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Decompression Bomb Warning & KeyError: 'pixel_x' #9

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Decompression Bomb Warning & KeyError: 'pixel_x'#9

Description

@johnchen99
johnchen99
opened on Aug 30, 2022

Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:

While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:

INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:

Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'

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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
      Skip to content
      Decompression Bomb Warning & KeyError: 'pixel_x' #9
      Open
      Open
      Decompression Bomb Warning & KeyError: 'pixel_x'#9
      Description
      @johnchen99
      johnchen99
      opened on Aug 30, 2022
      Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
      While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
      INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

      and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
      Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
          Skip to content
          Decompression Bomb Warning & KeyError: 'pixel_x' #9
          Open
          Open
          Decompression Bomb Warning & KeyError: 'pixel_x'#9
          Description
          @johnchen99
          johnchen99
          opened on Aug 30, 2022
          Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
          While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
          INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

          and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
          Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
              Skip to content
              Decompression Bomb Warning & KeyError: 'pixel_x' #9
              Open
              Open
              Decompression Bomb Warning & KeyError: 'pixel_x'#9
              Description
              @johnchen99
              johnchen99
              opened on Aug 30, 2022
              Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
              While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
              INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

              and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
              Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
                  Skip to content
                  Decompression Bomb Warning & KeyError: 'pixel_x' #9
                  Open
                  Open
                  Decompression Bomb Warning & KeyError: 'pixel_x'#9
                  Description
                  @johnchen99
                  johnchen99
                  opened on Aug 30, 2022
                  Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
                  While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
                  INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

                  and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
                  Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
                      Skip to content
                      Decompression Bomb Warning & KeyError: 'pixel_x' #9
                      Open
                      Open
                      Decompression Bomb Warning & KeyError: 'pixel_x'#9
                      Description
                      @johnchen99
                      johnchen99
                      opened on Aug 30, 2022
                      Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
                      While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
                      INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

                      and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
                      Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
                          Skip to content
                          Decompression Bomb Warning & KeyError: 'pixel_x' #9
                          Open
                          Open
                          Decompression Bomb Warning & KeyError: 'pixel_x'#9
                          Description
                          @johnchen99
                          johnchen99
                          opened on Aug 30, 2022
                          Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
                          While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
                          INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

                          and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
                          Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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Decompression Bomb Warning & KeyError: 'pixel_x' · Issue #9 · bryanhe/ST-Net · GitHub
                              Skip to content
                              Decompression Bomb Warning & KeyError: 'pixel_x' #9
                              Open
                              Open
                              Decompression Bomb Warning & KeyError: 'pixel_x'#9
                              Description
                              @johnchen99
                              johnchen99
                              opened on Aug 30, 2022
                              Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:
                              While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:
                              INFO [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00, 8.02it/s]
INFO [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO [08/29 09:46:29] Processing 1 / 23: BT23508
INFO [08/29 09:46:29] Processing BT23508 D2...
INFO [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
DecompressionBombWarning,
INFO [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

                              and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:
                              Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'
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