11
2- class StreamlineFile :
3- @staticmethod
4- def get_magic_number ():
5- raise NotImplementedError ()
2+ from nibabel .streamlines .header import Field
63
7- @staticmethod
8- def is_correct_format (cls , fileobj ):
9- raise NotImplementedError ()
4+ from ..externals .six .moves import zip_longest
5+
6+
7+ class HeaderError (Exception ):
8+ pass
9+
10+
11+ class DataError (Exception ):
12+ pass
13+
14+
15+ class Streamlines (object ):
16+ ''' Class containing information about streamlines.
17+
18+ Streamlines objects have three main properties: ``points``, ``scalars``
19+ and ``properties``. Streamlines objects can be iterate over producing
20+ tuple of ``points``, ``scalars`` and ``properties`` for each streamline.
21+
22+ Parameters
23+ ----------
24+ points : sequence of ndarray of shape (N, 3)
25+ Sequence of T streamlines. One streamline is an ndarray of shape (N, 3)
26+ where N is the number of points in a streamline.
27+
28+ scalars : sequence of ndarray of shape (N, M)
29+ Sequence of T ndarrays of shape (N, M) where T is the number of
30+ streamlines defined by ``points``, N is the number of points
31+ for a particular streamline and M is the number of scalars
32+ associated to each point (excluding the three coordinates).
33+
34+ properties : sequence of ndarray of shape (P,)
35+ Sequence of T ndarrays of shape (P,) where T is the number of
36+ streamlines defined by ``points``, P is the number of properties
37+ associated to each streamlines.
38+
39+ hdr : dict
40+ Header containing meta information about the streamlines. For a list
41+ of common header's fields to use as keys see `nibabel.streamlines.Field`.
42+ '''
43+ def __init__ (self , points = [], scalars = [], properties = [], hdr = {}):
44+ self .hdr = hdr
45+
46+ self .points = points
47+ self .scalars = scalars
48+ self .properties = properties
49+ self .data = lambda : zip_longest (self .points , self .scalars , self .properties , fillvalue = [])
50+
51+ try :
52+ self .length = len (points )
53+ except :
54+ if Field .NB_STREAMLINES in hdr :
55+ self .length = hdr [Field .NB_STREAMLINES ]
56+ else :
57+ raise HeaderError (("Neither parameter 'points' nor 'hdr' contain information about"
58+ " number of streamlines. Use key '{0}' to set the number of "
59+ "streamlines in 'hdr'." ).format (Field .NB_STREAMLINES ))
1060
1161 def get_header (self ):
12- raise NotImplementedError ()
62+ return self .hdr
63+
64+ @property
65+ def points (self ):
66+ return self ._points ()
67+
68+ @points .setter
69+ def points (self , value ):
70+ self ._points = value if callable (value ) else (lambda : value )
71+
72+ @property
73+ def scalars (self ):
74+ return self ._scalars ()
75+
76+ @scalars .setter
77+ def scalars (self , value ):
78+ self ._scalars = value if callable (value ) else lambda : value
79+
80+ @property
81+ def properties (self ):
82+ return self ._properties ()
1383
14- def get_streamlines (self , as_generator = False ):
84+ @properties .setter
85+ def properties (self , value ):
86+ self ._properties = value if callable (value ) else lambda : value
87+
88+ def __iter__ (self ):
89+ return self .data ()
90+
91+ def __len__ (self ):
92+ return self .length
93+
94+
95+ class StreamlinesFile :
96+ ''' Convenience class to encapsulate streamlines file format. '''
97+
98+ @classmethod
99+ def get_magic_number (cls ):
100+ ''' Return streamlines file's magic number. '''
15101 raise NotImplementedError ()
16102
17- def get_scalars (self , as_generator = False ):
103+ @classmethod
104+ def is_correct_format (cls , fileobj ):
105+ ''' Check if the file has the right streamlines file format.
106+
107+ Parameters
108+ ----------
109+ fileobj : string or file-like object
110+ If string, a filename; otherwise an open file-like object
111+ pointing to a streamlines file (and ready to read from the
112+ beginning of the header)
113+
114+ Returns
115+ -------
116+ is_correct_format : boolean
117+ Returns True if `fileobj` is in the right streamlines file format.
118+ '''
18119 raise NotImplementedError ()
19120
20- def get_properties (self , as_generator = False ):
121+ @classmethod
122+ def get_empty_header (cls ):
123+ ''' Return an empty streamlines file's header. '''
21124 raise NotImplementedError ()
22125
23126 @classmethod
24- def load (cls , fileobj ):
127+ def load (cls , fileobj , lazy_load = True ):
128+ ''' Loads streamlines from a file-like object.
129+
130+ Parameters
131+ ----------
132+ fileobj : string or file-like object
133+ If string, a filename; otherwise an open file-like object
134+ pointing to a streamlines file (and ready to read from the
135+ beginning of the header)
136+
137+ lazy_load : boolean
138+ Load streamlines in a lazy manner i.e. they will not be kept
139+ in memory. For postprocessing speed, turn off this option.
140+
141+ Returns
142+ -------
143+ streamlines : Streamlines object
144+ Returns an object containing streamlines' data and header
145+ information. See 'nibabel.Streamlines'.
146+ '''
25147 raise NotImplementedError ()
26148
27- def save (self , filename ):
149+ @classmethod
150+ def save (cls , streamlines , fileobj ):
151+ ''' Saves streamlines to a file-like object.
152+
153+ Parameters
154+ ----------
155+ streamlines : Streamlines object
156+ Object containing streamlines' data and header information.
157+ See 'nibabel.Streamlines'.
158+
159+ fileobj : string or file-like object
160+ If string, a filename; otherwise an open file-like object
161+ opened and ready to write.
162+ '''
28163 raise NotImplementedError ()
29164
30- def __iter__ (self ):
165+ @staticmethod
166+ def pretty_print (streamlines ):
167+ ''' Gets a formatted string contaning header's information
168+ relevant to the streamlines file format.
169+
170+ Parameters
171+ ----------
172+ streamlines : Streamlines object
173+ Object containing streamlines' data and header information.
174+ See 'nibabel.Streamlines'.
175+
176+ Returns
177+ -------
178+ info : string
179+ Header's information relevant to the streamlines file format.
180+ '''
31181 raise NotImplementedError ()
32182
33183
34- class DynamicStreamlineFile (StreamlineFile ):
184+ class DynamicStreamlineFile (StreamlinesFile ):
185+ ''' Convenience class to encapsulate streamlines file format
186+ that supports appending streamlines to an existing file.
187+ '''
188+
35189 def append (self , streamlines ):
36190 raise NotImplementedError ()
37191
38192 def __iadd__ (self , streamlines ):
39- return self .append (streamlines )
193+ return self .append (streamlines )
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