ENH: support of n segmentation for n series types for each finding

* list of findings is simple list
* upon finding selection a more detailed finding information widget
  is displayed and all available series types will be listed with an
  option to select one of three (segmentation, ruler, fiducial)
  annotation tools. For now we only support segmentations
* upon annotation tool selection display its annotation tool widget,
  which in the current situation will be a customized segment editor.
* added SeriesType class and subclasses where rules can be defined.
  Ideally this should also support the classification of DICOM files
  directly (issue SlicerProstate#1)
* added HangingProtocol class and three subclasses for PIRADS specific
  hanging.
* each finding can have n annotations of different annotation tools
  where n is the number of volumes used for PIRADS reading (issue SlicerProstate#3)

Documentation/Classes.puml

@@ -8,130 +8,155 @@ package SlicerPIRADSWidget {
   class MultiVolumeExplorerWidget {
   }
 
-  class AssessmentDialog {
-    + setAssessment(): Assessment
-  }
-
   class PatientInfoWidget {
   }
 
-  class FindingsWidget {
-    - __findingsTable
-    - __measurementToolWidget
-  }
+  package Finding {
+    class FindingsWidget {
+      - __findingList
+      - __findingsInformationWidget
+      - __AnnotationToolWidget
+    }
+
+    class FindingsList {
+      + createFinding(): Finding
+      + addAssessment()
+    }
+
+    class AnnotationToolSelectionWidget {
+      - __annotationTools: list
+      + addAnnotationTool(AnnotationTool tool)
+      + getAnnotationTools(): list
+      + setActiveAnnotationTool(id): bool
+    }
+
+    class FindingInformationWidget {
+
+    }
 
-  class FindingsTable {
-    + createFinding(): Finding
-    + assessLesion():
+    class AnnotationToolWidget {
+    }
   }
 
-  class MeasurementToolWidget {
-    - __measurementTools: list
-    + addMeasurementTool(MeasurementTool tool)
-    + getMeasurementTools(): list
-    + setActiveMeasurementTool(id): bool
+  class DataSelectionDialog {
+    # _patientTable
+    # _studiesTable
   }
 
   '  Connections
 
-  AssessmentDialog <|-- StudyAssessmentWidget
-  AssessmentDialog <|-- LesionAssessmentWidget
+  package Assessment {
 
-  FindingsWidget::__findingsTable ..> FindingsTable: has
-  FindingsWidget::__measurementToolWidget ..> MeasurementToolWidget: has
+    class AssessmentDialog {
+      + setAssessment(): Assessment
+    }
+    AssessmentDialog <|-- StudyAssessmentWidget
+    AssessmentDialog <|-- FindingAssessmentWidget
+  }
 
 }
 
-class AssessmentHelp {
 
-}
+package SlicerPIRADSLogic {
 
-interface Assessment {
-  - __schema: string
-  - __data=None
-  .. setter ..
-  + loadSchema(fileName)
-  + loadData(string): bool
-  .. getter ..
-  + getSchema(): string
-  + getData(): string
-}
+  package AssessmentLogic {
+    interface Assessment {
+      - __schema: string
+      - __data=None
+      .. setter ..
+      + loadSchema(fileName)
+      + loadData(string): bool
+      .. getter ..
+      + getSchema(): string
+      + getData(): string
+    }
 
-'interface DataHandler {
-'  + save()
-'  + load(fileName): bool
-'}
-'
-'class ReportDataHandler {
-'}
-'DataHandler <|-- ReportDataHandler
-'DataHandler <|-- StudyAssessmentHandler
-'
-'Assessment -> DataHandler: has_a
-
-class LesionAssessment {
-  -lesion: Lesion
-}
+    class FindingAssessment {
+    }
 
-class StudyAssessment {
-}
+    class StudyAssessment {
+    }
+  }
 
-class Report {
-- findings: Finding
-- studyAssessment: StudyAssessment
-__
-+ startReport(): bool
-+ closeReport(): bool
-+ saveReport(): bool
-+ loadReport(string jsonfilename): bool
-}
+  'interface DataHandler {
+  '  + save()
+  '  + load(fileName): bool
+  '}
+  '
+  'class ReportDataHandler {
+  '}
+  'DataHandler <|-- ReportDataHandler
+  'DataHandler <|-- StudyAssessmentHandler
+  '
+  'Assessment -> DataHandler: has_a
+
+
+  class Finding {
+    + createAnnotation(seriesType, mrmlNodeClass): Annotation
+    + getAnnotation(seriesType, mrmlNodeClass): Annotation
+  }
 
