Merge branch 'release/1.0.2'

CHANGELOG.md

@@ -6,6 +6,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+...
+
+## [1.0.2] - 2020-02-06
+
+### Added
+
+- New option for DicomRepopulator to put images in root subfolders e.g. by PatientID
+
+### Changed
+
+- Improved GUI usability 
+
 ## [1.0.1] - 2019-12-09
 
 ### Added 
@@ -18,7 +30,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Initial version
 
 
-[Unreleased]: https://github.com/HicServices/DicomTemplateBuilder/compare/v1.0.1...develop
+[Unreleased]: https://github.com/HicServices/DicomTemplateBuilder/compare/v1.0.2...develop
+[1.0.2]: https://github.com/HicServices/DicomTemplateBuilder/compare/v1.0.1...v1.0.2
 [1.0.1]: https://github.com/HicServices/DicomTemplateBuilder/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/HicServices/DicomTemplateBuilder/tree/v1.0.0
 [DicomTypeTranslation]: https://github.com/HicServices/DicomTypeTranslation

Repopulator/CsvToDicomColumn.cs

@@ -5,20 +5,38 @@
 
 namespace Repopulator
 {
+
+    public enum ColumnRole
+    {
+        None = 0,
+
+        /// <summary>
+        /// The column that contains the alleged location of dcm files on disk
+        /// </summary>
+        FilePath,
+
+        /// <summary>
+        /// The column should be a top level subfolder under which to create files e.g. PatientID
+        /// </summary>
+        SubFolder,
+    }
+
     public class CsvToDicomColumn
     {
         public string Name { get; }
         public int Index { get; }
         public HashSet<DicomTag> TagsToPopulate { get; }
-        public bool IsFilePath { get; set; }
-
+
+        public ColumnRole Role { get; }
 
-        public CsvToDicomColumn(string colName, int index, bool isFileColumn,params DicomTag[] mappedTags)
+        public CsvToDicomColumn(string colName, int index, ColumnRole role,params DicomTag[] mappedTags)
         {
-            if (mappedTags != null && mappedTags.Any() && isFileColumn)
+            //cannot be DicomTag AND FilePath
+            if (mappedTags != null && mappedTags.Any() && role == ColumnRole.FilePath)
                 throw new ArgumentException("Column has ambiguous role, it should either provide dicom tag substitutions or be the file path column not both");
 
-            if ((mappedTags == null || !mappedTags.Any())&& !isFileColumn)
+            //if you don't have DicomTags you must have some other role
+            if ((mappedTags == null || !mappedTags.Any())&& role == ColumnRole.None)
                 throw new ArgumentException("Column has no clear role, it should either provide dicom tag substitutions or be the file path column");
 
             if (index < 0)
@@ -35,7 +53,7 @@ public CsvToDicomColumn(string colName, int index, bool isFileColumn,params Dico
             Name = colName;
             Index = index;
             TagsToPopulate = new HashSet<DicomTag>(mappedTags?? new DicomTag[0]);
-            IsFilePath = isFileColumn;
+            Role = role;
         }
     }
 }

Repopulator/CsvToDicomTagMapping.cs

@@ -17,6 +17,12 @@ public class CsvToDicomTagMapping
         /// relatively (i.e. not absolute path names)
         /// </summary>
         public CsvToDicomColumn FilenameColumn;
+
+
+        /// <summary>
+        /// The column of the CSV which records.  The column should be a top level subfolder under which to create files e.g. PatientID
+        /// </summary>
+        public CsvToDicomColumn SubFolderColumn;
 
         /// <summary>
         /// Columns which contain dicom tag values.  This is not all the columns in the CSV.  It does not include <see cref="FilenameColumn"/>
@@ -84,19 +90,28 @@ public bool BuildMap(DicomRepopulatorOptions options, out string log)
 
                             if (match != null)
                             {
-                                if(match.IsFilePath)
+                                if(match.Role == ColumnRole.FilePath)
+                                {
                                     if (FilenameColumn != null)
                                         throw new Exception("There are 2+ FilenameColumn in the CSV");
                                     else
                                         FilenameColumn = match;
-                                else
+                                }
+
+                                if(match.Role == ColumnRole.SubFolder)
                                 {
-                                    if(TagColumns.Any(c=>c.TagsToPopulate.Intersect(match.TagsToPopulate).Any()))
-                                        throw new Exception($"There are 2+ columns that both populate for one of the DicomTag(s) '{string.Join(",",match.TagsToPopulate)}'");
-
-                                    TagColumns.Add(match);
+                                    if (SubFolderColumn != null)
+                                        throw new Exception("There are 2+ SubFolderColumn in the CSV");
+                                    else
+                                        SubFolderColumn = match;
                                 }
 
+                                if(TagColumns.Any(c=>c.TagsToPopulate.Intersect(match.TagsToPopulate).Any()))
+                                    throw new Exception($"There are 2+ columns that both populate for one of the DicomTag(s) '{string.Join(",",match.TagsToPopulate)}'");
+
+                                TagColumns.Add(match);
+
+
                                 sb.AppendLine($"Validated header '{header}'");
                             }
                             else
@@ -173,20 +188,23 @@ public CsvToDicomColumn GetKeyDicomTagAndColumnName(DicomRepopulatorOptions stat
         {
             CsvToDicomColumn toReturn = null;
             if(columnName.Equals(state.FileNameColumn,StringComparison.CurrentCultureIgnoreCase))
-                toReturn = new CsvToDicomColumn(columnName,index,true);
+                toReturn = new CsvToDicomColumn(columnName,index,ColumnRole.FilePath);
 
+            if(columnName.Equals(state.SubFolderColumn, StringComparison.CurrentCultureIgnoreCase))
+                toReturn = new CsvToDicomColumn(columnName,index,ColumnRole.SubFolder);
+
             var found = DicomDictionary.Default.SingleOrDefault(entry => string.Equals(entry.Keyword ,columnName,StringComparison.CurrentCultureIgnoreCase));
 
             if(found != null)
                 if (toReturn == null)
-                    toReturn = new CsvToDicomColumn(columnName,index,false,found.Tag); 
+                    toReturn = new CsvToDicomColumn(columnName,index,ColumnRole.None,found.Tag); 
                 else
                     toReturn.TagsToPopulate.Add(found.Tag); //it's a file path AND a tag! ok...
 
 
             if (extraMappings != null && extraMappings.ContainsKey(columnName))
                 if(toReturn == null)
-                    toReturn = new CsvToDicomColumn(columnName,index,false,extraMappings[columnName].ToArray());
+                    toReturn = new CsvToDicomColumn(columnName,index,ColumnRole.None,extraMappings[columnName].ToArray());
                 else
                     toReturn.TagsToPopulate.UnionWith(extraMappings[columnName]);
 

Repopulator/DicomRepopulator.cd

@@ -38,7 +38,7 @@
   <Class Name="Repopulator.CsvToDicomColumn">
     <Position X="9.25" Y="6.5" Width="2.25" />
     <TypeIdentifier>
-      <HashCode>AAAAAAAAAAAAAAAAAgAAAAQAAAAAAAAAAAEAABAAAAA=</HashCode>
+      <HashCode>AAAAAAAAAAAAAAAAEgAAAAQAAAAAAAAAAAEAAAAAAAA=</HashCode>
       <FileName>CsvToDicomColumn.cs</FileName>
     </TypeIdentifier>
   </Class>
@@ -47,11 +47,13 @@
     <AssociationLine Name="FilenameColumn" Type="Repopulator.CsvToDicomColumn" FixedToPoint="true">
       <Path>
         <Point X="7" Y="7.923" />
+        <Point X="7.698" Y="7.923" Type="JumpStart" />
+        <Point X="7.865" Y="7.923" Type="JumpEnd" />
         <Point X="9.25" Y="7.923" />
       </Path>
     </AssociationLine>
     <TypeIdentifier>
-      <HashCode>AAACAAGAAAAAAAAAAAAAAABAAAAAAAAABAAAAARBAAA=</HashCode>
+      <HashCode>AAACAAGAAAQAAAAAAAAAAABAAAAAAAAABAAAAARBAAA=</HashCode>
       <FileName>CsvToDicomTagMapping.cs</FileName>
     </TypeIdentifier>
     <ShowAsAssociation>
@@ -67,7 +69,7 @@
       <Compartment Name="Properties" Collapsed="true" />
     </Compartments>
     <TypeIdentifier>
-      <HashCode>AAAAgQgABAAAAAAAQAECAAQQCAAAEAgEASAAAAACAAA=</HashCode>
+      <HashCode>AAAAgQgABAQAAAAAQAECAAQQCQAAEAgEASAAAAACAAA=</HashCode>
       <FileName>DicomRepopulatorOptions.cs</FileName>
     </TypeIdentifier>
   </Class>
@@ -77,7 +79,7 @@
       <Compartment Name="Fields" Collapsed="true" />
     </Compartments>
     <TypeIdentifier>
-      <HashCode>AAhAAAAIACAAQQAAAgAAAIBAMAAABACAAAAQAAAAgAA=</HashCode>
+      <HashCode>AAhAAAAIACAAQQAAAgAAAIBAMgAABACAAAAQAAAAgAA=</HashCode>
       <FileName>DicomRepopulatorProcessor.cs</FileName>
     </TypeIdentifier>
     <ShowAsAssociation>

Repopulator/DicomRepopulatorOptions.cs

@@ -20,8 +20,12 @@ public class DicomRepopulatorOptions
         public string FileNameColumn = DefaultFileNameColumn;
         public bool Anonymise;
         public int ErrorThreshold = 100;
+        public string CultureName;
+
+        [YamlIgnore]
         public CultureInfo Culture = CultureInfo.CurrentCulture;
-
+
+        public string SubFolderColumn;
 
         [YamlIgnore]
         public DirectoryInfo OutputDirectoryInfo => new DirectoryInfo(OutputFolder);
@@ -34,6 +38,7 @@ public class DicomRepopulatorOptions
 
         [YamlIgnore]
         public FileInfo ExtraMappings => new FileInfo(InputExtraMappings);
+
 
     }
 }

Repopulator/DicomRepopulatorProcessor.cs

@@ -1,21 +1,17 @@
 using System;
-using System.Collections.Generic;
 using System.Diagnostics;
 using System.IO;
 using System.Linq;
 using System.Text;
 using System.Threading;
 using System.Threading.Tasks;
 using Dicom;
-using DicomTypeTranslation;
 using DicomTypeTranslation.Helpers;
-using FAnsi.Discovery.QuerySyntax.Update;
 using NLog;
 using NLog.Config;
 using NLog.Targets;
 using Repopulator.Matchers;
 using Repopulator.TagUpdaters;
-using TypeGuesser.Deciders;
 
 namespace Repopulator
 {
@@ -66,7 +62,7 @@ public DicomRepopulatorProcessor(string currentDirectory = null)
 
         public int Process(DicomRepopulatorOptions options)
         {
-            _parallelOptions = new ParallelOptions { MaxDegreeOfParallelism = options.NumThreads };
+            _parallelOptions = new ParallelOptions { MaxDegreeOfParallelism = Math.Max(1,options.NumThreads) };
             _tagUpdater = new ParseStringsUpdater(options.Culture);
             _anonymizer = options.Anonymise ? new DicomAnonymizer() : null;
 
@@ -162,7 +158,10 @@ private void ProcessJob(RepopulatorJob job, DicomRepopulatorOptions options)
             _logger.Debug("Saving output file");
 
             // Preserves any sub-directory structures
-            var outPath = Path.Combine(options.OutputDirectoryInfo.FullName, inputRelativePath);
+            var outPath = job.Map.SubFolderColumn != null
+                ? Path.Combine(options.OutputDirectoryInfo.FullName, job.Cells[job.Map.SubFolderColumn.Index],inputRelativePath)
+                : Path.Combine(options.OutputDirectoryInfo.FullName, inputRelativePath);
+
             Directory.CreateDirectory(Path.GetDirectoryName(outPath));
 
             job.File.Save(outPath);

SharedAssemblyInfo.cs

@@ -7,6 +7,6 @@
 [assembly: AssemblyCulture("")]
 
 // These should be replaced with correct values by the release process
-[assembly: AssemblyVersion("1.0.1")]
-[assembly: AssemblyFileVersion("1.0.1")]
-[assembly: AssemblyInformationalVersion("1.0.1")]
+[assembly: AssemblyVersion("1.0.2")]
+[assembly: AssemblyFileVersion("1.0.2")]
+[assembly: AssemblyInformationalVersion("1.0.2")]