def __init__(self, userDetails, inpath, outpath, compression, section_id, total_sections, input_data, pixelregion, outChan, scalefact, rotation): OMEBase.__init__(self) self.outputtif_path = outpath self.ID = section_id self.Total = total_sections self.InputPath = inpath self.InputFilename = self.InputPath.split("\\")[-1] self.imarray = input_data self.outChan = outChan self.rotation = rotation self.roi = pixelregion self.meta = SlideImage(self.InputPath) self.mode = self.meta.micro_mode() self.scalefact = scalefact self.tile_width = 1024 self.tile_height = 1024 self.compression = compression if not userDetails: current_user = '******' current_group = 'QBIgroup' else: current_user = userDetails[0] current_group = userDetails[1] if current_user not in people: people[current_user] = dict(first_name = userDetails[2], last_name = userDetails[3], email = userDetails[0]+'@uq.edu.au', user_name = userDetails[0], institution='Queensland Brain Institute', groups = current_group) if current_group not in groups: groups[current_group] = dict(name = userDetails[1], contact_id = userDetails[0]) self.current_user = current_user self.current_group = current_group
def __init__(self,conn=None,source=None,input_dir=None,filename=None,box=None,theZ=None,theC=None,theT=None,ROI=None): OMEBase.__init__(self) self.store = ome_xml.OME() self.conn = conn self.source = source self.input_dir = input_dir self.filename = filename self.box = box if source: if box: self.sizeX = int(box[2]) self.sizeY = int(box[3]) else: self.sizeX = int(source.getSizeX()) self.sizeY = int(source.getSizeY()) if theZ is not None: if isinstance(theZ,list): self.sizeZ = len(theZ) self.slicesZ = theZ else: self.sizeZ = 1 self.slicesZ = [theZ] else: self.sizeZ = int(source.getSizeZ()) self.slicesZ = range(self.sizeZ) if theC is not None: if isinstance(theC,list): self.sizeC = len(theC) self.slicesC = theC else: self.sizeC = 1 self.slicesC = [theC] else: self.sizeC = int(source.getSizeC()) self.slicesC = range(self.sizeC) if theT is not None: if isinstance(theT,list): self.sizeT = len(theT) self.slicesT = theT else: self.sizeT = 1 self.slicesT = [theT] else: self.sizeT = int(source.getSizeT()) self.slicesT = range(self.sizeT) self.roi_count = 0 if ROI: self.ROI = ROI self.roi_count = len(ROI) self.Xres = source.getPrimaryPixels().physicalSizeX.getValue() self.Yres = source.getPrimaryPixels().physicalSizeY.getValue() self.Zres = source.getPrimaryPixels().physicalSizeZ.getValue() self.dtype = source.getPixelsType() self.date = str(source.getDate())
def __init__(self, userDetails, inpath, outpath, compression, section_id, total_sections, input_data, pixelregion, outChan, scalefact, rotation): OMEBase.__init__(self) self.outputtif_path = outpath self.ID = section_id self.Total = total_sections self.InputPath = inpath self.InputFilename = self.InputPath.split("\\")[-1] self.imarray = input_data self.outChan = outChan self.rotation = rotation self.roi = pixelregion self.meta = SlideImage(self.InputPath) self.mode = self.meta.micro_mode() self.scalefact = scalefact self.tile_width = 1024 self.tile_height = 1024 self.compression = compression if not userDetails: current_user = '******' current_group = 'QBIgroup' else: current_user = userDetails[0] current_group = userDetails[1] if current_user not in people: people[current_user] = dict( first_name=userDetails[2], last_name=userDetails[3], email=userDetails[0] + '@uq.edu.au', user_name=userDetails[0], institution='Queensland Brain Institute', groups=current_group) if current_group not in groups: groups[current_group] = dict(name=userDetails[1], contact_id=userDetails[0]) self.current_user = current_user self.current_group = current_group