Hard code np.log1p(10000)

Teichlab · Sep 22, 2023 · 0fbf8d9 · 0fbf8d9
1 parent dd7e6a5
commit 0fbf8d9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/celltypist/classifier.py b/celltypist/classifier.py
@@ -301,7 +301,7 @@ def __init__(self, filename: Union[AnnData,str] = "", model: Union[Model,str] =
  elif isinstance(filename, AnnData) or (isinstance(filename, str) and filename.endswith('.h5ad')):
  self.adata = sc.read(filename) if isinstance(filename, str) else filename
  self.adata.var_names_make_unique()
- if (self.adata.X[:1000].min() < 0) or (self.adata.X[:1000].max() > np.log1p(10000)):
+ if (self.adata.X[:1000].min() < 0) or (self.adata.X[:1000].max() > 9.22):
  logger.info("👀 Invalid expression matrix in `.X`, expect log1p normalized expression to 10000 counts per cell; will try the `.raw` attribute")
  try:
  self.indata = self.adata.raw.X
@@ -310,7 +310,7 @@ def __init__(self, filename: Union[AnnData,str] = "", model: Union[Model,str] =
  except Exception as e:
  raise Exception(
  f"🛑 Fail to use the `.raw` attribute in the input object. {e}")
- if (self.indata[:1000].min() < 0) or (self.indata[:1000].max() > np.log1p(10000)):
+ if (self.indata[:1000].min() < 0) or (self.indata[:1000].max() > 9.22):
  raise ValueError(
  "🛑 Invalid expression matrix in both `.X` and `.raw.X`, expect log1p normalized expression to 10000 counts per cell")
  else: