Merged in feature/RAM-4011_cirs_bad_dataset_fix (pull request #456)

RAM-4011 part2: revert symmetric check Approved-by: Randy Taylor
jrkerns · Oct 11, 2024 · efc9656 · efc9656
2 parents 851d22c + bdb7170
commit efc9656
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Showing 4 changed files with 117 additions and 34 deletions.
diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml
@@ -40,7 +40,7 @@ definitions:
         name: Run CBCT Tests
         size: 2x
         script:
-          - uv run --locked pytest tests_basic/test_cbct.py -n 2 --cov=pylinac.cbct --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_cbct.py -n 2 --cov=pylinac.cbct --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -52,7 +52,7 @@ definitions:
     - step: &quart-tests
         name: Run Quart Tests
         script:
-          - uv run --locked pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_quart.py --cov=pylinac.quart --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -65,7 +65,7 @@ definitions:
     - step: &acr-tests
         name: Run ACR CT/MRI Tests
         script:
-          - uv run --locked pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_acr.py --cov=pylinac.acr --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -78,7 +78,7 @@ definitions:
     - step: &cheese-tests
         name: Run Cheese Phantom Tests
         script:
-          - uv run --locked pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_cheese.py --cov=pylinac.cheese --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -91,7 +91,7 @@ definitions:
     - step: &planar-tests
         name: Run Planar Imaging Tests
         script:
-          - uv run --locked pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_planar_imaging.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -103,7 +103,7 @@ definitions:
     - step: &dlg-tests
         name: Run DLG Tests
         script:
-          - uv run --locked pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_dlg.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -115,7 +115,7 @@ definitions:
     - step: &field-analysis-tests
         name: Run Field Analysis Tests
         script:
-          - uv run --locked pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_field_analysis.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -127,7 +127,7 @@ definitions:
     - step: &machine-log-tests
         name: Run Machine Logs Tests
         script:
-          - uv run --locked pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_logs.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -139,7 +139,7 @@ definitions:
     - step: &picket-fence-tests
         name: Run Picket Fence Tests
         script:
-          - uv run --locked pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_picketfence.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -151,7 +151,7 @@ definitions:
     - step: &starshot-tests
         name: Run Starshot Tests
         script:
-          - uv run --locked pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_starshot.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -163,7 +163,7 @@ definitions:
     - step: &calibration-tests
         name: Run TG-51/TRS-398 Tests
         script:
-          - uv run --locked pytest tests_basic/test_tg51.py tests_basic/test_trs398.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_tg51.py tests_basic/test_trs398.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -176,7 +176,7 @@ definitions:
     - step: &vmat-tests
         name: Run VMAT Tests
         script:
-          - uv run --locked pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_vmat.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -189,7 +189,7 @@ definitions:
         name: Run Winston-Lutz Tests
         size: 2x
         script:
-          - uv run --locked pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_winstonlutz.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         condition:
           changesets:
             includePaths:
@@ -200,7 +200,7 @@ definitions:
         name: Run Winston-Lutz Multi-Target Multi-Field Tests
         size: 2x
         script:
-          - uv run --locked pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/test_winstonlutz_mtmf.py --cov-report term --junitxml=./test-reports/pytest_results.xml
         condition:
           changesets:
             includePaths:
@@ -210,7 +210,7 @@ definitions:
     - step: &plan-generator-tests
         name: Plan generator tests
         script:
-          - uv run --locked pytest tests_basic/test_plan_generator.py tests_basic/test_generated_plans.py --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run 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:
@@ -221,7 +221,7 @@ definitions:
     - step: &core-module-tests
         name: Run core module tests
         script:
-          - uv run --locked pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml
+          - uv run pytest tests_basic/core --cov-report term --junitxml=./test-reports/pytest_results.xml
         caches:
           - testfiles
         condition:
@@ -239,7 +239,7 @@ definitions:
           - tar -xf gcloud_cli.tar.gz
           - ./google-cloud-sdk/install.sh --quiet
           - export PATH="./google-cloud-sdk/bin:$PATH"
-          - uv run --locked nox -s update_dev_kraken
+          - uv run nox -s update_dev_kraken
     - step: &run-min-python-version
         name: Run against min Python version
         image: ghcr.io/astral-sh/uv:python3.9-bookworm-slim

diff --git a/pylinac/ct.py b/pylinac/ct.py
@@ -404,8 +404,7 @@ def phantom_roi(self) -> RegionProperties:
         )[0]
         is_too_large = self.catphan_size * 1.3 < catphan_region.filled_area
         is_too_small = catphan_region.filled_area < self.catphan_size / 1.3
-        not_symmetric = not is_symmetric(catphan_region)
-        if is_too_small or is_too_large or not_symmetric:
+        if is_too_small or is_too_large:
             raise ValueError("Unable to find ROI of expected size of the phantom")
         return catphan_region
 
