Merged in bugfix/plan_prefab_energies (pull request #436)

Bugfix/plan prefab energies Approved-by: Randy Taylor Approved-by: Hasan Ammar
jrkerns · Aug 30, 2024 · fb30659 · fb30659
2 parents 1c93855 + 1da8398
commit fb30659
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diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml
@@ -234,13 +234,14 @@ definitions:
         name: Plan generator tests
         script:
           - source venv/bin/activate
-          - pytest tests_basic/test_plan_generator.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - pytest tests_basic/test_plan_generator.py tests_basic/test_generated_plans.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         condition:
             changesets:
                 includePaths:
                 - "pylinac/core/**"
                 - "pylinac/plan_generator/**"
                 - "tests_basic/test_plan_generator.py"
+                - "scripts/prefab_plan_generator.py"
     - step: &core-module-tests
         name: Run core module tests
         script:

diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -19,6 +19,8 @@ Plan Generator
 * It is now possible to export generated images from the plan generator to DICOM files.
   This can useful for end-to-end testing of workflows before delivering the plan itself on the machine.
   See the new section :ref:`plan_generator_dicom_fluence` for details.
+* Manual names can now be passed for Winston-Lutz beams.
+* The R2 prefabricated plan files have been fixed to have the same energy and dose rate for all beams of a given plan.
 
 Image Generator
 ^^^^^^^^^^^^^^^

diff --git a/docs/source/plan_generator.rst b/docs/source/plan_generator.rst
@@ -197,7 +197,33 @@ If you're too "busy" to generate your own plans, you can use the following gener
   be if you used the plan generator itself. On a Varian machine you will need to
   perform a machine override authorization every time.
 
-These plans contain a picket fence at each cardinal gantry angle, a Winston-Lutz batch, dose rate constancy, MLC speed tests, and gantry speed tests.
+These plans contain the following fields:
+
+* "PF 3mm G0": Picket fence, Gantry 0, 3mm strips, 100 MU
+* "PF 3mm G90": Picket fence, Gantry 90, 3mm strips, 100 MU
+* "PF 3mm G180": Picket fence, Gantry 180, 3mm strips, 100 MU
+* "PF 3mm G270": Picket fence, Gantry 270, 3mm strips, 100 MU
+* "G0C0P0": Winston-Lutz, Gantry 0, Collimator 0, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G90C0P0": Winston-Lutz, Gantry 90, Collimator 0, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G180C0P0": Winston-Lutz, Gantry 180, Collimator 0, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G270C0P0": Winston-Lutz, Gantry 270, Collimator 0, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G0C270P0": Winston-Lutz, Gantry 0, Collimator 270, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G0C90P0": Winston-Lutz, Gantry 0, Collimator 90, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G0C315P0": Winston-Lutz, Gantry 0, Collimator 315, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G0C45P0": Winston-Lutz, Gantry 0, Collimator 45, Couch 0, 2x2cm, 5 MU, MLC-defined
+* "G0C0P45": Winston-Lutz, Gantry 0, Collimator 0, Couch 45, 2x2cm, 5 MU, MLC-defined
+* "G0C0P90": Winston-Lutz, Gantry 0, Collimator 0, Couch 90, 2x2cm, 5 MU, MLC-defined
+* "G0C0P315": Winston-Lutz, Gantry 0, Collimator 0, Couch 315, 2x2cm, 5 MU, MLC-defined
+* "G0C0P270": Winston-Lutz, Gantry 0, Collimator 0, Couch 270, 2x2cm, 5 MU, MLC-defined
+* "G45C15P15": Winston-Lutz, Gantry 45, Collimator 15, Couch 15, 2x2cm, 5 MU, MLC-defined
+* "G5C330P60": Winston-Lutz, Gantry 5, Collimator 330, Couch 60, 2x2cm, 5 MU, MLC-defined
+* "G330C350P350": Winston-Lutz, Gantry 330, Collimator 350, Couch 350, 2x2cm, 5 MU, MLC-defined
+* "DR100-600": Dose Rate Constancy, 4 ROIs, 100, 200, 400, 600 MU/min
+* "DR Ref": Dose Rate Constancy, Reference Field
+* "MLC Speed": MLC Speed, 4 ROIs, 5, 10, 15, 20 mm/s
+* "MLC Speed Ref": MLC Speed, Reference Field
+* "GS": Gantry Speed, 4 ROIs, 1, 2, 3, 4 deg/s
+* "GS Ref": Gantry Speed, Reference Field
 
 .. tab-set::
    :sync-group: mlc-type
@@ -397,6 +423,24 @@ more efficiently. Adding a Winston-Lutz field can be done like so:
 
 This will create 4 open fields of a 1x1cm, MLC-defined WL fields. See the :meth:`~pylinac.plan_generator.dicom.PlanGenerator.add_winston_lutz_beams` method for more information.
 
