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 decode_event_description(self, protocol):
meta = ExperimentSettings.getInstance()
instance = exp.get_tag_attribute(protocol)
header = ''
footer = []
info = []
if exp.get_tag_type(protocol) == 'Overview':
header += meta.get_field('Overview|Project|Title', default='Not specified')
info.append(('Aims', meta.get_field('Overview|Project|Aims', default='Not specified')))
info.append(('Funding Code', meta.get_field('Overview|Project|Fund', default='Not specified')))
info.append(('Keywords', meta.get_field('Overview|Project|Keywords', default='Not specified')))
info.append(('Experiment Number', meta.get_field('Overview|Project|ExptNum', default='Not specified')))
info.append(('Experiment date', meta.get_field('Overview|Project|ExptDate', default='Not specified')))
info.append(('Relevant publications', meta.get_field('Overview|Project|Publications', default='Not specified')))
info.append(('Experimenter', meta.get_field('Overview|Project|Experimenter', default='Not specified')))
info.append(('Institution', meta.get_field('Overview|Project|Institution', default='Not specified')))
info.append(('Department', meta.get_field('Overview|Project|Department', default='Not specified')))
info.append(('Address', meta.get_field('Overview|Project|Address', default='Not specified')))
info.append(('Experiment Status', meta.get_field('Overview|Project|Status', default='Not specified')))
return (header, info)
if exp.get_tag_type(protocol) == 'StockCulture':
header += '%s cell line (Authority %s, Ref: %s) was used. This will be referred as Stock Instance %s' %(meta.get_field('StockCulture|Sample|CellLine|%s'%instance, default='Not specified'),
meta.get_field('StockCulture|Sample|Authority|%s'%instance, default='Not specified'),
str(instance),
meta.get_field('StockCulture|Sample|CatalogueNo|%s'%instance, default='Not specified'),
str(instance))
info.append(('Depositors', meta.get_field('StockCulture|Sample|Depositors|%s'%instance, default='Not specified')))
info.append(('Biosafety Level', meta.get_field('StockCulture|Sample|Biosafety|%s'%instance, default='Not specified')))
info.append(('Shipment', meta.get_field('StockCulture|Sample|Shipment|%s'%instance, default='Not specified')))
info.append(('Permit', meta.get_field('StockCulture|Sample|Permit|%s'%instance, default='Not specified')))
info.append(('Growth Property', meta.get_field('StockCulture|Sample|GrowthProperty|%s'%instance, default='Not specified')))
info.append(('Organism', meta.get_field('StockCulture|Sample|Organism|%s'%instance, default='Not specified')))
info.append(('Morphology', meta.get_field('StockCulture|Sample|Morphology|%s'%instance, default='Not specified')))
info.append(('Organ', meta.get_field('StockCulture|Sample|Organ|%s'%instance, default='Not specified')))
info.append(('Disease', meta.get_field('StockCulture|Sample|Disease|%s'%instance, default='Not specified')))
info.append(('Products', meta.get_field('StockCulture|Sample|Products|%s'%instance, default='Not specified')))
info.append(('Applications', meta.get_field('StockCulture|Sample|Applications|%s'%instance, default='Not specified')))
info.append(('Receptors', meta.get_field('StockCulture|Sample|Receptors|%s'%instance, default='Not specified')))
info.append(('Antigen', meta.get_field('StockCulture|Sample|Antigen|%s'%instance, default='Not specified')))
info.append(('DNA', meta.get_field('StockCulture|Sample|DNA|%s'%instance, default='Not specified')))
info.append(('Cytogenetic', meta.get_field('StockCulture|Sample|Cytogenetic|%s'%instance, default='Not specified')))
info.append(('Isoenzymes', meta.get_field('StockCulture|Sample|Isoenzymes|%s'%instance, default='Not specified')))
info.append(('Age of Organism (days)', meta.get_field('StockCulture|Sample|Age|%s'%instance, default='Not specified')))
info.append(('Gender', meta.get_field('StockCulture|Sample|Gender|%s'%instance, default='Not specified')))
info.append(('Ethnicity', meta.get_field('StockCulture|Sample|Ethnicity|%s'%instance, default='Not specified')))
info.append(('Comments', meta.get_field('StockCulture|Sample|Comments|%s'%instance, default='Not specified')))
info.append(('Publications', meta.get_field('StockCulture|Sample|Publications|%s'%instance, default='Not specified')))
info.append(('Related Products', meta.get_field('StockCulture|Sample|RelProduct|%s'%instance, default='Not specified')))
info.append(('Original Passage Number', meta.get_field('StockCulture|Sample|OrgPassageNo|%s'%instance, default='Not specified')))
