medpy.io.load.load#

medpy.io.load.load(image)[source]#

Loads the image and returns a ndarray with the image’s pixel content as well as a header object.

The header can, with restrictions, be used to extract additional meta-information about the image (e.g. using the methods in Header). Additionally it serves as meta-data container that can be passes to save when the altered image is saved to the hard drive again. Note that the transfer of meta-data is only possible, and even then not guaranteed, when the source and target image formats are the same.

MedPy relies on SimpleITK, which enables the power of ITK for image loading and saving. The supported image file formats should include at least the following.

Medical formats:

  • ITK MetaImage (.mha/.raw, .mhd)

  • Neuroimaging Informatics Technology Initiative (NIfTI) (.nia, .nii, .nii.gz, .hdr, .img, .img.gz)

  • Analyze (plain, SPM99, SPM2) (.hdr/.img, .img.gz)

  • Digital Imaging and Communications in Medicine (DICOM) (.dcm, .dicom)

  • Digital Imaging and Communications in Medicine (DICOM) series (<directory>/)

  • Nearly Raw Raster Data (Nrrd) (.nrrd, .nhdr)

  • Medical Imaging NetCDF (MINC) (.mnc, .MNC)

  • Guys Image Processing Lab (GIPL) (.gipl, .gipl.gz)

Microscopy formats:

  • Medical Research Council (MRC) (.mrc, .rec)

  • Bio-Rad (.pic, .PIC)

  • LSM (Zeiss) microscopy images (.tif, .TIF, .tiff, .TIFF, .lsm, .LSM)

  • Stimulate / Signal Data (SDT) (.sdt)

Visualization formats:

  • VTK images (.vtk)

Other formats:

  • Portable Network Graphics (PNG) (.png, .PNG)

  • Joint Photographic Experts Group (JPEG) (.jpg, .JPG, .jpeg, .JPEG)

  • Tagged Image File Format (TIFF) (.tif, .TIF, .tiff, .TIFF)

  • Windows bitmap (.bmp, .BMP)

  • Hierarchical Data Format (HDF5) (.h5 , .hdf5 , .he5)

  • MSX-DOS Screen-x (.ge4, .ge5)

For informations about which image formats, dimensionalities and pixel data types your current configuration supports, run python3 tests/support.py > myformats.log.

Further information see https://simpleitk.readthedocs.io .

Parameters:
imagestring

Path to the image to load.

Returns:
image_datandarray

The image data as numpy array with order x,y,z,c.

image_headerHeader

The image metadata as medpy.io.Header.

Raises:
ImageLoadingError

If the image could not be loaded due to some reason.

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