MSS-58 Updated API to make it compatible with fo-dicom 4.0.3. Bumped …

…version.
SMI · Oct 28, 2019 · 2220f15 · 2220f15
1 parent b704b09
commit 2220f15
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diff --git a/BadMedicine.Dicom.Tests/DicomDataGeneratorTests.cs b/BadMedicine.Dicom.Tests/DicomDataGeneratorTests.cs
@@ -51,21 +51,20 @@ public void ExampleUsage()
             var person = new Person(r);
 
             //create a generator 
-            var generator = new DicomDataGenerator(r,null,"CT");
-
-            //create a dataset in memory
-            DicomDataset dataset = generator.GenerateTestDataset(person);
+            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);
+                //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);
-
-            generator.Dispose();
+                //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]
@@ -80,7 +79,7 @@ public void Test_CreatingInMemory_ModalityCT()
             for(int i = 0 ; i < 100 ; i++)
             {
                 //all should be CT because we said CT only
-                var ds = generator.GenerateTestDataset(person);
+                var ds = generator.GenerateTestDataset(person, r);
                 Assert.AreEqual("CT",ds.GetSingleValue<string>(DicomTag.Modality));
             }
 
@@ -99,7 +98,7 @@ public void Test_CreatingInMemory_Modality_CTAndMR()
             for(int i = 0 ; i < 100 ; i++)
             {
                 //all should be CT because we said CT only
-                var ds = generator.GenerateTestDataset(person);
+                var ds = generator.GenerateTestDataset(person, r);
                 var modality = ds.GetSingleValue<string>(DicomTag.Modality);
 
                 Assert.IsTrue(modality == "CT" || modality == "MR","Unexpected modality {0}",modality);
@@ -155,8 +154,6 @@ public void Test_CsvOption()
                 }
 
             }
-
-
         }
     }
 }
diff --git a/BadMedicine.Dicom/BadMedicine.Dicom.csproj b/BadMedicine.Dicom/BadMedicine.Dicom.csproj
@@ -21,8 +21,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="fo-dicom.NetCore" Version="4.0.1" />
-    <PackageReference Include="HIC.BadMedicine" Version="0.1.4" />
+    <PackageReference Include="fo-dicom.NetCore" Version="4.0.3" />
+    <PackageReference Include="HIC.BadMedicine" Version="0.1.5" />
     <PackageReference Include="System.Drawing.Common" Version="4.5.1" />
   </ItemGroup>
 

diff --git a/BadMedicine.Dicom/BadMedicine.Dicom.nuspec b/BadMedicine.Dicom/BadMedicine.Dicom.nuspec
@@ -6,16 +6,16 @@
     <title>HIC.BadMedicine.Dicom</title>
     <authors>Health Informatics Centre - University of Dundee</authors>
     <owners>Health Informatics Centre - University of Dundee</owners>
-    <projectUrl>https://github.com/HicServices/BadMedicine</projectUrl>
+    <projectUrl>https://github.com/HicServices/BadMedicine.Dicom</projectUrl>
     <license type="expression">GPL-3.0-or-later</license>
     <requireLicenseAcceptance>false</requireLicenseAcceptance>
     <description>Generate large volumes of complex (in terms of tags) dicom images for integration/stress testing ETL and image management tools.  BadMedicine.Dicom generates dicom images on demand based on an anonymous aggregate model of tag data found in scottish medical imaging with a small memory footprint.</description>
     <copyright>Copyright 2019</copyright>
     <tags>Dicom,Test Data,Random,Synthetic Data,Health</tags>
     <dependencies>
       <dependency id="MathNet.Numerics" version="4.7.0" exclude="Build,Analyzers" />
-      <dependency id="fo-dicom.NetCore" version="4.0.1" />
-      <dependency id="HIC.BadMedicine" version="0.1.4" />
+      <dependency id="fo-dicom.NetCore" version="4.0.3" />
+      <dependency id="HIC.BadMedicine" version="0.1.5" />
       <dependency id="System.Drawing.Common" version="4.5.1" />
     </dependencies>
   </metadata>

diff --git a/BadMedicine.Dicom/DicomDataGenerator.cs b/BadMedicine.Dicom/DicomDataGenerator.cs
@@ -152,21 +152,21 @@ protected override string[] GetHeaders()
         public DicomDataset[] GenerateStudyImages(Person p, out Study study)
         {        
             //generate a study
-            study = new Study(this,p,GetRandomModality(),r);
+            study = new Study(this,p,GetRandomModality(r),r);
 
             return study.SelectMany(series=>series).Select(image=>image).ToArray();
         }
 
