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Merged in v3.21.1_hotfix (pull request #374)
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V3.21.1 hotfix

Approved-by: Randy Taylor
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@jrkerns
jrkerns committed Apr 10, 2024
2 parents f749f5a + c0896e9 commit cb1f9cc
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Showing 3 changed files with 158 additions and 23 deletions.
13 changes: 13 additions & 0 deletions docs/source/changelog.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,19 @@ Image Generator
* The Winston-Lutz image generator has a machine scale input.


v 3.21.1
--------

VMAT
^^^^

* A bug in the VMAT analysis was causing apparent shifts in the ROI position. This would happen if the gaps between the
ROIs were below 50% of the maximum. The ROI position is now based on the center position of the open field rather than the center
of the DMLC image. This caused a shift in some of the ROI positions of the test images of a few pixels (2-7 pixels). This
also caused the ROI values to change by anywhere between 0 and 0.2% in our test suite.
* This same bug was causing identification issues of open vs DMLC images occassionally, usually for Halcyon datasets. The identification algorithm
has been adjusted to better detect these scenarios.

v 3.21.0
--------

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21 changes: 18 additions & 3 deletions pylinac/vmat.py
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Expand Up @@ -252,7 +252,22 @@ def _identify_images(self, image1: DicomImage, image2: DicomImage):
profile1, profile2 = self._median_profiles(image1=image1, image2=image2)
field_profile1 = profile1.field_values()
field_profile2 = profile2.field_values()
if np.std(field_profile1) > np.std(field_profile2):
# first check if the profiles have a very different length
# if so, the longer one is the open field
# this leverages the shortcoming in FWXMProfile where the field might be very small because
# it "caught" on one of the first dips of the DMLC image
# catches most often with Halcyon images
if abs(len(field_profile1) - len(field_profile2)) > min(
len(field_profile1), len(field_profile2)
):
if len(field_profile1) > len(field_profile2):
self.open_image = image1
self.dmlc_image = image2
else:
self.open_image = image2
self.dmlc_image = image1
# normal check of the STD compared; for flat-ish beams this works well.
elif np.std(field_profile1) > np.std(field_profile2):
self.dmlc_image = image1
self.open_image = image2
else:
Expand Down Expand Up @@ -308,8 +323,8 @@ def _generate_results_data(self) -> VMATResult:
def _calculate_segment_centers(self) -> list[Point]:
"""Construct the center points of the segments based on the field center and known x-offsets."""
points = []
dmlc_prof, _ = self._median_profiles(self.dmlc_image, self.open_image)
x_field_center = round(dmlc_prof.center_idx)
_, open_prof = self._median_profiles(self.dmlc_image, self.open_image)
x_field_center = round(open_prof.center_idx)
for roi_data in self.roi_config.values():
x_offset_mm = roi_data["offset_mm"]
y = self.open_image.center.y
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147 changes: 127 additions & 20 deletions tests_basic/test_vmat.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
import io
import json
import tempfile
from functools import partial
from pathlib import Path
from typing import Iterable, Type, Union
from unittest import TestCase

Expand All @@ -9,6 +11,12 @@

from pylinac import DRGS, DRMLC
from pylinac.core.geometry import Point
from pylinac.core.image_generator import (
AS1200Image,
FilterFreeFieldLayer,
GaussianFilterLayer,
RandomNoiseLayer,
)
from pylinac.vmat import VMATResult
from tests_basic.utils import (
FromDemoImageTesterMixin,
Expand Down Expand Up @@ -131,7 +139,8 @@ class VMATMixin:
0: {"r_dev": 0, "r_corr": 100},
4: {"r_dev": 0, "r_corr": 100},
}
kwargs = {}
init_kwargs = {}
analyze_kwargs = {}
avg_abs_r_deviation = 0
avg_r_deviation = 0
max_r_deviation = 0
Expand All @@ -151,10 +160,10 @@ def absolute_path(cls):

