def processFiles(flist, roi='roi.txt', background=None,
verbose=True, ext=fileIO.FRET_FILE, **calcOptions):
"Process files given in flist as images"
if isinstance(background, str):
BG = image.fromFile(background,background=True)
elif isinstance(background, int):
BG = background
else:
BG = constants.default_background_subtract
if isinstance(roi,str):
roi = image.ROI.fromFile(roi)
for fname in flist:
try:
if verbose: info('Opening %s...' % fname)
img = image.fromFile(fname) - BG
img.addROI(*roi)
output = calculate(img, **calcOptions)
if verbose: info('Saving .fret data to file...')
toFile(fileIO.change_extension(fname,ext), output, img.metadata)
except IOError as e:
warning("Error processing file {0}: {1}".format(
fname, e.strerror)
)
def processFiles(flist,
roi='roi.txt',
background=None,
verbose=True,
ext=fileIO.FRET_FILE,
**calcOptions):
"Calculate donor, acceptor, and FRET values for files in flist argument."
if isinstance(roi, str):
roi = image.ROI.fromFile(roi)
if len(roi) < 2:
raise ValueError('Need 2 ROIs; given %s' % repr(roi))
don_roi, acc_roi = roi
BG = image.fromBackground(background)
for fname in flist:
try:
if verbose: info('Opening %s...' % fname)
img = image.fromFile(fname, roi=roi, background=BG)
calculated_fret = fret_from_image(img, **calcOptions)
if verbose:
info('Saving .fret data to file...')
calculated_fret.metadata.update(img.metadata)
save_fret(calculated_fret, fileIO.change_extension(fname, ext))
except IOError as e:
warning("Error processing file {0}: {1}".format(fname, e.strerror))
except image.StackError as e:
warning("\n** Error processing file {}:\n\t{!s}**\n".format(
fname, e))
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 processFiles(flist, roi='roi.txt', background=None,
verbose=True, ext=fileIO.FRET_FILE, **calcOptions):
"Calculate donor, acceptor, and FRET values for files in flist argument."
if isinstance(roi,str):
roi = image.ROI.fromFile(roi)
if len(roi) < 2:
raise ValueError('Need 2 ROIs; given %s' % repr(roi))
don_roi,acc_roi = roi
BG = image.fromBackground(background)
for fname in flist:
try:
if verbose: info('Opening %s...' % fname)
img = image.fromFile(fname, roi=roi, background=BG)
calculated_fret = fret_from_image(img, **calcOptions)
if verbose:
info('Saving .fret data to file...')
calculated_fret.metadata.update(img.metadata)
save_fret(calculated_fret, fileIO.change_extension(fname,ext))
except IOError as e:
warning("Error processing file {0}: {1}".format(
fname, e.strerror))
except image.StackError as e:
warning("\n** Error processing file {}:\n\t{!s}**\n".format(fname, e))
def loadimg(self, path='.', **kwargs): filename = self.filename return image.Stack(fileIO.add_img_ext(filename)) return image.fromFile(filename, **kwargs)