-        public DicomDataset GenerateTestDataset(Person p)
+        public DicomDataset GenerateTestDataset(Person p,Random r)
         {
             //get a random modality
-            var modality = GetRandomModality();
+            var modality = GetRandomModality(r);
             return GenerateTestDataset(p,new Study(this,p,modality,r).Series[0]);
         }
 
-        private ModalityStats GetRandomModality()
+        private ModalityStats GetRandomModality(Random r)
         {
-            return DicomDataGeneratorStats.GetInstance(r).ModalityFrequency.GetRandom(_modalities);
+            return DicomDataGeneratorStats.GetInstance(r).ModalityFrequency.GetRandom(_modalities,r);
         }
 
         /// <summary>
@@ -189,8 +189,16 @@ public DicomDataset GenerateTestDataset(Person p,Series series)
             ds.AddOrUpdate(DicomTag.PatientID, p.CHI);
             ds.AddOrUpdate(DicomTag.PatientName, p.Forename + " " + p.Surname);
             ds.AddOrUpdate(DicomTag.PatientBirthDate, p.DateOfBirth);
-            ds.AddOrUpdate(DicomTag.PatientAddress,p.Address.Line1 + " " + p.Address.Line2 + " " + p.Address.Line3 + " " + p.Address.Line4 + " " + p.Address.Postcode.Value);
 
+            if (p.Address != null)
+            {
+                string s = p.Address.Line1 + " " + p.Address.Line2 + " " + p.Address.Line3 + " " + p.Address.Line4 +
+                           " " + p.Address.Postcode.Value;
+
+                ds.AddOrUpdate(DicomTag.PatientAddress,
+                    s.Substring(0,Math.Min(s.Length,64)) //LO only allows 64 characters
+                    );
+            }
 
             ds.AddOrUpdate(new DicomDate(DicomTag.StudyDate, series.Study.StudyDate));
             ds.AddOrUpdate(new DicomTime(DicomTag.StudyTime, DateTime.Today + series.Study.StudyTime));
@@ -235,11 +243,11 @@ public DicomDataset GenerateTestDataset(Person p,Series series)
             ds.AddOrUpdate(DicomTag.AcquisitionNumber, "0");
             ds.AddOrUpdate(DicomTag.AcquisitionDate, series.SeriesDate);
             ds.AddOrUpdate(new DicomTime(DicomTag.AcquisitionTime, DateTime.Today + series.SeriesTime));
-            ds.AddOrUpdate(DicomTag.ImagePositionPatient, "0");
-            ds.AddOrUpdate(DicomTag.PixelSpacing, "0");
+            ds.AddOrUpdate(DicomTag.ImagePositionPatient, "0","0","0");
+            ds.AddOrUpdate(new DicomDecimalString(DicomTag.PixelSpacing,"0.3","0.25"));
             ds.AddOrUpdate(DicomTag.FieldOfViewDimensions, "0");
             ds.AddOrUpdate(DicomTag.FieldOfViewDimensionsInFloat, "0");
-            ds.AddOrUpdate(DicomTag.TransferSyntaxUID, "0");
+            //ds.AddOrUpdate(DicomTag.TransferSyntaxUID, "1.2.840.10008.1.2"); this seems to break saving of files lets not set it
             ds.AddOrUpdate(DicomTag.LossyImageCompression, "00");
             ds.AddOrUpdate(DicomTag.LossyImageCompressionMethod, "ISO_10918_1");
             ds.AddOrUpdate(DicomTag.LossyImageCompressionRatio, "1");

diff --git a/BadMedicine.Dicom/DicomDataGeneratorStats.cs b/BadMedicine.Dicom/DicomDataGeneratorStats.cs
@@ -30,9 +30,9 @@ internal class DicomDataGeneratorStats
 
         private DicomDataGeneratorStats(Random r)
         {
-            InitializeTagValuesByModalityAndTag(r);
+            InitializeTagValuesByModalityAndTag();
             InitializeModalityFrequency(r);
-            InitializeImageType(r);
+            InitializeImageType();
 
             InitializeHourOfDay(r);
         }
@@ -42,7 +42,7 @@ private void InitializeHourOfDay(Random r)
             //Provenance:
             //select DATEPART(HOUR,StudyTime),work.dbo.get_aggregate_value(count(*)) from CT_Godarts_StudyTable group by DATEPART(HOUR,StudyTime)
 
-            HourOfDay = new BucketList<int>(r);
+            HourOfDay = new BucketList<int>();
 
             HourOfDay.Add(1,1);
             HourOfDay.Add(4,1);
@@ -73,7 +73,7 @@ private void InitializeHourOfDay(Random r)
         /// <returns></returns>
         public TimeSpan GetRandomTimeOfDay(Random r)
         {
-            var ts = new TimeSpan(0,HourOfDay.GetRandom(),r.Next(60),r.Next(60),0);
+            var ts = new TimeSpan(0,HourOfDay.GetRandom(r),r.Next(60),r.Next(60),0);
 
             ts = ts.Subtract(new TimeSpan(ts.Days,0,0,0));
 
@@ -83,9 +83,9 @@ public TimeSpan GetRandomTimeOfDay(Random r)
             return ts;
         }
 
-        public string GetRandomImageType()
+        public string GetRandomImageType(Random r)
         {
-            return ImageType.GetRandom();
+            return ImageType.GetRandom(r);
         }
 
         /// <summary>
@@ -109,7 +109,7 @@ private void InitializeModalityFrequency(Random r)
 
             DicomDataGenerator.EmbeddedCsvToDataTable(typeof(DicomDataGenerator), "DicomDataGeneratorModalities.csv",dt);
 
-            ModalityFrequency = new BucketList<ModalityStats>(r);
+            ModalityFrequency = new BucketList<ModalityStats>();
 
             int idx=0;
             foreach(DataRow dr in dt.Rows)
@@ -130,7 +130,7 @@ private void InitializeModalityFrequency(Random r)
 
         }
 
-        private void InitializeTagValuesByModalityAndTag(Random r)
+        private void InitializeTagValuesByModalityAndTag()
         {
             DataTable dt = new DataTable();
             dt.Columns.Add("Frequency", typeof(int));
@@ -146,16 +146,16 @@ private void InitializeTagValuesByModalityAndTag(Random r)
                     TagValuesByModalityAndTag.Add(modality,new Dictionary<DicomTag, BucketList<string>>());
 
                 if(!TagValuesByModalityAndTag[modality].ContainsKey(tag))
-                    TagValuesByModalityAndTag[modality].Add(tag,new BucketList<string>(r));
+                    TagValuesByModalityAndTag[modality].Add(tag,new BucketList<string>());
 
                 int frequency = (int) dr["Frequency"];
                 TagValuesByModalityAndTag[modality][tag].Add(frequency,(string)dr["Value"]);
             }
         }
 
-        private void InitializeImageType(Random r)
+        private void InitializeImageType()
         {
-            ImageType = new BucketList<string>(r);
+            ImageType = new BucketList<string>();
 
             ImageType.Add(96,"ORIGINAL\\PRIMARY\\AXIAL");
             ImageType.Add(1,"ORIGINAL\\PRIMARY\\LOCALIZER");

diff --git a/BadMedicine.Dicom/Study.cs b/BadMedicine.Dicom/Study.cs
@@ -44,7 +44,7 @@ public Study(DicomDataGenerator parent, Person person, ModalityStats modalitySta
 
                     //if it's a study level one record it here
                     if(dict.Key == DicomTag.StudyDescription)
-                        StudyDescription = dict.Value.GetRandom();
+                        StudyDescription = dict.Value.GetRandom(r);
                 }
 
             AccessionNumber = stats.GetRandomAccessionNumber(r);
@@ -58,7 +58,7 @@ public Study(DicomDataGenerator parent, Person person, ModalityStats modalitySta
             if(modalityStats.Modality == "CT")
             {
                 // Set ImageType
-                imageType = stats.GetRandomImageType();
+                imageType = stats.GetRandomImageType(r);
                 if(imageType == "ORIGINAL\\PRIMARY\\AXIAL")
                 {
                     NumberOfStudyRelatedInstances = Math.Max(1,(int)modalityStats.SeriesPerStudyNormal.Sample());
@@ -67,7 +67,7 @@ public Study(DicomDataGenerator parent, Person person, ModalityStats modalitySta
             }
             else
             {
-                imageType = "UNKNOWN";
+                imageType = "ORIGINAL\\PRIMARY";
                 NumberOfStudyRelatedInstances = Math.Max(1,(int)modalityStats.SeriesPerStudyNormal.Sample());
                 imageCount = Math.Max(1,(int)modalityStats.ImagesPerSeriesNormal.Sample());
             }

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ...
+## [0.0.4] - 2019-10-28
+
+## Changed
+
+- Updated dependencies to latest fo Dicom library 4.0.3
+
+## Fixed
+
+- Fixed dodgy tags in test data generated which results in broken images with fo Dicom 4.0.3
+
+## [0.0.3] - 2019-10-28
+
+### Added 
+
+ - Added Csv mode where by dicom tags are output in full to series/study/instance level CSV files
 
