Fix major bug

.gitignore

@@ -13,3 +13,4 @@ docs/jupyter_execute
 twiss.tfs
 .vscode/
 dist/
+issues/

README.md

@@ -3,7 +3,7 @@
 [![ci](https://github.com/ULB-Metronu/georges/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/ULB-Metronu/georges/actions/workflows/master.yml)
 [![documentation](https://github.com/ULB-Metronu/georges/actions/workflows/documentation.yml/badge.svg?branch=master)](https://github.com/ULB-Metronu/georges/actions/workflows/documentation.yml)
 ![Python](docs/_static/python_versions.svg)
-![version](https://img.shields.io/badge/version-2024.1-blue)
+![version](https://img.shields.io/badge/version-2024.2-blue)
 
 [![Bugs](https://sonarcloud.io/api/project_badges/measure?project=ULB-Metronu_georges&metric=bugs)](https://sonarcloud.io/summary/overall?id=ULB-Metronu_georges)
 [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=ULB-Metronu_georges&metric=coverage)](https://sonarcloud.io/summary/overall?id=ULB-Metronu_georges)

docs/index.rst

@@ -66,7 +66,7 @@ Indices and tables
 
 .. |Python version| image:: _static/python_versions.svg
 
-.. |version| image:: https://img.shields.io/badge/version-2023.1-blue
+.. |version| image:: https://img.shields.io/badge/version-2024.2-blue
 
 .. |Bugs| image:: https://sonarcloud.io/api/project_badges/measure?project=ULB-Metronu_georges&metric=bugs
    :target: https://sonarcloud.io/summary/overall?id=ULB-Metronu_georges

georges/manzoni/input.py

@@ -212,6 +212,7 @@ def from_sequence(
 
         input_sequence = list()
         df_sequence = sequence.df.loc[from_element:to_element]
+        # df_sequence = get_cleaned_sequence(df_sequence)
         if "MATERIAL" in df_sequence.columns:
             idx = df_sequence[sequence.df["MATERIAL"].notnull()].index
             for ele in idx:
@@ -222,8 +223,9 @@ def from_sequence(
             element = element.replace({_np.nan: None})
             element_class = getattr(elements, MANZONI_FLAVOR.get(element["CLASS"], element["CLASS"]))
             parameters = list(set(list(element.index.values)).intersection(element_class.PARAMETERS.keys()))
+            params = element[parameters].dropna()  # Remove the None from the parameters.
             input_sequence.append(
-                element_class(name, **element[parameters]),
+                element_class(name, **params),
             )
         element_mapper = {k: v for v, k in enumerate(list(df_sequence.index.values))}
         return cls(sequence=input_sequence, mapper=element_mapper)

pyproject.toml

@@ -30,7 +30,7 @@ exclude = ['docs/**', '.venv/**']
 
 [tool.poetry]
 name = "georges"
-version = "2024.1"
+version = "2024.2"
 description = "Georges' accelerator physics library - Core"
 authors = ["Cédric Hernalsteens <[email protected]>",
            "Robin Tesse <[email protected]>",

tests/test_manzoni_tracking.py

@@ -0,0 +1,99 @@
+import matplotlib.pyplot as plt
+
+import georges
+from georges import ureg as _ureg
+from georges import vis
+from georges.manzoni import Input, observers
+from georges.manzoni.beam import MadXBeam
+
+
+def test_manzoni_tracking():
+    d1 = georges.Element.Drift(
+        NAME="D1",
+        L=2.145 * _ureg.m,
+        APERTYPE="CIRCULAR",
+        APERTURE=[3.645 * _ureg.cm, 3.645 * _ureg.cm],
+    )
+
+    d8 = georges.Element.Drift(
+        NAME="D8",
+        L=0.403 * _ureg.m,
+        APERTYPE="CIRCULAR",
+        APERTURE=[3.645 * _ureg.cm, 3.645 * _ureg.cm],
+    )
+
+    B2G2 = georges.Element.SBend(
+        NAME="B2G2",
+        L=1.492 * _ureg.m,
+        ANGLE=-57 * _ureg.degrees,
+        K1=0 * _ureg.m**-2,
+        HGAP=0.0 * _ureg.m,
+        APERTYPE="RECTANGULAR",
+        APERTURE=[5 * _ureg.cm, 2.8 * _ureg.cm],
+    )
+
+    d9 = georges.Element.Drift(
+        NAME="D9",
+        L=0.684 * _ureg.m,
+        APERTYPE="CIRCULAR",
+        APERTURE=[3.645 * _ureg.cm, 3.645 * _ureg.cm],
+    )
+
+    B3G2 = georges.Element.SBend(
+        NAME="B2G2",
+        L=1.492 * _ureg.m,
+        ANGLE=-90 * _ureg.degrees,
+        K1=0 * _ureg.m**-2,
+        APERTYPE="RECTANGULAR",
+        APERTURE=[5 * _ureg.cm, 2.8 * _ureg.cm],
+        HGAP=0.0315 * _ureg.m,
+        E1=-0.4346 * _ureg.radians,
+        E2=-0.2889 * _ureg.radians,
+        FINT=0.5,
+        FINTX=0.5,
+    )
+
+    d10 = georges.Element.Drift(
+        NAME="D10",
+        L=3.5 * _ureg.m,
+        APERTYPE="CIRCULAR",
+        APERTURE=[3.645 * _ureg.cm, 3.645 * _ureg.cm],
+    )
+
+    sequence = georges.PlacementSequence(name="Sequence")
+    sequence.place(d1, at_entry=0 * _ureg.m)
+    sequence.place_after_last(d8)
+    sequence.place_after_last(B2G2)
+    sequence.place_after_last(d9)
+    sequence.place_after_last(B3G2)
+    sequence.place_after_last(d10)
+
+    kin = georges.Kinematics(250 * _ureg.MeV, particle=georges.particles.Proton, kinetic=True)
+    sequence.metadata.kinematics = kin
+
+    beam = MadXBeam(
+        kinematics=kin,
+        distribution=georges.Distribution.from_twiss_parameters(
+            n=100,
+            x=2.5 * _ureg.mm,
+            y=2.5 * _ureg.mm,
+            emitx=7 * _ureg.mm * _ureg.mradians,
+            emity=7 * _ureg.mm * _ureg.mradians,
+        ).distribution.values,
+    )
+
+    mi = Input.from_sequence(sequence=sequence)
+    mi.freeze()
+    beam_observer_std = mi.track(beam=beam, observers=observers.SigmaObserver())
+    beam_observer_beam = mi.track(beam=beam, observers=observers.BeamObserver(with_input_beams=True))
+    beam_observer_losses = mi.track(beam=beam, observers=observers.LossesObserver())
+
+    fig = plt.figure(figsize=(10, 4))
+    ax = fig.add_subplot(111)
+    manzoni_plot = vis.ManzoniMatplotlibArtist(ax=ax)
+    manzoni_plot.plot_beamline(sequence.df, with_cartouche=True, print_label=True, with_aperture=True)
+    manzoni_plot.tracking(beam_observer_std, plane="both")
+
+    assert beam_observer_std is not None
+    assert beam_observer_beam is not None
+    assert beam_observer_losses is not None