RF - move datatype def and intents back to nifti1 to reduce duplication

nipy · Apr 2, 2011 · 02310a5 · 02310a5
1 parent 2d3eae0
commit 02310a5
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diff --git a/nibabel/gifti/gifti.py b/nibabel/gifti/gifti.py
@@ -16,8 +16,8 @@
 
 import numpy as np
 
-from .util import (data_type_codes, xform_codes, intent_codes,
-                   array_index_order_codes, gifti_encoding_codes,
+from ..nifti1 import data_type_codes, xform_codes, intent_codes
+from .util import (array_index_order_codes, gifti_encoding_codes,
                    gifti_endian_codes, KIND2FMT)
 
 class GiftiMetaData(object):
@@ -286,7 +286,7 @@ def to_xml(self):
         if not self.coordsys is None:
             result += self.coordsys.to_xml()
         # write data array depending on the encoding
-        dt_kind = np.dtype(data_type_codes.type[self.datatype]).kind
+        dt_kind = data_type_codes.dtype[self.datatype].kind
         result += data_tag(self.data,
                            gifti_encoding_codes.specs[self.encoding],
                            KIND2FMT[dt_kind],

diff --git a/nibabel/gifti/parse_gifti_fast.py b/nibabel/gifti/parse_gifti_fast.py
@@ -15,9 +15,9 @@
 
 import numpy as np
 
+from ..nifti1 import data_type_codes, xform_codes, intent_codes
 from . import gifti as gi
-from .util import (data_type_codes, xform_codes, intent_codes,
-                   array_index_order_codes, gifti_encoding_codes,
+from .util import (array_index_order_codes, gifti_encoding_codes,
                    gifti_endian_codes)
 
 

diff --git a/nibabel/gifti/util.py b/nibabel/gifti/util.py
@@ -7,51 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 
-from nibabel.volumeutils import Recoder
-import numpy as np
-
-xform_codes = Recoder(( # code, label
-    (0, 'unknown', "NIFTI_XFORM_UNKNOWN"), # Code for transform unknown or absent
-    (1, 'scanner', "NIFTI_XFORM_SCANNER_ANAT"),
-    (2, 'aligned', "NIFTI_XFORM_ALIGNED_ANAT"),
-    (3, 'talairach', "NIFTI_XFORM_TALAIRACH"),
-    (4, 'mni', "NIFTI_XFORM_MNI_152")), fields=('code', 'label', 'niistring'))
-
-try:
-    _float128t = np.float128
-except AttributeError:
-    _float128t = np.void
-try:
-    _complex256t = np.complex256
-except AttributeError:
-    _complex256t = np.void
-
-dtdefs = ( # code, label, dtype definition, niistring, XXX: format for store in txt
-    (0, 'none', np.void, "", ""),
-    (1, 'binary', np.void, "", ""), # 1 bit per voxel, needs thought
-    (2, 'uint8', np.uint8, "NIFTI_TYPE_UINT8", "%i"),
-    (4, 'int16', np.int16, "NIFTI_TYPE_INT16", "%i"),
-    (8, 'int32', np.int32, "NIFTI_TYPE_INT32", "%i"),
-    (16, 'float32', np.float32, "NIFTI_TYPE_FLOAT32", "%10.6f"),
-    (32, 'complex64', np.complex64, "NIFTI_TYPE_COMPLEX64", "%10.6f"), # numpy complex format?
-    (64, 'float64', np.float64, "NIFTI_TYPE_FLOAT64", "%10.6f"),
-    (128, 'RGB', np.dtype([('R','u1'),
-                  ('G', 'u1'),
-                  ('B', 'u1')]), "NIFTI_TYPE_RGB24", ""),
-    (256, 'int8', np.int8, "NIFTI_TYPE_INT8", "%i"),
-    (512, 'uint16', np.uint16, "NIFTI_TYPE_UINT16", "%i"),
-    (768, 'uint32', np.uint32, "NIFTI_TYPE_UINT32", "%i"),
-    (1024,'int64', np.int64, "NIFTI_TYPE_INT64", "%i"),
-    (1280, 'uint64', np.uint64, "NIFTI_TYPE_UINT64", "%i"),
-    (1536, 'float128', _float128t, "NIFTI_TYPE_FLOAT128", "%10.6f"), # Only numpy defined on 64 bit
-    (1792, 'complex128', np.complex128, "NIFTI_TYPE_COMPLEX128", "%10.6f"),
-    (2048, 'complex256', _complex256t, "NIFTI_TYPE_COMPLEX256", "%10.6f"), # 64 bit again
-    (2304, 'RGBA', np.dtype([('R','u1'),
-                    ('G', 'u1'),
-                    ('B', 'u1'),
-                    ('A', 'u1')]), "NIFTI_TYPE_RGBA32", ""),
-    )
-
+from ..volumeutils import Recoder
 