info.append(('Preservation', meta.get_field('StockCulture|Sample|Preservation|%s'%instance, default='Not specified')))
info.append(('GrowthMedium', meta.get_field('StockCulture|Sample|GrowthMedium|%s'%instance, default='Not specified')))
passages = [attr for attr in meta.get_attribute_list_by_instance('StockCulture|Sample', instance)
if attr.startswith('Passage')]
if passages:
footer += '%s passages were carried out according to the specifications' %str(len(passages))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Microscope':
header += '%s settings' %meta.get_field('Instrument|Microscope|ChannelName|%s'%instance, default = 'Not specified')
if meta.get_field('Instrument|Microscope|Stand|%s'%instance) is not None:
info.append(('Component', 'Stand'))
info.append(('Type', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[2]))
info.append(('Orientation', meta.get_field('Instrument|Microscope|Stand|%s'%instance)[3]))
info.append(('Number of Lampss', str(meta.get_field('Instrument|Microscope|Stand|%s'%instance)[4])))
info.append(('Number of Detectors', str(meta.get_field('Instrument|Microscope|Stand|%s'%instance)[5])))
if meta.get_field('Instrument|Microscope|Condensor|%s'%instance) is not None:
info.append(('Component', 'Condensor'))
info.append(('Type', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Condensor|%s'%instance)[2]))
if meta.get_field('Instrument|Microscope|Stage|%s'%instance) is not None:
info.append(('Component', 'Stage'))
info.append(('Type', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[2]))
info.append(('Stage Holder', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[3]))
info.append(('Holder Code', meta.get_field('Instrument|Microscope|Stage|%s'%instance)[4]))
if meta.get_field('Instrument|Microscope|Incubator|%s'%instance) is not None:
info.append(('Component', 'Incubator'))
info.append(('Make', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[0]))
info.append(('Model', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[1]))
info.append(('Temperature(C)', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[2]))
info.append(('CO2%', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[3]))
info.append(('Humidity', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[4]))
info.append(('Pressure', meta.get_field('Instrument|Microscope|Incubator|%s'%instance)[5]))
if meta.get_field('Instrument|Microscope|LightSource|%s'%instance) is not None:
info.append(('Component', 'Light Source'))
info.append(('Type', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[0]))
info.append(('Source', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[1]))
info.append(('Make', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[3]))
info.append(('Measured Power (User)', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[4]))
info.append(('Measured Power (Instrument)', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[5]))
info.append(('Shutter Used', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[6]))
info.append(('Shutter Type', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[7]))
info.append(('Shutter Make', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[8]))
info.append(('Shutter Model', meta.get_field('Instrument|Microscope|LightSource|%s'%instance)[9]))
if meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance) is not None:
info.append(('Component', 'Excitation Filter'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[1])))
info.append(('Make', meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|ExtFilter|%s'%instance)[3]))
if meta.get_field('Instrument|Microscope|Mirror|%s'%instance) is not None:
info.append(('Component', 'Dichroic Mirror'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[1])))
info.append(('Mode', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[2]))
info.append(('Make', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[3]))
info.append(('Model', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[4]))
info.append(('Modification', meta.get_field('Instrument|Microscope|Mirror|%s'%instance)[5]))
if meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance) is not None:
info.append(('Component', 'Emission Filter'))
info.append(('Wavelength Range (nm)', str(meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[0])+' - '+str(meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[1])))
info.append(('Make', meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[2]))
info.append(('Model', meta.get_field('Instrument|Microscope|EmsFilter|%s'%instance)[3]))
