Feature/cleanup

BadDicom/BadDicom.csproj

@@ -15,6 +15,8 @@
     <DebugType>embedded</DebugType>
     <SymbolPackageFormat>snupkg</SymbolPackageFormat>
     <PublishSingleFile>true</PublishSingleFile>
+    <Nullable>enable</Nullable>
+    <EmitCompilerGeneratedFiles>true</EmitCompilerGeneratedFiles>
   </PropertyGroup>
 
   <ItemGroup>
@@ -34,6 +36,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.9.1" />
     <PackageReference Include="HIC.DicomTypeTranslation" Version="4.0.3" />
+    <PackageReference Include="Vecc.YamlDotNet.Analyzers.StaticGenerator" Version="13.0.2" />
     <PackageReference Include="YamlDotNet" Version="13.1.1" />
   </ItemGroup>
   <ItemGroup>

BadDicom/Configuration/Config.cs

@@ -1,7 +1,10 @@
-namespace BadDicom.Configuration;
+using YamlDotNet.Serialization;
 
+namespace BadDicom.Configuration;
+
+[YamlSerializable]
 internal class Config
 {
-    public TargetDatabase Database { get;set; }
-    public ExplicitUIDs UIDs { get; set; }
+    public TargetDatabase? Database { get;set; }
+    public ExplicitUIDs? UIDs { get; set; }
 }

BadDicom/Configuration/ConfigContext.cs

@@ -0,0 +1,8 @@
+using YamlDotNet.Serialization;
+
+namespace BadDicom.Configuration;
+
+[YamlStaticContext]
+public partial class ConfigContext : StaticContext
+{
+}

BadDicom/Configuration/ExplicitUIDs.cs

@@ -2,28 +2,30 @@
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
+using YamlDotNet.Serialization;
 
 namespace BadDicom.Configuration;
 
 /// <summary>
 /// Config section for loading explicit UIDs from disk and using those in file creation
 /// </summary>
+[YamlSerializable]
 public class ExplicitUIDs
 {
     /// <summary>
     /// Path to a file containing a list of study instance UIDs to use
     /// </summary>
-    public string StudyInstanceUIDs { get; set; }
+    public string? StudyInstanceUIDs { get; set; }
 
     /// <summary>
     /// Path to a file containing a list of series instance UIDs to use
     /// </summary>
-    public string SeriesInstanceUIDs { get; set; }
+    public string? SeriesInstanceUIDs { get; set; }
 
     /// <summary>
     /// Path to a file containing a list of SOP instance UIDs to use
     /// </summary>
-    public string SOPInstanceUIDs { get; set; }
+    public string? SOPInstanceUIDs { get; set; }
 
     /// <summary>
     /// Loads the UID files referenced (if they exist) in the configuration
@@ -46,10 +48,10 @@ public void Load()
             UIDAllocator.SOPUIDs.Enqueue(u);
     }
 
-    private IEnumerable<string> GetUIDsFrom(string path)
+    private static IEnumerable<string> GetUIDsFrom(string? path)
     {
         if (string.IsNullOrWhiteSpace(path) || !File.Exists(path)) return Enumerable.Empty<string>();
 
-        return File.ReadLines(StudyInstanceUIDs).Where(l => !string.IsNullOrWhiteSpace(l));
+        return File.ReadLines(path).Where(l => !string.IsNullOrWhiteSpace(l));
     }
 }

BadDicom/Configuration/TargetDatabase.cs

@@ -1,10 +1,12 @@
 using FAnsi;
+using YamlDotNet.Serialization;
 
 namespace BadDicom.Configuration;
 
 /// <summary>
 /// Identify the target database and configuration for generated data
 /// </summary>
+[YamlSerializable]
 public class TargetDatabase
 {
     /// <summary>
@@ -14,17 +16,17 @@ public class TargetDatabase
     /// <summary>
     /// The ConnectionString containing the server name, credentials and other parameters for the connection
     /// </summary>
-    public string ConnectionString { get; set; }
+    public string? ConnectionString { get; set; }
 
     /// <summary>
     /// The name of database
     /// </summary>
-    public string DatabaseName { get; set; }
+    public string? DatabaseName { get; set; }
 
     /// <summary>
     /// The filename of a YAML template file to be used for this database
     /// </summary>
-    public string Template { get; set; }
+    public string? Template { get; set; }
 
     /// <summary>
     /// Pass true to create tables from template that do not have primary key.  Do bulk insert

