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,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
