[pre-commit.ci] auto fixes from pre-commit.com hooks

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ETSInitiative · Dec 13, 2024 · e60458c · e60458c
1 parent 254323e
commit e60458c
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Showing 130 changed files with 3,882 additions and 4,288 deletions.
diff --git a/matlab/buildfile.m b/matlab/buildfile.m
@@ -1,49 +1,57 @@
-function plan = buildfile
-    % import matlab.buildtool.tasks.CodeIssuesTask
-    % import matlab.buildtool.tasks.TestTask
+function plan = buildfile % import matlab.buildtool.tasks.CodeIssuesTask
+                % import matlab.buildtool.tasks.TestTask
 
-    plan = buildplan(localfunctions);
-    % plan("check") = CodeIssuesTask(Results="tests/results/static-analysis-results.sarif");
-    % plan("test") = TestTask("tests", SourceFiles="toolbox", TestResults="tests/results/test-results.xml");
+                      plan
+    = buildplan (localfunctions);
+% plan ("check")
+    = CodeIssuesTask (Results = "tests/results/static-analysis-results.sarif");
+% plan ("test") = TestTask ("tests", SourceFiles = "toolbox",
+                            TestResults = "tests/results/test-results.xml");
 
-    % plan("packageToolbox").Dependencies = ["check" "test"];
+% plan ("packageToolbox").Dependencies = ["check"
+                                          "test"];
 
-    plan.DefaultTasks = ["packageToolbox"];
+plan.DefaultTasks = ["packageToolbox"];
 end
 
-function packageToolboxTask(~)
-    buildToolbox("release");
+    function packageToolboxTask (~) buildToolbox ("release");
 end
 
-function buildToolbox(outdir)
-    if ~exist(outdir, 'dir')
-        mkdir(outdir);
-    end
+    function buildToolbox (outdir) if ~exist (outdir, 'dir') mkdir (outdir);
+end
 
-    uuid = string(java.util.UUID.randomUUID());
-    toolboxFolder = "./toolbox/";
-    opts = matlab.addons.toolbox.ToolboxOptions(toolboxFolder, uuid);
+    uuid
+    = string (java.util.UUID.randomUUID ());
+toolboxFolder = "./toolbox/";
+opts = matlab.addons.toolbox.ToolboxOptions (toolboxFolder, uuid);
 
-    toolboxDirs = unique(fileparts(opts.ToolboxFiles));
-    if ~all(contains(toolboxDirs, opts.ToolboxFolder))
-        error("No symbolic links allowed in toolboxFolder (BUG through at least R2023a)");
-    end
+toolboxDirs = unique (fileparts (opts.ToolboxFiles));
+if
+  ~all (contains (toolboxDirs, opts.ToolboxFolder))
+      error ("No symbolic links allowed in toolboxFolder (BUG through at "
+             "least R2023a)");
+end
 
-    opts.ToolboxName = "PETSIRD";
+    opts.ToolboxName
+    = "PETSIRD";
 
-    opts.ToolboxVersion = "0.2.0";
-    opts.OutputFile = fullfile(outdir, sprintf("petsird-%s.mltbx", opts.ToolboxVersion));
+opts.ToolboxVersion = "0.2.0";
+opts.OutputFile
+    = fullfile (outdir, sprintf ("petsird-%s.mltbx", opts.ToolboxVersion));
 
-    opts.Description = "Positron Emission Tomography Standardization Initiative Raw Data (PETSIRD) toolbox for MATLAB";
-    % opts.Summary = "";
-    % opts.AuthorCompany = "";
+opts.Description = "Positron Emission Tomography Standardization Initiative "
+                   "Raw Data (PETSIRD) toolbox for MATLAB";
+% opts.Summary = "";
+% opts.AuthorCompany = "";
 
-    opts.MinimumMatlabRelease = "R2022b";
+opts.MinimumMatlabRelease = "R2022b";
 
-    % Must also specify which folders should be added to MATLAB path upon toolbox installation.
-    % Must also include at least one *file* in the toolbox folder.
-    % This seems to be bug on Linux, Matlab R2023a. On Windows, this isn't required.
-    opts.ToolboxMatlabPath = toolboxFolder;
+% Must also specify which folders should be added to MATLAB path upon toolbox
+        installation.
+    % Must also include at least one *file *in the toolbox folder.
+    % This seems to be bug on Linux,
+    Matlab R2023a.On Windows,
+    this isn't required. opts.ToolboxMatlabPath = toolboxFolder;
 
-    matlab.addons.toolbox.packageToolbox(opts);
+matlab.addons.toolbox.packageToolbox (opts);
 end
diff --git a/matlab/toolbox/+petsird/+binary/AnnulusShapeSerializer.m b/matlab/toolbox/+petsird/+binary/AnnulusShapeSerializer.m
@@ -1,27 +1,31 @@
-% This file was generated by the "yardl" tool. DO NOT EDIT.
+% This file was generated by the "yardl" tool.DO NOT EDIT.
 
-classdef AnnulusShapeSerializer < yardl.binary.RecordSerializer
-  methods
-    function self = AnnulusShapeSerializer()
-      field_serializers{1} = yardl.binary.Float32Serializer;
-      field_serializers{2} = yardl.binary.Float32Serializer;
-      field_serializers{3} = yardl.binary.Float32Serializer;
-      field_serializers{4} = yardl.binary.FixedVectorSerializer(yardl.binary.Float32Serializer, 2);
-      [email protected]('petsird.AnnulusShape', field_serializers);
-    end
-
-    function write(self, outstream, value)
-      arguments
-        self
-        outstream (1,1) yardl.binary.CodedOutputStream
-        value (1,1) petsird.AnnulusShape
-      end
-      self.write_(outstream, value.inner_radius, value.outer_radius, value.thickness, value.angular_range);
-    end
+        classdef AnnulusShapeSerializer
+    < yardl.binary.RecordSerializer methods function self
+    = AnnulusShapeSerializer () field_serializers{ 1 }
+= yardl.binary.Float32Serializer;
+field_serializers{ 2 } = yardl.binary.Float32Serializer;
+field_serializers{ 3 } = yardl.binary.Float32Serializer;
+field_serializers{ 4 }
+= yardl.binary.FixedVectorSerializer (yardl.binary.Float32Serializer, 2);
+self
+    @yardl.binary.RecordSerializer ('petsird.AnnulusShape', field_serializers);
+end
 
-    function value = read(self, instream)
-      fields = self.read_(instream);
-      value = petsird.AnnulusShape(inner_radius=fields{1}, outer_radius=fields{2}, thickness=fields{3}, angular_range=fields{4});
-    end
-  end
+    function
+    write (self, outstream, value)
+arguments
+    self outstream (1, 1) yardl.binary.CodedOutputStream
+    value (1, 1) petsird.AnnulusShape end self.write_ (outstream,
+                                                       value.inner_radius,
+                                                       value.outer_radius,
+                                                       value.thickness,
+                                                       value.angular_range);
 end
+
+    function value
+    = read (self, instream) fields = self.read_ (instream);
+value = petsird.AnnulusShape (
+    inner_radius = fields{ 1 }, outer_radius = fields{ 2 },
+    thickness = fields{ 3 }, angular_range = fields{ 4 });
+end end end
diff --git a/matlab/toolbox/+petsird/+binary/AtomSerializer.m b/matlab/toolbox/+petsird/+binary/AtomSerializer.m
@@ -1,25 +1,21 @@
-% This file was generated by the "yardl" tool. DO NOT EDIT.
+% This file was generated by the "yardl" tool.DO NOT EDIT.
 
-classdef AtomSerializer < yardl.binary.RecordSerializer
-  methods
-    function self = AtomSerializer()
-      field_serializers{1} = yardl.binary.Uint32Serializer;
-      field_serializers{2} = yardl.binary.Uint32Serializer;
-      [email protected]('petsird.Atom', field_serializers);
-    end
-
-    function write(self, outstream, value)
-      arguments
-        self
-        outstream (1,1) yardl.binary.CodedOutputStream
-        value (1,1) petsird.Atom
-      end
-      self.write_(outstream, value.mass_number, value.atomic_number);
-    end
+        classdef AtomSerializer
+    < yardl.binary.RecordSerializer methods function self
+    = AtomSerializer () field_serializers{ 1 } = yardl.binary.Uint32Serializer;
+field_serializers{ 2 } = yardl.binary.Uint32Serializer;
+self @yardl.binary.RecordSerializer ('petsird.Atom', field_serializers);
+end
 
-    function value = read(self, instream)
-      fields = self.read_(instream);
-      value = petsird.Atom(mass_number=fields{1}, atomic_number=fields{2});
-    end
-  end
+    function
+    write (self, outstream, value)
+arguments
+    self outstream (1, 1) yardl.binary.CodedOutputStream
+    value (1, 1) petsird.Atom end self.write_ (outstream, value.mass_number,
+                                               value.atomic_number);
 end
+
+    function value
+    = read (self, instream) fields = self.read_ (instream);
+value = petsird.Atom (mass_number = fields{ 1 }, atomic_number = fields{ 2 });
+end end end
diff --git a/matlab/toolbox/+petsird/+binary/BedMovementTimeBlockSerializer.m b/matlab/toolbox/+petsird/+binary/BedMovementTimeBlockSerializer.m
@@ -1,25 +1,26 @@
-% This file was generated by the "yardl" tool. DO NOT EDIT.
+% This file was generated by the "yardl" tool.DO NOT EDIT.
 
-classdef BedMovementTimeBlockSerializer < yardl.binary.RecordSerializer
-  methods
-    function self = BedMovementTimeBlockSerializer()
-      field_serializers{1} = yardl.binary.Uint32Serializer;
-      field_serializers{2} = petsird.binary.RigidTransformationSerializer();
-      [email protected]('petsird.BedMovementTimeBlock', field_serializers);
-    end
-
-    function write(self, outstream, value)
-      arguments
-        self
-        outstream (1,1) yardl.binary.CodedOutputStream
-        value (1,1) petsird.BedMovementTimeBlock
-      end
-      self.write_(outstream, value.start, value.transform);
-    end
+        classdef BedMovementTimeBlockSerializer
+    < yardl.binary.RecordSerializer methods function self
+    = BedMovementTimeBlockSerializer () field_serializers{ 1 }
+= yardl.binary.Uint32Serializer;
+field_serializers{ 2 } = petsird.binary.RigidTransformationSerializer ();
+self @yardl.binary.RecordSerializer ('petsird.BedMovementTimeBlock',
+                                     field_serializers);
+end
 
-    function value = read(self, instream)
-      fields = self.read_(instream);
-      value = petsird.BedMovementTimeBlock(start=fields{1}, transform=fields{2});
-    end
-  end
+    function
+    write (self, outstream, value)
+arguments
+    self outstream (1, 1) yardl.binary.CodedOutputStream
+    value (1,
+           1) petsird.BedMovementTimeBlock end self.write_ (outstream,
+                                                            value.start,
+                                                            value.transform);
 end
+
+    function value
+    = read (self, instream) fields = self.read_ (instream);
+value = petsird.BedMovementTimeBlock (start = fields{ 1 },
+                                      transform = fields{ 2 });
+end end end
diff --git a/matlab/toolbox/+petsird/+binary/BoxShapeSerializer.m b/matlab/toolbox/+petsird/+binary/BoxShapeSerializer.m
@@ -1,24 +1,21 @@
-% This file was generated by the "yardl" tool. DO NOT EDIT.
+% This file was generated by the "yardl" tool.DO NOT EDIT.
 
-classdef BoxShapeSerializer < yardl.binary.RecordSerializer
-  methods
-    function self = BoxShapeSerializer()
-      field_serializers{1} = yardl.binary.FixedVectorSerializer(petsird.binary.CoordinateSerializer(), 8);
-      [email protected]('petsird.BoxShape', field_serializers);
-    end
-
-    function write(self, outstream, value)
-      arguments
-        self
-        outstream (1,1) yardl.binary.CodedOutputStream
-        value (1,1) petsird.BoxShape
-      end
-      self.write_(outstream, value.corners);
-    end
+        classdef BoxShapeSerializer
+    < yardl.binary.RecordSerializer methods function self
+    = BoxShapeSerializer () field_serializers{ 1 }
+= yardl.binary.FixedVectorSerializer (petsird.binary.CoordinateSerializer (),
+                                      8);
+self @yardl.binary.RecordSerializer ('petsird.BoxShape', field_serializers);
+end
 
-    function value = read(self, instream)
-      fields = self.read_(instream);
-      value = petsird.BoxShape(corners=fields{1});
-    end
-  end
+    function
+    write (self, outstream, value)
+arguments
+    self outstream (1, 1) yardl.binary.CodedOutputStream
+    value (1, 1) petsird.BoxShape end self.write_ (outstream, value.corners);
 end
+
+    function value
+    = read (self, instream) fields = self.read_ (instream);
+value = petsird.BoxShape (corners = fields{ 1 });
+end end end
diff --git a/matlab/toolbox/+petsird/+binary/BulkMaterialSerializer.m b/matlab/toolbox/+petsird/+binary/BulkMaterialSerializer.m
@@ -1,28 +1,33 @@
-% This file was generated by the "yardl" tool. DO NOT EDIT.
+% This file was generated by the "yardl" tool.DO NOT EDIT.
 
