def _on_mouse_click(self, evt):
if self.current_node is None:
return
for tag in self.current_node.get_tags():
if (tag.startswith('DataAcquis|TLM') or
tag.startswith('DataAcquis|HCS')):
for well in self.current_node.get_well_ids():
image_tag = '%s|Images|%s|%s|%s'%(exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well)
urls = meta.get_field(image_tag, [])
for url in urls:
im = Image.open(url)
im.show()
elif tag.startswith('DataAcquis|FCS'):
for well in self.current_node.get_well_ids():
image_tag = '%s|Images|%s|%s|%s'%(exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well)
urls = meta.get_field(image_tag, [])
for url in urls:
os.startfile(url)
## message = ''
## for well in sorted(self.current_node.get_well_ids()):
## message += ', '.join(well)
## message += '\n'
## msg = wx.MessageDialog(self, message, caption='Info', style=wx.OK | wx.ICON_INFORMATION | wx.STAY_ON_TOP, pos=(200,200))
## msg.ShowModal()
## msg.Destroy()
try:
bench = wx.GetApp().get_bench()
except:
return
# --- Update the Bench view ---
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols(
[exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0])
for well in self.current_node.get_well_ids()])
bench.update_plate_groups()
bench.update_well_selections()
def get_ancestral_tags(self, node):
#ancestral_tags = []
#for pnode in timeline.reverse_iter_tree(node):
#if pnode:
#if 'CellTransfer|Seed' in node.tags:
#for tag in node.tags:
##if (tag.startswith('CellTransfer|Seed') and
##meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) is not None):
#h_instance = meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag))
#for tpnode in self.nodes_by_timepoint[node.get_timepoint()-1]:
#if tpnode:
#for tptag in tpnode.tags:
#if exp.get_tag_protocol(tptag) == 'CellTransfer|Harvest|'+h_instance:
#for npnode in timeline.reverse_iter_tree(tpnode):
#if npnode:
#for nptag in npnode.tags:
#ancestral_tags.append(exp.get_tag_stump(nptag, 2))
#else:
#for ptag in pnode.tags:
#ancestral_tags.append(exp.get_tag_stump(ptag, 2))
#return ancestral_tags
return [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]
def get_children_tags(self, node): """returns the children node tags""" return [exp.get_tag_stump(ctag, 2) for cnodes in timeline.get_progeny(node) if cnodes for ctag in cnodes.tags]
def get_ancestral_tags(self, node):
#ancestral_tags = []
#for pnode in timeline.reverse_iter_tree(node):
#if pnode:
#if 'CellTransfer|Seed' in node.tags:
#for tag in node.tags:
##if (tag.startswith('CellTransfer|Seed') and
##meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) is not None):
#h_instance = meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag))
#for tpnode in self.nodes_by_timepoint[node.get_timepoint()-1]:
#if tpnode:
#for tptag in tpnode.tags:
#if exp.get_tag_protocol(tptag) == 'CellTransfer|Harvest|'+h_instance:
#for npnode in timeline.reverse_iter_tree(tpnode):
#if npnode:
#for nptag in npnode.tags:
#ancestral_tags.append(exp.get_tag_stump(nptag, 2))
#else:
#for ptag in pnode.tags:
#ancestral_tags.append(exp.get_tag_stump(ptag, 2))
#return ancestral_tags
return [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]
def get_children_tags(self, node): """returns the children node tags""" return [exp.get_tag_stump(ctag, 2) for cnodes in timeline.get_progeny(node) if cnodes for ctag in cnodes.tags]
def OnSavingData(self, event):
#TO DO: make this method coherent with other instances of this method
ctrl = event.GetEventObject()
tag = [t for t, c in self.settings_controls.items() if c == ctrl][0]
if tag.startswith('Admin'): # if this is an Admin
myDate = ''
if isinstance(ctrl, wx.DatePickerCtrl):
date = ctrl.GetValue()
self.myDate = '%02d/%02d/%4d' % (date.Day, date.Month + 1,
date.Year)
if isinstance(ctrl,
wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
self.curr_protocol['ADMIN'] = [
self.settings_controls['Admin|0'].GetValue(), self.myDate,
self.settings_controls['Admin|2'].GetValue(),
self.settings_controls['Admin|3'].GetValue(),
self.settings_controls['Admin|4'].GetStringSelection()
]
else: # if this is a step
step = tag.split('|')[0]
# get the sibling controls like description, duration, temp controls for this step
info = []
for tg in [t for t, c in self.settings_controls.items()]:
if exp.get_tag_stump(tag, 1) == exp.get_tag_stump(
tg, 1) and tg.startswith('Step'):
c_num = int(tg.split('|')[1])
if isinstance(self.settings_controls[tg], wx.Choice):
info.insert(
c_num,
self.settings_controls[tg].GetStringSelection())
elif isinstance(self.settings_controls[tg], wx.ListBox):
info.insert(
c_num,
self.settings_controls[tg].GetStringSelection())
else:
user_input = self.settings_controls[tg].GetValue()
user_input.rstrip('\n')
user_input.rstrip('\t')
info.insert(c_num, user_input)
self.curr_protocol[step] = info
def OnSavingData(self, event):
#TO DO: make this method coherent with other instances of this method
ctrl = event.GetEventObject()
tag = [t for t, c in self.settings_controls.items() if c==ctrl][0]
if tag.startswith('Admin'): # if this is an Admin
myDate = ''
if isinstance(ctrl, wx.DatePickerCtrl):
date = ctrl.GetValue()
self.myDate = '%02d/%02d/%4d'%(date.Day, date.Month+1, date.Year)
if isinstance(ctrl, wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
self.curr_protocol['ADMIN'] = [self.settings_controls['Admin|0'].GetValue(),
self.myDate,
self.settings_controls['Admin|2'].GetValue(),
self.settings_controls['Admin|3'].GetValue(),
self.settings_controls['Admin|4'].GetStringSelection()]
else: # if this is a step
step = tag.split('|')[0]
# get the sibling controls like description, duration, temp controls for this step
info = []
for tg in [t for t, c in self.settings_controls.items()]:
if exp.get_tag_stump(tag, 1) == exp.get_tag_stump(tg, 1) and tg.startswith('Step'):
c_num = int(tg.split('|')[1])
if isinstance(self.settings_controls[tg], wx.Choice):
info.insert(c_num, self.settings_controls[tg].GetStringSelection())
elif isinstance(self.settings_controls[tg], wx.ListBox):
info.insert(c_num, self.settings_controls[tg].GetStringSelection())
else:
user_input = self.settings_controls[tg].GetValue()
user_input.rstrip('\n')
user_input.rstrip('\t')
info.insert(c_num, user_input)
self.curr_protocol[step] = info
def _recalculate_min_size(self):
if self.timepoints is not None and len(self.timepoints) > 0:
timeline = exp.ExperimentSettings.getInstance().get_timeline()
max_event_types_per_timepoint = \
max([len(set([exp.get_tag_stump(evt.get_welltag()) for evt in evts]))
for t, evts in self.events_by_timepoint.items()])
min_h = (max_event_types_per_timepoint+1) * self.ICON_SIZE + self.PAD * 2 + self.FONT_SIZE[1] + self.TIC_SIZE * 2 + 1
if self.time_x:
self.SetMinSize((self.PAD * 2 + self.MIN_X_GAP * self.timepoints[-1],
min_h))
else:
self.SetMinSize((len(self.timepoints) * self.MIN_X_GAP + self.PAD * 2,
min_h))
def __init__(self, parent, protocol, token, col_details, mandatory_tags, **kwargs):
wx.Panel.__init__(self, parent, **kwargs)
self.protocol = protocol
self.token = token
self.col_details = col_details
self.col_headers = self.col_details.keys()
self.mandatory_tags = mandatory_tags
self.tag_stump = exp.get_tag_stump(self.protocol, 2)
self.instance = exp.get_tag_attribute(self.protocol)
self.settings_controls = {}
self.showRows()
def __init__(self, parent, protocol, **kwargs):
wx.ScrolledWindow.__init__(self, parent, **kwargs)
self.SetScrollbars(20, 20, self.Size[0] + 20, self.Size[1] + 20, 0, 0)
self.tag_stump = exp.get_tag_stump(protocol, 2)
self.instance = exp.get_tag_attribute(protocol)
# Attach a flexi sizer for the text controler and labels
self.fgs = wx.FlexGridSizer(rows=15000, cols=6, hgap=5, vgap=5)
#Create the first step as empty
if not meta.get_field(self.tag_stump + '|Step1|%s' % self.instance):
meta.set_field(self.tag_stump + '|Step1|%s' % self.instance,
['', '', ''])
self.showSteps()
def __init__(self, parent, protocol, **kwargs):
wx.ScrolledWindow.__init__(self, parent, **kwargs)
self.SetScrollbars(20, 20, self.Size[0]+20, self.Size[1]+20, 0, 0)
self.tag_stump = exp.get_tag_stump(protocol, 2)
self.instance = exp.get_tag_attribute(protocol)
# Attach a flexi sizer for the text controler and labels
self.fgs = wx.FlexGridSizer(rows=15000, cols=6, hgap=5, vgap=5)
#Create the first step as empty
if not meta.get_field(self.tag_stump+'|Step1|%s'%self.instance):
meta.set_field(self.tag_stump+'|Step1|%s'%self.instance, ['','',''])
self.showSteps()
def _on_paint(self, evt=None):
'''Handler for paint events.
'''
if not self.timepoints:
evt.Skip()
return
PAD = self.PAD + self.ICON_SIZE / 2.0
ICON_SIZE = self.ICON_SIZE
MIN_X_GAP = self.MIN_X_GAP
TIC_SIZE = self.TIC_SIZE
FONT_SIZE = self.FONT_SIZE
MAX_TIMEPOINT = self.timepoints[-1]
self.hover_timepoint = None
dc = wx.PaintDC(self)
dc.Clear()
dc.BeginDrawing()
w_win, h_win = (float(self.Size[0]), float(self.Size[1]))
if self.time_x:
if MAX_TIMEPOINT == 0:
px_per_time = 1
else:
px_per_time = max((w_win - PAD * 2.0) / MAX_TIMEPOINT,
MIN_X_GAP)
if len(self.timepoints) == 1:
x_gap = 1
else:
x_gap = max(MIN_X_GAP,
(w_win - PAD * 2) / (len(self.timepoints) - 1))
# y pos of line
y = h_win - PAD - FONT_SIZE[1] - TIC_SIZE - 1
# draw the timeline
if self.time_x:
dc.DrawLine(PAD, y,
px_per_time * MAX_TIMEPOINT + PAD, y)
else:
dc.DrawLine(PAD, y,
x_gap * (len(self.timepoints) - 1) + PAD, y)
font = dc.Font
font.SetPixelSize(FONT_SIZE)
dc.SetFont(font)
# draw event icons
for i, timepoint in enumerate(self.timepoints):
# x position of timepoint on the line
if self.time_x:
x = timepoint * px_per_time + PAD
else:
x = i * x_gap + PAD
if (self.cursor_pos is not None and
x - ICON_SIZE/2 < self.cursor_pos < x + ICON_SIZE/2):
dc.SetPen(wx.Pen(wx.BLACK, 3))
self.hover_timepoint = timepoint
else:
dc.SetPen(wx.Pen(wx.BLACK, 1))
# Draw tic marks
dc.DrawLine(x, y - TIC_SIZE,
x, y + TIC_SIZE)
#dc.DrawRectangle(x, y, ICON_SIZE, ICON_SIZE)
prefixes = set([exp.get_tag_stump(ev.get_welltag(), 2) for ev in self.events_by_timepoint[timepoint]])
for i, stump in enumerate(prefixes):
if stump.startswith('CellTransfer|Seed'):
bmp = icons.seed.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('CellTransfer|Harvest'):
bmp = icons.harvest.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('Perturbation|Chem'):
bmp = icons.treat.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('Perturbation|Bio'):
bmp = icons.dna.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('Labeling|Stain'):
bmp = icons.stain.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('Labeling|Antibody'):
bmp = icons.antibody.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('Labeling|Primer'):
bmp = icons.primer.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('AddProcess|Spin'):
bmp = icons.spin.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('AddProcess|Wash'):
bmp = icons.wash.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('AddProcess|Dry'):
bmp = icons.dry.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('AddProcess|Medium'):
bmp = icons.medium.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('AddProcess|Incubator'):
bmp = icons.incubator.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('DataAcquis|HCS'):
bmp = icons.staticimage.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('DataAcquis|FCS'):
bmp = icons.fcs.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
elif stump.startswith('DataAcquis|TLM'):
bmp = icons.tlm.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
dc.DrawBitmap(bmp, x - ICON_SIZE / 2.0,
y - ((i+1)*ICON_SIZE) - TIC_SIZE - 1)
# draw the timepoint beneath the line
time_string = exp.format_time_string(timepoint)
wtext = FONT_SIZE[0] * len(time_string)
dc.DrawText(time_string, x - wtext/2.0, y + TIC_SIZE + 1)
dc.EndDrawing()
def formatProtocolInfo(self):
''' this method format the information of the annoted protocols
ready for printing'''
meta = exp.ExperimentSettings.getInstance()
self.printfile = file('screenshot.htm', 'w')
timepoints = meta.get_timeline().get_unique_timepoints()
timeline = meta.get_timeline()
self.events_by_timepoint = timeline.get_events_by_timepoint()
#---- Overview Secion ---#
protocol_info = self.decode_event_description('Overview|Project|1') #this 1 is psedo to make it coherent with other instance based tabs
self.printfile.write('<html><head><title>Experiment Protocol</title></head>'
'<br/><body><h1>'+protocol_info[0]+'</h1>'
'<h3>1. Experiment Overview</h3>'
)
for element in protocol_info[1]:
self.printfile.write('<dfn>'+element[0]+': </dfn><code>'+element[1]+'</code><br />')
#---- Stock Culture ----#
stockcultures = meta.get_field_instances('StockCulture|Sample')
self.printfile.write('<h3>2. Stock Culture</h3>')
if stockcultures:
for instance in stockcultures:
protocol_info = self.decode_event_description('StockCulture|Sample|%s'%instance)
self.printfile.write('<i>'+protocol_info[0]+' </i><br />')
for element in protocol_info[1]:
self.printfile.write('<dfn>'+element[0]+': </dfn><code>'+element[1]+'</code><br />')
#self.printfile.write('<code>'+protocol_info[2]+' </code><br />')
self.printfile.write('<br />')
self.printfile.write('<dfn>'+protocol_info[2][0]+'</dfn><br />'
else:
self.printfile.write('<code>No stock culture was used for this experiment</code>')
#---- Instrument Secion ---#
self.printfile.write('<h3>3. Instrument Settings</h3>')
microscopes = meta.get_field_instances('Instrument|Microscope')
flowcytometers = meta.get_field_instances('Instrument|Flowcytometer')
if microscopes:
for instance in microscopes:
protocol_info = self.decode_event_description('Instrument|Microscope|%s'%instance)
self.printfile.write('<i>Channel Name: '+protocol_info[0]+' (microscope instance %s)'%instance+'</i><br />')
for component in protocol_info[1]:
if component[0] == 'Component':
self.printfile.write('<strong>'+component[1]+'</strong><br />')
else:
self.printfile.write('<code><b>'+component[0]+': </b>'+component[1]+'</code><br />')
self.printfile.write('<p></p>')
if flowcytometers:
for instance in flowcytometers:
protocol_info = self.decode_event_description('Instrument|Flowcytometer|%s'%instance)
self.printfile.write('<i>'+protocol_info[0]+' </i><br />')
for element in protocol_info[1]: # channels
self.printfile.write('<ul><li><code><b>'+element[0]+': </b>') # channel name
for i, component in enumerate(element[1]): # config of each component of this channel
if i == len(element[1])-1:
self.printfile.write(meta.decode_ch_component(component[0]))
else:
self.printfile.write(meta.decode_ch_component(component[0])+' >> ')
self.printfile.write('</code></li></ul>')
self.printfile.write('<p></p>')
#---- Material and Method Secion ---#
self.printfile.write('<h3>4. Materials and Methods</h3>')
for i, timepoint in enumerate(timepoints):
for protocol in set([exp.get_tag_protocol(ev.get_welltag()) for ev in self.events_by_timepoint[timepoint]]):
instance = exp.get_tag_attribute(protocol)
# protocol info includes the description of the attributes for each of the protocol e.g. Perturbation|Chem|1 is passed
protocol_info = self.decode_event_description(protocol)
# spatial info includes plate well inforamtion for this event well tag e.g. Perturbation|Bio|Wells|1|793
####spatial_info = self.decode_event_location(ev.get_welltag()) ##THIS THING DOES NOT WORK WHEN SAME EVENT AT SAME TIME POINT HAPPENS
welltag = exp.get_tag_stump(protocol, 2)+'|Wells|%s|%s'%(instance, str(timepoint))
spatial_info = self.decode_event_location(welltag)
# -- write the description and location of the event --#
if (exp.get_tag_event(protocol) == 'Seed') and (meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance) is not None):
self.printfile.write('Step '+str(i+1)+': <em><b>Seeding</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />')
self.printlocation(spatial_info)
# if harvest precede seeding
#if meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance) is not None:
## origin(harvesting instance), destination(seeding instance), timepoint
#self.printCellTransfer(meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance),
#instance, timepoint)
if exp.get_tag_event(protocol) == 'Harvest':
self.printfile.write('Step '+str(i+1)+': <em><b>Harvest-Seed (Cell Transfer)</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printCellTransfer(instance, timepoint)
if exp.get_tag_event(protocol) == 'Chem': #TO DO
self.printfile.write('Step '+str(i+1)+': <em><b>Chemical Perturbation</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Bio':
self.printfile.write('Step '+str(i+1)+': <em><b>Biological Perturbation</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />')
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Dye':
self.printfile.write('Step '+str(i+1)+': <em><b>Staining with chemical dye</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
duration = element[1]
temp = element[2]
if len(duration) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
if len(temp) > 0: # duration is mentioned
temp = ' at %s C.'%element[2]
self.printfile.write('<ul><li><code>'+description+duration+temp+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Immuno':
self.printfile.write('Step '+str(i+1)+': <em><b>Staining with immunofluorescence</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code>'+element+'</code><br />') #footer part
for element in protocol_info[1]: # step description
description = element[0]
duration = element[1]
temp = element[2]
if len(duration) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
if len(temp) > 0: # duration is mentioned
temp = ' at %s C.'%element[2]
self.printfile.write('<ul><li><code>'+description+duration+temp+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Genetic':
self.printfile.write('Step '+str(i+1)+': <em><b>Staining with genetic materials</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')#footer part
for element in protocol_info[1]: # step description
description = element[0]
duration = element[1]
temp = element[2]
if len(duration) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
if len(temp) > 0: # duration is mentioned
temp = ' at %s C.'%element[2]
self.printfile.write('<ul><li><code>'+description+duration+temp+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Spin':
self.printfile.write('Step '+str(i+1)+': <em><b>Spinning</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Wash':
self.printfile.write('Step '+str(i+1)+': <em><b>Washing</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Dry':
self.printfile.write('Step '+str(i+1)+': <em><b>Drying</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Medium':
self.printfile.write('Step '+str(i+1)+': <em><b>Addition of medium</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code>'+element+'</code><br />') #footer part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Incubator':
self.printfile.write('Step '+str(i+1)+': <em><b>Incubation</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />') #footer part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'TLM':
self.printfile.write('Step '+str(i+1)+': <em><b>Timelapse image acquisition</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />') # header part wrtie wich setting instance being used
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
# write the image urls
self.printfile.write('<table border="0">')
for plate, wells in spatial_info.iteritems():
for well in wells:
pw = plate, well
self.printfile.write('<code><b>Well '+well+'</b></code><br />')
for url in meta.get_field('DataAcquis|TLM|Images|%s|%s|%s'%(instance,timepoint, pw), []):
self.printfile.write('<small>'+url+'</small><br />')
#self.printfile.write('<tr><code><td>'+well+':</td><td>'+('<br />'.join(meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), [])))+'</td></code></tr>')
self.printfile.write('</table><br />')
if exp.get_tag_event(protocol) == 'HCS':
self.printfile.write('Step '+str(i+1)+': <em><b>Static image acquisition</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />') # header part wrtie wich setting instance being used
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
# write the image urls
self.printfile.write('<table border="0">')
for plate, wells in spatial_info.iteritems():
for well in wells:
pw = plate, well
self.printfile.write('<code><b>Well '+well+'</b></code><br />')
for url in meta.get_field('DataAcquis|HCS|Images|%s|%s|%s'%(instance,timepoint, pw), []):
self.printfile.write('<small>'+url+'</small><br />')
#self.printfile.write('<tr><code><td>'+well+':</td><td>'+('<br />'.join(meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), [])))+'</td></code></tr>')
self.printfile.write('</table><br />')
if exp.get_tag_event(protocol) == 'FCS':
self.printfile.write('Step '+str(i+1)+': <em><b> FCS file acquisition</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />') # header part wrtie wich setting instance being used
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
# write the image urls
self.printfile.write('<table border="0">')
for plate, wells in spatial_info.iteritems():
for well in wells:
pw = plate, well
self.printfile.write('<code><b>'+plate+'['+well+']'+'</b></code><br />')
for url in meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), []):
self.printfile.write('<small>'+url+'</small><br />')
#self.printfile.write('<tr><code><td>'+well+':</td><td>'+('<br />'.join(meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), [])))+'</td></code></tr>')
self.printfile.write('</table><br />')
if exp.get_tag_event(protocol) == 'CriticalPoint': # to implement if there are events at the same timepoint write those event first then the critical point
