gifti¶
GIfTI format IO
giftiio |
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gifti |
Module: gifti.gifti¶
GiftiCoordSystem([dataspace, xformspace, xform]) |
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GiftiDataArray([data]) |
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GiftiImage([meta, labeltable, darrays, version]) |
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GiftiLabel([key, label, red, green, blue, alpha]) |
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GiftiLabelTable() |
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GiftiMetaData([nvpair]) |
A list of GiftiNVPairs in stored in |
GiftiNVPairs([name, value]) |
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data_tag(dataarray, encoding, datatype, ordering) |
Creates the data tag depending on the required encoding |
Module: gifti.giftiio¶
read(filename) |
Load a Gifti image from a file |
write(image, filename) |
Save the current image to a new file |
Module: gifti.parse_gifti_fast¶
Outputter() |
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parse_gifti_file(fname[, buffer_size]) |
Parse gifti file named fname, return image |
read_data_block(encoding, endian, ordering, ...) |
Tries to unzip, decode, parse the funny string data |
Module: gifti.util¶
GiftiDataArray¶
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class
nibabel.gifti.gifti.GiftiDataArray(data=None)¶ Bases:
object-
__init__(data=None)¶
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coordsys¶ alias of
GiftiCoordSystem
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data¶ alias of
ndarray
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datatype¶ alias of
int
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dims¶ alias of
list
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encoding¶ alias of
int
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endian¶ alias of
int
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ext_fname¶ alias of
str
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ext_offset¶ alias of
str
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classmethod
from_array(klass, darray, intent, datatype=None, encoding='GIFTI_ENCODING_B64GZ', endian='little', coordsys=None, ordering='C', meta=None)¶ Creates a new Gifti data array
Parameters: darray : ndarray
NumPy data array
intent : string
NIFTI intent code, see nifti1.intent_codes
datatype : None or string, optional
NIFTI data type codes, see nifti1.data_type_codes If None, the datatype of the NumPy array is taken.
encoding : string, optionaal
Encoding of the data, see util.gifti_encoding_codes; default: GIFTI_ENCODING_B64GZ
endian : string, optional
The Endianness to store the data array. Should correspond to the machine endianness. default: system byteorder
coordsys : GiftiCoordSystem, optional
If None, a identity transformation is taken.
ordering : string, optional
The ordering of the array. see util.array_index_order_codes; default: RowMajorOrder - C ordering
meta : None or dict, optional
A dictionary for metadata information. If None, gives empty dict.
Returns: da : instance of our own class
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get_metadata()¶ Returns metadata as dictionary
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ind_ord¶ alias of
int
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intent¶ alias of
int
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meta¶ alias of
GiftiMetaData
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num_dim¶ alias of
int
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print_summary()¶
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to_xml()¶
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to_xml_close()¶
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to_xml_open()¶
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GiftiImage¶
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class
nibabel.gifti.gifti.GiftiImage(meta=None, labeltable=None, darrays=None, version='1.0')¶ Bases:
object-
__init__(meta=None, labeltable=None, darrays=None, version='1.0')¶
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add_gifti_data_array(dataarr)¶ Adds a data array to the GiftiImage
Parameters: dataarr : GiftiDataArray
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filename¶ alias of
str
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getArraysFromIntent(intent)¶ Returns a a list of GiftiDataArray elements matching the given intent
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get_labeltable()¶
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get_metadata()¶
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numDA¶ alias of
int
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print_summary()¶
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remove_gifti_data_array(ith)¶ Removes the ith data array element from the GiftiImage
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remove_gifti_data_array_by_intent(intent)¶ Removes all the data arrays with the given intent type
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set_labeltable(labeltable)¶ Set the labeltable for this GiftiImage
Parameters: labeltable : GiftiLabelTable
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set_metadata(meta)¶ Set the metadata for this GiftiImage
Parameters: meta : GiftiMetaData Returns: None :
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to_xml()¶ Return XML corresponding to image content
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version¶ alias of
str
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GiftiLabel¶
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class
nibabel.gifti.gifti.GiftiLabel(key=0, label='', red=None, green=None, blue=None, alpha=None)¶ Bases:
object-
__init__(key=0, label='', red=None, green=None, blue=None, alpha=None)¶
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alpha¶ alias of
float
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blue¶ alias of
float
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get_rgba()¶ Returns RGBA as tuple
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green¶ alias of
float
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key¶ alias of
int
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label¶ alias of
str
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red¶ alias of
float
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data_tag¶
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nibabel.gifti.gifti.data_tag(dataarray, encoding, datatype, ordering)¶ Creates the data tag depending on the required encoding
read¶
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nibabel.gifti.giftiio.read(filename)¶ Load a Gifti image from a file
Parameters: filename : string
The Gifti file to open, it has usually ending .gii
Returns: img : GiftiImage
Returns a GiftiImage
write¶
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nibabel.gifti.giftiio.write(image, filename)¶ Save the current image to a new file
Parameters: image : GiftiImage
A GiftiImage instance to store
filename : string
Filename to store the Gifti file to
Returns: None :
Notes
We write all files with utf-8 encoding, and specify this at the top of the XML file with the
encodingattribute.The Gifti spec suggests using the following suffixes to your filename when saving each specific type of data:
- .gii
- Generic GIFTI File
- .coord.gii
- Coordinates
- .func.gii
- Functional
- .label.gii
- Labels
- .rgba.gii
- RGB or RGBA
- .shape.gii
- Shape
- .surf.gii
- Surface
- .tensor.gii
- Tensors
- .time.gii
- Time Series
- .topo.gii
- Topology
The Gifti file is stored in endian convention of the current machine.
Outputter¶
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class
nibabel.gifti.parse_gifti_fast.Outputter¶ Bases:
object-
__init__()¶
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CharacterDataHandler(data)¶ Collect character data chunks pending collation
The parser breaks the data up into chunks of size depending on the buffer_size of the parser. A large bit of character data, with standard parser buffer_size (such as 8K) can easily span many calls to this function. We thus collect the chunks and process them when we hit start or end tags.
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EndElementHandler(name)¶
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StartElementHandler(name, attrs)¶
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flush_chardata()¶ Collate and process collected character data
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initialize()¶ Initialize outputter
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pending_data¶ True if there is character data pending for processing
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parse_gifti_file¶
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nibabel.gifti.parse_gifti_fast.parse_gifti_file(fname, buffer_size=None)¶ Parse gifti file named fname, return image
Parameters: fname : str
filename of gifti file
buffer_size: None or int, optional :
size of read buffer. None gives default of 35000000 unless on python < 2.6, in which case it is read only in the parser. In that case values other than None cause a ValueError on execution
Returns: img : gifti image