
def clear(self):
self.global_settings = {}
PlateDesign.clear()
#
# TODO:
#
self.timeline = Timeline('TEST_STOCK')
for matchstring, callbacks in self.subscribers.items():
for callback in callbacks:
callback(None)
def get_timeline(self):
return self.timeline
def update_timeline(self, welltag):
'''Updates the experiment metadata timeline event associated with the
action and wells in welltag (eg: 'ExpNum|AddProcess|Spin|Wells|1|1')
'''
platewell_ids = self.get_field(welltag, [])
if platewell_ids == []:
self.timeline.delete_event(welltag)
else:
event = self.timeline.get_event(welltag)
if event is not None:
event.set_well_ids(platewell_ids)
else:
self.timeline.add_event(welltag, platewell_ids)
def save_to_file(self, file):
f = open(file, 'w')
for field, value in sorted(self.global_settings.items()):
f.write('%s = %s\n' % (field, repr(value)))
f.close()
def load_from_file(self, file):
# Populate the tag structure
self.clear()
f = open(file, 'r')
for line in f:
tag, value = line.split('=')
tag = tag.strip()
self.set_field(tag, eval(value), notify_subscribers=False)
f.close()
# Populate PlateDesign
PlateDesign.clear()
for vessel_type in ('Plate', 'Flask', 'Dish', 'Coverslip'):
prefix = 'ExptVessel|%s' % (vessel_type)
for inst in self.get_field_instances(prefix):
d = self.get_attribute_dict(prefix + '|' + inst)
shape = d.get('Design', None)
if shape is None:
shape = (1, 1)
group = d.get('GroupName', None)
PlateDesign.add_plate(vessel_type, inst, shape, group)
# Update everything
for tag in self.global_settings:
self.notify_subscribers(tag)
# Update the bench time-slider
# TODO: this is crappy
try:
import wx
bench = wx.GetApp().get_bench()
bench.set_time_interval(0, self.get_timeline().get_max_timepoint())
except:
return
def add_subscriber(self, callback, match_string):
'''callback -- the function to be called
match_string -- a regular expression string matching the tags you want
to be notified of changes to
'''
self.subscribers[match_string] = self.subscribers.get(
match_string, []) + [callback]
def remove_subscriber(self, callback):
'''unsubscribe the given callback function.
This MUST be called before a callback function is deleted.
'''
for k, v in self.subscribers:
if v == callback:
self.subscribers.pop(k)
def notify_subscribers(self, tag):
for matchstring, callbacks in self.subscribers.items():
if re.match(matchstring, tag):
for callback in callbacks:
callback(tag)
class ExperimentSettings(Singleton):
global_settings = {}
timeline = Timeline('TEST_STOCK')
subscribers = {}
def __init__(self):
pass
def set_field(self, tag, value, notify_subscribers=True):
self.global_settings[tag] = value
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'SET FIELD: %s = %s'%(tag, value)
def get_field(self, tag, default=None):
return self.global_settings.get(tag, default)
def remove_field(self, tag, notify_subscribers=True):
'''completely removes the specified tag from the metadata (if it exists)
'''
#if self.get_field(tag) is not None:
self.global_settings.pop(tag)
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'DEL FIELD: %s'%(tag)
def get_action_tags(self):
'''returns all existing TEMPORAL tags as list'''
return [tag for tag in self.global_settings
if tag.split('|')[0] in ('CellTransfer', 'Perturbation',
'Staining', 'AddProcess', 'DataAcquis', 'Notes')]
def get_field_instances(self, tag_prefix):
'''returns a list of unique instance ids for each tag beginning with
tag_prefix'''
ids = set([get_tag_instance(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_attribute_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([get_tag_attribute(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_attribute_list_by_instance(self, tag_prefix, instance=None):
'''returns a list of all attributes beginning with tag_prefix. If instance
is passed in, only attributes of the given instance will be returned'''
ids = set([get_tag_attribute(tag) for tag in self.global_settings
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance))])
return list(ids)
#tags = []
#for tag in self.global_settings:
#if ((tag_prefix is None or tag.startswith(tag_prefix)) and
#(instance is None or get_tag_instance(tag) == instance)):
#tag += [tag]
#ids= set([get_tag_attribute(tag)])
#return list(ids)
def get_attribute_dict(self, protocol):
'''returns a dict mapping attribute names to their values for a given
protocol.
eg: get_attribute_dict('CellTransfer|Seed|1') -->
{'SeedingDensity': 12, 'MediumUsed': 'agar',
'MediumAddatives': 'None', 'Trypsinization': True}
'''
d = {}
for tag in self.get_matching_tags('|*|'.join(protocol.rsplit('|',1))):
if (get_tag_attribute(tag) not in ('Wells', 'EventTimepoint', 'Images', 'OriginWells')):
d[get_tag_attribute(tag)] = self.global_settings[tag]
return d
def get_eventtype_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([tag.split('|')[1] for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_eventclass_list(self, tag_prefix):
'''returns a list of event class name for each tag beginning with
tag_prefix'''
ids = set([tag.split('|')[0] for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_field_tags(self, tag_prefix=None, instance=None):
'''returns a list of all tags beginning with tag_prefix. If instance
is passed in, only tags of the given instance will be returned'''
tags = []
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
tags += [tag]
return tags
def get_matching_tags(self, matchstring):
'''returns a list of all tags matching matchstring
matchstring -- a string that matches the tags you want
eg: CellTransfer|*
'''
tags = []
for tag in self.global_settings:
match = True
for m, subtag in map(None, matchstring.split('|'), tag.split('|')):
if m != subtag and m not in ('*', None):
match = False
break
if match:
tags += [tag]
return tags
def get_protocol_instances(self, prefix):
'''returns a list of protocol instance names for tags
matching the given prefix.
'''
return list(set([get_tag_instance(tag)
for tag in self.get_field_tags(prefix)]))
def get_new_protocol_id(self, prefix):
'''returns an id string that hasn't been used for the given tag prefix
prefix -- eg: CellTransfer|Seed
'''
instances = self.get_protocol_instances(prefix)
for i in xrange(1, 100000):
if str(i) not in instances:
return str(i)
def get_instance_by_field_value(self, prefix, field_value):
'''returns instance number given tag prefix and field value
'''
return get_tag_instance([tag for tag, value in self.global_settings.iteritems() if value == field_value][0])
def get_stack_ids(self, prefix):
'''returns the stack ids for a given type of vessels prefix e.g. ExptVessel|Tube'''
return set([self.get_field(prefix+'|StackNo|%s'%instance)
for instance in sorted(self.get_field_instances(prefix))])
def get_rep_vessel_instance(self, prefix, stack_id):
''' returns instance number of the vessel for this stack, since all vessels of a given stack has identical settings
one instance represents others'''
for instance in sorted(self.get_field_instances(prefix)):
if self.get_field(prefix+'|StackNo|%s'%(instance)) == stack_id:
return instance
def clear(self):
self.global_settings = {}
PlateDesign.clear()
#
# TODO:
#
self.timeline = Timeline('TEST_STOCK')
for matchstring, callbacks in self.subscribers.items():
for callback in callbacks:
callback(None)
def onTabClosing(self, event):
event.Veto()
dlg = wx.MessageDialog(None, 'Can not delete instance', 'Deleting..', wx.OK| wx.ICON_STOP)
dlg.ShowModal()
return
def get_timeline(self):
return self.timeline
def does_tag_exists(self, tag_prefix, instnace=None):
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and (instnace is None or get_tag_instance(tag) == instnace)):
return True
else:
return False
def is_supp_protocol_filled(self, tag_prefix, instance=None):
'''tag_prefix is always type|event e.g. AddProcess|Wash
'''
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and (instance is None or get_tag_instance(tag) == instance)):
if (self.get_field(tag_prefix+'|ProtocolName|%s'%instance) is None) or (self.get_field(tag_prefix+'|Step1|%s'%instance) == ['', '', '']):
return False
else:
return True
def update_timeline(self, welltag):
'''Updates the experiment metadata timeline event associated with the
action and wells in welltag (eg: 'ExpNum|AddProcess|Spin|Wells|1|1')
'''
platewell_ids = self.get_field(welltag, [])
if platewell_ids == []:
self.timeline.delete_event(welltag)
else:
event = self.timeline.get_event(welltag)
if event is not None:
event.set_well_ids(platewell_ids)
else:
self.timeline.add_event(welltag, platewell_ids)
def save_to_file(self, file):
f = open(file, 'w')
for field, value in sorted(self.global_settings.items()):
f.write('%s = %s\n'%(field, repr(value)))
f.close()
def save_settings(self, file, protocol):
'''
saves settings in text file. the settings may include instrument settings, supp protocol, stock flask
Format: attr = value where value may be text, int, list, etc.
'''
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
setting_type = get_tag_event(protocol)
f = open(file,'w')
f.write(setting_type+'\n')
attributes = self.get_attribute_list_by_instance(tag_stump, instance)
for attr in attributes:
info = self.get_field(tag_stump+'|%s|%s' %(attr, instance))
print info
f.write('%s = %s\n'%(attr, repr(info)))
f.close()
def save_supp_protocol_file(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
f = open(file,'w')
attributes = self.get_attribute_list_by_instance(tag_stump, instance)
for attr in attributes:
info = self.get_field(tag_stump+'|%s|%s' %(attr, instance))
if isinstance(info, list):
f.write('%s|'%attr)
for i, val in enumerate(info):
if isinstance(val, tuple):
print val
elif i == len(info)-1:
f.write('%s'%val)
else:
f.write('%s|'%val)
f.write('\n')
else:
f.write('%s|%s\n'%(attr, info))
f.close()
def load_from_file(self, file):
# Populate the tag structure
self.clear()
f = open(file, 'r')
for line in f:
tag, value = line.split('=', 1)
tag = tag.strip()
self.set_field(tag, eval(value), notify_subscribers=False)
f.close()
# Populate PlateDesign
PlateDesign.clear()
for vessel_type in ('Plate', 'Flask', 'Dish', 'Coverslip', 'Tube'):
prefix = 'ExptVessel|%s'%(vessel_type)
for inst in self.get_field_instances(prefix):
d = self.get_attribute_dict(prefix+'|'+inst)
shape = d.get('Design', None)
if shape is None:
shape = (1,1)
group = d.get('StackName', None)
PlateDesign.add_plate(vessel_type, inst, shape, group)
# Update everything
for tag in self.global_settings:
self.notify_subscribers(tag)
# Update the bench time-slider
# TODO: this is crappy
try:
import wx
bench = wx.GetApp().get_bench()
bench.set_time_interval(0, self.get_timeline().get_max_timepoint())
except:return
def load_supp_protocol_file(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
lines = [line.strip() for line in open(file)]
if not lines:
import wx
dial = wx.MessageDialog(None, 'Supplementary protocol file is empty!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
for line in lines:
#line.rstrip('\n')
line_info = line.split('|')
attr = line_info.pop(0)
if len(line_info)>1:
self.set_field(tag_stump+'|%s|%s'%(attr, instance), line_info)
else:
self.set_field(tag_stump+'|%s|%s'%(attr, instance), line_info[0])
def load_settings(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
f = open(file, 'r')
lines = [line.strip() for line in f]
lines.pop(0) # takes out the first line or the header where all setting type microscope/spin etc are written
for line in lines:
attr, value = line.split('=', 1)
attr = attr.strip()
tag = tag_stump+'|%s|%s'%(attr, instance)
self.set_field(tag, eval(value), notify_subscribers=False)
self.notify_subscribers(tag)
f.close()
def add_subscriber(self, callback, match_string):
'''callback -- the function to be called
match_string -- a regular expression string matching the tags you want
to be notified of changes to
'''
self.subscribers[match_string] = self.subscribers.get(match_string, []) + [callback]
def remove_subscriber(self, callback):
'''unsubscribe the given callback function.