self.printfile.write('<font size="2" color="red">Critical point: '+meta.get_field('Notes|CriticalPoint|Description|%s'%instance)+'</font></em><br />')
if exp.get_tag_event(protocol) == 'Hint':
self.printfile.write('<font size="2" color="blue">Hint: '+meta.get_field('Notes|Hint|Description|%s'%instance)+'</font></em><br />')
if exp.get_tag_event(protocol) == 'Rest':
self.printfile.write('<font size="2" color="green">Rest: '+meta.get_field('Notes|Rest|Description|%s'%instance)+'</font></em><br />')
if exp.get_tag_event(protocol) == 'URL':
self.printfile.write('<code>To find out more information please visit '+meta.get_field('Notes|URL|Description|%s'%instance)+'</code><br />')
if exp.get_tag_event(protocol) == 'Video':
self.printfile.write('<code>For more information please watch the media file: '+meta.get_field('Notes|Video|Description|%s'%instance)+'</code><br />')
self.printfile.write('<br />')
#---- Protocol Map ---#
self.printfile.write('<br />'.join(['<h3>5. Methodology Map</h3>',
'<br/><br/>',
'<center><img src=myImage.png width=500 height=600></center>',
'</body></html>']))
self.printfile.close()
#----------------------------------------------------------------------
def sendToPrinter(self):
""""""
self.printer.GetPrintData().SetPaperId(wx.PAPER_LETTER)
self.printer.PrintFile(self.html.GetOpenedPage())
def decode_event_description(self, protocol):
meta = ExperimentSettings.getInstance()
instance = exp.get_tag_attribute(protocol)
header = ''
footer = []
info = []
if exp.get_tag_type(protocol) == 'Overview':
header += meta.get_field('Overview|Project|Title', default='Not specified')
info.append(('Aims', meta.get_field('Overview|Project|Aims', default='Not specified')))
info.append(('Funding Code', meta.get_field('Overview|Project|Fund', default='Not specified')))
info.append(('Keywords', meta.get_field('Overview|Project|Keywords', default='Not specified')))
info.append(('Experiment Number', meta.get_field('Overview|Project|ExptNum', default='Not specified')))
info.append(('Experiment date', meta.get_field('Overview|Project|ExptDate', default='Not specified')))
info.append(('Relevant publications', meta.get_field('Overview|Project|Publications', default='Not specified')))
info.append(('Experimenter', meta.get_field('Overview|Project|Experimenter', default='Not specified')))
info.append(('Institution', meta.get_field('Overview|Project|Institution', default='Not specified')))
info.append(('Department', meta.get_field('Overview|Project|Department', default='Not specified')))
info.append(('Address', meta.get_field('Overview|Project|Address', default='Not specified')))
info.append(('Experiment Status', meta.get_field('Overview|Project|Status', default='Not specified')))
return (header, info)
if exp.get_tag_type(protocol) == 'StockCulture':
header += '%s cell line (Authority %s, Ref: %s) was used. This will be referred as Stock Instance %s' %(meta.get_field('StockCulture|Sample|CellLine|%s'%instance, default='Not specified'),
meta.get_field('StockCulture|Sample|Authority|%s'%instance, default='Not specified'),
str(instance),
meta.get_field('StockCulture|Sample|CatalogueNo|%s'%instance, default='Not specified'),
str(instance))
info.append(('Depositors', meta.get_field('StockCulture|Sample|Depositors|%s'%instance, default='Not specified')))
info.append(('Biosafety Level', meta.get_field('StockCulture|Sample|Biosafety|%s'%instance, default='Not specified')))
info.append(('Shipment', meta.get_field('StockCulture|Sample|Shipment|%s'%instance, default='Not specified')))
info.append(('Permit', meta.get_field('StockCulture|Sample|Permit|%s'%instance, default='Not specified')))
info.append(('Growth Property', meta.get_field('StockCulture|Sample|GrowthProperty|%s'%instance, default='Not specified')))
info.append(('Organism', meta.get_field('StockCulture|Sample|Organism|%s'%instance, default='Not specified')))
info.append(('Morphology', meta.get_field('StockCulture|Sample|Morphology|%s'%instance, default='Not specified')))
info.append(('Organ', meta.get_field('StockCulture|Sample|Organ|%s'%instance, default='Not specified')))
info.append(('Disease', meta.get_field('StockCulture|Sample|Disease|%s'%instance, default='Not specified')))
info.append(('Products', meta.get_field('StockCulture|Sample|Products|%s'%instance, default='Not specified')))
info.append(('Applications', meta.get_field('StockCulture|Sample|Applications|%s'%instance, default='Not specified')))
info.append(('Receptors', meta.get_field('StockCulture|Sample|Receptors|%s'%instance, default='Not specified')))
info.append(('Antigen', meta.get_field('StockCulture|Sample|Antigen|%s'%instance, default='Not specified')))
info.append(('DNA', meta.get_field('StockCulture|Sample|DNA|%s'%instance, default='Not specified')))
info.append(('Cytogenetic', meta.get_field('StockCulture|Sample|Cytogenetic|%s'%instance, default='Not specified')))
info.append(('Isoenzymes', meta.get_field('StockCulture|Sample|Isoenzymes|%s'%instance, default='Not specified')))
info.append(('Age of Organism (days)', meta.get_field('StockCulture|Sample|Age|%s'%instance, default='Not specified')))
info.append(('Gender', meta.get_field('StockCulture|Sample|Gender|%s'%instance, default='Not specified')))
info.append(('Ethnicity', meta.get_field('StockCulture|Sample|Ethnicity|%s'%instance, default='Not specified')))
info.append(('Comments', meta.get_field('StockCulture|Sample|Comments|%s'%instance, default='Not specified')))
info.append(('Publications', meta.get_field('StockCulture|Sample|Publications|%s'%instance, default='Not specified')))
info.append(('Related Products', meta.get_field('StockCulture|Sample|RelProduct|%s'%instance, default='Not specified')))
info.append(('Original Passage Number', meta.get_field('StockCulture|Sample|OrgPassageNo|%s'%instance, default='Not specified')))
info.append(('Preservation', meta.get_field('StockCulture|Sample|Preservation|%s'%instance, default='Not specified')))
info.append(('GrowthMedium', meta.get_field('StockCulture|Sample|GrowthMedium|%s'%instance, default='Not specified')))
passages = [attr for attr in meta.get_attribute_list_by_instance('StockCulture|Sample', instance)
if attr.startswith('Passage')]
if passages:
footer += '%s passages were carried out according to the specifications' %str(len(passages))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Microscope':
header += '%s settings' %meta.get_field('Instrument|Microscope|ChannelName|%s'%instance, default = 'Not specified')
if meta.get_field('Instrument|Microscope|Stand|%s'%instance) is not None:
info.append(('Component', 'Stand'))
info.append(('Type', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[2]))
info.append(('Orientation', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[3]))
info.append(('Number of Lampss', str(meta.get_field('Instrument|Microscope|Stand|%s'%instance)[4])))
info.append(('Number of Detectors', str(meta.get_field('Instrument|Microscope|Stand|%s'%instance)[5])))
if meta.get_field('Instrument|Microscope|Condensor|%s'%instance) is not None:
info.append(('Component', 'Condensor'))
info.append(('Type', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[2]))
if meta.get_field('Instrument|Microscope|Stage|%s'%instance) is not None:
info.append(('Component', 'Stage'))
info.append(('Type', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[2]))
info.append(('Stage Holder', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[3]))
info.append(('Holder Code', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[4]))
if meta.get_field('Instrument|Microscope|Incubator|%s'%instance) is not None:
info.append(('Component', 'Incubator'))
info.append(('Make', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[0]))
info.append(('Model', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[1]))
info.append(('Temperature(C)', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[2]))
info.append(('CO2%', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[3]))
info.append(('Humidity', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[4]))
info.append(('Pressure', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[5]))
if meta.get_field('Instrument|Microscope|LightSource|%s'%instance) is not None:
info.append(('Component', 'Light Source'))
info.append(('Type', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[0]))
info.append(('Source', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[1]))
info.append(('Make', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[3]))
info.append(('Measured Power (User)', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[4]))
info.append(('Measured Power (Instrument)', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[5]))
info.append(('Shutter Used', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[6]))
info.append(('Shutter Type', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[7]))
info.append(('Shutter Make', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[8]))
info.append(('Shutter Model', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[9]))
if meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance) is not None:
info.append(('Component', 'Excitation Filter'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[1])))
info.append(('Make', meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[3]))
if meta.get_field('Instrument|Microscope|Mirror|%s'%instance) is not None:
info.append(('Component', 'Dichroic Mirror'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[1])))
info.append(('Mode', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[2]))
info.append(('Make', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[3]))
info.append(('Model', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[4]))
info.append(('Modification', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[5]))
if meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance) is not None:
info.append(('Component', 'Emission Filter'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[1])))
info.append(('Make', meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[3]))
if meta.get_field('Instrument|Microscope|Lens|%s'%instance) is not None:
info.append(('Component', 'Lens'))
info.append(('Make', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[0]))
info.append(('Model', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[1]))
info.append(('Objective Magnification', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[2]))
info.append(('Objective NA', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[3]))
info.append(('Calibrated Magnification', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[4]))
info.append(('Immersion', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[5]))
info.append(('Correction Collar', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[6]))
info.append(('Correction Value', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[7]))
info.append(('Correction Type', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[8]))
if meta.get_field('Instrument|Microscope|Lens|%s'%instance) is not None:
info.append(('Component', 'Detector'))
info.append(('Type', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[2]))
info.append(('Binning', str(meta.get_field('Instrument|Microscope|Detector|%s'%instance)[3])))
info.append(('Exposure Time', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[4]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[5]))
info.append(('Gain', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[6]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[7]))
info.append(('Offset', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[8]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[9]))
return (header, info)
if exp.get_tag_event(protocol) == 'Flowcytometer':
header += meta.get_field('Instrument|Flowcytometer|Manufacter|%s'%instance, default='')
if meta.get_field('Instrument|Flowcytometer|Model|%s'%instance) is not None:
header += '(model: %s)' %meta.get_field('Instrument|Flowcytometer|Model|%s'%instance, default = 'not specified')
header += ' was used. '
for attribute, description in sorted(meta.get_attribute_dict('Instrument|Flowcytometer|%s'%instance).iteritems()):
if attribute.startswith('Manufacter') or attribute.startswith('Model'):
continue
else:
info.append((attribute, description)) # attribute is Ch# and description is the component list
return(header, info)
if exp.get_tag_event(protocol) == 'Seed':
if meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance) is not None:
header += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance))
header += ' cells were seeded with a density of %s from the stock flask (Instance %s). ' %(meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = ''), meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance))
#if meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance) is not None:
#header += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance))
