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src/n/i/nibabel-1.3.0/nibabel/externals/netcdf.py nibabel(Download)
import numpy as np from ..py3k import asbytes, asstr from numpy import fromstring, ndarray, dtype, empty, array, asarray from numpy import little_endian as LITTLE_ENDIAN ABSENT = asbytes('\x00\x00\x00\x00\x00\x00\x00\x00') ZERO = asbytes('\x00\x00\x00\x00') NC_BYTE = asbytes('\x00\x00\x00\x01')
ZERO = asbytes('\x00\x00\x00\x00') NC_BYTE = asbytes('\x00\x00\x00\x01') NC_CHAR = asbytes('\x00\x00\x00\x02') NC_SHORT = asbytes('\x00\x00\x00\x03') NC_INT = asbytes('\x00\x00\x00\x04')
src/n/i/nibabel-1.3.0/nibabel/nifti1.py nibabel(Download)
import numpy.linalg as npl from .py3k import ZEROB, ints2bytes, asbytes, asstr from .volumeutils import Recoder, make_dt_codes, endian_codes from .spatialimages import HeaderDataError, ImageFileError
magic = np.asscalar(hdr['magic']) offset = hdr['vox_offset'] if magic == asbytes('n+1'): # one file if offset >= 352: if not offset % 16:
hdr['vox_offset'] = 352 rep.fix_msg = 'setting to minimum value of 352' elif magic != asbytes('ni1'): # two files # unrecognized nii magic string, oh dear rep.problem_msg = ('magic string "%s" is not valid' %
src/n/i/nibabel-1.3.0/nibabel/minc.py nibabel(Download)
from .externals.netcdf import netcdf_file from .py3k import asbytes, asstr from .spatialimages import SpatialImage
# http://www.bic.mni.mcgill.ca/software/minc/minc1_format/node15.html for dim in self._dims: if dim.spacing != asbytes('regular__'): raise ValueError('Irregular spacing not supported') self._spatial_dims = [name for name in self._dim_names
src/n/i/nibabel-1.3.0/nibabel/nicom/csareader.py nibabel(Download)
import numpy as np from ..py3k import ZEROB, asbytes, asstr from .structreader import Unpacker
hdr_id = csa_str[:4] up_str = Unpacker(csa_str, endian='<') if hdr_id == asbytes('SV10'): # CSA2 hdr_type = 2 up_str.ptr = 4 # omit the SV10
src/n/i/nibabel-1.3.0/nibabel/loadsave.py nibabel(Download)
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## # module imports from .py3k import asbytes from .filename_parser import types_filenames, splitext_addext from . import volumeutils as vu
vu.allopen(filenames['header']), check=False) if hdr['magic'] in (asbytes('ni1'), asbytes('n+1')): # allow goofy nifti single magic for pair klass = nifti1.Nifti1Pair
src/n/i/nibabel-1.3.0/nibabel/trackvis.py nibabel(Download)
import numpy.linalg as npl from .py3k import asbytes, asstr from .volumeutils import (native_code, swapped_code, endian_codes, allopen, rec2dict)
dtype=header_2_dtype, buffer=hdr_str) if np.asscalar(hdr['id_string'])[:5] != asbytes('TRACK'): raise HeaderError('Expecting TRACK as first ' '5 characters of id_string')
hdr[key] = value # check header values if np.asscalar(hdr['id_string'])[:5] != asbytes('TRACK'): raise HeaderError('Expecting TRACK as first ' '5 characaters of id_string')
src/n/i/nibabel-HEAD/nibabel/externals/netcdf.py nibabel(Download)
import numpy as np from ..py3k import asbytes, asstr from numpy import fromstring, ndarray, dtype, empty, array, asarray from numpy import little_endian as LITTLE_ENDIAN
nc_type = REVERSE[var.typecode(), var.itemsize()] self.fp.write(asbytes(nc_type)) if not var.isrec:
values = asarray(values, dtype=dtype_) self.fp.write(asbytes(nc_type)) if values.dtype.char == 'S':
def _pack_string(self, s): count = len(s) self._pack_int(count) self.fp.write(asbytes(s)) self.fp.write(b'0' * (-count % 4)) # pad
src/n/i/nibabel-1.3.0/nibabel/nicom/tests/test_structreader.py nibabel(Download)
import struct from ...py3k import asbytes from ..structreader import Unpacker
def test_unpacker(): s = asbytes('1234\x00\x01') le_int, = struct.unpack('<h', asbytes('\x00\x01')) be_int, = struct.unpack('>h', asbytes('\x00\x01')) if sys.byteorder == 'little':
swapped_code = '<' up_str = Unpacker(s, endian='<') assert_equal(up_str.read(4), asbytes('1234')) up_str.ptr = 0 assert_equal(up_str.unpack('4s'), (asbytes('1234'),))
src/n/i/nibabel-1.3.0/nibabel/tests/test_nifti1.py nibabel(Download)
import os from ..py3k import BytesIO, ZEROB, asbytes import numpy as np
def test_empty(self): tana.TestAnalyzeHeader.test_empty(self) hdr = self.header_class() assert_equal(hdr['magic'], asbytes('ni1')) assert_equal(hdr['scl_slope'], 1)
def test_from_eg_file(self): hdr = Nifti1Header.from_fileobj(open(self.example_file, 'rb')) assert_equal(hdr.endianness, '<') assert_equal(hdr['magic'], asbytes('ni1')) assert_equal(hdr['sizeof_hdr'], 348)
hdr['magic'] = 'ooh' fhdr, message, raiser = self.log_chk(hdr, 45) assert_equal(fhdr['magic'], asbytes('ooh')) assert_equal(message, 'magic string "ooh" is not valid; ' 'leaving as is, but future errors are likely')
def test_empty(self): tana.TestAnalyzeHeader.test_empty(self) hdr = self.header_class() assert_equal(hdr['magic'], asbytes('n+1')) assert_equal(hdr['scl_slope'], 1)
src/n/i/nibabel-1.3.0/nibabel/tests/test_utils.py nibabel(Download)
''' Test for volumeutils module ''' from __future__ import with_statement from ..py3k import BytesIO, asbytes, ZEROB import tempfile
fd, fname = tempfile.mkstemp() with InTemporaryDirectory(): open(fname, 'wb').write(asbytes('1')) in_buf = open(fname, 'rb') # For windows this will raise a WindowsError from mmap, Unices
def buf_chk(in_arr, out_buf, in_buf, offset): ''' Write contents of in_arr into fileobj, read back, check same ''' instr = asbytes(' ') * offset + in_arr.tostring(order='F') out_buf.write(instr) out_buf.flush()
def test_a2f_offset(): # check that non-zero file offset works arr = np.array([[0.0, 1.0],[2.0, 3.0]]) str_io = BytesIO() str_io.write(asbytes('a') * 42)
def test_rec2dict(): r = np.zeros((), dtype = [('x', 'i4'), ('s', 'S10')]) d = rec2dict(r) assert_equal(d, {'x': 0, 's': asbytes('')})
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