Merge branch 'main' of https://gitea.pkm.physik.tu-darmstadt.de/IPKM/python3-damaris

bool("False") is True, so stored False description values were read back
as True. Compare the written text against "True" instead.

src/damaris/experiments/Experiment.py

@@ -13,7 +13,7 @@ class StateSimple(StateBase):
         super(StateSimple, self).__init__()
         if time < 0:
             raise AssertionError("time for state is negative!")
-        self.time = time
+        self.time = float(time)
         self.content = content
 
     def to_xml(self, indent: str = "") -> str:
@@ -191,7 +191,7 @@ class Experiment:
 
         Typically only used in very special cases.
         """
-        self.state_list.append('<state time="%s">\n' % repr(time))
+        self.state_list.append('<state time="%s">\n' % repr(float(time)))
         self.total_time[-1] += time
 
     ## End of *state_start*
@@ -404,10 +404,10 @@ class Experiment:
         The state length is 2 µs. Stabilisation time depends on RF source.
 
         :param float frequency: frequency to set in Hz
-        :param float phase: phase to set
+        :param float phase: phase to set, normalized to the range [0, 360)
         :param int ttls: default=0, additional ttl lines to set (integer)
         """
-        s_content = '<analogout id="0" f="%f" phase="%f"/>' % (frequency, phase)
+        s_content = '<analogout id="0" f="%f" phase="%f"/>' % (frequency, phase % 360)
         if ttls != 0:
             s_content += '<ttlout value="0x%06x"/>' % ttls
         self.state_list.append(StateSimple(2e-6, s_content))
@@ -582,8 +582,9 @@ class Experiment:
         - The state length for this command is 0.5 µs.
         - The stabilization time for the phase change is RF source dependent. A typical value for PTS310 is 2 µs.
         - The phase is relative to the initial phase set at start of the experiment.
+        - Negative phases are normalized to the range [0, 360) before writing the job file.
         """
-        s_content = '<analogout phase="%f" />' % (phase)
+        s_content = '<analogout phase="%f" />' % (phase % 360)
         if ttls!=0:
             s_content += '<ttlout value="%d"/>' % ttls
         self.state_list.append(StateSimple(0.5e-6, s_content))
@@ -680,19 +681,19 @@ class Experiment:
                     value=""
                 elif type(value) is float or isinstance(value, numpy.floating):
                     type_string="Float"
-                    value=repr(value)
+                    value=repr(float(value))
                 elif type(value) is int or isinstance(value, numpy.integer):
                     type_string="Int"
-                    value=repr(value)
+                    value=repr(int(value))
                 elif type(value) is int:
                     type_string="Long"
                     value=repr(value)
                 elif type(value) is complex or isinstance(value, numpy.complexfloating):
                     type_string="Complex"
-                    value=repr(value)
+                    value=repr(complex(value))
                 elif type(value) is bool or isinstance(value, numpy.bool_):
                     type_string="Boolean"
-                    value=repr(value)
+                    value=repr(bool(value))
                 elif type(value) in (str,):
                     type_string="String"
                 else:

src/damaris/gui/DamarisGUI.py

@@ -3945,7 +3945,7 @@ class MonitorWidgets:
             self.measurementresultline = None
         elif self.measurementresultline is not None:
             # clear line plot
-            self.matplot_axes.lines.remove( self.measurementresultline[ 0 ] )
+            self.measurementresultline[ 0 ].remove( )
             self.measurementresultline = None
         if hasattr(self, 'matplot_cursor') and self.matplot_cursor is not None:
             self.matplot_cursor.disconnect_events()
@@ -4205,17 +4205,17 @@ class MonitorWidgets:
 
             # remove lines and error bars
             if self.measurementresultgraph is not None:
-                self.matplot_axes.lines.remove( self.measurementresultgraph[ 0 ] )
+                self.measurementresultgraph[ 0 ].remove( )
                 # remove caps
                 for l in self.measurementresultgraph[ 1 ]:
-                    self.matplot_axes.lines.remove( l )
+                    l.remove( )
                 # and columns
                 for l in self.measurementresultgraph[ 2 ]:
-                    self.matplot_axes.collections.remove( l )
+                    l.remove( )
                 self.measurementresultgraph = None
 
                 if self.measurementresultline is not None:
-                    self.matplot_axes.lines.remove( self.measurementresultline[ 0 ] )
+                    self.measurementresultline[ 0 ].remove( )
                     self.measurementresultline = None
 
