medpy.io.save.save#

medpy.io.save.save(arr, filename, hdr=False, force=True, use_compression=False)[source]#

Save the image arr as filename using information encoded in hdr. The target image format is determined by the filename suffix. If the force parameter is set to true, an already existing image is overwritten silently. Otherwise an error is thrown.

The header (hdr) object is the one returned by load and is used opportunistically, possibly loosing some meta-information.

Generally this function does not guarantee, that metadata other than the image shape and pixel data type are kept.

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:
arrarray_like

The image data with order x,y,z,c.

filenamestring

Where to save the image; path and filename including the image suffix.

hdrobject

The image header containing the metadata.

forcebool

Set to True to overwrite already exiting image silently.

use_compressionbool

Use data compression of the target format supports it.

Raises:
ImageSavingError

If the image could not be saved due to various reasons

On this page