postprocessing.json #17

zhangjin506 · 2021-09-28T06:56:49Z

(nnFormer) toolman@modeling506:~/Heart_model/zhang/nnFormer/nnformer$ nnFormer_predict -i ../DATASET/nnFormer_raw/nnFormer_raw_data/Task001_ACDC/imagesTs -o ../DATASET/nnFormer_raw/nnFormer_raw_data/Task001_ACDC/inferTs/output -m 3d_fullres -f 0 -t 1 -chk model_best -tr nnFormerTrainerV2_ACDC
using model stored in /home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1
This model expects 1 input modalities for each image
Found 40 unique case ids, here are some examples: ['patient009_frame13_0000' 'patient095_frame12_0000'
'patient079_frame01_0000' 'patient053_frame12_0000'
'patient081_frame07_0000' 'patient081_frame07_0000'
'patient009_frame13_0000' 'patient064_frame12_0000'
'patient088_frame01_0000' 'patient003_frame15_0000']
If they don't look right, make sure to double check your filenames. They must end with _0000.nii.gz etc
number of cases: 40
number of cases that still need to be predicted: 0
emptying cuda cache
loading parameters for folds, [0]
2021-09-28 14:03:56.302944: Using dummy2d data augmentation
I am using the pre_train weight!!
using the following model files: ['/home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1/fold_0/model_best.model']
starting preprocessing generator
starting prediction...
inference done. Now waiting for the segmentation export to finish...
WARNING! Cannot run postprocessing because the postprocessing file is missing. Make sure to run consolidate_folds in the output folder of the model first!
The folder you need to run this in is /home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1

请问一下，为什么会出现上面问题？是缺少postprocessing.json文件还是我少了步骤？

282857341 · 2021-09-28T15:42:28Z

不影响，出现这个提示是正常的，我们并没有用到后处理。

zhangjin506 · 2021-09-29T06:33:42Z

您好，但是我最后得到的dice系数结果如下：

Mean_Dice
Dice_rv nan
Dice_myo nan
Dice_lv nan

DSC:nan

我之前执行的时候，提示找不到plans.pkl文件，于是我把nnFormerPlansv2.1_ACDC_plans_3D.pkl(这是 3 Generating plan files of our network的结果)改成了plans.pkl，不知道这样对不对？

282857341 · 2021-09-29T06:41:25Z

你好，请问是具体执行哪一步命令提示找不到plans.pkl文件的呢？

训练的时候需要读取nnFormerPlansv2.1_ACDC_plans_3D.pkl，如果更改了这个文件的名称，训练就会报错

zhangjin506 · 2021-09-29T06:45:15Z

在执行inference时

…

------------------ Original ------------------ From: jsguo ***@***.***> Date: Wed,Sep 29,2021 2:41 PM To: 282857341/nnFormer ***@***.***> Cc: zhangjin506 ***@***.***>, Author ***@***.***> Subject: Re: [282857341/nnFormer] postprocessing.json (#17) 你好，请问是具体执行哪一步命令提示找不到plans.pkl文件的呢？训练的时候需要读取nnFormerPlansv2.1_ACDC_plans_3D.pkl，如果更改了这个文件的名称，训练就会报错 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

282857341 · 2021-09-29T07:08:58Z

根据你推理的信息，你应该已经完成了40个case的推理，只需要运行inference.py计算dice。
计算dice得到nan的结果，应该是对空的list做了平均，你可以检查一下test()这个函数的for循环

zhangjin506 · 2021-09-29T08:11:11Z

您好，不好意思，我在目录里面去搜索了test()函数，但是没有找到，这个函数是在某一个.py 文件里么？还有一个问题是plans.pkl这个文件是怎么得到的？真的太麻烦您了

…

------------------ Original ------------------ From: jsguo ***@***.***> Date: Wed,Sep 29,2021 3:09 PM To: 282857341/nnFormer ***@***.***> Cc: zhangjin506 ***@***.***>, Author ***@***.***> Subject: Re: [282857341/nnFormer] postprocessing.json (#17) 根据你推理的信息，你应该已经完成了40个case的推理，只需要运行inference.py计算dice。计算dice得到nan的结果，应该是对空的list做了平均，你可以检查一下test()这个函数的for循环 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

wuliwan · 2021-09-29T10:49:18Z

我想问一下那个运行完nnFormer_predict -i....之后只生成了plans.pkl，没有nii.gz文件但计算DICE时需要，是我哪一步出现问题了嘛？

