ENH: Add Image dict and pixel set/get Python interfaces

[thewtex]

Provides a Python dictionary interface to image metadata, keys are
MetaDataDictionary entries along with 'origin', 'spacing', and
'direction' keys. The later reverse their order to be consistent with
the NumPy array index order resulting from array views of the image. The
entries can be accesses and set directly on the image, e.g.

print(image['0008|0008'])
image['origin'] = [4.0, 2.0, 2.0]

or a dictionary can be retrieved with:

meta_dict = dict(image)

For example:

In [3]: dict(image)
Out[3]:
{'0008|0005': 'ISO IR 100',
 '0008|0008': 'ORIGINAL\\PRIMARY\\AXIAL',
 '0008|0016': '1.2.840.10008.5.1.4.1.1.2',
 '0008|0018': '1.3.12.2.1107.5.8.99.484849.834848.79844848.2001082217554549',
 '0008|0020': '20010822',
 '0008|0021': '20010822',
 '0008|0022': '20010822',
 '0008|0023': '20010822',
 '0008|0030': '093652.000000 ',
 '0008|0031': '093652.000000 ',
 '0008|0032': '094028.820000 ',
 '0008|0033': '094335.532000 ',
 '0008|0040': '0',
 '0008|0041': 'IMA SPI ',
 '0008|0050': '                ',
 '0008|0060': 'CT',
 '0008|0070': 'SIEMENS ',
 '0008|0080': 'UNC HOSPITALS - BODY C    ',
 '0008|0090': '',
 '0008|1010': 'bodyct          ',
 '0008|1090': 'SOMATOM PLUS 4            ',
 '0010|0010': 'LIVER DONOR PHANTOM 2                                           ',
 '0010|0020': '2                                                               ',
 '0010|0030': '',
 '0010|0040': 'M ',
 '0018|0010': 'NONE    ',
 '0018|0015': 'BODY',
 '0018|0020': 'RM',
 '0018|0050': '003.000000E+00',
 '0018|0060': '000120',
 '0018|0090': '000500',
 '0018|1000': '                     20380',
 '0018|1020': 'VC10C   ',
 '0018|1110': '001005',
 '0018|1111': '000570',
 '0018|1120': '000.000000E+00',
 '0018|1130': '001.270000E+02',
 '0018|1140': 'CW',
 '0018|1150': '750 ',
 '0018|1151': '170 ',
 '0018|1152': '128 ',
 '0018|1170': '20',
 '0018|1190': '001.200000E+00',
 '0018|1200': '20010817',
 '0018|1201': '072320.877000 ',
 '0018|1210': '59 .10.AB50     ',
 '0018|5100': 'HFS ',
 '0020|000d': '1.3.12.2.1107.5.8.99.484849.834848.79844848.2001082213291053',
 '0020|000e': '1.3.12.2.1107.5.1.1.20380.52.36.9.22.8.2001.3                  ',
 '0020|0010': '000001',
 '0020|0011': '000004',
 '0020|0012': '000003',
 '0020|0013': '000052',
 '0020|0030': '-01.217578E+02\\-1.437578E+02\\-8.360000E+02',
 '0020|0032': '-122\\-144\\-836',
 '0020|0035': '001.000000E+00\\00.000000E+00\\00.000000E+00\\00.000000E+00\\01.000000E+00\\00.000000E+00',
 '0020|0037': '1\\0\\0\\0\\1\\0 ',
 '0020|0050': '-08.360000E+02',
 '0020|0052': '1.3.12.2.1107.5.1.1.20380.52.36.9.22.8.2001                    ',
 '0020|0070': 'PLANAR  ',
 '0020|0080': '',
 '0020|1040': '',
 '0020|1041': '-836',
 '0020|3100': '',
 '0020|3401': '',
 '0020|3402': '',
 '0020|3403': '',
 '0020|3404': '',
 '0020|3405': '',
 '0020|3406': '',
 '0020|5000': '',
 '0020|5002': '',
 '0028|0002': '1',
 '0028|0004': 'MONOCHROME2 ',
 '0028|0005': '2',
 '0028|0010': '512',
 '0028|0011': '512',
 '0028|0030': '004.843750E-01\\04.843750E-01',
 '0028|0040': 'RECT',
 '0028|0050': '',
 '0028|0100': '16',
 '0028|0101': '12',
 '0028|0102': '11',
 '0028|0103': '0',
 '0028|0200': '32736',
 '0028|1050': '000070\\-0700',
 '0028|1051': '000422\\02000',
 '0028|1052': '-01.024000E+03',
 '0028|1053': '001.000000E+00',
 'origin': array([-836., -144., -122.]),
 'spacing': array([1.      , 0.484375, 0.484375]),
 'direction': array([[1., 0., 0.],
        [0., 1., 0.],
        [0., 0., 1.]])}

For non-string keys, they are passed to the NumPy array view so array views can be set and get with NumPy indexing syntax, e.g.

In [6]: image[0,:2,4] = [5,5]

In [7]: image[0,:4,4:6]
Out[7]:
NDArrayITKBase([[    5,  -997],
                [    5, -1003],
                [ -993,  -999],
                [ -996,  -994]], dtype=int16)

NumPy 1.15 or later is required to support the axis=None argument to
np.flip.

[aylward]

Outstanding! Nicely done!

[Leengit]

Perhaps assert that origin, spacing, and direction are not supplied by meta_keys = self.GetMetaDataDictionary().GetKeys(). If they were, their values there would get hidden, which would be hard to debug.

[thewtex]

Worth considering, but for simplicity, origin, spacing, direction keys also in the MetaDataDictionary should not be a valid, supported state. We do not want duplication, and the Origin, Spacing, and Direction ivars should be used for these.