#header += ' cells were seeded with a density of %s from the Wells depicted bellow. ' %meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = '')
if meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance) is not None:
header += meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance)+' medium was used '
if meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance) is not None:
header += 'with following medium additives: %s. ' %meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance)
if meta.get_field('CellTransfer|Seed|Trypsinizatiton|%s'%instance) is 'Yes':
header += 'Also trypsinisation was performed'
return (header, info)
if exp.get_tag_event(protocol) == 'Chem':
if meta.get_field('Perturbation|Chem|ChemName|%s'%instance) is not None:
header += meta.get_field('Perturbation|Chem|ChemName|%s'%instance)
subtext = '%s,%s' %(meta.get_field('Perturbation|Chem|Manufacturer|%s'%instance, default=''), meta.get_field('Perturbation|Chem|CatNum|%s'%instance, default=''))
if re.search('\w+', subtext): #if the mfg and or cat number of the chemical is mentioned
header += '[%s]'%subtext
header += ' was added'
if meta.get_field('Perturbation|Chem|Conc|%s'%instance) is not None:
header += ' with a concentration of %s %s' %(meta.get_field('Perturbation|Chem|Conc|%s'%instance), meta.get_field('Perturbation|Chem|Unit|%s'%instance, default=''))
if meta.get_field('Perturbation|Chem|Additives|%s'%instance) is not None:
header += '. Following additives were included: %s' %meta.get_field('Perturbation|Chem|Additives|%s'%instance)
if meta.get_field('Perturbation|Chem|Other|%s'%instance) is not None:
header += '. Other information: %s'%meta.get_field('Perturbation|Chem|Other|%s'%instance)
return (header, info)
if exp.get_tag_event(protocol) == 'Bio':
header += 'Biological perturbation was done with following agent'
info.append(('RNAi Sequence', meta.get_field('Perturbation|Bio|SeqName|%s'%instance, default = 'Not specified')))
info.append(('Acession Number', meta.get_field('Perturbation|Bio|AccessNumber|%s'%instance, default = 'Not specified')))
info.append(('Target Gene Accession Number', meta.get_field('Perturbation|Bio|TargetGeneAccessNum|%s'%instance, default = 'Not specified')))
info.append(('Concentration', meta.get_field('Perturbation|Bio|Conc|%s'%instance, default = 'Not specified')+' '+meta.get_field('Perturbation|Bio|Unit|%s'%instance, default = '')))
info.append(('Additives', meta.get_field('Perturbation|Bio|Additives|%s'%instance, default = 'Not specified')))
info.append(('Other Information', meta.get_field('Perturbation|Bio|Other|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'Dye':
header += meta.get_field('Staining|Dye|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('Staining|Dye|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Dye|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Immuno':
header += meta.get_field('Staining|Immuno|ProtocolName|%s'%instance)
if meta.get_field('Staining|Immuno|Target|%s'%instance) is not None:
footer.append('Target antibody %s was used.'%meta.get_field('Staining|Immuno|Target|%s'%instance))
if meta.get_field('Staining|Immuno|Clonality|%s'%instance) is not None:
footer.append('Clonality was %s.'%meta.get_field('Staining|Immuno|Clonality|%s'%instance))
if meta.get_field('Staining|Immuno|Primary|%s'%instance) is not None:
token =''
token += 'Primary antibody %s was used'%meta.get_field('Staining|Immuno|Primary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Primary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Primary|%s'%instance)[1]
footer.append(token)
if meta.get_field('Staining|Immuno|Secondary|%s'%instance) is not None:
token =''
token += 'Secondary antibody %s was used'%meta.get_field('Staining|Immuno|Secondary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Secondary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Secondary|%s'%instance)[1]
footer.append(token)
if meta.get_field('Staining|Immuno|Tertiary|%s'%instance) is not None:
token =''
token += 'Tertiary antibody %s was used'%meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[1]
footer.append(token)
steps = sorted(meta.get_attribute_list_by_instance('Staining|Immuno|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Immuno|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Genetic':
header += meta.get_field('Staining|Genetic|ProtocolName|%s'%instance)
footer.append(('Target Sequence', meta.get_field('Staining|Genetic|Target|%s'%instance, default = 'Not specified')))
footer.append(('Primer Sequence', meta.get_field('Staining|Genetic|Primer|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('Staining|Genetic|Temp|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('Staining|Genetic|GC|%s'%instance, default = 'Not specified')))
steps = sorted(meta.get_attribute_list_by_instance('Staining|Genetic|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Genetic|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Spin':
header += meta.get_field('AddProcess|Spin|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Spin|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Spin|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Wash':
header += meta.get_field('AddProcess|Wash|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Wash|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Wash|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Dry':
header += meta.get_field('AddProcess|Dry|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Dry|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Dry|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Medium':
header += meta.get_field('AddProcess|Medium|ProtocolName|%s'%instance)
if meta.get_field('AddProcess|Medium|MediumAdditives|%s'%instance) is not None:
footer.append('Medium additives used: %s'%meta.get_field('AddProcess|Medium|MediumAdditives|%s'%instance))
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Medium|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Medium|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Incubator':
header += meta.get_field('AddProcess|Incubator|ProtocolName|%s'%instance)
footer.append(('Incubator settings', ''))
footer.append(('Manufacturer', meta.get_field('AddProcess|Incubator|Manufacter|%s'%instance, default = 'Not specified')))
footer.append(('Model', meta.get_field('AddProcess|Incubator|Model|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('AddProcess|Incubator|Temp|%s'%instance, default = 'Not specified')))
footer.append(('CO2%', meta.get_field('AddProcess|Incubator|CO2|%s'%instance, default = 'Not specified')))
footer.append(('Humidity', meta.get_field('AddProcess|Incubator|Humidity|%s'%instance, default = 'Not specified')))
footer.append(('Pressure', meta.get_field('AddProcess|Incubator|Pressure|%s'%instance, default = 'Not specified')))
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Medium|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Medium|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'TLM':
if meta.get_field('DataAcquis|TLM|MicroscopeInstance|%s'%instance) is not None:
ch_name = meta.get_field('DataAcquis|TLM|MicroscopeInstance|%s'%instance)
cytometer_instance=meta.get_instance_by_field_value('Instrument|Microscope|ChannelName|', ch_name)
header += ch_name+' channel was used (see microscope instance %s for details)'%cytometer_instance
info.append(('Image Format', meta.get_field('DataAcquis|TLM|Format|%s'%instance, default = 'Not specified')))
info.append(('Time Interval (min)', meta.get_field('DataAcquis|TLM|TimeInterval|%s'%instance, default = 'Not specified')))
info.append(('Total Frame/Pane Number', meta.get_field('DataAcquis|TLM|FrameNumber|%s'%instance, default = 'Not specified')))
info.append(('Stacking Order', meta.get_field('DataAcquis|TLM|StackProcess|%s'%instance, default = 'Not specified')))
info.append(('Pixel Size', meta.get_field('DataAcquis|TLM|PixelSize|%s'%instance, default = 'Not specified')))
info.append(('Pixel Conversion', meta.get_field('DataAcquis|TLM|PixelConvert|%s'%instance, default = 'Not specified')))
info.append(('Software', meta.get_field('DataAcquis|TLM|Software|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'HCS':
if meta.get_field('DataAcquis|HCS|MicroscopeInstance|%s'%instance) is not None:
ch_name = meta.get_field('DataAcquis|HCS|MicroscopeInstance|%s'%instance)
cytometer_instance=meta.get_instance_by_field_value('Instrument|Microscope|ChannelName|', ch_name)
header += ch_name+' channel was used (see microscope instance %s for details)'%cytometer_instance
info.append(('Image Format', meta.get_field('DataAcquis|HCS|Format|%s'%instance, default = 'Not specified')))
info.append(('Pixel Size', meta.get_field('DataAcquis|HCS|PixelSize|%s'%instance, default = 'Not specified')))
info.append(('Pixel Conversion', meta.get_field('DataAcquis|HCS|PixelConvert|%s'%instance, default = 'Not specified')))
info.append(('Software', meta.get_field('DataAcquis|HCS|Software|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'FCS':
if meta.get_field('DataAcquis|FCS|FlowcytInstance|%s'%instance) is not None:
cytometer_instance = meta.get_field('DataAcquis|FCS|FlowcytInstance|%s'%instance)
header += meta.get_field('Instrument|Flowcytometer|Manufacter|%s'%cytometer_instance, default='')+' flowcytometer '
if meta.get_field('Instrument|Flowcytometer|Model|%s'%cytometer_instance) is not None:
header += '(model: %s)' %meta.get_field('Instrument|Flowcytometer|Model|%s'%cytometer_instance, default = 'not specified')
header += ' was used (see flowcytometer instance %s for details).'%cytometer_instance
if meta.get_field('DataAcquis|FCS|Software|%s'%instance) is not None:
info.append(meta.get_field('DataAcquis|FCS|Software|%s'%instance)+' software was used for data acquisition. ')
if meta.get_field('DataAcquis|FCS|Format|%s'%instance) is not None:
info.append('FCS files in %s'%meta.get_field('DataAcquis|FCS|Format|%s'%instance)+' format were saved in following location\n')
return (header, info)
#if event == 'Harvest':
##if meta.get_field('CellTransfer|Harvest|StockInstance|%s'%instance) is not None:
##text += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Harvest|StockInstance|%s'%instance))
#if meta.get_field('CellTransfer|Seed|Trypsinizatiton|%s'%instance) is 'Yes':
#text += ' cells were harvested by trypsinisation '
#text += 'cell density was %s. ' %meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = '')
#if meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance) is not None:
#text += meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance)+' medium was used '
#if meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance) is not None:
#text += 'with following medium additives: %s. ' %meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance)
def decode_event_location(self, plate_well_info):
d = {}
for pw in meta.get_field(plate_well_info):
plate = pw[0]
well = pw[1]
if d.get(plate, None) is None:
d[plate] = [well]
else:
d[plate] += [well]
return d
def printlocation(self, spatial_info):
for plate, wells in spatial_info.iteritems():
self.printfile.write('<br /><cite>'+plate+'</cite><br />')
self.printfile.write('<table border="1">')
for row in exp.PlateDesign.get_row_labels(exp.PlateDesign.get_plate_format(plate)):
self.printfile.write('<tr>')
for col in exp.PlateDesign.get_col_labels(exp.PlateDesign.get_plate_format(plate)):
well = row+col
if well in wells:
self.printfile.write('<td BGCOLOR=yellow>'+well+'</td>')
else:
self.printfile.write('<td><code>'+well+'</code></td>')
self.printfile.write('</tr>')
self.printfile.write('</table><br />')
def printCellTransfer(self, harvest_inst, timepoint):
seed_instances = meta.get_protocol_instances('CellTransfer|Seed|HarvestInstance|')
for seed_inst in seed_instances:
if (meta.get_field('CellTransfer|Seed|Wells|%s|%s'%(seed_inst, str(timepoint+1))) is not None) and (meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%seed_inst) == harvest_inst):
harvest_spatial_info = self.decode_event_location('CellTransfer|Harvest|Wells|%s|%s'%(harvest_inst, str(timepoint)))
seed_spatial_info = self.decode_event_location('CellTransfer|Seed|Wells|%s|%s'%(seed_inst, str(timepoint+1)))
self.printfile.write('<table border="0">')
self.printfile.write('<tr><td>')
for plate, wells in harvest_spatial_info.iteritems():
self.printfile.write('<br /><cite>'+plate+'</cite><br />')
self.printfile.write('<table border="1">')
for row in exp.PlateDesign.get_row_labels(exp.PlateDesign.get_plate_format(plate)):
self.printfile.write('<tr>')
for col in exp.PlateDesign.get_col_labels(exp.PlateDesign.get_plate_format(plate)):
well = row+col
if well in wells:
self.printfile.write('<td BGCOLOR=yellow>'+well+'</td>')
else:
self.printfile.write('<td><code>'+well+'</code></td>')
self.printfile.write('</tr>')
self.printfile.write('</table>')
self.printfile.write('</td><td> -- Transferred to --> </td><td>')
for plate, wells in seed_spatial_info.iteritems():
self.printfile.write('<br /><cite>'+plate+'</cite><br />')
self.printfile.write('<table border="1">')
