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 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 __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)
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))