This MUST be called before a callback function is deleted.
'''
for k, v in self.subscribers:
if v == callback:
self.subscribers.pop(k)
def notify_subscribers(self, tag):
for matchstring, callbacks in self.subscribers.items():
if re.match(matchstring, tag):
for callback in callbacks:
callback(tag)
def getNM(self, nm):
return int(nm.split('-')[0]), int(nm.split('-')[1])
def belongsTo(self, value, rangeStart, rangeEnd):
if value >= rangeStart and value <= rangeEnd:
return True
return False
def partition(self, lst, n):
division = len(lst) / float(n)
rlist = [lst[int(round(division * i)): int(round(division * (i + 1)))] [-1] for i in xrange(n) ]
rlist.insert(0, lst[0])
return rlist
def stringSplitByNumbers(self, x):
r = re.compile('(\d+)')
l = r.split(x)
return [int(y) if y.isdigit() else y for y in l]
def nmToRGB(self, w):
# colour
if w >= 380 and w < 440:
R = -(w - 440.) / (440. - 350.)
G = 0.0
B = 1.0
elif w >= 440 and w < 490:
R = 0.0
G = (w - 440.) / (490. - 440.)
B = 1.0
elif w >= 490 and w < 510:
R = 0.0
G = 1.0
B = -(w - 510.) / (510. - 490.)
elif w >= 510 and w < 580:
R = (w - 510.) / (580. - 510.)
G = 1.0
B = 0.0
elif w >= 580 and w < 645:
R = 1.0
G = -(w - 645.) / (645. - 580.)
B = 0.0
elif w >= 645 and w <= 780:
R = 1.0
G = 0.0
B = 0.0
else:
R = 0.0
G = 0.0
B = 0.0
# intensity correction
if w >= 380 and w < 420:
SSS = 0.3 + 0.7*(w - 350) / (420 - 350)
elif w >= 420 and w <= 700:
SSS = 1.0
elif w > 700 and w <= 780:
SSS = 0.3 + 0.7*(780 - w) / (780 - 700)
else:
SSS = 0.0
SSS *= 255
return [int(SSS*R), int(SSS*G), int(SSS*B)]
def decode_ch_component(self, component):
'''this method decofify the components of the light path for a given channel
'LSR488' --> Laser 488nm, 'DMR567LP' ---> Long pass Dichroic Mirror 567nm etc..
'''
description = ''
if component.startswith('LSR'):
nm = re.sub('\D', '', component)
description = nm+' nm Excitation laser '
if component.startswith('DMR'):
nm = re.sub('\D', '', component)
if component.endswith('LP'):
description = nm+' nm Long Pass Dichroic Mirror'
if component.endswith('SP'):
description = nm+' nm Short Pass Dichroic Mirror'
if component.startswith('FLT'):
if component.endswith('LP'):
description = re.sub('\D', '', component)+' nm Long Pass Filter'
if component.endswith('SP'):
description = re.sub('\D', '', component)+' nm Short Pass Filter'
if component.endswith('BP'):
description = (component.split('FLT')[1]).split('BP')[0]+' nm Band pass Filter' # this needs to be adjusted
if component.startswith('DYE'):
dye = component.split('_')[1]
description = 'Dye used: %s' %dye
if component.startswith('DTC'):
volt = re.sub('\D', '', component)
description = 'PMT voltage %s volts' %volt
return description
def setDyeList(self, emLow, emHgh):
'''This method sets the list of dye for a given spectrum range'''
dyeList = []
for dye in FLUOR_SPECTRUM:
dyeLowNM, dyeHghNM = self.getNM(FLUOR_SPECTRUM[dye][1])
for wl in range(emLow, emHgh+1):
if wl in range(dyeLowNM, dyeHghNM+1):
dyeList.append(dye)
#self.dyeListBox.Clear()
return sorted(list(set(dyeList)))
def saveData(self, ctrl, tag, settings_controls):
if isinstance(ctrl, wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
if len(tag.split('|'))>4:
# get the relevant controls for this tag eg, duration, temp controls for this step
subtags = []
info = []
for subtag in [t for t, c in settings_controls.items()]:
if get_tag_stump(tag, 4) == get_tag_stump(subtag, 4):
subtags.append(subtag)
for i in range(0, len(subtags)):
info.append('')
for st in subtags:
if isinstance(settings_controls[st], wx.Choice) or isinstance(settings_controls[st], wx.ListBox):
info[int(st.split('|')[4])]=settings_controls[st].GetStringSelection()
else:
info[int(st.split('|')[4])]=settings_controls[st].GetValue()
self.set_field(get_tag_stump(tag, 4), info) # get the core tag like AddProcess|Spin|Step|<instance> = [duration, description, temp]
else:
if isinstance(ctrl, wx.Choice) or isinstance(ctrl, wx.ListBox):
self.set_field(tag, ctrl.GetStringSelection())
elif isinstance(ctrl, wx.DatePickerCtrl):
date = ctrl.GetValue()
self.set_field(tag, '%02d/%02d/%4d'%(date.Day, date.Month+1, date.Year))
else:
user_input = ctrl.GetValue()
self.set_field(tag, user_input)
def get_seeded_sample(self, platewell_id):
'''this method returns sample or cell line information for the selected well
'''
timeline = self.get_timeline()
timepoints = timeline.get_unique_timepoints()
events_by_timepoint = timeline.get_events_by_timepoint()
seeding_instances = []
for i, timepoint in enumerate(timepoints):
for ev in events_by_timepoint[timepoint]:
for well_id in ev.get_well_ids():
if well_id == platewell_id and ev.get_welltag().startswith('CellTransfer|Seed'):
seeding_instances.append(ev.get_welltag())
return seeding_instances
def get_sampleInstance(self, seed_tag):
'''This method returns the stock culutre or sample instance for a given seeding tag CellTransfer|Seed|Wells|<instance>
'''
instance = get_tag_instance(seed_tag)
# if seed from stock culture
if self.global_settings.has_key('CellTransfer|Seed|StockInstance|%s'%instance):
return self.get_field('CellTransfer|Seed|StockInstance|%s'%instance)
elif self.global_settings.has_key('CellTransfer|Seed|HarvestInstance|%s'%instance):
return self.get_field('CellTransfer|Harvest|StockInstance|%s'
%str(self.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance)))
#----------------------------------------------------------------------
def getStateRGB(self, trackTags):
"""This method returns the colour of the node given the history of the ancestor nodes events"""
currRGB = (255, 255, 255, 100)
for tag in trackTags:
event = get_tag_event(tag)
if event.startswith('Notes') or event.startswith('DataAcquis'): # since these are measurements or notes
continue
currRGB = (int((currRGB[0]+EVENT_RGB[event][0])/2), int((currRGB[1]+EVENT_RGB[event][1])/2), int((currRGB[2]+EVENT_RGB[event][2])/2), 100)
return currRGB
#----------------------------------------------------------------------
def getEventRGB(self, tag):
"""get all event tags for the passed node and returns the colour associated with the last event** Need to change**"""
#currRGB = (255, 255, 255, 100)
#if nodeTags:
#tag = nodeTags.pop()
event = get_tag_event(tag)
if not event.startswith('Notes') or not event.startswith('DataAcquis'): # since these are measurements or notes
return (EVENT_RGB[event][0], EVENT_RGB[event][1], EVENT_RGB[event][2], 100)
else:
return (255, 255, 255, 100)
#----------------------------------------------------------------------
def getEventIcon(self, icon_size, act):
"""get the associated icon for the given action/event"""
if act == 'Seed':
icon = icons.seed.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Stock':
icon = icons.stock.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Harvest':
icon = icons.harvest.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Chem':
icon = icons.treat.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Bio':
icon = icons.dna.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Dye':
icon = icons.stain.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Immuno':
icon = icons.antibody.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Genetic':
icon = icons.primer.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Spin':
icon = icons.spin.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Wash':
icon = icons.wash.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Dry':
icon = icons.dry.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Medium':
icon = icons.medium.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Incubator':
icon = icons.incubator.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='HCS':
icon = icons.staticimage.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='FCS':
icon = icons.arrow_up.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='TLM':
icon = icons.tlm.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Hint':
#icon = icons.hint.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='CriticalPoint':
#icon = icons.critical.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Rest':
#icon = icons.rest.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='URL':
#icon = icons.url.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Video':
#icon = icons.video.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
return icon
class ExperimentSettings(Singleton):
global_settings = {}
timeline = Timeline('TEST_STOCK')
subscribers = {}
def __init__(self):
pass
def set_field(self, tag, value, notify_subscribers=True):
self.global_settings[tag] = value
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'SET FIELD: %s = %s' % (tag, value)
def get_field(self, tag, default=None):
return self.global_settings.get(tag, default)
def remove_field(self, tag, notify_subscribers=True):
'''completely removes the specified tag from the metadata (if it exists)
'''
#if self.get_field(tag) is not None:
self.global_settings.pop(tag)
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'DEL FIELD: %s' % (tag)
def get_action_tags(self):
'''returns all existing TEMPORAL tags as list'''
return [
tag for tag in self.global_settings
if tag.split('|')[0] in ('CellTransfer', 'Perturbation',
'Staining', 'AddProcess', 'DataAcquis',
'Notes')
]
def get_field_instances(self, tag_prefix):
'''returns a list of unique instance ids for each tag beginning with
tag_prefix'''
ids = set([
get_tag_instance(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_attribute_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([
get_tag_attribute(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_attribute_list_by_instance(self, tag_prefix, instance=None):
'''returns a list of all attributes beginning with tag_prefix. If instance
is passed in, only attributes of the given instance will be returned'''
ids = set([
get_tag_attribute(tag) for tag in self.global_settings
if ((tag_prefix is None or tag.startswith(tag_prefix)) and (
instance is None or get_tag_instance(tag) == instance))
])
return list(ids)
#tags = []
#for tag in self.global_settings:
#if ((tag_prefix is None or tag.startswith(tag_prefix)) and
#(instance is None or get_tag_instance(tag) == instance)):
#tag += [tag]
#ids= set([get_tag_attribute(tag)])
#return list(ids)
def get_attribute_dict(self, protocol):
'''returns a dict mapping attribute names to their values for a given
protocol.
eg: get_attribute_dict('CellTransfer|Seed|1') -->
{'SeedingDensity': 12, 'MediumUsed': 'agar',
'MediumAddatives': 'None', 'Trypsinization': True}
'''
d = {}
for tag in self.get_matching_tags('|*|'.join(protocol.rsplit('|', 1))):
if (get_tag_attribute(tag) not in ('Wells', 'EventTimepoint',
'Images', 'OriginWells')):
d[get_tag_attribute(tag)] = self.global_settings[tag]
return d
def get_eventtype_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([
tag.split('|')[1] for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_eventclass_list(self, tag_prefix):
'''returns a list of event class name for each tag beginning with
tag_prefix'''
ids = set([
tag.split('|')[0] for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_field_tags(self, tag_prefix=None, instance=None):
'''returns a list of all tags beginning with tag_prefix. If instance
is passed in, only tags of the given instance will be returned'''
tags = []
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
tags += [tag]
return tags
def get_matching_tags(self, matchstring):
'''returns a list of all tags matching matchstring
matchstring -- a string that matches the tags you want
eg: CellTransfer|*
'''
tags = []
for tag in self.global_settings:
match = True
for m, subtag in map(None, matchstring.split('|'), tag.split('|')):
if m != subtag and m not in ('*', None):
match = False
break
if match:
tags += [tag]
return tags
def get_protocol_instances(self, prefix):
'''returns a list of protocol instance names for tags
matching the given prefix.
