def save_numpy(array, fname):
"""
Saves a numpy array to a file in MRC, EM or VTI format.
Args:
array (numpy.ndarray): input array
fname (str): full path to the tomogram, has to end with '.mrc', '.em' or
'.vti'
Returns:
None
"""
_, ext = os.path.splitext(fname)
# Parse input array for fulfilling format requirements
if (ext == '.mrc') or (ext == '.em'):
if ((array.dtype != 'ubyte') and (array.dtype != 'int16') and
(array.dtype != 'float32')):
array = array.astype('float32')
# if (len(array.shape) == 3) and (array.shape[2] == 1):
# array = np.reshape(array, (array.shape[0], array.shape[1]))
if ext == '.vti':
pname, fnameh = os.path.split(fname)
save_vti(numpy_to_vti(array), fnameh, pname)
# elif ext == '.fits':
# warnings.resetwarnings()
# warnings.filterwarnings('ignore', category=UserWarning, append=True)
# pyfits.writeto(fname, array, clobber=True, output_verify='silentfix')
# warnings.resetwarnings()
# warnings.filterwarnings('always', category=UserWarning, append=True)
elif ext == '.mrc':
img = ImageIO()
# img.setData(np.transpose(array, (1, 0, 2)))
img.setData(array)
img.writeMRC(fname)
elif ext == '.em':
img = ImageIO()
# img.setData(np.transpose(array, (1, 0, 2)))
img.setData(array)
img.writeEM(fname)
else:
error_msg = 'Format not valid %s.' % ext
raise pexceptions.PySegInputError(expr='save_numpy', msg=error_msg)
def save_numpy(array, fname):
"""
Saves a numpy array to a file in MRC, EM or VTI format.
Args:
array (numpy.ndarray): input array
fname (str): full path to the tomogram, has to end with '.mrc', '.em' or
'.vti'
Returns:
None
"""
_, ext = os.path.splitext(fname)
# Parse input array for fulfilling format requirements
if (ext == '.mrc') or (ext == '.em'):
if ((array.dtype != 'ubyte') and (array.dtype != 'int16')
and (array.dtype != 'float32')):
array = array.astype('float32')
# if (len(array.shape) == 3) and (array.shape[2] == 1):
# array = np.reshape(array, (array.shape[0], array.shape[1]))
if ext == '.vti':
pname, fnameh = os.path.split(fname)
save_vti(numpy_to_vti(array), fnameh, pname)
elif ext == '.mrc':
img = ImageIO()
# img.setData(np.transpose(array, (1, 0, 2)))
img.setData(array)
img.writeMRC(fname)
elif ext == '.em':
img = ImageIO()
# img.setData(np.transpose(array, (1, 0, 2)))
img.setData(array)
img.writeEM(fname)
else:
raise pexceptions.PySegInputError(
expr='save_numpy', msg='Format not valid {}.'.format(ext))