From c285c15acd9c464324dc70a0fc707c00f7010a99 Mon Sep 17 00:00:00 2001
From: Joost van Griethuysen <j.v.griethuysen@nki.nl>
Date: Wed, 12 Sep 2018 17:53:16 +0200
Subject: [PATCH] BUG: Fix some small bugs in the baseline generation script

---
 tests/add_baseline.py | 18 ++++++++----------
 tests/testUtils.py    | 10 +++++-----
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/tests/add_baseline.py b/tests/add_baseline.py
index 6786e8bc..0a484083 100644
--- a/tests/add_baseline.py
+++ b/tests/add_baseline.py
@@ -40,22 +40,20 @@ def process_testcase(self, test, featureClassName):
 
     featureClass = self.featureClasses[featureClassName](testImage, testMask, **self.testUtils.getSettings())
 
+    featureClass.enableAllFeatures()
+    featureClass.execute()
+
     if "_calculateMatrix" in dir(featureClass):
       cMat = getattr(featureClass, 'P_%s' % featureClassName)
       if cMat is not None:
         numpy.save(os.path.join(self.baselineDir, '%s_%s.npy' % (test, featureClassName)), cMat)
 
-    featureClass.enableAllFeatures()
-    featureClass.calculateFeatures()
-
     imageTypeName = 'original'
 
     # Update versions to reflect which configuration generated the baseline
-    versions = {}
-    versions['general_info_Version'] = generalinfo.GeneralInfo.getVersionValue()
-    versions['general_info_NumpyVersion'] = generalinfo.GeneralInfo.getNumpyVersionValue()
-    versions['general_info_SimpleITKVersion'] = generalinfo.GeneralInfo.getSimpleITKVersionValue()
-    versions['general_info_PyWaveletVersion'] = generalinfo.GeneralInfo.getPyWaveletVersionValue()
+    self.generalInfo = generalinfo.GeneralInfo()
+
+    versions = self.generalInfo.getGeneralInfo()
     self.new_baselines[featureClassName].configuration[test].update(versions)
 
     self.new_baselines[featureClassName].baseline[test] = {'%s_%s_%s' % (imageTypeName, featureClassName, key): val
@@ -70,7 +68,7 @@ def run(self, featureClass=None):
         if newClass not in self.new_baselines:
           self.logger.info('Adding class %s to the baseline', newClass)
           self.new_baselines[newClass] = PyRadiomicsBaseline(newClass)
-          self.new_baselines[newClass].config = config
+          self.new_baselines[newClass].configuration = config
           # add the new baseline to test utils so it's config can be used during processing
           self.testUtils._baseline[newClass] = self.new_baselines[newClass]
 
@@ -85,7 +83,7 @@ def run(self, featureClass=None):
       else:
         # Feature class not yet present in the baseline, generate a new one
         self.new_baselines[featureClass] = PyRadiomicsBaseline(featureClass)
-        self.new_baselines[featureClass].config = config
+        self.new_baselines[featureClass].configuration = config
 
       for test in self.testCases:
         self.process_testcase(test, featureClass)
diff --git a/tests/testUtils.py b/tests/testUtils.py
index 790b1cc1..5875ba30 100644
--- a/tests/testUtils.py
+++ b/tests/testUtils.py
@@ -149,10 +149,10 @@ class or test case is changed, function returns True.
 
       self._featureClassName = className
 
-      # Check if test settings have changed
-      if self._current_config != self._baseline[className].getTestConfig(test):
-        self._current_config = self._baseline[className].getTestConfig(test)
-        self._testCase = None  # forces image to be reloaded (as settings have changed)
+    # Check if test settings have changed
+    if self._current_config != self._baseline[className].getTestConfig(test):
+      self._current_config = self._baseline[className].getTestConfig(test)
+      self._testCase = None  # forces image to be reloaded (as settings have changed)
 
     # Next, set testCase if necessary
     if self._testCase != self._current_config['TestCase']:
@@ -367,7 +367,7 @@ def getBaselineValue(self, test, featureName):
 
   def writeBaselineFile(self, baselineDir):
     baselineFile = os.path.join(baselineDir, 'baseline_%s.csv' % self.cls)
-    testCases = list(self.baseline.keys())
+    testCases = sorted(self.baseline.keys())
     with open(baselineFile, 'wb') as baseline:
       csvWriter = csv.writer(baseline)
       header = ['featureName'] + testCases