'''
return list(
set([get_tag_instance(tag)
for tag in self.get_field_tags(prefix)]))
def get_new_protocol_id(self, prefix):
'''returns an id string that hasn't been used for the given tag prefix
prefix -- eg: CellTransfer|Seed
'''
instances = self.get_protocol_instances(prefix)
for i in xrange(1, 100000):
if str(i) not in instances:
return str(i)
def get_instance_by_field_value(self, prefix, field_value):
'''returns instance number given tag prefix and field value
'''
return get_tag_instance([
tag for tag, value in self.global_settings.iteritems()
if value == field_value
][0])
def get_stack_ids(self, prefix):
'''returns the stack ids for a given type of vessels prefix e.g. ExptVessel|Tube'''
return set([
self.get_field(prefix + '|StackNo|%s' % instance)
for instance in sorted(self.get_field_instances(prefix))
])
def get_rep_vessel_instance(self, prefix, stack_id):
''' returns instance number of the vessel for this stack, since all vessels of a given stack has identical settings
one instance represents others'''
for instance in sorted(self.get_field_instances(prefix)):
if self.get_field(prefix + '|StackNo|%s' % (instance)) == stack_id:
return instance
def clear(self):
self.global_settings = {}
PlateDesign.clear()
#
# TODO:
#
self.timeline = Timeline('TEST_STOCK')
for matchstring, callbacks in self.subscribers.items():
for callback in callbacks:
callback(None)
def onTabClosing(self, event):
event.Veto()
dlg = wx.MessageDialog(None, 'Can not delete instance', 'Deleting..',
wx.OK | wx.ICON_STOP)
dlg.ShowModal()
return
def get_timeline(self):
return self.timeline
def does_tag_exists(self, tag_prefix, instnace=None):
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instnace is None or get_tag_instance(tag) == instnace)):
return True
else:
return False
def is_supp_protocol_filled(self, tag_prefix, instance=None):
'''tag_prefix is always type|event e.g. AddProcess|Wash
'''
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
if (self.get_field(tag_prefix + '|ProtocolName|%s' % instance)
is None) or (self.get_field(tag_prefix +
'|Step1|%s' % instance)
== ['', '', '']):
return False
else:
return True
def update_timeline(self, welltag):
'''Updates the experiment metadata timeline event associated with the
action and wells in welltag (eg: 'ExpNum|AddProcess|Spin|Wells|1|1')
'''
platewell_ids = self.get_field(welltag, [])
if platewell_ids == []:
self.timeline.delete_event(welltag)
else:
event = self.timeline.get_event(welltag)
if event is not None:
event.set_well_ids(platewell_ids)
else:
self.timeline.add_event(welltag, platewell_ids)
def save_to_file(self, file):
f = open(file, 'w')
for field, value in sorted(self.global_settings.items()):
f.write('%s = %s\n' % (field, repr(value)))
f.close()
def save_settings(self, file, protocol):
'''
saves settings in text file. the settings may include instrument settings, supp protocol, stock flask
Format: attr = value where value may be text, int, list, etc.
'''
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
setting_type = get_tag_event(protocol)
f = open(file, 'w')
f.write(setting_type + '\n')
attributes = self.get_attribute_list_by_instance(tag_stump, instance)
for attr in attributes:
info = self.get_field(tag_stump + '|%s|%s' % (attr, instance))
print info
f.write('%s = %s\n' % (attr, repr(info)))
f.close()
def save_supp_protocol_file(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
f = open(file, 'w')
attributes = self.get_attribute_list_by_instance(tag_stump, instance)
for attr in attributes:
info = self.get_field(tag_stump + '|%s|%s' % (attr, instance))
if isinstance(info, list):
f.write('%s|' % attr)
for i, val in enumerate(info):
if isinstance(val, tuple):
print val
elif i == len(info) - 1:
f.write('%s' % val)
else:
f.write('%s|' % val)
f.write('\n')
else:
f.write('%s|%s\n' % (attr, info))
f.close()
def load_from_file(self, file):
# Populate the tag structure
self.clear()
f = open(file, 'r')
for line in f:
tag, value = line.split('=', 1)
tag = tag.strip()
self.set_field(tag, eval(value), notify_subscribers=False)
f.close()
# Populate PlateDesign
PlateDesign.clear()
for vessel_type in ('Plate', 'Flask', 'Dish', 'Coverslip', 'Tube'):
prefix = 'ExptVessel|%s' % (vessel_type)
for inst in self.get_field_instances(prefix):
d = self.get_attribute_dict(prefix + '|' + inst)
shape = d.get('Design', None)
if shape is None:
shape = (1, 1)
group = d.get('StackName', None)
PlateDesign.add_plate(vessel_type, inst, shape, group)
# Update everything
for tag in self.global_settings:
self.notify_subscribers(tag)
# Update the bench time-slider
# TODO: this is crappy
try:
import wx
bench = wx.GetApp().get_bench()
bench.set_time_interval(0, self.get_timeline().get_max_timepoint())
except:
return
def load_supp_protocol_file(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
lines = [line.strip() for line in open(file)]
if not lines:
import wx
dial = wx.MessageDialog(None,
'Supplementary protocol file is empty!!',
'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
for line in lines:
#line.rstrip('\n')
line_info = line.split('|')
attr = line_info.pop(0)
if len(line_info) > 1:
self.set_field(tag_stump + '|%s|%s' % (attr, instance),
line_info)
else:
self.set_field(tag_stump + '|%s|%s' % (attr, instance),
line_info[0])
def load_settings(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
f = open(file, 'r')
lines = [line.strip() for line in f]
lines.pop(
0
) # takes out the first line or the header where all setting type microscope/spin etc are written
for line in lines:
attr, value = line.split('=', 1)
attr = attr.strip()
tag = tag_stump + '|%s|%s' % (attr, instance)
self.set_field(tag, eval(value), notify_subscribers=False)
self.notify_subscribers(tag)
f.close()
def add_subscriber(self, callback, match_string):
'''callback -- the function to be called
match_string -- a regular expression string matching the tags you want
to be notified of changes to
'''
self.subscribers[match_string] = self.subscribers.get(
match_string, []) + [callback]
def remove_subscriber(self, callback):
'''unsubscribe the given callback function.
This MUST be called before a callback function is deleted.
'''
for k, v in self.subscribers:
if v == callback:
self.subscribers.pop(k)
def notify_subscribers(self, tag):
for matchstring, callbacks in self.subscribers.items():
if re.match(matchstring, tag):
for callback in callbacks:
callback(tag)
def getNM(self, nm):
return int(nm.split('-')[0]), int(nm.split('-')[1])
def belongsTo(self, value, rangeStart, rangeEnd):
if value >= rangeStart and value <= rangeEnd:
return True
return False
def partition(self, lst, n):
division = len(lst) / float(n)
rlist = [
lst[int(round(division * i)):int(round(division * (i + 1)))][-1]
for i in xrange(n)
]
rlist.insert(0, lst[0])
return rlist
def stringSplitByNumbers(self, x):
r = re.compile('(\d+)')
l = r.split(x)
return [int(y) if y.isdigit() else y for y in l]
def nmToRGB(self, w):
# colour
if w >= 380 and w < 440:
R = -(w - 440.) / (440. - 350.)
G = 0.0
B = 1.0
elif w >= 440 and w < 490:
R = 0.0
G = (w - 440.) / (490. - 440.)
B = 1.0
elif w >= 490 and w < 510:
R = 0.0
G = 1.0
B = -(w - 510.) / (510. - 490.)
elif w >= 510 and w < 580:
R = (w - 510.) / (580. - 510.)
G = 1.0
B = 0.0
elif w >= 580 and w < 645:
R = 1.0
G = -(w - 645.) / (645. - 580.)
B = 0.0
elif w >= 645 and w <= 780:
R = 1.0
G = 0.0
B = 0.0
else:
R = 0.0
G = 0.0
B = 0.0
# intensity correction
if w >= 380 and w < 420:
SSS = 0.3 + 0.7 * (w - 350) / (420 - 350)
elif w >= 420 and w <= 700:
SSS = 1.0
elif w > 700 and w <= 780:
SSS = 0.3 + 0.7 * (780 - w) / (780 - 700)
else:
SSS = 0.0
SSS *= 255
return [int(SSS * R), int(SSS * G), int(SSS * B)]
def decode_ch_component(self, component):
'''this method decofify the components of the light path for a given channel
'LSR488' --> Laser 488nm, 'DMR567LP' ---> Long pass Dichroic Mirror 567nm etc..