 # Translate dtype.kind char codes to XML text output strings
 KIND2FMT = {
@@ -61,78 +17,20 @@
     'c': '%10.6f',
     'V': ''}
 
-
-# XXX: do i need the extensions provided by volumeutils.make_dt_codes()
-data_type_codes = Recoder( dtdefs,  fields=('code', 'label', 'type', 'niistring', 'fmt') )
-
-
-array_index_order_codes = Recoder((
-    (1, "RowMajorOrder", 'C'),
-    (2, "ColumnMajorOrder", 'F')),
-    fields = ('code', 'label', 'npcode'))
-
-gifti_encoding_codes = Recoder((
-    (0, "undef", "GIFTI_ENCODING_UNDEF", "undef"),
-    (1, "ASCII", "GIFTI_ENCODING_ASCII", "ASCII"),
-    (2, "B64BIN", "GIFTI_ENCODING_B64BIN", "Base64Binary" ),
-    (3, "B64GZ", "GIFTI_ENCODING_B64GZ", "GZipBase64Binary"),
-    (4, "External", "GIFTI_ENCODING_EXTBIN", "ExternalFileBinary")),
-    fields = ('code', 'label', 'giistring', 'specs'))
-
-gifti_endian_codes = Recoder((
-    (0, "GIFTI_ENDIAN_UNDEF", "Undef", "undef"),
-    (1, "GIFTI_ENDIAN_BIG", "BigEndian", "big"),
-    (2, "GIFTI_ENDIAN_LITTLE", "LittleEndian", "little")),
-    fields = ('code', 'giistring', 'specs', 'byteorder'))
-
-intent_codes = Recoder((
-    # code, label, parameters description tuple
-    (0, 'none', (), "NIFTI_INTENT_NONE"),
-    (2, 'correlation',('p1 = DOF',), "NIFTI_INTENT_CORREL"),
-    (3, 't test', ('p1 = DOF',), "NIFTI_INTENT_TTEST"),
-    (4, 'f test', ('p1 = numerator DOF', 'p2 = denominator DOF'), "NIFTI_INTENT_FTEST"),
-    (5, 'z score', (), "NIFTI_INTENT_ZSCORE"),
-    (6, 'chi2', ('p1 = DOF',), "NIFTI_INTENT_CHISQ"),
-    (7, 'beta', ('p1=a', 'p2=b'), "NIFTI_INTENT_BETA"), # two parameter beta distribution
-    (8, 'binomial', ('p1 = number of trials', 'p2 = probability per trial'), "NIFTI_INTENT_BINOM"),
-    # Prob(x) = (p1 choose x) * p2^x * (1-p2)^(p1-x), for x=0,1,...,p1
-    (9, 'gamma', ('p1 = shape, p2 = scale', 2), "NIFTI_INTENT_GAMMA"), # 2 parameter gamma
-    (10, 'poisson', ('p1 = mean',), "NIFTI_INTENT_POISSON"), # Density(x) proportional to
-                                     # x^(p1-1) * exp(-p2*x)
-    (11, 'normal', ('p1 = mean', 'p2 = standard deviation',), "NIFTI_INTENT_NORMAL"),
-    (12, 'non central f test', ('p1 = numerator DOF',
-                                'p2 = denominator DOF',
-                                'p3 = numerator noncentrality parameter',), "NIFTI_INTENT_FTEST_NONC"),
-    (13, 'non central chi2', ('p1 = DOF', 'p2 = noncentrality parameter',), "NIFTI_INTENT_CHISQ_NONC"),
-    (14, 'logistic', ('p1 = location', 'p2 = scale',), "NIFTI_INTENT_LOGISTIC"),
-    (15, 'laplace', ('p1 = location', 'p2 = scale'), "NIFTI_INTENT_LAPLACE"),
-    (16, 'uniform', ('p1 = lower end', 'p2 = upper end'), "NIFTI_INTENT_UNIFORM"),
-    (17, 'non central t test', ('p1 = DOF', 'p2 = noncentrality parameter'), "NIFTI_INTENT_TTEST_NONC"),
-    (18, 'weibull', ('p1 = location', 'p2 = scale, p3 = power'), "NIFTI_INTENT_WEIBULL"),
-    (19, 'chi', ('p1 = DOF',), "NIFTI_INTENT_CHI"),
-    # p1 = 1 = 'half normal' distribution
-    # p1 = 2 = Rayleigh distribution
-    # p1 = 3 = Maxwell-Boltzmann distribution.
-    (20, 'inverse gaussian', ('pi = mu', 'p2 = lambda'), "NIFTI_INTENT_INVGAUSS"),
-    (21, 'extreme value 1', ('p1 = location', 'p2 = scale'), "NIFTI_INTENT_EXTVAL"),
-    (22, 'p value', (), "NIFTI_INTENT_PVAL"),
-    (23, 'log p value', (), "NIFTI_INTENT_LOGPVAL"),
-    (24, 'log10 p value', (), "NIFTI_INTENT_LOG10PVAL"),
-    (1001, 'estimate', (), "NIFTI_INTENT_ESTIMATE"),
-    (1002, 'label', (), "NIFTI_INTENT_LABEL"),
-    (1003, 'neuroname', (), "NIFTI_INTENT_NEURONAME"),
-    (1004, 'general matrix', ('p1 = M', 'p2 = N'), "NIFTI_INTENT_GENMATRIX"),
-    (1005, 'symmetric matrix', ('p1 = M',), "NIFTI_INTENT_SYMMATRIX"),
-    (1006, 'displacement vector', (), "NIFTI_INTENT_DISPVECT"),
-    (1007, 'vector', (), "NIFTI_INTENT_VECTOR"),
-    (1008, 'pointset', (), "NIFTI_INTENT_POINTSET"),
-    (1009, 'triangle', (), "NIFTI_INTENT_TRIANGLE"),
-    (1010, 'quaternion', (), "NIFTI_INTENT_QUATERNION"),
-    (1011, 'dimensionless', (), "NIFTI_INTENT_DIMLESS"),
-    (2001, 'time series', (), "NIFTI_INTENT_TIMESERIES"),
-    (2002, 'node index', (), "NIFTI_INTENT_NODE_INDEX"),
-    (2003, 'rgb vector', (), "NIFTI_INTENT_RGB_VECTOR"),
-    (2004, 'rgba vector', (), "NIFTI_INTENT_RGBA_VECTOR"),
-    (2005, 'shape', (), "NIFTI_INTENT_SHAPE")),
-                       fields=('code', 'label', 'parameters', 'niistring'))
-
+array_index_order_codes = Recoder(((1, "RowMajorOrder", 'C'),
+                                   (2, "ColumnMajorOrder", 'F')),
+                                   fields = ('code', 'label', 'npcode'))
+
+gifti_encoding_codes = Recoder(
+    ((0, "undef", "GIFTI_ENCODING_UNDEF", "undef"),
