From a7e88db4253401348ef6d4e005009f5213169437 Mon Sep 17 00:00:00 2001
From: Artur Glavic <artur.glavic@psi.ch>
Date: Tue, 24 Sep 2024 14:51:27 +0200
Subject: [PATCH] Update test cases and make old datafile work

---
 libeos/file_reader.py       |  7 +++++--
 tests/test_full_analysis.py | 16 ++++++++++++----
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/libeos/file_reader.py b/libeos/file_reader.py
index e7b7dbd..8217533 100644
--- a/libeos/file_reader.py
+++ b/libeos/file_reader.py
@@ -352,11 +352,14 @@ class AmorData:
         self.pixelID_e = np.array(self.hdf['/entry1/Amor/detector/data/event_id'][:], dtype=int)
         self.dataPacket_p = np.array(self.hdf['/entry1/Amor/detector/data/event_index'][:], dtype=np.uint64)
         #self.dataPacketTime_p = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][:], dtype=np.uint64)/1e9
-        self.dataPacketTime_p = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][:], dtype=int)
+        self.dataPacketTime_p = np.array(self.hdf['/entry1/Amor/detector/data/event_time_zero'][:], dtype=float)
         try:
             self.currentTime = np.array(self.hdf['entry1/Amor/detector/proton_current/time'][:], dtype=int)
             self.current = np.array(self.hdf['entry1/Amor/detector/proton_current/value'][:,0], dtype=float)
-            self.monitorType = 'protonCharge'
+            if len(self.current)>0:
+                self.monitorType = 'protonCharge'
+            else:
+                self.monitorType = 'countingTime'
         except(KeyError, IndexError):
             self.monitorType = 'countingTime'
 
diff --git a/tests/test_full_analysis.py b/tests/test_full_analysis.py
index 44a6878..9eff6d0 100644
--- a/tests/test_full_analysis.py
+++ b/tests/test_full_analysis.py
@@ -6,6 +6,8 @@ from libeos import options, reduction, logconfig
 logconfig.setup_logging()
 logconfig.update_loglevel(True, False)
 
+# TODO: add test for new features like proton charge normalization
+
 class FullAmorTest(TestCase):
     @classmethod
     def setUpClass(cls):
@@ -19,7 +21,9 @@ class FullAmorTest(TestCase):
         self.pr.enable()
         self.reader_config = options.ReaderConfig(
                 year=2023,
-                dataPath=os.path.join('..', "test_data"))
+                dataPath=os.path.join('..', "test_data"),
+                raw=(os.path.join('..', "test_data"),)
+                )
 
     def tearDown(self):
         self.pr.disable()
@@ -37,14 +41,16 @@ class FullAmorTest(TestCase):
                 yRange=(11., 41.),
                 lambdaRange=(2., 15.),
                 qzRange=(0.005, 0.30),
-                offSpecular=False,
+                incidentAngle=options.Defaults.incidentAngle,
                 mu=0,
                 nu=0,
                 muOffset=0.0,
                 sampleModel='air | 10 H2O | D2O'
                 )
         reduction_config = options.ReductionConfig(
+                normalisationMethod=options.Defaults.normalisationMethod,
                 qResolution=0.01,
+                qzRange=options.Defaults.qzRange,
                 thetaRange=(-12., 12.),
                 thetaRangeR=(-12., 12.),
                 fileIdentifier=["610"],
@@ -72,19 +78,21 @@ class FullAmorTest(TestCase):
                 yRange=(11., 41.),
                 lambdaRange=(2., 15.),
                 qzRange=(0.005, 0.30),
-                offSpecular=False,
+                incidentAngle=options.Defaults.incidentAngle,
                 mu=0,
                 nu=0,
                 muOffset=0.0
                 )
         reduction_config = options.ReductionConfig(
                 qResolution=0.01,
+                qzRange=options.Defaults.qzRange,
+                normalisationMethod=options.Defaults.normalisationMethod,
                 thetaRange=(-12., 12.),
                 thetaRangeR=(-12., 12.),
                 fileIdentifier=["610", "611", "608,612-613", "609"],
                 scale=[1],
                 normalisationFileIdentifier=["614"],
-                autoscale=(0.005, 0.008)
+                autoscale=(True, True)
                 )
         output_config = options.OutputConfig(
                 outputFormats=["Rqz.ort"],