def _on_click(self, evt):
if self.hover_timepoint is not None:
try:
bench = wx.GetApp().get_bench()
except:
return
bench.set_timepoint(self.hover_timepoint)
bench.update_well_selections()
if self.curr_note_tag is not None:
note_type = exp.get_tag_event(self.curr_note_tag)
timepoint = exp.get_tag_attribute(self.curr_note_tag)
self.page_counter = exp.get_tag_instance(self.curr_note_tag)
if exp.get_tag_type(self.curr_note_tag) == "Notes":
note_dia = NotePad(self, note_type, timepoint, self.page_counter)
if note_dia.ShowModal() == wx.ID_OK:
# Notes|<type>|<timepoint>|<instance> = value
meta.set_field(
"Notes|%s|%s|%s" % (note_dia.noteType, timepoint, str(self.page_counter)),
note_dia.noteDescrip.GetValue(),
)
elif exp.get_tag_type(self.curr_note_tag) == "Attachments":
attfileTAG = "Attachments|Files|%s|%s" % (timepoint, str(self.page_counter))
dia = FileListDialog(self, attfileTAG, meta.get_field(attfileTAG, []), None)
if dia.ShowModal() == wx.ID_OK:
f_list = dia.file_list
if f_list:
meta.set_field(attfileTAG, f_list)
def ShowTooltipsInfo(self):
what = ""
where = ""
for tag in self.current_node.get_tags():
what = exp.get_tag_event(exp.get_tag_protocol(tag)) + " instance %s was used on" % exp.get_tag_attribute(
exp.get_tag_protocol(tag)
)
for pw in self.current_node.get_well_ids():
where += str(pw)
return what + "\n" + where
def _on_click(self, evt):
if self.hover_timepoint is not None:
try:
bench = wx.GetApp().get_bench()
except: return
bench.set_timepoint(self.hover_timepoint)
bench.update_well_selections()
if self.current_ntag is not None:
note_type = exp.get_tag_event(self.current_ntag)
timepoint = exp.get_tag_attribute(self.current_ntag)
self.page_counter = exp.get_tag_instance(self.current_ntag)
note_dia = NotePad(self, note_type, timepoint, self.page_counter)
if note_dia.ShowModal() == wx.ID_OK:
# Notes|<type>|<timepoint>|<instance> = value
meta.set_field('Notes|%s|%s|%s' %(note_dia.noteType, timepoint, str(self.page_counter)), note_dia.noteDescrip.GetValue())
def _on_click(self, evt):
if self.hover_timepoint is not None:
try:
bench = wx.GetApp().get_bench()
except: return
bench.set_timepoint(self.hover_timepoint)
bench.update_well_selections()
if self.current_ntag is not None:
note_type = exp.get_tag_event(self.current_ntag)
timepoint = exp.get_tag_attribute(self.current_ntag)
self.page_counter = exp.get_tag_instance(self.current_ntag)
note_dia = NotePad(self, note_type, timepoint, self.page_counter)
if note_dia.ShowModal() == wx.ID_OK:
# Notes|<type>|<timepoint>|<instance> = value
meta.set_field('Notes|%s|%s|%s' %(note_dia.noteType, timepoint, str(self.page_counter)), note_dia.noteDescrip.GetValue())
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
SM_NODE_R = self.SM_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)
else:
px_per_time = 1
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.BufferedPaintDC(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: # for the root node which is not shown
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
# Draw longitudinal time lines
if t != -1:
dc.SetPen(wx.Pen('#E1E2ED', 1, wx.DOT))
dc.DrawLine(X, 0, X, h_win)
# LEAF NODES
if i == 0:
for node in sorted(nodes_by_tp[t], key=self.order_nodes):
ancestor_tags = self.get_ancestral_tags(node)
node_tags = node.get_tags()
stateRGB = meta.getStateRGB([tags for tags in reversed(ancestor_tags)]+node_tags)# reverse the ancestal line so that it become progeny + curr node
if node_tags:
eventRGB = meta.getEventRGB(node_tags[0]) #get all event tags for the passed node and returns the colour associated with the last event** Need to change
else:
eventRGB = (255, 255, 255, 100)
empty_path = False # whether this path follows a harvesting
event_status = False # whether any event occured to this node
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush(eventRGB))
dc.SetPen(wx.Pen(stateRGB, 3))
event_status = True
else:
# No event
if eventRGB == (255,255,255,100) and stateRGB == (255,255,255,100):
dc.SetBrush(wx.Brush(wx.WHITE))
dc.SetPen(wx.Pen(wx.WHITE))
if 'CellTransfer|Harvest' in self.get_ancestral_tags(node):
