Merge pull request #162 from haesleinhuepf/negative_labels

Warn of and display negative labels

Author: haesleinhuepf

docs/label_display.ipynb

@@ -104,7 +104,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 4,
    "id": "814c1423-4e97-444a-b391-d071770b61fb",
    "metadata": {
     "tags": []
@@ -136,7 +136,7 @@
        "                  [2, 3]])"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -149,9 +149,52 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "58966dc1-2eb9-44fb-bdee-c1e78c2c7ab7",
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table>\n",
+       "<tr>\n",
+       "<td>\n",
+       "<img src=\"data:image/png;base64,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\"></img>\n",
+       "</td>\n",
+       "<td style=\"text-align: center; vertical-align: top;\">\n",
+       "\n",
+       "<table>\n",
+       "<tr><td>shape</td><td>(2,&nbsp;2)</td></tr>\n",
+       "<tr><td>dtype</td><td>int32</td></tr>\n",
+       "<tr><td>size</td><td>16.0 B</td></tr>\n",
+       "<tr><td>min</td><td>-3</td></tr><tr><td>max</td><td>4</td></tr><tr><td>n labels</td><td>4</td></tr><tr><td colspan=\"2\" style=\"color:darkred; font-weight:bold\">Negative label values detected!</td></tr>\n",
+       "</table>\n",
+       "\n",
+       "</td>\n",
+       "</tr>\n",
+       "</table>"
+      ],
+      "text/plain": [
+       "StackViewNDArray([[ 4,  1],\n",
+       "                  [ 2, -3]])"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "labels = [[4,1],[2,-3]]\n",
+    "\n",
+    "stackview.insight(labels)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "78c31759-b9f0-4729-beaa-e7381b15fb20",
+   "metadata": {},
    "outputs": [],
    "source": []
   }

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="stackview",
-    version="0.15.3",
+    version="0.15.4",
     author="Robert Haase",
     author_email="[email protected]",
     description="Interactive image stack viewing in jupyter notebooks",

stackview/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.15.3"
+__version__ = "0.15.4"
 
 from ._static_view import jupyter_displayable_output, insight
 from ._utilities import merge_rgb

stackview/_imshow.py

@@ -96,6 +96,9 @@ def imshow(image,
         if max_display_intensity is None:
             max_display_intensity = 65536
 
+        if image.min() < 0:
+            image = np.abs(image)
+
     if plot is None:
         import matplotlib.pyplot as plt
         plt.imshow(image, cmap=colormap, vmin=min_display_intensity, vmax=max_display_intensity, interpolation='nearest',

stackview/_static_view.py

@@ -113,8 +113,9 @@ def _repr_html_(self):
 
                 histogram = _png_to_html(_plt_to_png())
 
+            min_intensity = self.obj.min()
             max_intensity = self.obj.max()
-            min_max = "<tr><td>min</td><td>" + str(self.obj.min()) + "</td></tr>" + \
+            min_max = "<tr><td>min</td><td>" + str(min_intensity) + "</td></tr>" + \
                       "<tr><td>max</td><td>" + str(max_intensity) + "</td></tr>"
 
             if labels:
@@ -126,9 +127,9 @@ def _repr_html_(self):
                 min_max += "<tr><td>n labels</td><td>" + str(num_labels) + "</td></tr>"
                 if max_intensity != num_labels:
                     min_max += "<tr><td colspan=\"2\"><a href=\"https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/20h_segmentation_post_processing/sequential_labeling.html\" style=\"color:darkred; font-weight:bold\">Not sequentially labeled!</a></td></tr>"
-
+                if min_intensity < 0:
+                    min_max += "<tr><td colspan=\"2\" style=\"color:darkred; font-weight:bold\">Negative label values detected!</td></tr>"
         else:
-
             min_max = ""
 
         help_text = ""