DICOM not loading

[JumpLK]

Describe the bug
I'm trying to load some data from the CHAOS challenge : https://zenodo.org/record/3431873#.YEX2o7rPyUk
I got an ITK error while trying to load it but I think that my version is up to date

To Reproduce
Download the dataset from the link above
Run this code (replace root_dir by the folder where you downloaded the data) :

from monai.transforms import LoadImage
import os

root_dir = r'..\datas\data_chaos\\'
CT_dir = root_dir + r'\train\Train_Sets\CT'

train_images_chaos = [os.path.join(CT_dir, x, 'DICOM_anon')  for x in os.listdir(CT_dir)]
data, meta = LoadImage()(train_images_chaos[0] +  "\i0000,0000b.dcm")

Expected behavior
Data should load

Environment

================================
Printing MONAI config...
================================
MONAI version: 0.4.0+127.g380f042
Numpy version: 1.19.2
Pytorch version: 1.7.1
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 380f042dec9c55ba1a5ab241ae6b1a7b3e2b07fb

Optional dependencies:
Pytorch Ignite version: 0.4.2
Nibabel version: 3.2.1
scikit-image version: 0.18.1
Pillow version: 8.1.1
Tensorboard version: 2.4.1
gdown version: 3.12.2
TorchVision version: 0.8.2
ITK version: 5.1.2
tqdm version: 4.56.0
lmdb version: 1.1.1
psutil version: 5.8.0

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies


================================
Printing system config...
================================
System: Windows
Win32 version: ('10', '10.0.18362', 'SP0', 'Multiprocessor Free')
Win32 edition: Core
Platform: Windows-10-10.0.18362-SP0
Processor: Intel64 Family 6 Model 158 Stepping 10, GenuineIntel
Machine: AMD64
Python version: 3.8.8
Process name: python.exe
Command: ['C:\\Users\\Camille\\anaconda3\\envs\\kitware\\python.exe', 'c:\\Users\\Camille\\Desktop\\important\\Kitware\\liver-segmentation\\segmentation\\tmp2.py']
Open files: [popenfile(path='C:\\Program Files\\WindowsApps\\Microsoft.LanguageExperiencePackfr-FR_18362.35.108.0_neutral__8wekyb3d8bbwe\\Windows\\System32\\fr-FR\\kernel32.dll.mui', fd=-1), popenfile(path='C:\\Program Files\\WindowsApps\\Microsoft.LanguageExperiencePackfr-FR_18362.35.108.0_neutral__8wekyb3d8bbwe\\Windows\\System32\\fr-FR\\KernelBase.dll.mui', fd=-1)]
Num physical CPUs: 6
Num logical CPUs: 12
Num usable CPUs: 12
CPU usage (%): [55.9, 22.3, 46.7, 11.4, 36.4, 12.4, 29.5, 25.8, 26.1, 22.5, 30.3, 48.9]
CPU freq. (MHz): 2208
Load avg. in last 1, 5, 15 mins (%): [0.0, 0.0, 0.0]
Disk usage (%): 90.1
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 15.9
Available memory (GB): 8.8
Used memory (GB): 7.0

================================
Printing GPU config...
================================
Num GPUs: 1
Has CUDA: True
CUDA version: 10.2
cuDNN enabled: True
cuDNN version: 7605
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_61', 'sm_70', 'sm_75', 'compute_37']
GPU 0 Name: GeForce GTX 1070 with Max-Q Design
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 16
GPU 0 Total memory (GB): 8.0
GPU 0 Cached memory (GB): 0.0
GPU 0 Allocated memory (GB): 0.0
GPU 0 CUDA capability (maj.min): 6.1

Additional Context
Here is the error message I got :