zhangjin506 · 2021-09-29T10:52:51Z

plans.pkl你是这一步之后生成的么？我那个上面提示好像是执行这一步需要这个文件…我们可以加个好友讨论讨论

…

------------------ Original ------------------ From: wuliwan ***@***.***> Date: Wed,Sep 29,2021 6:49 PM To: 282857341/nnFormer ***@***.***> Cc: zhangjin506 ***@***.***>, Author ***@***.***> Subject: Re: [282857341/nnFormer] postprocessing.json (#17) 我想问一下那个运行完nnFormer_predict -i....之后只生成了plans.pkl，没有nii.gz文件但计算DICE时需要，是我哪一步出现问题了嘛？ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

282857341 · 2021-09-29T11:08:52Z

也有可能完成了推理，但是保存的文件目录位置错了，因为我在指令和inference.py里使用的是相对路径
我看楼主运行nnFormer_predict 后有如下的结果
number of cases: 40
number of cases that still need to be predicted: 0
程序会检查目标文件夹还有多少个case需要被预测，这里number of cases that still need to be predicted=0说明目标文件夹40个case推理已经推理完了

至于plans.pkl这个文件是在nnFormer_predict这个指令后自动生成的

wuliwan · 2021-09-30T03:33:42Z

plans.pkl你是这一步之后生成的么？我那个上面提示好像是执行这一步需要这个文件…我们可以加个好友讨论讨论
…
------------------ Original ------------------ From: wuliwan @.> Date: Wed,Sep 29,2021 6:49 PM To: 282857341/nnFormer @.> Cc: zhangjin506 @.>, Author @.> Subject: Re: [282857341/nnFormer] postprocessing.json (#17) 我想问一下那个运行完nnFormer_predict -i....之后只生成了plans.pkl，没有nii.gz文件但计算DICE时需要，是我哪一步出现问题了嘛？ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

好啊我q:1256281294

wuliwan · 2021-09-30T05:32:05Z

也有可能完成了推理，但是保存的文件目录位置错了，因为我在指令和inference.py里使用的是相对路径我看楼主运行nnFormer_predict 后有如下的结果 number of cases: 40 number of cases that still need to be predicted: 0 程序会检查目标文件夹还有多少个case需要被预测，这里number of cases that still need to be predicted=0说明目标文件夹40个case推理已经推理完了

至于plans.pkl这个文件是在nnFormer_predict这个指令后自动生成的

我的是number of cases that still need to be predicted: 28 没有进行推理是什么原因呢

282857341 · 2021-09-30T05:49:08Z

也有可能完成了推理，但是保存的文件目录位置错了，因为我在指令和inference.py里使用的是相对路径我看楼主运行nnFormer_predict 后有如下的结果 number of cases: 40 number of cases that still need to be predicted: 0 程序会检查目标文件夹还有多少个case需要被预测，这里number of cases that still need to be predicted=0说明目标文件夹40个case推理已经推理完了
至于plans.pkl这个文件是在nnFormer_predict这个指令后自动生成的

我的是number of cases that still need to be predicted: 28 没有进行推理是什么原因呢

没有进行推理说明程序在哪卡住了，而nnunet的框架即使推理卡住了也不会报错。

请问是对synapse或是acdc的数据进行推理吗？因为如果对这两个数据进行推理number of cases that still need to be predicted这个数字应该是12和40。如果是对其他数据进行推理，请严格按照数据放置的格式要求。

wuliwan · 2021-09-30T09:04:56Z

也有可能完成了推理，但是保存的文件目录位置错了，因为我在指令和inference.py里使用的是相对路径我看楼主运行nnFormer_predict 后有如下的结果 number of cases: 40 number of cases that still need to be predicted: 0 程序会检查目标文件夹还有多少个case需要被预测，这里number of cases that still need to be predicted=0说明目标文件夹40个case推理已经推理完了
至于plans.pkl这个文件是在nnFormer_predict这个指令后自动生成的

我的是number of cases that still need to be predicted: 28 没有进行推理是什么原因呢

没有进行推理说明程序在哪卡住了，而nnunet的框架即使推理卡住了也不会报错。

请问是对synapse或是acdc的数据进行推理吗？因为如果对这两个数据进行推理number of cases that still need to be predicted这个数字应该是12和40。如果是对其他数据进行推理，请严格按照数据放置的格式要求。