+     (1, "ASCII", "GIFTI_ENCODING_ASCII", "ASCII"),
+     (2, "B64BIN", "GIFTI_ENCODING_B64BIN", "Base64Binary" ),
+     (3, "B64GZ", "GIFTI_ENCODING_B64GZ", "GZipBase64Binary"),
+     (4, "External", "GIFTI_ENCODING_EXTBIN", "ExternalFileBinary"),
+    ), fields = ('code', 'label', 'giistring', 'specs'))
+
+gifti_endian_codes = Recoder(
+    ((0, "GIFTI_ENDIAN_UNDEF", "Undef", "undef"),
+     (1, "GIFTI_ENDIAN_BIG", "BigEndian", "big"),
+     (2, "GIFTI_ENDIAN_LITTLE", "LittleEndian", "little"),
+    ), fields = ('code', 'giistring', 'specs', 'byteorder'))
diff --git a/nibabel/nifti1.py b/nibabel/nifti1.py
@@ -82,31 +82,45 @@
     _complex256t = np.complex256
 except AttributeError:
     _complex256t = np.void
-_added_dtdefs = ( # code, label, dtype definition
-    (256, 'int8', np.int8),
-    (512, 'uint16', np.uint16),
-    (768, 'uint32', np.uint32),
-    (1024,'int64', np.int64),
-    (1280, 'uint64', np.uint64),
-    (1536, 'float128', _float128t), # Only numpy defined on 64 bit
-    (1792, 'complex128', np.complex128),
-    (2048, 'complex256', _complex256t), # 64 bit again
+
+_dtdefs = ( # code, label, dtype definition, niistring
+    (0, 'none', np.void, ""),
+    (1, 'binary', np.void, ""),
+    (2, 'uint8', np.uint8, "NIFTI_TYPE_UINT8"),
+    (4, 'int16', np.int16, "NIFTI_TYPE_INT16"),
+    (8, 'int32', np.int32, "NIFTI_TYPE_INT32"),
+    (16, 'float32', np.float32, "NIFTI_TYPE_FLOAT32"),
+    (32, 'complex64', np.complex64, "NIFTI_TYPE_COMPLEX64"),
+    (64, 'float64', np.float64, "NIFTI_TYPE_FLOAT64"),
+    (128, 'RGB', np.dtype([('R','u1'),
+                  ('G', 'u1'),
+                  ('B', 'u1')]), "NIFTI_TYPE_RGB24"),
+    (255, 'all', np.void, ''),
+    (256, 'int8', np.int8, "NIFTI_TYPE_INT8"),
+    (512, 'uint16', np.uint16, "NIFTI_TYPE_UINT16"),
+    (768, 'uint32', np.uint32, "NIFTI_TYPE_UINT32"),
+    (1024,'int64', np.int64, "NIFTI_TYPE_INT64"),
+    (1280, 'uint64', np.uint64, "NIFTI_TYPE_UINT64"),
+    (1536, 'float128', _float128t, "NIFTI_TYPE_FLOAT128"),
+    (1792, 'complex128', np.complex128, "NIFTI_TYPE_COMPLEX128"),
+    (2048, 'complex256', _complex256t, "NIFTI_TYPE_COMPLEX256"),
     (2304, 'RGBA', np.dtype([('R','u1'),
                     ('G', 'u1'),
                     ('B', 'u1'),
-                    ('A', 'u1')]))
+                    ('A', 'u1')]), "NIFTI_TYPE_RGBA32"),
     )
 
