![]() ![]() Before you write the image, you can use the setter methods to change the parameters. When using the default settings for the ImageFileReader class or the ReadImage function you have minimal control over the reading. You can write the image to disk using sitk.WriteImage(). You can convert any NumPy array to an ITK image using the GetImageFromArray() function. Each of the Get* methods has a similar Set* method to change the parameter, e.g. Because the names of the methods and parameters in the header file do not match at all, we give a summary of the most important ones below. SimpleITK image objects like itk_image have some methods to get and set these parameters. The MET_DOUBLE type will be converted to the numpy.float64 dtype. ![]() This shows that this chest X-ray is a 2D image, consisting of uncompressed binary data, with 1 mm x 1 mm pixels ( ElementSpacing) and a size of 1024 by 1024. ![]() ObjectType = Image NDims = 2 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 1 Offset = 0 0 CenterOfRotation = 0 0 ElementSpacing = 1 1 DimSize = 1024 1024 ElementType = MET_DOUBLE ElementDataFile = chest_xray. For example, to install the package SimpleITK, use datadirectory directory seriesIDs (datadirectory) if not seriesIDs: print ('ERROR: given directory \'' datadirectory '\' does not contain a DICOM series.') sys. In the Terminal, the Windows Prompt, or the Anaconda Terminal, you can use pip to install packages. First obtain the series file names using the image series reader. Therefore, it is common to read the images and specify their pixel type as sitk.sitkFloat32 or sitk.sitkFloat64. Alternatively, you can open a prompt or terminal from the Anaconda Navigator by clicking on Environments in the left side bar, clicking on the green triangle, and then 'Open Terminal'. This framework only accepts images with float pixel types. You can run pip from a Terminal window (on Linux or macOS) or a Command Prompt or Cygwin window on Windows, provided you have added the Anaconda distribution to your PATH during installation. import SimpleITK as sitk mhd sitk.ReadImage (filename) origin mhd.GetOrigin () spacing mhd.GetSpacing () direction mhd. You can read '.mhd' files using using FileIO img load ( 'myimage.mhd') This package is a work-in-progress, and writing is not yet supported. Installing extra Python packagesĪnaconda comes with the pip package manager. README.md MetaImageFormat This package supports the MetaImage file format for the Julia language. Therefore this chapter will also discuss how to install packages in Python. These packages are not included with the Anaconda installation you In this chapter, a few modules and methods for working with medical images areĭiscussed. You can call EraseMetaData to remove the extraneous/redundant tags. Currently, when MetaImage Reader encounters an ITK tag it results in an exception: net.sf.ijplugins.io.metaimage.MiException: 'ITKFileNotes' is no. With ITK, when an image if filtered the meta-data tags are not propagated, the this issue is not frequently encountered. I’m guessing that the itk::NifTiImageIO reader is trying to do something “smart” with the NifTi tags to preserve them. (sform_code_name) = "NIFTI_XFORM_UNKNOWN" (qform_code_name) = "NIFTI_XFORM_SCANNER_ANAT" I did a test with NifTi and there were quite a lot of NifTi tags: In : import SimpleITK as sitk When you first read an image in ITK, the Image may contain additional meta data tags from the reader. Print('\nGetImageFromArray, written with ITK') Nib.Nifti1Image(array, affine).to_filename(filepath_nib) With gzip.open(image_path, 'rb') as f_in: With NamedTemporaryFile(suffix='.nii') as f: Here’s some code to show what I mean, and the output: import gzip If I read and write and image with SimpleITK, the header is incorrect. When I create an image using GetImageFromArray, the written header is fine. qfac is the first value of the pixdim array in the header and is expected to be -1 or 1. NIfTI docs say that it “should not occur” that qfac is 0. I’m using SimpleITK 1.2.4 to read and write NIfTI images. ![]()
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