+.. versionadded:: 3.27
+
+You can pass your own beam name for a given axes position by adding a ``name`` key to the dictionary. If no name
+key is passed the beam name will be of the form "G<gantry>C<collimator>P<couch>".
+
+.. code-block:: python
+
+    pg.add_winston_lutz_beams(
+        axes_positions=(
+            {"gantry": 0, "collimator": 0, "couch": 0, "name": "Ref"},
+            {"gantry": 90, "collimator": 15, "couch": 0},  # auto-name: G90C15P0
+            {"gantry": 180, "collimator": 0, "couch": 90},  # auto-name: G180C0P90
+            {"gantry": 270, "collimator": 0, "couch": 0},  # auto-name: G270C0P0
+        ),
+        ...,
+    )
+
+
 Picket Fence
 ^^^^^^^^^^^^
 

diff --git a/pylinac/plan_generator/dicom.py b/pylinac/plan_generator/dicom.py
@@ -1324,7 +1324,7 @@ def add_mlc_speed_beams(
             )
         ref_beam = Beam(
             plan_dataset=self.ds,
-            beam_name="MLC Sp Ref",
+            beam_name=f"{beam_name} Ref",
             beam_type=BeamType.DYNAMIC,
             energy=energy,
             dose_rate=default_dose_rate,
@@ -1410,7 +1410,7 @@ def add_winston_lutz_beams(
         dose_rate : int
             The dose rate of the beam.
         axes_positions : Iterable[dict]
-            The positions of the axes. Each dict should have keys 'gantry', 'collimator', and 'couch'.
+            The positions of the axes. Each dict should have keys 'gantry', 'collimator', 'couch', and optionally 'name'.
         couch_vrt : float
             The couch vertical position.
         couch_lng : float
@@ -1440,9 +1440,13 @@ def add_winston_lutz_beams(
                 meterset_at_target=1.0,
                 x_outfield_position=x1 - mlc_padding - jaw_padding - 20,
             )
+            beam_name = (
+                axes.get("name")
+                or f"G{axes['gantry']:g}C{axes['collimator']:g}P{axes['couch']:g}"
+            )
             beam = Beam(
                 plan_dataset=self.ds,
-                beam_name=f"G{axes['gantry']:g}C{axes['collimator']:g}P{axes['couch']:g}",
+                beam_name=beam_name,
                 beam_type=BeamType.DYNAMIC,
                 energy=energy,
                 dose_rate=dose_rate,
@@ -1554,7 +1558,7 @@ def add_gantry_speed_beams(
         g_angles_uncorrected = [start_gantry_angle] + (
             start_gantry_angle + gantry_sign * np.cumsum(gantry_deltas)
         ).tolist()
-        gantry_angles = [wrap360(angle) for angle in g_angles_uncorrected]
+        gantry_angles = [round(wrap360(angle), 2) for angle in g_angles_uncorrected]
 
         if sum(gantry_deltas) >= 360:
             raise ValueError(
@@ -1620,7 +1624,7 @@ def add_gantry_speed_beams(
         self.add_beam(beam.as_dicom(), mu=mu)
         ref_beam = Beam(
             plan_dataset=self.ds,
-            beam_name="G Sp Ref",
+            beam_name=f"{beam_name} Ref",
             beam_type=BeamType.DYNAMIC,
             energy=energy,
             dose_rate=max_dose_rate,

diff --git a/scripts/prefab_plan_generator.py b/scripts/prefab_plan_generator.py
@@ -2,17 +2,18 @@
 
 from pylinac.plan_generator.dicom import FluenceMode, PlanGenerator
 
-rt_plan_file = (
+rt_plan_dir = (
     Path(__file__).parent.parent.absolute()
     / "Files"
     / "RapidArc QA Test Procedures and Files for TrueBeam"
     / "Plans"
-    / "HDMLC"
-    / "T0.2_PicketFenceStatic_HD120_TB_Rev02.dcm"
 )
 
-MLC = "HD120"
-REVISION = 1
+REVISION = 2
+MLCS = (
+    ("HD120", rt_plan_dir / "HDMLC" / "T0.2_PicketFenceStatic_HD120_TB_Rev02.dcm"),
+    ("M120", rt_plan_dir / "Millennium" / "T0.2_PicketFenceStatic_M120_TB_Rev02.dcm"),
+)
 CONTEXTS = [
     # energy, mode, max dose rate
     (6, FluenceMode.STANDARD, 600),
@@ -23,89 +24,96 @@
     (18, FluenceMode.STANDARD, 600),
 ]
 
