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Data Analyzer uses "None" as NoneType for label key#5428

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wyli merged 6 commits intoProject-MONAI:devfrom
mingxin-zheng:fix-5247
Oct 31, 2022
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Data Analyzer uses "None" as NoneType for label key#5428
wyli merged 6 commits intoProject-MONAI:devfrom
mingxin-zheng:fix-5247

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@mingxin-zheng mingxin-zheng commented Oct 28, 2022

Signed-off-by: Mingxin Zheng [email protected]

Fixes #5427 .

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • New tests added to cover the changes.
  • In-line docstrings updated.

@mingxin-zheng mingxin-zheng changed the title Allow Data Analyzer to take label_key is "None" as NoneType Data Analyzer uses "None" as NoneType for label key Oct 28, 2022
@mingxin-zheng mingxin-zheng requested a review from wyli October 28, 2022 14:27
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wyli commented Oct 28, 2022

I still have the issue using this PR, it's from the hard-coded string "label" in this line:

MONAI/monai/apps/auto3dseg/data_analyzer.py

Line 265 in 6e77d57

del d["image"], d["label"]

also this hard-coded ["label"] looks suspicious as well:

MONAI/monai/apps/auto3dseg/data_analyzer.py

Line 223 in 6e77d57

SqueezeDimd(keys=["label"], dim=0) if self.label_key else None,

I think they should be something like self.label_key instead of "label".

log:

python -m monai.apps.auto3dseg  DataAnalyzer get_all_case_stats --dataroot="/Users/Documents/bundles/MedNIST/Hand" --datalist="data_list.yaml" --label_key=None  
File ./data_stats.yaml already exists and will be overwritten.
  0%|                                                                                                                                                        | 0/3 [00:00<?, ?it/s]axcodes ('RAS') length is smaller than the number of input spatial dimensions D=2.
Orientation: input spatial shape is (64, 64), num. channels is 1,please make sure the input is in the channel-first format.
axcodes ('RAS') length is smaller than the number of input spatial dimensions D=2.
Orientation: input spatial shape is (64, 64), num. channels is 1,please make sure the input is in the channel-first format.
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:15<00:00,  5.30s/it]
Traceback (most recent call last):
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/Documents/MONAI/monai/apps/auto3dseg/__main__.py", line 22, in <module>
    fire.Fire(
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/Users/Documents/MONAI/monai/apps/auto3dseg/data_analyzer.py", line 265, in get_all_case_stats
    del d["image"], d["label"]
KeyError: 'label'

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mingxin-zheng commented Oct 31, 2022

I still have the issue using this PR, it's from the hard-coded string "label" in this line:

MONAI/monai/apps/auto3dseg/data_analyzer.py

Line 265 in 6e77d57

del d["image"], d["label"]

also this hard-coded ["label"] looks suspicious as well:

MONAI/monai/apps/auto3dseg/data_analyzer.py

Line 223 in 6e77d57

SqueezeDimd(keys=["label"], dim=0) if self.label_key else None,

I think they should be something like self.label_key instead of "label".

log:

python -m monai.apps.auto3dseg  DataAnalyzer get_all_case_stats --dataroot="/Users/Documents/bundles/MedNIST/Hand" --datalist="data_list.yaml" --label_key=None  
File ./data_stats.yaml already exists and will be overwritten.
  0%|                                                                                                                                                        | 0/3 [00:00<?, ?it/s]axcodes ('RAS') length is smaller than the number of input spatial dimensions D=2.
Orientation: input spatial shape is (64, 64), num. channels is 1,please make sure the input is in the channel-first format.
axcodes ('RAS') length is smaller than the number of input spatial dimensions D=2.
Orientation: input spatial shape is (64, 64), num. channels is 1,please make sure the input is in the channel-first format.
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:15<00:00,  5.30s/it]
Traceback (most recent call last):
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/Documents/MONAI/monai/apps/auto3dseg/__main__.py", line 22, in <module>
    fire.Fire(
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/Users/Documents/MONAI/monai/apps/auto3dseg/data_analyzer.py", line 265, in get_all_case_stats
    del d["image"], d["label"]
KeyError: 'label'

@wyli Since the issue is not caused by the None input as commented in the original ticket, it is obvious that these lines need fixed.

@mingxin-zheng
fix flake8
1b51d1c 
Signed-off-by: Mingxin Zheng <[email protected]>
wyli
wyli approved these changes Oct 31, 2022
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thanks!

@wyli wyli enabled auto-merge (squash) October 31, 2022 11:02
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wyli commented Oct 31, 2022

/build

@wyli wyli disabled auto-merge October 31, 2022 12:32
@wyli wyli enabled auto-merge (squash) October 31, 2022 12:33
@wyli wyli merged commit fe60832 into Project-MONAI:dev Oct 31, 2022
KumoLiu pushed a commit that referenced this pull request Nov 2, 2022
@mingxin-zheng @KumoLiu
Data Analyzer uses "None" as NoneType for label key (#5428)
015f06c 
Signed-off-by: Mingxin Zheng
<[email protected]>

Fixes #5427 .

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [x] In-line docstrings updated.

Signed-off-by: Mingxin Zheng <[email protected]>
Signed-off-by: KumoLiu <[email protected]>
yiheng-wang-nv pushed a commit to yiheng-wang-nv/MONAI that referenced this pull request Nov 2, 2022
@mingxin-zheng @yiheng-wang-nv
Data Analyzer uses "None" as NoneType for label key (Project-MONAI#5428)
4a01d19 
Signed-off-by: Mingxin Zheng
<[email protected]>

Fixes Project-MONAI#5427 .

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [x] In-line docstrings updated.

Signed-off-by: Mingxin Zheng <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
@mingxin-zheng mingxin-zheng deleted the fix-5247 branch December 1, 2022 04:59
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KeyError: 'label' monai/apps/auto3dseg/data_analyzer.py

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