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 1))
self.current_node = node
else:
# No MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 3))
if not empty_path and event_status:
#dc.DrawCircle(X, Y, NODE_R)
#evt_categories = list(set([exp.get_tag_stump(tag, 1) for tag in node.get_tags()]))
#if all(evt_categories[0] == cat and cat == 'DataAcquis' for cat in evt_categories):
if 'CellTransfer|Seed|StockInstance' in node_tags:
event = 'Stock'
else:
event = exp.get_tag_event(node_tags[0])
dc.DrawBitmap(meta.getEventIcon(16.0, event), X - 16.0 / 2.0, Y - 16.0 / 2.0)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
nodeY[node.id] = Y
Y += y_gap
# INTERNAL NODES
else:
for node in sorted(nodes_by_tp[t], key=self.order_nodes):
ancestor_tags = self.get_ancestral_tags(node)
children_tags = self.get_children_tags(node)
node_tags = node.get_tags()
stateRGB = meta.getStateRGB([tags for tags in reversed(ancestor_tags)]+node_tags)# reverse the ancestal line so that it become progeny + curr node
if node_tags:
eventRGB = meta.getEventRGB(node_tags[0]) #get all event tags for the passed node and returns the colour associated with the last event** Need to change
else:
eventRGB = (255, 255, 255, 100)
empty_path = False # whether this path follows a harvesting
event_status = False # whether this node has event
children_status = False # whether the children nodes have any events associated
if children_tags:
children_status = True
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(eventRGB))
dc.SetPen(wx.Pen(stateRGB, 3))
event_status = True
else:
#No event
if eventRGB == (255,255,255,100) and stateRGB == (255,255,255,100):
dc.SetBrush(wx.Brush(wx.WHITE))
dc.SetPen(wx.Pen(wx.WHITE))
else:
if children_status:
#dc.SetBrush(wx.Brush(wx.BLACK))
#dc.SetPen(wx.Pen(wx.BLACK))
dc.SetBrush(wx.Brush('#D1CDCF'))
dc.SetPen(wx.Pen('#D1CDCF'))
else:
dc.SetBrush(wx.Brush(wx.WHITE))
dc.SetPen(wx.Pen(wx.WHITE))
if 'CellTransfer|Harvest' in self.get_ancestral_tags(node):
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 1))
self.current_node = node
self.SetToolTipString(self.ShowTooltipsInfo())
else:
# No MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 3))
#if t == -1:
#dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
#else:
if not empty_path:
if event_status:
if (node_tags[0].startswith('CellTransfer|Seed') and
meta.get_field('CellTransfer|Seed|StockInstance|'+exp.get_tag_instance(node_tags[0])) is not None):
event = 'Stock'
else:
event = exp.get_tag_event(node_tags[0])
#dc.DrawCircle(X, Y, NODE_R)
#dc.SetPen(wx.Pen('BLACK'))
#dc.DrawCircle(X, Y, NODE_R-3/2)
dc.DrawBitmap(meta.getEventIcon(16.0, event), X - 16.0 / 2.0, Y - 16.0 / 2.0)
else:
#dc.DrawCircle(X-NODE_R,Y, SM_NODE_R) # draws the node slightly left hand side on the furcation point
#dc.SetBrush(wx.Brush(stateRGB))
dc.DrawCircle(X,Y, SM_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))
dc.SetPen(wx.Pen('#D1CDCF'))
#dc.SetPen(wx.Pen(stateRGB))
harvest_tag = False
for tag in node.get_tags():
if tag.startswith('CellTransfer|Harvest'):
harvest_tag = tag
# for children of this node check whether furhter event had occured to them if not do not draw the line
for child in node.get_children():
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('#948BB3', 1, wx.SHORT_DASH))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R ,nodeY[nn.id])
else:
if not empty_path:
if event_status:
if children_status:
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R, nodeY[child.id])
else:
if children_status and stateRGB != (255,255,255,100):
dc.SetPen(wx.Pen('#D1CDCF'))
#dc.SetPen(wx.Pen(stateRGB))
dc.DrawLine(X, Y,
X + x_gap, nodeY[child.id])
nodeY[node.id] = Y
#if self.timepoint_cursor is not None: # BUG: New addition of 24hr will not work, i.e. the timeline cant hover over no event time zone****
#timepoints = meta.get_timeline().get_unique_timepoints()
#ti = bisect.bisect_left(timepoints, self.timepoint_cursor)
#time_interval = timepoints[ti]-timepoints[ti-1]
##according to the time interval calculate the px per time.