-for context in CONTEXTS:
-    energy, fluence_mode, max_dose_rate = context
-    plan_name = f"{energy}MV{'' + fluence_mode.value if fluence_mode != FluenceMode.STANDARD else ''}"
-    generator = PlanGenerator.from_rt_plan_file(
-        rt_plan_file, plan_name=plan_name, plan_label=plan_name
-    )
-    # picket fence
-    for gantry_angle in (0, 90, 180, 270):
-        generator.add_picketfence_beam(
-            strip_width_mm=3,
-            strip_positions_mm=(-60, -30, 0, 30, 60),  # 5 pickets
-            mu=100,
-            beam_name=f"PF 3mm G{gantry_angle}",
-            gantry_angle=gantry_angle,
-            fluence_mode=fluence_mode,
+for mlc, rt_plan_file in MLCS:
+    for context in CONTEXTS:
+        energy, fluence_mode, max_dose_rate = context
+        plan_name = f"{energy}MV{'' + fluence_mode.value if fluence_mode != FluenceMode.STANDARD else ''}"
+        generator = PlanGenerator.from_rt_plan_file(
+            rt_plan_file, plan_name=plan_name, plan_label=plan_name
+        )
+        # picket fence
+        for gantry_angle in (0, 90, 180, 270):
+            generator.add_picketfence_beam(
+                strip_width_mm=3,
+                strip_positions_mm=(-60, -30, 0, 30, 60),  # 5 pickets
+                mu=100,
+                beam_name=f"PF 3mm G{gantry_angle}",
+                gantry_angle=gantry_angle,
+                fluence_mode=fluence_mode,
+                energy=energy,
+                dose_rate=max_dose_rate,
+            )
+        # winston lutz
+        generator.add_winston_lutz_beams(
+            axes_positions=(
+                # basic gantry
+                {"gantry": 0, "collimator": 0, "couch": 0},
+                {"gantry": 90, "collimator": 0, "couch": 0},
+                {"gantry": 180, "collimator": 0, "couch": 0},
+                {"gantry": 270, "collimator": 0, "couch": 0},
+                # collimator-rotation
+                {"gantry": 0, "collimator": 270, "couch": 0},
+                {"gantry": 0, "collimator": 90, "couch": 0},
+                {"gantry": 0, "collimator": 315, "couch": 0},
+                {"gantry": 0, "collimator": 45, "couch": 0},
+                # couch-rotation
+                {"gantry": 0, "collimator": 0, "couch": 45},
+                {"gantry": 0, "collimator": 0, "couch": 90},
+                {"gantry": 0, "collimator": 0, "couch": 315},
+                {"gantry": 0, "collimator": 0, "couch": 270},
+                # combo
+                {"gantry": 45, "collimator": 15, "couch": 15},
+                {"gantry": 5, "collimator": 330, "couch": 60},
+                {"gantry": 330, "collimator": 350, "couch": 350},
+            ),
+            x1=-10,
+            x2=10,
+            y1=-10,
+            y2=10,
+            defined_by_mlcs=True,
+            mu=5,
             energy=energy,
             dose_rate=max_dose_rate,
+            fluence_mode=fluence_mode,
         )
-    # winston lutz
-    generator.add_winston_lutz_beams(
-        axes_positions=(
-            # basic gantry
-            {"gantry": 0, "collimator": 0, "couch": 0},
-            {"gantry": 90, "collimator": 0, "couch": 0},
-            {"gantry": 180, "collimator": 0, "couch": 0},
-            {"gantry": 270, "collimator": 0, "couch": 0},
-            # collimator-rotation
-            {"gantry": 0, "collimator": 270, "couch": 0},
-            {"gantry": 0, "collimator": 90, "couch": 0},
-            {"gantry": 0, "collimator": 315, "couch": 0},
-            {"gantry": 0, "collimator": 45, "couch": 0},
-            # couch-rotation
-            {"gantry": 0, "collimator": 0, "couch": 45},
-            {"gantry": 0, "collimator": 0, "couch": 90},
-            {"gantry": 0, "collimator": 0, "couch": 315},
-            {"gantry": 0, "collimator": 0, "couch": 270},
-            # combo
-            {"gantry": 45, "collimator": 15, "couch": 15},
-            {"gantry": 5, "collimator": 330, "couch": 60},
-            {"gantry": 330, "collimator": 350, "couch": 350},
-        ),
-        x1=-10,
-        x2=10,
-        y1=-10,
-        y2=10,
-        defined_by_mlcs=True,
-        mu=5,
-        energy=energy,
-        dose_rate=max_dose_rate,
-    )
 
-    # dose rate
-    generator.add_dose_rate_beams(
-        dose_rates=(100, 200, 400, 600),
-        y1=-50,
-        y2=50,
-        default_dose_rate=600,
-        desired_mu=100,
-    )
+        # dose rate
+        generator.add_dose_rate_beams(
+            dose_rates=(100, 200, 400, 600),
+            y1=-50,
+            y2=50,
+            default_dose_rate=max_dose_rate,
+            desired_mu=100,
+            fluence_mode=fluence_mode,
+            energy=energy,
+        )
 