 # Make full code alias bank, including dtype column
-data_type_codes = make_dt_codes(analyze._dtdefs + _added_dtdefs)
+data_type_codes = make_dt_codes(_dtdefs)
 
 # Transform (qform, sform) codes
-xform_codes = Recoder(( # code, label
-    (0, 'unknown'), # Code for transform unknown or absent
-    (1, 'scanner'),
-    (2, 'aligned'),
-    (3, 'talairach'),
-    (4, 'mni')), fields=('code', 'label'))
+xform_codes = Recoder(( # code, label, niistring
+                       (0, 'unknown', "NIFTI_XFORM_UNKNOWN"),
+                       (1, 'scanner', "NIFTI_XFORM_SCANNER_ANAT"),
+                       (2, 'aligned', "NIFTI_XFORM_ALIGNED_ANAT"),
+                       (3, 'talairach', "NIFTI_XFORM_TALAIRACH"),
+                       (4, 'mni', "NIFTI_XFORM_MNI_152")),
+                      fields=('code', 'label', 'niistring'))
 
 # unit codes
 unit_codes = Recoder(( # code, label
@@ -133,54 +147,88 @@
 
 intent_codes = Recoder((
     # code, label, parameters description tuple
-    (0, 'none', ()),
-    (2, 'correlation',('p1 = DOF',)),
-    (3, 't test', ('p1 = DOF',)),
-    (4, 'f test', ('p1 = numerator DOF', 'p2 = denominator DOF')),
-    (5, 'z score', ()),
-    (6, 'chi2', ('p1 = DOF',)),
-    (7, 'beta', ('p1=a', 'p2=b')), # two parameter beta distribution
-    (8, 'binomial', ('p1 = number of trials', 'p2 = probability per trial')),
+    (0, 'none', (), "NIFTI_INTENT_NONE"),
+    (2, 'correlation',('p1 = DOF',), "NIFTI_INTENT_CORREL"),
+    (3, 't test', ('p1 = DOF',), "NIFTI_INTENT_TTEST"),
+    (4, 'f test',
+     ('p1 = numerator DOF', 'p2 = denominator DOF'),
+     "NIFTI_INTENT_FTEST"),
+    (5, 'z score', (), "NIFTI_INTENT_ZSCORE"),
+    (6, 'chi2', ('p1 = DOF',), "NIFTI_INTENT_CHISQ"),
+    # two parameter beta distribution
+    (7, 'beta',
+     ('p1=a', 'p2=b'),
+     "NIFTI_INTENT_BETA"),
     # Prob(x) = (p1 choose x) * p2^x * (1-p2)^(p1-x), for x=0,1,...,p1
-    (9, 'gamma', ('p1 = shape, p2 = scale', 2)), # 2 parameter gamma
-    (10, 'poisson', ('p1 = mean',)), # Density(x) proportional to
-                                     # x^(p1-1) * exp(-p2*x)
-    (11, 'normal', ('p1 = mean', 'p2 = standard deviation',)),
-    (12, 'non central f test', ('p1 = numerator DOF',
-                                'p2 = denominator DOF',
-                                'p3 = numerator noncentrality parameter',)),
-    (13, 'non central chi2', ('p1 = DOF', 'p2 = noncentrality parameter',)),
-    (14, 'logistic', ('p1 = location', 'p2 = scale',)),
-    (15, 'laplace', ('p1 = location', 'p2 = scale')),
-    (16, 'uniform', ('p1 = lower end', 'p2 = upper end')),
-    (17, 'non central t test', ('p1 = DOF', 'p2 = noncentrality parameter')),
-    (18, 'weibull', ('p1 = location', 'p2 = scale, p3 = power')),
-    (19, 'chi', ('p1 = DOF',)),
+    (8, 'binomial',
+     ('p1 = number of trials', 'p2 = probability per trial'),
+     "NIFTI_INTENT_BINOM"),
+    # 2 parameter gamma
+    # Density(x) proportional to # x^(p1-1) * exp(-p2*x)
+    (9, 'gamma',
+     ('p1 = shape, p2 = scale', 2),
+     "NIFTI_INTENT_GAMMA"),
+    (10, 'poisson',
+     ('p1 = mean',),
+     "NIFTI_INTENT_POISSON"),
+    (11, 'normal',
+     ('p1 = mean', 'p2 = standard deviation',),