BadDicom/Program.cs

@@ -10,7 +10,6 @@
 using System.Runtime.InteropServices;
 using System.Threading.Tasks;
 using BadDicom.Configuration;
-using FellowOakDicom;
 using DicomTypeTranslation;
 using DicomTypeTranslation.TableCreation;
 using FAnsi.Discovery;
@@ -61,13 +60,12 @@ private static void RunOptionsAndReturnExitCode(ProgramOptions opts)
 
             try
             {
-                var d = new Deserializer();
+                var d = new StaticDeserializerBuilder(new ConfigContext()).Build();
                 config = d.Deserialize<Config>(File.ReadAllText(ConfigFile));
             }
             catch (Exception e)
             {
-                Console.WriteLine($"Error deserializing '{ConfigFile}'");
-                Console.Write(e.ToString());
+                Console.WriteLine($"Error deserializing '{ConfigFile}'{Environment.NewLine}{e}");
                 _returnCode = -1;
                 return;
             }
@@ -112,12 +110,12 @@ private static void RunOptionsAndReturnExitCode(ProgramOptions opts)
         _returnCode = 0;
     }
 
-    private static DicomDataGenerator GetDataGenerator(ProgramOptions opts,Random r, out DirectoryInfo dir)
+    private static DicomDataGenerator GetDataGenerator(ProgramOptions opts,Random r, out DirectoryInfo? dir)
     {
         //Generate the dicom files (of the modalities that the user requested)
-        var modalities = !string.IsNullOrWhiteSpace(opts.Modalities)? opts.Modalities.Split(",") :Array.Empty<string>();
+        var modalities = string.IsNullOrWhiteSpace(opts.Modalities)? Array.Empty<string>() :opts.Modalities.Split(",");
 
-        dir = opts.OutputDirectory.Equals("/dev/null",StringComparison.InvariantCulture) ? null : Directory.CreateDirectory(opts.OutputDirectory);
+        dir = opts.OutputDirectory?.Equals("/dev/null",StringComparison.InvariantCulture)!=false ? null : Directory.CreateDirectory(opts.OutputDirectory);
         return new DicomDataGenerator(r, opts.OutputDirectory, modalities)
         {
             NoPixels = opts.NoPixels,
@@ -144,14 +142,10 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
         var batchSize = Math.Max(1, configDatabase.Batches);
 
         //if we are going into a database we definitely do not need pixels!
-        if (opts.NoPixels == false)
-            opts.NoPixels = true;
+        opts.NoPixels = true;
 
 
-        Stopwatch swTotal = new();
-
-        swTotal.Start();
-
+        var swTotal = Stopwatch.StartNew();
         const string neverDistinct = "SOPInstanceUID";
 
         if (!File.Exists(configDatabase.Template))
@@ -167,8 +161,7 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
         }
         catch (Exception e)
         {
-            Console.WriteLine($"Error reading yaml from '{configDatabase.Template}'");
-            Console.WriteLine(e.ToString());
+            Console.WriteLine($"Error reading yaml from '{configDatabase.Template}'{Environment.NewLine}{e}");
             return -2;
         }
 
@@ -220,7 +213,7 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
         for (var i = 0; i < uploaders.Length; i++)
             uploaders[i] = new IBulkCopy[template.Tables.Count];
 
-        var pks = new string[template.Tables.Count];
+        var pks = new string?[template.Tables.Count];
 
         for (var i = 0; i < template.Tables.Count; i++)
         {
@@ -286,22 +279,9 @@ private static int RunDatabaseTarget(TargetDatabase configDatabase, ProgramOptio
                 uploaders[j][i] = tbl.BeginBulkInsert();
             }
         }
-        var tasks = new Task[batchSize];
-
         var identifiers = GetPeople(opts, out var r);
 
-        for (var i = 0; i < batchSize; i++)
-        {
-            var batch = i;
-            tasks[i] = new Task(() =>  // lgtm[cs/local-not-disposed]
-            {
-                RunBatch(identifiers,opts,r,batches[batch],uploaders[batch]);
-
-            });
-            tasks[i].Start();
-        }
-
-        Task.WaitAll(tasks);
+        Parallel.For(0, batchSize, i => RunBatch(identifiers, opts, r, batches[i], uploaders[i]));
 
         swTotal.Stop();
 