##px_per_time = max((w_win - PAD * 2 - FLASK_GAP) / MAX_TIMEPOINT,
##MIN_X_GAP)
#px_per_ti = (w_win - PAD * 2 - FLASK_GAP) /(len(timepoints)-1)
#adjusted_factor = px_per_ti/time_interval
#X = PAD + FLASK_GAP +px_per_ti*(ti-1)+(self.timepoint_cursor - timepoints[ti-1])* adjusted_factor
#dc.SetPen(wx.Pen(wx.BLACK, 3))
#dc.DrawLine(X, 0, X, h_win)
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 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)
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
SM_NODE_R = self.SM_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)
else:
px_per_time = 1
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.BufferedPaintDC(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: # for the root node which is not shown
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
# Draw longitudinal time lines
if t != -1:
dc.SetPen(wx.Pen('#E1E2ED', 1, wx.DOT))
dc.DrawLine(X, 0, X, h_win)
# LEAF NODES
if i == 0:
for node in sorted(nodes_by_tp[t], key=self.order_nodes):
ancestor_tags = self.get_ancestral_tags(node)
node_tags = node.get_tags()
stateRGB = meta.getStateRGB([tags for tags in reversed(ancestor_tags)]+node_tags)# reverse the ancestal line so that it become progeny + curr node
if node_tags:
eventRGB = meta.getEventRGB(node_tags[0]) #get all event tags for the passed node and returns the colour associated with the last event** Need to change
else:
eventRGB = (255, 255, 255, 100)
empty_path = False # whether this path follows a harvesting
event_status = False # whether any event occured to this node
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush(eventRGB))
dc.SetPen(wx.Pen(stateRGB, 3))
event_status = True
else:
# No event
if eventRGB == (255,255,255,100) and stateRGB == (255,255,255,100):
dc.SetBrush(wx.Brush(wx.WHITE))
dc.SetPen(wx.Pen(wx.WHITE))
if 'CellTransfer|Harvest' in self.get_ancestral_tags(node):
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 1))
self.current_node = node
else:
# No MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 3))
if not empty_path and event_status:
#dc.DrawCircle(X, Y, NODE_R)
#evt_categories = list(set([exp.get_tag_stump(tag, 1) for tag in node.get_tags()]))
#if all(evt_categories[0] == cat and cat == 'DataAcquis' for cat in evt_categories):
if 'CellTransfer|Seed|StockInstance' in node_tags:
event = 'Stock'
else:
event = exp.get_tag_event(node_tags[0])
dc.DrawBitmap(meta.getEventIcon(16.0, event), X - 16.0 / 2.0, Y - 16.0 / 2.0)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
nodeY[node.id] = Y
Y += y_gap
# INTERNAL NODES
else:
for node in sorted(nodes_by_tp[t], key=self.order_nodes):
ancestor_tags = self.get_ancestral_tags(node)
children_tags = self.get_children_tags(node)
node_tags = node.get_tags()
stateRGB = meta.getStateRGB([tags for tags in reversed(ancestor_tags)]+node_tags)# reverse the ancestal line so that it become progeny + curr node
if node_tags:
eventRGB = meta.getEventRGB(node_tags[0]) #get all event tags for the passed node and returns the colour associated with the last event** Need to change
else:
eventRGB = (255, 255, 255, 100)
empty_path = False # whether this path follows a harvesting
event_status = False # whether this node has event
children_status = False # whether the children nodes have any events associated
if children_tags:
children_status = True
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(eventRGB))
dc.SetPen(wx.Pen(stateRGB, 3))
event_status = True
else:
#No event
if eventRGB == (255,255,255,100) and stateRGB == (255,255,255,100):
dc.SetBrush(wx.Brush(wx.WHITE))
dc.SetPen(wx.Pen(wx.WHITE))
else:
if children_status:
#dc.SetBrush(wx.Brush(wx.BLACK))
#dc.SetPen(wx.Pen(wx.BLACK))
dc.SetBrush(wx.Brush('#D1CDCF'))
dc.SetPen(wx.Pen('#D1CDCF'))
else:
dc.SetBrush(wx.Brush(wx.WHITE))
dc.SetPen(wx.Pen(wx.WHITE))
if 'CellTransfer|Harvest' in self.get_ancestral_tags(node):
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 1))
self.current_node = node
self.SetToolTipString(self.ShowTooltipsInfo())
else:
# No MouseOver
if event_status:
dc.SetPen(wx.Pen(stateRGB, 3))
#if t == -1:
#dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
#else:
if not empty_path:
if event_status:
if (node_tags[0].startswith('CellTransfer|Seed') and
meta.get_field('CellTransfer|Seed|StockInstance|'+exp.get_tag_instance(node_tags[0])) is not None):
event = 'Stock'
else:
event = exp.get_tag_event(node_tags[0])
#dc.DrawCircle(X, Y, NODE_R)
#dc.SetPen(wx.Pen('BLACK'))
#dc.DrawCircle(X, Y, NODE_R-3/2)
dc.DrawBitmap(meta.getEventIcon(16.0, event), X - 16.0 / 2.0, Y - 16.0 / 2.0)
else:
#dc.DrawCircle(X-NODE_R,Y, SM_NODE_R) # draws the node slightly left hand side on the furcation point
#dc.SetBrush(wx.Brush(stateRGB))
dc.DrawCircle(X,Y, SM_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))
dc.SetPen(wx.Pen('#D1CDCF'))
#dc.SetPen(wx.Pen(stateRGB))
harvest_tag = False
for tag in node.get_tags():
if tag.startswith('CellTransfer|Harvest'):
harvest_tag = tag
# for children of this node check whether furhter event had occured to them if not do not draw the line
for child in node.get_children():
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('#948BB3', 1, wx.SHORT_DASH))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R ,nodeY[nn.id])
else:
if not empty_path:
if event_status:
if children_status:
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R, nodeY[child.id])
else:
if children_status and stateRGB != (255,255,255,100):
dc.SetPen(wx.Pen('#D1CDCF'))
#dc.SetPen(wx.Pen(stateRGB))
dc.DrawLine(X, Y,
X + x_gap, nodeY[child.id])
nodeY[node.id] = Y
#if self.timepoint_cursor is not None: # BUG: New addition of 24hr will not work, i.e. the timeline cant hover over no event time zone****
#timepoints = meta.get_timeline().get_unique_timepoints()
#ti = bisect.bisect_left(timepoints, self.timepoint_cursor)
#time_interval = timepoints[ti]-timepoints[ti-1]
##according to the time interval calculate the px per time.
##px_per_time = max((w_win - PAD * 2 - FLASK_GAP) / MAX_TIMEPOINT,
##MIN_X_GAP)
#px_per_ti = (w_win - PAD * 2 - FLASK_GAP) /(len(timepoints)-1)
#adjusted_factor = px_per_ti/time_interval
#X = PAD + FLASK_GAP +px_per_ti*(ti-1)+(self.timepoint_cursor - timepoints[ti-1])* adjusted_factor
#dc.SetPen(wx.Pen(wx.BLACK, 3))
#dc.DrawLine(X, 0, X, h_win)
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 _on_mouse_click(self, evt):
if self.current_node is None:
return
# first check whehter the tag is Harvest if so call the method.
# self.remove_harvest_seed_track(self.current_node.tags[0])
# meta.remove_field(ctags)
# --- Update the Bench view ---
try:
bench = wx.GetApp().get_bench()
except:
return
bench.selected_harvest_inst = self.current_node.tags[0]
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():
tag = self.current_node.get_tags()[
0
] # TO DO: if multiple event tag are there need to itterate through the list
if (
meta.get_field("Transfer|Seed|HarvestInstance|" + exp.get_tag_instance(tag)) is None
or exp.get_tag_event(tag) is "Harvest"
):
exptsettings.ShowInstance(tag)
# -- 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(),
self.current_node.get_timepoint(),
self.find_ancestral_tags(self.current_node),
)
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])
try:
myfile = open(file_dlg.GetPath(), "wb")
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.get_selected_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
except:
err_dlg = wx.MessageDialog(
None, "Cant open file for writing", "Error", wx.OK | wx.ICON_ERROR
)
err_dlg.ShowModal()
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.get_all_urls():
wr.writerow(filter(None, row))
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 2:
image_urls = []
for row in dia.get_selected_urls():
image_urls.append(row[3])
if os.path.isfile("C:\Program Files\ImageJ\ImageJ.exe") is False:
for r, d, f in os.walk("c:\\"):
if r.endswith("ImageJ"):
for files in f:
if files == "ImageJ.exe":
ImageJPath = os.path.join(r, files)
if not ImageJPath:
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 and image path are compatible with mageJ
ImageJPath = "C:\Program Files\ImageJ\ImageJ.exe"
subprocess.Popen("%s %s" % (ImageJPath, " ".join('"' + item + '"' for item in image_urls)))
dia.Destroy()