'''
description = ''
if component.startswith('LSR'):
nm = re.sub('\D', '', component)
description = nm + ' nm Excitation laser '
if component.startswith('DMR'):
nm = re.sub('\D', '', component)
if component.endswith('LP'):
description = nm + ' nm Long Pass Dichroic Mirror'
if component.endswith('SP'):
description = nm + ' nm Short Pass Dichroic Mirror'
if component.startswith('FLT'):
if component.endswith('LP'):
description = re.sub('\D', '',
component) + ' nm Long Pass Filter'
if component.endswith('SP'):
description = re.sub('\D', '',
component) + ' nm Short Pass Filter'
if component.endswith('BP'):
description = (component.split('FLT')[1]).split('BP')[
0] + ' nm Band pass Filter' # this needs to be adjusted
if component.startswith('DYE'):
dye = component.split('_')[1]
description = 'Dye used: %s' % dye
if component.startswith('DTC'):
volt = re.sub('\D', '', component)
description = 'PMT voltage %s volts' % volt
return description
def setDyeList(self, emLow, emHgh):
'''This method sets the list of dye for a given spectrum range'''
dyeList = []
for dye in FLUOR_SPECTRUM:
dyeLowNM, dyeHghNM = self.getNM(FLUOR_SPECTRUM[dye][1])
for wl in range(emLow, emHgh + 1):
if wl in range(dyeLowNM, dyeHghNM + 1):
dyeList.append(dye)
#self.dyeListBox.Clear()
return sorted(list(set(dyeList)))
def saveData(self, ctrl, tag, settings_controls):
if isinstance(ctrl,
wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
if len(tag.split('|')) > 4:
# get the relevant controls for this tag eg, duration, temp controls for this step
subtags = []
info = []
for subtag in [t for t, c in settings_controls.items()]:
if get_tag_stump(tag, 4) == get_tag_stump(subtag, 4):
subtags.append(subtag)
for i in range(0, len(subtags)):
info.append('')
for st in subtags:
if isinstance(settings_controls[st], wx.Choice) or isinstance(
settings_controls[st], wx.ListBox):
info[int(st.split(
'|')[4])] = settings_controls[st].GetStringSelection()
else:
info[int(
st.split('|')[4])] = settings_controls[st].GetValue()
self.set_field(
get_tag_stump(tag, 4), info
) # get the core tag like AddProcess|Spin|Step|<instance> = [duration, description, temp]
else:
if isinstance(ctrl, wx.Choice) or isinstance(ctrl, wx.ListBox):
self.set_field(tag, ctrl.GetStringSelection())
elif isinstance(ctrl, wx.DatePickerCtrl):
date = ctrl.GetValue()
self.set_field(
tag,
'%02d/%02d/%4d' % (date.Day, date.Month + 1, date.Year))
else:
user_input = ctrl.GetValue()
self.set_field(tag, user_input)
def get_seeded_sample(self, platewell_id):
'''this method returns sample or cell line information for the selected well
'''
timeline = self.get_timeline()
timepoints = timeline.get_unique_timepoints()
events_by_timepoint = timeline.get_events_by_timepoint()
seeding_instances = []
for i, timepoint in enumerate(timepoints):
for ev in events_by_timepoint[timepoint]:
for well_id in ev.get_well_ids():
if well_id == platewell_id and ev.get_welltag().startswith(
'CellTransfer|Seed'):
seeding_instances.append(ev.get_welltag())
return seeding_instances
def get_sampleInstance(self, seed_tag):
'''This method returns the stock culutre or sample instance for a given seeding tag CellTransfer|Seed|Wells|<instance>
'''
instance = get_tag_instance(seed_tag)
# if seed from stock culture
if self.global_settings.has_key('CellTransfer|Seed|StockInstance|%s' %
instance):
return self.get_field('CellTransfer|Seed|StockInstance|%s' %
instance)
elif self.global_settings.has_key(
'CellTransfer|Seed|HarvestInstance|%s' % instance):
return self.get_field(
'CellTransfer|Harvest|StockInstance|%s' % str(
self.get_field(
'CellTransfer|Seed|HarvestInstance|%s' % instance)))
#----------------------------------------------------------------------
def getStateRGB(self, trackTags):
"""This method returns the colour of the node given the history of the ancestor nodes events"""
currRGB = (255, 255, 255, 100)
for tag in trackTags:
event = get_tag_event(tag)
if event.startswith('Notes') or event.startswith(
'DataAcquis'): # since these are measurements or notes
continue
currRGB = (int((currRGB[0] + EVENT_RGB[event][0]) / 2),
int((currRGB[1] + EVENT_RGB[event][1]) / 2),
int((currRGB[2] + EVENT_RGB[event][2]) / 2), 100)
return currRGB
#----------------------------------------------------------------------
def getEventRGB(self, tag):
"""get all event tags for the passed node and returns the colour associated with the last event** Need to change**"""
#currRGB = (255, 255, 255, 100)
#if nodeTags:
#tag = nodeTags.pop()
event = get_tag_event(tag)
if not event.startswith('Notes') or not event.startswith(
'DataAcquis'): # since these are measurements or notes
return (EVENT_RGB[event][0], EVENT_RGB[event][1],
EVENT_RGB[event][2], 100)
else:
return (255, 255, 255, 100)
#----------------------------------------------------------------------
def getEventIcon(self, icon_size, act):
"""get the associated icon for the given action/event"""
if act == 'Seed':
icon = icons.seed.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Stock':
icon = icons.stock.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Harvest':
icon = icons.harvest.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Chem':
icon = icons.treat.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Bio':
icon = icons.dna.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Dye':
icon = icons.stain.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Immuno':
icon = icons.antibody.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Genetic':
icon = icons.primer.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Spin':
icon = icons.spin.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Wash':
icon = icons.wash.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Dry':
icon = icons.dry.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Medium':
icon = icons.medium.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Incubator':
icon = icons.incubator.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'HCS':
icon = icons.staticimage.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'FCS':
icon = icons.arrow_up.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'TLM':
icon = icons.tlm.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Hint':
#icon = icons.hint.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='CriticalPoint':
#icon = icons.critical.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Rest':
#icon = icons.rest.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='URL':
#icon = icons.url.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Video':
#icon = icons.video.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
return icon
class ExperimentSettings(Singleton):
global_settings = {}
timeline = Timeline('TEST_STOCK')
subscribers = {}
#curr_dir = os.path.dirname(os.path.abspath(__file__))
#save_file_path = curr_dir+'\\temporary_experiment.txt' # first assign it to the temp directory
save_file_path = None
def __init__(self):
pass
def set_field(self, tag, value, notify_subscribers=True):
self.global_settings[tag] = value
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'SET FIELD: %s = %s' % (tag, value)
def get_field(self, tag, default=None):
return self.global_settings.get(tag, default)
def remove_field(self, tag, notify_subscribers=True):
'''completely removes the specified tag from the metadata (if it exists)
'''
#if self.get_field(tag) is not None:
self.global_settings.pop(tag)
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'DEL FIELD: %s' % (tag)
def remove_harvest_seed_tags(self, h_inst, s_inst):
'''removes all associated tags with coupled harvest seed tags e.g density, steps etc'''
h_attrs = self.get_attribute_list_by_instance('Transfer|Harvest',
h_inst)
s_attrs = self.get_attribute_list_by_instance('Transfer|Seed', s_inst)
if h_attrs:
for h_attr in h_attrs:
self.remove_field('Transfer|Harvest|%s|%s' % (h_attr, h_inst),
notify_subscribers=False)
if s_attrs:
for s_attr in s_attrs:
self.remove_field('Transfer|Seed|%s|%s' % (s_attr, s_inst),
notify_subscribers=False)
def remove_associated_dataacquis_tag(self, wells):
'''removes all image tags associated with this timepoint and wells e.g. DataAcquis|*|Images|*|timepoint|[(Plate_Well), ()]'''
image_tags = self.get_matching_tags('DataAcquis|*|Images|*|*|%s' %
str(wells))
if image_tags:
for i_tag in image_tags:
self.remove_field(i_tag)
def remove_timeline_attachments(self, timepoint):
'''removes all notes and attachment from the timeline at the given timepoint'''
note_tags = self.get_matching_tags('Notes|*|%s|*' % timepoint)
attach_tags = self.get_matching_tags('Attachments|*|%s|*' % timepoint)
if note_tags:
for n_tag in note_tags:
self.remove_field(n_tag)
if attach_tags:
for a_tag in attach_tags:
self.remove_field(a_tag)
def get_action_tags(self):
'''returns all existing TEMPORAL tags as list'''
return [
tag for tag in self.global_settings
if tag.split('|')[0] in ('Transfer', 'Perturbation', 'Labeling',
'AddProcess', 'DataAcquis', 'InstProcess',
'Notes')
]
def get_field_instances(self, tag_prefix):
'''returns a list of unique instance ids for each tag beginning with
tag_prefix'''
ids = set([
get_tag_instance(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_attribute_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([
get_tag_attribute(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_attribute_list_by_instance(self, tag_prefix, instance=None):
'''returns a list of all attributes beginning with tag_prefix. If instance
is passed in, only attributes of the given instance will be returned'''
ids = set([
get_tag_attribute(tag) for tag in self.global_settings
if ((tag_prefix is None or tag.startswith(tag_prefix)) and (
instance is None or get_tag_instance(tag) == instance))
])
return list(ids)
#tags = []
#for tag in self.global_settings:
#if ((tag_prefix is None or tag.startswith(tag_prefix)) and
#(instance is None or get_tag_instance(tag) == instance)):
#tag += [tag]
#ids= set([get_tag_attribute(tag)])
#return list(ids)
def get_attribute_dict(self, protocol):
'''returns a dict mapping attribute names to their values for a given
protocol.
eg: get_attribute_dict('Transfer|Seed|1') -->
{'SeedingDensity': 12, 'MediumUsed': 'agar',
'MediumAddatives': 'None', 'Trypsinization': True}
'''
d = {}
for tag in self.get_matching_tags('|*|'.join(protocol.rsplit('|', 1))):
if (get_tag_attribute(tag) not in ('Wells', 'EventTimepoint',
'Images', 'OriginWells')):
d[get_tag_attribute(tag)] = self.global_settings[tag]
return d
def get_eventtype_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([
tag.split('|')[1] for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_eventclass_list(self, tag_prefix):
'''returns a list of event class name for each tag beginning with
tag_prefix'''
ids = set([
tag.split('|')[0] for tag in self.global_settings
if tag.startswith(tag_prefix)
])
return list(ids)
def get_field_tags(self, tag_prefix=None, instance=None):
'''returns a list of all tags beginning with tag_prefix. If instance
is passed in, only tags of the given instance will be returned'''
tags = []
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
tags += [tag]
return tags
def get_matching_tags(self, matchstring):
'''returns a list of all tags matching matchstring
matchstring -- a string that matches the tags you want
eg: Transfer|*
'''
tags = []
for tag in self.global_settings:
match = True
for m, subtag in map(None, matchstring.split('|'), tag.split('|')):
if m != subtag and m not in ('*', None):
match = False
break
if match:
tags += [tag]
return tags
def get_protocol_instances(self, prefix):
'''returns a list of protocol instance names for tags
matching the given prefix.
