def czi2tif(czifile, tiffile=None, squeeze=True, verbose=True, **kwargs):
"""Convert CZI file to memory-mappable TIFF file.
To read the image data from the created TIFF file: Read the 'StripOffsets'
and 'ImageDescription' tags from the first TIFF page. Get the 'dtype' and
'shape' attributes from the ImageDescription string using a JSON decoder.
Memory-map 'product(shape) * sizeof(dtype)' bytes in the file starting at
StripOffsets[0]. Cast the mapped bytes to an array of 'dtype' and 'shape'.
"""
verbose = print_ if verbose else lambda *a, **b: None
if tiffile is None:
tiffile = czifile + '.tif'
elif tiffile.lower() == 'none':
tiffile = None
verbose("\nOpening CZI file... ", end='', flush=True)
start_time = time.time()
with CziFile(czifile) as czi:
if squeeze:
shape, axes = squeeze_axes(czi.shape, czi.axes, '')
else:
shape = czi.shape
axes = czi.axes
dtype = str(czi.dtype)
size = product(shape) * czi.dtype.itemsize
verbose("%.3f s" % (time.time() - start_time))
verbose("Image\n axes: %s\n shape: %s\n dtype: %s\n size: %s" %
(axes, shape, dtype, format_size(size)),
flush=True)
if not tiffile:
verbose("Copying image from CZI file to RAM... ",
end='',
flush=True)
start_time = time.time()
czi.asarray(order=0)
else:
verbose("Creating empty TIF file... ", end='', flush=True)
start_time = time.time()
if 'software' not in kwargs:
kwargs['software'] = 'czi2tif'
metadata = kwargs.pop('metadata', {})
metadata.update(axes=axes, dtype=dtype)
data = memmap(tiffile,
shape=shape,
dtype=dtype,
metadata=metadata,
**kwargs)
data = data.reshape(czi.shape)
verbose("%.3f s" % (time.time() - start_time))
verbose("Copying image from CZI to TIF file... ",
end='',
flush=True)
start_time = time.time()
czi.asarray(order=0, out=data)
verbose("%.3f s" % (time.time() - start_time), flush=True)
def czi2tif(czifile, tiffile=None, squeeze=True, verbose=True, **kwargs):
"""Convert CZI file to memory-mappable TIFF file.
To read the image data from the created TIFF file: Read the 'StripOffsets'
and 'ImageDescription' tags from the first TIFF page. Get the 'dtype' and
'shape' attributes from the ImageDescription string using a JSON decoder.
Memory-map 'product(shape) * sizeof(dtype)' bytes in the file starting at
StripOffsets[0]. Cast the mapped bytes to an array of 'dtype' and 'shape'.
"""
verbose = print_ if verbose else lambda *a, **b: None
if tiffile is None:
tiffile = czifile + '.tif'
elif tiffile.lower() == 'none':
tiffile = None
verbose("\nOpening CZI file... ", end='', flush=True)
start_time = time.time()
with CziFile(czifile) as czi:
if squeeze:
shape, axes = squeeze_axes(czi.shape, czi.axes, '')
else:
shape = czi.shape
axes = czi.axes
dtype = str(czi.dtype)
size = product(shape) * czi.dtype.itemsize
verbose("%.3f s" % (time.time() - start_time))
verbose("Image\n axes: %s\n shape: %s\n dtype: %s\n size: %s"
% (axes, shape, dtype, format_size(size)), flush=True)
if not tiffile:
verbose("Copying image from CZI file to RAM... ",
end='', flush=True)
start_time = time.time()
czi.asarray(order=0)
else:
verbose("Creating empty TIF file... ", end='', flush=True)
start_time = time.time()
if 'software' not in kwargs:
kwargs['software'] = 'czi2tif'
metadata = kwargs.pop('metadata', {})
metadata.update(axes=axes, dtype=dtype)
data = memmap(tiffile, shape=shape, dtype=dtype,
metadata=metadata, **kwargs)
data = data.reshape(czi.shape)
verbose("%.3f s" % (time.time() - start_time))
verbose("Copying image from CZI to TIF file... ",
end='', flush=True)
start_time = time.time()
czi.asarray(order=0, out=data)
verbose("%.3f s" % (time.time() - start_time), flush=True)