MNT: Various removals not listed in removal schedule

Author: effigies

nibabel/dataobj_images.py

@@ -48,13 +48,6 @@ def __init__(self, dataobj, header=None, extra=None, file_map=None):
     def dataobj(self):
         return self._dataobj
 
-    @property
-    @deprecate_with_version('_data attribute not part of public API. '
-                            'please use "dataobj" property instead.',
-                            '2.0', '4.0')
-    def _data(self):
-        return self._dataobj
-
     @deprecate_with_version('get_data() is deprecated in favor of get_fdata(),'
                             ' which has a more predictable return type. To '
                             'obtain get_data() behavior going forward, use '

nibabel/freesurfer/mghformat.py

@@ -24,7 +24,6 @@
 from ..openers import ImageOpener
 from ..batteryrunners import BatteryRunner, Report
 from ..wrapstruct import LabeledWrapStruct
-from ..deprecated import deprecate_with_version
 
 # mgh header
 # See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
@@ -462,45 +461,6 @@ def diagnose_binaryblock(klass, binaryblock, endianness=None):
         return '\n'.join([report.message
                           for report in reports if report.message])
 
-    class _HeaderData:
-        """ Provide interface to deprecated MGHHeader fields"""
-        def __init__(self, structarr):
-            self._structarr = structarr
-
-        def __getitem__(self, item):
-            sa = self._structarr
-            if item == 'mrparams':
-                return np.hstack((sa['tr'], sa['flip_angle'], sa['te'], sa['ti']))
-            return sa[item]
-
-        def __setitem__(self, item, val):
-            sa = self._structarr
-            if item == 'mrparams':
-                sa['tr'], sa['flip_angle'], sa['te'], sa['ti'] = val
-            else:
-                sa[item] = val
-
-    @property
-    @deprecate_with_version('_header_data is deprecated.\n'
-                            'Please use the _structarr interface instead.\n'
-                            'Note also that some fields have changed name and '
-                            'shape.',
-                            '2.3', '4.0')
-    def _header_data(self):
-        """ Deprecated field-access interface """
-        return self._HeaderData(self._structarr)
-
-    def __getitem__(self, item):
-        if item == 'mrparams':
-            return self._header_data[item]
-        return super(MGHHeader, self).__getitem__(item)
-
-    def __setitem__(self, item, value):
-        if item == 'mrparams':
-            self._header_data[item] = value
-        else:
-            super(MGHHeader, self).__setitem__(item, value)
-
 
 class MGHImage(SpatialImage, SerializableImage):
     """ Class for MGH format image

nibabel/freesurfer/tests/test_mghformat.py

@@ -22,7 +22,6 @@
 from ...volumeutils import sys_is_le
 from ...wrapstruct import WrapStructError
 from ... import imageglobals
-from ...deprecator import ExpiredDeprecationError
 
 
 import pytest
@@ -340,20 +339,6 @@ def test_mghheader_default_structarr():
             MGHHeader.default_structarr(endianness=endianness)
 
 
-def test_deprecated_fields():
-    hdr = MGHHeader()
-    hdr_data = MGHHeader._HeaderData(hdr.structarr)
-
-    # mrparams is the only deprecated field at the moment
-    # Accessing hdr_data is equivalent to accessing hdr, so double all checks,
-    # but expect success on hdr_data['mrparams']
-    with pytest.raises(ExpiredDeprecationError):
-        hdr['mrparams']
-    with pytest.raises(ExpiredDeprecationError):
-        hdr['mrparams'] = [1, 2, 3, 4]
-    assert_array_equal(hdr_data['mrparams'], 0)
-
-
 class TestMGHImage(tsi.TestSpatialImage, tsi.MmapImageMixin):
     """ Apply general image tests to MGHImage
     """

nibabel/gifti/__init__.py

@@ -17,6 +17,5 @@
    gifti
 """
 
