Official PyTorch implementation for paper Context Matters: Graph-based Self-supervised Representation Learning for Medical Images

Related tags

Deep Learning Context_Aware_SSL
Overview

Context Matters: Graph-based Self-supervised Representation Learning for Medical Images

Official PyTorch implementation for paper Context Matters: Graph-based Self-supervised Representation Learning for Medical Images, accepted by AAAI 2021.

Li Sun*, Ke Yu* and Kayhan Batmanghelich

Absrtact

Supervised learning method requires a large volume of annotated datasets. Collecting such datasets is time-consuming and expensive. Until now, very few annotated COVID-19 imaging datasets are available. Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learnt embedding to quantify the clinical progression of COVID-19 and show that our method generalizes well to COVID-19 patients from different hospitals. Qualitative results suggest that our model can identify clinically relevant regions in the images.

Bibtex

@misc{sun2020context,
      title={Context Matters: Graph-based Self-supervised Representation Learning for Medical Images}, 
      author={Li Sun and Ke Yu and Kayhan Batmanghelich},
      year={2020},
      eprint={2012.06457},
      archivePrefix={arXiv},
      primaryClass={eess.IV}
}

Requirements

Preprocess Data

Please follow the instructions in ./preprocess/README.md

Training

sh train.sh

The hyperparameter setting can be found in train.sh

Evaluation

python test.py
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Comments
  • NameError: name 'input_csv' is not defined

    NameError: name 'input_csv' is not defined

    Any hints for the following error reporting?

