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_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 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_description(self, protocol): return '\n'.join(['%s=%s'%(k, v) for k, v in meta.get_attribute_dict(exp.get_tag_protocol(protocol))])
def ShowTooltipsInfo(self): info_string = '' for tag in self.current_node.get_tags(): info_string += str(meta.get_attribute_dict(exp.get_tag_protocol(tag))) return info_string
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 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 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()