'''
return list(
set([get_tag_instance(tag)
for tag in self.get_field_tags(prefix)]))
def get_new_protocol_id(self, prefix):
'''returns an id string that hasn't been used for the given tag prefix
prefix -- eg: Transfer|Seed
'''
instances = self.get_protocol_instances(prefix)
for i in xrange(1, 100000):
if str(i) not in instances:
return str(i)
def get_instance_by_field_value(self, prefix, field_value):
'''returns instance number given tag prefix and field value
'''
return get_tag_instance([
tag for tag, value in self.global_settings.iteritems()
if value == field_value
][0])
def get_stack_ids(self, prefix):
'''returns the stack ids for a given type of vessels prefix e.g. ExptVessel|Tube'''
return set([
self.get_field(prefix + '|StackNo|%s' % instance)
for instance in sorted(self.get_field_instances(prefix))
])
def get_rep_vessel_instance(self, prefix, stack_id):
''' returns instance number of the vessel for this stack, since all vessels of a given stack has identical settings
one instance represents others'''
for instance in sorted(self.get_field_instances(prefix)):
if self.get_field(prefix + '|StackNo|%s' % (instance)) == stack_id:
return instance
def clear(self):
self.global_settings = {}
PlateDesign.clear()
#
# TODO:
#
self.timeline = Timeline('TEST_STOCK')
for matchstring, callbacks in self.subscribers.items():
for callback in callbacks:
callback(None)
def onTabClosing(self, event):
event.Veto()
dlg = wx.MessageDialog(None, 'Can not delete instance', 'Deleting..',
wx.OK | wx.ICON_STOP)
dlg.ShowModal()
return
def get_timeline(self):
return self.timeline
def does_tag_exists(self, tag_prefix, instnace=None):
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instnace is None or get_tag_instance(tag) == instnace)):
return True
else:
return False
def is_supp_protocol_filled(self, tag_prefix, instance=None):
'''tag_prefix is always type|event e.g. AddProcess|Wash
'''
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
if (self.get_field(tag_prefix + '|ProtocolName|%s' % instance)
is None) or (self.get_field(tag_prefix +
'|Step1|%s' % instance)
== ['', '', '']):
return False
else:
return True
def update_timeline(self, welltag):
'''Updates the experiment metadata timeline event associated with the
action and wells in welltag (eg: 'ExpNum|AddProcess|Spin|Wells|1|1')
'''
platewell_ids = self.get_field(welltag, [])
if platewell_ids == []:
self.timeline.delete_event(welltag)
else:
event = self.timeline.get_event(welltag)
if event is not None:
event.set_well_ids(platewell_ids)
else:
self.timeline.add_event(welltag, platewell_ids)
def save_file_dialogue(self):
exp_date = self.get_field('Overview|Project|ExptDate')
exp_num = self.get_field('Overview|Project|ExptNum')
exp_title = self.get_field('Overview|Project|Title')
if self.save_file_path:
self.save_to_file()
#import ntpath
#filename = os.path.splitext(ntpath.basename(self.save_file_path))[0]
else:
filename = 'new_experiment.txt'
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt' % (year, month, day, exp_num,
exp_title)
dlg = wx.FileDialog(None,
message='Saving experimental protocol...',
defaultDir=os.getcwd(),
defaultFile=filename,
wildcard='.txt',
style=wx.SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
self.save_file_path = dlg.GetPath()
self.save_to_file()
def save_as_file_dialogue(self):
exp_date = self.get_field('Overview|Project|ExptDate')
exp_num = self.get_field('Overview|Project|ExptNum')
exp_title = self.get_field('Overview|Project|Title')
if self.save_file_path:
import ntpath
filename = os.path.splitext(ntpath.basename(
self.save_file_path))[0]
else:
filename = 'new_experiment.txt'
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt' % (year, month, day, exp_num,
exp_title)
dlg = wx.FileDialog(None,
message='Saving experimental protocol...',
defaultDir=os.getcwd(),
defaultFile=filename,
wildcard='.txt',
style=wx.SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
self.save_file_path = dlg.GetPath()
self.save_to_file()
def save_to_file(self):
if self.save_file_path:
try:
f = open(self.save_file_path, 'w')
f.write(VERSION + '\n')
for field, value in sorted(self.global_settings.items()):
f.write('%s = %s\n' % (field, repr(value)))
f.close()
except IOError:
import wx
dial = wx.MessageDialog(
None,
'No permission to create temporary experimental file in current directory\nPlease save file in separate directory.',
'Error', wx.OK | wx.ICON_ERROR)
if dial.ShowModal() == wx.ID_OK:
self.save_as_file_dialogue()
def saveData(self, ctrl, tag, settings_controls):
if isinstance(ctrl,
wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
if len(tag.split('|')) > 4:
# get the relevant controls for this tag eg, duration, temp controls for this step
subtags = []
info = []
for subtag in [t for t, c in settings_controls.items()]:
if get_tag_stump(tag, 4) == get_tag_stump(subtag, 4):
subtags.append(subtag)
for i in range(0, len(subtags)):
info.append('')
for st in subtags:
if isinstance(settings_controls[st], wx.Choice) or isinstance(
settings_controls[st], wx.ListBox):
info[int(st.split(
'|')[4])] = settings_controls[st].GetStringSelection()
#settings_controls[st].SetToolTipString(settings_controls[st].GetStringSelection())
else:
info[int(
st.split('|')[4])] = settings_controls[st].GetValue()
#settings_controls[st].SetToolTipString(settings_controls[st].GetValue())
self.set_field(
get_tag_stump(tag, 4), info
) # get the core tag like AddProcess|Spin|Step|<instance> = [duration, description, temp]
else:
if isinstance(ctrl, wx.Choice) or isinstance(ctrl, wx.ListBox):
self.set_field(tag, ctrl.GetStringSelection())
#ctrl.SetToolTipString(ctrl.GetStringSelection())
elif isinstance(ctrl, wx.DatePickerCtrl):
date = ctrl.GetValue()
self.set_field(
tag,
'%02d/%02d/%4d' % (date.Day, date.Month + 1, date.Year))
else:
user_input = ctrl.GetValue()
self.set_field(tag, user_input)
#ctrl.SetToolTipString(ctrl.GetValue())
def saving_settings(self, protocol, tag, m_tags):
import wx
if not self.get_field(tag):
dial = wx.MessageDialog(None,
'Please provide a settings/protocol name',
'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
if self.checkMandatoryTags(m_tags):
filename = self.get_field(tag) + '.txt'
dlg = wx.FileDialog(None,
message='Saving ...',
defaultDir=os.getcwd(),
defaultFile=filename,
wildcard='.txt',
style=wx.SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
dirname = dlg.GetDirectory()
filename = dlg.GetFilename()
file_path = os.path.join(dirname, filename)
self.save_settings(file_path, protocol)
def save_settings(self, file, protocol):
'''
saves settings in text file. the settings may include instrument settings, supp protocol, stock flask
Format: attr = value where value may be text, int, list, etc.
'''
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
setting_type = get_tag_event(protocol)
f = open(file, 'w')
f.write(setting_type + '\n')
attributes = list(
set(self.get_attribute_list_by_instance(tag_stump, instance)))
if 'Wells' in attributes: attributes.remove('Wells')
for attr in attributes:
value = self.get_field(tag_stump + '|%s|%s' % (attr, instance))
if attr.endswith('Instance'):
f.write('Dependency%s = %s\n' % (attr, repr(value))
) # to get the ...Instance which will be overwritten
for d_attr, d_val in self.get_attribute_dict(
'%s|%s' %
(DEPENDENCY[get_tag_event(protocol)], value)).iteritems():
f.write('Dependency%s = %s\n' % (d_attr, repr(d_val)))
else:
f.write('%s = %s\n' % (attr, repr(value)))
f.close()
def load_from_file(self, file, menuitem):
# Populate the tag structure
self.clear()
f = open(file, 'r')
lines = [line.strip() for line in f]
if not lines.pop(0).startswith('ProtocolNavigator'):
import wx
dial = wx.MessageDialog(
None, 'Selected file is not a ProtocolNavigator file', 'Error',
wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
for line in lines:
tag, value = line.split('=', 1)
tag = tag.strip()
self.set_field(tag, eval(value), notify_subscribers=False)
f.close()
# Disable the open file menu
menuitem.Enable(False)
# index the file path
self.save_file_path = file
#import ntpath
#self.temp_file_path = os.path.dirname(os.path.abspath(file))+os.path.splitext(ntpath.basename(self.save_file_path))[0]+'_temp.txt'
# Populate PlateDesign
PlateDesign.clear()
for vessel_type in ('Plate', 'Flask', 'Dish', 'Coverslip', 'Tube'):
prefix = 'ExptVessel|%s' % (vessel_type)
for inst in self.get_field_instances(prefix):
d = self.get_attribute_dict(prefix + '|' + inst)
shape = d.get('Design', None)
if shape is None:
shape = (1, 1)
group = d.get('StackName', None)
PlateDesign.add_plate(vessel_type, inst, shape, group)
# Update everything
for tag in self.global_settings:
self.notify_subscribers(tag)
# Update the bench time-slider
# TODO: this is crappy
try:
import wx
bench = wx.GetApp().get_bench()
bench.set_time_interval(0, self.get_timeline().get_max_timepoint())
except:
return
def load_supp_protocol_file(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
lines = [line.strip() for line in open(file)]
if not lines:
import wx
dial = wx.MessageDialog(None, 'Sub-process file is empty!!',
'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
for line in lines:
#line.rstrip('\n')
line_info = line.split('|')
attr = line_info.pop(0)
if len(line_info) > 1:
self.set_field(tag_stump + '|%s|%s' % (attr, instance),
line_info)
else:
self.set_field(tag_stump + '|%s|%s' % (attr, instance),
line_info[0])
def load_settings(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
f = open(file, 'r')
lines = [line.strip() for line in f]
event = lines.pop(
0
) # takes out the first line or the header where all setting type microscope/spin etc are written
attributes = {}
for line in lines:
attr, value = line.split('=', 1)
attributes[attr.strip()] = value
# set all dependency attributes e.g. Centifugation depends on Centrifuge
dependecny_attrs = [s for s in attributes if 'Dependency' in s]
if dependecny_attrs:
d_inst = self.get_new_protocol_id(DEPENDENCY[event])
for d_attr in dependecny_attrs:
if d_attr.endswith('Instance'):
tag = tag_stump + '|%s|%s' % (
d_attr.split('Dependency')[1], instance)
self.set_field(tag, d_inst, notify_subscribers=False)
self.notify_subscribers(tag)
del attributes[d_attr]
else:
tag = DEPENDENCY[event] + '|%s|%s' % (
d_attr.split('Dependency')[1], d_inst)
self.set_field(tag,
eval(attributes[d_attr]),
notify_subscribers=False)
self.notify_subscribers(tag)
del attributes[d_attr]
# set rest of the attributes
for attr in attributes:
tag = tag_stump + '|%s|%s' % (attr, instance)
self.set_field(tag,
eval(attributes[attr]),
notify_subscribers=False)
self.notify_subscribers(tag)
f.close()
#for line in lines:
#attr, value = line.split('=', 1)
#attr = attr.strip()
#tag = tag_stump+'|%s|%s'%(attr, instance)
#self.set_field(tag, eval(value), notify_subscribers=False)
#self.notify_subscribers(tag)
#f.close()
def add_subscriber(self, callback, match_string):
'''callback -- the function to be called
match_string -- a regular expression string matching the tags you want
to be notified of changes to
'''
self.subscribers[match_string] = self.subscribers.get(
match_string, []) + [callback]
def remove_subscriber(self, callback):
'''unsubscribe the given callback function.
This MUST be called before a callback function is deleted.
'''
for k, v in self.subscribers:
if v == callback:
self.subscribers.pop(k)
def notify_subscribers(self, tag):
for matchstring, callbacks in self.subscribers.items():
if re.match(matchstring, tag):
#self.save_to_temp_file() # update info to the temp file
for callback in callbacks:
callback(tag)
def getNM(self, nm):
return int(nm.split('-')[0]), int(nm.split('-')[1])
def belongsTo(self, value, rangeStart, rangeEnd):
if value >= rangeStart and value <= rangeEnd:
return True
return False
def partition(self, lst, n):
division = len(lst) / float(n)
rlist = [
lst[int(round(division * i)):int(round(division * (i + 1)))][-1]
for i in xrange(n)
]
rlist.insert(0, lst[0])
return rlist
def stringSplitByNumbers(self, x):
r = re.compile('(\d+)')
l = r.split(x)
return [int(y) if y.isdigit() else y for y in l]
def nmToRGB(self, w):
# colour
if w >= 380 and w < 440:
R = -(w - 440.) / (440. - 350.)
G = 0.0
B = 1.0
elif w >= 440 and w < 490:
R = 0.0
G = (w - 440.) / (490. - 440.)
B = 1.0
elif w >= 490 and w < 510:
R = 0.0
G = 1.0
B = -(w - 510.) / (510. - 490.)
elif w >= 510 and w < 580:
R = (w - 510.) / (580. - 510.)
G = 1.0
B = 0.0
elif w >= 580 and w < 645:
R = 1.0
G = -(w - 645.) / (645. - 580.)
B = 0.0
elif w >= 645 and w <= 780:
R = 1.0
G = 0.0
B = 0.0
else:
R = 0.0
G = 0.0
B = 0.0
# intensity correction
if w >= 380 and w < 420:
SSS = 0.3 + 0.7 * (w - 350) / (420 - 350)
elif w >= 420 and w <= 700:
SSS = 1.0
elif w > 700 and w <= 780:
SSS = 0.3 + 0.7 * (780 - w) / (780 - 700)
else:
SSS = 0.0
SSS *= 255
return [int(SSS * R), int(SSS * G), int(SSS * B)]
def decode_ch_component(self, component):
'''this method decofify the components of the light path for a given channel
'LSR488' --> Laser 488nm, 'DMR567LP' ---> Long pass Dichroic Mirror 567nm etc..
