/usr/lib/python2.7/dist-packages/nibabel/spm2analyze.py is in python-nibabel 2.1.0-1.
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#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
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''' Read / write access to SPM2 version of analyze image format '''
import numpy as np
from . import spm99analyze as spm99 # module import
image_dimension_dtd = spm99.image_dimension_dtd[:]
image_dimension_dtd[
image_dimension_dtd.index(('funused2', 'f4'))
] = ('scl_inter', 'f4')
# Full header numpy dtype combined across sub-fields
header_dtype = np.dtype(spm99.header_key_dtd +
image_dimension_dtd +
spm99.data_history_dtd)
class Spm2AnalyzeHeader(spm99.Spm99AnalyzeHeader):
''' Class for SPM2 variant of basic Analyze header
SPM2 variant adds the following to basic Analyze format:
* voxel origin;
* slope scaling of data;
* reading - but not writing - intercept of data.
'''
# Copies of module level definitions
template_dtype = header_dtype
def get_slope_inter(self):
''' Get data scaling (slope) and intercept from header data
Uses the algorithm from SPM2 spm_vol_ana.m by John Ashburner
Parameters
----------
self : header
Mapping with fields:
* scl_slope - slope
* scl_inter - possible intercept (SPM2 use - shared by nifti)
* glmax - the (recorded) maximum value in the data (unscaled)
* glmin - recorded minimum unscaled value
* cal_max - the calibrated (scaled) maximum value in the dataset
* cal_min - ditto minimum value
Returns
-------
scl_slope : None or float
slope. None if there is no valid scaling from these fields
scl_inter : None or float
intercept. Also None if there is no valid slope, intercept
Examples
--------
>>> fields = {'scl_slope': 1, 'scl_inter': 0, 'glmax': 0, 'glmin': 0,
... 'cal_max': 0, 'cal_min': 0}
>>> hdr = Spm2AnalyzeHeader()
>>> for key, value in fields.items():
... hdr[key] = value
>>> hdr.get_slope_inter()
(1.0, 0.0)
>>> hdr['scl_inter'] = 0.5
>>> hdr.get_slope_inter()
(1.0, 0.5)
>>> hdr['scl_inter'] = np.nan
>>> hdr.get_slope_inter()
(1.0, 0.0)
If 'scl_slope' is 0, nan or inf, cannot use 'scl_slope'.
Without valid information in the gl / cal fields, we cannot get
scaling, and return None
>>> hdr['scl_slope'] = 0
>>> hdr.get_slope_inter()
(None, None)
>>> hdr['scl_slope'] = np.nan
>>> hdr.get_slope_inter()
(None, None)
Valid information in the gl AND cal fields are needed
>>> hdr['cal_max'] = 0.8
>>> hdr['cal_min'] = 0.2
>>> hdr.get_slope_inter()
(None, None)
>>> hdr['glmax'] = 110
>>> hdr['glmin'] = 10
>>> np.allclose(hdr.get_slope_inter(), [0.6/100, 0.2-0.6/100*10])
True
'''
# get scaling factor from 'scl_slope' (funused1)
slope = float(self['scl_slope'])
if np.isfinite(slope) and slope:
# try to get offset from scl_inter
inter = float(self['scl_inter'])
if not np.isfinite(inter):
inter = 0.0
return slope, inter
# no non-zero and finite scaling, try gl/cal fields
unscaled_range = self['glmax'] - self['glmin']
scaled_range = self['cal_max'] - self['cal_min']
if unscaled_range and scaled_range:
slope = float(scaled_range) / unscaled_range
inter = self['cal_min'] - slope * self['glmin']
return slope, inter
return None, None
@classmethod
def may_contain_header(klass, binaryblock):
if len(binaryblock) < klass.sizeof_hdr:
return False
hdr_struct = np.ndarray(shape=(), dtype=header_dtype,
buffer=binaryblock[:klass.sizeof_hdr])
bs_hdr_struct = hdr_struct.byteswap()
return (binaryblock[344:348] not in (b'ni1\x00', b'n+1\x00') and
348 in (hdr_struct['sizeof_hdr'], bs_hdr_struct['sizeof_hdr']))
class Spm2AnalyzeImage(spm99.Spm99AnalyzeImage):
""" Class for SPM2 variant of basic Analyze image
"""
header_class = Spm2AnalyzeHeader
load = Spm2AnalyzeImage.load
save = Spm2AnalyzeImage.instance_to_filename
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