def _getFilenameSuggestion(dirname='', seriesname=SERIES_PATTERN):
from PYME.IO.FileUtils import nameUtils
from PYME.IO import clusterIO
import os
if dirname == '':
dirname = nameUtils.genClusterDataFilepath()
else:
dirname = dirname.split(nameUtils.getUsername())[-1]
dir_parts = dirname.split(os.path.sep)
if len(dirname) < 1 or len(dir_parts) > 3:
#path is either too complex, or too easy - revert to default
dirname = nameUtils.genClusterDataFilepath()
else:
dirname = nameUtils.getUsername() + '/'.join(dir_parts)
#dirname = defDir % nameUtils.dateDict
seriesStub = dirname + '/' + seriesname % nameUtils.dateDict
seriesCounter = 0
seriesName = seriesStub % {'counter': nameUtils.numToAlpha(seriesCounter)}
#try to find the next available serie name
while clusterIO.exists(seriesName + '/'):
seriesCounter += 1
if '%(counter)' in seriesName:
seriesName = seriesStub % {
'counter': nameUtils.numToAlpha(seriesCounter)
}
else:
seriesName = seriesStub + '_' + nameUtils.numToAlpha(seriesCounter)
return seriesName
def PopulateMetadata(self, mdh, acquiring=True):
global lastCreator, lastSlideRef
currentSlide[0] = self.slide
creator = self.slide['creator']
slideRef = self.slide['reference']
sampleNotes = self.slide['notes']
#notes = self.tNotes.GetValue()
#sampleNotes = self.tSlideNotes.GetValue()
if not slideRef == lastSlideRef or not creator == lastCreator:
lastCreator = creator
lastSlideRef = slideRef
for f in WantSlideChangeNotification:
f()
#if len(creator) == 0:
# creator = '<none>'
#if len(slideRef) == 0:
# slideRef = '<none>'
#if len(notes) == 0:
# notes = '<none>'
#if len(sampleNotes) == 0:
# sampleNotes = '<none>'
mdh.setEntry('Sample.Creator', creator)
mdh.setEntry('Sample.SlideRef', slideRef)
if len(sampleNotes) > 0:
mdh.setEntry('Sample.Notes', sampleNotes)
#mdh.setEntry('AcquisitionNotes', notes)
# labels = []
# for i in range(self.gLabelling.GetNumberRows()):
# labels.append((self.gLabelling.GetCellValue(i, 0),self.gLabelling.GetCellValue(i, 1)))
#mdh.setEntry('Sample.Labelling', [(l.structure, l.dye.shortName) for l in self.slide.labelling.all()])
mdh.setEntry('Sample.Labelling', self.slide['labels'])
mdh['Sample.SlideID'] = self.slide['slideID']
mdh['Sample.Specimen'] = self.slide['sample']
mdh.setEntry('AcquiringUser', nameUtils.getUsername())
#slide = models.Slide.Get(creator, slideRef)
# if not self.slideExists:
# for struct, label in self.labels:
# l = models.Labelling(slideID=slide, structure=struct, label=label)
# l.notes = sampleNotes
# l.save()
if acquiring:
notes = self.tNotes.GetValue()
mdh.setEntry('Notes', notes)
import wx.lib.mixins.listctrl as listmix
import sys
import os
import requests
import logging
logging.getLogger("requests").setLevel(logging.WARNING)
logging.getLogger("urllib3").setLevel(logging.WARNING)
from PYME.IO.FileUtils import nameUtils
from PYME.contrib import TextCtrlAutoComplete
#from PYME.SampleDB2 import populate #just to setup the Django environment
#from PYME.SampleDB2.samples import models
lastCreator = nameUtils.getUsername()
lastSlideRef = ''
currentSlide = [None]
WantSlideChangeNotification = []
from PYME.IO import MetaDataHandler
from PYME.IO.MetaDataHandler import NestedClassMDHandler
slideMD = NestedClassMDHandler()
if 'PYME_DATABASE_HOST' in os.environ.keys():
dbhost = os.environ['PYME_DATABASE_HOST']
else:
dbhost = 'dbsrv1'
def createImage(mdh, slide, comments=''):
im = models.Image.GetOrCreate(mdh.getEntry('imageID'),
nameUtils.getUsername(), slide,
mdh.getEntry('StartTime'))
im.comments = comments
im.save()
