isort

docs/source/code_snippets/tg51_class.py

@@ -1,7 +1,6 @@
 """A script to calculate TG-51 dose using pylinac classes and following the TG-51 photon form"""
 from pylinac.calibration import tg51
 
-
 ENERGY = 6
 TEMP = 22.1
 PRESS = tg51.mmHg2kPa(755.0)

docs/source/code_snippets/tg51_function.py

@@ -1,7 +1,6 @@
 """A script to calculate TG-51 dose using pylinac functions and following the TG-51 photon form"""
 from pylinac.calibration import tg51
 
-
 ENERGY = 6
 TEMP = 22.1
 PRESS = tg51.mmHg2kPa(755.0)

docs/source/code_snippets/trs398_class.py

@@ -1,7 +1,6 @@
 """A script to calculate TRS-398 dose using pylinac classes and following the TRS-398 photon form"""
 from pylinac.calibration import trs398
 
-
 ENERGY = 6
 TEMP = 22.1
 PRESS = trs398.mmHg2kPa(755.0)

docs/source/code_snippets/trs398_function.py

@@ -1,7 +1,6 @@
 """A script to calculate TRS-398 dose using pylinac functions and following the TRS-398 photon form"""
 from pylinac.calibration import trs398
 
-
 TEMP = 22.1
 PRESS = trs398.mmHg2kPa(755.0)
 CHAMBER = "30013"  # PTW

docs/source/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # pylinac documentation build configuration file, created by
 # sphinx-quickstart on Thu Sep 10 11:56:25 2015.

pylinac/__init__.py

@@ -8,45 +8,45 @@
         "Pylinac is only supported on Python 3.7+. Please update your environment."
     )
 
+# alphabetized modules
+from .acr import ACRCT, ACRMRILarge
+from .calibration import tg51, trs398
+
 # import shortcuts
 # core first
 from .core import decorators, geometry, image, io, mask, profile, roi, utilities
-
-# alphabetized modules
-from .acr import ACRCT, ACRMRILarge
-from .ct import CatPhan504, CatPhan600, CatPhan503, CatPhan604
-from .quart import QuartDVT
-from .core.utilities import clear_data_files, assign2machine
+from .core.utilities import assign2machine, clear_data_files
+from .ct import CatPhan503, CatPhan504, CatPhan600, CatPhan604
 from .field_analysis import (
-    FieldAnalysis,
-    DeviceFieldAnalysis,
-    Protocol,
+    Centering,
     Device,
+    DeviceFieldAnalysis,
     Edge,
+    FieldAnalysis,
     Interpolation,
     Normalization,
-    Centering,
+    Protocol,
 )
+from .log_analyzer import Dynalog, MachineLogs, TrajectoryLog, load_log
+from .picketfence import PicketFence  # must be after log analyzer
 from .planar_imaging import (
-    LeedsTOR,
-    StandardImagingQC3,
-    LasVegas,
-    DoselabMC2kV,
-    DoselabMC2MV,
-    StandardImagingQCkV,
     PTWEPIDQC,
-    SNCMV,
-    SNCkV,
-    StandardImagingFC2,
-    IMTLRad,
     SNCFSQA,
-    LeedsTORBlue,
+    SNCMV,
     SNCMV12510,
+    DoselabMC2kV,
+    DoselabMC2MV,
     IBAPrimusA,
+    IMTLRad,
+    LasVegas,
+    LeedsTOR,
+    LeedsTORBlue,
+    SNCkV,
+    StandardImagingFC2,
+    StandardImagingQC3,
+    StandardImagingQCkV,
 )
-from .log_analyzer import load_log, Dynalog, TrajectoryLog, MachineLogs
-from .picketfence import PicketFence  # must be after log analyzer
+from .quart import QuartDVT
 from .starshot import Starshot
-from .vmat import DRMLC, DRGS
+from .vmat import DRGS, DRMLC
 from .winston_lutz import WinstonLutz, WinstonLutzMultiTargetMultiField
-from .calibration import tg51, trs398

pylinac/acr.py

@@ -6,7 +6,7 @@
 from dataclasses import dataclass
 from io import BytesIO
 from pathlib import Path
-from typing import Union, List, Dict, Optional, Tuple
+from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np
 from matplotlib import pyplot as plt
@@ -15,10 +15,10 @@
 from .core import pdf
 from .core.geometry import Line, Point
 from .core.mtf import MTF
-from .core.profile import SingleProfile, Interpolation
+from .core.profile import Interpolation, SingleProfile
 from .core.roi import HighContrastDiskROI, RectangleROI
 from .core.utilities import ResultBase
-from .ct import CatPhanBase, CatPhanModule, ThicknessROI, Slice, get_regions
+from .ct import CatPhanBase, CatPhanModule, Slice, ThicknessROI, get_regions
 
 # CT
 CT_UNIFORMITY_MODULE_OFFSET_MM = 70

pylinac/calibration/trs398.py

@@ -1,29 +1,29 @@
 import webbrowser
 from abc import ABC
 from datetime import datetime
-from typing import Union, Optional
+from typing import Optional, Union
 
 import argue
 import numpy as np
 
+from ..core.pdf import PylinacCanvas
+from ..core.typing import NumberOrArray
+from ..core.utilities import Structure, is_close
 from . import tg51 as _tg51
+from .tg51 import MAX_PPOL  # make available to module
 from .tg51 import (
-    mmHg2kPa,
-    mbar2kPa,
-    fahrenheit2celsius,
-    tpr2010_from_pdd2010,
-    MIN_PTP,
+    MAX_PELEC,
+    MAX_PION,
     MAX_PTP,
     MIN_PELEC,
-    MAX_PELEC,
-    MIN_PPOL,
-    MAX_PPOL,
     MIN_PION,
-    MAX_PION,
-)  # make available to module
-from ..core.pdf import PylinacCanvas
-from ..core.typing import NumberOrArray
-from ..core.utilities import is_close, Structure
+    MIN_PPOL,
+    MIN_PTP,
+    fahrenheit2celsius,
+    mbar2kPa,
+    mmHg2kPa,
+    tpr2010_from_pdd2010,
+)
 
 V1_V2_FITS = {
     2.0: {"a0": 2.337, "a1": -3.636, "a2": 2.299},
@@ -1137,7 +1137,7 @@ def publish_pdf(
             metadata is at the top of every page while notes is at the bottom of the report.
         """
         was_adjusted = "Yes" if self.output_was_adjusted else "No"
-        title = "TRS-398 Electron Report - {} MV".format(self.energy)
+        title = f"TRS-398 Electron Report - {self.energy} MV"
 
         canvas = PylinacCanvas(filename, page_title=title, metadata=metadata)
         text = [

pylinac/core/geometry.py

@@ -3,12 +3,13 @@
 
 import math
 from itertools import zip_longest
-from typing import Union, Optional, List, Iterable, Tuple
+from typing import Iterable, List, Optional, Tuple, Union
 
 import argue
 import matplotlib.pyplot as plt
 import numpy as np
-from matplotlib.patches import Circle as mpl_Circle, Rectangle as mpl_Rectangle
+from matplotlib.patches import Circle as mpl_Circle
+from matplotlib.patches import Rectangle as mpl_Rectangle
 
 from .utilities import is_iterable
 
@@ -39,16 +40,16 @@ class Point:
     z: float
     y: float
     x: float
-    _attr_list: List[str] = ["x", "y", "z", "idx", "value"]
-    _coord_list: List[str] = ["x", "y", "z"]
+    _attr_list: list[str] = ["x", "y", "z", "idx", "value"]
+    _coord_list: list[str] = ["x", "y", "z"]
 
     def __init__(
         self,
-        x: Union[float, tuple, Point] = 0,
+        x: float | tuple | Point = 0,
         y: float = 0,
         z: float = 0,
-        idx: Optional[int] = None,
-        value: Optional[float] = None,
+        idx: int | None = None,
+        value: float | None = None,
         as_int: bool = False,
     ):
         """
@@ -85,7 +86,7 @@ def __init__(
             self.y = int(round(self.y))
             self.z = int(round(self.z))
 
-    def distance_to(self, thing: Union["Point", "Circle"]) -> float:
+    def distance_to(self, thing: Point | Circle) -> float:
         """Calculate the distance to the given point.
 
         Parameters
@@ -116,7 +117,7 @@ def as_array(self, only_coords: bool = True) -> np.array:
                 ]
             )
 
-    def as_vector(self) -> "Vector":
+    def as_vector(self) -> Vector:
         return Vector(x=self.x, y=self.y, z=self.z)
 
     def __repr__(self):
@@ -160,9 +161,7 @@ class Circle:
     center: Point
     radius: float
 
-    def __init__(
-        self, center_point: Union[Point, Iterable] = (0, 0), radius: float = 0
-    ):
+    def __init__(self, center_point: Point | Iterable = (0, 0), radius: float = 0):
         """
         Parameters
         ----------
@@ -229,7 +228,7 @@ def as_scalar(self) -> float:
         """Return the scalar equivalent of the vector."""
         return math.sqrt(self.x**2 + self.y**2 + self.z**2)
 
-    def distance_to(self, thing: Union[Circle, Point]) -> float:
+    def distance_to(self, thing: Circle | Point) -> float:
         """Calculate the distance to the given point.
 
         Parameters
@@ -248,19 +247,19 @@ def distance_to(self, thing: Union[Circle, Point]) -> float:
                 (self.x - p.x) ** 2 + (self.y - p.y) ** 2 + (self.z - p.z) ** 2
             )
 
-    def __sub__(self, other: "Vector") -> "Vector":
+    def __sub__(self, other: Vector) -> Vector:
         new_x = self.x - other.x
         new_y = self.y - other.y
         new_z = self.z - other.z
         return Vector(x=new_x, y=new_y, z=new_z)
 
-    def __add__(self, other: "Vector") -> "Vector":
+    def __add__(self, other: Vector) -> Vector:
         new_x = self.x + other.x
         new_y = self.y + other.y
         new_z = self.z + other.z
         return Vector(x=new_x, y=new_y, z=new_z)
 
-    def __truediv__(self, other: float) -> "Vector":
+    def __truediv__(self, other: float) -> Vector:
         for attr in ("x", "y", "z"):
             val = getattr(self, attr)
             setattr(self, attr, val / other)
@@ -297,8 +296,8 @@ class Line:
 
     def __init__(
         self,
-        point1: Union[Point, Tuple[float, float]],
-        point2: Union[Point, Tuple[float, float]],
+        point1: Point | tuple[float, float],
+        point2: Point | tuple[float, float],
     ):
         """
         Parameters
@@ -355,7 +354,7 @@ def length(self) -> float:
         """Return length of the line, if finite."""
         return self.point1.distance_to(self.point2)
 
-    def distance_to(self, point: "Point") -> float:
+    def distance_to(self, point: Point) -> float:
         """Calculate the minimum distance from the line to a point.
 
         Equations are from here: http://mathworld.wolfram.com/Point-LineDistance2-Dimensional.html #14
@@ -397,16 +396,16 @@ def plot2axes(
 class Rectangle:
     """A rectangle with width, height, center Point, top-left corner Point, and bottom-left corner Point."""
 
-    width: Union[int, float]
-    height: Union[int, float]
+    width: int | float
+    height: int | float
     _as_int: bool
     center: Point
 
     def __init__(
         self,
         width: float,
         height: float,
-        center: Union[Point, Tuple],
+        center: Point | tuple,
         as_int: bool = False,
     ):
         """

pylinac/core/image.py

@@ -9,9 +9,9 @@
 import typing
 from collections import Counter
 from datetime import datetime
-from io import BytesIO, BufferedReader
+from io import BufferedReader, BytesIO
 from pathlib import Path
-from typing import Union, Sequence, List, Any, Tuple, Optional, BinaryIO
+from typing import Any, BinaryIO, List, Optional, Sequence, Tuple, Union
 
 import argue
 import matplotlib.pyplot as plt
@@ -24,17 +24,17 @@
 from scipy import ndimage
 from skimage.draw import disk
 
+from ..settings import PATH_TRUNCATION_LENGTH, get_dicom_cmap
 from .geometry import Point
 from .io import (
-    get_url,
     TemporaryZipDirectory,
-    retrieve_filenames,
+    get_url,
     is_dicom_image,
     retrieve_dicom_file,
+    retrieve_filenames,
 )
 from .profile import stretch as stretcharray
-from .utilities import is_close, decode_binary
-from ..settings import get_dicom_cmap, PATH_TRUNCATION_LENGTH
+from .utilities import decode_binary, is_close
 
 ARRAY = "Array"
 DICOM = "DICOM"
@@ -129,7 +129,7 @@ def retrieve_image_files(path: str) -> List[str]:
 def load(
     path: Union[str, Path, ImageLike, np.ndarray, BinaryIO], **kwargs
 ) -> ImageLike:
-    """Load a DICOM image, JPG/TIF/BMP image, or numpy 2D array.
+    r"""Load a DICOM image, JPG/TIF/BMP image, or numpy 2D array.
 
     Parameters
     ----------
@@ -1169,9 +1169,7 @@ def _get_axis_value(self, axis_str: str, axis_dcm_attr: str) -> float:
                 axis_found = True
             # if it is, then make sure it follows the naming convention of <axis###>
             else:
-                match = re.search(
-                    r"(?<={})\d+".format(axis_str.lower()), filename.lower()
-                )
+                match = re.search(rf"(?<={axis_str.lower()})\d+", filename.lower())
                 if match is None:
                     raise ValueError(
                         f"The filename contains '{axis_str}' but could not read a number following it. Use the format '...{axis_str}<#>...'"