-classdef BulkMaterialSerializer < yardl.binary.RecordSerializer
-  methods
-    function self = BulkMaterialSerializer()
-      field_serializers{1} = yardl.binary.Uint32Serializer;
-      field_serializers{2} = yardl.binary.StringSerializer;
-      field_serializers{3} = yardl.binary.Float32Serializer;
-      field_serializers{4} = yardl.binary.VectorSerializer(petsird.binary.AtomSerializer());
-      field_serializers{5} = yardl.binary.VectorSerializer(yardl.binary.Float32Serializer);
-      [email protected]('petsird.BulkMaterial', field_serializers);
-    end
-
-    function write(self, outstream, value)
-      arguments
-        self
-        outstream (1,1) yardl.binary.CodedOutputStream
-        value (1,1) petsird.BulkMaterial
-      end
-      self.write_(outstream, value.id, value.name, value.density, value.atoms, value.mass_fractions);
-    end
+        classdef BulkMaterialSerializer
+    < yardl.binary.RecordSerializer methods function self
+    = BulkMaterialSerializer () field_serializers{ 1 }
+= yardl.binary.Uint32Serializer;
+field_serializers{ 2 } = yardl.binary.StringSerializer;
+field_serializers{ 3 } = yardl.binary.Float32Serializer;
+field_serializers{ 4 }
+= yardl.binary.VectorSerializer (petsird.binary.AtomSerializer ());
+field_serializers{ 5 }
+= yardl.binary.VectorSerializer (yardl.binary.Float32Serializer);
+self
+    @yardl.binary.RecordSerializer ('petsird.BulkMaterial', field_serializers);
+end
 
-    function value = read(self, instream)
-      fields = self.read_(instream);
-      value = petsird.BulkMaterial(id=fields{1}, name=fields{2}, density=fields{3}, atoms=fields{4}, mass_fractions=fields{5});
-    end
-  end
+    function
+    write (self, outstream, value)
+arguments
+    self outstream (1, 1) yardl.binary.CodedOutputStream
+    value (1, 1) petsird.BulkMaterial end self.write_ (outstream, value.id,
+                                                       value.name,
+                                                       value.density,
+                                                       value.atoms,
+                                                       value.mass_fractions);
 end
+
+    function value
+    = read (self, instream) fields = self.read_ (instream);
+value = petsird.BulkMaterial (id = fields{ 1 }, name = fields{ 2 },
+                              density = fields{ 3 }, atoms = fields{ 4 },
+                              mass_fractions = fields{ 5 });
+end end end
diff --git a/matlab/toolbox/+petsird/+binary/CoincidenceEventSerializer.m b/matlab/toolbox/+petsird/+binary/CoincidenceEventSerializer.m
@@ -1,26 +1,27 @@
-% This file was generated by the "yardl" tool. DO NOT EDIT.
+% This file was generated by the "yardl" tool.DO NOT EDIT.
 
-classdef CoincidenceEventSerializer < yardl.binary.RecordSerializer
-  methods
-    function self = CoincidenceEventSerializer()
-      field_serializers{1} = yardl.binary.FixedVectorSerializer(yardl.binary.Uint32Serializer, 2);
-      field_serializers{2} = yardl.binary.Uint32Serializer;
-      field_serializers{3} = yardl.binary.FixedVectorSerializer(yardl.binary.Uint32Serializer, 2);
-      [email protected]('petsird.CoincidenceEvent', field_serializers);
-    end
-
-    function write(self, outstream, value)
-      arguments
-        self
-        outstream (1,1) yardl.binary.CodedOutputStream
-        value (1,1) petsird.CoincidenceEvent
-      end
-      self.write_(outstream, value.detector_ids, value.tof_idx, value.energy_indices);
-    end
+        classdef CoincidenceEventSerializer
+    < yardl.binary.RecordSerializer methods function self
+    = CoincidenceEventSerializer () field_serializers{ 1 }
+= yardl.binary.FixedVectorSerializer (yardl.binary.Uint32Serializer, 2);
+field_serializers{ 2 } = yardl.binary.Uint32Serializer;
+field_serializers{ 3 }
+= yardl.binary.FixedVectorSerializer (yardl.binary.Uint32Serializer, 2);
+self @yardl.binary.RecordSerializer ('petsird.CoincidenceEvent',
+                                     field_serializers);
+end
 
-    function value = read(self, instream)
-      fields = self.read_(instream);
-      value = petsird.CoincidenceEvent(detector_ids=fields{1}, tof_idx=fields{2}, energy_indices=fields{3});
-    end
-  end
+    function
+    write (self, outstream, value)
+arguments
+    self outstream (1, 1) yardl.binary.CodedOutputStream
+    value (1, 1) petsird.CoincidenceEvent end self.write_ (
+        outstream, value.detector_ids, value.tof_idx, value.energy_indices);
 end
+
+    function value
+    = read (self, instream) fields = self.read_ (instream);
+value = petsird.CoincidenceEvent (detector_ids = fields{ 1 },
+                                  tof_idx = fields{ 2 },
+                                  energy_indices = fields{ 3 });
+end end end