if meta.get_field('Instrument|Microscope|Lens|%s'%instance) is not None:
info.append(('Component', 'Lens'))
info.append(('Make', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[0]))
info.append(('Model', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[1]))
info.append(('Objective Magnification', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[2]))
info.append(('Objective NA', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[3]))
info.append(('Calibrated Magnification', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[4]))
info.append(('Immersion', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[5]))
info.append(('Correction Collar', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[6]))
info.append(('Correction Value', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[7]))
info.append(('Correction Type', meta.get_field('Instrument|Microscope|Lens|%s'%instance)[8]))
if meta.get_field('Instrument|Microscope|Lens|%s'%instance) is not None:
info.append(('Component', 'Detector'))
info.append(('Type', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[0]))
info.append(('Make', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[1]))
info.append(('Model', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[2]))
info.append(('Binning', str(meta.get_field('Instrument|Microscope|Detector|%s'%instance)[3])))
info.append(('Exposure Time', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[4]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[5]))
info.append(('Gain', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[6]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[7]))
info.append(('Offset', meta.get_field('Instrument|Microscope|Detector|%s'%instance)[8]+' '+meta.get_field('Instrument|Microscope|Detector|%s'%instance)[9]))
return (header, info)
if exp.get_tag_event(protocol) == 'Flowcytometer':
header += meta.get_field('Instrument|Flowcytometer|Manufacter|%s'%instance, default='')
if meta.get_field('Instrument|Flowcytometer|Model|%s'%instance) is not None:
header += '(model: %s)' %meta.get_field('Instrument|Flowcytometer|Model|%s'%instance, default = 'not specified')
header += ' was used. '
for attribute, description in sorted(meta.get_attribute_dict('Instrument|Flowcytometer|%s'%instance).iteritems()):
if attribute.startswith('Manufacter') or attribute.startswith('Model'):
continue
else:
info.append((attribute, description)) # attribute is Ch# and description is the component list
return(header, info)
if exp.get_tag_event(protocol) == 'Seed':
if meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance) is not None:
header += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance))
header += ' cells were seeded with a density of %s from the stock flask (Instance %s). ' %(meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = ''), meta.get_field('CellTransfer|Seed|StockInstance|%s'%instance))
#if meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance) is not None:
#header += meta.get_field('StockCulture|Sample|CellLine|%s'%meta.get_field('CellTransfer|Seed|HarvestInstance|%s'%instance))
#header += ' cells were seeded with a density of %s from the Wells depicted bellow. ' %meta.get_field('CellTransfer|Seed|SeedingDensity|%s'%instance, default = '')
if meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance) is not None:
header += meta.get_field('CellTransfer|Seed|MediumUsed|%s'%instance)+' medium was used '
if meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance) is not None:
header += 'with following medium additives: %s. ' %meta.get_field('CellTransfer|Seed|MediumAddatives|%s'%instance)
if meta.get_field('CellTransfer|Seed|Trypsinizatiton|%s'%instance) is 'Yes':
header += 'Also trypsinisation was performed'
return (header, info)
if exp.get_tag_event(protocol) == 'Chem':
if meta.get_field('Perturbation|Chem|ChemName|%s'%instance) is not None:
header += meta.get_field('Perturbation|Chem|ChemName|%s'%instance)
subtext = '%s,%s' %(meta.get_field('Perturbation|Chem|Manufacturer|%s'%instance, default=''), meta.get_field('Perturbation|Chem|CatNum|%s'%instance, default=''))
if re.search('\w+', subtext): #if the mfg and or cat number of the chemical is mentioned
header += '[%s]'%subtext
header += ' was added'
if meta.get_field('Perturbation|Chem|Conc|%s'%instance) is not None:
header += ' with a concentration of %s %s' %(meta.get_field('Perturbation|Chem|Conc|%s'%instance), meta.get_field('Perturbation|Chem|Unit|%s'%instance, default=''))
if meta.get_field('Perturbation|Chem|Additives|%s'%instance) is not None:
header += '. Following additives were included: %s' %meta.get_field('Perturbation|Chem|Additives|%s'%instance)
if meta.get_field('Perturbation|Chem|Other|%s'%instance) is not None:
header += '. Other information: %s'%meta.get_field('Perturbation|Chem|Other|%s'%instance)
return (header, info)
if exp.get_tag_event(protocol) == 'Bio':
header += 'Biological perturbation was done with following agent'
info.append(('RNAi Sequence', meta.get_field('Perturbation|Bio|SeqName|%s'%instance, default = 'Not specified')))
info.append(('Acession Number', meta.get_field('Perturbation|Bio|AccessNumber|%s'%instance, default = 'Not specified')))
info.append(('Target Gene Accession Number', meta.get_field('Perturbation|Bio|TargetGeneAccessNum|%s'%instance, default = 'Not specified')))
info.append(('Concentration', meta.get_field('Perturbation|Bio|Conc|%s'%instance, default = 'Not specified')+' '+meta.get_field('Perturbation|Bio|Unit|%s'%instance, default = '')))
info.append(('Additives', meta.get_field('Perturbation|Bio|Additives|%s'%instance, default = 'Not specified')))
info.append(('Other Information', meta.get_field('Perturbation|Bio|Other|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'Dye':
header += meta.get_field('Staining|Dye|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('Staining|Dye|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Dye|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Immuno':
header += meta.get_field('Staining|Immuno|ProtocolName|%s'%instance)
if meta.get_field('Staining|Immuno|Target|%s'%instance) is not None:
footer.append('Target antibody %s was used.'%meta.get_field('Staining|Immuno|Target|%s'%instance))
if meta.get_field('Staining|Immuno|Clonality|%s'%instance) is not None:
footer.append('Clonality was %s.'%meta.get_field('Staining|Immuno|Clonality|%s'%instance))
if meta.get_field('Staining|Immuno|Primary|%s'%instance) is not None:
token =''
token += 'Primary antibody %s was used'%meta.get_field('Staining|Immuno|Primary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Primary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Primary|%s'%instance)[1]
footer.append(token)
if meta.get_field('Staining|Immuno|Secondary|%s'%instance) is not None:
token =''
token += 'Secondary antibody %s was used'%meta.get_field('Staining|Immuno|Secondary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Secondary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Secondary|%s'%instance)[1]
footer.append(token)
if meta.get_field('Staining|Immuno|Tertiary|%s'%instance) is not None:
token =''
token += 'Tertiary antibody %s was used'%meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[0]
if len(meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[1])>0:
token += ' with %s'%meta.get_field('Staining|Immuno|Tertiary|%s'%instance)[1]
footer.append(token)
steps = sorted(meta.get_attribute_list_by_instance('Staining|Immuno|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Immuno|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Genetic':
header += meta.get_field('Staining|Genetic|ProtocolName|%s'%instance)
footer.append(('Target Sequence', meta.get_field('Staining|Genetic|Target|%s'%instance, default = 'Not specified')))
footer.append(('Primer Sequence', meta.get_field('Staining|Genetic|Primer|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('Staining|Genetic|Temp|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('Staining|Genetic|GC|%s'%instance, default = 'Not specified')))
steps = sorted(meta.get_attribute_list_by_instance('Staining|Genetic|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('Staining|Genetic|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Spin':
header += meta.get_field('AddProcess|Spin|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Spin|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Spin|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Wash':
header += meta.get_field('AddProcess|Wash|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Wash|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Wash|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Dry':
header += meta.get_field('AddProcess|Dry|ProtocolName|%s'%instance)
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Dry|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Dry|%s|%s'%(step,instance)))
return (header, info)
if exp.get_tag_event(protocol) == 'Medium':
header += meta.get_field('AddProcess|Medium|ProtocolName|%s'%instance)
if meta.get_field('AddProcess|Medium|MediumAdditives|%s'%instance) is not None:
footer.append('Medium additives used: %s'%meta.get_field('AddProcess|Medium|MediumAdditives|%s'%instance))
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Medium|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Medium|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'Incubator':
header += meta.get_field('AddProcess|Incubator|ProtocolName|%s'%instance)
footer.append(('Incubator settings', ''))
footer.append(('Manufacturer', meta.get_field('AddProcess|Incubator|Manufacter|%s'%instance, default = 'Not specified')))
footer.append(('Model', meta.get_field('AddProcess|Incubator|Model|%s'%instance, default = 'Not specified')))
footer.append(('Temperature', meta.get_field('AddProcess|Incubator|Temp|%s'%instance, default = 'Not specified')))
footer.append(('CO2%', meta.get_field('AddProcess|Incubator|CO2|%s'%instance, default = 'Not specified')))
footer.append(('Humidity', meta.get_field('AddProcess|Incubator|Humidity|%s'%instance, default = 'Not specified')))
footer.append(('Pressure', meta.get_field('AddProcess|Incubator|Pressure|%s'%instance, default = 'Not specified')))
steps = sorted(meta.get_attribute_list_by_instance('AddProcess|Medium|Step', str(instance)), key = meta.stringSplitByNumbers)
for step in steps:
info.append(meta.get_field('AddProcess|Medium|%s|%s'%(step,instance)))
return (header, info, footer)
if exp.get_tag_event(protocol) == 'TLM':
if meta.get_field('DataAcquis|TLM|MicroscopeInstance|%s'%instance) is not None:
ch_name = meta.get_field('DataAcquis|TLM|MicroscopeInstance|%s'%instance)
cytometer_instance=meta.get_instance_by_field_value('Instrument|Microscope|ChannelName|', ch_name)
header += ch_name+' channel was used (see microscope instance %s for details)'%cytometer_instance
info.append(('Image Format', meta.get_field('DataAcquis|TLM|Format|%s'%instance, default = 'Not specified')))
info.append(('Time Interval (min)', meta.get_field('DataAcquis|TLM|TimeInterval|%s'%instance, default = 'Not specified')))
info.append(('Total Frame/Pane Number', meta.get_field('DataAcquis|TLM|FrameNumber|%s'%instance, default = 'Not specified')))
info.append(('Stacking Order', meta.get_field('DataAcquis|TLM|StackProcess|%s'%instance, default = 'Not specified')))
info.append(('Pixel Size', meta.get_field('DataAcquis|TLM|PixelSize|%s'%instance, default = 'Not specified')))
info.append(('Pixel Conversion', meta.get_field('DataAcquis|TLM|PixelConvert|%s'%instance, default = 'Not specified')))
info.append(('Software', meta.get_field('DataAcquis|TLM|Software|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'HCS':
if meta.get_field('DataAcquis|HCS|MicroscopeInstance|%s'%instance) is not None:
ch_name = meta.get_field('DataAcquis|HCS|MicroscopeInstance|%s'%instance)
cytometer_instance=meta.get_instance_by_field_value('Instrument|Microscope|ChannelName|', ch_name)
header += ch_name+' channel was used (see microscope instance %s for details)'%cytometer_instance
info.append(('Image Format', meta.get_field('DataAcquis|HCS|Format|%s'%instance, default = 'Not specified')))
info.append(('Pixel Size', meta.get_field('DataAcquis|HCS|PixelSize|%s'%instance, default = 'Not specified')))
info.append(('Pixel Conversion', meta.get_field('DataAcquis|HCS|PixelConvert|%s'%instance, default = 'Not specified')))
info.append(('Software', meta.get_field('DataAcquis|HCS|Software|%s'%instance, default = 'Not specified')))
return (header, info)
if exp.get_tag_event(protocol) == 'FCS':
if meta.get_field('DataAcquis|FCS|FlowcytInstance|%s'%instance) is not None:
cytometer_instance = meta.get_field('DataAcquis|FCS|FlowcytInstance|%s'%instance)
header += meta.get_field('Instrument|Flowcytometer|Manufacter|%s'%cytometer_instance, default='')+' flowcytometer '
if meta.get_field('Instrument|Flowcytometer|Model|%s'%cytometer_instance) is not None:
header += '(model: %s)' %meta.get_field('Instrument|Flowcytometer|Model|%s'%cytometer_instance, default = 'not specified')
header += ' was used (see flowcytometer instance %s for details).'%cytometer_instance
if meta.get_field('DataAcquis|FCS|Software|%s'%instance) is not None:
info.append(meta.get_field('DataAcquis|FCS|Software|%s'%instance)+' software was used for data acquisition. ')
if meta.get_field('DataAcquis|FCS|Format|%s'%instance) is not None:
info.append('FCS files in %s'%meta.get_field('DataAcquis|FCS|Format|%s'%instance)+' format were saved in following location\n')
return (header, info)
def 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_paint(self, evt=None):
"""Handler for paint events.