-from .giftiio import read, write
 from .gifti import (GiftiMetaData, GiftiNVPairs, GiftiLabelTable, GiftiLabel,
                     GiftiCoordSystem, GiftiDataArray, GiftiImage)

nibabel/gifti/giftiio.py

@@ -24,7 +24,6 @@
                    gifti_endian_codes)
 from ..nifti1 import data_type_codes, xform_codes, intent_codes
 from ..xmlutils import XmlParser
-from ..deprecated import deprecate_with_version
 
 
 class GiftiParseError(ExpatError):
@@ -409,23 +408,3 @@ def flush_chardata(self):
     def pending_data(self):
         """True if there is character data pending for processing"""
         return self._char_blocks is not None
-
-
-class Outputter(GiftiImageParser):
-
-    @deprecate_with_version('Outputter class deprecated. '
-                            "Use GiftiImageParser instead.",
-                            '2.1', '4.0')
-    def __init__(self):
-        super(Outputter, self).__init__()
-
-    def initialize(self):
-        """ Initialize outputter"""
-        self.__init__()
-
-
-@deprecate_with_version('parse_gifti_file deprecated. '
-                        "Use GiftiImageParser.parse() instead.",
-                        '2.1', '4.0')
-def parse_gifti_file(fname=None, fptr=None, buffer_size=None):
-    GiftiImageParser(buffer_size=buffer_size).parse(fname=fname, fptr=fptr)

nibabel/gifti/parse_gifti_fast.py

@@ -17,12 +17,10 @@
 
 from .. import gifti as gi
 from ..util import gifti_endian_codes
-from ..parse_gifti_fast import (Outputter, parse_gifti_file, GiftiParseError,
-                                GiftiImageParser)
+from ..parse_gifti_fast import GiftiParseError, GiftiImageParser
 from ...loadsave import load, save
 from ...nifti1 import xform_codes
 from ...tmpdirs import InTemporaryDirectory
-from ...deprecator import ExpiredDeprecationError
 
 from numpy.testing import assert_array_almost_equal
 
@@ -354,16 +352,6 @@ def test_parse_dataarrays():
             assert img.numDA == 0
 
 
-def test_parse_deprecated():
-
-    # Test deprecation
-    with pytest.raises(ExpiredDeprecationError):
-        Outputter()
-
-    with pytest.raises(ExpiredDeprecationError):
-        parse_gifti_file()
-
-
 def test_parse_with_buffersize():
     for buff_sz in [None, 1, 2**12]:
         img2 = load(DATA_FILE2, buffer_size=buff_sz)

nibabel/gifti/tests/test_giftiio.py

@@ -137,7 +137,6 @@
 from .nifti1 import unit_codes
 from .fileslice import fileslice, strided_scalar
 from .openers import ImageOpener
-from .deprecated import deprecate_with_version
 
 # PSL to RAS affine
 PSL_TO_RAS = np.array([[0, 0, -1, 0],  # L -> R
@@ -871,29 +870,6 @@ def _get_unique_image_prop(self, name):
                               f'({props}). This is not supported.')
         return props[0]
 
-    @deprecate_with_version('get_voxel_size deprecated. '
-                            'Please use "get_zooms" instead.',
-                            '2.0', '4.0')
-    def get_voxel_size(self):
-        """Returns the spatial extent of a voxel.
-
-        Does not include the slice gap in the slice extent.
-
-        If you need the slice thickness not including the slice gap, use
-        ``self.image_defs['slice thickness']``.
-
-        Returns
-        -------
-        vox_size: shape (3,) ndarray
-        """
-        # slice orientation for the whole image series
-        slice_thickness = self._get_unique_image_prop('slice thickness')
-        voxsize_inplane = self._get_unique_image_prop('pixel spacing')
-        voxsize = np.array((voxsize_inplane[0],
-                            voxsize_inplane[1],
-                            slice_thickness))
-        return voxsize
-
     def get_data_offset(self):
         """ PAR header always has 0 data offset (into REC file) """
         return 0

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -412,16 +412,6 @@ def _check_array_caching(self, imaker, meth_name, caching):
                 data = get_data_func(dtype=float_type)
             assert (data is img.dataobj) == (arr_dtype == float_type)
 
-    def validate_data_deprecated(self, imaker, params):
-        # Check _data property still exists, but raises warning
-        img = imaker()
-        with pytest.raises(ExpiredDeprecationError):
-            assert_data_similar(img._data, params)
-        # Check setting _data raises error
-        fake_data = np.zeros(img.shape).astype(img.get_data_dtype())
-        with pytest.raises(AttributeError):
-            img._data = fake_data
-
     def validate_shape(self, imaker, params):
         # Validate shape
         img = imaker()