Traceback (most recent call last):
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\itkTemplate.py", line 336, in __getitem__
    return(self.__template__[tuple(cleanParameters)])
KeyError: (<itkCType signed int>, 3)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\itkTemplate.py", line 340, in __getitem__
    return(self.__template__[tuple(cleanParameters)])
KeyError: (<itkCType signed int>, 3)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "c:\Users\Camille\Desktop\important\Kitware\liver-segmentation\segmentation\tmp2.py", line 9, in <module>
    data, meta = LoadImage()(train_images_chaos[0] +  "\i0000,0000b.dcm")
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\monai\transforms\io\array.py", line 149, in __call__
    img = reader.read(filename)
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\monai\data\image_reader.py", line 191, in read
    img_.append(itk.imread(name, **kwargs_))
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\itkExtras.py", line 645, in imread
    reader = TemplateReaderType.New(**kwargs)
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\itkTemplate.py", line 469, in New
    return self._NewImageReader(itk.ImageFileReader, False, 'FileName', *args, **kwargs)
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\itkTemplate.py", line 579, in _NewImageReader
    ImageType = itk.Image[PixelType, dimension]
  File "C:\Users\Camille\anaconda3\envs\kitware\lib\site-packages\itkTemplate.py", line 342, in __getitem__
    raise TemplateTypeError(self, tuple(cleanParameters))
itkTemplate.TemplateTypeError: itk.Image is not wrapped for input type `itk.SI, int`.

To limit the size of the package, only a limited number of
types are available in ITK Python. To print the supported
types, run the following command in your python environment:

    itk.Image.GetTypes()

Possible solutions:
* If you are an application user:
** Convert your input image into a supported format (see below).
** Contact developer to report the issue.
* If you are an application developer, force input images to be
loaded in a supported pixel type.

    e.g.: instance = itk.Image[itk.RGBPixel[itk.UC], int].New(my_input)

* (Advanced) If you are an application developer, build ITK Python yourself and
turned to `ON` the corresponding CMake option to wrap the pixel type or image
dimension you need. When configuring ITK with CMake, you can set
`ITK_WRAP_${type}` (replace ${type} with appropriate pixel type such as
`double`). If you need to support images with 4 or 5 dimensions, you can add
these dimensions to the list of dimensions in the CMake variable
`ITK_WRAP_IMAGE_DIMS`.

Supported input types:

itk.RGBPixel[itk.UC]
itk.RGBAPixel[itk.UC]
itk.Vector[itk.F,2]
itk.Vector[itk.F,3]
itk.Vector[itk.F,4]
itk.CovariantVector[itk.F,2]
itk.CovariantVector[itk.F,3]
itk.CovariantVector[itk.F,4]
itk.SS
itk.UC
itk.US
itk.F
itk.D
itk.complex[itk.F]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.UL
itk.ULL
itk.B
itk.FixedArray[itk.F,2]
itk.FixedArray[itk.D,2]
itk.Offset[2]
itk.SymmetricSecondRankTensor[itk.D,2]
itk.RGBPixel[itk.UC]
itk.RGBAPixel[itk.UC]
itk.Vector[itk.F,2]
itk.Vector[itk.F,3]
itk.Vector[itk.F,4]
itk.CovariantVector[itk.F,2]
itk.CovariantVector[itk.F,3]
itk.CovariantVector[itk.F,4]
itk.SS
itk.UC
itk.US
itk.F
itk.D
itk.complex[itk.F]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.UL
itk.ULL
itk.B
itk.FixedArray[itk.F,3]
itk.FixedArray[itk.D,3]
itk.Offset[3]
itk.SymmetricSecondRankTensor[itk.D,3]
itk.Vector[itk.F,1]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.Vector[itk.F,1]
itk.CovariantVector[itk.D,2]
itk.CovariantVector[itk.D,3]
itk.CovariantVector[itk.D,4]
itk.CovariantVector[itk.D,2]
itk.CovariantVector[itk.D,3]
itk.CovariantVector[itk.D,4]
itk.NormalBandNode[itk.Image[itk.F,2]]
itk.NormalBandNode[itk.Image[itk.D,2]]
itk.NormalBandNode[itk.Image[itk.F,3]]
itk.NormalBandNode[itk.Image[itk.D,3]]

[Nic-Ma]

Hi @thewtex ,

Could you please help share some comments here?

Thanks in advance.

[thewtex]

Hi @JumpLK , @Nic-Ma ,

KeyError: (<itkCType signed int>, 3)

This means that the IO classes are not wrapped for 32 bit signed integers. These particular files have 32 bit signed integer pixels.

As a workaround, we can add pixel_type=itk.F, fallback_only=True to the itk.imread default kwargs, which will read in the pixels as 32 bit floats (a good default).

This patch will add direct 32 bit signed int IO support in itk-5.2.0.

[JumpLK]

Hi, thank you for the answer !