deftest_save2():# A test to ensure that when a file is saved, the affine and the# data agree. This image comes from a NIFTI fileshape = (13,5,7,3) step = np.array([3.45,2.3,4.5,6.93]) cmap = api.AffineTransform.from_start_step('ijkt','xyzt', [1,3,5,0], step) data...
image_output.data[int(coord.x), int(coord.y), int(coord.z)] = int(round(coord.value))ifsymmetry:# image_output_ref = Image(self.image_ref.dim, orientation=self.image_ref.orientation, hdr=self.image_ref.hdr, verbose=self.verbose)image_output_ref = Image(self.image_ref, verbose=self....
I am going to read a nifti image and change the values of the voxels and save the new nifti image similar to the main image but only different voxel values. In other words I want my labels in segmentation image be from 0 to 7 instead of having different numbers. o wrote the code bel...
def save_as_nifti_file(data: np.ndarray, affine: np.ndarray, path: Union[str, Path]) -> None: """Create a Nifti file and save it. Parameters --- data Brain data. affine Affine of the image, usually inherited from an existing image. path Output filename. """ if not isinstance(pa...
I used this puyhon code to convert nifti file to .vtk polydata meshes import itk import vtk input_filename = '/home/nour/Bureau/7ans/244/whatIneed/244seg_pve_2.nii.gz' reader=itk.ImageFileReader[itk.Image[itk.UC,3]].New() reader.SetFileName(input_filename) reader.Update() itkToVt...
使用SimpleITK读取和保存NIfTIDICOM文件实例 image3D.GetOrigin() spacing = image3D.GetSpacing() print("origin:",origin," spacing:",spacing) 读取DICOM单个文件...我就废话不多说了,大家还是直接看代码吧~ /*** 控制台运行程序 输入: 程序名称 读取图像文件名...保存图像文件名 输出:保存另一种类型的...
Nifti1Image(slice_img_np, img_affine) nib.save(nft_img, slice_dir_path + 'FLAIR_' + str(i) + '.nii.gz') if os.path.basename(sf) == '0': slice_img = nib.load(slice_dir_path + 'FLAIR_' + str(i) + '.nii.gz').get_data() / 5 print('DID I GET HERE?') print('...
nImg = nb.Nifti1Image(clustermask,None) nb.save(nImg, os.path.abspath(clusterfile+'_clustermask'+str(x)+'.nii')) cluster2masks(volume_file) dataset_file ='/home/raid3/watanabe/neurosynth/data/dataset.pkl'ifnotos.path.exists(dataset_file): ...
header['descrip'] ='mask image'output_image = nifti1.Nifti1Image(grp_mask.astype(np.uint8), affine=affine, header=header, )save(output_image, output_filename)returngrp_mask >0 开发者ID:bergtholdt,项目名称:nipy,代码行数:60,代码来源:mask.py ...
get_target_class(image_val['dataset_image_id']) f.write('{0}.png,{1}\n'.format(image_id, target_class)) Example 2Source File: nifti_saver.py From MONAI with Apache License 2.0 6 votes def save_batch(self, batch_data: Union[torch.Tensor, np.ndarray], meta_data=None): """ ...