aspect

Author: kevinjohncutler

src/.DS_Store

@@ -2,7 +2,9 @@
 import os
 import multiprocessing
 os.environ['NUMEXPR_MAX_THREADS'] = str(multiprocessing.cpu_count())
-
+# apparently there is another function in numexpr that can detect number of cores too 
+# this might be a reason why loading takes so long 
+# "and can increase import times for NumExpr or packages that import it such as Pandas or PyTables."
 
 # controlled import to prevent MIP print statement 
 # import mip

src/omnipose/__init__.py

@@ -1724,9 +1724,11 @@ def div_rescale(dP,mask,p=1):
         dP *= div
     return dP
 
+from scipy.special import expit
 def sigmoid(x):
     """The sigmoid function."""
-    return 1 / (1 + np.exp(-x))
+    expit(x) # this is the same as 1 / (1 + np.exp(-x))
+    # return 1 / (1 + np.exp(-x))
 
 # def bd_rescale(dP,mask,bd):
 #     dP = dP.copy()

src/omnipose/core.py

@@ -11,6 +11,8 @@
 import torch
 import fastremap
 
+from ncolor import unique_nonzero
+
 def vector_to_arrow(vectors, flip_y: bool = False):
     """
     Convert one or many 2-D vectors (in y,x order) into Unicode arrow glyphs.
@@ -62,16 +64,7 @@ def vector_to_arrow(vectors, flip_y: bool = False):
 
     glyphs = [arrow_map.get(sig, '?') for sig in signs]
     return glyphs[0] if len(glyphs) == 1 else glyphs
-    
-def unique_nonzero(labels):
-    """
-    Get unique nonzero labels
-    """
-    # return np.sort(np.array(list(set(fastremap.unique(labels))-set((0,)))))
-    if np.any(labels):
-        return fastremap.unique(labels[labels > 0])
-    else:
-        return np.array([0])
+
 
 
 def random_int(N, M=None, seed=None):

src/omnipose/misc.py

@@ -86,10 +86,10 @@ def _legend(self, *args, **kwargs):
     _Axes.legend = _legend
 
 
-def figure(nrow=None, ncol=None, **kwargs):
+def figure(nrow=None, ncol=None, aspect=1, **kwargs):
     figsize = kwargs.get('figsize', 2)
     if not isinstance(figsize, (list, tuple, np.ndarray)) and figsize is not None:
-        figsize = (figsize, figsize)
+        figsize = (figsize*aspect, figsize)
 
     kwargs['figsize'] = figsize
     fig = Figure(**kwargs)