Class NiftiImage

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Parameters:

• source, str, |, ndarray - If source is a string, it is assumed to be a filename and an attempt will be made to open the corresponding NIfTI file. In case of an ndarray the array data will be used for the to be created nifti image and a matching nifti header is generated. If an object of a different type is supplied as 'source' a ValueError exception will be thrown.
• header, dict - Additional header data might be supplied. However, dimensionality and datatype are determined from the ndarray and not taken from a header dictionary.
• load, Boolean - If set to True the image data will be loaded into memory. This is only useful if loading a NIfTI image from file.

Overrides: object.__init__

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Overrides: niftiformat.NiftiFormat.__del__

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Save the image.

If the image was created using array data (not loaded from a file) one has to specify a filename.

Warning: There will be no exception if writing fails for any reason, as the underlying function nifti_write_hdr_img() from libniftiio does not provide any feedback. Suggestions for improvements are appreciated.

If not yet done already, the image data will be loaded into memory before saving the file.

Parameters:

• filename, str, |, None - Calling save() with filename equal None on a NiftiImage loaded from a file, it will overwrite the original file.

  Usually setting the filename also determines the filetype (NIfTI/ANALYZE). Please see the documentation of the setFilename() method for some more details.

• filetype, str - Override filetype. Please see the documentation of the setFilename() method for some more details.

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Load the image data into memory, if it is not already accessible.

It is save to call this method several times successively.

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Unload image data and free allocated memory.

This methods does nothing in case of memory mapped files.

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Return the NIfTI image data wrapped into a NumPy array.

The data property is an alternative way to access this function.

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Parameters:

• copy, Boolean - If set to False the array only wraps the image data, while True will return a copy of the data array.

Returns a scaled copy of the data array.

Scaling is done by multiplying with the slope and adding the intercept that is stored in the NIfTI header.

Returns:

ndarray

Get the bounding box of the image.

This functions returns a tuple of (min, max) tuples. It contains as many tuples as image dimensions. The order of dimensions is identical to that in the data array.

The bbox property is an alternative way to access this function.

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Set the filename for the NIfTI image.

Setting the filename also determines the filetype. If the filename
ends with '.nii' the type will be set to NIfTI single file. A '.hdr'
extension can be used for NIfTI file pairs. If the desired filetype
is ANALYZE the extension should be '.img'. However, one can use the
'.hdr' extension and force the filetype to ANALYZE by setting the
filetype argument to ANALYZE. Setting filetype if the filename
extension is '.nii' has no effect, the file will always be in NIFTI
format.

If the filename carries an additional '.gz' the resulting file(s) will
be compressed.

Uncompressed NIfTI single files are the default filetype that will be
used if the filename has no valid extension. The '.nii' extension is
appended automatically. The 'filetype' argument can be used to force a
certain filetype when no extension can be used to determine it. 
'filetype' can be one of the nifticlibs filtetypes or any of 'NIFTI',
'NIFTI_GZ', 'NIFTI_PAIR', 'NIFTI_PAIR_GZ', 'ANALYZE', 'ANALYZE_GZ'.

Setting the filename will cause the image data to be loaded into memory
if not yet done already. This has to be done, because without the
filename of the original image file there would be no access to the
image data anymore. As a side-effect a simple operation like setting a
filename may take a significant amount of time (e.g. for a large 4d
dataset).

By passing an empty string or none as filename one can reset the
filename and detach the NiftiImage object from any file on disk.

Examples:

  Filename          Output of save()
  ----------------------------------
  exmpl.nii         exmpl.nii (NIfTI)
  exmpl.hdr         exmpl.hdr, exmpl.img (NIfTI)
  exmpl.img         exmpl.hdr, exmpl.img (ANALYZE)
  exmpl             exmpl.nii (NIfTI)
  exmpl.hdr.gz      exmpl.hdr.gz, exmpl.img.gz (NIfTI)

! exmpl.gz          exmpl.gz.nii (uncompressed NIfTI)

Setting the filename is also possible by assigning to the 'filename'
property.

Deprecated method only here for backward compatibility.

Please refer to NiftiFormat.updateFromDict()

data

Return the NIfTI image data wrapped into a NumPy array.

The data property is an alternative way to access this function.

Get Method:

getDataArray(self) - Return the NIfTI image data wrapped into a NumPy array.

bbox

Get the bounding box of the image.

This functions returns a tuple of (min, max) tuples. It contains as many tuples as image dimensions. The order of dimensions is identical to that in the data array.

The bbox property is an alternative way to access this function.

Get Method:

getBoundingBox(self) - Get the bounding box of the image.