Open johnchen99 opened 2 years ago
have you solved this problem? @johnchen99
I also meet this error, have you solved this problem? @johnchen99 @Rnxh Thanks for your help!
I slove it, just change the file read style, it is a csv file not tsv file.
@Boli-trainee how did you solve it? Can you describe it in details?
Previously, I have solved it by lowering PIL's MAX_IMAGEPIXELS, not sure if it's directly related: /anaconda3/envs/stnet/lib/python3.7/site-packages/PIL_
MAX_IMAGE_PIXELS = 100000000MAX_IMAGE_PIXELS = 100000000
@johnchen99 Hi john, i download in https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=md_ensembl_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit as ensembl.tsv, and i doing command $python3 -m stnet prepare spatial$, do your have same step with me? but My output is not same with your, i hava a ValueError for concatenate.
INFO [05/09 14:27:56] Loading raw data... 0it [00:00, ?it/s] INFO [05/09 14:27:56] Loading raw data took 0.0007731914520263672 seconds. INFO [05/09 14:27:56] Finding list of genes: 1.9788742065429688e-05 INFO [05/09 14:27:56] Preprocessing took 6.723403930664062e-05 seconds INFO [05/09 14:27:56] Computing statistics of dataset 0it [00:00, ?it/s] Traceback (most recent call last): File "/home/bio-3090ti/anaconda3/envs/ST-Net/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/bio-3090ti/anaconda3/envs/ST-Net/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/bio-3090ti/Benz_code/ST-Net/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/bio-3090ti/Benz_code/ST-Net/stnet/main.py", line 15, in main func(args) File "/home/bio-3090ti/Benz_code/ST-Net/stnet/cmd/prepare/spatial.py", line 136, in spatial gene = np.concatenate(gene, 1) ValueError: need at least one array to concatenate
Do you have some advice? Thansk a lot
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: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'