def _on_mouse_click(self, evt):
if self.current_node is None:
return
for tag in self.current_node.get_tags():
if (tag.startswith('DataAcquis|TLM') or
tag.startswith('DataAcquis|HCS')):
for well in self.current_node.get_well_ids():
image_tag = '%s|Images|%s|%s|%s'%(exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well)
urls = meta.get_field(image_tag, [])
for url in urls:
im = Image.open(url)
im.show()
elif tag.startswith('DataAcquis|FCS'):
for well in self.current_node.get_well_ids():
image_tag = '%s|Images|%s|%s|%s'%(exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well)
urls = meta.get_field(image_tag, [])
for url in urls:
os.startfile(url)
## message = ''
## for well in sorted(self.current_node.get_well_ids()):
## message += ', '.join(well)
## message += '\n'
## msg = wx.MessageDialog(self, message, caption='Info', style=wx.OK | wx.ICON_INFORMATION | wx.STAY_ON_TOP, pos=(200,200))
## msg.ShowModal()
## msg.Destroy()
try:
bench = wx.GetApp().get_bench()
except:
return
# --- Update the Bench view ---
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols(
[exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0])
for well in self.current_node.get_well_ids()])
bench.update_plate_groups()
bench.update_well_selections()
def remove_harvest_seed_track(self, h_tag):
"""Completely removes all events associated with a harvest_seed (sample transfer) track including the harvest seed coupled event"""
h_instance = exp.get_tag_instance(h_tag)
harvest_tp = exp.get_tag_timepoint(h_tag)
tag_list = [h_tag]
for s_instance in meta.get_field_instances("Transfer|Seed|HarvestInstance"):
if meta.get_field("Transfer|Seed|HarvestInstance|%s" % s_instance) == h_instance:
s_tag = "Transfer|Seed|Wells|%s|%s" % (
s_instance,
str(harvest_tp + 1),
) # coupled seed is always 1 min after from harvest
for tpnode in self.nodes_by_timepoint[harvest_tp + 1]:
if tpnode:
if s_tag in tpnode.tags:
for c_tag in self.get_children_tags(tpnode, 5):
if c_tag.startswith(
"Transfer|Harvest"
): # in case further harvest-seed is there then make it recursive
self.remove_harvest_seed_track(c_tag)
else:
for s_well in meta.get_field(s_tag):
c_wells = meta.get_field(c_tag)
if s_well in c_wells:
c_wells.remove(s_well)
meta.remove_associated_dataacquis_tag([s_well])
if c_wells: # if at least one other affected well
meta.set_field(c_tag, c_wells)
else:
meta.remove_field(c_tag) # tag with single well
meta.remove_timeline_attachments(exp.get_tag_timepoint(c_tag))
meta.remove_field(h_tag)
meta.remove_field(s_tag)
meta.remove_harvest_seed_tags(h_instance, s_instance)
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 find_ancestral_tags(self, node):
ancestral_tags = []
for pnode in timeline.reverse_iter_tree(node):
if pnode:
for ptag in pnode.tags:
if (
ptag.startswith("Transfer|Seed")
and meta.get_field("Transfer|Seed|HarvestInstance|" + exp.get_tag_instance(ptag)) is not None
):
for tpnode in self.nodes_by_timepoint[pnode.get_timepoint() - 1]:
if tpnode:
for tptag in tpnode.tags:
if exp.get_tag_protocol(tptag) == "Transfer|Harvest|%s" % meta.get_field(
"Transfer|Seed|HarvestInstance|" + exp.get_tag_instance(ptag)
):
for npnode in timeline.reverse_iter_tree(tpnode):
if npnode:
for nptag in npnode.tags:
ancestral_tags.append(nptag)
else:
ancestral_tags.append(ptag)
return list(reversed(ancestral_tags))
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
MIN_X_GAP = self.MIN_X_GAP
MIN_Y_GAP = self.MIN_Y_GAP
FLASK_GAP = self.FLASK_GAP
MAX_TIMEPOINT = self.timepoints[0]
timepoints = self.timepoints
nodes_by_tp = self.nodes_by_timepoint
self.current_node = None # Node with the mouse over it
w_win, h_win = (float(self.Size[0]), float(self.Size[1]))
if self.time_x:
if timepoints[0] == 0:
px_per_time = 1
else:
px_per_time = max((w_win - PAD * 2 - FLASK_GAP) / MAX_TIMEPOINT,
MIN_X_GAP)
if len(nodes_by_tp) == 2:
x_gap = 1
else:
# calculate the number of pixels to separate each generation timepoint
x_gap = max(MIN_X_GAP,
(w_win - PAD * 2 - FLASK_GAP) / (len(nodes_by_tp) - 2))
if len(nodes_by_tp[timepoints[0]]) == 1:
y_gap = MIN_Y_GAP
else:
# calcuate the minimum number of pixels to separate nodes on the y axis
y_gap = max(MIN_Y_GAP,
(h_win - PAD * 2) / (len(nodes_by_tp[MAX_TIMEPOINT]) - 1))
nodeY = {} # Store y coords of children so we can calculate where to draw the parents
Y = PAD
X = w_win - PAD
dc = wx.PaintDC(self)
dc.Clear()
dc.BeginDrawing()
#dc.SetPen(wx.Pen("BLACK",1))
def hover(mouse_pos, node_pos, node_r):
'''returns whether the mouse is hovering over a node
mouse_pos - the mouse position
node_pos - the node position
node_r - the node radius
'''
if mouse_pos is None:
return False
MX,MY = mouse_pos
X,Y = node_pos
return (X - node_r < MX < X + node_r and
Y - node_r < MY < Y + node_r)
# Iterate from leaf nodes up to the root, and draw R->L, Top->Bottom
for i, t in enumerate(timepoints):
if t == -1:
X = PAD
elif self.time_x:
X = PAD + FLASK_GAP + t * px_per_time
x_gap = PAD + FLASK_GAP + timepoints[i-1] * px_per_time - X
else:
X = PAD + FLASK_GAP + (len(timepoints) - i - 2) * x_gap
# NO EVENTS. JUST DRAW THE STOCK, CENTERED.
if len(nodes_by_tp) == 1:
X = w_win / 2
Y = h_win / 2
if hover(self.cursor_pos, (X,Y), self.NODE_R):
dc.SetBrush(wx.Brush('#FFFFAA'))
self.current_node = nodes_by_tp.values()[t][0]
else:
dc.SetBrush(wx.Brush('#FAF9F7'))
self.current_node = None
dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
## dc.DrawText(str(nodes_by_tp[t][0].get_timepoint()), X, Y+NODE_R)
# LEAF NODES
elif i == 0:
for node in nodes_by_tp[t]:
empty_path = False # whether this path follows a harvesting
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush('YELLOW'))
else:
# No event
dc.SetBrush(wx.Brush('WHITE'))
if 'CellTransfer|Harvest' in [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]:
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
dc.SetPen(wx.Pen('#000000', 3))
self.current_node = node
else:
# No MouseOver
dc.SetPen(wx.Pen('#000000', 1))
if not empty_path:
dc.DrawCircle(X, Y, NODE_R)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
nodeY[node.id] = Y
Y += y_gap
# INTERNAL NODES
else:
for node in nodes_by_tp[t]:
empty_path = False # whether this path follows a harvesting
ys = []
for child in node.get_children():
ys.append(nodeY[child.id])
Y = (min(ys) + max(ys)) / 2
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush('YELLOW'))
else:
# No event
dc.SetBrush(wx.Brush('WHITE'))
if 'CellTransfer|Harvest' in [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]:
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
dc.SetPen(wx.Pen(wx.BLACK, 3))
self.current_node = node
else:
# No MouseOver
dc.SetPen(wx.Pen(wx.BLACK, 1))
if t == -1:
dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
else:
if not empty_path:
dc.DrawCircle(X, Y, NODE_R)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
# DRAW LINES CONNECTING THIS NODE TO ITS CHILDREN
dc.SetBrush(wx.Brush('#FAF9F7'))
dc.SetPen(wx.Pen(wx.BLACK, 1))
harvest_tag = False
for tag in node.get_tags():
if tag.startswith('CellTransfer|Harvest'):
harvest_tag = tag
for child in node.get_children():
if t == -1:
if self.time_x:
dc.DrawLine(X + NODE_R, Y,
X + FLASK_GAP + px_per_time * timepoints[i-1] - NODE_R ,nodeY[child.id])
else:
dc.DrawLine(X + NODE_R, Y,
X + FLASK_GAP - NODE_R ,nodeY[child.id])
else:
if harvest_tag:
# TODO: improve performance by caching reseed
# events from the previous timepoint
for nn in nodes_by_tp[timepoints[i-1]]:
for tag in nn.get_tags():
if (tag.startswith('CellTransfer|Seed') and
meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) == exp.get_tag_instance(harvest_tag)):
dc.SetPen(wx.Pen('BLACK', 1, wx.SHORT_DASH))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R ,nodeY[nn.id])
else:
if not empty_path:
dc.SetPen(wx.Pen(wx.BLACK, 1))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R,
nodeY[child.id])
nodeY[node.id] = Y
dc.EndDrawing()
def _on_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 _on_mouse_click(self, evt):
if self.current_node is None:
return
for tag in self.current_node.get_tags():
if tag.startswith("DataAcquis|TLM") or tag.startswith("DataAcquis|HCS"):
for well in self.current_node.get_well_ids():
image_tag = "%s|Images|%s|%s|%s" % (
exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well,
)
urls = meta.get_field(image_tag, [])
image_viewer_path = ""
if os.path.isfile("C:\Program Files\ImageJ\ImageJ.exe"):
ImageJPath = "C:\Program Files\ImageJ\ImageJ.exe"
subprocess.Popen("%s %s" % (ImageJPath, " ".join(urls)))
else:
dlg = wx.lib.dialogs.ScrolledMessageDialog(
self,
str("\n".join(urls)),
"ERROR!! ImageJ was not found in C\Program Files directory to show following images",
)
dlg.ShowModal()
return
# for url in urls:
# im = Image.open(url)
# im.show()
##TODO: make it Try with ImageJ first then Exception is Image.open(url)
# ImageJPath = r'C:\Program Files\ImageJ\ImageJ'
# subprocess.Popen("%s %s" % (ImageJPath, url))
elif tag.startswith("DataAcquis|FCS"):
for well in self.current_node.get_well_ids():
image_tag = "%s|Images|%s|%s|%s" % (
exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well,
)
urls = meta.get_field(image_tag, [])
for url in urls:
os.startfile(url)
# print self.current_node.get_well_ids()
# print self.current_node.get_parent()
## message = ''
## for well in sorted(self.current_node.get_well_ids()):
## message += ', '.join(well)
## message += '\n'
## msg = wx.MessageDialog(self, message, caption='Info', style=wx.OK | wx.ICON_INFORMATION | wx.STAY_ON_TOP, pos=(200,200))
## msg.ShowModal()
## msg.Destroy()
try:
bench = wx.GetApp().get_bench()
except:
return
# --- Update the Bench view ---
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols([exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0]) for well in self.current_node.get_well_ids()]
)
bench.update_plate_groups()
bench.update_well_selections()
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
# -- Update the expt setting/metadata view --#
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [
exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node)
if pnode
for ptag in pnode.tags
]
def _on_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 _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()
