From 64206a26d40ae1d1aaf0787e565e005f5ad8c64c Mon Sep 17 00:00:00 2001
From: Andriy <andre.ixar@gmail.com>
Date: Tue, 23 May 2023 15:59:08 -0400
Subject: [PATCH] fixed a bug in README, added argument type check in
 featurize()

---
 README.md                     | 34 ++++++++++++++++------------------
 src/nyx/python/nyxus/nyxus.py | 15 +++++++++++----
 2 files changed, 27 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index 3e7db3d0..f7538ad5 100644
--- a/README.md
+++ b/README.md
@@ -77,33 +77,31 @@ or a pair of 3D arrays containing 2D intensity and mask images. There is also tw
 from nyxus import Nyxus
 import numpy as np
 
-
 nyx = Nyxus(["*ALL*"])
 
-intens = [
+intens = np.array([
     [[1, 4, 4, 1, 1],
-        [1, 4, 6, 1, 1],
-        [4, 1, 6, 4, 1],
-        [4, 4, 6, 4, 1]],
+     [1, 4, 6, 1, 1],
+     [4, 1, 6, 4, 1],
+     [4, 4, 6, 4, 1]],
                    
     [[1, 4, 4, 1, 1],
-    [1, 1, 6, 1, 1],
-    [1, 1, 3, 1, 1],
-    [4, 4, 6, 1, 1]]
-]
+     [1, 1, 6, 1, 1],
+     [1, 1, 3, 1, 1],
+     [4, 4, 6, 1, 1]]
+])
 
-seg = [
+seg = np.array([
     [[1, 1, 1, 1, 1],
-    [1, 1, 1, 1, 1],
-    [1, 1, 1, 1, 1],
-    [1, 1, 1, 1, 1]],
+     [1, 1, 1, 1, 1],
+     [1, 1, 1, 1, 1],
+     [1, 1, 1, 1, 1]],
                 
     [[1, 1, 1, 1, 1],
-    [1, 1, 1, 1, 1],
-    [0, 1, 1, 1, 1],
-    [1, 1, 1, 1, 1]]
-]
-
+     [1, 1, 1, 1, 1],
+     [0, 1, 1, 1, 1],
+     [1, 1, 1, 1, 1]]
+])
 
 features = nyx.featurize(intens, seg)
 ```
diff --git a/src/nyx/python/nyxus/nyxus.py b/src/nyx/python/nyxus/nyxus.py
index 913a4487..8f6d1832 100644
--- a/src/nyx/python/nyxus/nyxus.py
+++ b/src/nyx/python/nyxus/nyxus.py
@@ -203,8 +203,8 @@ def featurize_directory(
     
     def featurize(
         self,
-        intensity_images: np.array,
-        label_images: np.array,
+        intensity_images: np.ndarray,
+        label_images: np.ndarray,
         intensity_names: list = [],
         label_names: list = []
     ):
@@ -218,9 +218,9 @@ def featurize(
 
         Parameters
         ----------
-        intensity_dir : np.array
+        intensity_images : np.ndarray
             2D image or 3D collection of intensity images.
-        label_images : np.array
+        label_images : np.ndarray
             2D image or 3D collection of label images.
         intensity_names (optional): list
             names for the images in for the DataFrame output. 
@@ -234,6 +234,13 @@ def featurize(
             per image.
         """
         
+        # verify argument types
+        if not isinstance(intensity_images, np.ndarray):
+            raise ValueError("intensity_images parameter must be numpy.ndarray")
+
+        if not isinstance(label_images, np.ndarray):
+            raise ValueError("label_images parameter must be numpy.ndarray")
+        
         # verify dimensions of images are the same
         if(intensity_images.ndim == 2):
             if(label_images.ndim != 2):