├── .gitignore ├── ComplexityScript.py ├── LICENSE ├── README.md ├── complexity ├── ApertureMetric.py ├── EsapiApertureMetric.py ├── PyApertureMetric.py ├── PyComplexityMetric.py ├── __init__.py ├── dicomrt.py └── misc.py ├── metrics_examples.py ├── requirements.txt ├── setup.py ├── test-requirements.txt └── tests ├── __init__.py ├── conftest.py ├── test_aperture.py ├── test_apertureIrregularityMetric.py ├── test_jaw.py ├── test_leafPair.py ├── test_leafSequenceVariability.py ├── test_modulationComplexityScore.py ├── test_modulationIndexScore.py ├── test_modulationIndexTotal.py ├── test_pyAperture.py ├── test_pyAperturesFromBeamCreator.py ├── test_pyComplexityMetric.py ├── test_pyMetersetsFromMetersetWeightsCreator.py └── tests_data └── RP_FiF.dcm /.gitignore: -------------------------------------------------------------------------------- 1 | # Created by .ignore support plugin (hsz.mobi) 2 | ### JetBrains template 3 | # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider 4 | # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839 5 | ### Python ### 6 | # Byte-compiled / optimized / DLL files 7 | __pycache__/ 8 | *.py[cod] 9 | *$py.class 10 | /test.py 11 | /Test2.py 12 | # C extensions 13 | *.so 14 | 15 | # Distribution / packaging 16 | .Python 17 | build/ 18 | develop-eggs/ 19 | dist/ 20 | downloads/ 21 | eggs/ 22 | .eggs/ 23 | lib/ 24 | lib64/ 25 | parts/ 26 | sdist/ 27 | var/ 28 | wheels/ 29 | pip-wheel-metadata/ 30 | share/python-wheels/ 31 | *.egg-info/ 32 | .installed.cfg 33 | *.egg 34 | MANIFEST 35 | # User-specific stuff 36 | .idea/**/workspace.xml 37 | .idea/**/tasks.xml 38 | .idea/**/usage.statistics.xml 39 | .idea/**/dictionaries 40 | .idea/**/shelf 41 | 42 | # Generated files 43 | .idea/**/contentModel.xml 44 | 45 | # Sensitive or high-churn files 46 | .idea/**/dataSources/ 47 | .idea/**/dataSources.ids 48 | .idea/**/dataSources.local.xml 49 | .idea/**/sqlDataSources.xml 50 | .idea/**/dynamic.xml 51 | .idea/**/uiDesigner.xml 52 | .idea/**/dbnavigator.xml 53 | 54 | # Gradle 55 | .idea/**/gradle.xml 56 | .idea/**/libraries 57 | 58 | # Gradle and Maven with auto-import 59 | # When using Gradle or Maven with auto-import, you should exclude module files, 60 | # since they will be recreated, and may cause churn. Uncomment if using 61 | # auto-import. 62 | # .idea/artifacts 63 | # .idea/compiler.xml 64 | # .idea/jarRepositories.xml 65 | # .idea/modules.xml 66 | # .idea/*.iml 67 | # .idea/modules 68 | # *.iml 69 | # *.ipr 70 | 71 | # CMake 72 | cmake-build-*/ 73 | 74 | # Mongo Explorer plugin 75 | .idea/**/mongoSettings.xml 76 | 77 | # File-based project format 78 | *.iws 79 | 80 | # IntelliJ 81 | out/ 82 | 83 | # mpeltonen/sbt-idea plugin 84 | .idea_modules/ 85 | 86 | # JIRA plugin 87 | atlassian-ide-plugin.xml 88 | 89 | # Cursive Clojure plugin 90 | .idea/replstate.xml 91 | 92 | # Crashlytics plugin (for Android Studio and IntelliJ) 93 | com_crashlytics_export_strings.xml 94 | crashlytics.properties 95 | crashlytics-build.properties 96 | fabric.properties 97 | 98 | # Editor-based Rest Client 99 | .idea/httpRequests 100 | 101 | # Android studio 3.1+ serialized cache file 102 | .idea/caches/build_file_checksums.ser 103 | 104 | .idea/.gitignore 105 | .idea/ApertureComplexity.iml 106 | .idea/deployment.xml 107 | .idea/inspectionProfiles/ 108 | .idea/misc.xml 109 | .idea/modules.xml 110 | .idea/vcs.xml 111 | -------------------------------------------------------------------------------- /ComplexityScript.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | import time 4 | 5 | from complexity.PyComplexityMetric import PyComplexityMetric 6 | from complexity.dicomrt import RTPlan 7 | 8 | if len(sys.argv) != 2: 9 | print("Usage: %s path to DICOM RT-PLAN file *.dcm" % (sys.argv[0])) 10 | sys.exit(1) 11 | 12 | st = time.time() 13 | plan_info = RTPlan(filename=sys.argv[1]) 14 | plan_dict = plan_info.get_plan() 15 | beams = [beam for k, beam in plan_dict["beams"].items()] 16 | complexity_obj = PyComplexityMetric() 17 | 18 | complexity_metric = complexity_obj.CalculateForPlan(None, plan_dict) 19 | ed = time.time() 20 | print("elapsed", ed - st) 21 | 22 | _, plan_file = os.path.split(sys.argv[1]) 23 | 24 | print("Reference: https://github.com/umro/Complexity") 25 | print("Python version by Victor Gabriel Leandro Alves, D.Sc. - victorgabr@gmail.com") 26 | print("Plan %s aperture complexity: %1.3f [mm-1]: " % (sys.argv[1], complexity_metric)) 27 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Aperture Complexity - IMRT/VMAT Plans 2 | 3 | It is a Python 3.x port of the Eclipse ESAPI plug-in script. 4 | As such, it aims to contain the complete functionality of the aperture complexity analysis. 5 | 6 | Since it uses DICOM standard, this module extends the methodology to any TPS that exports DICOM-RP files. 7 | 8 | More on misc.py file 9 | 10 | ## Getting Started 11 | 12 | Calculating weighed plan complexity - only IMRT or VMAT. 13 | 14 | 15 | python ComplexityScript.py path_to_dicom_RP_file 16 | 17 | Plotting aperture complexity per beam aperture using matplotlib. 18 | 19 | ```python 20 | import matplotlib.pyplot as plt 21 | 22 | from complexity.PyComplexityMetric import ( 23 | PyComplexityMetric, 24 | MeanAreaMetricEstimator, 25 | AreaMetricEstimator, 26 | ApertureIrregularityMetric, 27 | ) 28 | from complexity.dicomrt import RTPlan 29 | 30 | if __name__ == "__main__": 31 | # Path to DICOM RTPLAN file - IMRT/VMAT 32 | # pfile = "RP.dcm" 33 | path_to_rtplan_file = "RP.dcm" 34 | 35 | # Getting planning data from DICOM file. 36 | plan_info = RTPlan(filename=path_to_rtplan_file) 37 | plan_dict = plan_info.get_plan() 38 | 39 | metrics_list = [ 40 | PyComplexityMetric, 41 | MeanAreaMetricEstimator, 42 | AreaMetricEstimator, 43 | ApertureIrregularityMetric, 44 | ] 45 | units = ["CI [mm^-1]", "mm^2", "mm^2", "dimensionless"] 46 | 47 | # plotting results 48 | for unit, cc in zip(units, metrics_list): 49 | cc_obj = cc() 50 | # compute per plan 51 | plan_metric = cc_obj.CalculateForPlan(None, plan_dict) 52 | print(f"{cc.__name__} Plan Metric - {plan_metric} {unit}") 53 | for k, beam in plan_dict["beams"].items(): 54 | # skip setup fields 55 | if beam["TreatmentDeliveryType"] == "TREATMENT" and beam["MU"] > 0: 56 | fig = plt.figure(figsize=(6, 6)) 57 | # create a subplot 58 | ax = fig.add_subplot(111) 59 | cpx_beam_cp = cc_obj.CalculateForBeamPerAperture( 60 | None, plan_dict, beam 61 | ) 62 | ax.plot(cpx_beam_cp) 63 | ax.set_xlabel("Control Point") 64 | ax.set_ylabel(f"${unit}$") 65 | txt = f"{file_name} - Beam name: {beam['BeamName']} - {cc.__name__}" 66 | ax.set_title(txt) 67 | plt.show() 68 | 69 | ``` 70 | ## Example result 71 | Beam 1 72 | 73 | ![beam_1_complexity](https://user-images.githubusercontent.com/6777517/37774893-336082a8-2dc0-11e8-9c3f-6b15d8488d9f.png) 74 | 75 | 76 | ## Requirements 77 | pydicom, numpy, pandas, pytest for unit testing 78 | 79 | ## Installing 80 | python setup.py install 81 | 82 | ## Contributing 83 | 84 | Any bug fixes or improvements are welcome. 85 | 86 | ## Author 87 | Victor Gabriel Leandro Alves, D.Sc. 88 | Copyright 2017-2018 89 | 90 | ## Acknowledgments 91 | 92 | University of Michigan, Radiation Oncology 93 | [https://github.com/umro/Complexity](https://github.com/umro/Complexity) 94 | -------------------------------------------------------------------------------- /complexity/ApertureMetric.py: -------------------------------------------------------------------------------- 1 | """ 2 | ApertureMetric.py 3 | 4 | This module is a Python port of namespace Complexity.ApertureMetric of the Eclipse plug-in script used in the study: 5 | [Predicting deliverability of volumetric-modulated arc therapy (VMAT) plans using aperture complexity analysis] 6 | (http://www.jacmp.org/index.php/jacmp/article/view/6241). 7 | Also, see the blog post [Calculating Aperture Complexity Metrics] 8 | (http://www.carlosjanderson.com/calculating-aperture-complexity-metrics). 9 | 10 | Notes 11 | ----- 12 | 13 | .. Original Code: 14 | https://github.com/umro/Complexity 15 | 16 | Python port by. Victor Gabriel Leandro Alves 17 | victorgabr@gmail.com 18 | 19 | """ 20 | 21 | 22 | class Rect: 23 | def __init__(self, left: float, top: float, right: float, bottom: float) -> None: 24 | """ 25 | Rectangular dimension (used for leaf and jaw positions) 26 | it is relative to the top of the first leaf and the isocenter 27 | :param left: 28 | :param top: 29 | :param right: 30 | :param bottom: 31 | """ 32 | self.Left = left 33 | self.Top = top 34 | self.Right = right 35 | self.Bottom = bottom 36 | 37 | def __repr__(self): 38 | return "Position: left: %1.1f top: %1.1f right: %1.1f botton: %1.1f" % ( 39 | self.Left, 40 | self.Top, 41 | self.Right, 42 | self.Bottom, 43 | ) 44 | 45 | 46 | class Jaw: 47 | def __init__(self, left: float, top: float, right: float, bottom: float) -> None: 48 | self.jaw_position = Rect(left, top, right, bottom) 49 | 50 | @property 51 | def Position(self): 52 | return self.jaw_position 53 | 54 | @Position.setter 55 | def Position(self, value): 56 | self.jaw_position = value 57 | 58 | @property 59 | def Left(self): 60 | return self.jaw_position.Left 61 | 62 | @property 63 | def Top(self): 64 | return self.jaw_position.Top 65 | 66 | @property 67 | def Right(self): 68 | return self.jaw_position.Right 69 | 70 | @property 71 | def Bottom(self): 72 | return self.jaw_position.Bottom 73 | 74 | 75 | class LeafPair: 76 | def __init__(self, left, right, width, top, jaw): 77 | """ 78 | Left and right represent the bank A and B, respectively 79 | :param left: float 80 | :param right: float 81 | :param width: float 82 | :param top: float 83 | :param jaw: Jaw object 84 | """ 85 | self.position = Rect(left, top, right, top - width) 86 | self.width = width 87 | self.jaw = jaw 88 | 89 | @property 90 | def Position(self): 91 | return self.position 92 | 93 | @Position.setter 94 | def Position(self, value): 95 | self.position = value 96 | 97 | @property 98 | def Left(self): 99 | return self.position.Left 100 | 101 | @property 102 | def Top(self): 103 | return self.position.Top 104 | 105 | @property 106 | def Right(self): 107 | return self.position.Right 108 | 109 | @property 110 | def Bottom(self): 111 | return self.position.Bottom 112 | 113 | @property 114 | def Width(self): 115 | return self.width 116 | 117 | @Width.setter 118 | def Width(self, value): 119 | self.width = value 120 | 121 | @property 122 | def Jaw(self): 123 | """ 124 | Each leaf pair contains a reference to the jaw 125 | :return: 126 | """ 127 | return self.jaw 128 | 129 | @Jaw.setter 130 | def Jaw(self, value): 131 | self.jaw = value 132 | 133 | def FieldSize(self): 134 | if self.IsOutsideJaw(): 135 | return 0.0 136 | 137 | left = max(self.Jaw.Left, self.Left) 138 | right = min(self.Jaw.Right, self.Right) 139 | return right - left 140 | 141 | def FieldArea(self): 142 | return self.FieldSize() * self.OpenLeafWidth() 143 | 144 | def IsOutsideJaw(self): 145 | """ 146 | The reason for <= or >= instead of just < or > 147 | is that if the jaw edge is equal to the leaf edge, 148 | it's as if the jaw edge was the leaf edge, 149 | so it's safer to count the leaf as outside, 150 | so that the edges are not counted twice (leaf and jaw edge) 151 | """ 152 | return ( 153 | (self.Jaw.Top <= self.Bottom) 154 | or (self.Jaw.Bottom >= self.Top) 155 | or (self.Jaw.Left >= self.Right) 156 | or (self.Jaw.Right <= self.Left) 157 | ) 158 | 159 | def IsOpen(self): 160 | return self.FieldSize() > 0.0 161 | 162 | def IsOpenButBehindJaw(self): 163 | """ 164 | Used to warn the user that there is a leaf behind the jaws, 165 | even though it is open and within the top and bottom jaw edges 166 | """ 167 | return (self.FieldSize() > 0.0) and ( 168 | self.Jaw.Left > self.Left or self.Jaw.Right < self.Right 169 | ) 170 | 171 | def OpenLeafWidth(self): 172 | """ 173 | Returns the amount of leaf width that is open, 174 | considering the Position of the jaw 175 | """ 176 | if self.IsOutsideJaw(): 177 | return 0.0 178 | 179 | top = min(self.Jaw.Top, self.Top) 180 | bottom = max(self.Jaw.Bottom, self.Bottom) 181 | 182 | return top - bottom 183 | 184 | 185 | class Aperture: 186 | """ 187 | The first dimension of leafPositions corresponds to the bank, 188 | and the second dimension corresponds to the leaf pair. 189 | Leaf coordinates follow the IEC 61217 standard: 190 | 191 | Negative Y x = isocenter (0, 0) 192 | - 193 | | 194 | | 195 | | 196 | Negative X |----------x----------| Positive X 197 | | 198 | | 199 | | 200 | - 201 | Positive Y 202 | 203 | leafPositions and leafWidths must not be null, 204 | and they must have the same number of leaves 205 | 206 | jaw is the Position of the jaw (cannot be null), 207 | given as: 208 | 209 | left, top, right, bottom; for a completely open jaw, use: 210 | 211 | new double[] { double.MinValue, double.MinValue, 212 | double.MaxValue, double.MaxValue }; 213 | """ 214 | 215 | # todo translate this doc to python 216 | def __init__(self, leaf_positions, leaf_widths, jaw): 217 | """ 218 | :param leaf_positions: Numpy 2D array of floats 219 | :param leaf_widths: Numpy array 1D 220 | :param jaw: list with jaw positions 221 | """ 222 | self.jaw = self.CreateJaw(jaw) 223 | self.leaf_pairs = self.CreateLeafPairs(leaf_positions, leaf_widths, self.Jaw) 224 | 225 | def CreateLeafPairs(self, positions, widths, jaw): 226 | """ 227 | 228 | :param positions: 229 | :param widths: 230 | :param jaw: 231 | :return: 232 | """ 233 | leaf_tops = self.GetLeafTops(widths) 234 | 235 | pairs = [] 236 | for i in range(len(widths)): 237 | lp = LeafPair( 238 | positions[0, i], positions[1, i], widths[i], leaf_tops[i], jaw 239 | ) 240 | pairs.append(lp) 241 | return pairs 242 | 243 | @staticmethod 244 | def GetLeafTops(widths): 245 | """ 246 | Using the leaf widths, creates an array of the location 247 | of all the leaf tops (relative to the isocenter) 248 | 249 | :param widths: 250 | :return: 251 | """ 252 | # Todo add unit test 253 | leaf_tops = [0.0] * len(widths) 254 | 255 | # Leaf index right below isocenter 256 | middle_index = int(len(widths) / 2) 257 | 258 | # Do bottom half 259 | for i in range(middle_index + 1, len(widths)): 260 | leaf_tops[i] = leaf_tops[i - 1] - widths[i - 1] 261 | 262 | # Do top half 263 | i = middle_index - 1 264 | while i >= 0: 265 | leaf_tops[i] = leaf_tops[i + 1] + widths[i] 266 | i -= 1 267 | 268 | return leaf_tops 269 | 270 | @staticmethod 271 | def CreateJaw(pos): 272 | """ 273 | Creates Jaw object using x and y positions 274 | :param pos: [] position 275 | :return: Jaw 276 | """ 277 | return Jaw(pos[0], pos[1], pos[2], pos[3]) 278 | 279 | @property 280 | def Jaw(self): 281 | return self.jaw 282 | 283 | @Jaw.setter 284 | def Jaw(self, value): 285 | self.jaw = value 286 | 287 | @property 288 | def LeafPairs(self): 289 | return self.leaf_pairs 290 | 291 | @LeafPairs.setter 292 | def LeafPairs(self, value): 293 | self.leaf_pairs = value 294 | 295 | def HasOpenLeafBehindJaws(self): 296 | truth = [lp.IsOpenButBehindJaw() for lp in self.LeafPairs] 297 | return any(truth) 298 | 299 | def Area(self): 300 | return sum([lp.FieldArea() for lp in self.LeafPairs]) 301 | 302 | def side_perimeter(self): 303 | # Python does not support method overloading 304 | if len(self.LeafPairs) == 0: 305 | return 0.0 306 | 307 | # Top end of first leaf pair 308 | perimeter = self.LeafPairs[0].FieldSize() 309 | 310 | for i in range(len(self.LeafPairs)): 311 | perimeter += self.SidePerimeter(self.LeafPairs[i - 1], self.LeafPairs[i]) 312 | 313 | # Bottom end of last leaf pair 314 | 315 | perimeter += self.LeafPairs[-1].FieldSize() 316 | 317 | return perimeter 318 | 319 | def SidePerimeter(self, topLeafPair, bottomLeafPair): 320 | 321 | if self.LeafPairsAreOutsideJaw(topLeafPair, bottomLeafPair): 322 | # _____ ________ 323 | # | | 324 | # _____|___ |________ 325 | # +-------|------|---+ 326 | # _|_______| |___|_ 327 | 328 | return 0.0 329 | 330 | if self.JawTopIsBelowTopLeafPair(topLeafPair): 331 | # 332 | # _|___ ______|_ 333 | # +---|-------|------+ 334 | # _____|___ |________ 335 | # | | 336 | # _________| |_____ 337 | 338 | return bottomLeafPair.FieldSize() 339 | 340 | if self.JawBottomIsAboveBottomLeafPair(bottomLeafPair): 341 | # At this point, the edge between the top and bottom leaf pairs 342 | # should be fully or partially exposed (depending on the jaw) 343 | # ___ _______________ 344 | # +-|--|-------+ 345 | # _|_|__|_______|_______ 346 | # +-------|----+ | 347 | # _________| |_____ 348 | return topLeafPair.FieldSize() 349 | 350 | if self.LeafPairsAreDisjoint(topLeafPair, bottomLeafPair): 351 | # ___ __________ 352 | # +-|-------|--+ 353 | # _|_|___ |__|_______ 354 | # +-----|------+ | 355 | # _______| |_____ 356 | 357 | return topLeafPair.FieldSize() + bottomLeafPair.FieldSize() 358 | 359 | topEdgeLeft = max(self.Jaw.Left, topLeafPair.Left) 360 | bottomEdgeLeft = max(self.Jaw.Left, bottomLeafPair.Left) 361 | topEdgeRight = min(self.Jaw.Right, topLeafPair.Right) 362 | bottomEdgeRight = min(self.Jaw.Right, bottomLeafPair.Right) 363 | 364 | return abs(topEdgeLeft - bottomEdgeLeft) + abs(topEdgeRight - bottomEdgeRight) 365 | 366 | def LeafPairsAreOutsideJaw(self, topLeafPair, bottomLeafPair): 367 | return topLeafPair.IsOutsideJaw() and bottomLeafPair.IsOutsideJaw() 368 | 369 | def JawTopIsBelowTopLeafPair(self, topLeafPair): 370 | return self.Jaw.Top <= topLeafPair.Bottom 371 | 372 | def JawBottomIsAboveBottomLeafPair(self, bottomLeafPair): 373 | return self.Jaw.Bottom >= bottomLeafPair.Top 374 | 375 | def LeafPairsAreDisjoint(self, topLeafPair, bottomLeafPair): 376 | 377 | return (bottomLeafPair.Left > topLeafPair.Right) or ( 378 | bottomLeafPair.Right < topLeafPair.Left 379 | ) 380 | 381 | 382 | class EdgeMetricBase: 383 | def Calculate(self, aperture): 384 | return self.DivisionOrDefault(aperture.SidePerimeter(), aperture.Area()) 385 | 386 | @staticmethod 387 | def DivisionOrDefault(a, b): 388 | return a / b if b != 0 else 0 389 | -------------------------------------------------------------------------------- /complexity/EsapiApertureMetric.py: -------------------------------------------------------------------------------- 1 | """ 2 | EsapiApertureMetric.py 3 | 4 | This module is a Python port of namespace Complexity.ApertureMetric of the Eclipse plug-in script used in the study: 5 | [Predicting deliverability of volumetric-modulated arc therapy (VMAT) plans using aperture complexity analysis] 6 | (http://www.jacmp.org/index.php/jacmp/article/view/6241). 7 | Also, see the blog post [Calculating Aperture Complexity Metrics] 8 | (http://www.carlosjanderson.com/calculating-aperture-complexity-metrics). 9 | 10 | Notes 11 | ----- 12 | 13 | 14 | 15 | .. Original Code: 16 | https://github.com/umro/Complexity 17 | 18 | Python port by. Victor Gabriel Leandro Alves 19 | victorgabr@gmail.com 20 | 21 | """ 22 | 23 | from complexity import ApertureMetric 24 | from complexity.ApertureMetric import Aperture 25 | 26 | 27 | class ComplexityMetric: 28 | """ 29 | Abstract class that represents any complexity metric 30 | it implements many common methods, but leaves 31 | the actual metric calculation to subclasses 32 | """ 33 | 34 | def CalculateForPlan(self, patient, plan): 35 | """ 36 | Returns the complexity metric of a plan, calculated as 37 | the weighted sum of the individual metrics for each beam 38 | :param patient: Patient Class 39 | :param plan: Plan class 40 | :return: metric 41 | """ 42 | weights = self.GetWeightsPlan(plan) 43 | metrics = self.GetMetricsPlan(patient, plan) 44 | return self.WeightedSum(weights, metrics) 45 | 46 | def GetWeightsPlan(self, plan): 47 | """ 48 | Returns the weights of a plan's beams 49 | by default, the weights are the meterset values per beam 50 | :param plan: DicomParser plan dict 51 | """ 52 | return self.GetMeterSetsPlan(plan) 53 | 54 | def GetMeterSetsPlan(self, plan): 55 | """ 56 | Returns the total metersets of a plan's beams 57 | :param plan: 58 | :return: metersets of a plan's beams 59 | """ 60 | return NotImplementedError 61 | 62 | def GetMetricsPlan(self, patient, plan): 63 | """ 64 | Returns the unweighted metrics of a plan's beams 65 | :param patient: 66 | :param plan: 67 | :return: 68 | """ 69 | return self.CalculateForPlanPerBeam(patient, plan) 70 | 71 | def CalculateForPlanPerBeam(self, patient, plan): 72 | """ 73 | Returns the unweighted metrics of a plan's non-setup beams 74 | :param patient: 75 | :param plan: 76 | :return: 77 | """ 78 | return NotImplementedError 79 | 80 | def CalculateForBeam(self, patient, plan, beam): 81 | """ 82 | Returns the complexity metric of a beam, calculated as 83 | the weighted sum of the individual metrics for each control point 84 | :param patient: 85 | :param plan: 86 | :param beam: 87 | :return: 88 | """ 89 | weights = self.GetWeightsBeam(beam) 90 | values = self.GetMetricsBeam(patient, plan, beam) 91 | 92 | return self.WeightedSum(weights, values) 93 | 94 | def GetWeightsBeam(self, beam): 95 | """ 96 | Returns the weights of a beam's control points 97 | by default, the weights are the meterset values per control point 98 | :param beam: 99 | :return: 100 | """ 101 | return self.GetMetersetsBeam(beam) 102 | 103 | def GetMetersetsBeam(self, beam): 104 | """ 105 | Returns the metersets of a beam's control points 106 | :param beam: 107 | :return: 108 | """ 109 | 110 | return MetersetsFromMetersetWeightsCreator().Create(beam) 111 | 112 | def GetMetricsBeam(self, patient, plan, beam): 113 | """ 114 | Returns the unweighted metrics of a beam's control points 115 | :param patient: 116 | :param plan: 117 | :param beam: 118 | :return: 119 | """ 120 | return self.CalculateForBeamPerAperture(patient, plan, beam) 121 | 122 | def CalculateForBeamPerAperture(self, patient, plan, beam): 123 | apertures = self.CreateApertures(patient, plan, beam) 124 | return self.CalculatePerAperture(apertures) 125 | 126 | def CalculatePerAperture(self, param): 127 | """ 128 | Returns the unweighted metrics of a list of apertures 129 | it must be overridden by a subclass 130 | :param param: 131 | :return: 132 | """ 133 | return NotImplementedError 134 | 135 | def CreateApertures(self, patient, plan, beam): 136 | """ 137 | Returns the apertures created from a beam 138 | :param patient: 139 | :param plan: 140 | :param beam: 141 | :return: 142 | """ 143 | return AperturesFromBeamCreator().Create(patient, plan, beam) 144 | 145 | def CalculatePerControlPointWeighted(self, patient, plan, beam): 146 | """ 147 | Returns the weighted metrics of a beam's control points 148 | :param patient: 149 | :param plan: 150 | :param beam: 151 | :return: 152 | """ 153 | return self.WeightedValues( 154 | self.GetWeightsBeam(beam), self.GetMetricsBeam(patient, plan, beam) 155 | ) 156 | 157 | def CalculatePerControlPointUnweighted(self, patient, plan, beam): 158 | """ 159 | Returns the unweighted metrics of a beam's control points 160 | :param patient: 161 | :param plan: 162 | :param beam: 163 | :return: 164 | """ 165 | return self.GetMetricsBeam(patient, plan, beam) 166 | 167 | def CalculatePerControlPointWeightsOnly(self, beam): 168 | """ 169 | Returns the weights of a beam's control points 170 | :param beam: 171 | :return: 172 | """ 173 | return self.GetWeightsBeam(beam) 174 | 175 | def WeightedSum(self, weights, values): 176 | """ 177 | Returns the weighted sum of the given values and weights 178 | :param weights: 179 | :param values: 180 | :return: 181 | """ 182 | return sum(self.WeightedValues(weights, values)) 183 | 184 | @staticmethod 185 | def WeightedValues(weights, values): 186 | weightSum = sum(weights) 187 | result = [] 188 | for i in range(len(values)): 189 | v = (weights[i] / weightSum) * values[i] 190 | result.append(v) 191 | return result 192 | 193 | 194 | class MetersetsFromMetersetWeightsCreator: 195 | def Create(self, beam): 196 | if beam["PrimaryDosimeterUnit"] != "MU" or "MU" not in beam: 197 | return None 198 | 199 | metersetWeights = self.GetMetersetWeights(beam["ControlPointSequence"]) 200 | metersets = self.ConvertMetersetWeightsToMetersets(beam["MU"], metersetWeights) 201 | 202 | return self.UndoCummulativeSum(metersets) 203 | 204 | @staticmethod 205 | def GetMetersetWeights(ControlPoints): 206 | return [float(cp.CumulativeMetersetWeight) for cp in ControlPoints] 207 | 208 | @staticmethod 209 | def ConvertMetersetWeightsToMetersets(beamMeterset, metersetWeights): 210 | finalMetersetWeight = metersetWeights[-1] 211 | return [beamMeterset * x / finalMetersetWeight for x in metersetWeights] 212 | 213 | @staticmethod 214 | def UndoCummulativeSum(cummulativeSum): 215 | """ 216 | Returns the values whose cummulative sum is "cummulativeSum" 217 | :param cummulativeSum: 218 | :return: 219 | """ 220 | values = [0] * len(cummulativeSum) 221 | 222 | delta_prev = 0.0 223 | for i in range(len(values) - 1): 224 | delta_curr = cummulativeSum[i + 1] - cummulativeSum[i] 225 | values[i] = 0.5 * delta_prev + 0.5 * delta_curr 226 | delta_prev = delta_curr 227 | 228 | values[-1] = 0.5 * delta_prev 229 | 230 | return values 231 | 232 | 233 | class AperturesFromBeamCreator: 234 | def Create(self, patient, plan, beam): 235 | apertures = [] 236 | leafWidths = self.GetLeafWidths(patient, plan, beam) 237 | 238 | for controlPoint in beam.ControlPointSequence: 239 | leafPositions = self.GetLeafPositions(controlPoint) 240 | jaw = self.CreateJaw(controlPoint) 241 | apertures.append(Aperture(leafPositions, leafWidths, jaw)) 242 | 243 | return apertures 244 | 245 | @staticmethod 246 | def CreateJaw(cp): 247 | left = cp.JawPositions.X1 248 | top = cp.JawPositions.Y2 249 | right = cp.JawPositions.X2 250 | bottom = cp.JawPositions.Y1 251 | 252 | return [left, top, right, bottom] 253 | 254 | def GetLeafWidths(self, patient, plan, beam): 255 | return self.GetLeafWidthsFromAria(patient, plan, beam) 256 | 257 | def GetLeafWidthsFromAria(self, patient, plan, beam): 258 | return NotImplementedError 259 | 260 | def GetLeafPositions(self, controlPoint): 261 | # Leaf positions are given from bottom to top by ESAPI, 262 | # but the Aperture class expects them from top to bottom 263 | # leafPositions[i, j] = controlPoint.LeafPositions[i, n - j - 1] 264 | 265 | # return leafPositions 266 | return NotImplementedError 267 | 268 | 269 | class EdgeMetric(ComplexityMetric): 270 | def CalculatePerAperture(self, apertures): 271 | metric = ApertureMetric.EdgeMetricBase() 272 | return [metric.Calculate(aperture) for aperture in apertures] 273 | -------------------------------------------------------------------------------- /complexity/PyApertureMetric.py: -------------------------------------------------------------------------------- 1 | # Typing imports 2 | from typing import List, Dict 3 | from pydicom.dataset import Dataset 4 | 5 | import numpy as np 6 | 7 | from complexity.ApertureMetric import Aperture, LeafPair, Jaw 8 | 9 | 10 | class PyLeafPair(LeafPair): 11 | def __init__( 12 | self, left: float, right: float, width: float, top: float, jaw: Jaw 13 | ) -> None: 14 | super().__init__(left, right, width, top, jaw) 15 | 16 | def __repr__(self): 17 | txt = "Leaf Pair: left: %1.1f top: %1.1f right: %1.1f botton: %1.1f" % ( 18 | self.Left, 19 | self.Top, 20 | self.Right, 21 | self.Bottom, 22 | ) 23 | 24 | return txt 25 | 26 | 27 | class PyAperture(Aperture): 28 | def __init__( 29 | self, 30 | leaf_positions: np.ndarray, 31 | leaf_widths: np.ndarray, 32 | jaw: List[float], 33 | gantry_angle: float, 34 | ) -> None: 35 | super().__init__(leaf_positions, leaf_widths, jaw) 36 | self.gantry_angle = gantry_angle 37 | 38 | def CreateLeafPairs( 39 | self, positions: np.ndarray, widths: np.ndarray, jaw: Jaw 40 | ) -> List[PyLeafPair]: 41 | leaf_tops = self.GetLeafTops(widths) 42 | 43 | pairs = [] 44 | for i in range(len(widths)): 45 | lp = PyLeafPair( 46 | positions[0, i], positions[1, i], widths[i], leaf_tops[i], jaw 47 | ) 48 | pairs.append(lp) 49 | return pairs 50 | 51 | @property 52 | def LeafPairArea(self) -> List[float]: 53 | return [lp.FieldArea() for lp in self.LeafPairs] 54 | 55 | @property 56 | def GantryAngle(self) -> float: 57 | return self.gantry_angle 58 | 59 | @GantryAngle.setter 60 | def GantryAngle(self, value: float): 61 | self.gantry_angle = value 62 | 63 | def __repr__(self): 64 | txt = "Aperture - Gantry: %1.1f" % self.GantryAngle 65 | return txt 66 | 67 | 68 | class PyAperturesFromBeamCreator: 69 | def Create(self, beam: Dict[str, str]) -> List[PyAperture]: 70 | 71 | apertures = [] 72 | 73 | leafWidths = self.GetLeafWidths(beam) 74 | cp_jaw = self.CreateJaw(beam) 75 | for controlPoint in beam["ControlPointSequence"]: 76 | gantry_angle = ( 77 | float(controlPoint.GantryAngle) 78 | if "GantryAngle" in controlPoint 79 | else beam["GantryAngle"] 80 | ) 81 | leafPositions = self.GetLeafPositions(controlPoint) 82 | new_jaw_position = self.get_jaw_position_per_control_point(controlPoint, leafWidths) 83 | if new_jaw_position: 84 | cp_jaw = new_jaw_position 85 | if leafPositions is not None: 86 | apertures.append( 87 | PyAperture(leafPositions, leafWidths, cp_jaw, gantry_angle) 88 | ) 89 | 90 | return apertures 91 | 92 | @staticmethod 93 | def CreateJaw(beam: dict) -> List[float]: 94 | """ 95 | but the Aperture class expects cartesian y-axis 96 | :param beam: 97 | :return: 98 | """ 99 | 100 | # if there is no X jaws, consider open 400 mm 101 | left = float(beam["ASYMX"][0]) if "ASYMX" in beam else -200.0 102 | right = float(beam["ASYMX"][1]) if "ASYMX" in beam else 200.0 103 | top = float(beam["ASYMY"][0]) if "ASYMY" in beam else -200.0 104 | bottom = float(beam["ASYMY"][1]) if "ASYMY" in beam else 200.0 105 | 106 | # invert y axis to match apperture class -top, -botton that uses Varian standard ESAPI 107 | return [left, -top, right, -bottom] 108 | 109 | def GetLeafWidths(self, beam_dict: Dict) -> np.ndarray: 110 | """ 111 | Get MLCX leaf width from BeamLimitingDeviceSequence 112 | (300a, 00be) Leaf Position Boundaries Tag 113 | 114 | #TODO HALCYON leaf widths 115 | :param beam_dict: Dicomparser Beam dict from plan_dict 116 | :return: MLCX leaf width 117 | """ 118 | 119 | bs = beam_dict["BeamLimitingDeviceSequence"] 120 | # the script only takes MLCX as parameter 121 | for b in bs: 122 | if b.RTBeamLimitingDeviceType in ["MLCX", "MLCX1", "MLCX2"]: 123 | return np.diff(b.LeafPositionBoundaries) 124 | 125 | def GetLeafTops(self, beam_dict: Dict) -> np.ndarray: 126 | """ 127 | Get MLCX leaf Tops from BeamLimitingDeviceSequence 128 | (300a, 00be) Leaf Position Boundaries Tag 129 | :param beam_dict: Dicomparser Beam dict from plan_dict 130 | :return: MLCX leaf width 131 | """ 132 | bs = beam_dict["BeamLimitingDeviceSequence"] 133 | for b in bs: 134 | if b.RTBeamLimitingDeviceType == "MLCX": 135 | return np.array(b.LeafPositionBoundaries[:-1], dtype=float) 136 | 137 | def GetLeafPositions(self, control_point: Dataset) -> np.ndarray: 138 | """ 139 | Leaf positions are given from bottom to top by ESAPI, 140 | but the Aperture class expects them from top to bottom 141 | Leaf Positions are mechanical boundaries projected onto Isocenter plane 142 | # TODO add halcyon MLC positions 143 | :param control_point: 144 | """ 145 | if "BeamLimitingDevicePositionSequence" in control_point: 146 | pos = control_point.BeamLimitingDevicePositionSequence[-1] 147 | mlc_open = pos.LeafJawPositions 148 | n_pairs = int(len(mlc_open) / 2) 149 | bank_a_pos = mlc_open[:n_pairs] 150 | bank_b_pos = mlc_open[n_pairs:] 151 | 152 | return np.vstack((bank_a_pos, bank_b_pos)) 153 | 154 | def return_jaw_position_from_mlc(self, positions, leafwidths: np.ndarray): 155 | """ 156 | Finding left/right isn't hard, just take min and max when they aren't equal 157 | Finding top/bottom is difficult. We need to find the first and last leaf pairs that are touching 158 | Then use the leaf thicknesses to identify that physical location as a distance from the center 159 | """ 160 | left_leaves = np.asarray(positions[:len(positions) // 2]) 161 | right_leaves = np.asarray(positions[len(positions) // 2:]) 162 | left = np.min(left_leaves[left_leaves != right_leaves]) 163 | right = np.max(right_leaves[left_leaves != right_leaves]) 164 | center = len(positions)//4 165 | top_bottom = np.where(left_leaves != right_leaves) 166 | diff_bottom = center - top_bottom[0][0] 167 | if diff_bottom > 0: 168 | bottom = np.sum(leafwidths[center-diff_bottom:center]) 169 | else: 170 | bottom = -np.sum(leafwidths[center:center-diff_bottom]) 171 | diff_top = center - top_bottom[0][-1] 172 | if diff_top > 0: 173 | top = np.sum(leafwidths[center-diff_top:center]) 174 | else: 175 | top = -np.sum(leafwidths[center:center-diff_top]) 176 | return [left, top, right, bottom] 177 | 178 | def get_jaw_position_per_control_point(self, control_point: Dataset, leafwidths: np.ndarray) -> List[float]: 179 | """ 180 | Get jaw positions from control point 181 | :param 182 | """ 183 | if "BeamLimitingDevicePositionSequence" in control_point: 184 | sequence = control_point.BeamLimitingDevicePositionSequence 185 | # check if there's a jaw position per control point 186 | mlc_jaws = [s.LeafJawPositions for s in sequence if s.RTBeamLimitingDeviceType.find("MLCX") == 0] 187 | x_jaws = [s.LeafJawPositions for s in sequence if s.RTBeamLimitingDeviceType == "X"] 188 | y_jaws = [s.LeafJawPositions for s in sequence if s.RTBeamLimitingDeviceType == "Y"] 189 | x_jaws_asym = [s.LeafJawPositions for s in sequence if s.RTBeamLimitingDeviceType == "ASYMX"] 190 | y_jaws_asym = [s.LeafJawPositions for s in sequence if s.RTBeamLimitingDeviceType == "ASYMY"] 191 | """ 192 | Checking first to see if we have jaw positions, which will be 2 points 193 | """ 194 | if ((x_jaws and y_jaws) or (x_jaws_asym and y_jaws_asym)) and len(leafwidths) != 28: 195 | if x_jaws: 196 | left, right = x_jaws[0] 197 | top, bottom = y_jaws[0] 198 | return [float(left), float(-top), float(right), float(-bottom)] 199 | if x_jaws_asym: 200 | left, right = x_jaws_asym[0] 201 | top, bottom = y_jaws_asym[0] 202 | return [float(left), float(-top), float(right), float(-bottom)] 203 | elif mlc_jaws and len(leafwidths) == 28: # Make sure it is a Halcyon MLC 204 | """ 205 | If we have halcyon style, which has 2N values, 101, 102, ..., 201, 202, ... 206 | https://dicom.innolitics.com/ciods/rt-image/rt-image/30020030/300a00b6/300a011c 207 | """ 208 | for mlc_jaw in mlc_jaws: 209 | left, top, right, bottom = self.return_jaw_position_from_mlc(mlc_jaw, leafwidths) 210 | return [float(left), float(-top), float(right), float(-bottom)] 211 | return [] 212 | 213 | class PyMetersetsFromMetersetWeightsCreator: 214 | def Create(self, beam: Dict[str, str]) -> np.ndarray: 215 | if beam["PrimaryDosimeterUnit"] != "MU": 216 | return None 217 | 218 | metersetWeights = self.GetMetersetWeights(beam["ControlPointSequence"]) 219 | metersets = self.ConvertMetersetWeightsToMetersets(beam["MU"], metersetWeights) 220 | 221 | return self.UndoCummulativeSum(metersets) 222 | 223 | def GetCumulativeMetersets(self, beam): 224 | metersetWeights = self.GetMetersetWeights(beam["ControlPointSequence"]) 225 | metersets = self.ConvertMetersetWeightsToMetersets(beam["MU"], metersetWeights) 226 | return metersets 227 | 228 | @staticmethod 229 | def GetMetersetWeights(ControlPoints): 230 | return np.array( 231 | [cp.CumulativeMetersetWeight for cp in ControlPoints], dtype=float 232 | ) 233 | 234 | @staticmethod 235 | def ConvertMetersetWeightsToMetersets(beamMeterset, metersetWeights): 236 | return beamMeterset * metersetWeights / metersetWeights[-1] 237 | 238 | @staticmethod 239 | def UndoCummulativeSum(cummulativeSum): 240 | """ 241 | Returns the values whose cummulative sum is "cummulativeSum" 242 | :param cummulativeSum: 243 | :return: 244 | """ 245 | 246 | values = np.zeros(len(cummulativeSum)) 247 | delta_prev = 0.0 248 | for i in range(len(values) - 1): 249 | delta_curr = cummulativeSum[i + 1] - cummulativeSum[i] 250 | values[i] = 0.5 * delta_prev + 0.5 * delta_curr 251 | delta_prev = delta_curr 252 | 253 | values[-1] = 0.5 * delta_prev 254 | 255 | return values 256 | -------------------------------------------------------------------------------- /complexity/PyComplexityMetric.py: -------------------------------------------------------------------------------- 1 | import numpy 2 | import numpy as np 3 | 4 | from complexity.ApertureMetric import EdgeMetricBase 5 | from complexity.EsapiApertureMetric import ComplexityMetric 6 | from complexity.PyApertureMetric import ( 7 | PyAperturesFromBeamCreator, 8 | PyMetersetsFromMetersetWeightsCreator, 9 | PyAperture, 10 | ) 11 | 12 | from typing import Dict, List 13 | 14 | 15 | class PyEdgeMetricBase(EdgeMetricBase): 16 | def Calculate(self, aperture: PyAperture) -> float: 17 | return self.DivisionOrDefault(aperture.side_perimeter(), aperture.Area()) 18 | 19 | @staticmethod 20 | def DivisionOrDefault(a: float, b: float) -> float: 21 | return a / b if b != 0 else 0.0 22 | 23 | 24 | class PyComplexityMetric(ComplexityMetric): 25 | # TODO add unit tests 26 | 27 | def CalculateForPlan( 28 | self, patient: None = None, plan: Dict[str, str] = None 29 | ) -> float: 30 | """ 31 | Returns the complexity metric of a plan, calculated as 32 | the weighted sum of the individual metrics for each beam 33 | :param patient: Patient Class 34 | :param plan: Plan class 35 | :return: metric 36 | """ 37 | weights = self.GetWeightsPlan(plan) 38 | metrics = self.GetMetricsPlan(patient, plan) 39 | 40 | return self.WeightedSum(weights, metrics) 41 | 42 | def GetWeightsPlan(self, plan: Dict[str, str]) -> List[float]: 43 | """ 44 | Returns the weights of a plan's beams 45 | by default, the weights are the meterset values per beam 46 | :param plan: DicomParser plan dict 47 | """ 48 | return self.GetMeterSetsPlan(plan) 49 | 50 | def GetMeterSetsPlan(self, plan: Dict[str, str]) -> List[float]: 51 | """ 52 | Returns the total metersets of a plan's beams 53 | :param plan: DicomParser plan dictionaty 54 | :return: metersets of a plan's beams 55 | """ 56 | 57 | metersets = [] 58 | for k, beam in plan["beams"].items(): 59 | if "MU" in beam: 60 | if beam["MU"] > 0: 61 | metersets.append(float(beam["MU"])) 62 | 63 | return metersets 64 | 65 | def GetMetersetsBeam(self, beam: Dict[str, str]) -> np.ndarray: 66 | """ 67 | Returns the metersets of a beam's control points 68 | :param beam: 69 | :return: 70 | """ 71 | return PyMetersetsFromMetersetWeightsCreator().Create(beam) 72 | 73 | def CalculateForPlanPerBeam( 74 | self, patient: None, plan: Dict[str, str] 75 | ) -> List[float]: 76 | """ 77 | Returns the unweighted metrics of a plan's non-setup beams 78 | :param patient: 79 | :param plan: 80 | :return: 81 | """ 82 | values = [] 83 | for k, beam in plan["beams"].items(): 84 | # check if treatment beam 85 | if beam["TreatmentDeliveryType"] == "TREATMENT": 86 | if beam["MU"] > 0.0: 87 | v = self.CalculateForBeam(patient, plan, beam) 88 | values.append(v) 89 | 90 | return values 91 | 92 | def CalculatePerAperture(self, apertures: List[PyAperture]) -> List[float]: 93 | metric = PyEdgeMetricBase() 94 | return [metric.Calculate(aperture) for aperture in apertures] 95 | 96 | def CalculateForBeamPerAperture( 97 | self, patient: None, plan: Dict[str, str], beam: Dict[str, str] 98 | ) -> List[float]: 99 | apertures = self.CreateApertures(patient, plan, beam) 100 | return self.CalculatePerAperture(apertures) 101 | 102 | def CreateApertures( 103 | self, patient: None, plan: Dict[str, str], beam: Dict[str, str] 104 | ) -> List[PyAperture]: 105 | """ 106 | Added default parameter to meet Liskov substitution principle 107 | :param patient: 108 | :param plan: 109 | :param beam: 110 | :return: 111 | """ 112 | return PyAperturesFromBeamCreator().Create(beam) 113 | 114 | 115 | class MeanApertureAreaMetric: 116 | def Calculate(self, aperture): 117 | """ 118 | Calculates the mean aperture area of all leaf pairs 119 | :param aperture: 120 | :return: 121 | """ 122 | areas = np.array(aperture.LeafPairArea) 123 | return areas[np.nonzero(areas)].mean() 124 | 125 | 126 | class MeanAreaMetricEstimator(PyComplexityMetric): 127 | def CalculatePerAperture(self, apertures): 128 | metric = MeanApertureAreaMetric() 129 | return [metric.Calculate(aperture) for aperture in apertures] 130 | 131 | 132 | class ApertureAreaMetric: 133 | def Calculate(self, aperture): 134 | """ 135 | return the aperture area. 136 | :param aperture: 137 | :return: 138 | """ 139 | return aperture.Area() 140 | 141 | 142 | class AreaMetricEstimator(PyComplexityMetric): 143 | def CalculatePerAperture(self, apertures): 144 | metric = ApertureAreaMetric() 145 | return [metric.Calculate(aperture) for aperture in apertures] 146 | 147 | 148 | class ApertureIrregularity: 149 | def Calculate(self, aperture): 150 | aa = aperture.Area() 151 | ap = aperture.side_perimeter() 152 | return self.DivisionOrDefault(ap ** 2, 4 * np.pi * aa) 153 | 154 | @staticmethod 155 | def DivisionOrDefault(a, b): 156 | return a / b if b != 0 else 0 157 | 158 | 159 | class ApertureIrregularityMetric(PyComplexityMetric): 160 | def CalculatePerAperture(self, apertures): 161 | """ 162 | Du W, Cho SH, Zhang X, Hoffman KE, Kudchadker RJ. Quantification of beam 163 | complexity in intensity-modulated radiation therapy treatment plans. Med 164 | Phys 2014;41:21716. http://dx.doi.org/10.1118/1.4861821. 165 | :param apertures: list of beam apertures 166 | :return: 167 | """ 168 | metric = ApertureIrregularity() 169 | return [metric.Calculate(aperture) for aperture in apertures] 170 | -------------------------------------------------------------------------------- /complexity/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/victorgabr/ApertureComplexity/fbb25e756dd2a7b265a77cb6903fe69e868cce6e/complexity/__init__.py -------------------------------------------------------------------------------- /complexity/dicomrt.py: -------------------------------------------------------------------------------- 1 | # Copyright (c) 2009-2016 Aditya Panchal 2 | # Copyright (c) 2009-2010 Roy Keyes 3 | # This class is derived from dicomparser.py of dicompyler-core, released under a BSD license. 4 | # See the file license.txt included with this distribution, also 5 | # available at https://github.com/dicompyler/dicompyler-core/ 6 | from typing import Dict 7 | 8 | import numpy as np 9 | import pydicom as dicom 10 | from pydicom.valuerep import IS 11 | 12 | 13 | class RTPlan: 14 | """Class that parses and returns formatted DICOM RT Plan data.""" 15 | 16 | def __init__(self, filename: str) -> None: 17 | 18 | if filename: 19 | self.plan = dict() 20 | try: 21 | # Only pydicom 0.9.5 and above supports the force read argument 22 | if dicom.__version__ >= "0.9.5": 23 | self.ds = dicom.read_file(filename, defer_size=100, force=True) 24 | else: 25 | self.ds = dicom.read_file(filename, defer_size=100) 26 | except (EOFError, IOError): 27 | # Raise the error for the calling method to handle 28 | raise 29 | else: 30 | # Sometimes DICOM files may not have headers, but they should always 31 | # have a SOPClassUID to declare what type of file it is. If the 32 | # file doesn't have a SOPClassUID, then it probably isn't DICOM. 33 | if "SOPClassUID" not in self.ds: 34 | raise AttributeError 35 | else: 36 | raise AttributeError 37 | 38 | def get_plan(self) -> Dict[str, str]: 39 | """Returns the plan information.""" 40 | self.plan["label"] = self.ds.RTPlanLabel 41 | self.plan["date"] = self.ds.RTPlanDate 42 | self.plan["time"] = self.ds.RTPlanTime 43 | self.plan["name"] = "" 44 | self.plan["rxdose"] = 0.0 45 | if "DoseReferenceSequence" in self.ds: 46 | for item in self.ds.DoseReferenceSequence: 47 | if item.DoseReferenceStructureType == "SITE": 48 | self.plan["name"] = "N/A" 49 | if "DoseReferenceDescription" in item: 50 | self.plan["name"] = item.DoseReferenceDescription 51 | if "TargetPrescriptionDose" in item: 52 | rxdose = item.TargetPrescriptionDose * 100 53 | if rxdose > self.plan["rxdose"]: 54 | self.plan["rxdose"] = rxdose 55 | elif item.DoseReferenceStructureType == "VOLUME": 56 | if "TargetPrescriptionDose" in item: 57 | self.plan["rxdose"] = item.TargetPrescriptionDose * 100 58 | if ("FractionGroupSequence" in self.ds) and (self.plan["rxdose"] == 0): 59 | fg = self.ds.FractionGroupSequence[0] 60 | if ("ReferencedBeamSequence" in fg) and ("NumberofFractionsPlanned" in fg): 61 | beams = fg.ReferencedBeamSequence 62 | fx = fg.NumberofFractionsPlanned 63 | for beam in beams: 64 | if "BeamDose" in beam: 65 | self.plan["rxdose"] += beam.BeamDose * fx * 100 66 | 67 | if "FractionGroupSequence" in self.ds: 68 | fg = self.ds.FractionGroupSequence[0] 69 | if "ReferencedBeamSequence" in fg: 70 | self.plan["fractions"] = fg.NumberOfFractionsPlanned 71 | self.plan["rxdose"] = int(self.plan["rxdose"]) 72 | 73 | # referenced beams 74 | ref_beams = self.get_beams() 75 | self.plan["beams"] = ref_beams 76 | 77 | # try estimate the number of isocenters 78 | isos = np.array([ref_beams[i]["IsocenterPosition"] for i in ref_beams]) 79 | 80 | # round to 2 decimals 81 | isos = np.round(isos, 2) 82 | dist = np.sqrt(np.sum((isos - isos[0]) ** 2, axis=1)) 83 | self.plan["n_isocenters"] = len(np.unique(dist)) 84 | 85 | # Total number of MU 86 | total_mu = np.sum( 87 | [ref_beams[b]["MU"] for b in ref_beams if "MU" in ref_beams[b]] 88 | ) 89 | self.plan["Plan_MU"] = total_mu 90 | 91 | tmp = self.get_study_info() 92 | self.plan["description"] = tmp["description"] 93 | if "RTPlanName" in self.ds: 94 | self.plan["plan_name"] = self.ds.RTPlanName 95 | else: 96 | self.plan["plan_name"] = "" 97 | if "PatientsName" in self.ds: 98 | name = ( 99 | self.ds.PatientsName.family_comma_given() 100 | .replace(",", "") 101 | .replace("^", " ") 102 | .strip() 103 | ) 104 | self.plan["patient_name"] = name 105 | else: 106 | self.plan["patient_name"] = "" 107 | return self.plan 108 | 109 | def get_beams(self, fx: int = 0) -> Dict[IS, Dict[str, str]]: 110 | """Return the referenced beams from the specified fraction.""" 111 | 112 | beams = {} 113 | if "BeamSequence" in self.ds: 114 | bdict = self.ds.BeamSequence 115 | elif "IonBeamSequence" in self.ds: 116 | bdict = self.ds.IonBeamSequence 117 | else: 118 | return beams 119 | # Obtain the beam information 120 | for bi in bdict: 121 | beam = dict() 122 | beam["Manufacturer"] = bi.Manufacturer if "Manufacturer" in bi else "" 123 | beam["InstitutionName"] = ( 124 | bi.InstitutionName if "InstitutionName" in bi else "" 125 | ) 126 | beam["TreatmentMachineName"] = ( 127 | bi.TreatmentMachineName if "TreatmentMachineName" in bi else "" 128 | ) 129 | beam["BeamName"] = bi.BeamName if "BeamName" in bi else "" 130 | beam["SourcetoSurfaceDistance"] = ( 131 | bi.SourcetoSurfaceDistance if "SourcetoSurfaceDistance" in bi else "" 132 | ) 133 | beam["BeamDescription "] = ( 134 | bi.BeamDescription if "BeamDescription" in bi else "" 135 | ) 136 | beam["BeamType"] = bi.BeamType if "BeamType" in bi else "" 137 | beam["RadiationType"] = bi.RadiationType if "RadiationType" in bi else "" 138 | beam["ManufacturerModelName"] = ( 139 | bi.ManufacturerModelName if "ManufacturerModelName" in bi else "" 140 | ) 141 | beam["PrimaryDosimeterUnit"] = ( 142 | bi.PrimaryDosimeterUnit if "PrimaryDosimeterUnit" in bi else "" 143 | ) 144 | beam["NumberofWedges"] = bi.NumberofWedges if "NumberofWedges" in bi else "" 145 | beam["NumberofCompensators"] = ( 146 | bi.NumberofCompensators if "NumberofCompensators" in bi else "" 147 | ) 148 | beam["NumberofBoli"] = bi.NumberofBoli if "NumberofBoli" in bi else "" 149 | beam["NumberofBlocks"] = bi.NumberofBlocks if "NumberofBlocks" in bi else "" 150 | ftemp = ( 151 | bi.FinalCumulativeMetersetWeight 152 | if "FinalCumulativeMetersetWeight" in bi 153 | else "" 154 | ) 155 | beam["FinalCumulativeMetersetWeight"] = ftemp 156 | beam["NumberofControlPoints"] = ( 157 | bi.NumberofControlPoints if "NumberofControlPoints" in bi else "" 158 | ) 159 | beam["TreatmentDeliveryType"] = ( 160 | bi.TreatmentDeliveryType if "TreatmentDeliveryType" in bi else "" 161 | ) 162 | 163 | # adding mlc info from BeamLimitingDeviceSequence 164 | beam_limits = ( 165 | bi.BeamLimitingDeviceSequence 166 | if "BeamLimitingDeviceSequence" in bi 167 | else "" 168 | ) 169 | beam["BeamLimitingDeviceSequence"] = beam_limits 170 | 171 | # Check control points if exists 172 | if "ControlPointSequence" in bi: 173 | beam["ControlPointSequence"] = bi.ControlPointSequence 174 | # control point 0 175 | cp0 = bi.ControlPointSequence[0] 176 | # final control point 177 | final_cp = bi.ControlPointSequence[-1] 178 | 179 | beam["NominalBeamEnergy"] = ( 180 | cp0.NominalBeamEnergy if "NominalBeamEnergy" in cp0 else "" 181 | ) 182 | beam["DoseRateSet"] = cp0.DoseRateSet if "DoseRateSet" in cp0 else "" 183 | beam["IsocenterPosition"] = ( 184 | cp0.IsocenterPosition if "IsocenterPosition" in cp0 else "" 185 | ) 186 | beam["GantryAngle"] = cp0.GantryAngle if "GantryAngle" in cp0 else "" 187 | 188 | # check VMAT delivery 189 | if "GantryRotationDirection" in cp0: 190 | if cp0.GantryRotationDirection != "NONE": 191 | 192 | # VMAT Delivery 193 | beam["GantryRotationDirection"] = ( 194 | cp0.GantryRotationDirection 195 | if "GantryRotationDirection" in cp0 196 | else "" 197 | ) 198 | 199 | # last control point angle 200 | if final_cp.GantryRotationDirection == "NONE": 201 | final_angle = ( 202 | bi.ControlPointSequence[-1].GantryAngle 203 | if "GantryAngle" in cp0 204 | else "" 205 | ) 206 | beam["GantryFinalAngle"] = final_angle 207 | 208 | btmp = ( 209 | cp0.BeamLimitingDeviceAngle 210 | if "BeamLimitingDeviceAngle" in cp0 211 | else "" 212 | ) 213 | beam["BeamLimitingDeviceAngle"] = btmp 214 | beam["TableTopEccentricAngle"] = ( 215 | cp0.TableTopEccentricAngle 216 | if "TableTopEccentricAngle" in cp0 217 | else "" 218 | ) 219 | 220 | # check beam limits 221 | if "BeamLimitingDevicePositionSequence" in cp0: 222 | for bl in cp0.BeamLimitingDevicePositionSequence: 223 | beam[bl.RTBeamLimitingDeviceType] = bl.LeafJawPositions 224 | 225 | # Ion control point sequence 226 | if "IonControlPointSequence" in bi: 227 | beam["IonControlPointSequence"] = bi.IonControlPointSequence 228 | cp0 = bi.IonControlPointSequence[0] 229 | beam["NominalBeamEnergyUnit"] = ( 230 | cp0.NominalBeamEnergyUnit if "NominalBeamEnergyUnit" in cp0 else "" 231 | ) 232 | beam["NominalBeamEnergy"] = ( 233 | cp0.NominalBeamEnergy if "NominalBeamEnergy" in cp0 else "" 234 | ) 235 | beam["DoseRateSet"] = cp0.DoseRateSet if "DoseRateSet" in cp0 else "" 236 | beam["IsocenterPosition"] = ( 237 | cp0.IsocenterPosition if "IsocenterPosition" in cp0 else "" 238 | ) 239 | beam["GantryAngle"] = cp0.GantryAngle if "GantryAngle" in cp0 else "" 240 | btmp1 = ( 241 | cp0.BeamLimitingDeviceAngle 242 | if "BeamLimitingDeviceAngle" in cp0 243 | else "" 244 | ) 245 | beam["BeamLimitingDeviceAngle"] = btmp1 246 | 247 | # add each beam to beams dict 248 | beams[bi.BeamNumber] = beam 249 | 250 | # Obtain the referenced beam info from the fraction info 251 | if "FractionGroupSequence" in self.ds: 252 | fg = self.ds.FractionGroupSequence[fx] 253 | if "ReferencedBeamSequence" in fg: 254 | rb = fg.ReferencedBeamSequence 255 | nfx = fg.NumberOfFractionsPlanned 256 | for bi in rb: 257 | if "BeamDose" in bi: 258 | # dose in cGy 259 | beams[bi.ReferencedBeamNumber]["dose"] = bi.BeamDose * nfx * 100 260 | if "BeamMeterset" in bi: 261 | beams[bi.ReferencedBeamNumber]["MU"] = float(bi.BeamMeterset) 262 | return beams 263 | 264 | def get_study_info(self) -> Dict[str, str]: 265 | """Return the study information of the current file.""" 266 | 267 | study = {} 268 | if "StudyDescription" in self.ds: 269 | desc = self.ds.StudyDescription 270 | else: 271 | desc = "No description" 272 | study["description"] = desc 273 | # Don't assume that every dataset includes a study UID 274 | study["id"] = self.ds.SeriesInstanceUID 275 | if "StudyInstanceUID" in self.ds: 276 | study["id"] = self.ds.StudyInstanceUID 277 | 278 | return study 279 | -------------------------------------------------------------------------------- /complexity/misc.py: -------------------------------------------------------------------------------- 1 | """Classes to estimate many complexity metrics""" 2 | # Copyright (c) 2017-2018 Victor G. L. Alves 3 | 4 | import numpy as np 5 | import pandas as pd 6 | from scipy import integrate 7 | 8 | from complexity.PyApertureMetric import ( 9 | PyMetersetsFromMetersetWeightsCreator, 10 | PyAperturesFromBeamCreator, 11 | ) 12 | from complexity.PyComplexityMetric import PyComplexityMetric 13 | 14 | 15 | class LeafSequenceVariability: 16 | def Calculate(self, aperture, aav_norm): 17 | """ 18 | variability in segment shape for a 19 | specific plan. The shape of each segment is considered, 20 | based on the change in leaf position between adjacent MLC 21 | leaves. This is calculated for leaves on each bank that define 22 | a specific segment. The LSV is defined using N, the number 23 | of open leaves constituting the beam and the coordinates of 24 | the leaf positions. Leaves are not considered if they are 25 | positioned under the jaws. The position of each leaf is incor- 26 | porated by defining pos max . 27 | The second IMRT segment characteristic that is considered 28 | for the overall determination of complexity is the area 29 | of the beam aperture. The aperture area variability AAV is 30 | used to characterize the variation in segment area relative to 31 | the maximum aperture defined by all of the segments. Segments 32 | that are more similar in area to the maximum beam 33 | aperture contribute to a larger score. 34 | 35 | Reference: 36 | McNiven AL, Sharpe MB, Purdie TG. A new metric for assessing IMRT 37 | modulation complexity and plan deliverability. Med Phys 2010;37:505–15. 38 | http://dx.doi.org/10.1118/1.3276775. 39 | 40 | :param aav_norm: Maximum aperture area 41 | :param aperture: Control point PyAperture class 42 | :return: product LSV * AAV 43 | """ 44 | 45 | pos = [ 46 | (lp.Left, lp.Right) for lp in aperture.LeafPairs if not lp.IsOutsideJaw() 47 | ] 48 | N = len(pos) 49 | pos_max = np.max(pos, axis=0) - np.min(pos, axis=0) 50 | tmp = np.sum(pos_max + np.diff(pos, axis=0), axis=0) / (N * pos_max) 51 | LSV = np.prod(tmp) 52 | 53 | num = sum( 54 | ([lp.FieldSize() for lp in aperture.LeafPairs if not lp.IsOutsideJaw()]) 55 | ) 56 | AAV = self.DivisionOrDefault(num, aav_norm) 57 | 58 | return LSV * AAV 59 | 60 | @staticmethod 61 | def DivisionOrDefault(a, b): 62 | return a / b if b != 0 else 0 63 | 64 | 65 | class ModulationComplexityScore(PyComplexityMetric): 66 | """ Reference: 67 | McNiven AL, Sharpe MB, Purdie TG. A new metric for assessing IMRT 68 | modulation complexity and plan deliverability. Med Phys 2010;37:505–15. 69 | http://dx.doi.org/10.1118/1.3276775.""" 70 | 71 | def CalculatePerAperture(self, apertures): 72 | aav_norm = 0 73 | for aperture in apertures: 74 | posi = [ 75 | (lp.Left, lp.Right) 76 | for lp in aperture.LeafPairs 77 | if not lp.IsOutsideJaw() 78 | ] 79 | posi_max = np.max(posi, axis=0) 80 | aav_norm += abs(posi_max[1] - posi_max[0]) 81 | metric = LeafSequenceVariability() 82 | 83 | return [metric.Calculate(aperture, aav_norm) for aperture in apertures] 84 | 85 | 86 | class ModulationIndexScore(PyComplexityMetric): 87 | 88 | def CalculateForPlan(self, patient=None, plan=None, k=0.02): 89 | """ 90 | Jong Min Park et al - "Modulation indices for volumetric modulated arc therapy" 91 | https://iopscience.iop.org/article/10.1088/0031-9155/59/23/7315 92 | See table 1 93 | """ 94 | apertures = [] 95 | cumulative_metersets = [] 96 | meterset_creator = PyMetersetsFromMetersetWeightsCreator() 97 | for k, beam in plan["beams"].items(): 98 | if "MU" in beam: 99 | apertures += PyAperturesFromBeamCreator().Create(beam) 100 | cum = meterset_creator.GetCumulativeMetersets(beam) 101 | cumulative_metersets.append(cum) 102 | 103 | cumulative_mu = np.concatenate(cumulative_metersets) 104 | mid = ModulationIndexTotal(apertures, cumulative_mu) 105 | return mid.calculate_integrate(k=k) 106 | 107 | def CalculateForBeam(self, patient, plan, beam, k=0.02): 108 | apertures = PyAperturesFromBeamCreator().Create(beam) 109 | cumulative_metersets = PyMetersetsFromMetersetWeightsCreator().GetCumulativeMetersets( 110 | beam 111 | ) 112 | mid = ModulationIndexTotal(apertures, cumulative_metersets) 113 | return mid.calculate_integrate(k=k) 114 | 115 | 116 | class ModulationIndexTotal: 117 | def __init__(self, apertures, cumulative_mu): 118 | # beam data 119 | self.apertures = apertures 120 | self.Ncp = len(self.apertures) 121 | 122 | # meterset data 123 | self.cumulative_mu = self.get_mu_data(cumulative_mu) 124 | 125 | # MLC position data 126 | self.mlc_positions = self.get_positions(self.apertures) 127 | self.mlc_speed = ( 128 | self.mlc_positions.diff().abs().T / self.cumulative_mu["time"] 129 | ).T 130 | self.mlc_speed_std = self.mlc_speed.std() 131 | self.mlc_acceleration = ( 132 | self.mlc_speed.diff().abs().T / self.cumulative_mu["time"] 133 | ).T 134 | self.mlc_acceleration_std = self.mlc_acceleration.std() 135 | 136 | # gantry data 137 | gantry_angles = np.array([ap.GantryAngle for ap in self.apertures]) 138 | self.gantry = pd.DataFrame(gantry_angles, columns=["gantry"]) 139 | self.gantry["delta_gantry"] = self.rolling_apply( 140 | self.delta_gantry, gantry_angles 141 | ) 142 | self.gantry["gantry_speed"] = ( 143 | self.gantry["delta_gantry"] / self.cumulative_mu["time"] 144 | ) 145 | self.gantry["delta_gantry_speed"] = self.gantry["gantry_speed"].diff().abs() 146 | self.gantry["gantry_acc"] = ( 147 | self.gantry["delta_gantry_speed"] / self.cumulative_mu["time"] 148 | ) 149 | 150 | # dose rate data 151 | self.dose_rate = pd.DataFrame( 152 | self.cumulative_mu["delta_mu"] / self.cumulative_mu["time"], columns=["DR"] 153 | ) 154 | self.dose_rate["delta_dose_rate"] = self.dose_rate.diff().abs() 155 | 156 | def get_mu_data(self, cumulative_mu): 157 | # meterset data 158 | tmp = pd.DataFrame(cumulative_mu, columns=["MU"]) 159 | tmp["delta_mu"] = tmp.diff().abs() 160 | tmp["time"] = tmp["delta_mu"].apply(self.calculate_time) 161 | return tmp 162 | 163 | @staticmethod 164 | def calculate_time(delta_mu): 165 | """ 166 | Calculate time between control points in seconds 167 | :param delta_mu: 168 | :return: time in seconds 169 | """ 170 | if delta_mu <= 4.238: 171 | return 2.0341 / 4.8 172 | elif delta_mu > 4.238: 173 | return delta_mu / 10 174 | 175 | @staticmethod 176 | def delta_gantry(param): 177 | alpha, beta = param 178 | phi = abs(beta - alpha) % 360 179 | return 360 - phi if phi > 180 else phi 180 | 181 | @staticmethod 182 | def rolling_apply(fun, a, w=2): 183 | r = np.empty(a.shape) 184 | r.fill(np.nan) 185 | for i in range(w - 1, a.shape[0]): 186 | r[i] = fun(a[(i - w + 1) : i + 1]) 187 | return r 188 | 189 | @staticmethod 190 | def get_positions(apertures): 191 | pos = [] 192 | for aperture in apertures: 193 | cp_pos = [(lp.Left, lp.Right) for lp in aperture.LeafPairs] 194 | arr = np.ravel(cp_pos) 195 | pos.append(arr) 196 | 197 | return pd.DataFrame(pos) 198 | 199 | def calc_mi_speed(self, mlc_speed, speed_std, k=1.0): 200 | 201 | calc_z = ( 202 | lambda f: 1 / (self.Ncp - 1) * np.sum(np.sum(mlc_speed > f * speed_std)) 203 | ) 204 | res = integrate.quad(calc_z, 0, k) 205 | return res[0] 206 | 207 | def calc_mi_acceleration( 208 | self, mlc_speed, speed_std, mlc_acc, mlc_acc_std, k=1.0, alpha=1.0 209 | ): 210 | 211 | z_acc = lambda f: (1 / (self.Ncp - 2)) * np.nansum( 212 | np.nansum( 213 | np.logical_or( 214 | mlc_speed > f * speed_std, mlc_acc > alpha * f * mlc_acc_std 215 | ) 216 | ) 217 | ) 218 | res = integrate.quad(z_acc, 0, k) 219 | return res[0] 220 | 221 | def calc_mi_total( 222 | self, 223 | mlc_speed, 224 | speed_std, 225 | mlc_acc, 226 | mlc_acc_std, 227 | k=1.0, 228 | alpha=1.0, 229 | WGA=None, 230 | WMU=None, 231 | ): 232 | 233 | z_total = lambda f: (1 / (self.Ncp - 2)) * np.nansum( 234 | np.nansum( 235 | np.logical_or( 236 | mlc_speed > f * speed_std, mlc_acc > alpha * f * mlc_acc_std 237 | ), 238 | axis=1, 239 | ) 240 | * WGA 241 | * WMU 242 | ) 243 | 244 | res = integrate.quad(z_total, 0, k) 245 | 246 | return res[0] 247 | 248 | def calculate_integrate(self, k=1.0, beta=2.0, alpha=2.0): 249 | 250 | # fill NAN 251 | mlc_speed = np.nan_to_num(self.mlc_speed) 252 | mlc_acc = np.nan_to_num(self.mlc_acceleration) 253 | 254 | mis = self.calc_mi_speed(mlc_speed, self.mlc_speed_std.values, k) 255 | 256 | alpha_acc = 1.0 / self.cumulative_mu["time"].mean() 257 | mia = self.calc_mi_acceleration( 258 | mlc_speed, 259 | self.mlc_speed_std.values, 260 | mlc_acc, 261 | self.mlc_acceleration_std.values, 262 | k=k, 263 | alpha=alpha_acc, 264 | ) 265 | 266 | gantry_acc = self.gantry["gantry_acc"].values 267 | WGA = beta / (1 + (beta - 1) * np.exp(-gantry_acc / alpha)) 268 | 269 | # Wmu 270 | delta_dose_rate = self.dose_rate["delta_dose_rate"].values 271 | WMU = beta / (1 + (beta - 1) * np.exp(-delta_dose_rate / alpha)) 272 | 273 | mit = self.calc_mi_total( 274 | mlc_speed, 275 | self.mlc_speed_std.values, 276 | mlc_acc, 277 | self.mlc_acceleration_std.values, 278 | k=k, 279 | alpha=alpha_acc, 280 | WGA=WGA, 281 | WMU=WMU, 282 | ) 283 | 284 | return mis, mia, mit 285 | 286 | def calculate(self, f=1.0, beta=2.0, alpha=2.0): 287 | 288 | # speed MI 289 | mask_speed_std = self.mlc_speed > f * self.mlc_speed_std 290 | Ns = mask_speed_std.sum().sum() 291 | z_speed = 1 / (self.Ncp - 1) * Ns 292 | 293 | # acc MI 294 | alpha_acc = 1.0 / self.cumulative_mu["time"].mean() 295 | mask_acc_std = self.mlc_acceleration > alpha_acc * f * self.mlc_acceleration_std 296 | 297 | mask_acc_mi = np.logical_or(mask_speed_std, mask_acc_std) 298 | Nacc = mask_acc_mi.sum().sum() 299 | z_acc = 1 / (self.Ncp - 2) * Nacc 300 | 301 | # Total MI 302 | gantry_acc = self.gantry["gantry_acc"] 303 | WGA = beta / (1 + (beta - 1) * np.exp(-gantry_acc / alpha)) 304 | 305 | # Wmu 306 | delta_dose_rate = self.dose_rate["delta_dose_rate"] 307 | WMU = beta / (1 + (beta - 1) * np.exp(-delta_dose_rate / alpha)) 308 | 309 | tmp = mask_acc_mi.multiply(WGA, axis="index").multiply(WMU, axis="index") 310 | Mti = tmp.sum().sum() / (self.Ncp - 2) 311 | 312 | return z_speed, z_acc, Mti 313 | -------------------------------------------------------------------------------- /metrics_examples.py: -------------------------------------------------------------------------------- 1 | import matplotlib.pyplot as plt 2 | import os 3 | 4 | from complexity.PyComplexityMetric import ( 5 | PyComplexityMetric, 6 | MeanAreaMetricEstimator, 7 | AreaMetricEstimator, 8 | ApertureIrregularityMetric, 9 | ) 10 | from complexity.misc import ModulationIndexScore 11 | from complexity.dicomrt import RTPlan 12 | 13 | if __name__ == "__main__": 14 | # Path to DICOM RTPLAN file - IMRT/VMAT 15 | # pfile = "RP.dcm" 16 | path_to_rtplan_file = "RP.dcm" 17 | 18 | # Getting planning data from DICOM file. 19 | plan_info = RTPlan(filename=path_to_rtplan_file) 20 | plan_dict = plan_info.get_plan() 21 | 22 | metrics_list = [ 23 | #ModulationIndexScore, 24 | PyComplexityMetric, 25 | MeanAreaMetricEstimator, 26 | AreaMetricEstimator, 27 | ApertureIrregularityMetric, 28 | ] 29 | units = ["CI [mm^-1]", "mm^2", "mm^2", "dimensionless"] 30 | 31 | # plotting results 32 | for unit, cc in zip(units, metrics_list): 33 | cc_obj = cc() 34 | # compute per plan 35 | plan_metric = cc_obj.CalculateForPlan(None, plan_dict) 36 | print(f"{cc.__name__} Plan Metric - {plan_metric} {unit}") 37 | for k, beam in plan_dict["beams"].items(): 38 | # skip setup fields 39 | if beam["TreatmentDeliveryType"] == "TREATMENT" and beam["MU"] > 0: 40 | fig = plt.figure(figsize=(6, 6)) 41 | # create a subplot 42 | ax = fig.add_subplot(111) 43 | cpx_beam_cp = cc_obj.CalculateForBeamPerAperture( 44 | None, plan_dict, beam 45 | ) 46 | ax.plot(cpx_beam_cp) 47 | ax.set_xlabel("Control Point") 48 | ax.set_ylabel(f"${unit}$") 49 | txt = f"Output - Beam name: {beam['BeamName']} - {cc.__name__}" 50 | ax.set_title(txt) 51 | plt.show() 52 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | pydicom 2 | numpy 3 | pandas 4 | scipy 5 | matplotlib -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | 3 | with open("README.md") as f: 4 | readme = f.read() 5 | 6 | with open("LICENSE") as f: 7 | license = f.read() 8 | 9 | setup( 10 | name="Complexity", 11 | version="0.1.0", 12 | description="Python 3.x port of the Eclipse ESAPI plug-in script", 13 | long_description=readme, 14 | author="Victor G. L Alves", 15 | author_email="victorgabr@gmail.com", 16 | url="https://github.com/victorgabr/ApertureComplexity", 17 | license=license, 18 | # packages=find_packages(exclude=('tests', 'docs')) 19 | packages=["complexity"], 20 | ) 21 | -------------------------------------------------------------------------------- /test-requirements.txt: -------------------------------------------------------------------------------- 1 | pytest -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/victorgabr/ApertureComplexity/fbb25e756dd2a7b265a77cb6903fe69e868cce6e/tests/__init__.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | from complexity.dicomrt import RTPlan 4 | import pytest 5 | 6 | 7 | @pytest.fixture() 8 | def plan_dcm(): 9 | plan_file = os.path.join(DATA_DIR, "RP_FiF.dcm") 10 | plan_info = RTPlan(filename=plan_file) 11 | return plan_info 12 | -------------------------------------------------------------------------------- /tests/test_aperture.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestAperture(TestCase): 5 | def test_CreateLeafPairs(self): 6 | self.fail() 7 | 8 | def test_GetLeafTops(self): 9 | self.fail() 10 | 11 | def test_CreateJaw(self): 12 | self.fail() 13 | 14 | def test_Jaw(self): 15 | self.fail() 16 | 17 | def test_LeafPairs(self): 18 | self.fail() 19 | 20 | def test_HasOpenLeafBehindJaws(self): 21 | self.fail() 22 | 23 | def test_Area(self): 24 | self.fail() 25 | 26 | def test_side_perimeter(self): 27 | self.fail() 28 | 29 | def test_SidePerimeter(self): 30 | self.fail() 31 | 32 | def test_LeafPairsAreOutsideJaw(self): 33 | self.fail() 34 | 35 | def test_JawTopIsBelowTopLeafPair(self): 36 | self.fail() 37 | 38 | def test_JawBottomIsAboveBottomLeafPair(self): 39 | self.fail() 40 | 41 | def test_LeafPairsAreDisjoint(self): 42 | self.fail() 43 | -------------------------------------------------------------------------------- /tests/test_apertureIrregularityMetric.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestApertureIrregularityMetric(TestCase): 5 | def test_CalculatePerAperture(self): 6 | self.fail() 7 | -------------------------------------------------------------------------------- /tests/test_jaw.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | from complexity.ApertureMetric import Jaw, Rect 4 | 5 | left, top, right, botton = -50, -50, 50, 50 6 | jaw = Jaw(left, top, right, botton) 7 | 8 | 9 | class TestJaw(TestCase): 10 | def test_Position(self): 11 | assert isinstance(jaw.Position, Rect) 12 | 13 | def test_Left(self): 14 | assert jaw.Left == -50 15 | 16 | def test_Top(self): 17 | assert jaw.Top == -50 18 | 19 | def test_Right(self): 20 | assert jaw.Right == 50 21 | 22 | def test_Bottom(self): 23 | assert jaw.Bottom == 50 24 | -------------------------------------------------------------------------------- /tests/test_leafPair.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | from complexity.ApertureMetric import LeafPair, Jaw, Rect 4 | 5 | left, top, right, botton = -50, -50, 50, 50 6 | jaw = Jaw(left, top, right, botton) 7 | lp = LeafPair(-25, 25, 5, -5, jaw) 8 | 9 | 10 | class TestLeafPair(TestCase): 11 | def test_Position(self): 12 | assert isinstance(lp.Position, Rect) 13 | 14 | def test_Left(self): 15 | self.assertAlmostEqual(lp.Left, -25) 16 | 17 | def test_Top(self): 18 | self.assertAlmostEqual(lp.Top, 5) 19 | 20 | def test_Right(self): 21 | self.assertAlmostEqual(lp.Right, 25) 22 | 23 | def test_Bottom(self): 24 | self.assertAlmostEqual(lp.Bottom, 0) 25 | 26 | def test_Width(self): 27 | self.assertAlmostEqual(lp.Width, 0) 28 | 29 | def test_Jaw(self): 30 | assert lp.jaw.Left == -50 31 | 32 | assert lp.jaw.Top == -50 33 | 34 | assert lp.jaw.Right == 50 35 | 36 | assert lp.jaw.Bottom == 50 37 | 38 | def test_FieldSize(self): 39 | target = 50 * 5 40 | self.assertAlmostEqual(lp.FieldSize(), target) 41 | 42 | def test_FieldArea(self): 43 | self.fail() 44 | 45 | def test_IsOutsideJaw(self): 46 | self.fail() 47 | 48 | def test_IsOpen(self): 49 | self.fail() 50 | 51 | def test_IsOpenButBehindJaw(self): 52 | self.fail() 53 | 54 | def test_OpenLeafWidth(self): 55 | self.fail() 56 | -------------------------------------------------------------------------------- /tests/test_leafSequenceVariability.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestLeafSequenceVariability(TestCase): 5 | def test_Calculate(self): 6 | self.fail() 7 | -------------------------------------------------------------------------------- /tests/test_modulationComplexityScore.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestModulationComplexityScore(TestCase): 5 | def test_CalculatePerAperture(self): 6 | self.fail() 7 | -------------------------------------------------------------------------------- /tests/test_modulationIndexScore.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestModulationIndexScore(TestCase): 5 | def test_CalculateForPlan(self): 6 | self.fail() 7 | 8 | def test_CalculateForBeam(self): 9 | self.fail() 10 | -------------------------------------------------------------------------------- /tests/test_modulationIndexTotal.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestModulationIndexTotal(TestCase): 5 | def test_get_mu_data(self): 6 | self.fail() 7 | 8 | def test_calculate_time(self): 9 | self.fail() 10 | 11 | def test_delta_gantry(self): 12 | self.fail() 13 | 14 | def test_rolling_apply(self): 15 | self.fail() 16 | 17 | def test_get_positions(self): 18 | self.fail() 19 | 20 | def test_calc_mi_speed(self): 21 | self.fail() 22 | 23 | def test_calc_mi_acceleration(self): 24 | self.fail() 25 | 26 | def test_calc_mi_total(self): 27 | self.fail() 28 | 29 | def test_calculate_integrate(self): 30 | self.fail() 31 | 32 | def test_calculate(self): 33 | self.fail() 34 | -------------------------------------------------------------------------------- /tests/test_pyAperture.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestPyAperture(TestCase): 5 | def test_CreateLeafPairs(self): 6 | self.fail() 7 | 8 | def test_LeafPairArea(self): 9 | self.fail() 10 | 11 | def test_GantryAngle(self): 12 | self.fail() 13 | -------------------------------------------------------------------------------- /tests/test_pyAperturesFromBeamCreator.py: -------------------------------------------------------------------------------- 1 | from complexity.PyApertureMetric import PyAperturesFromBeamCreator 2 | 3 | 4 | def test_Create(plan_dcm): 5 | # given 10 x 10 cm field size 6 | plan_dict = plan_dcm.get_plan() 7 | beam = plan_dict["beams"][1] 8 | apertures = PyAperturesFromBeamCreator().Create(beam) 9 | 10 | assert apertures[1].side_perimeter() == 200.0 11 | assert apertures[3].side_perimeter() == 100.0 12 | assert len(apertures) == 4 13 | assert apertures[0].Area() == 100 * 100 14 | assert apertures[2].Area() == 50 * 50 15 | -------------------------------------------------------------------------------- /tests/test_pyComplexityMetric.py: -------------------------------------------------------------------------------- 1 | from complexity.PyComplexityMetric import PyComplexityMetric 2 | 3 | 4 | def test_CalculateForPlan(plan_dcm): 5 | plan_dict = plan_dcm.get_plan() 6 | complexity_metric = PyComplexityMetric().CalculateForPlan(None, plan_dict) 7 | 8 | cp0 = 100 * 2 / (100 ** 2) 9 | cp1 = 50 * 2 / (50 ** 2) 10 | expected = (100 * cp0 + 100 * cp1) / 200.0 11 | assert complexity_metric == expected 12 | -------------------------------------------------------------------------------- /tests/test_pyMetersetsFromMetersetWeightsCreator.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | 3 | 4 | class TestPyMetersetsFromMetersetWeightsCreator(TestCase): 5 | def test_Create(self): 6 | self.fail() 7 | 8 | def test_GetCumulativeMetersets(self): 9 | self.fail() 10 | 11 | def test_GetMetersetWeights(self): 12 | self.fail() 13 | 14 | def test_ConvertMetersetWeightsToMetersets(self): 15 | self.fail() 16 | 17 | def test_UndoCummulativeSum(self): 18 | self.fail() 19 | -------------------------------------------------------------------------------- /tests/tests_data/RP_FiF.dcm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/victorgabr/ApertureComplexity/fbb25e756dd2a7b265a77cb6903fe69e868cce6e/tests/tests_data/RP_FiF.dcm --------------------------------------------------------------------------------