-interface Lesion {
-- mrmlNode=None
-- mrmlClass=None
-__
-+ setMRMLNode(mrmlNode)
-}
+  class Report {
+  - findings: Finding
+  - studyAssessment: StudyAssessment
+  __
+  + startReport(): bool
+  + closeReport(): bool
+  + saveReport(): bool
+  + loadReport(string jsonfilename): bool
+  }
 
-class Fiducial {
-}
+  package AnnotationLogic {
 
-class Segmentation {
-}
+    interface Annotation {
+    - mrmlNode=None
+    - mrmlClass=None
+    __
+    + setMRMLNode(mrmlNode)
+    }
 
-class Ruler {
-}
+    interface Annotation {
+      +id=None
+    }
+
+    class Fiducial {
+    }
+
+    class Segmentation {
+    }
 
-interface MeasurementTool {
-  +id=None
+    class Ruler {
+    }
+  }
 }
 
+
 SlicerPIRADSWidget ..> Report: has_a
 
-LesionAssessmentWidget ..> AssessmentHelp
+'FindingAssessmentWidget ..> AssessmentHelp
 
-LesionAssessmentWidget ..> LesionAssessment:generated_from
+FindingAssessmentWidget ..> FindingAssessment:generated_from
 StudyAssessmentWidget ..> StudyAssessment:generated_from
 
-FindingsTable "1" ..> "0..*" Finding:has/creates
-
-MeasurementToolWidget::__measurementTool "1" ..> "1" MeasurementTool: has
+FindingsList "1" ..> "0..*" Finding:has/creates
+FindingsWidget ..> FindingInformationWidget: has
+FindingsWidget::_AnnotationToolWidget ..> AnnotationToolWidget: has
+FindingsWidget::__FindingsList ..> FindingsList: has
 
-MeasurementTool <|-- Fiducial
-MeasurementTool <|-- Segmentation
-MeasurementTool <|-- Ruler
+Annotation <|-- Fiducial
+Annotation <|-- Segmentation
+Annotation <|-- Ruler
 
-MeasurementTool ..> Lesion
+FindingInformationWidget "1" .> "n" AnnotationToolSelectionWidget: has
 
-Finding "1" *-- "1" LesionAssessment: has_a
-Finding "1" *-- "1" Lesion: has_a
-LesionAssessment::lesion "1" ..> "1" Lesion: has_a
 
+Finding "1" *-- "1" FindingAssessment: has_a
+Finding::_annotations "1" *-- "n" Annotation: has
 
 Report::findings "1" ..> "n" Finding
 Report::studyAssessment "1" ..> "1" StudyAssessment
 
-Assessment <|-- LesionAssessment
+Assessment <|-- FindingAssessment
 Assessment <|-- StudyAssessment
 
 @enduml

SlicerPIRADS/CMakeLists.txt

@@ -4,8 +4,15 @@ set(MODULE_PYTHON_SCRIPTS
   ${MODULE_NAME}.py
   SlicerPIRADSLogic/__init__.py
   SlicerPIRADSLogic/Configuration.py
+  SlicerPIRADSLogic/Annotation.py
+  SlicerPIRADSLogic/Finding.py
+  SlicerPIRADSLogic/HangingProtocol.py
+  SlicerPIRADSLogic/SeriesType.py
   SlicerPIRADSWidgets/__init__.py
   SlicerPIRADSWidgets/AssessmentDialog.py
+  SlicerPIRADSWidgets/AnnotationWidget.py
+  SlicerPIRADSWidgets/FindingsWidget.py
+  SlicerPIRADSWidgets/ProstateSectorMapDialog.py
   SlicerPIRADSWidgets/DataSelectionDialog.py
   )
 
@@ -15,11 +22,16 @@ set(MODULE_PYTHON_RESOURCES
   Resources/Forms/Procedure_Information.json
   Resources/UI/AssessmentDialog.ui
   Resources/UI/DataSelectionDialog.ui
-  Resources/UI/FindingItemWidget.ui
+  Resources/UI/AnnotationItemWidget.ui
   Resources/UI/FindingsWidget.ui
-  Resources/UI/MeasurementToolSelectionDialog.ui
+  Resources/UI/FindingInformationWidget.ui
+  Resources/UI/AnnotationItemWidget.ui
   Resources/UI/ProstateSectorMapDialog.ui
   Resources/UI/StudyLevelAssessmentWidget.ui
+  Resources/Icons/Fiducials.png
+  Resources/Icons/ProstateMap.png
+  Resources/Icons/Ruler.png
+  Resources/Icons/SegmentEditor.png
 )
 
 slicerMacroBuildScriptedModule(