-    # MLC speed
-    generator.add_mlc_speed_beams(
-        speeds=(5, 10, 15, 20),
-        roi_size_mm=20,
-        y1=-50,
-        y2=50,
-        mu=100,
-        default_dose_rate=600,
-        beam_name="MLC Speed",
-    )
+        # MLC speed
+        generator.add_mlc_speed_beams(
+            speeds=(5, 10, 15, 20),
+            roi_size_mm=20,
+            y1=-50,
+            y2=50,
+            mu=100,
+            default_dose_rate=max_dose_rate,
+            fluence_mode=fluence_mode,
+            energy=energy,
+        )
 
-    # gantry speed
-    generator.add_gantry_speed_beams(
-        speeds=(1, 2, 3, 4),
-        max_dose_rate=600,
-        start_gantry_angle=179,
-        roi_size_mm=20,
-        y1=-50,
-        y2=50,
-        mu=100,
-    )
+        # gantry speed
+        generator.add_gantry_speed_beams(
+            speeds=(1, 2, 3, 4),
+            max_dose_rate=max_dose_rate,
+            start_gantry_angle=179,
+            roi_size_mm=20,
+            y1=-50,
+            y2=50,
+            mu=100,
+            fluence_mode=fluence_mode,
+            energy=energy,
+        )
 
-    # save file
-    generator.to_file(
-        filename=f"R{REVISION}_{plan_name}_{MLC}_prefab.dcm".replace(" ", "_")
-    )
+        # save file
+        file_name = f"R{REVISION}_{plan_name}_{mlc}_prefab.dcm".replace(" ", "_")
+        generator.to_file(filename=file_name)
+        print(f"Generated {file_name} plan")
diff --git a/tests_basic/contrib/test_orthogonality.py b/tests_basic/contrib/test_orthogonality.py
@@ -2,15 +2,13 @@
 from unittest import TestCase
 
 from pylinac.contrib.orthogonality import JawOrthogonality
-from tests_basic.utils import get_folder_from_cloud_test_repo
+from tests_basic.utils import get_folder_from_cloud_repo
 
 
 class TestOrthogonality(TestCase):
     @classmethod
     def setUpClass(cls) -> None:
-        cls.dir = Path(
-            get_folder_from_cloud_test_repo(["planar_imaging", "Orthogonality"])
-        )
+        cls.dir = Path(get_folder_from_cloud_repo(["planar_imaging", "Orthogonality"]))
 
     def test_analyze(self):
         for file in self.dir.iterdir():

diff --git a/tests_basic/contrib/test_quasar.py b/tests_basic/contrib/test_quasar.py
@@ -2,13 +2,13 @@
 from unittest import TestCase
 
 from pylinac.contrib.quasar import QuasarLightRadScaling
-from tests_basic.utils import get_folder_from_cloud_test_repo
+from tests_basic.utils import get_folder_from_cloud_repo
 
 
 class TestQuasar(TestCase):
     @classmethod
     def setUpClass(cls) -> None:
-        cls.dir = Path(get_folder_from_cloud_test_repo(["planar_imaging", "Quasar"]))
+        cls.dir = Path(get_folder_from_cloud_repo(["planar_imaging", "Quasar"]))
 
     def test_analyze(self):
         for file in self.dir.iterdir():

diff --git a/tests_basic/core/test_image.py b/tests_basic/core/test_image.py
@@ -36,7 +36,7 @@
 from pylinac.core.io import TemporaryZipDirectory
 from tests_basic.utils import (
     get_file_from_cloud_test_repo,
-    get_folder_from_cloud_test_repo,
+    get_folder_from_cloud_repo,
     save_file,
 )
 
@@ -763,7 +763,7 @@ class TestTiff(TestCase):
 
     def test_all_tiffs_have_tags_and_are_2d(self):
         """Test all tiffs will load. Just raw ingestion"""
-        all_starshot_files = get_folder_from_cloud_test_repo(["Starshot"])
+        all_starshot_files = get_folder_from_cloud_repo(["Starshot"])
         for img in Path(all_starshot_files).iterdir():
             if img.suffix in (".tif", ".tiff"):
                 fimg = FileImage(img)
@@ -896,7 +896,7 @@ def test_conversion_goes_to_uint16(self):
 
     def test_mass_conversion(self):
         """Mass conversion; shouldn't fail. All images have dpi tag"""
-        all_starshot_files = get_folder_from_cloud_test_repo(["Starshot"])
+        all_starshot_files = get_folder_from_cloud_repo(["Starshot"])
         for img in Path(all_starshot_files).iterdir():
             if img.suffix in (".tif", ".tiff"):
                 tiff_to_dicom(img, sid=1000, gantry=10, coll=11, couch=12)