是其他数据，后来发现是我可能用windows跑然后只能将进程设为0，遍历进程的时候没有读取到好像，不知如何解决

zhangjin506 · 2021-10-09T05:15:48Z

你好，最近我重新试了一下，没有更改之前的文件名，但是又出现了之前说的问题，就是找不到plans.pkl
问题如下：
(nnFormer) toolman@modeling506:~/Heart_model/zhang/nnFormer/nnformer$ nnFormer_predict -i ../DATASET/nnFormer_raw/nnFormer_raw_data/Task001_ACDC/imagesTs -o ../DATASET/nnFormer_raw/nnFormer_raw_data/Task001_ACDC/inferTs/output -m 3d_fullres -f 0 -t 1 -chk model_best -tr nnFormerTrainerV2_ACDC
using model stored in /home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1
Traceback (most recent call last):
File "/home/toolman/anaconda3/envs/nnFormer/bin/nnFormer_predict", line 33, in
sys.exit(load_entry_point('nnformer', 'console_scripts', 'nnFormer_predict')())
File "/home/toolman/Heart_model/zhang/nnFormer/nnformer/inference/predict_simple.py", line 221, in main
step_size=step_size, checkpoint_name=args.chk)
File "/home/toolman/Heart_model/zhang/nnFormer/nnformer/inference/predict.py", line 603, in predict_from_folder
shutil.copy(join(model, 'plans.pkl'), output_folder)
File "/home/toolman/anaconda3/envs/nnFormer/lib/python3.6/shutil.py", line 245, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/home/toolman/anaconda3/envs/nnFormer/lib/python3.6/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1/plans.pkl'

282857341 · 2021-10-09T11:27:17Z

你好，最近我重新试了一下，没有更改之前的文件名，但是又出现了之前说的问题，就是找不到plans.pkl 问题如下： (nnFormer) toolman@modeling506:~/Heart_model/zhang/nnFormer/nnformer$ nnFormer_predict -i ../DATASET/nnFormer_raw/nnFormer_raw_data/Task001_ACDC/imagesTs -o ../DATASET/nnFormer_raw/nnFormer_raw_data/Task001_ACDC/inferTs/output -m 3d_fullres -f 0 -t 1 -chk model_best -tr nnFormerTrainerV2_ACDC using model stored in /home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1 Traceback (most recent call last): File "/home/toolman/anaconda3/envs/nnFormer/bin/nnFormer_predict", line 33, in sys.exit(load_entry_point('nnformer', 'console_scripts', 'nnFormer_predict')()) File "/home/toolman/Heart_model/zhang/nnFormer/nnformer/inference/predict_simple.py", line 221, in main step_size=step_size, checkpoint_name=args.chk) File "/home/toolman/Heart_model/zhang/nnFormer/nnformer/inference/predict.py", line 603, in predict_from_folder shutil.copy(join(model, 'plans.pkl'), output_folder) File "/home/toolman/anaconda3/envs/nnFormer/lib/python3.6/shutil.py", line 245, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/home/toolman/anaconda3/envs/nnFormer/lib/python3.6/shutil.py", line 120, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: '/home/toolman/Heart_model/zhang/nnFormer/DATASET/nnFormer_trained_models/nnFormer/3d_fullres/Task001_ACDC/nnFormerTrainerV2_ACDC__nnFormerPlansv2.1/plans.pkl'

nnFormer/nnformer/inference/predict_simple.py

Lines 217 to 223 in 79f803c

    
           import os 
        
           import shutil 
        
           if not os.path.exists(join(model_folder_name, "plans.pkl")): 
        
               plans_file = join(preprocessing_output_dir, task_name, args.plans_identifier + "_plans_3D.pkl") 
        
               shutil.copy(plans_file, join(model_folder_name, "plans.pkl"))

在文件下补充这些代码，由于我的部分代码已经做了一些修改，所以如果你clone的是今天之前的代码，就将"_plans_3D.pkl"修改为"_ACDC_plans_3D.pkl"

zhangjin506 · 2021-10-09T13:04:37Z

好的，十分感谢🙏

…

------------------ Original ------------------ From: jsguo ***@***.***> Date: Sat,Oct 9,2021 7:27 PM To: 282857341/nnFormer ***@***.***> Cc: zhangjin506 ***@***.***>, Author ***@***.***> Subject: Re: [282857341/nnFormer] postprocessing.json (#17)

282857341 closed this as completed Sep 28, 2021

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postprocessing.json #17

postprocessing.json #17

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postprocessing.json #17

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