    (r-reticulate) (base) zhangzhhengsMBP:Context_Aware_SSL zhangzhongheng$ python /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py  --atlas_image ./misc/atlas_lung_mask.nii.gz --atlas_patch_loc /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/patch_data_32_6_reg/COPD_Atlas_INSP_BSpline_Iso1mm_patch_loc.npy --lowerThreshold -1024 --upperThreshold 240  --input_csv /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/dataset.csv  --output_dir ./results/processed_patch   --patch_size 32  --step_size 26
Process Process-1:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-2:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-5:
Process Process-4:
Process Process-7:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
Process Process-3:
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
Process Process-15:
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-13:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-16:
Process Process-11:
Process Process-14:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Process Process-12:
Process Process-10:
Process Process-8:
Process Process-6:
Process Process-9:
Traceback (most recent call last):
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
NameError: name 'input_csv' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
(r-reticulate) (base) zhangzhhengsMBP:Context_Aware_SSL zhangzhongheng$ python /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py  --atlas_image /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/COPD_Atlas_INSP_BSpline_Iso1mm.nii.gz  --atlas_patch_loc /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/patch_data_32_6_reg/COPD_Atlas_INSP_BSpline_Iso1mm_patch_loc.npy --lowerThreshold -1024 --upperThreshold 240  --input_csv /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/dataset.csv  --output_dir ./results/processed_patch   --patch_size 32  --step_size 26
Process Process-4:
Process Process-2:
Process Process-3:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Process Process-6:
Process Process-9:
Traceback (most recent call last):
Process Process-13:
Process Process-8:
Process Process-1:
Process Process-10:
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
Process Process-11:
Process Process-14:
Process Process-12:
Process Process-15:
Process Process-5:
NameError: name 'input_csv' is not defined
Process Process-7:
Process Process-16:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
Traceback (most recent call last):
Traceback (most recent call last):
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/ContenTraceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
ts/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/NameError: name 'input_csv' is not defined
Traceback (most recent call last):
python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
NameError: name 'input_csv' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
(r-reticulate) (base) zhangzhhengsMBP:Context_Aware_SSL zhangzhongheng$ python /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py  --atlas_image /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/COPD_Atlas_INSP_BSpline_Iso1mm.nii.gz  --atlas_patch_loc /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/patch_data_32_6_reg/COPD_Atlas_INSP_BSpline_Iso1mm_patch_loc.npy --lowerThreshold -1024 --upperThreshold 240  --input_csv /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/dataset.csv  --output_dir ./results/processed_patch   --patch_size 32  --step_size 26
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 245, in <module>
    main(sys.argv[1:])
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 225, in main
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
(r-reticulate) (base) zhangzhhengsMBP:Context_Aware_SSL zhangzhongheng$ python /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py  --atlas_image /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/COPD_Atlas_INSP_BSpline_Iso1mm.nii.gz  --atlas_patch_loc /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/patch_data_32_6_reg/COPD_Atlas_INSP_BSpline_Iso1mm_patch_loc.npy --lowerThreshold -1024 --upperThreshold 240  --input_csv /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/dataset.csv  --output_dir ./results/processed_patch   --patch_size 32  --step_size 26
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 245, in <module>
    main(sys.argv[1:])
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 225, in main
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
(r-reticulate) (base) zhangzhhengsMBP:Context_Aware_SSL zhangzhongheng$ python /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py  --atlas_image /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/COPD_Atlas_INSP_BSpline_Iso1mm.nii.gz  --atlas_patch_loc /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/patch_data_32_6_reg/COPD_Atlas_INSP_BSpline_Iso1mm_patch_loc.npy --lowerThreshold -1024 --upperThreshold 240  --input_csv /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/dataset.csv  --output_dir ./results/processed_patch   --patch_size 32  --step_size 26
Process Process-1:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
Process Process-6:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
Process Process-11:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/pytProcess Process-2:
hon3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Process Process-7:
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
Process Process-4:
Process Process-15:
Process Process-3:
Process Process-5:
Process Process-8:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Process Process-9:
Traceback (most recent call last):
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
NameError: name 'input_csv_path' is not defined
Process Process-14:
Process Process-12:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.pyProcess Process-16:
Traceback (most recent call last):
Process Process-13:
Traceback (most recent call last):
Traceback (most recent call last):
Process Process-10:
", line 132, in run
    df = pd.read_csv(input_csv_path)
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
NameError: name 'input_csv_path' is not defined
NameError: name 'input_csv_path' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
NameError: name 'input_csv_path' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv_path)
NameError: name 'input_csv_path' is not defined
NameError: name 'input_csv_path' is not defined
NameError: name 'input_csv_path' is not defined
(r-reticulate) (base) zhangzhhengsMBP:Context_Aware_SSL zhangzhongheng$ python /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py  --atlas_image /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/COPD_Atlas_INSP_BSpline_Iso1mm.nii.gz  --atlas_patch_loc /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/patch_data_32_6_reg/COPD_Atlas_INSP_BSpline_Iso1mm_patch_loc.npy --lowerThreshold -1024 --upperThreshold 240  --input_csv /Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/dataset.csv  --output_dir ./results/processed_patch   --patch_size 32  --step_size 26
Process Process-1:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-5:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-4:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multProcess Process-10:
iprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Process Process-8:
Process Process-3:
Process Process-6:
Process Process-7:
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
Process Process-13:
Process Process-2:
Process Process-12:
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
Traceback (most recent call last):
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
Traceback (most recent call last):
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Devel  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
oper/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Process Process-11:
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
Process Process-15:
Process Process-9:
Traceback (most recent call last):
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
NameError: name 'input_csv' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
Process Process-14:
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
Process Process-16:
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/NameError: name 'input_csv' is not defined
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
Traceback (most recent call last):
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
Traceback (most recent call last):
NameError: name 'input_csv' is not defined
Traceback (most recent call last):
Traceback (most recent call last):
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
NameError: name 'input_csv' is not defined
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/zhangzhongheng/Documents/2022/ARDS_CT_radiomics/Context_Aware_SSL/src/preprocess/4_patchify_images.py", line 132, in run
    df = pd.read_csv(input_csv)
NameError: name 'input_csv' is not defined
    opened by zh-zhang1984 0
  • torch_geometric installation

    torch_geometric installation

    Great work! Trying to reproduce your results, and having some difficulty installing torch_geometric with torch1.4 and cuda10.1 Could you share your environment yml file or setup.py with the package versions? Thanks :)

    opened by aleshem 1
Owner
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