 ## [0.0.2] - 2019-07-16
 
@@ -24,6 +39,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Support for PatientAge, Modality, Address, UIDs, StudyDate/Time
 - Support for pixel data / NoPixels flag
 
-[Unreleased]: https://github.com/HicServices/BadMedicine.Dicom/compare/5517d7e29aaf3742e91b86288b85f692a063dba4...develop
+[Unreleased]: https://github.com/HicServices/BadMedicine.Dicom/compare/v0.0.4...develop
+[0.0.4]: https://github.com/HicServices/BadMedicine.Dicom/compare/v0.0.3...v0.0.4
+[0.0.3]: https://github.com/HicServices/BadMedicine.Dicom/compare/5517d7e29aaf3742e91b86288b85f692a063dba4...v0.0.3
 [0.0.2]: https://github.com/HicServices/BadMedicine.Dicom/compare/v0.0.1...5517d7e29aaf3742e91b86288b85f692a063dba4
 [0.0.1]: https://github.com/HicServices/BadMedicine.Dicom/compare/bdea963df0337e47434c3e72bde7a16a111b99a8...v0.0.1
diff --git a/Packages.md b/Packages.md
@@ -9,8 +9,8 @@
 
 | Package | Source Code | Version | License | Purpose | Additional Risk Assessment |
 | ------- | ------------| --------| ------- | ------- | -------------------------- |
-| HIC.BadMedicine | [GitHub](https://github.com/HicServices/BadMedicine) | [0.1.4](https://www.nuget.org/packages/HIC.BadMedicine/0.1.4) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Handles generating baseline random data (patient date of birth, CHI numberts etc)| |
-| fo-dicom.NetCore | [GitHub](https://github.com/fo-dicom/fo-dicom) |[4.0.1](https://www.nuget.org/packages/fo-dicom.NetCore/4.0.1)|[MS-PL](https://opensource.org/licenses/MS-PL) | Handles reading/writing dicom tags from dicom datasets | |
+| HIC.BadMedicine | [GitHub](https://github.com/HicServices/BadMedicine) | [0.1.5](https://www.nuget.org/packages/HIC.BadMedicine/0.1.5) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Handles generating baseline random data (patient date of birth, CHI numberts etc)| |
+| fo-dicom.NetCore | [GitHub](https://github.com/fo-dicom/fo-dicom) |[4.0.3](https://www.nuget.org/packages/fo-dicom.NetCore/4.0.3)|[MS-PL](https://opensource.org/licenses/MS-PL) | Handles reading/writing dicom tags from dicom datasets | |
 | YamlDotNet | [GitHub](https://github.com/aaubry/YamlDotNet)  | [6.0.0](https://www.nuget.org/packages/YamlDotNet/6.0.0) | [MIT](https://opensource.org/licenses/MIT) |Loading configuration files|
 | [Nunit](https://nunit.org/) |[GitHub](https://github.com/nunit/nunit) | [3.11.0](https://www.nuget.org/packages/NUnit/3.11.0) | [MIT](https://opensource.org/licenses/MIT) | Unit testing |
 | NUnit3TestAdapter | [GitHub](https://github.com/nunit/nunit3-vs-adapter)| [3.13.0](https://www.nuget.org/packages/NUnit3TestAdapter/3.13.0) | [MIT](https://opensource.org/licenses/MIT) | Run unit tests from within Visual Studio |

diff --git a/README.md b/README.md
@@ -52,14 +52,18 @@ var r = new Random(23);
 var person = new Person(r);
 
 //create a generator 
-var generator = new DicomDataGenerator(r,null,"CT");
-
-//create a dataset in memory
-DicomDataset dataset = generator.GenerateTestDataset(person);
-
-//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);
+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));   
+}
 ```
 
 ## Building

diff --git a/SharedAssemblyInfo.cs b/SharedAssemblyInfo.cs
@@ -9,6 +9,6 @@
 [assembly: AssemblyCulture("")]
 
 // These should be replaced with correct values by the release process
-[assembly: AssemblyVersion("0.0.3")]
-[assembly: AssemblyFileVersion("0.0.3")]
-[assembly: AssemblyInformationalVersion("0.0.3")]
+[assembly: AssemblyVersion("0.0.4")]
+[assembly: AssemblyFileVersion("0.0.4")]
+[assembly: AssemblyInformationalVersion("0.0.4")]