def fromFile(filename, **kwargs):
"""fromFile(filename, [background='' or True]):
Load Image from filename with optional background file or constant to subtract.
fromFile('image.img', background = 'filename') => load background file and subtract (SLOW!)
fromFile('background.img', background=True, [filter='median']) => load background.img as background file
fromFile('image.img', background=100) => subtract 100 from image as background level
"""
bg = kwargs.pop('background', False)
roi = kwargs.pop('roi', None)
try:
img = Stack(fileIO.add_img_ext(filename), **kwargs)
except IOError:
raise IOError("File %s can't be found/loaded" % filename)
if bg is True:
return img.toBackground(**kwargs)
elif isinstance(bg,str):
bg = Stack(bg)
bg.toBackground(**kwargs)
result = img - bg
if roi is not None:
rois = ROI.fromFile(roi)
result.addROI(*rois)
return result
def fromFile(filename, background=None, **kwargs):
"""fromFile(filename, [background='' or True]):
Load Image from filename with optional background file or constant to subtract.
fromFile('image.img', background = 'filename') => load background file and subtract (SLOW!)
fromFile('image.img', background=100) => subtract 100 from image as background level
"""
roi = kwargs.pop('roi', None)
img = Stack.fromfile(fileIO.add_img_ext(filename))
bgimg = fromBackground(background)
bg_exposure = bgimg.metadata['exposurems']
if not isinstance(bgimg, ConstantStack) and bg_exposure != img.metadata['exposurems']:
print '''WARNING Trying to subtract background with exposure time {}
from image with exposure time {}'''.format(
bg_exposure,
img.metadata['exposurems'])
img.metadata['background'] = bgimg.metadata['filename'] or background
img -= bgimg
if roi is not None:
if isinstance(roi, basestring):
roi = ROI.fromFile(roi)
img.addROI(*roi)
return img
def loadimg(p, directory='.', **kwargs):
'''Return the Stack image using ROI and background stored in experiment metadata.
Must be in current or specified directory.
'''
filename = p.filename if directory=='.' else opath.join(directory, p.filename)
meta = p.fret.metadata
if 'roi' not in kwargs:
# If keyword roi= is not specified,
# get the ROIs from the experiment metadata
rois = [ meta[roi_key]
for roi_key in ('roi_donor', 'roi_acceptor')
if roi_key in meta
]
kwargs['roi'] = map(ROI.fromDict, rois)
kwargs.setdefault('background', meta.get('background', '') )
return image.fromFile(fileIO.add_img_ext(filename), **kwargs)
def loadimg(self, path='.', **kwargs): filename = self.filename return image.Stack(fileIO.add_img_ext(filename)) return image.fromFile(filename, **kwargs)