for row in exp.PlateDesign.get_row_labels(exp.PlateDesign.get_plate_format(plate)):
self.printfile.write('<tr>')
for col in exp.PlateDesign.get_col_labels(exp.PlateDesign.get_plate_format(plate)):
well = row+col
if well in wells:
self.printfile.write('<td BGCOLOR=yellow>'+well+'</td>')
else:
self.printfile.write('<td><code>'+well+'</code></td>')
self.printfile.write('</tr>')
self.printfile.write('</table>')
self.printfile.write('</td></tr>')
self.printfile.write('</table><br />')
class wxHTML(HtmlWindow):
#----------------------------------------------------------------------
def __init__(self, parent, id):
html.HtmlWindow.__init__(self, parent, id, style=wx.NO_FULL_REPAINT_ON_RESIZE)
if __name__ == '__main__':
app = wx.App(False)
frame = PrintProtocol()
#frame.Show()
app.MainLoop()
def OnSavingData(self, event):
ctrl = event.GetEventObject()
tag = [t for t, c in self.settings_controls.items() if c==ctrl][0]
if isinstance(ctrl, wx.ListBox) and ctrl.GetStringSelection() == 'Other':
other = wx.GetTextFromUser('Insert Other', 'Other')
ctrl.Append(other)
ctrl.SetStringSelection(other)
if tag.startswith('Admin'): # if this is an Admin
date = self.settings_controls['Admin|1'].GetValue()
self.curr_protocol['ADMIN'] = [self.settings_controls['Admin|0'].GetValue(),
'%02d/%02d/%4d'%(date.Day, date.Month+1, date.Year),
self.settings_controls['Admin|2'].GetValue()
]
elif tag.startswith('Seed'):
self.curr_protocol['SEED'] = [self.settings_controls['Seed|0'].GetValue(),
self.settings_controls['Seed|1'].GetStringSelection()
]
elif tag.startswith('Harvest'):
self.curr_protocol['HARVEST'] = [self.settings_controls['Harvest|0'].GetValue(),
self.settings_controls['Harvest|1'].GetStringSelection()
]
elif tag.startswith('Reseed'):
self.curr_protocol['SEED'] = [self.settings_controls['Reseed|0'].GetValue(),
self.settings_controls['Reseed|1'].GetStringSelection()
]
elif tag.startswith('Vessel'):
self.curr_protocol['VESSEL'] = [self.settings_controls['Vessel|0'].GetStringSelection()]
else: # if this is a step
step = tag.split('|')[0]
# get the sibling controls like description, duration, temp controls for this step
info = []
for tg in [t for t, c in self.settings_controls.items()]:
if exp.get_tag_stump(tag, 1) == exp.get_tag_stump(tg, 1) and tg.startswith('Step'):
c_num = int(tg.split('|')[1])
if isinstance(self.settings_controls[tg], wx.Choice):
info.insert(c_num, self.settings_controls[tg].GetStringSelection())
elif isinstance(self.settings_controls[tg], wx.ListBox):
info.insert(c_num, self.settings_controls[tg].GetStringSelection())
else:
user_input = self.settings_controls[tg].GetValue()
user_input.rstrip('\n')
user_input.rstrip('\t')
info.insert(c_num, user_input)
self.curr_protocol[step] = info
date = self.curr_protocol['ADMIN'][1].split('/')
time = self.curr_protocol['ADMIN'][2].split(':')
self.sel_date_time = map(int, [date[2],date[1],date[0],time[0],time[1], time[2]])
self.selected_datetime = datetime.datetime(*map(int, [date[2],date[1],date[0],time[0],time[1], time[2]]))
if (self.initial_datetime and self.initial_seed_density and self.curr_protocol['HARVEST']):
# *** Harvest density can be less then seed density if cells die
# the forumula is different check with Paul #=elapsedtime*LN(2)/LN(harvest density/seed density)
# ** time resloution can be days or hours
time_elapsed = (self.selected_datetime-self.initial_datetime)
elapsed_minutes = (time_elapsed.days * 1440) + (time_elapsed.seconds / 60)
if elapsed_minutes < 360:
dlg = wx.MessageDialog(None, 'Difference of seed-harvest time should be minimum 6 hr.\nReselect time', 'Time selection error', wx.OK| wx.ICON_STOP)
dlg.ShowModal()
return
if (self.selected_datetime>self.initial_datetime and self.curr_protocol['HARVEST'][0] > self.initial_seed_density):
cell_growth = max(math.log(self.curr_protocol['HARVEST'][0]/self.initial_seed_density), 1)
pdt = (elapsed_minutes*math.log(2)/cell_growth)/60
self.pd_text.SetLabel('PD Time %.2f Hr' %pdt)
self.curr_protocol['PD'].append(pdt)
self.curr_protocol['PD'].append((elapsed_minutes/60)/pdt)
self.curr_protocol['PD'].append((elapsed_minutes/60))
if self.initial_seed_density and self.curr_protocol['HARVEST']:
self.selection_btn.Enable()
if (self.initial_seed_density is None) and self.curr_protocol['SEED']:
self.selection_btn.Enable()
def __init__(self, parent, protocol, currpassageNo, action_type):
wx.Dialog.__init__(self, parent, -1, size=(850,500), style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
self.protocol = protocol
self.currpassageNo = currpassageNo
self.action_type = action_type
self.SetTitle(self.action_type.title())
self.top_panel = wx.Panel(self)
self.bot_panel = wx.ScrolledWindow(self)
self.settings_controls = {}
self.curr_protocol = {}
self.admin_info = {}
self.today_datetime = datetime.datetime.now()
self.tag_stump = exp.get_tag_stump(self.protocol, 2)
self.instance = exp.get_tag_attribute(self.protocol)
if meta.get_field(self.tag_stump+'|Passage%s|%s' %(str(self.currpassageNo-1), self.instance)) is None:
self.curr_protocol = Default_Protocol
else:
d = meta.get_field(self.tag_stump+'|Passage%s|%s' %(str(self.currpassageNo-1), self.instance))
for k, v in d:
self.curr_protocol[k] = v
date= None
self.initial_datetime = None
self.initial_seed_density = None
self.curr_protocol['PD'] = []
self.curr_protocol['HARVEST'] = []
self.curr_protocol['RESEED'] = []
#datetime.datetime.fromtimestamp(wx.DateTime.Now().GetTicks())
#wx.DateTimeFromTimeT(time.mktime(datetime.datetime.now().timetuple()))
if self.curr_protocol['ADMIN'][1]:
date = self.curr_protocol['ADMIN'][1].split('/')
time = self.curr_protocol['ADMIN'][2].split(':')
self.initial_datetime = datetime.datetime(*map(int, [date[2],date[1],date[0],time[0],time[1], time[2]]))
if self.curr_protocol['SEED']:
self.initial_seed_density = self.curr_protocol['SEED'][0]
#Admin
self.settings_controls['Admin|0'] = wx.TextCtrl(self.top_panel, size=(70,-1), value=self.curr_protocol['ADMIN'][0])
self.settings_controls['Admin|1'] = wx.DatePickerCtrl(self.top_panel, style = wx.DP_DROPDOWN | wx.DP_SHOWCENTURY)
if date is None:
self.curr_protocol['ADMIN'][1] = str(self.today_datetime.day)+'/'+str(self.today_datetime.month)+'/'+str(self.today_datetime.year)
else:
self.settings_controls['Admin|1'].SetValue(wx.DateTimeFromDMY(int(date[0]), int(date[1])-1, int(date[2])))
self.settings_controls['Admin|2'] = masked.TimeCtrl( self.top_panel, -1, name="24 hour control", fmt24hr=True )
h = self.settings_controls['Admin|2'].GetSize().height
spin1 = wx.SpinButton( self.top_panel, -1, wx.DefaultPosition, (-1,h), wx.SP_VERTICAL )
self.settings_controls['Admin|2'].BindSpinButton( spin1 )
self.curr_protocol['ADMIN'][2] = str(self.today_datetime.hour)+':'+str(self.today_datetime.minute)+':'+str(self.today_datetime.second)
self.settings_controls['Admin|2'].SetValue(self.curr_protocol['ADMIN'][2])
self.set_curr_time = wx.Button(self.top_panel, -1, 'Set Current Date Time')
if (self.action_type == 'passage') or (self.action_type == 'seed'):
self.settings_controls['Seed|0'] = wx.lib.masked.NumCtrl(self.top_panel, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Seed|1'] = wx.ListBox(self.top_panel, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
if self.curr_protocol['SEED']:
self.settings_controls['Seed|0'].SetValue(self.curr_protocol['SEED'][0])
self.settings_controls['Seed|0'].Disable()
self.settings_controls['Seed|1'].Append(self.curr_protocol['SEED'][1])
self.settings_controls['Seed|1'].SetStringSelection(self.curr_protocol['SEED'][1])
self.settings_controls['Seed|1'].Disable()
self.settings_controls['Seed|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
if (self.action_type == 'passage'):
self.settings_controls['Harvest|0'] = wx.lib.masked.NumCtrl(self.top_panel, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Harvest|1'] = wx.ListBox(self.top_panel, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Reseed|0'] = wx.lib.masked.NumCtrl(self.top_panel, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Reseed|1'] = wx.ListBox(self.top_panel, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Harvest|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Harvest|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.settings_controls['Reseed|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Reseed|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
# CHANGE IT VESSEL DESIGN TWO SELECTIONS
vessel_types =['T75', 'T25', '6WellPlate','12WellPlate', 'Other']
self.settings_controls['Vessel|0'] = wx.ListBox(self.top_panel, -1, wx.DefaultPosition, (100,20), vessel_types, wx.LB_SINGLE)
if self.curr_protocol['VESSEL']:
self.settings_controls['Vessel|0'].Append(self.curr_protocol['VESSEL'][0])
self.settings_controls['Vessel|0'].SetStringSelection(self.curr_protocol['VESSEL'][0])
self.pd_text = wx.StaticText(self.top_panel, -1, '')
font = wx.Font(12, wx.FONTFAMILY_MODERN, wx.FONTSTYLE_NORMAL, wx.FONTWEIGHT_BOLD)
self.pd_text.SetFont(font)
self.selection_btn = wx.Button(self, wx.ID_OK, 'Record Passage')
self.close_btn = wx.Button(self, wx.ID_CANCEL)
#self.selection_btn.Disable()
#Bind
self.settings_controls['Admin|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|1'].Bind(wx.EVT_DATE_CHANGED, self.OnSavingData)
self.settings_controls['Admin|2'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Vessel|0'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.set_curr_time.Bind(wx.EVT_BUTTON, self.setCurrDateTime)
# Sizers and layout
staticbox = wx.StaticBox(self.top_panel, -1, "Admin")
adminsizer = wx.StaticBoxSizer(staticbox, wx.HORIZONTAL)
adminsizer.Add(wx.StaticText(self.top_panel, -1, 'Operator Name'),0, wx.RIGHT, 5)
adminsizer.Add(self.settings_controls['Admin|0'] , 0, wx.EXPAND)
adminsizer.Add(wx.StaticText(self.top_panel, -1, 'Date'),0, wx.RIGHT|wx.LEFT, 5)
adminsizer.Add(self.settings_controls['Admin|1'], 0, wx.EXPAND)
adminsizer.Add(wx.StaticText(self.top_panel, -1, 'Time'),0, wx.LEFT, 5)
adminsizer.Add(self.settings_controls['Admin|2'], 0, wx.EXPAND)
adminsizer.Add( spin1, 0, wx.ALIGN_CENTRE )
adminsizer.Add(self.set_curr_time, 0, wx.ALIGN_RIGHT|wx.LEFT, 15)
stat_fgs = wx.FlexGridSizer(cols=4, hgap=5, vgap=5)
if (self.action_type == 'passage') or (self.action_type == 'seed'):
stat_fgs.Add(wx.StaticText(self.top_panel, -1, 'Seed Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Seed|0'], 0, wx.EXPAND)
stat_fgs.Add(wx.StaticText(self.top_panel, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Seed|1'], 0, wx.EXPAND)
if (self.action_type == 'passage'):
stat_fgs.Add(wx.StaticText(self.top_panel, -1, 'Harvest Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Harvest|0'], 0, wx.EXPAND)
stat_fgs.Add(wx.StaticText(self.top_panel, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Harvest|1'], 0, wx.EXPAND)
stat_fgs.Add(wx.StaticText(self.top_panel, -1, 'Reseed Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Reseed|0'], 0, wx.EXPAND)
stat_fgs.Add(wx.StaticText(self.top_panel, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Reseed|1'], 0, wx.EXPAND)
stat_fgs.Add(wx.StaticText(self.top_panel, -1, 'Vessel Type'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
stat_fgs.Add(self.settings_controls['Vessel|0'], 0, wx.EXPAND)
staticbox = wx.StaticBox(self.top_panel, -1, "Statistics")
statsizer = wx.StaticBoxSizer(staticbox, wx.HORIZONTAL)
statsizer.Add(stat_fgs, 0, wx.ALIGN_LEFT)
statsizer.Add(self.pd_text, 0, wx.ALIGN_CENTRE|wx.ALIGN_RIGHT|wx.ALL, 20)
self.top_panel_sizer = wx.BoxSizer(wx.VERTICAL)
self.top_panel_sizer.Add(adminsizer, 0, wx.EXPAND|wx.ALL, 5)
self.top_panel_sizer.Add(statsizer, 0, wx.EXPAND|wx.ALL, 5)
self.fgs = wx.FlexGridSizer(cols=7, hgap=5, vgap=5)
self.showSteps()
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add(self.selection_btn , 0, wx.ALL, 5)
btnSizer.Add(self.close_btn , 0, wx.ALL, 5)
self.top_panel.SetSizer(self.top_panel_sizer)
self.bot_panel.SetSizer(self.fgs)
self.bot_panel.SetScrollbars(20, 20, self.Size[0]+20, self.Size[1]+20, 0, 0)
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add(self.selection_btn , 0, wx.ALL, 5)
btnSizer.Add(self.close_btn , 0, wx.ALL, 5)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.top_panel, 0, wx.EXPAND|wx.ALL, 5)
self.Sizer.Add(wx.StaticLine(self), 0, wx.EXPAND|wx.ALL, 5)
self.Sizer.Add(self.bot_panel, 1, wx.EXPAND|wx.ALL, 5)
self.Sizer.Add(btnSizer)
self.Show()
def _on_mouse_click(self, evt):
if self.current_node is None:
return
for tag in self.current_node.get_tags():
if tag.startswith("DataAcquis|TLM") or tag.startswith("DataAcquis|HCS"):
for well in self.current_node.get_well_ids():
image_tag = "%s|Images|%s|%s|%s" % (
exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well,
)
urls = meta.get_field(image_tag, [])
image_viewer_path = ""
if os.path.isfile("C:\Program Files\ImageJ\ImageJ.exe"):
ImageJPath = "C:\Program Files\ImageJ\ImageJ.exe"
subprocess.Popen("%s %s" % (ImageJPath, " ".join(urls)))
else:
dlg = wx.lib.dialogs.ScrolledMessageDialog(
self,
str("\n".join(urls)),
"ERROR!! ImageJ was not found in C\Program Files directory to show following images",