+     "NIFTI_INTENT_NORMAL"),
+    (12, 'non central f test',
+     ('p1 = numerator DOF',
+      'p2 = denominator DOF',
+      'p3 = numerator noncentrality parameter',),
+     "NIFTI_INTENT_FTEST_NONC"),
+    (13, 'non central chi2',
+     ('p1 = DOF', 'p2 = noncentrality parameter',), 
+     "NIFTI_INTENT_CHISQ_NONC"),
+    (14, 'logistic',
+     ('p1 = location', 'p2 = scale',),
+     "NIFTI_INTENT_LOGISTIC"),
+    (15, 'laplace',
+     ('p1 = location', 'p2 = scale'),
+     "NIFTI_INTENT_LAPLACE"),
+    (16, 'uniform',
+     ('p1 = lower end', 'p2 = upper end'),
+     "NIFTI_INTENT_UNIFORM"),
+    (17, 'non central t test',
+     ('p1 = DOF', 'p2 = noncentrality parameter'),
+     "NIFTI_INTENT_TTEST_NONC"),
+    (18, 'weibull',
+     ('p1 = location', 'p2 = scale, p3 = power'),
+     "NIFTI_INTENT_WEIBULL"),
     # p1 = 1 = 'half normal' distribution
     # p1 = 2 = Rayleigh distribution
     # p1 = 3 = Maxwell-Boltzmann distribution.
-    (20, 'inverse gaussian', ('pi = mu', 'p2 = lambda')),
-    (21, 'extreme value 1', ('p1 = location', 'p2 = scale')),
-    (22, 'p value', ()),
-    (23, 'log p value', ()),
-    (24, 'log10 p value', ()),
-    (1001, 'estimate', ()),
-    (1002, 'label', ()),
-    (1003, 'neuroname', ()),
-    (1004, 'general matrix', ('p1 = M', 'p2 = N')),
-    (1005, 'symmetric matrix', ('p1 = M',)),
-    (1006, 'displacement vector', ()),
-    (1007, 'vector', ()),
-    (1008, 'poinset', ()),
-    (1009, 'triangle', ()),
-    (1010, 'quaternion', ()),
-    (1011, 'dimensionless', ()),
-    (2001, 'time series', ()),
-    (2002, 'node index', ()),
-    (2003, 'rgb vector', ()),
-    (2004, 'rgba vector', ()),
-    (2005, 'shape', ())),
-                       fields=('code', 'label', 'parameters'))
+    (19, 'chi', ('p1 = DOF',), "NIFTI_INTENT_CHI"),
+    (20, 'inverse gaussian',
+     ('pi = mu', 'p2 = lambda'),
+     "NIFTI_INTENT_INVGAUSS"),
+    (21, 'extreme value 1',
+     ('p1 = location', 'p2 = scale'),
+     "NIFTI_INTENT_EXTVAL"),
+    (22, 'p value', (), "NIFTI_INTENT_PVAL"),
+    (23, 'log p value', (), "NIFTI_INTENT_LOGPVAL"),
+    (24, 'log10 p value', (), "NIFTI_INTENT_LOG10PVAL"),
+    (1001, 'estimate', (), "NIFTI_INTENT_ESTIMATE"),
+    (1002, 'label', (), "NIFTI_INTENT_LABEL"),
+    (1003, 'neuroname', (), "NIFTI_INTENT_NEURONAME"),
+    (1004, 'general matrix',
+     ('p1 = M', 'p2 = N'),
+     "NIFTI_INTENT_GENMATRIX"),
+    (1005, 'symmetric matrix', ('p1 = M',), "NIFTI_INTENT_SYMMATRIX"),
+    (1006, 'displacement vector', (), "NIFTI_INTENT_DISPVECT"),
+    (1007, 'vector', (), "NIFTI_INTENT_VECTOR"),
+    (1008, 'pointset', (), "NIFTI_INTENT_POINTSET"),
+    (1009, 'triangle', (), "NIFTI_INTENT_TRIANGLE"),
+    (1010, 'quaternion', (), "NIFTI_INTENT_QUATERNION"),
+    (1011, 'dimensionless', (), "NIFTI_INTENT_DIMLESS"),
+    (2001, 'time series', (), "NIFTI_INTENT_TIMESERIES"),
+    (2002, 'node index', (), "NIFTI_INTENT_NODE_INDEX"),
+    (2003, 'rgb vector', (), "NIFTI_INTENT_RGB_VECTOR"),
+    (2004, 'rgba vector', (), "NIFTI_INTENT_RGBA_VECTOR"),
+    (2005, 'shape', (), "NIFTI_INTENT_SHAPE")),
+    fields=('code', 'label', 'parameters', 'niistring'))
 
 
 class Nifti1Extension(object):