Merge pull request #79 from HicServices/dependabot/nuget/develop/HIC.…

…DicomTypeTranslation-4.0.0

.github/workflows/testpack.yml

@@ -10,6 +10,12 @@ jobs:
       - uses: actions/setup-dotnet@v1
         with:
           dotnet-version: '5.0.x'
+      - uses: actions/cache@v2
+        with:
+          path: ~/.nuget/packages
+          key: ${{ runner.os }}-nuget-${{ hashFiles('**/*.csproj') }}
+          restore-keys: |
+            ${{ runner.os }}-nuget-
       - name: Start MySQL for testing
         run: sudo systemctl start mysql.service
       - name: Test

BadDicom/BadDicom.csproj

@@ -42,7 +42,7 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.8.0" />
-    <PackageReference Include="HIC.DicomTypeTranslation" Version="3.0.0" />
+    <PackageReference Include="HIC.DicomTypeTranslation" Version="4.0.0" />
     <PackageReference Include="YamlDotNet" Version="11.2.1" />
   </ItemGroup>
   <ItemGroup>

BadDicom/Program.cs

@@ -9,7 +9,7 @@
 using System.Linq;
 using System.Threading.Tasks;
 using BadDicom.Configuration;
-using Dicom;
+using FellowOakDicom;
 using DicomTypeTranslation;
 using DicomTypeTranslation.TableCreation;
 using FAnsi.Discovery;
@@ -92,12 +92,10 @@ private static void RunOptionsAndReturnExitCode(ProgramOptions opts)
             try
             {
                 IPersonCollection identifiers = GetPeople(opts, out Random r);
-                using(var dicomGenerator = GetDataGenerator(opts, identifiers,r, out DirectoryInfo dir))
-                {
-                    Console.WriteLine($"{DateTime.Now} Starting file generation (to {dir.FullName})" );
-                    var targetFile = new FileInfo(Path.Combine(dir.FullName, "DicomFiles.csv"));
-                    dicomGenerator.GenerateTestDataFile(identifiers,targetFile,opts.NumberOfStudies);
-                }
+                using var dicomGenerator = GetDataGenerator(opts, identifiers,r, out DirectoryInfo dir);
+                Console.WriteLine($"{DateTime.Now} Starting file generation (to {dir.FullName})" );
+                var targetFile = new FileInfo(Path.Combine(dir.FullName, "DicomFiles.csv"));
+                dicomGenerator.GenerateTestDataFile(identifiers,targetFile,opts.NumberOfStudies);
             }
             catch (Exception e)
             {
@@ -116,9 +114,9 @@ private static DicomDataGenerator GetDataGenerator(ProgramOptions opts, IPersonC
             dir = Directory.CreateDirectory(opts.OutputDirectory);
 
             //Generate the dicom files (of the modalities that the user requested)
-            string[] modalities = !string.IsNullOrWhiteSpace(opts.Modalities)? opts.Modalities.Split(",") :new string[0];
+            string[] modalities = !string.IsNullOrWhiteSpace(opts.Modalities)? opts.Modalities.Split(",") :Array.Empty<string>();
 
-            return new DicomDataGenerator(r, dir, modalities)
+            return new(r, dir, modalities)
             {
                 NoPixels = opts.NoPixels,
                 Anonymise = opts.Anonymise,
@@ -130,7 +128,7 @@ private static DicomDataGenerator GetDataGenerator(ProgramOptions opts, IPersonC
 
         private static IPersonCollection GetPeople(ProgramOptions opts, out Random r)
         {
-            r = opts.Seed == -1 ? new Random() : new Random(opts.Seed);
+            r = opts.Seed == -1 ? new() : new Random(opts.Seed);
 
             //create a cohort of people
             IPersonCollection identifiers = new PersonCollection();
@@ -148,7 +146,7 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
                 opts.NoPixels = true;
 
 
-            Stopwatch swTotal = new Stopwatch();
+            Stopwatch swTotal = new();
 
             swTotal.Start();
 
@@ -293,7 +291,7 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
             for (int i = 0; i < batchSize; i++)
             {
                 var batch = i;
-                tasks[i] = new Task(() =>  // lgtm[cs/local-not-disposed]
+                tasks[i] = new(() =>  // lgtm[cs/local-not-disposed]
                 {
                     RunBatch(identifiers,opts,r,batches[batch],uploaders[batch]);
 
@@ -323,70 +321,67 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
             foreach (DiscoveredTable t in tables)
                 Console.WriteLine($"{t.GetFullyQualifiedName()}: {t.GetRowCount():0,0}");
 
