mvpa2.misc.plot.lightbox.SpatialImage¶
- class mvpa2.misc.plot.lightbox.SpatialImage(data, affine, header=None, extra=None, file_map=None)¶
Initialize image
The image is a combination of (array, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.
Parameters : data : array-like
image data. It should be some object that retuns an array from np.asanyarray
affine : None or (4,4) array-like
homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.get_affine() also returns None, and the affine as written to disk will depend on the file format.
header : None or mapping or header instance, optional
metadata for this image format
extra : None or mapping, optional
metadata to associate with image that cannot be stored in the metadata of this image type
file_map : mapping, optional
mapping giving file information for this image format
- files_types = (('image', None),)¶
- classmethod filespec_to_file_map(klass, filespec)¶
- classmethod filespec_to_files(klass, filespec)¶
- classmethod from_file_map(klass, file_map)¶
- classmethod from_filename(klass, filename)¶
- classmethod from_files(klass, file_map)¶
- classmethod from_filespec(klass, filespec)¶
- classmethod from_image(klass, img)¶
Class method to create new instance of own class from img
Parameters : img : spatialimage instance
In fact, an object with the API of spatialimage - specifically get_data, get_affine, get_header and extra.
Returns : cimg : spatialimage instance
Image, of our own class
- get_affine()¶
- get_data()¶
- get_data_dtype()¶
- get_filename()¶
Fetch the image filename
Parameters : None :
Returns : fname : None or str
Returns None if there is no filename, or a filename string. If an image may have several filenames assoctiated with it (e.g Analyze .img, .hdr pair) then we return the more characteristic filename (the .img filename in the case of Analyze’)
- get_header()¶
- header_class¶
alias of Header
- classmethod instance_to_filename(klass, img, filename)¶
Save img in our own format, to name implied by filename
This is a class method
Parameters : img : spatialimage instance
In fact, an object with the API of spatialimage - specifically get_data, get_affine, get_header and extra.
filename : str
Filename, implying name to which to save image.
- classmethod load(klass, filename)¶
- classmethod make_file_map(klass, mapping=None)¶
Class method to make files holder for this image type
Parameters : mapping : None or mapping, optional
mapping with keys corresponding to image file types (such as ‘image’, ‘header’ etc, depending on image class) and values that are filenames or file-like. Default is None
Returns : file_map : dict
dict with string keys given by first entry in tuples in sequence klass.files_types, and values of type FileHolder, where FileHolder objects have default values, other than those given by mapping
- set_data_dtype(dtype)¶
- set_filename(filename)¶
Sets the files in the object from a given filename
The different image formats may check whether the filename has an extension characteristic of the format, and raise an error if not.
Parameters : filename : str
If the image format only has one file associated with it, this will be the only filename set into the image .file_map attribute. Otherwise, the image instance will try and guess the other filenames from this given filename.
- shape¶
- to_file_map(file_map=None)¶
- to_filename(filename)¶
Write image to files implied by filename string
Parameters : filename : str
filename to which to save image. We will parse filename with filespec_to_file_map to work out names for image, header etc.
Returns : None :
- to_files(file_map=None)¶
- to_filespec(filename)¶
- update_header()¶
Update header from information in image