)
dlg.ShowModal()
return
# for url in urls:
# im = Image.open(url)
# im.show()
##TODO: make it Try with ImageJ first then Exception is Image.open(url)
# ImageJPath = r'C:\Program Files\ImageJ\ImageJ'
# subprocess.Popen("%s %s" % (ImageJPath, url))
elif tag.startswith("DataAcquis|FCS"):
for well in self.current_node.get_well_ids():
image_tag = "%s|Images|%s|%s|%s" % (
exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well,
)
urls = meta.get_field(image_tag, [])
for url in urls:
os.startfile(url)
# print self.current_node.get_well_ids()
# print self.current_node.get_parent()
## message = ''
## for well in sorted(self.current_node.get_well_ids()):
## message += ', '.join(well)
## message += '\n'
## msg = wx.MessageDialog(self, message, caption='Info', style=wx.OK | wx.ICON_INFORMATION | wx.STAY_ON_TOP, pos=(200,200))
## msg.ShowModal()
## msg.Destroy()
try:
bench = wx.GetApp().get_bench()
except:
return
# --- Update the Bench view ---
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols([exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0]) for well in self.current_node.get_well_ids()]
)
bench.update_plate_groups()
bench.update_well_selections()
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
# -- Update the expt setting/metadata view --#
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [
exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node)
if pnode
for ptag in pnode.tags
]
def _on_mouse_click(self, evt):
if self.current_node is None:
return
# --- Update the Bench view ---
try:
bench = wx.GetApp().get_bench()
except:
return
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols(
[exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0])
for well in self.current_node.get_well_ids()])
bench.update_plate_groups()
bench.update_well_selections()
bench.del_evt_button.Enable()
# -- Update the expt setting/metadata view --#
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node) if pnode
for ptag in pnode.tags]
# -- show the data url list --- #
data_acquis = False
for tag in self.current_node.get_tags():
if tag.startswith('DataAcquis'):
data_acquis = True
break
if data_acquis:
dia = DataLinkListDialog(self, self.current_node.get_well_ids())
if dia.ShowModal() == wx.ID_OK:
if dia.output_options.GetSelection() == 0:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_selected_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 1:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_all_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 2:
image_urls = []
for row in dia.listctrl.get_selected_urls():
image_urls.append(row[2])
if os.path.isfile('C:\Program Files\ImageJ\ImageJ.exe') is False:
#err_dlg = wx.lib.dialogs.ScrolledMessageDialog(self, str("\n".join(urls)), "ERROR!! ImageJ was not found in C\Program Files directory to show following images")
err_dlg = wx.MessageDialog(None, 'ImageJ was not found in C\Program Files directory to show images!!', 'Error', wx.OK | wx.ICON_ERROR)
err_dlg.ShowModal()
return
else:
#TO DO: check the image format to be shown in ImageJ
ImageJPath = 'C:\Program Files\ImageJ\ImageJ.exe'
subprocess.Popen("%s %s" % (ImageJPath, ' '.join(image_urls)))
dia.Destroy()
def __init__(self, parent, protocol, currpassageNo):
wx.Dialog.__init__(self,
parent,
-1,
size=(700, 500),
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER,
title='Passage %s' % str(currpassageNo))
self.protocol = protocol
self.currpassageNo = currpassageNo
self.top_panel = wx.Panel(self)
self.bot_panel = wx.ScrolledWindow(self)
self.settings_controls = {}
self.curr_protocol = {}
self.admin_info = {}
self.tag_stump = exp.get_tag_stump(self.protocol, 2)
self.instance = exp.get_tag_attribute(self.protocol)
if meta.get_field(
self.tag_stump + '|Passage%s|%s' %
(str(self.currpassageNo - 1), self.instance)) is None:
self.curr_protocol = Default_Protocol
else:
#self.curr_protocol = meta.get_field(self.tag_stump+'|Passage%s|%s' %(str(self.currpassageNo-1), self.instance))
d = meta.get_field(self.tag_stump + '|Passage%s|%s' %
(str(self.currpassageNo - 1), self.instance))
for k, v in d:
self.curr_protocol[k] = v
today = datetime.date.today()
self.myDate = '%02d/%02d/%4d' % (today.day, today.month, today.year)
self.curr_protocol['ADMIN'][
1] = self.myDate # set todays date as current
self.settings_controls['Admin|0'] = wx.TextCtrl(
self.top_panel,
size=(70, -1),
value=self.curr_protocol['ADMIN'][0])
self.settings_controls['Admin|1'] = wx.DatePickerCtrl(
self.top_panel, style=wx.DP_DROPDOWN | wx.DP_SHOWCENTURY)
self.settings_controls['Admin|2'] = wx.TextCtrl(
self.top_panel,
size=(20, -1),
value=self.curr_protocol['ADMIN'][2])
#self.settings_controls['Admin|3'] = wx.TextCtrl(self.top_panel, size=(20,-1), value=self.curr_protocol['ADMIN'][3])
self.settings_controls['Admin|3'] = wx.lib.masked.NumCtrl(
self.top_panel, size=(20, -1), style=wx.TE_PROCESS_ENTER)
if isinstance(self.curr_protocol['ADMIN'][3], int): #it had value
self.settings_controls['Admin|3'].SetValue(
self.curr_protocol['ADMIN'][3])
unit_choices = ['nM2', 'uM2', 'mM2', 'Other']
self.settings_controls['Admin|4'] = wx.ListBox(self.top_panel, -1,
wx.DefaultPosition,
(50, 20), unit_choices,
wx.LB_SINGLE)
if self.curr_protocol['ADMIN'][4] is not None:
self.settings_controls['Admin|4'].Append(
self.curr_protocol['ADMIN'][4])
self.settings_controls['Admin|4'].SetStringSelection(
self.curr_protocol['ADMIN'][4])
self.settings_controls['Admin|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|1'].Bind(wx.EVT_DATE_CHANGED,
self.OnSavingData)
self.settings_controls['Admin|2'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|3'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|4'].Bind(wx.EVT_LISTBOX,
self.OnSavingData)
self.selection_btn = wx.Button(self, wx.ID_OK, 'Record Passage')
self.close_btn = wx.Button(self, wx.ID_CANCEL)
# Sizers and layout
top_fgs = wx.FlexGridSizer(cols=10, vgap=5)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Operator Name'), 0,
wx.RIGHT, 5)
top_fgs.Add(self.settings_controls['Admin|0'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Date'), 0,
wx.RIGHT | wx.LEFT, 5)
top_fgs.Add(self.settings_controls['Admin|1'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Split 1:'), 0, wx.LEFT,
5)
top_fgs.Add(self.settings_controls['Admin|2'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Cell Count'), 0,
wx.RIGHT | wx.LEFT, 5)
top_fgs.Add(self.settings_controls['Admin|3'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, ' cells/'), 0)
top_fgs.Add(self.settings_controls['Admin|4'], 0, wx.EXPAND)
self.fgs = wx.FlexGridSizer(cols=7, hgap=5, vgap=5)
self.showSteps()
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add(self.selection_btn, 0, wx.ALL, 5)
btnSizer.Add(self.close_btn, 0, wx.ALL, 5)
self.top_panel.SetSizer(top_fgs)
self.bot_panel.SetSizer(self.fgs)
self.bot_panel.SetScrollbars(20, 20, self.Size[0] + 20,
self.Size[1] + 20, 0, 0)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.top_panel, 0, wx.EXPAND | wx.ALL, 5)
self.Sizer.Add(wx.StaticLine(self), 0, wx.EXPAND | wx.ALL, 5)
self.Sizer.Add(self.bot_panel, 1, wx.EXPAND | wx.ALL, 10)
self.Sizer.Add(btnSizer)
self.Show()
def __init__(self, parent, protocol, currpassageNo):
wx.Dialog.__init__(self, parent, -1, size=(700,500), style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER, title = 'Passage %s' %str(currpassageNo))
self.protocol = protocol
self.currpassageNo = currpassageNo
self.top_panel = wx.Panel(self)
self.bot_panel = wx.ScrolledWindow(self)
self.settings_controls = {}
self.curr_protocol = {}
self.admin_info = {}
self.tag_stump = exp.get_tag_stump(self.protocol, 2)
self.instance = exp.get_tag_attribute(self.protocol)
if meta.get_field(self.tag_stump+'|Passage%s|%s' %(str(self.currpassageNo-1), self.instance)) is None:
self.curr_protocol = Default_Protocol
else:
#self.curr_protocol = meta.get_field(self.tag_stump+'|Passage%s|%s' %(str(self.currpassageNo-1), self.instance))
d = meta.get_field(self.tag_stump+'|Passage%s|%s' %(str(self.currpassageNo-1), self.instance))
for k, v in d:
self.curr_protocol[k] = v
today = datetime.date.today()
self.myDate = '%02d/%02d/%4d'%(today.day, today.month, today.year)
self.curr_protocol['ADMIN'][1] = self.myDate # set todays date as current
self.settings_controls['Admin|0'] = wx.TextCtrl(self.top_panel, size=(70,-1), value=self.curr_protocol['ADMIN'][0])
self.settings_controls['Admin|1'] = wx.DatePickerCtrl(self.top_panel, style = wx.DP_DROPDOWN | wx.DP_SHOWCENTURY)
self.settings_controls['Admin|2'] = wx.TextCtrl(self.top_panel, size=(20,-1), value=self.curr_protocol['ADMIN'][2])
#self.settings_controls['Admin|3'] = wx.TextCtrl(self.top_panel, size=(20,-1), value=self.curr_protocol['ADMIN'][3])
self.settings_controls['Admin|3'] = wx.lib.masked.NumCtrl(self.top_panel, size=(20,-1), style=wx.TE_PROCESS_ENTER)
if isinstance(self.curr_protocol['ADMIN'][3], int): #it had value
self.settings_controls['Admin|3'].SetValue(self.curr_protocol['ADMIN'][3])
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Admin|4'] = wx.ListBox(self.top_panel, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
if self.curr_protocol['ADMIN'][4] is not None:
self.settings_controls['Admin|4'].Append(self.curr_protocol['ADMIN'][4])
self.settings_controls['Admin|4'].SetStringSelection(self.curr_protocol['ADMIN'][4])
self.settings_controls['Admin|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|1'].Bind(wx.EVT_DATE_CHANGED, self.OnSavingData)
self.settings_controls['Admin|2'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|3'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|4'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.selection_btn = wx.Button(self, wx.ID_OK, 'Record Passage')
self.close_btn = wx.Button(self, wx.ID_CANCEL)
# Sizers and layout
top_fgs = wx.FlexGridSizer(cols=10, vgap=5)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Operator Name'),0, wx.RIGHT, 5)
top_fgs.Add(self.settings_controls['Admin|0'] , 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Date'),0, wx.RIGHT|wx.LEFT, 5)
top_fgs.Add(self.settings_controls['Admin|1'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Split 1:'),0, wx.LEFT, 5)
top_fgs.Add(self.settings_controls['Admin|2'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, 'Cell Count'),0, wx.RIGHT|wx.LEFT, 5)
top_fgs.Add(self.settings_controls['Admin|3'], 0, wx.EXPAND)
top_fgs.Add(wx.StaticText(self.top_panel, -1, ' cells/'),0)
top_fgs.Add(self.settings_controls['Admin|4'], 0, wx.EXPAND)
self.fgs = wx.FlexGridSizer(cols=7, hgap=5, vgap=5)
self.showSteps()
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add(self.selection_btn , 0, wx.ALL, 5)
btnSizer.Add(self.close_btn , 0, wx.ALL, 5)
self.top_panel.SetSizer(top_fgs)
self.bot_panel.SetSizer(self.fgs)
self.bot_panel.SetScrollbars(20, 20, self.Size[0]+20, self.Size[1]+20, 0, 0)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.top_panel, 0, wx.EXPAND|wx.ALL, 5)
self.Sizer.Add(wx.StaticLine(self), 0, wx.EXPAND|wx.ALL, 5)
self.Sizer.Add(self.bot_panel, 1, wx.EXPAND|wx.ALL, 10)
self.Sizer.Add(btnSizer)
self.Show()
def get_ancestral_tags(self, node):
return [
exp.get_tag_stump(ptag, 2) for pnode in timeline.reverse_iter_tree(node) if pnode for ptag in pnode.tags
]
def _on_paint(self, evt=None):
'''Handler for paint events.
'''
if self.nodes_by_timepoint == {}:
evt.Skip()
return
t0 = time()
PAD = self.PAD + self.NODE_R
NODE_R = self.NODE_R
MIN_X_GAP = self.MIN_X_GAP
MIN_Y_GAP = self.MIN_Y_GAP
FLASK_GAP = self.FLASK_GAP
MAX_TIMEPOINT = self.timepoints[0]
timepoints = self.timepoints
nodes_by_tp = self.nodes_by_timepoint
self.current_node = None # Node with the mouse over it
w_win, h_win = (float(self.Size[0]), float(self.Size[1]))
if self.time_x:
if timepoints[0] == 0:
px_per_time = 1
else:
px_per_time = max((w_win - PAD * 2 - FLASK_GAP) / MAX_TIMEPOINT,
MIN_X_GAP)
if len(nodes_by_tp) == 2:
x_gap = 1
else:
# calculate the number of pixels to separate each generation timepoint
x_gap = max(MIN_X_GAP,
(w_win - PAD * 2 - FLASK_GAP) / (len(nodes_by_tp) - 2))
if len(nodes_by_tp[timepoints[0]]) == 1:
y_gap = MIN_Y_GAP
else:
# calcuate the minimum number of pixels to separate nodes on the y axis
y_gap = max(MIN_Y_GAP,
(h_win - PAD * 2) / (len(nodes_by_tp[MAX_TIMEPOINT]) - 1))
nodeY = {} # Store y coords of children so we can calculate where to draw the parents
Y = PAD
X = w_win - PAD
dc = wx.PaintDC(self)
dc.Clear()
dc.BeginDrawing()
#dc.SetPen(wx.Pen("BLACK",1))
def hover(mouse_pos, node_pos, node_r):
'''returns whether the mouse is hovering over a node
mouse_pos - the mouse position
node_pos - the node position
node_r - the node radius
'''
if mouse_pos is None:
return False
MX,MY = mouse_pos
X,Y = node_pos
return (X - node_r < MX < X + node_r and
Y - node_r < MY < Y + node_r)
# Iterate from leaf nodes up to the root, and draw R->L, Top->Bottom
for i, t in enumerate(timepoints):
if t == -1:
X = PAD
elif self.time_x:
X = PAD + FLASK_GAP + t * px_per_time
x_gap = PAD + FLASK_GAP + timepoints[i-1] * px_per_time - X
else:
X = PAD + FLASK_GAP + (len(timepoints) - i - 2) * x_gap
# NO EVENTS. JUST DRAW THE STOCK, CENTERED.
if len(nodes_by_tp) == 1:
X = w_win / 2
Y = h_win / 2
if hover(self.cursor_pos, (X,Y), self.NODE_R):
dc.SetBrush(wx.Brush('#FFFFAA'))
self.current_node = nodes_by_tp.values()[t][0]
else:
dc.SetBrush(wx.Brush('#FAF9F7'))
self.current_node = None
dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
## dc.DrawText(str(nodes_by_tp[t][0].get_timepoint()), X, Y+NODE_R)
# LEAF NODES
elif i == 0:
for node in nodes_by_tp[t]:
empty_path = False # whether this path follows a harvesting
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush('YELLOW'))
else:
# No event
dc.SetBrush(wx.Brush('WHITE'))
if 'CellTransfer|Harvest' in [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]:
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
dc.SetPen(wx.Pen('#000000', 3))
self.current_node = node
else:
# No MouseOver
dc.SetPen(wx.Pen('#000000', 1))
if not empty_path:
dc.DrawCircle(X, Y, NODE_R)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
nodeY[node.id] = Y
Y += y_gap
# INTERNAL NODES
else:
for node in nodes_by_tp[t]:
empty_path = False # whether this path follows a harvesting
ys = []
for child in node.get_children():
ys.append(nodeY[child.id])
Y = (min(ys) + max(ys)) / 2
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush('YELLOW'))
else:
# No event
dc.SetBrush(wx.Brush('WHITE'))
if 'CellTransfer|Harvest' in [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]:
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
dc.SetPen(wx.Pen(wx.BLACK, 3))
self.current_node = node
else:
# No MouseOver
dc.SetPen(wx.Pen(wx.BLACK, 1))
if t == -1:
dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
else:
if not empty_path:
dc.DrawCircle(X, Y, NODE_R)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
# DRAW LINES CONNECTING THIS NODE TO ITS CHILDREN
dc.SetBrush(wx.Brush('#FAF9F7'))
dc.SetPen(wx.Pen(wx.BLACK, 1))
harvest_tag = False
for tag in node.get_tags():
if tag.startswith('CellTransfer|Harvest'):
harvest_tag = tag
for child in node.get_children():
if t == -1:
if self.time_x:
dc.DrawLine(X + NODE_R, Y,
X + FLASK_GAP + px_per_time * timepoints[i-1] - NODE_R ,nodeY[child.id])
else:
dc.DrawLine(X + NODE_R, Y,
X + FLASK_GAP - NODE_R ,nodeY[child.id])
else:
if harvest_tag:
# TODO: improve performance by caching reseed
# events from the previous timepoint
for nn in nodes_by_tp[timepoints[i-1]]:
for tag in nn.get_tags():
if (tag.startswith('CellTransfer|Seed') and
meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) == exp.get_tag_instance(harvest_tag)):
dc.SetPen(wx.Pen('BLACK', 1, wx.SHORT_DASH))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R ,nodeY[nn.id])
else:
if not empty_path:
dc.SetPen(wx.Pen(wx.BLACK, 1))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R,
nodeY[child.id])
nodeY[node.id] = Y
dc.EndDrawing()
def _on_mouse_click(self, evt):
if self.current_node is None:
return
# --- Update the Bench view ---
try:
bench = wx.GetApp().get_bench()
except:
return
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols(
[exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0])
for well in self.current_node.get_well_ids()])
bench.update_plate_groups()
bench.update_well_selections()
bench.del_evt_button.Enable()
# -- Update the expt setting/metadata view --#
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node) if pnode
for ptag in pnode.tags]
# -- show the data url list --- #
data_acquis = False
for tag in self.current_node.get_tags():
if tag.startswith('DataAcquis'):
data_acquis = True
break
if data_acquis:
dia = DataLinkListDialog(self, self.current_node.get_well_ids())
if dia.ShowModal() == wx.ID_OK:
if dia.output_options.GetSelection() == 0:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_selected_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 1:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_all_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 2:
image_urls = []
for row in dia.listctrl.get_selected_urls():
image_urls.append(row[2])
if os.path.isfile('C:\Program Files\ImageJ\ImageJ.exe') is False:
#err_dlg = wx.lib.dialogs.ScrolledMessageDialog(self, str("\n".join(urls)), "ERROR!! ImageJ was not found in C\Program Files directory to show following images")
err_dlg = wx.MessageDialog(None, 'ImageJ was not found in C\Program Files directory to show images!!', 'Error', wx.OK | wx.ICON_ERROR)
err_dlg.ShowModal()
return
else:
#TO DO: check the image format to be shown in ImageJ
ImageJPath = 'C:\Program Files\ImageJ\ImageJ.exe'
subprocess.Popen("%s %s" % (ImageJPath, ' '.join(image_urls)))
dia.Destroy()
def formatProtocolInfo(self):
''' this method format the information of the annoted protocols
ready for printing'''
meta = exp.ExperimentSettings.getInstance()
self.printfile = file('screenshot.htm', 'w')
timepoints = meta.get_timeline().get_unique_timepoints()
timeline = meta.get_timeline()
self.events_by_timepoint = timeline.get_events_by_timepoint()
#---- Overview Secion ---#
protocol_info = self.decode_event_description('Overview|Project|1') #this 1 is psedo to make it coherent with other instance based tabs
self.printfile.write('<html><head><title>Experiment Protocol</title></head>'
'<br/><body><h1>'+protocol_info[0]+'</h1>'
'<h3>1. Experiment Overview</h3>'
)
for element in protocol_info[1]:
self.printfile.write('<dfn>'+element[0]+': </dfn><code>'+element[1]+'</code><br />')
#---- Stock Culture ----#
stockcultures = meta.get_field_instances('StockCulture|Sample')
self.printfile.write('<h3>2. Stock Culture</h3>')
if stockcultures:
for instance in stockcultures:
protocol_info = self.decode_event_description('StockCulture|Sample|%s'%instance)
self.printfile.write('<i>'+protocol_info[0]+' </i><br />')
for element in protocol_info[1]:
self.printfile.write('<dfn>'+element[0]+': </dfn><code>'+element[1]+'</code><br />')
#self.printfile.write('<code>'+protocol_info[2]+' </code><br />')
self.printfile.write('<br />')
self.printfile.write('<dfn>'+protocol_info[2][0]+'</dfn><br />')
else:
self.printfile.write('<code>No stock culture was used for this experiment</code>')
#---- Instrument Secion ---#
self.printfile.write('<h3>3. Instrument Settings</h3>')
microscopes = meta.get_field_instances('Instrument|Microscope')
flowcytometers = meta.get_field_instances('Instrument|Flowcytometer')
if microscopes:
for instance in microscopes:
protocol_info = self.decode_event_description('Instrument|Microscope|%s'%instance)
self.printfile.write('<i>Channel Name: '+protocol_info[0]+' (microscope instance %s)'%instance+'</i><br />')
for component in protocol_info[1]:
if component[0] == 'Component':
self.printfile.write('<strong>'+component[1]+'</strong><br />')
else:
self.printfile.write('<code><b>'+component[0]+': </b>'+component[1]+'</code><br />')
self.printfile.write('<p></p>')
if flowcytometers:
for instance in flowcytometers:
protocol_info = self.decode_event_description('Instrument|Flowcytometer|%s'%instance)
self.printfile.write('<i>'+protocol_info[0]+' </i><br />')
for element in protocol_info[1]: # channels
self.printfile.write('<ul><li><code><b>'+element[0]+': </b>') # channel name
for i, component in enumerate(element[1]): # config of each component of this channel
if i == len(element[1])-1:
self.printfile.write(meta.decode_ch_component(component[0]))
else:
self.printfile.write(meta.decode_ch_component(component[0])+' >> ')
self.printfile.write('</code></li></ul>')
self.printfile.write('<p></p>')
#---- Material and Method Secion ---#
self.printfile.write('<h3>4. Materials and Methods</h3>')
for i, timepoint in enumerate(timepoints):
for protocol in set([exp.get_tag_protocol(ev.get_welltag()) for ev in self.events_by_timepoint[timepoint]]):
instance = exp.get_tag_attribute(protocol)
# protocol info includes the description of the attributes for each of the protocol e.g. Perturbation|Chem|1 is passed
protocol_info = self.decode_event_description(protocol)
# spatial info includes plate well inforamtion for this event well tag e.g. Perturbation|Bio|Wells|1|793
####spatial_info = self.decode_event_location(ev.get_welltag()) ##THIS THING DOES NOT WORK WHEN SAME EVENT AT SAME TIME POINT HAPPENS
welltag = exp.get_tag_stump(protocol, 2)+'|Wells|%s|%s'%(instance, str(timepoint))
spatial_info = self.decode_event_location(welltag)
# -- write the description and location of the event --#
if (exp.get_tag_event(protocol) == 'Seed') and (meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance) is not None):
self.printfile.write('Step '+str(i+1)+': <em><b>Seeding</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />')
self.printlocation(spatial_info)
# if harvest precede seeding
#if meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance) is not None:
## origin(harvesting instance), destination(seeding instance), timepoint
#self.printCellTransfer(meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance),
#instance, timepoint)
if exp.get_tag_event(protocol) == 'Harvest':
self.printfile.write('Step '+str(i+1)+': <em><b>Harvest-Seed (Cell Transfer)</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printCellTransfer(instance, timepoint)
if exp.get_tag_event(protocol) == 'Chem': #TO DO
self.printfile.write('Step '+str(i+1)+': <em><b>Chemical Perturbation</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Bio':
self.printfile.write('Step '+str(i+1)+': <em><b>Biological Perturbation</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />')
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Dye':
self.printfile.write('Step '+str(i+1)+': <em><b>Staining with chemical dye</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
duration = element[1]
temp = element[2]
if len(duration) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
if len(temp) > 0: # duration is mentioned
temp = ' at %s C.'%element[2]
self.printfile.write('<ul><li><code>'+description+duration+temp+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Immuno':
self.printfile.write('Step '+str(i+1)+': <em><b>Staining with immunofluorescence</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code>'+element+'</code><br />') #footer part
for element in protocol_info[1]: # step description
description = element[0]
duration = element[1]
temp = element[2]
if len(duration) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
if len(temp) > 0: # duration is mentioned
temp = ' at %s C.'%element[2]
self.printfile.write('<ul><li><code>'+description+duration+temp+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Genetic':
self.printfile.write('Step '+str(i+1)+': <em><b>Staining with genetic materials</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')#footer part
for element in protocol_info[1]: # step description
description = element[0]
duration = element[1]
temp = element[2]
if len(duration) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
if len(temp) > 0: # duration is mentioned
temp = ' at %s C.'%element[2]
self.printfile.write('<ul><li><code>'+description+duration+temp+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Spin':
self.printfile.write('Step '+str(i+1)+': <em><b>Spinning</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Wash':
self.printfile.write('Step '+str(i+1)+': <em><b>Washing</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Dry':
self.printfile.write('Step '+str(i+1)+': <em><b>Drying</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Medium':
self.printfile.write('Step '+str(i+1)+': <em><b>Addition of medium</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code>'+element+'</code><br />') #footer part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'Incubator':
self.printfile.write('Step '+str(i+1)+': <em><b>Incubation</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<i>'+protocol_info[0]+'</i><br />') # header part
for element in protocol_info[2]: #footer part goes here
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />') #footer part
for element in protocol_info[1]: # step description
description = element[0]
if len(element[1]) > 0: # duration is mentioned
duration = ' for %s minutes'%element[1]
else:
duration = ''
self.printfile.write('<ul><li><code>'+description+duration+'</code></li></ul>')
self.printlocation(spatial_info)
if exp.get_tag_event(protocol) == 'TLM':
self.printfile.write('Step '+str(i+1)+': <em><b>Timelapse image acquisition</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />') # header part wrtie wich setting instance being used
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
# write the image urls
self.printfile.write('<table border="0">')
for plate, wells in spatial_info.iteritems():
for well in wells:
pw = plate, well
self.printfile.write('<code><b>Well '+well+'</b></code><br />')
for url in meta.get_field('DataAcquis|TLM|Images|%s|%s|%s'%(instance,timepoint, pw), []):
self.printfile.write('<small>'+url+'</small><br />')
#self.printfile.write('<tr><code><td>'+well+':</td><td>'+('<br />'.join(meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), [])))+'</td></code></tr>')
self.printfile.write('</table><br />')
if exp.get_tag_event(protocol) == 'HCS':
self.printfile.write('Step '+str(i+1)+': <em><b>Static image acquisition</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />') # header part wrtie wich setting instance being used
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
# write the image urls
self.printfile.write('<table border="0">')
for plate, wells in spatial_info.iteritems():
for well in wells:
pw = plate, well
self.printfile.write('<code><b>Well '+well+'</b></code><br />')
for url in meta.get_field('DataAcquis|HCS|Images|%s|%s|%s'%(instance,timepoint, pw), []):
