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 get_ancestral_tags(self, node):
#ancestral_tags = []
#for pnode in timeline.reverse_iter_tree(node):
#if pnode:
#if 'CellTransfer|Seed' in node.tags:
#for tag in node.tags:
##if (tag.startswith('CellTransfer|Seed') and
##meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) is not None):
#h_instance = meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag))
#for tpnode in self.nodes_by_timepoint[node.get_timepoint()-1]:
#if tpnode:
#for tptag in tpnode.tags:
#if exp.get_tag_protocol(tptag) == 'CellTransfer|Harvest|'+h_instance:
#for npnode in timeline.reverse_iter_tree(tpnode):
#if npnode:
#for nptag in npnode.tags:
#ancestral_tags.append(exp.get_tag_stump(nptag, 2))
#else:
#for ptag in pnode.tags:
#ancestral_tags.append(exp.get_tag_stump(ptag, 2))
#return ancestral_tags
return [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]
def get_ancestral_tags(self, node):
#ancestral_tags = []
#for pnode in timeline.reverse_iter_tree(node):
#if pnode:
#if 'CellTransfer|Seed' in node.tags:
#for tag in node.tags:
##if (tag.startswith('CellTransfer|Seed') and
##meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) is not None):
#h_instance = meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag))
#for tpnode in self.nodes_by_timepoint[node.get_timepoint()-1]:
#if tpnode:
#for tptag in tpnode.tags:
#if exp.get_tag_protocol(tptag) == 'CellTransfer|Harvest|'+h_instance:
#for npnode in timeline.reverse_iter_tree(tpnode):
#if npnode:
#for nptag in npnode.tags:
#ancestral_tags.append(exp.get_tag_stump(nptag, 2))
#else:
#for ptag in pnode.tags:
#ancestral_tags.append(exp.get_tag_stump(ptag, 2))
#return ancestral_tags
return [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]
def 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_paint(self, evt=None):
'''Handler for paint events.
'''
if self.nodes_by_timepoint == {}:
evt.Skip()
return
t0 = time()
PAD = self.PAD + self.NODE_R
NODE_R = self.NODE_R
MIN_X_GAP = self.MIN_X_GAP
MIN_Y_GAP = self.MIN_Y_GAP
FLASK_GAP = self.FLASK_GAP
MAX_TIMEPOINT = self.timepoints[0]
timepoints = self.timepoints
nodes_by_tp = self.nodes_by_timepoint
self.current_node = None # Node with the mouse over it
w_win, h_win = (float(self.Size[0]), float(self.Size[1]))
if self.time_x:
if timepoints[0] == 0:
px_per_time = 1
else:
px_per_time = max((w_win - PAD * 2 - FLASK_GAP) / MAX_TIMEPOINT,
MIN_X_GAP)
if len(nodes_by_tp) == 2:
x_gap = 1
else:
# calculate the number of pixels to separate each generation timepoint
x_gap = max(MIN_X_GAP,
(w_win - PAD * 2 - FLASK_GAP) / (len(nodes_by_tp) - 2))
if len(nodes_by_tp[timepoints[0]]) == 1:
y_gap = MIN_Y_GAP
else:
# calcuate the minimum number of pixels to separate nodes on the y axis
y_gap = max(MIN_Y_GAP,
(h_win - PAD * 2) / (len(nodes_by_tp[MAX_TIMEPOINT]) - 1))
nodeY = {} # Store y coords of children so we can calculate where to draw the parents
Y = PAD
X = w_win - PAD
dc = wx.PaintDC(self)
dc.Clear()
dc.BeginDrawing()
#dc.SetPen(wx.Pen("BLACK",1))
def hover(mouse_pos, node_pos, node_r):
'''returns whether the mouse is hovering over a node
mouse_pos - the mouse position
node_pos - the node position
node_r - the node radius
'''
if mouse_pos is None:
return False
MX,MY = mouse_pos
X,Y = node_pos
return (X - node_r < MX < X + node_r and
Y - node_r < MY < Y + node_r)
# Iterate from leaf nodes up to the root, and draw R->L, Top->Bottom
for i, t in enumerate(timepoints):
if t == -1:
X = PAD
elif self.time_x:
X = PAD + FLASK_GAP + t * px_per_time
x_gap = PAD + FLASK_GAP + timepoints[i-1] * px_per_time - X
else:
X = PAD + FLASK_GAP + (len(timepoints) - i - 2) * x_gap
# NO EVENTS. JUST DRAW THE STOCK, CENTERED.
if len(nodes_by_tp) == 1:
X = w_win / 2
Y = h_win / 2
if hover(self.cursor_pos, (X,Y), self.NODE_R):
dc.SetBrush(wx.Brush('#FFFFAA'))
self.current_node = nodes_by_tp.values()[t][0]
else:
dc.SetBrush(wx.Brush('#FAF9F7'))
self.current_node = None
dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
## dc.DrawText(str(nodes_by_tp[t][0].get_timepoint()), X, Y+NODE_R)
# LEAF NODES
elif i == 0:
for node in nodes_by_tp[t]:
empty_path = False # whether this path follows a harvesting
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush('YELLOW'))
else:
# No event
dc.SetBrush(wx.Brush('WHITE'))
if 'CellTransfer|Harvest' in [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]:
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
dc.SetPen(wx.Pen('#000000', 3))
self.current_node = node
else:
# No MouseOver
dc.SetPen(wx.Pen('#000000', 1))
if not empty_path:
dc.DrawCircle(X, Y, NODE_R)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
nodeY[node.id] = Y
Y += y_gap
# INTERNAL NODES
else:
for node in nodes_by_tp[t]:
empty_path = False # whether this path follows a harvesting
ys = []
for child in node.get_children():
ys.append(nodeY[child.id])
Y = (min(ys) + max(ys)) / 2
if len(node.get_tags()) > 0:
# Event occurred
dc.SetBrush(wx.Brush('YELLOW'))
else:
# No event
dc.SetBrush(wx.Brush('WHITE'))
if 'CellTransfer|Harvest' in [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags]:
empty_path = True
if hover(self.cursor_pos, (X,Y), self.NODE_R):
# MouseOver
dc.SetPen(wx.Pen(wx.BLACK, 3))
self.current_node = node
else:
# No MouseOver
dc.SetPen(wx.Pen(wx.BLACK, 1))
if t == -1:
dc.DrawRectangle(X-NODE_R, Y-NODE_R, NODE_R*2, NODE_R*2)
else:
if not empty_path:
dc.DrawCircle(X, Y, NODE_R)
## dc.DrawText(str(node.get_tags()), X, Y+NODE_R)
# DRAW LINES CONNECTING THIS NODE TO ITS CHILDREN
dc.SetBrush(wx.Brush('#FAF9F7'))
dc.SetPen(wx.Pen(wx.BLACK, 1))
harvest_tag = False
for tag in node.get_tags():
if tag.startswith('CellTransfer|Harvest'):
harvest_tag = tag
for child in node.get_children():
if t == -1:
if self.time_x:
dc.DrawLine(X + NODE_R, Y,
X + FLASK_GAP + px_per_time * timepoints[i-1] - NODE_R ,nodeY[child.id])
else:
dc.DrawLine(X + NODE_R, Y,
X + FLASK_GAP - NODE_R ,nodeY[child.id])
else:
if harvest_tag:
# TODO: improve performance by caching reseed
# events from the previous timepoint
for nn in nodes_by_tp[timepoints[i-1]]:
for tag in nn.get_tags():
if (tag.startswith('CellTransfer|Seed') and
meta.get_field('CellTransfer|Seed|HarvestInstance|'+exp.get_tag_instance(tag)) == exp.get_tag_instance(harvest_tag)):
dc.SetPen(wx.Pen('BLACK', 1, wx.SHORT_DASH))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R ,nodeY[nn.id])
else:
if not empty_path:
dc.SetPen(wx.Pen(wx.BLACK, 1))
dc.DrawLine(X + NODE_R, Y,
X + x_gap - NODE_R,
nodeY[child.id])
nodeY[node.id] = Y
dc.EndDrawing()
def _on_mouse_click(self, evt):
if self.current_node is None:
return
# --- Update the Bench view ---
try:
bench = wx.GetApp().get_bench()
except:
return
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols(
[exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0])
for well in self.current_node.get_well_ids()])
bench.update_plate_groups()
bench.update_well_selections()
bench.del_evt_button.Enable()
# -- Update the expt setting/metadata view --#
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node) if pnode
for ptag in pnode.tags]
# -- show the data url list --- #
data_acquis = False
for tag in self.current_node.get_tags():
if tag.startswith('DataAcquis'):
data_acquis = True
break
if data_acquis:
dia = DataLinkListDialog(self, self.current_node.get_well_ids())
if dia.ShowModal() == wx.ID_OK:
if dia.output_options.GetSelection() == 0:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_selected_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 1:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_all_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 2:
image_urls = []
for row in dia.listctrl.get_selected_urls():
image_urls.append(row[2])
if os.path.isfile('C:\Program Files\ImageJ\ImageJ.exe') is False:
#err_dlg = wx.lib.dialogs.ScrolledMessageDialog(self, str("\n".join(urls)), "ERROR!! ImageJ was not found in C\Program Files directory to show following images")
err_dlg = wx.MessageDialog(None, 'ImageJ was not found in C\Program Files directory to show images!!', 'Error', wx.OK | wx.ICON_ERROR)
err_dlg.ShowModal()
return
else:
#TO DO: check the image format to be shown in ImageJ
ImageJPath = 'C:\Program Files\ImageJ\ImageJ.exe'
subprocess.Popen("%s %s" % (ImageJPath, ' '.join(image_urls)))
dia.Destroy()
def _on_mouse_click(self, evt):
if self.current_node is None:
return
for tag in self.current_node.get_tags():
if tag.startswith("DataAcquis|TLM") or tag.startswith("DataAcquis|HCS"):
for well in self.current_node.get_well_ids():
image_tag = "%s|Images|%s|%s|%s" % (
exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well,
)
urls = meta.get_field(image_tag, [])
image_viewer_path = ""
if os.path.isfile("C:\Program Files\ImageJ\ImageJ.exe"):
ImageJPath = "C:\Program Files\ImageJ\ImageJ.exe"
subprocess.Popen("%s %s" % (ImageJPath, " ".join(urls)))
else:
dlg = wx.lib.dialogs.ScrolledMessageDialog(
self,
str("\n".join(urls)),
"ERROR!! ImageJ was not found in C\Program Files directory to show following images",
)
dlg.ShowModal()
return
# for url in urls:
# im = Image.open(url)
# im.show()
##TODO: make it Try with ImageJ first then Exception is Image.open(url)
# ImageJPath = r'C:\Program Files\ImageJ\ImageJ'
# subprocess.Popen("%s %s" % (ImageJPath, url))
elif tag.startswith("DataAcquis|FCS"):
for well in self.current_node.get_well_ids():
image_tag = "%s|Images|%s|%s|%s" % (
exp.get_tag_stump(tag, 2),
exp.get_tag_instance(tag),
exp.get_tag_timepoint(tag),
well,
)
urls = meta.get_field(image_tag, [])
for url in urls:
os.startfile(url)
# print self.current_node.get_well_ids()
# print self.current_node.get_parent()
## message = ''
## for well in sorted(self.current_node.get_well_ids()):
## message += ', '.join(well)
## message += '\n'
## msg = wx.MessageDialog(self, message, caption='Info', style=wx.OK | wx.ICON_INFORMATION | wx.STAY_ON_TOP, pos=(200,200))
## msg.ShowModal()
## msg.Destroy()
try:
bench = wx.GetApp().get_bench()
except:
return
# --- Update the Bench view ---
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols([exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0]) for well in self.current_node.get_well_ids()]
)
bench.update_plate_groups()
bench.update_well_selections()
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
# -- Update the expt setting/metadata view --#
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [
exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node)
if pnode
for ptag in pnode.tags
]
def _on_mouse_click(self, evt):
if self.current_node is None:
return
# --- Update the Bench view ---
try:
bench = wx.GetApp().get_bench()
except:
return
bench.set_timepoint(self.current_node.get_timepoint())
bench.taglistctrl.set_selected_protocols(
[exp.get_tag_protocol(tag) for tag in self.current_node.get_tags()])
bench.group_checklist.SetCheckedStrings(
[exp.PlateDesign.get_plate_group(well[0])
for well in self.current_node.get_well_ids()])
bench.update_plate_groups()
bench.update_well_selections()
bench.del_evt_button.Enable()
# -- Update the expt setting/metadata view --#
try:
exptsettings = wx.GetApp().get_exptsettings()
except:
return
exptsettings.OnLeafSelect()
if self.current_node.get_tags():
exptsettings.ShowInstance(self.current_node.get_tags()[0])
ancestors = [exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(self.current_node) if pnode
for ptag in pnode.tags]
# -- show the data url list --- #
data_acquis = False
for tag in self.current_node.get_tags():
if tag.startswith('DataAcquis'):
data_acquis = True
break
if data_acquis:
dia = DataLinkListDialog(self, self.current_node.get_well_ids())
if dia.ShowModal() == wx.ID_OK:
if dia.output_options.GetSelection() == 0:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_selected_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 1:
file_dlg = wx.FileDialog(None, message='Exporting Data URL...',
defaultDir=os.getcwd(), defaultFile='data urls',
wildcard='.csv',
style=wx.SAVE|wx.FD_OVERWRITE_PROMPT)
if file_dlg.ShowModal() == wx.ID_OK:
os.chdir(os.path.split(file_dlg.GetPath())[0])
myfile = open(file_dlg.GetPath(), 'wb')
wr = csv.writer(myfile, quoting=csv.QUOTE_ALL)
for row in dia.listctrl.get_all_urls():
wr.writerow(row)
myfile.close()
file_dlg.Destroy()
if dia.output_options.GetSelection() == 2:
image_urls = []
for row in dia.listctrl.get_selected_urls():
image_urls.append(row[2])
if os.path.isfile('C:\Program Files\ImageJ\ImageJ.exe') is False:
#err_dlg = wx.lib.dialogs.ScrolledMessageDialog(self, str("\n".join(urls)), "ERROR!! ImageJ was not found in C\Program Files directory to show following images")
err_dlg = wx.MessageDialog(None, 'ImageJ was not found in C\Program Files directory to show images!!', 'Error', wx.OK | wx.ICON_ERROR)
err_dlg.ShowModal()
return
else:
#TO DO: check the image format to be shown in ImageJ
ImageJPath = 'C:\Program Files\ImageJ\ImageJ.exe'
subprocess.Popen("%s %s" % (ImageJPath, ' '.join(image_urls)))
dia.Destroy()
def get_ancestral_tags(self, node): return [exp.get_tag_stump(ptag, 2) for pnode in timeline.reverse_iter_tree(node) if pnode for ptag in pnode.tags]
def get_ancestral_tags(self, node):
return [
exp.get_tag_stump(ptag, 2)
for pnode in timeline.reverse_iter_tree(node) if pnode
for ptag in pnode.tags
]