-            Console.WriteLine("Total Running Time:" + swTotal.Elapsed);
+            Console.WriteLine($"Total Running Time:{swTotal.Elapsed}");
             return 0;
         }
 
         private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts, Random r,DataTable[] batches, IBulkCopy[] uploaders)
         {
-            Stopwatch swGeneration = new Stopwatch();
-            Stopwatch swReading = new Stopwatch();
-            Stopwatch swUploading = new Stopwatch();
+            Stopwatch swGeneration = new();
+            Stopwatch swReading = new();
+            Stopwatch swUploading = new();
 
             try
             {
-                using(var dicomGenerator = GetDataGenerator(opts, identifiers,r, out _))
+                using var dicomGenerator = GetDataGenerator(opts, identifiers,r, out _);
+                for (int i = 0; i < opts.NumberOfStudies; i++)
                 {
-
-                    for (int i = 0; i < opts.NumberOfStudies; i++)
-                    {
-                        swGeneration.Start();
+                    swGeneration.Start();
 
-                        var p = identifiers.People[r.Next(identifiers.People.Length)];
-                        var ds = dicomGenerator.GenerateStudyImages(p,out Study s);
+                    var p = identifiers.People[r.Next(identifiers.People.Length)];
+                    var ds = dicomGenerator.GenerateStudyImages(p,out Study s);
 
-                        swGeneration.Stop();
+                    swGeneration.Stop();
 
-                        foreach (DicomDataset dataset in ds)
-                        {
-                            var rows = new DataRow[batches.Length];
+                    foreach (DicomDataset dataset in ds)
+                    {
+                        var rows = new DataRow[batches.Length];
 
-                            for (int j = 0; j < batches.Length; j++) 
-                                rows[j] = batches[j].NewRow();
+                        for (int j = 0; j < batches.Length; j++) 
+                            rows[j] = batches[j].NewRow();
+
+                        swReading.Start();
+                        foreach (DicomItem item in dataset)
+                        {
+                            var column = DicomTypeTranslaterReader.GetColumnNameForTag(item.Tag, false);
+                            var value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(dataset, item));
 
-                            swReading.Start();
-                            foreach (DicomItem item in dataset)
+                            foreach (DataRow row in rows)
                             {
-                                var column = DicomTypeTranslaterReader.GetColumnNameForTag(item.Tag, false);
-                                var value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(dataset, item));
-
-                                foreach (DataRow row in rows)
-                                {
-                                    if (row.Table.Columns.Contains(column))
-                                        row[column] = value ?? DBNull.Value;
-                                }
+                                if (row.Table.Columns.Contains(column))
+                                    row[column] = value ?? DBNull.Value;
                             }
+                        }
 
-                            for (int j = 0; j < batches.Length; j++)
-                                batches[j].Rows.Add(rows[j]);
+                        for (int j = 0; j < batches.Length; j++)
+                            batches[j].Rows.Add(rows[j]);
 
-                            swReading.Stop();
-                        }
+                        swReading.Stop();
+                    }
 
-                        //every 100 and last batch
-                        if (i % 100 == 0 || i == opts.NumberOfStudies - 1)
+                    //every 100 and last batch
+                    if (i % 100 == 0 || i == opts.NumberOfStudies - 1)
+                    {
+                        swUploading.Start();
+                        for (var j = 0; j < uploaders.Length; j++)
                         {
-                            swUploading.Start();
-                            for (var j = 0; j < uploaders.Length; j++)
-                            {
-                                uploaders[j].Upload(batches[j]);
-                                batches[j].Rows.Clear();
-                            }
-                            swUploading.Stop();
-                            Console.WriteLine($"{DateTime.Now} Done {i} studies");
+                            uploaders[j].Upload(batches[j]);
+                            batches[j].Rows.Clear();
                         }
-
+                        swUploading.Stop();
+                        Console.WriteLine($"{DateTime.Now} Done {i} studies");
                     }
+
                 }
             }
             finally
@@ -398,9 +393,9 @@ private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts,
                 }
             }
 
-            Console.WriteLine("Total time Generating Dicoms:" + swGeneration.Elapsed);
-            Console.WriteLine("Total time Reading Dicoms:" + swReading.Elapsed);
-            Console.WriteLine("Total time Uploading Records:" + swUploading.Elapsed);
+            Console.WriteLine($"Total time Generating Dicoms:{swGeneration.Elapsed}");
+            Console.WriteLine($"Total time Reading Dicoms:{swReading.Elapsed}");
+            Console.WriteLine($"Total time Uploading Records:{swUploading.Elapsed}");
 
         }
     }

BadMedicine.Dicom.Tests/DicomDataGeneratorTests.cs

@@ -1,4 +1,4 @@
-using Dicom;
+using FellowOakDicom;
 using NUnit.Framework;
 using System;
 using System.Globalization;
@@ -39,7 +39,7 @@ public void Test_CreatingOnDisk_OneFile()
 
             Assert.IsNotEmpty(datasetCreated.Dataset.GetSingleValue<String>(DicomTag.AccessionNumber));
 
-            Console.WriteLine("Created file "+ f.FullName);
+            Console.WriteLine($"Created file {f.FullName}");
 
             generator.Dispose();
         }
@@ -53,20 +53,18 @@ public void ExampleUsage()
             var person = new Person(r);
 
             //create a generator 
-            using (var generator = new DicomDataGenerator(r, null, "CT"))
-            {
-                //create a dataset in memory
-                DicomDataset dataset = generator.GenerateTestDataset(person, r);
-
-                //values should match the patient details
-                Assert.AreEqual(person.CHI,dataset.GetValue<string>(DicomTag.PatientID,0));
-                Assert.GreaterOrEqual(dataset.GetValue<DateTime>(DicomTag.StudyDate,0),person.DateOfBirth);
-
-                //should have a study description
-                Assert.IsNotNull(dataset.GetValue<string>(DicomTag.StudyDescription,0));
-                //should have a study description
-                Assert.IsNotNull(dataset.GetSingleValue<DateTime>(DicomTag.StudyTime).TimeOfDay);
-            }
+            using var generator = new DicomDataGenerator(r, null, "CT");
+            //create a dataset in memory
+            DicomDataset dataset = generator.GenerateTestDataset(person, r);
+
+            //values should match the patient details
+            Assert.AreEqual(person.CHI,dataset.GetValue<string>(DicomTag.PatientID,0));
+            Assert.GreaterOrEqual(dataset.GetValue<DateTime>(DicomTag.StudyDate,0),person.DateOfBirth);
+
+            //should have a study description
+            Assert.IsNotNull(dataset.GetValue<string>(DicomTag.StudyDescription,0));
+            //should have a study description
+            Assert.IsNotNull(dataset.GetSingleValue<DateTime>(DicomTag.StudyTime).TimeOfDay);
         }
 
         [Test]
@@ -75,7 +73,7 @@ public void Test_CreatingInMemory_ModalityCT()
             var r = new Random(23);
             var person = new Person(r);
 
-            var generator = new DicomDataGenerator(r,new DirectoryInfo(TestContext.CurrentContext.WorkDirectory),"CT");
+            var generator = new DicomDataGenerator(r,new(TestContext.CurrentContext.WorkDirectory),"CT");
 
             //generate 100 images
             for(int i = 0 ; i < 100 ; i++)
@@ -94,7 +92,7 @@ public void Test_Anonymise()
             var r = new Random(23);
             var person = new Person(r);
 
-            var generator = new DicomDataGenerator(r,new DirectoryInfo(TestContext.CurrentContext.WorkDirectory),"CT");
+            var generator = new DicomDataGenerator(r,new(TestContext.CurrentContext.WorkDirectory),"CT");
 
             // without anonymisation (default) we get the normal patient ID
             var ds = generator.GenerateTestDataset(person, r);
@@ -120,7 +118,7 @@ public void Test_CreatingInMemory_Modality_CTAndMR()
             var r = new Random(23);
             var person = new Person(r);
 
-            var generator = new DicomDataGenerator(r,new DirectoryInfo(TestContext.CurrentContext.WorkDirectory),"CT","MR");
+            var generator = new DicomDataGenerator(r,new(TestContext.CurrentContext.WorkDirectory),"CT","MR");
 
             //generate 100 images
             for(int i = 0 ; i < 100 ; i++)
@@ -139,7 +137,7 @@ public void Test_CreatingInMemory_Modality_CTAndMR()
         public void TestFail_CreatingInMemory_Modality_Unknown()
         {
             var r = new Random(23);
-            Assert.Throws<ArgumentException>(()=>new DicomDataGenerator(r,new DirectoryInfo(TestContext.CurrentContext.WorkDirectory),"LOLZ"));
+            Assert.Throws<ArgumentException>(()=>new DicomDataGenerator(r,new(TestContext.CurrentContext.WorkDirectory),"LOLZ"));
 
         }
 
@@ -160,27 +158,24 @@ public void Test_CsvOption()
                 generator.NoPixels = true;
                 generator.MaximumImages = 500;
 
-                generator.GenerateTestDataFile(people,new FileInfo(Path.Combine(outputDir.FullName,"index.csv")),500);
+                generator.GenerateTestDataFile(people,new(Path.Combine(outputDir.FullName,"index.csv")),500);
             }
 
             //3 csv files + index.csv (the default one
             Assert.AreEqual(4,outputDir.GetFiles().Length);
 
             foreach (FileInfo f in outputDir.GetFiles())
             {
-                using(var reader = new CsvReader(new StreamReader(f.FullName),CultureInfo.CurrentCulture))
-                {
-                    int rowcount = 0;
-
-                    //confirms that the CSV is intact (no dodgy commas, unquoted newlines etc)
-                    while (reader.Read())
-                        rowcount++;
+                using var reader = new CsvReader(new StreamReader(f.FullName),CultureInfo.CurrentCulture);
+                int rowcount = 0;
 
-                    //should be 1 row per image + 1 for header
-                    if(f.Name == DicomDataGenerator.ImageCsvFilename)
-                        Assert.AreEqual(501,rowcount);
-                }
+                //confirms that the CSV is intact (no dodgy commas, unquoted newlines etc)
+                while (reader.Read())
+                    rowcount++;
 
+                //should be 1 row per image + 1 for header
+                if(f.Name == DicomDataGenerator.ImageCsvFilename)
+                    Assert.AreEqual(501,rowcount);
             }
         }
     }

BadMedicine.Dicom.Tests/NuspecIsCorrectTests.cs

@@ -40,10 +40,10 @@ public void TestDependencyCorrect(string csproj, string nuspec, string packagesM
                 Assert.Fail("Could not find file {0}", packagesMarkdown);
 
             //<PackageReference Include="NUnit3TestAdapter" Version="3.13.0" />
-            Regex rPackageRef = new Regex(@"<PackageReference\s+Include=""(.*)""\s+Version=""([^""]*)""", RegexOptions.IgnoreCase);
+            Regex rPackageRef = new(@"<PackageReference\s+Include=""(.*)""\s+Version=""([^""]*)""", RegexOptions.IgnoreCase);
 
             //<dependency id="CsvHelper" version="12.1.2" />
-            Regex rDependencyRef = new Regex(@"<dependency\s+id=""(.*)""\s+version=""([^""]*)""", RegexOptions.IgnoreCase);
+            Regex rDependencyRef = new(@"<dependency\s+id=""(.*)""\s+version=""([^""]*)""", RegexOptions.IgnoreCase);
 
             //For each dependency listed in the csproj
             foreach (Match p in rPackageRef.Matches(File.ReadAllText(csproj)))
@@ -81,7 +81,7 @@ public void TestDependencyCorrect(string csproj, string nuspec, string packagesM
                     found = false;
                     foreach (string line in File.ReadAllLines(packagesMarkdown))
                     {
-                        if (Regex.IsMatch(line, @"[\s[]" + Regex.Escape(package) + @"[\s\]]", RegexOptions.IgnoreCase))
+                        if (Regex.IsMatch(line, $@"[\s[]{Regex.Escape(package)}[\s\]]", RegexOptions.IgnoreCase))
                         {
                             int count = new Regex(Regex.Escape(version)).Matches(line).Count;
 
@@ -97,14 +97,15 @@ public void TestDependencyCorrect(string csproj, string nuspec, string packagesM
             }
         }
 
-        private object BuildRecommendedDependencyLine(string package, string version)
+        private static object BuildRecommendedDependencyLine(string package, string version)
         {
             return $"<dependency id=\"{package}\" version=\"{version}\" />";
         }
 
-        private object BuildRecommendedMarkdownLine(string package, string version)
+        private static object BuildRecommendedMarkdownLine(string package, string version)
         {
-            return string.Format("| {0} | [GitHub]() | [{1}](https://www.nuget.org/packages/{0}/{1}) | | | |", package, version);
+            return
+                $"| {package} | [GitHub]() | [{version}](https://www.nuget.org/packages/{package}/{version}) | | | |";
         }
     }
 }

BadMedicine.Dicom.Tests/StudyTests.cs

@@ -1,4 +1,4 @@
-using Dicom;
+using FellowOakDicom;
 using NUnit.Framework;
 using System;
 
@@ -16,7 +16,7 @@ public void Test_CreatingNewStudy_HasSomeImages()
 
             var p = new Person(r);
 
-            Study study = new Study(generator,p,new ModalityStats("MR",2,0,50,0,r),r);
+            Study study = new(generator,p,new("MR",2,0,50,0,r),r);
 
             Assert.AreEqual(2,study.Series.Count);
             Assert.AreEqual(50,study.Series[0].Datasets.Count);