'''
description = ''
if component.startswith('LSR'):
nm = re.sub('\D', '', component)
description = nm + ' nm Excitation laser '
if component.startswith('DMR'):
nm = re.sub('\D', '', component)
if component.endswith('LP'):
description = nm + ' nm Long Pass Dichroic Mirror'
if component.endswith('SP'):
description = nm + ' nm Short Pass Dichroic Mirror'
if component.startswith('FLT'):
if component.endswith('LP'):
description = re.sub('\D', '',
component) + ' nm Long Pass Filter'
if component.endswith('SP'):
description = re.sub('\D', '',
component) + ' nm Short Pass Filter'
if component.endswith('BP'):
description = (component.split('FLT')[1]).split('BP')[
0] + ' nm Band pass Filter' # this needs to be adjusted
if component.startswith('SLT'):
ratio = component.split('SLT')[1]
description = re.sub('/', ':', ratio) + ' Beam Splitter'
if component.startswith('DYE'):
dye = component.split('_')[1]
description = 'Dye used: %s' % dye
if component.startswith('DTC'):
volt = re.sub('\D', '', component)
description = 'PMT voltage %s volts' % volt
return description
def setDyeList(self, emLow, emHgh):
'''This method sets the list of dye for a given spectrum range'''
dyeList = []
for dye in FLUOR_SPECTRUM:
dyeLowNM, dyeHghNM = self.getNM(FLUOR_SPECTRUM[dye][1])
for wl in range(emLow, emHgh + 1):
if wl in range(dyeLowNM, dyeHghNM + 1):
dyeList.append(dye)
#self.dyeListBox.Clear()
return sorted(list(set(dyeList)))
def get_seeded_sample(self, platewell_id):
'''this method returns sample or cell line information for the selected well
'''
timeline = self.get_timeline()
timepoints = timeline.get_unique_timepoints()
events_by_timepoint = timeline.get_events_by_timepoint()
seeding_instances = []
for i, timepoint in enumerate(timepoints):
for ev in events_by_timepoint[timepoint]:
for well_id in ev.get_well_ids():
if well_id == platewell_id and ev.get_welltag().startswith(
'Transfer|Seed'):
seeding_instances.append(ev.get_welltag())
return seeding_instances
#----------------------------------------------------------------------
def get_sampleInstance(self, seed_tag):
'''This method returns the stock culutre or sample instance for a given seeding tag Transfer|Seed|Wells|<instance>
'''
instance = get_tag_instance(seed_tag)
# if seed from stock culture
if self.global_settings.has_key('Transfer|Seed|CellLineInstance|%s' %
instance):
return self.get_field('Transfer|Seed|CellLineInstance|%s' %
instance)
elif self.global_settings.has_key('Transfer|Seed|HarvestInstance|%s' %
instance):
return self.get_field('Transfer|Harvest|CellLineInstance|%s' % str(
self.get_field('Transfer|Seed|HarvestInstance|%s' % instance)))
#----------------------------------------------------------------------
def getStateRGB(self, trackTags):
"""This method returns the colour of the node given the history of the ancestor nodes events"""
currRGB = (255, 255, 255, 100)
for tag in trackTags:
event = get_tag_event(tag)
if event.startswith('Notes') or event.startswith(
'DataAcquis'): # since these are measurements or notes
continue
currRGB = (int((currRGB[0] + EVENT_RGB[event][0]) / 2),
int((currRGB[1] + EVENT_RGB[event][1]) / 2),
int((currRGB[2] + EVENT_RGB[event][2]) / 2), 100)
return currRGB
#----------------------------------------------------------------------
def getEventRGB(self, tag):
"""get all event tags for the passed node and returns the colour associated with the last event** Need to change**"""
#currRGB = (255, 255, 255, 100)
#if nodeTags:
#tag = nodeTags.pop()
event = get_tag_event(tag)
if not event.startswith('Notes') or not event.startswith(
'DataAcquis'): # since these are measurements or notes
return (EVENT_RGB[event][0], EVENT_RGB[event][1],
EVENT_RGB[event][2], 100)
else:
return (255, 255, 255, 100)
#----------------------------------------------------------------------
def getEventIcon(self, icon_size, act):
"""get the associated icon for the given action/event"""
if act == 'Seed':
icon = icons.seed.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'CellLine':
icon = icons.stock.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Harvest':
icon = icons.harvest.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Chemical':
icon = icons.treat.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Biological':
icon = icons.dna.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Physical':
icon = icons.physical.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Dye':
icon = icons.stain.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Immuno':
icon = icons.antibody.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Genetic':
icon = icons.primer.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Centrifugation':
icon = icons.spin.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Wash':
icon = icons.wash.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Drying':
icon = icons.drying.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Medium':
icon = icons.medium.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Initiation':
icon = icons.initiation.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Storage':
icon = icons.storage.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'Incubation':
icon = icons.incubator.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'RheoManipulation':
icon = icons.rheometer.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'HCS':
icon = icons.hcs.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'FCS':
icon = icons.fcs.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'TLM':
icon = icons.tlm.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'RHE':
icon = icons.rhe.Scale(
icon_size, icon_size,
quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Hint':
#icon = icons.hint.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Text':
#icon = icons.critical.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Rest':
#icon = icons.rest.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='URL':
#icon = icons.url.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='MultiMedia':
#icon = icons.video.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
return icon
#----------------------------------------------------------------------
def get_Row_Numbers(self, protocol, token):
"""This method returs TAGS with similar elements
eg. 'AddProcess|Rheology|Gas1|1' 'AddProcess|Rheology|Gas2|1' etc"""
tag_stump = get_tag_stump(protocol, 2)
instance = get_tag_attribute(protocol)
return sorted(self.get_attribute_list_by_instance(
tag_stump + '|%s' % token, instance),
key=self.stringSplitByNumbers)
#----------------------------------------------------------------------
def setLabelColour(self, tags, labels):
"""Change mandatory label colour Red-->Green when filled"""
for tag in tags:
if self.get_field(tag):
labels[tag].SetForegroundColour(('#006600'))
labels[tag].Refresh()
else:
labels[tag].SetForegroundColour(wx.RED)
labels[tag].Refresh()
#----------------------------------------------------------------------
def checkMandatoryTags(self, tags):
"""Checks whether the mandatory fields/tags being filled"""
for tag in tags:
if not self.get_field(tag):
import wx
dial = wx.MessageDialog(
None,
'Please fill %s mandatory field' % get_tag_attribute(tag),
'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
return True
#----------------------------------------------------------------------
def alphanumeric_sort(self, lst):
"""sort alphanumeric strings in a list e.g. [Plate1, Plate11, Tube2]"""
re_natural = re.compile('[0-9]+|[^0-9]+')
return [(1, int(c)) if c.isdigit() else (0, c.lower())
for c in re_natural.findall(lst)] + [lst]
#----------------------------------------------------------------------
def last_seed_instance(self, instance):
"""finds the last seeding instance that is associated with a harvest instance"""
for inst in list(reversed(range(int(instance)))):
if 'Transfer|Seed|HarvestInstance|%s' % str(inst) is not None:
return str(inst)
#----------------------------------------------------------------------
def get_cellLine_Name(self, inst, mode):
"""returns cell Line name given the seeding/harvesting (mode) instance that is realted with a harvest instance
if mode is None, it refers to Harvest_Seed type of seeding instance"""
if mode is 'H':
return self.get_field('Sample|CellLine|Name|%s' % str(
self.get_field(
'Transfer|Harvest|CellLineInstance|%s' % str(inst))))
if mode is 'S':
return self.get_field('Sample|CellLine|Name|%s' % str(
self.get_field(
'Transfer|Seed|CellLineInstance|%s' % str(inst))))
if mode is 'HS':
return self.get_field('Sample|CellLine|Name|%s' % str(
self.get_field('Transfer|Harvest|CellLineInstance|%s' % str(
self.get_field(
'Transfer|Seed|HarvestInstance|%s' % str(inst))))))
class ExperimentSettings(Singleton):
global_settings = {}
timeline = Timeline('TEST_STOCK')
subscribers = {}
#curr_dir = os.path.dirname(os.path.abspath(__file__))
#save_file_path = curr_dir+'\\temporary_experiment.txt' # first assign it to the temp directory
save_file_path = None
def __init__(self):
pass
def set_field(self, tag, value, notify_subscribers=True):
self.global_settings[tag] = value
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'SET FIELD: %s = %s'%(tag, value)
def get_field(self, tag, default=None):
return self.global_settings.get(tag, default)
def remove_field(self, tag, notify_subscribers=True):
'''completely removes the specified tag from the metadata (if it exists)
'''
#if self.get_field(tag) is not None:
self.global_settings.pop(tag)
if re.match(get_matchstring_for_subtag(2, 'Well'), tag):
self.update_timeline(tag)
if notify_subscribers:
self.notify_subscribers(tag)
print 'DEL FIELD: %s'%(tag)
def remove_harvest_seed_tags(self, h_inst, s_inst):
'''removes all associated tags with coupled harvest seed tags e.g density, steps etc'''
h_attrs = self.get_attribute_list_by_instance('Transfer|Harvest', h_inst)
s_attrs = self.get_attribute_list_by_instance('Transfer|Seed', s_inst)
if h_attrs:
for h_attr in h_attrs:
self.remove_field('Transfer|Harvest|%s|%s'%(h_attr, h_inst), notify_subscribers =False)
if s_attrs:
for s_attr in s_attrs:
self.remove_field('Transfer|Seed|%s|%s'%(s_attr, s_inst), notify_subscribers =False)
def remove_associated_dataacquis_tag(self, wells):
'''removes all image tags associated with this timepoint and wells e.g. DataAcquis|*|Images|*|timepoint|[(Plate_Well), ()]'''
image_tags = self.get_matching_tags('DataAcquis|*|Images|*|*|%s'%str(wells))
if image_tags:
for i_tag in image_tags:
self.remove_field(i_tag)
def remove_timeline_attachments(self, timepoint):
'''removes all notes and attachment from the timeline at the given timepoint'''
note_tags = self.get_matching_tags('Notes|*|%s|*'%timepoint)
attach_tags = self.get_matching_tags('Attachments|*|%s|*'%timepoint)
if note_tags:
for n_tag in note_tags:
self.remove_field(n_tag)
if attach_tags:
for a_tag in attach_tags:
self.remove_field(a_tag)
def get_action_tags(self):
'''returns all existing TEMPORAL tags as list'''
return [tag for tag in self.global_settings
if tag.split('|')[0] in ('Transfer', 'Perturbation',
'Labeling', 'AddProcess', 'DataAcquis', 'InstProcess', 'Notes')]
def get_field_instances(self, tag_prefix):
'''returns a list of unique instance ids for each tag beginning with
tag_prefix'''
ids = set([get_tag_instance(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_attribute_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([get_tag_attribute(tag) for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_attribute_list_by_instance(self, tag_prefix, instance=None):
'''returns a list of all attributes beginning with tag_prefix. If instance
is passed in, only attributes of the given instance will be returned'''
ids = set([get_tag_attribute(tag) for tag in self.global_settings
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance))])
return list(ids)
#tags = []
#for tag in self.global_settings:
#if ((tag_prefix is None or tag.startswith(tag_prefix)) and
#(instance is None or get_tag_instance(tag) == instance)):
#tag += [tag]
#ids= set([get_tag_attribute(tag)])
#return list(ids)
def get_attribute_dict(self, protocol):
'''returns a dict mapping attribute names to their values for a given
protocol.
eg: get_attribute_dict('Transfer|Seed|1') -->
{'SeedingDensity': 12, 'MediumUsed': 'agar',
'MediumAddatives': 'None', 'Trypsinization': True}
'''
d = {}
for tag in self.get_matching_tags('|*|'.join(protocol.rsplit('|',1))):
if (get_tag_attribute(tag) not in ('Wells', 'EventTimepoint', 'Images', 'OriginWells')):
d[get_tag_attribute(tag)] = self.global_settings[tag]
return d
def get_eventtype_list(self, tag_prefix):
'''returns a list of attributes name for each tag beginning with
tag_prefix'''
ids = set([tag.split('|')[1] for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_eventclass_list(self, tag_prefix):
'''returns a list of event class name for each tag beginning with
tag_prefix'''
ids = set([tag.split('|')[0] for tag in self.global_settings
if tag.startswith(tag_prefix)])
return list(ids)
def get_field_tags(self, tag_prefix=None, instance=None):
'''returns a list of all tags beginning with tag_prefix. If instance
is passed in, only tags of the given instance will be returned'''
tags = []
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and
(instance is None or get_tag_instance(tag) == instance)):
tags += [tag]
return tags
def get_matching_tags(self, matchstring):
'''returns a list of all tags matching matchstring
matchstring -- a string that matches the tags you want
eg: Transfer|*
'''
tags = []
for tag in self.global_settings:
match = True
for m, subtag in map(None, matchstring.split('|'), tag.split('|')):
if m != subtag and m not in ('*', None):
match = False
break
if match:
tags += [tag]
return tags
def get_protocol_instances(self, prefix):
'''returns a list of protocol instance names for tags
matching the given prefix.