def setUp(self):
if self.is_zip:
self.vmat = self.klass.from_zip(self.absolute_path(), **self.kwargs)
self.vmat = self.klass.from_zip(self.absolute_path(), **self.init_kwargs)
else:
self.vmat = self.klass(self.absolute_path(), **self.kwargs)
self.vmat.analyze()
self.vmat = self.klass(self.absolute_path(), **self.init_kwargs)
self.vmat.analyze(**self.analyze_kwargs)
if self.print_debug:
print(self.vmat.results())
print(
Expand Down Expand Up @@ -218,7 +227,7 @@ class TestDRGSDemo(VMATMixin, TestCase):
0: {"r_dev": 0.965, "r_corr": 6.2, "stdev": 0.0008},
4: {"r_dev": -0.459, "r_corr": 6, "stdev": 0.0007},
}
avg_abs_r_deviation = 0.66
avg_abs_r_deviation = 0.74
max_r_deviation = 1.8
passes = False

Expand Down Expand Up @@ -249,7 +258,7 @@ class TestDRMLCDemo(VMATMixin, TestCase):
max_r_deviation = 0.89

def setUp(self):
self.vmat = DRMLC.from_demo_images(**self.kwargs)
self.vmat = DRMLC.from_demo_images(**self.init_kwargs)
self.vmat.analyze()

def test_demo(self):
Expand All @@ -259,7 +268,7 @@ def test_demo(self):
class TestDRMLCDemoRawPixels(TestDRMLCDemo):
"""Use raw DICOM pixel values, like doselab does."""

kwargs = {"raw_pixels": True, "ground": False, "check_inversion": False}
init_kwargs = {"raw_pixels": True, "ground": False, "check_inversion": False}
segment_values = {
0: {"r_dev": -0.55, "r_corr": 138.55},
2: {"r_dev": 0.56, "r_corr": 140},
Expand Down Expand Up @@ -291,7 +300,7 @@ class TestDRGS105(VMATMixin, TestCase):

filepaths = ("DRGSopen-105-example.dcm", "DRGSdmlc-105-example.dcm")
klass = DRGS
segment_positions = {0: Point(371, 384), 2: Point(478, 384)}
segment_positions = {0: Point(378, 384), 2: Point(485, 384)}
segment_values = {
0: {
"r_dev": 1.385,
Expand All @@ -314,7 +323,7 @@ class TestDRMLC2(VMATMixin, TestCase):
2: {"r_dev": -1.1, "r_corr": 6},
}
avg_abs_r_deviation = 1.4
max_r_deviation = 1.98
max_r_deviation = 2.11
passes = False


Expand Down Expand Up @@ -373,15 +382,25 @@ class TestHalcyonDRGS(VMATMixin, TestCase):

klass = DRGS
filepaths = ("HalcyonDRGS.zip",)
analyze_kwargs = {
"roi_config": {
"ROI 1": {"offset_mm": -120},
"ROI 2": {"offset_mm": -80},
"ROI 3": {"offset_mm": -40},
"ROI 4": {"offset_mm": 0},
"ROI 5": {"offset_mm": 40},
"ROI 6": {"offset_mm": 80},
"ROI 7": {"offset_mm": 120},
}
}
is_zip = True
segment_positions = {0: Point(364, 640), 2: Point(547, 640)}
segment_positions = {0: Point(89, 640), 2: Point(456, 640)}
segment_values = {
0: {"r_dev": 41.4, "r_corr": 1689.2},
2: {"r_dev": 28, "r_corr": 1529.5},
0: {"r_dev": 0.583, "r_corr": 13.62},
2: {"r_dev": -0.30, "r_corr": 13.5},
}
avg_abs_r_deviation = 32.64
max_r_deviation = 41.4
passes = False
avg_abs_r_deviation = 0.266
max_r_deviation = 0.58