             # remove fit overlay lines
@@ -4303,13 +4303,13 @@ class MonitorWidgets:
 
                     # finally decide about x log plot
                     if x_scale == "log10" and xmin > 0:
-                        self.matplot_axes.set_xscale( "log", basex=10.0 )
+                        self.matplot_axes.set_xscale( "log", base=10.0 )
                         self.matplot_axes.fmt_xdata = lambda x: "%g" % x
                     #elif x_scale=="log" and xmin>0:
                     # e scaling implementation not really useful
                     #    self.matplot_axes.set_xscale("log", basex=numpy.e)
                     if y_scale == "log10" and ymin > 0:
-                        self.matplot_axes.set_yscale( "log", basex=10.0 )
+                        self.matplot_axes.set_yscale( "log", base=10.0 )
                         self.matplot_axes.fmt_ydata = lambda x: "%g" % x
 
                     self.__rescale = False

src/damaris/gui/ResultReader.py

@@ -135,7 +135,8 @@ class ResultReader:
                     elif t == "Complex":
                         self.result_description[k]=complex(v)
                     elif t == "Boolean":
-                        self.result_description[k]=bool(v)
+                        # bool("False") would be True, compare the text instead
+                        self.result_description[k]=(v == "True")
                     elif t == "String":
                         self.result_description[k]=v
                     else:
@@ -502,7 +503,8 @@ class ResultReader:
             elif t == "Complex":
                 self.result_description[k]=complex(v)
             elif t == "Boolean":
-                self.result_description[k]=bool(v)
+                # bool("False") would be True, compare the text instead
+                self.result_description[k]=(v == "True")
             elif t == "String":
                 self.result_description[k]=v
             else:

tests/test_Experiment.py

@@ -0,0 +1,75 @@
+import re
+import unittest
+
+from damaris.experiments.Experiment import Experiment
+
+
+def phase_of_state(state):
+    "extracts the phase value from a state's XML content"
+    match = re.search(r'phase="([-0-9.]+)"', state.content)
+    assert match, "no phase in state: %s" % state.content
+    return float(match.group(1))
+
+
+class TestExperimentPhase(unittest.TestCase):
+    def test_set_phase_negative_normalized(self):
+        """Test that set_phase() normalizes negative phases to [0, 360)."""
+        e = Experiment()
+        for degrees, expected in ((-90, 270.0), (-45.5, 314.5),
+                                  (-270, 90.0), (-360, 0.0)):
+            e.set_phase(degrees)
+            self.assertEqual(phase_of_state(e.state_list.list[-1]), expected)
+
+    def test_set_phase_positive_unchanged(self):
+        """Test that set_phase() passes positive phases through unchanged."""
+        e = Experiment()
+        for degrees, expected in ((0, 0.0), (90, 90.0), (270, 270.0),
+                                  (45.5, 45.5)):
+            e.set_phase(degrees)
+            self.assertEqual(phase_of_state(e.state_list.list[-1]), expected)
+
+    def test_set_frequency_negative_phase_normalized(self):
+        """Test that set_frequency() normalizes a negative phase."""
+        e = Experiment()
+        e.set_frequency(85e6, -90)
+        state = e.state_list.list[-1]
+        self.assertEqual(phase_of_state(state), 270.0)
+        self.assertIn('f="85000000.000000"', state.content)
+
+    def test_rf_pulse_negative_phase_normalized(self):
+        """Test that rf_pulse() normalizes a negative pulse phase."""
+        e = Experiment(gating=1e-6, rf_sources=[1], rf_gates=[2])
+        e.rf_pulse(length=1e-6, phase=-90, source=0)
+        self.assertEqual(phase_of_state(e.state_list.list[0]), 270.0)
+
+    def test_numpy_scalars_in_description(self):
+        """Test that description items with numpy scalars (e.g. from lin_range)
+        are written as plain numbers so the result script can parse them again."""
+        import numpy as np
+        from damaris.tools.ranges import lin_range
+        e = Experiment()
+        e.set_description("tau", lin_range(1e-6, 3e-6, 1e-6)[0])
+        e.set_description("n", np.int64(42))
+        xml = e.write_xml_string()
+        items = {key: (typ, text)
+                 for key, typ, text in
+                 re.findall(r'<item key="([^"]+)" type="([^"]+)">([^<]*)</item>', xml)}
+        self.assertEqual(items["tau"][0], "Float")
+        self.assertEqual(items["n"][0], "Int")
+        self.assertEqual(float(items["tau"][1]), 1e-6)
+        self.assertEqual(int(items["n"][1]), 42)
+
+    def test_numpy_scalar_state_times(self):
+        """Test that numpy scalar times do not end up as np.float64(...) in the XML."""
+        import numpy as np
+        e = Experiment()
+        e.wait(np.float64(1e-6))
+        e.state_start(np.float64(2e-6))
+        xml = e.write_xml_string()
+        self.assertNotIn("np.float64", xml)
+        self.assertIn('<state time="1e-06"/>', xml)
+        self.assertIn('<state time="2e-06">', xml)
+
+
+if __name__ == "__main__":
+    unittest.main()