'''
return list(set([get_tag_instance(tag)
for tag in self.get_field_tags(prefix)]))
def get_new_protocol_id(self, prefix):
'''returns an id string that hasn't been used for the given tag prefix
prefix -- eg: Transfer|Seed
'''
instances = self.get_protocol_instances(prefix)
for i in xrange(1, 100000):
if str(i) not in instances:
return str(i)
def get_instance_by_field_value(self, prefix, field_value):
'''returns instance number given tag prefix and field value
'''
return get_tag_instance([tag for tag, value in self.global_settings.iteritems() if value == field_value][0])
def get_stack_ids(self, prefix):
'''returns the stack ids for a given type of vessels prefix e.g. ExptVessel|Tube'''
return set([self.get_field(prefix+'|StackNo|%s'%instance)
for instance in sorted(self.get_field_instances(prefix))])
def get_rep_vessel_instance(self, prefix, stack_id):
''' returns instance number of the vessel for this stack, since all vessels of a given stack has identical settings
one instance represents others'''
for instance in sorted(self.get_field_instances(prefix)):
if self.get_field(prefix+'|StackNo|%s'%(instance)) == stack_id:
return instance
def clear(self):
self.global_settings = {}
PlateDesign.clear()
#
# TODO:
#
self.timeline = Timeline('TEST_STOCK')
for matchstring, callbacks in self.subscribers.items():
for callback in callbacks:
callback(None)
def onTabClosing(self, event):
event.Veto()
dlg = wx.MessageDialog(None, 'Can not delete instance', 'Deleting..', wx.OK| wx.ICON_STOP)
dlg.ShowModal()
return
def get_timeline(self):
return self.timeline
def does_tag_exists(self, tag_prefix, instnace=None):
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and (instnace is None or get_tag_instance(tag) == instnace)):
return True
else:
return False
def is_supp_protocol_filled(self, tag_prefix, instance=None):
'''tag_prefix is always type|event e.g. AddProcess|Wash
'''
for tag in self.global_settings:
if ((tag_prefix is None or tag.startswith(tag_prefix)) and (instance is None or get_tag_instance(tag) == instance)):
if (self.get_field(tag_prefix+'|ProtocolName|%s'%instance) is None) or (self.get_field(tag_prefix+'|Step1|%s'%instance) == ['', '', '']):
return False
else:
return True
def update_timeline(self, welltag):
'''Updates the experiment metadata timeline event associated with the
action and wells in welltag (eg: 'ExpNum|AddProcess|Spin|Wells|1|1')
'''
platewell_ids = self.get_field(welltag, [])
if platewell_ids == []:
self.timeline.delete_event(welltag)
else:
event = self.timeline.get_event(welltag)
if event is not None:
event.set_well_ids(platewell_ids)
else:
self.timeline.add_event(welltag, platewell_ids)
def save_file_dialogue(self):
exp_date = self.get_field('Overview|Project|ExptDate')
exp_num = self.get_field('Overview|Project|ExptNum')
exp_title = self.get_field('Overview|Project|Title')
if self.save_file_path:
self.save_to_file()
#import ntpath
#filename = os.path.splitext(ntpath.basename(self.save_file_path))[0]
else:
filename = 'new_experiment.txt'
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt'%(year, month, day , exp_num, exp_title)
dlg = wx.FileDialog(None, message='Saving experimental protocol...',
defaultDir=os.getcwd(), defaultFile=filename,
wildcard='.txt',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
self.save_file_path = dlg.GetPath()
self.save_to_file()
def save_as_file_dialogue(self):
exp_date = self.get_field('Overview|Project|ExptDate')
exp_num = self.get_field('Overview|Project|ExptNum')
exp_title = self.get_field('Overview|Project|Title')
if self.save_file_path:
import ntpath
filename = os.path.splitext(ntpath.basename(self.save_file_path))[0]
else:
filename = 'new_experiment.txt'
if None not in [exp_date, exp_num, exp_title]:
day, month, year = exp_date.split('/')
filename = '%s%s%s_%s_%s.txt'%(year, month, day , exp_num, exp_title)
dlg = wx.FileDialog(None, message='Saving experimental protocol...',
defaultDir=os.getcwd(), defaultFile=filename,
wildcard='.txt',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
self.save_file_path = dlg.GetPath()
self.save_to_file()
def save_to_file(self):
if self.save_file_path:
try:
f = open(self.save_file_path, 'w')
f.write(VERSION+'\n')
for field, value in sorted(self.global_settings.items()):
f.write('%s = %s\n'%(field, repr(value)))
f.close()
except IOError:
import wx
dial = wx.MessageDialog(None, 'No permission to create temporary experimental file in current directory\nPlease save file in separate directory.', 'Error', wx.OK | wx.ICON_ERROR)
if dial.ShowModal() == wx.ID_OK:
self.save_as_file_dialogue()
def saveData(self, ctrl, tag, settings_controls):
if isinstance(ctrl, wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
if len(tag.split('|'))>4:
# get the relevant controls for this tag eg, duration, temp controls for this step
subtags = []
info = []
for subtag in [t for t, c in settings_controls.items()]:
if get_tag_stump(tag, 4) == get_tag_stump(subtag, 4):
subtags.append(subtag)
for i in range(0, len(subtags)):
info.append('')
for st in subtags:
if isinstance(settings_controls[st], wx.Choice) or isinstance(settings_controls[st], wx.ListBox):
info[int(st.split('|')[4])]=settings_controls[st].GetStringSelection()
#settings_controls[st].SetToolTipString(settings_controls[st].GetStringSelection())
else:
info[int(st.split('|')[4])]=settings_controls[st].GetValue()
#settings_controls[st].SetToolTipString(settings_controls[st].GetValue())
self.set_field(get_tag_stump(tag, 4), info) # get the core tag like AddProcess|Spin|Step|<instance> = [duration, description, temp]
else:
if isinstance(ctrl, wx.Choice) or isinstance(ctrl, wx.ListBox):
self.set_field(tag, ctrl.GetStringSelection())
#ctrl.SetToolTipString(ctrl.GetStringSelection())
elif isinstance(ctrl, wx.DatePickerCtrl):
date = ctrl.GetValue()
self.set_field(tag, '%02d/%02d/%4d'%(date.Day, date.Month+1, date.Year))
else:
user_input = ctrl.GetValue()
self.set_field(tag, user_input)
#ctrl.SetToolTipString(ctrl.GetValue())
def saving_settings(self, protocol, tag, m_tags):
import wx
if not self.get_field(tag):
dial = wx.MessageDialog(None, 'Please provide a settings/protocol name', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
if self.checkMandatoryTags(m_tags):
filename = self.get_field(tag)+'.txt'
dlg = wx.FileDialog(None, message='Saving ...',
defaultDir=os.getcwd(), defaultFile=filename,
wildcard='.txt',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
dirname=dlg.GetDirectory()
filename=dlg.GetFilename()
file_path = os.path.join(dirname, filename)
self.save_settings(file_path, protocol)
def save_settings(self, file, protocol):
'''
saves settings in text file. the settings may include instrument settings, supp protocol, stock flask
Format: attr = value where value may be text, int, list, etc.
'''
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
setting_type = get_tag_event(protocol)
f = open(file,'w')
f.write(setting_type+'\n')
attributes = list(set(self.get_attribute_list_by_instance(tag_stump, instance)))
if 'Wells' in attributes: attributes.remove('Wells')
for attr in attributes:
value = self.get_field(tag_stump+'|%s|%s' %(attr, instance))
if attr.endswith('Instance'):
f.write('Dependency%s = %s\n'%(attr, repr(value))) # to get the ...Instance which will be overwritten
for d_attr, d_val in self.get_attribute_dict('%s|%s' %(DEPENDENCY[get_tag_event(protocol)], value)).iteritems():
f.write('Dependency%s = %s\n'%(d_attr, repr(d_val)))
else:
f.write('%s = %s\n'%(attr, repr(value)))
f.close()
def load_from_file(self, file, menuitem):
# Populate the tag structure
self.clear()
f = open(file, 'r')
lines = [line.strip() for line in f]
if not lines.pop(0).startswith('ProtocolNavigator'):
import wx
dial = wx.MessageDialog(None, 'Selected file is not a ProtocolNavigator file', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
for line in lines:
tag, value = line.split('=', 1)
tag = tag.strip()
self.set_field(tag, eval(value), notify_subscribers=False)
f.close()
# Disable the open file menu
menuitem.Enable(False)
# index the file path
self.save_file_path = file
#import ntpath
#self.temp_file_path = os.path.dirname(os.path.abspath(file))+os.path.splitext(ntpath.basename(self.save_file_path))[0]+'_temp.txt'
# Populate PlateDesign
PlateDesign.clear()
for vessel_type in ('Plate', 'Flask', 'Dish', 'Coverslip', 'Tube'):
prefix = 'ExptVessel|%s'%(vessel_type)
for inst in self.get_field_instances(prefix):
d = self.get_attribute_dict(prefix+'|'+inst)
shape = d.get('Design', None)
if shape is None:
shape = (1,1)
group = d.get('StackName', None)
PlateDesign.add_plate(vessel_type, inst, shape, group)
# Update everything
for tag in self.global_settings:
self.notify_subscribers(tag)
# Update the bench time-slider
# TODO: this is crappy
try:
import wx
bench = wx.GetApp().get_bench()
bench.set_time_interval(0, self.get_timeline().get_max_timepoint())
except:return
def load_supp_protocol_file(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
lines = [line.strip() for line in open(file)]
if not lines:
import wx
dial = wx.MessageDialog(None, 'Sub-process file is empty!!', 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
for line in lines:
#line.rstrip('\n')
line_info = line.split('|')
attr = line_info.pop(0)
if len(line_info)>1:
self.set_field(tag_stump+'|%s|%s'%(attr, instance), line_info)
else:
self.set_field(tag_stump+'|%s|%s'%(attr, instance), line_info[0])
def load_settings(self, file, protocol):
instance = get_tag_attribute(protocol)
tag_stump = get_tag_stump(protocol, 2)
f = open(file, 'r')
lines = [line.strip() for line in f]
event = lines.pop(0) # takes out the first line or the header where all setting type microscope/spin etc are written
attributes = {}
for line in lines:
attr, value = line.split('=', 1)
attributes[attr.strip()] = value
# set all dependency attributes e.g. Centifugation depends on Centrifuge
dependecny_attrs = [s for s in attributes if 'Dependency' in s]
if dependecny_attrs:
d_inst = self.get_new_protocol_id(DEPENDENCY[event])
for d_attr in dependecny_attrs:
if d_attr.endswith('Instance'):
tag = tag_stump+'|%s|%s'%(d_attr.split('Dependency')[1], instance)
self.set_field(tag, d_inst, notify_subscribers=False)
self.notify_subscribers(tag)
del attributes[d_attr]
else:
tag = DEPENDENCY[event]+'|%s|%s'%(d_attr.split('Dependency')[1], d_inst)
self.set_field(tag, eval(attributes[d_attr]), notify_subscribers=False)
self.notify_subscribers(tag)
del attributes[d_attr]
# set rest of the attributes
for attr in attributes:
tag = tag_stump+'|%s|%s'%(attr, instance)
self.set_field(tag, eval(attributes[attr]), notify_subscribers=False)
self.notify_subscribers(tag)
f.close()
#for line in lines:
#attr, value = line.split('=', 1)
#attr = attr.strip()
#tag = tag_stump+'|%s|%s'%(attr, instance)
#self.set_field(tag, eval(value), notify_subscribers=False)
#self.notify_subscribers(tag)
#f.close()
def add_subscriber(self, callback, match_string):
'''callback -- the function to be called
match_string -- a regular expression string matching the tags you want
to be notified of changes to
'''
self.subscribers[match_string] = self.subscribers.get(match_string, []) + [callback]
def remove_subscriber(self, callback):
'''unsubscribe the given callback function.