"""
if not self.timepoints:
evt.Skip()
return
PAD = self.PAD + self.ICON_SIZE / 2.0
ICON_SIZE = self.ICON_SIZE
MIN_X_GAP = self.MIN_X_GAP
TIC_SIZE = self.TIC_SIZE
FONT_SIZE = self.FONT_SIZE
MAX_TIMEPOINT = self.timepoints[-1]
WIGGEL_NUM = 100
self.hover_timepoint = None
self.curr_note_tag = None
self.on_note_icon_add()
# self.current_atag = None
# self.on_attach_icon_add()
dc = wx.BufferedPaintDC(self)
dc.Clear()
dc.BeginDrawing()
w_win, h_win = (float(self.Size[0]), float(self.Size[1]))
if self.time_x:
if MAX_TIMEPOINT == 0:
px_per_time = 1
else:
px_per_time = max((w_win - PAD * 2.0) / MAX_TIMEPOINT, MIN_X_GAP)
else:
px_per_time = 1
if len(self.timepoints) == 1:
x_gap = 1
else:
x_gap = max(MIN_X_GAP, (w_win - PAD * 2) / (len(self.timepoints) - 1))
# y pos of line
y = h_win - PAD - FONT_SIZE[1] - TIC_SIZE - 1
def icon_hover(mouse_pos, icon_pos, icon_size):
"""returns whether the mouse is hovering over an icon
"""
if mouse_pos is None:
return False
MX, MY = mouse_pos
X, Y = icon_pos
return X - icon_size / 2.0 < MX < X + icon_size / 2.0 and Y - icon_size / 2.0 < MY < Y + icon_size / 2.0
# draw the timeline
if self.time_x:
dc.DrawLine(PAD, y, px_per_time * MAX_TIMEPOINT + PAD, y)
else:
dxs = range(WIGGEL_NUM + 1)
dxs = [float(dx) / WIGGEL_NUM for dx in dxs]
x = PAD
for i, timepoint in enumerate(self.timepoints):
if i > 0:
n = math.sqrt(((self.timepoints[i] - self.timepoints[i - 1]))) # instead of log can use square root
ys = [
5 * (math.sin((math.pi) * dx)) * math.sin(2 * math.pi * dx * n) for dx in dxs
] # 10 is px height fow wiggles can change it
for p, dx in enumerate(dxs[:-1]):
dc.DrawLine(x + x_gap * dxs[p], y + ys[p], x + x_gap * dxs[p + 1], y + ys[p + 1])
x += x_gap
font = dc.Font
font.SetPixelSize(FONT_SIZE)
dc.SetFont(font)
# draw the ticks
for i, timepoint in enumerate(self.timepoints):
# if data acquisition is the only event in this timepoint skip it
# evt_categories = list(set([exp.get_tag_stump(ev.get_welltag(), 1) for ev in self.events_by_timepoint[timepoint]]))
# if all(evt_categories[0] == cat and cat == 'DataAcquis' for cat in evt_categories):
# continue
# x position of timepoint on the line
if self.time_x:
x = timepoint * px_per_time + PAD
else:
x = i * x_gap + PAD
if self.cursor_pos is not None and x - ICON_SIZE / 2 < self.cursor_pos[0] < x + ICON_SIZE / 2:
dc.SetPen(wx.Pen(wx.BLACK, 3))
self.hover_timepoint = timepoint
else:
dc.SetPen(wx.Pen(wx.BLACK, 1))
# Draw tic marks
dc.DrawLine(x, y - TIC_SIZE, x, y + TIC_SIZE)
# Draw the note/attachment icon above the tick
note_tags = [
tag
for tag in meta.global_settings
if (tag.startswith("Notes") or tag.startswith("Attachments"))
and exp.get_tag_attribute(tag) == str(timepoint)
]
for i, note_tag in enumerate(note_tags):
if exp.get_tag_type(note_tag) == "Notes":
bmp = icons.note.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
if exp.get_tag_type(note_tag) == "Attachments":
bmp = icons.clip.Scale(ICON_SIZE, ICON_SIZE, quality=wx.IMAGE_QUALITY_HIGH).ConvertToBitmap()
dc.DrawBitmap(bmp, x - ICON_SIZE / 2.0, y - ((i + 1) * ICON_SIZE) - TIC_SIZE - 1)
if icon_hover(
self.cursor_pos, (x - ICON_SIZE / 2.0, y - ((i + 1) * ICON_SIZE) - TIC_SIZE - 1), ICON_SIZE
):
self.curr_note_tag = note_tag
# draw the timepoint beneath the line
time_string = exp.format_time_string(timepoint)
wtext = FONT_SIZE[0] * len(time_string)
htext = FONT_SIZE[1]
dc.DrawText(time_string, x - wtext / 2.0, y + TIC_SIZE + 1)
dc.DrawLine(x, y + TIC_SIZE + 1 + htext, x, h_win) # extension of tick towards the lineage panel
dc.EndDrawing()
