fix the case where there is no scoring data

dfci · Jul 18, 2024 · 4d98033 · 4d98033
1 parent ae04ac2
commit 4d98033
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -40,7 +40,8 @@ RUN pip3 install pandas \
     && pip3 install scikit-image \
     && pip3 install imagecodecs \
     && pip3 install jsonschema \
-    && pip3 install opencv-python-headless
+    && pip3 install opencv-python-headless \
+    && pip3 install pythologist-test-images
 
 ARG user=jupyter_user
 ARG user_id=999

diff --git a/pythologist/reader/formats/inform/frame.py b/pythologist/reader/formats/inform/frame.py
@@ -369,10 +369,11 @@ def _read_data(self,
         #    t_feature_definition.append([_v,'-',0])
         #    t_feature_basics.append([_v,'InForm threshold analysis'])
 
-        for i,r in _thresholds.iterrows():
-            t_feature_definition.append([r['gate_label'],'+',1])
-            t_feature_definition.append([r['gate_label'],'-',0])
-            t_feature_basics.append([r['gate_label'],'InForm threshold analysis'])
+        if score_data_file is not None:
+            for i,r in _thresholds.iterrows():
+                t_feature_definition.append([r['gate_label'],'+',1])
+                t_feature_definition.append([r['gate_label'],'-',0])
+                t_feature_basics.append([r['gate_label'],'InForm threshold analysis'])
 
         features = pd.DataFrame(me_feature_basics+t_feature_basics,columns=['feature_label','feature_description'])
         features.index.name = 'feature_index'

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 
 setup(
   name='pythologist',
-  version='2.1.0',
+  version='2.1.1',
   test_suite='nose2.collector.collector',
   description='inForm PerkinElmer Reader - Python interface to read outputs of the PerkinElmer inForm software;\
     Pythologist-image-utilities: Functions to assist in working with image files;\