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_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 _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 get_timepoint(self):
return exp.get_tag_timepoint(self.welltag)
def get_timepoint(self):
return exp.get_tag_timepoint(self.welltag)