class TestHalcyonDRMLC(VMATMixin, TestCase):
Expand All @@ -390,11 +409,99 @@ class TestHalcyonDRMLC(VMATMixin, TestCase):
klass = DRMLC
filepaths = ("HalcyonDRMLC.zip",)
is_zip = True
segment_positions = {0: Point(433, 640), 2: Point(708, 640)}
analyze_kwargs = {
"roi_config": {
"ROI 1": {"offset_mm": -115},
"ROI 2": {"offset_mm": -57.5},
"ROI 3": {"offset_mm": 0},
"ROI 4": {"offset_mm": 57.5},
"ROI 5": {"offset_mm": 115},
}
}
segment_positions = {0: Point(112, 640), 2: Point(639, 640)}
segment_values = {
0: {"r_dev": -0.34, "r_corr": 2.8},
2: {"r_dev": 1.15, "r_corr": 2.85},
}
avg_abs_r_deviation = 0.66
max_r_deviation = 1.15
passes = True


class TestHalcyonDRGS2(VMATMixin, TestCase):
"""A Hal image w/ deep gaps between the ROIs. Causes a shift in the ROIs from RAM-3483"""

klass = DRGS
filepaths = ("DRGS_Halcyon2.zip",)
is_zip = True
segment_positions = {0: Point(364, 640), 2: Point(543, 640)}
segment_values = {
0: {"r_dev": 1.17, "r_corr": 13.73},
2: {"r_dev": -0.206, "r_corr": 13.56},
}
avg_abs_r_deviation = 0.44
max_r_deviation = 0.803
passes = True


class TestHalcyonDRGS3(VMATMixin, TestCase):
"""A TB image w/ deep gaps between the ROIs. Causes a shift in the ROIs from RAM-3483"""

klass = DRGS
filepaths = ("DRGS_example_PM.zip",)
is_zip = True
segment_positions = {0: Point(280, 384), 2: Point(433, 384)}
segment_values = {
0: {"r_dev": 1.17, "r_corr": 3602},
2: {"r_dev": -0.206, "r_corr": 3552.8},
0: {"r_dev": -0.37, "r_corr": 13.73},
2: {"r_dev": -0.206, "r_corr": 13.56},
}
avg_abs_r_deviation = 0.585
max_r_deviation = 1.17
avg_abs_r_deviation = 0.89
max_r_deviation = 1.87
passes = False


class TestContrivedWideGapTest(VMATMixin, TestCase):
"""A contrived test with a wide gap between the segments."""

klass = DRMLC
is_zip = False
segment_positions = {0: Point(506, 640), 2: Point(685, 640)}
segment_values = {
0: {"r_dev": 0, "r_corr": 100},
2: {"r_dev": 0, "r_corr": 100},
}
avg_abs_r_deviation = 0
max_r_deviation = 0.0
passes = True

def create_synthetic_images(self):
tmp_dir = Path(tempfile.gettempdir())
as1200_open = AS1200Image(1000)
as1200_open.add_layer(FilterFreeFieldLayer(field_size_mm=(110, 110)))
as1200_open.add_layer(GaussianFilterLayer())
open_path = tmp_dir / "contrived_wide_gap_open.dcm"
as1200_open.generate_dicom(open_path)
# generate the DMLC image
as1200_dmlc = AS1200Image(1000)
as1200_dmlc.add_layer(
FilterFreeFieldLayer(field_size_mm=(150, 20), cax_offset_mm=(0, 45))
)
as1200_dmlc.add_layer(
FilterFreeFieldLayer(field_size_mm=(150, 20), cax_offset_mm=(0, 15))
)
as1200_dmlc.add_layer(
FilterFreeFieldLayer(field_size_mm=(150, 20), cax_offset_mm=(0, -15))
)
as1200_dmlc.add_layer(
FilterFreeFieldLayer(field_size_mm=(150, 20), cax_offset_mm=(0, -45))
)
as1200_dmlc.add_layer(GaussianFilterLayer())
as1200_dmlc.add_layer(RandomNoiseLayer(sigma=0.005))
dmlc_path = tmp_dir / "contrived_wide_gap_dmlc.dcm"
as1200_dmlc.generate_dicom(dmlc_path)
return open_path, dmlc_path

def setUp(self):
open_path, dmlc_path = self.create_synthetic_images()
self.vmat = self.klass(image_paths=(open_path, dmlc_path), **self.init_kwargs)
self.vmat.analyze(**self.analyze_kwargs)

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