def fromfile(cls, imgfile, camfile=''): img = fileIO.loadimg(imgfile) camfile = camfile or fileIO.to_cam_filename(imgfile) metadata = fileIO.loadcam(camfile) metadata['filename'] = imgfile stack = cls(img, metadata) # Keeping the .filename attribute for backward compatibility, but should move to # metadata lookup stack.filename = metadata['filename'] return stack
def __init__(self, filename, filetype="img", camFile='', deepcopy=False):
if filetype != 'img':
raise ValueError, "Only filetype 'img' is supported!"
self._showROI = False
#################################################
## Load data from file called filename if string
#################################################
if isinstance(filename, str):
self.filename = filename
self._img = fileIO.loadimg(filename)
self._roi = {}
self._donorROIName = Stack.defaultDonorROI
self._acceptorROIName = Stack.defaultAcceptorROI
camFile = camFile or fileIO.change_extension(filename, '.cam')
settings = fileIO.loadcam(camFile)
self.metadata = {}
for setting,value in settings.iteritems():
self.metadata[setting] = value
if not hasattr(self, setting):
setattr(self, setting, value)
# check cam and img file correspondence
if self._img.shape != (settings['frames'],settings['height'],settings['width']):
raise StackError, ".img file and .cam file dimensions do not agree"
self.origin = (self.roileft,self.roibottom)
self.addROI(*self.__class__.defaultROI.values())
#################################################
## Make a copy of filename if actually another Stack
#################################################
elif isinstance(filename, Stack):
if deepcopy:
self._img=filename._img.copy()
else:
self._img=filename._img
self._roi=filename._roi
self._donorROIName = filename._donorROIName
self._acceptorROIName = filename._acceptorROIName
self.origin = filename.origin
self.metadata = filename.metadata
for setting in self.metadata:
if not hasattr(self,setting.lower()):
setattr(self, setting, getattr(filename,setting))
else:
raise StackError, "Invalid constructor call using %s" % str(filename)
