def export_averages(self, filenames, fmt='TIFF16', scale_values=True):
"""Save TIFF files with the time average of each channel.
For datasets with multiple frames, the resulting TIFF files
have multiple pages.
Parameters
----------
filenames : str or list of str
A single (.h5) output filename, or a list of (.tif) output
filenames with one per channel.
fmt : {'TIFF8', 'TIFF16', 'HDF5'}, optional
The format of the output files. Defaults to 16-bit TIFF.
scale_values : bool, optional
Whether to scale the values to use the full range of the
output format. Defaults to False.
"""
if fmt == 'HDF5':
if not isinstance(filenames, basestring):
raise ValueError(
'A single filename must be passed for HDF5 format.')
elif not len(filenames) == self.frame_shape[-1]:
raise ValueError(
"The number of filenames must equal the number of channels.")
if fmt == 'HDF5':
if not h5py_available:
raise ImportError('h5py >= 2.2.1 required')
f = h5py.File(filenames, 'w')
im = self.time_averages
if scale_values:
im = sima.misc.to16bit(im)
else:
im = im.astype('uint16')
f.create_dataset(name='time_average', data=im)
for idx, label in enumerate(['z', 'y', 'x', 'c']):
f['time_average'].dims[idx].label = label
if self.channel_names is not None:
f['time_average'].attrs['channel_names'] = [
np.string_(s) for s in self.channel_names
]
# Note: https://github.com/h5py/h5py/issues/289
f.close()
else:
for chan, filename in enumerate(filenames):
im = self.time_averages[:, :, :, chan]
if dirname(filename):
mkdir_p(dirname(filename))
if fmt == 'TIFF8':
if scale_values:
out = sima.misc.to8bit(im)
else:
out = im.astype('uint8')
elif fmt == 'TIFF16':
if scale_values:
out = sima.misc.to16bit(im)
else:
out = im.astype('uint16')
else:
raise ValueError('Unrecognized format.')
imsave(filename, out)
def export_averages(self, filenames, fmt='TIFF16', scale_values=True):
"""Save TIFF files with the time average of each channel.
For datasets with multiple frames, the resulting TIFF files
have multiple pages.
Parameters
----------
filenames : str or list of str
A single (.h5) output filename, or a list of (.tif) output
filenames with one per channel.
fmt : {'TIFF8', 'TIFF16', 'HDF5'}, optional
The format of the output files. Defaults to 16-bit TIFF.
scale_values : bool, optional
Whether to scale the values to use the full range of the
output format. Defaults to False.
"""
if fmt == 'HDF5':
if not isinstance(filenames, basestring):
raise ValueError(
'A single filename must be passed for HDF5 format.')
elif not len(filenames) == self.frame_shape[-1]:
raise ValueError(
"The number of filenames must equal the number of channels.")
if fmt == 'HDF5':
if not h5py_available:
raise ImportError('h5py >= 2.2.1 required')
f = h5py.File(filenames, 'w')
im = self.time_averages
if scale_values:
im = sima.misc.to16bit(im)
else:
im = im.astype('uint16')
f.create_dataset(name='time_average', data=im)
for idx, label in enumerate(['z', 'y', 'x', 'c']):
f['time_average'].dims[idx].label = label
if self.channel_names is not None:
f['time_average'].attrs['channel_names'] = [
np.string_(s) for s in self.channel_names]
# Note: https://github.com/h5py/h5py/issues/289
f.close()
else:
for chan, filename in enumerate(filenames):
im = self.time_averages[:, :, :, chan]
if dirname(filename):
mkdir_p(dirname(filename))
if fmt == 'TIFF8':
if scale_values:
out = sima.misc.to8bit(im)
else:
out = im.astype('uint8')
elif fmt == 'TIFF16':
if scale_values:
out = sima.misc.to16bit(im)
else:
out = im.astype('uint16')
else:
raise ValueError('Unrecognized format.')
imsave(filename, out)
def export_averages(self, filenames, fmt='TIFF16', scale_values=True):
"""Save TIFF files with the time average of each channel.
For datasets with multiple frames, the resulting TIFF files
have multiple pages.
Parameters
----------
filenames : str or list of str
A single (.h5) output filename, or a list of (.tif) output
filenames with one per channel.
fmt : {'TIFF8', 'TIFF16'}, optional
The format of the output files. Defaults to 16-bit TIFF.
scale_values : bool, optional
Whether to scale the values to use the full range of the
output format. Defaults to False.
"""
if fmt == 'HDF5':
if not isinstance(filenames, str):
raise ValueError(
'A single filename must be passed for HDF5 format.')
elif not len(filenames) == self.frame_shape[-1]:
raise ValueError(
"The number of filenames must equal the number of channels.")
for chan, filename in enumerate(filenames):
im = self.time_averages[:, :, :, chan]
if dirname(filename):
mkdir_p(dirname(filename))
if fmt is 'TIFF8':
if scale_values:
out = sima.misc.to8bit(im)
else:
out = im.astype('uint8')
elif fmt is 'TIFF16':
if scale_values:
out = sima.misc.to16bit(im)
else:
out = im.astype('uint16')
else:
raise ValueError('Unrecognized format.')
imsave(filename, out)