DIR-lab 4DCT dataset #8
Description
I'm trying to load the DIR-lab 4DCT dataset, but I've run into some trouble.
I downloaded the dataset from dir-lab.com, and applied the following pre-processing steps:
-downloaded all 10 data sets.
-renamed *-ssm.img to *_s.img (to silence errors from dirlab.py).
-ran the dirlab.py module on the img files.
-copied the resulting mha directory to /srv/mymachine/hsokooti/Data/DIR-Lab/4DCT/.
However, running RegNet3D.py throws the following error:
[MainThread ] ---------------------------------Fri Nov 9 11:21:44 2018--------------------------------
[MainThread ] ----------------------------------start experiment------------------------------
[MainThread ] number of images in the last chunk=12
[MainThread ] SyntheticDeformation[generation]: start DIR-Lab_4D/3D_max7_D9//T40/case2/Dsmooth0/DNext3/nextIm.mha
[MainThread ] Process Process-1:
[MainThread ] Traceback (most recent call last):
[MainThread ] File "/usr/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
[MainThread ] self.run()
[MainThread ] File "/usr/lib/python3.5/multiprocessing/process.py", line 93, in run
[MainThread ] self._target(*self._args, **self._kwargs)
[MainThread ] File "/home/markemus/dev/RegNet/functions/reading/direct_1st_epoch.py", line 49, in run
[MainThread ] self.fill()
[MainThread ] File "/home/markemus/dev/RegNet/functions/reading/direct_1st_epoch.py", line 85, in fill
[MainThread ] mode_synthetic_dvf='generation'
[MainThread ] File "/home/markemus/dev/RegNet/functions/synthetic_deformation.py", line 63, in get_dvf_and_deformed_images
[MainThread ] generate_next_im(setting, im_info=im_info)
[MainThread ] File "/home/markemus/dev/RegNet/functions/synthetic_deformation.py", line 495, in generate_next_im
[MainThread ] original_im_sitk = sitk.ReadImage(su.address_generator(setting, 'originalIm', **im_info_su))
[MainThread ] File "/home/markemus/.local/lib/python3.5/site-packages/SimpleITK/SimpleITK.py", line 8614, in ReadImage
[MainThread ] return _SimpleITK.ReadImage(*args)
[MainThread ] RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:89:
[MainThread ] sitk::ERROR: The file "/srv/markemus-VirtualBox/hsokooti/Data/DIR-Lab/4DCT/mha/case2/case2_T40_RS1.mha" does not exist.
[MainThread ] total number of variables 1116164
[Thread-4 ] SyntheticDeformation[reading]: waiting 5s for DIR-Lab_4D/3D_max7_D9//T40/case2/Dsmooth0/DNext3/nextIm.mha
Is there an additional/different preprocessing step I need to do? Renaming */case2_T40.mha to */case2_T40_RS1.mha seems to fix this error and creates a nextIm.mha file, but there are more errors after that.