Dear all members in 3d slicer
Describe the bug
[2022-11-22 10:24:37,281] [19036] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last):
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\starlette\routing.py”, line 635, in lifespan
async with self.lifespan_context(app):
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\starlette\routing.py”, line 530, in aenter
await self.router.startup()
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\starlette\routing.py”, line 612, in startup
await handler()
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monailabel\app.py”, line 106, in startup_event
instance = app_instance()
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monailabel\interfaces\utils\app.py”, line 51, in app_instance
app = c(app_dir=app_dir, studies=studies, conf=conf)
File “C:\Users\AA\apps\monaibundle\main.py”, line 90, in init
super().init(
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monailabel\interfaces\app.py”, line 96, in init
self.trainers = self.init_trainers() if settings.MONAI_LABEL_TASKS_TRAIN else {}
File “C:\Users\AA\apps\monaibundle\main.py”, line 116, in init_trainers
t = BundleTrainTask(b, self.conf)
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monailabel\tasks\train\bundle.py”, line 83, in init
self.bundle_config.read_config(self.bundle_config_path)
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\bundle\config_parser.py”, line 300, in read_config
content.update(self.load_config_files(f, **kwargs))
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\bundle\config_parser.py”, line 403, in load_config_files
for k, v in (cls.load_config_file(i, **kwargs)).items():
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\site-packages\monai\bundle\config_parser.py”, line 382, in load_config_file
return json.load(f, **kwargs)
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\json_init.py”, line 293, in load
return loads(fp.read(),
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\json_init.py”, line 346, in loads
return _default_decoder.decode(s)
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\json\decoder.py”, line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File “C:\Users\AA\AppData\Local\Programs\Python\Python39\lib\json\decoder.py”, line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ‘,’ delimiter: line 63 column 43 (char 1947)
[2022-11-22 10:24:37,282] [19036] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.
To Reproduce
Steps to reproduce the behavior:
- ‘in_channel’ value edited 4 into 1 and added 'ensure_channel_first": ture in train.json as following.
“target”: “SegResNet”,
“blocks_down”: [
1,
2,
2,
4
],
“blocks_up”: [
1,
1,
1
],
“init_filters”: 16,
“in_channels”: 1,
“out_channels”: 3,
“dropout_prob”: 0.2
},
“network”: “$@network_def.to(@device)”,
“preprocessing”: {
“target”: “Compose”,
“transforms”: [
{
“target”: “LoadImaged”,
“keys”: “image”,
“ensure_channel_first”: true
},
- ‘in_channel’ value edited 4 into 1 and added 'ensure_channel_first": ture in train.json as following.
edited train.json code>
“target”: “SegResNet”,
“blocks_down”: [
1,
2,
2,
4
],
“blocks_up”: [
1,
1,
1
],
“init_filters”: 16,
“in_channels”: 1,
“out_channels”: 3,
“dropout_prob”: 0.2
},
.
.
.
“train”: {
“preprocessing_transforms”: [
{
“target”: “LoadImaged”,
“keys”: [
“image”,
“label”,
“ensure_channel_first”: true
]
},
- ‘(“inputs”) num_channel’ value edits 4 into 1 train.json as following.
“network_data_format”: {
“inputs”: {
“image”: {
“type”: “image”,
“format”: “magnitude”,
“modality”: “MR”,
“num_channels”: 1,
“spatial_shape”: [
“8n”,
“8n”,
“8*n”
],
Expected behavior
I can expect result when I press ‘run’ button in Auto Segmentation option, after I edited and added inference.json, train.josn and metadata.json.
Screenshots
But I can’t extract brain tumor as following figure.
Environment
Printing MONAI config…
MONAI version: 1.0.1
Numpy version: 1.23.4
Pytorch version: 1.12.1+cu113
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 8271a193229fe4437026185e218d5b06f7c8ce69
MONAI file: C:\Users\TRL 3D\AppData\Local\Programs\Python\Python39\lib\site-packages\monai_init_.py
Optional dependencies:
Pytorch Ignite version: 0.4.10
Nibabel version: 4.0.2
scikit-image version: 0.19.3
Pillow version: 9.3.0
Tensorboard version: 2.10.1
gdown version: 4.5.3
TorchVision version: 0.13.1+cu113
tqdm version: 4.64.1
lmdb version: 1.3.0
psutil version: 5.9.4
pandas version: 1.5.1
einops version: 0.6.0
transformers version: 4.24.0
mlflow version: 2.0.1
pynrrd version: 0.4.3
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’, ‘10.0.22000’, ‘SP0’, ‘Multiprocessor Free’)
Win32 edition: Core
Platform: Windows-10-10.0.22000-SP0
Processor: AMD64 Family 25 Model 80 Stepping 0, AuthenticAMD
Machine: AMD64
Python version: 3.9.13
Process name: python.exe
Command: [‘C:\Users\TRL 3D\AppData\Local\Programs\Python\Python39\python.exe’, ‘-c’, ‘import monai; monai.config.print_debug_info()’]
Open files: [popenfile(path=‘C:\Program Files\WindowsApps\Microsoft.LanguageExperiencePackko-KR_22000.29.134.0_neutral__8wekyb3d8bbwe\Windows\System32\ko-KR\39386f74d1967f5c37a5b4171f81c8f3\kernel32.dll.mui’, fd=-1), popenfile(path=‘C:\Program Files\WindowsApps\Microsoft.LanguageExperiencePackko-KR_22000.29.134.0_neutral__8wekyb3d8bbwe\Windows\System32\ko-KR\fe441ef3ed396a241e46f9f354057863\tzres.dll.mui’, fd=-1), popenfile(path=‘C:\Program Files\WindowsApps\Microsoft.LanguageExperiencePackko-KR_22000.29.134.0_neutral__8wekyb3d8bbwe\Windows\System32\ko-KR\a7c1941e6709c10ab525083b61805316\KernelBase.dll.mui’, fd=-1)]
Num physical CPUs: 8
Num logical CPUs: 16
Num usable CPUs: 16
CPU usage (%): [10.3, 9.4, 6.9, 3.8, 4.4, 0.6, 1.9, 2.2, 6.6, 15.2, 7.8, 3.2, 2.2, 0.9, 6.0, 41.1]
CPU freq. (MHz): 3301
Load avg. in last 1, 5, 15 mins (%): [0.0, 0.0, 0.0]
Disk usage (%): 60.3
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 15.4
Available memory (GB): 7.1
Used memory (GB): 8.3
================================
Printing GPU config…
Num GPUs: 1
Has CUDA: True
CUDA version: 11.3
cuDNN enabled: True
cuDNN version: 8302
Current device: 0
Library compiled for CUDA architectures: [‘sm_37’, ‘sm_50’, ‘sm_60’, ‘sm_61’, ‘sm_70’, ‘sm_75’, ‘sm_80’, ‘sm_86’, ‘compute_37’]
GPU 0 Name: NVIDIA GeForce RTX 3070 Laptop GPU
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 40
GPU 0 Total memory (GB): 8.0
GPU 0 CUDA capability (maj.min): 8.6