This MUST be called before a callback function is deleted.
'''
for k, v in self.subscribers:
if v == callback:
self.subscribers.pop(k)
def notify_subscribers(self, tag):
for matchstring, callbacks in self.subscribers.items():
if re.match(matchstring, tag):
#self.save_to_temp_file() # update info to the temp file
for callback in callbacks:
callback(tag)
def getNM(self, nm):
return int(nm.split('-')[0]), int(nm.split('-')[1])
def belongsTo(self, value, rangeStart, rangeEnd):
if value >= rangeStart and value <= rangeEnd:
return True
return False
def partition(self, lst, n):
division = len(lst) / float(n)
rlist = [lst[int(round(division * i)): int(round(division * (i + 1)))] [-1] for i in xrange(n) ]
rlist.insert(0, lst[0])
return rlist
def stringSplitByNumbers(self, x):
r = re.compile('(\d+)')
l = r.split(x)
return [int(y) if y.isdigit() else y for y in l]
def nmToRGB(self, w):
# colour
if w >= 380 and w < 440:
R = -(w - 440.) / (440. - 350.)
G = 0.0
B = 1.0
elif w >= 440 and w < 490:
R = 0.0
G = (w - 440.) / (490. - 440.)
B = 1.0
elif w >= 490 and w < 510:
R = 0.0
G = 1.0
B = -(w - 510.) / (510. - 490.)
elif w >= 510 and w < 580:
R = (w - 510.) / (580. - 510.)
G = 1.0
B = 0.0
elif w >= 580 and w < 645:
R = 1.0
G = -(w - 645.) / (645. - 580.)
B = 0.0
elif w >= 645 and w <= 780:
R = 1.0
G = 0.0
B = 0.0
else:
R = 0.0
G = 0.0
B = 0.0
# intensity correction
if w >= 380 and w < 420:
SSS = 0.3 + 0.7*(w - 350) / (420 - 350)
elif w >= 420 and w <= 700:
SSS = 1.0
elif w > 700 and w <= 780:
SSS = 0.3 + 0.7*(780 - w) / (780 - 700)
else:
SSS = 0.0
SSS *= 255
return [int(SSS*R), int(SSS*G), int(SSS*B)]
def decode_ch_component(self, component):
'''this method decofify the components of the light path for a given channel
'LSR488' --> Laser 488nm, 'DMR567LP' ---> Long pass Dichroic Mirror 567nm etc..
'''
description = ''
if component.startswith('LSR'):
nm = re.sub('\D', '', component)
description = nm+' nm Excitation laser '
if component.startswith('DMR'):
nm = re.sub('\D', '', component)
if component.endswith('LP'):
description = nm+' nm Long Pass Dichroic Mirror'
if component.endswith('SP'):
description = nm+' nm Short Pass Dichroic Mirror'
if component.startswith('FLT'):
if component.endswith('LP'):
description = re.sub('\D', '', component)+' nm Long Pass Filter'
if component.endswith('SP'):
description = re.sub('\D', '', component)+' nm Short Pass Filter'
if component.endswith('BP'):
description = (component.split('FLT')[1]).split('BP')[0]+' nm Band pass Filter' # this needs to be adjusted
if component.startswith('SLT'):
ratio = component.split('SLT')[1]
description = re.sub('/', ':', ratio)+' Beam Splitter'
if component.startswith('DYE'):
dye = component.split('_')[1]
description = 'Dye used: %s' %dye
if component.startswith('DTC'):
volt = re.sub('\D', '', component)
description = 'PMT voltage %s volts' %volt
return description
def setDyeList(self, emLow, emHgh):
'''This method sets the list of dye for a given spectrum range'''
dyeList = []
for dye in FLUOR_SPECTRUM:
dyeLowNM, dyeHghNM = self.getNM(FLUOR_SPECTRUM[dye][1])
for wl in range(emLow, emHgh+1):
if wl in range(dyeLowNM, dyeHghNM+1):
dyeList.append(dye)
#self.dyeListBox.Clear()
return sorted(list(set(dyeList)))
def get_seeded_sample(self, platewell_id):
'''this method returns sample or cell line information for the selected well
'''
timeline = self.get_timeline()
timepoints = timeline.get_unique_timepoints()
events_by_timepoint = timeline.get_events_by_timepoint()
seeding_instances = []
for i, timepoint in enumerate(timepoints):
for ev in events_by_timepoint[timepoint]:
for well_id in ev.get_well_ids():
if well_id == platewell_id and ev.get_welltag().startswith('Transfer|Seed'):
seeding_instances.append(ev.get_welltag())
return seeding_instances
#----------------------------------------------------------------------
def get_sampleInstance(self, seed_tag):
'''This method returns the stock culutre or sample instance for a given seeding tag Transfer|Seed|Wells|<instance>
'''
instance = get_tag_instance(seed_tag)
# if seed from stock culture
if self.global_settings.has_key('Transfer|Seed|CellLineInstance|%s'%instance):
return self.get_field('Transfer|Seed|CellLineInstance|%s'%instance)
elif self.global_settings.has_key('Transfer|Seed|HarvestInstance|%s'%instance):
return self.get_field('Transfer|Harvest|CellLineInstance|%s'
%str(self.get_field('Transfer|Seed|HarvestInstance|%s'%instance)))
#----------------------------------------------------------------------
def getStateRGB(self, trackTags):
"""This method returns the colour of the node given the history of the ancestor nodes events"""
currRGB = (255, 255, 255, 100)
for tag in trackTags:
event = get_tag_event(tag)
if event.startswith('Notes') or event.startswith('DataAcquis'): # since these are measurements or notes
continue
currRGB = (int((currRGB[0]+EVENT_RGB[event][0])/2), int((currRGB[1]+EVENT_RGB[event][1])/2), int((currRGB[2]+EVENT_RGB[event][2])/2), 100)
return currRGB
#----------------------------------------------------------------------
def getEventRGB(self, tag):
"""get all event tags for the passed node and returns the colour associated with the last event** Need to change**"""
#currRGB = (255, 255, 255, 100)
#if nodeTags:
#tag = nodeTags.pop()
event = get_tag_event(tag)
if not event.startswith('Notes') or not event.startswith('DataAcquis'): # since these are measurements or notes
return (EVENT_RGB[event][0], EVENT_RGB[event][1], EVENT_RGB[event][2], 100)
else:
return (255, 255, 255, 100)
#----------------------------------------------------------------------
def getEventIcon(self, icon_size, act):
"""get the associated icon for the given action/event"""
if act == 'Seed':
icon = icons.seed.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act == 'CellLine':
icon = icons.stock.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Harvest':
icon = icons.harvest.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Chemical':
icon = icons.treat.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Biological':
icon = icons.dna.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Physical':
icon = icons.physical.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Dye':
icon = icons.stain.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Immuno':
icon = icons.antibody.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Genetic':
icon = icons.primer.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Centrifugation':
icon = icons.spin.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Wash':
icon = icons.wash.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Drying':
icon = icons.drying.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Medium':
icon = icons.medium.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Initiation':
icon = icons.initiation.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Storage':
icon = icons.storage.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='Incubation':
icon = icons.incubator.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='RheoManipulation':
icon = icons.rheometer.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='HCS':
icon = icons.hcs.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='FCS':
icon = icons.fcs.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='TLM':
icon = icons.tlm.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif act =='RHE':
icon = icons.rhe.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Hint':
#icon = icons.hint.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Text':
#icon = icons.critical.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='Rest':
#icon = icons.rest.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='URL':
#icon = icons.url.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
#elif act =='MultiMedia':
#icon = icons.video.Scale(icon_size, icon_size, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
return icon
#----------------------------------------------------------------------
def get_Row_Numbers(self, protocol, token):
"""This method returs TAGS with similar elements
eg. 'AddProcess|Rheology|Gas1|1' 'AddProcess|Rheology|Gas2|1' etc"""
tag_stump = get_tag_stump(protocol, 2)
instance = get_tag_attribute(protocol)
return sorted(self.get_attribute_list_by_instance(tag_stump+'|%s'%token, instance), key = self.stringSplitByNumbers)
#----------------------------------------------------------------------
def setLabelColour(self, tags, labels):
"""Change mandatory label colour Red-->Green when filled"""
for tag in tags:
if self.get_field(tag):
labels[tag].SetForegroundColour(('#006600'))
labels[tag].Refresh()
else:
labels[tag].SetForegroundColour(wx.RED)
labels[tag].Refresh()
#----------------------------------------------------------------------
def checkMandatoryTags(self, tags):
"""Checks whether the mandatory fields/tags being filled"""
for tag in tags:
if not self.get_field(tag):
import wx
dial = wx.MessageDialog(None, 'Please fill %s mandatory field' %get_tag_attribute(tag), 'Error', wx.OK | wx.ICON_ERROR)
dial.ShowModal()
return
return True
#----------------------------------------------------------------------
def alphanumeric_sort(self, lst):
"""sort alphanumeric strings in a list e.g. [Plate1, Plate11, Tube2]"""
re_natural = re.compile('[0-9]+|[^0-9]+')
return [(1, int(c)) if c.isdigit() else (0, c.lower()) for c in re_natural.findall(lst)] + [lst]
#----------------------------------------------------------------------
def last_seed_instance(self, instance):
"""finds the last seeding instance that is associated with a harvest instance"""
for inst in list(reversed(range(int(instance)))):
if 'Transfer|Seed|HarvestInstance|%s'%str(inst) is not None:
return str(inst)
#----------------------------------------------------------------------
def get_cellLine_Name(self, inst, mode):
"""returns cell Line name given the seeding/harvesting (mode) instance that is realted with a harvest instance
if mode is None, it refers to Harvest_Seed type of seeding instance"""
if mode is 'H':
return self.get_field('Sample|CellLine|Name|%s'
%str(self.get_field('Transfer|Harvest|CellLineInstance|%s'%str(inst))))
if mode is 'S':
return self.get_field('Sample|CellLine|Name|%s'
%str(self.get_field('Transfer|Seed|CellLineInstance|%s'%str(inst))))
if mode is 'HS':
return self.get_field('Sample|CellLine|Name|%s'
%str(self.get_field('Transfer|Harvest|CellLineInstance|%s'
%str(self.get_field('Transfer|Seed|HarvestInstance|%s'
%str(inst))))))