@@ -341,7 +321,7 @@ private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts,
                 swGeneration.Start();
 
                 var p = identifiers.People[r.Next(identifiers.People.Length)];
-                var ds = dicomGenerator.GenerateStudyImages(p,out var s);
+                var ds = dicomGenerator.GenerateStudyImages(p,out _);
 
                 swGeneration.Stop();
 
@@ -358,11 +338,8 @@ private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts,
                         var column = DicomTypeTranslaterReader.GetColumnNameForTag(item.Tag, false);
                         var value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(dataset, item));
 
-                        foreach (var row in rows)
-                        {
-                            if (row.Table.Columns.Contains(column))
-                                row[column] = value ?? DBNull.Value;
-                        }
+                        foreach (var row in rows.Where(row=>row.Table.Columns.Contains(column)))
+                            row[column] = value ?? DBNull.Value;
                     }
 
                     for (var j = 0; j < batches.Length; j++)
@@ -372,7 +349,7 @@ private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts,
                 }
 
                 //every 100 and last batch
-                if (i % 100 == 0 || i == opts.NumberOfStudies - 1)
+                if (i % 100 != 0 && i != opts.NumberOfStudies - 1) continue;
                 {
                     swUploading.Start();
                     for (var j = 0; j < uploaders.Length; j++)
@@ -383,7 +360,7 @@ private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts,
                     swUploading.Stop();
                     Console.WriteLine($"{DateTime.Now} Done {i} studies");
                 }
-                            
+
             }
         }
         finally

BadDicom/ProgramOptions.cs

@@ -8,7 +8,7 @@ namespace BadDicom;
 internal class ProgramOptions
 {
     [Value(0,HelpText = "Output directory to create CSV files in",Required=true)]
-    public string OutputDirectory { get; set; }
+    public string? OutputDirectory { get; set; }
 
     [Value(1, HelpText = "The number of unique patient identifiers to generate up front and then use in test data",Default = 500)]
     public int NumberOfPatients { get; set; } = 500;

BadMedicine.Dicom.Tests/DicomDataGeneratorTests.cs

@@ -84,7 +84,7 @@ public void Test_Anonymise()
         var r = new Random(23);
         var person = new Person(r);
 
-        var generator = new DicomDataGenerator(r,new string(TestContext.CurrentContext.WorkDirectory),"CT");
+        using var generator = new DicomDataGenerator(r,new string(TestContext.CurrentContext.WorkDirectory),"CT");
 
         // without anonymisation (default) we get the normal patient ID
         var ds = generator.GenerateTestDataset(person, r);
@@ -100,9 +100,6 @@ public void Test_Anonymise()
         // we get a blank patient ID
         Assert.IsTrue(ds2.Contains(DicomTag.PatientID));
         Assert.AreEqual(string.Empty,ds2.GetString(DicomTag.PatientID));
-
-        generator.Dispose();
-
     }
     [Test]
     public void Test_CreatingInMemory_Modality_CTAndMR()

BadMedicine.Dicom/BadMedicine.Dicom.csproj

@@ -14,6 +14,7 @@
     <PackageLicenseExpression>GPL-3.0-or-later</PackageLicenseExpression>
     <Copyright>Copyright 2019</Copyright>
     <PackageTags>DICOM,Test Data,Random,Synthetic Data,Health</PackageTags>
+    <Nullable>enable</Nullable>
   </PropertyGroup>
 
   <ItemGroup>

BadMedicine.Dicom/DescBodyPart.cs

@@ -22,17 +22,17 @@ public class DescBodyPart
     /// A known value of <see cref="DicomTag.StudyDescription"/> which is consistent with
     /// <see cref="BodyPartExamined"/> and <see cref="SeriesDescription"/> (of this class)
     /// </summary>
-    public string StudyDescription { get; init; }
+    public string? StudyDescription { get; init; }
 
     /// <summary>
     /// A known value of <see cref="DicomTag.BodyPartExamined"/> which is consistent with
     /// <see cref="StudyDescription"/> and <see cref="SeriesDescription"/> (of this class)
     /// </summary>
-    public string BodyPartExamined { get; init; }
+    public string? BodyPartExamined { get; init; }
 
     /// <summary>
     /// A known value of <see cref="DicomTag.SeriesDescription"/> which is consistent with
     /// <see cref="BodyPartExamined"/> and <see cref="StudyDescription"/> (of this class)
     /// </summary>
-    public string SeriesDescription { get; init; }
+    public string? SeriesDescription { get; init; }
 }