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- Committer: Matthew Brett
- Date: 2009-04-11 23:55:20 UTC
- Revision ID: matthew.brett@gmail.com-20090411235520-5oze2nny7pndp519
Prettier output of strings for codes; more private files
- files modified:
- volumeimages/analyze.py
added
removed
volumeimages/nifti1.py
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info = info | (((slice+1) & 3) << 4)
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self._header_data['dim_info'] = info
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def get_intent_code(self, code_repr='label'):
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''' Return representation of intent code
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Parameters
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----------
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code_repr : string
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string giving output form of intent code representation.
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Default is 'label'; use 'code' for integer representation.
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Returns
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-------
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intent_code : string or integer
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string label for intent code or code
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Examples
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--------
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>>> hdr = Nifti1Header()
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>>> hdr.set_intent('t test', (10,), name='some score')
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>>> hdr.get_intent_code()
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't test'
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'''
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return self._get_code_field(
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code_repr,
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'intent_code',
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self._intent_codes)
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def get_intent(self, code_repr='label'):
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''' Get intent code, parameters and name
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'''
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hdr = self._header_data
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code = int(hdr['intent_code'])
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recode = self._get_code_field(
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code_repr,
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'intent_code',
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self._intent_codes)
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recode = self.get_intent_code(code_repr)
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n_params = len(self._intent_codes.parameters[code])
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params = (float(hdr['intent_p%d' % (i+1)]) for i in range(n_params))
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return recode, tuple(params), str(hdr['intent_name'])
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>>> hdr.set_dim_info(slice=2)
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>>> hdr.set_data_shape((1, 1, 7))
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>>> hdr.set_slice_duration(0.1)
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>>> hdr['slice_code'] = slice_order_codes.code['sequential increasing']
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We need a function to print out the Nones and floating point
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values in a predictable way, for the tests below
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values in a predictable way, for the tests below.
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>>> _stringer = lambda val: val is not None and '%2.1f' % val or None
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>>> printable_seq = lambda s: map(_stringer, s)
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The following examples are from the nifti1.h documentation
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>>> printable_seq(hdr.get_slice_times())
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>>> _print_me = lambda s: map(_stringer, s)
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The following examples are from the nifti1.h documentation.
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>>> hdr['slice_code'] = slice_order_codes['sequential increasing']
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>>> _print_me(hdr.get_slice_times())
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['0.0', '0.1', '0.2', '0.3', '0.4', '0.5', '0.6']
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>>> hdr['slice_start'] = 1
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>>> hdr['slice_end'] = 5
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>>> printable_seq(hdr.get_slice_times())
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>>> _print_me(hdr.get_slice_times())
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[None, '0.0', '0.1', '0.2', '0.3', '0.4', None]
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>>> hdr['slice_code'] = slice_order_codes.code['sequential decreasing']
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>>> printable_seq(hdr.get_slice_times())
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>>> hdr['slice_code'] = slice_order_codes['sequential decreasing']
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>>> _print_me(hdr.get_slice_times())
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[None, '0.4', '0.3', '0.2', '0.1', '0.0', None]
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>>> hdr['slice_code'] = slice_order_codes.code['alternating increasing']
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>>> printable_seq(hdr.get_slice_times())
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>>> hdr['slice_code'] = slice_order_codes['alternating increasing']
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>>> _print_me(hdr.get_slice_times())
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[None, '0.0', '0.3', '0.1', '0.4', '0.2', None]
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>>> hdr['slice_code'] = slice_order_codes.code['alternating decreasing']
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>>> printable_seq(hdr.get_slice_times())
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>>> hdr['slice_code'] = slice_order_codes['alternating decreasing']
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>>> _print_me(hdr.get_slice_times())
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[None, '0.2', '0.4', '0.1', '0.3', '0.0', None]
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>>> hdr['slice_code'] = slice_order_codes.code['alternating increasing 2']
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>>> printable_seq(hdr.get_slice_times())
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>>> hdr['slice_code'] = slice_order_codes['alternating increasing 2']
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>>> _print_me(hdr.get_slice_times())
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[None, '0.2', '0.0', '0.3', '0.1', '0.4', None]
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>>> hdr['slice_code'] = slice_order_codes.code['alternating decreasing 2']
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>>> printable_seq(hdr.get_slice_times())
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>>> hdr['slice_code'] = slice_order_codes['alternating decreasing 2']
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>>> _print_me(hdr.get_slice_times())
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[None, '0.4', '0.1', '0.3', '0.0', '0.2', None]
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'''
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hdr = self._header_data
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>>> data = np.zeros((2,3,4))
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>>> affine = np.diag([1.0,2.0,3.0,1.0])
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>>> img = Nifti1Image(data, affine)
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At this stage the image files are not defined, and there are no
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checks we should run on the nifti magic and offset
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>>> meta = img.get_metadata()
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>>> str(meta['magic'])
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'n+1'
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True
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>>> str(meta['magic'])
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'n+1'
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>>> img.files = {'header':'tmp.nii','image':'tmp.nii'}
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>>> img.update_metadata()
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Now we change the files, to reveal the checks.
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>>> from StringIO import StringIO
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>>> str_io = StringIO()
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>>> files = {'header':str_io,'image':str_io}
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>>> img.to_files(files) # implies img.update_metadata()
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>>> str(meta['magic'])
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'n+1'
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>>> int(meta['vox_offset'])
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>>> img.files = {'header':'tmp.hdr','image':'tmp.img'}
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>>> img.update_metadata()
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>>> str_io2 = StringIO()
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>>> files = {'header':str_io,'image':str_io2}
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>>> img.to_files(files) # implies img.update_metadata()
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>>> str(meta['magic'])
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'ni1'
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>>> int(meta['vox_offset'])
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if not self._affine is None:
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hdr.set_sform(self._affine)
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hdr.set_qform(self._affine)
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if not self.files:
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if not self._files:
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return
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if self.files['header'] == self.files['image']:
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if self._files['header'] == self._files['image']:
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# one file version
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if hdr['magic'] == 'n+1':
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return
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def save(img, filespec):
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img = Nifti1Image.from_image(img)
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img.to_files(filespec)
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img.to_filespec(filespec)
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