self.printfile.write('<small>'+url+'</small><br />')
#self.printfile.write('<tr><code><td>'+well+':</td><td>'+('<br />'.join(meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), [])))+'</td></code></tr>')
self.printfile.write('</table><br />')
if exp.get_tag_event(protocol) == 'FCS':
self.printfile.write('Step '+str(i+1)+': <em><b> FCS file acquisition</b></em> at '+exp.format_time_string(timepoint)+' hrs<br />')
self.printfile.write('<code>'+protocol_info[0]+'</code><br />') # header part wrtie wich setting instance being used
for element in protocol_info[1]:
self.printfile.write('<code><i>'+element[0]+': </i>'+element[1]+'</code><br />')
self.printlocation(spatial_info)
# write the image urls
self.printfile.write('<table border="0">')
for plate, wells in spatial_info.iteritems():
for well in wells:
pw = plate, well
self.printfile.write('<code><b>'+plate+'['+well+']'+'</b></code><br />')
for url in meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), []):
self.printfile.write('<small>'+url+'</small><br />')
#self.printfile.write('<tr><code><td>'+well+':</td><td>'+('<br />'.join(meta.get_field('DataAcquis|FCS|Images|%s|%s|%s'%(instance,timepoint, pw), [])))+'</td></code></tr>')
self.printfile.write('</table><br />')
if exp.get_tag_event(protocol) == 'CriticalPoint': # to implement if there are events at the same timepoint write those event first then the critical point
self.printfile.write('<font size="2" color="red">Critical point: '+meta.get_field('Notes|CriticalPoint|Description|%s'%instance)+'</font></em><br />')
if exp.get_tag_event(protocol) == 'Hint':
self.printfile.write('<font size="2" color="blue">Hint: '+meta.get_field('Notes|Hint|Description|%s'%instance)+'</font></em><br />')
if exp.get_tag_event(protocol) == 'Rest':
self.printfile.write('<font size="2" color="green">Rest: '+meta.get_field('Notes|Rest|Description|%s'%instance)+'</font></em><br />')
if exp.get_tag_event(protocol) == 'URL':
self.printfile.write('<code>To find out more information please visit '+meta.get_field('Notes|URL|Description|%s'%instance)+'</code><br />')
if exp.get_tag_event(protocol) == 'Video':
self.printfile.write('<code>For more information please watch the media file: '+meta.get_field('Notes|Video|Description|%s'%instance)+'</code><br />')
self.printfile.write('<br />')
#---- Protocol Map ---#
self.printfile.write('<br />'.join(['<h3>5. Methodology Map</h3>',
'<br/><br/>',
'<center><img src=myImage.png width=500 height=600></center>',
'</body></html>']))
self.printfile.close()
def __init__(self, parent, protocol, curractionNo, action_type, ldt):
wx.Dialog.__init__(self, parent, -1, size=(850,500), style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
self.protocol = protocol
self.curractionNo = curractionNo
self.action_type = action_type
self.last_date_time = ldt
self.action_attr = '%s %s'%(self.action_type, str(self.curractionNo))
self.tag_stump = exp.get_tag_stump(self.protocol, 2)
self.instance = exp.get_tag_attribute(self.protocol)
self.SetTitle(self.action_attr)
self.sw = wx.ScrolledWindow(self)
self.swsizer = wx.BoxSizer(wx.VERTICAL)
self.settings_controls = {}
self.curr_protocol = {}
self.admin_info = {}
self.mandatory_tags = []
self.labels = {}
# Set Protocol (if prev instance is there copy that else set STD protocol
if meta.get_field(self.tag_stump+'|%s%s|%s' %(self.action_type, str(self.curractionNo-1), self.instance)):
d = meta.get_field(self.tag_stump+'|%s%s|%s' %(self.action_type, str(self.curractionNo-1), self.instance))
for k, v in d:
self.curr_protocol[k] = v
else:
self.curr_protocol = STD_PROTOCOLS[self.action_type]
# Set the time prev or curr
if self.last_date_time:
self.initial_datetime = datetime.datetime(*map(int,self.last_date_time))
else:
self.initial_datetime = datetime.datetime.now()
self.sel_date_time = map(int, [self.initial_datetime.year,self.initial_datetime.month,self.initial_datetime.day,
self.initial_datetime.hour,self.initial_datetime.minute, self.initial_datetime.second])
# set the cell density
self.initial_seed_density = None
#self.curr_protocol['PD'] = []
self.curr_protocol['HARVEST'] = []
if self.curr_protocol['SEED']:
self.initial_seed_density = self.curr_protocol['SEED'][0]
#Admin
self.settings_controls['Admin|0'] = wx.TextCtrl(self.sw, size=(70,-1), value=self.curr_protocol['ADMIN'][0])
self.settings_controls['Admin|1'] = wx.DatePickerCtrl(self.sw, style = wx.DP_DROPDOWN | wx.DP_SHOWCENTURY)
self.settings_controls['Admin|1'].SetValue(wx.DateTimeFromDMY(self.initial_datetime.day, self.initial_datetime.month-1, self.initial_datetime.year))
self.curr_protocol['ADMIN'][1] = str(self.initial_datetime.day)+'/'+str(self.initial_datetime.month)+'/'+str(self.initial_datetime.year)
self.settings_controls['Admin|2'] = masked.TimeCtrl( self.sw, -1, name="24 hour control", fmt24hr=True )
h = self.settings_controls['Admin|2'].GetSize().height
spin1 = wx.SpinButton( self.sw, -1, wx.DefaultPosition, (-1,h), wx.SP_VERTICAL )
self.settings_controls['Admin|2'].BindSpinButton( spin1 )
self.settings_controls['Admin|2'].SetValue(wx.DateTimeFromHMS(self.initial_datetime.hour, self.initial_datetime.minute, self.initial_datetime.second))
self.curr_protocol['ADMIN'][2] = str(self.initial_datetime.hour)+':'+str(self.initial_datetime.minute)+':'+str(self.initial_datetime.second)
self.set_curr_time = wx.Button(self.sw, -1, 'Set Current Date Time')
self.attr_fgs = wx.FlexGridSizer(cols=4, hgap=5, vgap=5)
if self.action_type == 'Seed':
self.settings_controls['Seed|0'] = wx.lib.masked.NumCtrl(self.sw, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Seed|1'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Seed|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
vessel_types =['T75', 'T25', '6WellPlate','12WellPlate', 'Other']
self.settings_controls['Vessel|0'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (100,20), vessel_types, wx.LB_SINGLE)
if self.curr_protocol['VESSEL']:
self.settings_controls['Vessel|0'].Append(self.curr_protocol['VESSEL'][0])
self.settings_controls['Vessel|0'].SetStringSelection(self.curr_protocol['VESSEL'][0])
self.settings_controls['Vessel|0'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Seed Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|0'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|1'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Vessel Type'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Vessel|0'], 0, wx.EXPAND)
if self.action_type == 'Passage':
self.settings_controls['Harvest|0'] = wx.lib.masked.NumCtrl(self.sw, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Harvest|1'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Harvest|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Harvest|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.settings_controls['Seed|0'] = wx.lib.masked.NumCtrl(self.sw, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Seed|1'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Seed|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
vessel_types =['T75', 'T25', '6WellPlate','12WellPlate', 'Other']
self.settings_controls['Vessel|0'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (100,20), vessel_types, wx.LB_SINGLE)
if self.curr_protocol['VESSEL']:
self.settings_controls['Vessel|0'].Append(self.curr_protocol['VESSEL'][0])
self.settings_controls['Vessel|0'].SetStringSelection(self.curr_protocol['VESSEL'][0])
self.settings_controls['Vessel|0'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Harvest Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Harvest|0'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Harvest|1'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, '(Re)seed Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|0'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|1'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Vessel Type'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Vessel|0'], 0, wx.EXPAND)
if self.action_type == 'Freeze':
self.settings_controls['Split'] = wx.Choice(self.sw, -1, choices= map(str, range(1,21)), style=wx.TE_PROCESS_ENTER)
self.settings_controls['Split'].Bind(wx.EVT_CHOICE, self.OnSavingData)
self.settings_controls['Make'] = wx.TextCtrl(self.sw, size=(70,-1), value='Test')
self.settings_controls['Make'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Model'] = wx.TextCtrl(self.sw, size=(70,-1), value='Test')
self.settings_controls['Make'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|0'] = wx.lib.masked.NumCtrl(self.sw, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Seed|1'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Seed|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
vessel_types =['T75', 'T25', '6WellPlate','12WellPlate', 'Other']
self.settings_controls['Vessel|0'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (100,20), vessel_types, wx.LB_SINGLE)
self.settings_controls['Vessel|0'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Split 1: '),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Split'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Make'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Make'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' Model'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Model'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, '(Re)seed Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|0'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|1'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Vessel Type'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Vessel|0'], 0, wx.EXPAND)
if self.action_type == 'Enrich':
self.settings_controls['Split'] = wx.Choice(self.sw, -1, choices= map(str, range(1,21)), style=wx.TE_PROCESS_ENTER)
self.settings_controls['Split'].Bind(wx.EVT_CHOICE, self.OnSavingData)
self.settings_controls['Make'] = wx.TextCtrl(self.sw, size=(70,-1), value='Test')
self.settings_controls['Make'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Model'] = wx.TextCtrl(self.sw, size=(70,-1), value='Test')
self.settings_controls['Make'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|0'] = wx.lib.masked.NumCtrl(self.sw, size=(20,-1), style=wx.TE_PROCESS_ENTER)
unit_choices =['nM2', 'uM2', 'mM2','Other']
self.settings_controls['Seed|1'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (50,20), unit_choices, wx.LB_SINGLE)
self.settings_controls['Seed|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Seed|1'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
vessel_types =['T75', 'T25', '6WellPlate','12WellPlate', 'Other']
self.settings_controls['Vessel|0'] = wx.ListBox(self.sw, -1, wx.DefaultPosition, (100,20), vessel_types, wx.LB_SINGLE)
self.settings_controls['Vessel|0'].Bind(wx.EVT_LISTBOX, self.OnSavingData)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Split 1: '),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Split'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Flow Cytometer'),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ''),0)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Make'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Make'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' Model'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Model'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, '(Re)seed Density'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|0'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, ' cells/'),0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Seed|1'], 0, wx.EXPAND)
self.attr_fgs.Add(wx.StaticText(self.sw, -1, 'Vessel Type'),0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.attr_fgs.Add(self.settings_controls['Vessel|0'], 0, wx.EXPAND)
self.selection_btn = wx.Button(self, wx.ID_OK, 'Record')
self.close_btn = wx.Button(self, wx.ID_CANCEL)
#self.selection_btn.Disable()
#Bind
self.settings_controls['Admin|0'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.settings_controls['Admin|1'].Bind(wx.EVT_DATE_CHANGED, self.OnSavingData)
self.settings_controls['Admin|2'].Bind(wx.EVT_TEXT, self.OnSavingData)
self.set_curr_time.Bind(wx.EVT_BUTTON, self.setCurrDateTime)
# Sizers and layout
staticbox = wx.StaticBox(self.sw, -1, "Admin")
adminsizer = wx.StaticBoxSizer(staticbox, wx.HORIZONTAL)
adminsizer.Add(wx.StaticText(self.sw, -1, 'Operator Name'),0, wx.RIGHT, 5)
adminsizer.Add(self.settings_controls['Admin|0'] , 0, wx.EXPAND)
adminsizer.Add(wx.StaticText(self.sw, -1, 'Date'),0, wx.RIGHT|wx.LEFT, 5)
adminsizer.Add(self.settings_controls['Admin|1'], 0, wx.EXPAND)
adminsizer.Add(wx.StaticText(self.sw, -1, 'Time'),0, wx.LEFT, 5)
adminsizer.Add(self.settings_controls['Admin|2'], 0, wx.EXPAND)
adminsizer.Add( spin1, 0, wx.ALIGN_CENTRE )
adminsizer.Add(self.set_curr_time, 0, wx.ALIGN_RIGHT|wx.LEFT, 15)
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add(self.selection_btn , 0, wx.ALL, 5)
btnSizer.Add(self.close_btn , 0, wx.ALL, 5)
self.step_fgs = wx.FlexGridSizer(cols=8, hgap=5, vgap=5)
self.staticbox = wx.StaticBox(self.sw, -1, "Actions")
self.staticbox_sizer = wx.StaticBoxSizer(self.staticbox, wx.VERTICAL)
self.staticbox_sizer.Add(self.attr_fgs, 0, wx.EXPAND|wx.ALL, 5)
self.staticbox_sizer.Add((-1,10))
self.staticbox_sizer.Add(self.step_fgs, 0, wx.EXPAND|wx.ALL, 5)
self.swsizer.Add(adminsizer, 0, wx.EXPAND|wx.ALL, 5)
self.swsizer.Add(self.staticbox_sizer,0,wx.EXPAND|wx.ALL, 5)
self.sw.SetSizer(self.swsizer)
self.sw.SetScrollbars(20, 20, self.Size[0]+10, self.Size[1]+10, 0, 0)
self.Sizer = wx.BoxSizer(wx.VERTICAL)
self.Sizer.Add(self.sw, 1, wx.EXPAND)
self.Sizer.Add(btnSizer)
self.SetSizer(self.Sizer)
self.showSteps()