@@ -2823,6 +2822,9 @@ def refine_origin_slice(self, initial_slice_num: int) -> int:
                     "angle": angle,
                     "left width": troi["Left"].long_profile.field_width_px,
                     "right width": troi["Right"].long_profile.field_width_px,
+                    # the values AT the FWXM
+                    "left center": troi["Left"].long_profile.y_at_x(left_wire),
+                    "right center": troi["Right"].long_profile.y_at_x(right_wire),
                     "left profile": troi["Left"].long_profile.values,
                     "right profile": troi["Right"].long_profile.values,
                 }
@@ -2858,11 +2860,9 @@ def refine_origin_slice(self, initial_slice_num: int) -> int:
                 continue
             # if the max pixel value of the angle set is closer to the overall median than the max
             # it means the wire isn't in the slice; drop it
-            max_pixel = max(
-                angle_set["left profile"].max(), angle_set["right profile"].max()
-            )
-            delta_median = abs(median_pixel_val - max_pixel)
-            delta_max = abs(max_pixel_val - max_pixel)
+            fwxm_pixel = np.mean((angle_set["left center"], angle_set["right center"]))
+            delta_median = abs(median_pixel_val - fwxm_pixel)
+            delta_max = abs(max_pixel_val - fwxm_pixel)
             if delta_median < delta_max:
                 angles.remove(angle_set)
 
@@ -2915,16 +2915,6 @@ def find_phantom_roll(self, func: Callable | None = None) -> float:
         return angle + 75
 
 
-def is_symmetric(region: RegionProperties, tolerance: float = 0.3) -> bool:
-    """Check symmetry of ROI by comparing x-axis size to y-axis size"""
-    ymin, xmin, ymax, xmax = region.bbox
-    y = abs(ymax - ymin)
-    x = abs(xmax - xmin)
-    if x > y * (1 + tolerance) or x < y * (1 - tolerance):
-        return False
-    return True
-
-
 def get_regions(
     slice_or_arr: Slice | np.array,
     fill_holes: bool = False,

diff --git a/tests_basic/test_cbct.py b/tests_basic/test_cbct.py
@@ -1773,6 +1773,86 @@ class CatPhan604CoCr(CatPhan604Mixin, TestCase):
     lowcon_visible = 2
 
 
+@mark.directdensity
+@mark.catphan604
+class CatPhan604SliceRefinementLocalization(CatPhan604Mixin, TestCase):
+    """A crazy scenario where the refinement algorithm failed due to the wire being at the edge of the
+    "long_profile". Also, this is a direct density scan.
+    """
+
+    file_name = "CatPhan604 - ramp edge.zip"
+    hu_origin_variance = 200
+    origin_slice = 71
+    hu_values = {
+        "Poly": -67,
+        "Acrylic": 94,
+        "Delrin": 114,
+        "Air": -997,
+        "Teflon": 364,
+        "PMP": -212,
+        "LDPE": -129,
+        "50% Bone": 335,
+        "20% Bone": 104,
+    }
+    thickness_slice_straddle = 0
+    slice_thickness = 2.35
+    unif_values = {"Center": -18, "Left": -17, "Right": -17, "Top": -17, "Bottom": -18}
+    mtf_values = {50: 0.30}
+    lowcon_visible = 6
+
+
+@mark.directdensity
+@mark.catphan604
+class CatPhan604DD2(CatPhan604Mixin, TestCase):
+    """Direct density scan"""
+
+    file_name = "CatPhan604 - DD2.zip"
+    hu_origin_variance = 200
+    origin_slice = 74
+    hu_values = {
+        "Poly": -36,
+        "Acrylic": 118,
+        "Delrin": 191,
+        "Air": -1017,
+        "Teflon": 540,
+        "PMP": -187,
+        "LDPE": -97,
+        "50% Bone": 380,
+        "20% Bone": 124,
+    }
+    thickness_slice_straddle = 0
+    slice_thickness = 2.35
+    unif_values = {"Center": 9, "Left": 9, "Right": 9, "Top": 9, "Bottom": 9}
+    mtf_values = {50: 0.30}
+    lowcon_visible = 6
+
+
+@mark.directdensity
+@mark.catphan604
+class CatPhan604DD3(CatPhan604Mixin, TestCase):
+    """Direct density scan"""
+
+    file_name = "CatPhan604 - DD3.zip"
+    hu_origin_variance = 200
+    origin_slice = 71
+    hu_values = {
+        "Poly": -65,
+        "Acrylic": 95,
+        "Delrin": 115,
+        "Air": -999,
+        "Teflon": 363,
+        "PMP": -212,
+        "LDPE": -125,
+        "50% Bone": 335,
+        "20% Bone": 105,
+    }
+    thickness_slice_straddle = 0
+    slice_thickness = 2.35
+    unif_values = {"Center": -20, "Left": -20, "Right": -20, "Top": -20, "Bottom": -20}
+    mtf_values = {50: 0.30}
+    lowcon_visible = 6
+
+
 class CatPhan504NearEdge(CatPhan504Mixin, TestCase):
     file_name = "phantom_edge.zip"
     expected_roll = 1.4

diff --git a/tests_basic/test_cheese.py b/tests_basic/test_cheese.py
@@ -395,3 +395,16 @@ class TestCIRS062MButsonEmptyButoOuter(CheeseMixin, TestCase):
         "16": 214,
         "17": 856,
     }
+
+
+class TestCIRS062MShifted(CheeseMixin, TestCase):
+    model = CIRS062M
+    origin_slice = 30
+    dir_path = ["Tomo", "CIRS062M"]
+    file_name = "CIRS bad, shifted.zip"
+    expected_roll = -0.55
+    hu_values = {
+        "1": -3,
+        "8": 45,
+        "17": -489,
+    }