Merge pull request #317 from michaelschwier/MeasurementReportUtils

Util Classes to build Measurement Report and generate JSON

Author: fedorov

.gitignore

@@ -35,3 +35,7 @@ CMakeLists.txt.user*
 __pycache__/
 *.py[cod]
 *$py.class
+
+# VSCode             #
+######################
+.vscode

util/measurementReportUtils/__init__.py

@@ -0,0 +1,7 @@
+# Defining convenience import shortcuts for those classes which are
+# supposed to be used publicly
+from .measurementReport import MeasurementReport
+from .measurementGroup import MeasurementGroup
+from .measurementItem import VolumeMeasurementItem, MeanADCMeasurementItem
+from .codeSequences import CodeSequence, Finding, FindingSite, ProcedureReported
+

util/measurementReportUtils/codeSequences.py

@@ -0,0 +1,47 @@
+
+class CodeSequence(object):
+
+  def __init__(self, codeMeaning, codingSchemeDesignator, codeValue):
+    self.CodeValue = codeValue
+    self.CodingSchemeDesignator = codingSchemeDesignator
+    self.CodeMeaning = codeMeaning
+
+
+class Finding(CodeSequence):
+
+  def __init__(self, segmentedStructure):
+    if segmentedStructure == "NormalROI_PZ_1":
+      super().__init__("Normal", "SRT", "G-A460")
+    elif segmentedStructure == "PeripheralZone":
+      super().__init__("Entire", "SRT", "R-404A4")
+    elif segmentedStructure == "TumorROI_PZ_1":
+      super().__init__("Abnormal", "SRT", "R-42037")
+    elif segmentedStructure == "WholeGland":
+      super().__init__("Entire Gland", "SRT", "T-F6078")
+    else:
+      raise ValueError("Segmented Structure Type {} is not supported yet. Build your own Finding code sequence using the class CodeSequence".format(segmentedStructure))
+  
+
+class FindingSite(CodeSequence):
+  
+  def __init__(self, segmentedStructure):
+    if segmentedStructure == "NormalROI_PZ_1":
+      super().__init__("Peripheral zone of the prostate", "SRT", "T-D05E4")
+    elif segmentedStructure == "PeripheralZone":
+      super().__init__("Peripheral zone of the prostate", "SRT", "T-D05E4")
+    elif segmentedStructure == "TumorROI_PZ_1":
+      super().__init__("Peripheral zone of the prostate", "SRT", "T-D05E4")
+    elif segmentedStructure == "WholeGland":
+      super().__init__("Prostate", "SRT", "T-9200B")
+    else:
+      raise ValueError("Segmented Structure Type {} is not supported yet. Build your own FindingSite code sequence using the class CodeSequence".format(segmentedStructure))
+
+
+class ProcedureReported(CodeSequence):
+
+  def __init__(self, codeMeaning):
+    if codeMeaning == "Multiparametric MRI of prostate":
+      super().__init__("Multiparametric MRI of prostate", "DCM", "126021")
+    else:
+      raise ValueError("Procedure Type {} is not supported yet. Build your own ProcedureReported code sequence using the class CodeSequence".format(codeMeaning))
+

util/measurementReportUtils/measurementGroup.py

@@ -0,0 +1,27 @@
+
+class MeasurementGroup(object):
+  """
+  Data structure plus convenience methods to create measurment groups following
+  the required format to be processed by the DCMQI tid1500writer tool. Use this
+  to populate the Measurements list in :class:`MeasurementReport`.
+  """
+
+  def __init__(self, 
+               trackingIdentifier, trackingUniqueIdentifier, referencedSegment, 
+               sourceSeriesInstanceUID, segmentationSOPInstanceUID,
+               finding, findingSite):
+    self.TrackingIdentifier = trackingIdentifier
+    self.TrackingUniqueIdentifier = trackingUniqueIdentifier
+    self.ReferencedSegment = referencedSegment
+    self.SourceSeriesForImageSegmentation = sourceSeriesInstanceUID
+    self.segmentationSOPInstanceUID = segmentationSOPInstanceUID
+    self.Finding = finding
+    self.FindingSite = findingSite
+    self.measurementItems = []
+
+  def addMeasurementItem(self, measurementItem):
+    self.measurementItems.append(measurementItem)
+
+    
+
+

util/measurementReportUtils/measurementItem.py

@@ -0,0 +1,53 @@
+
+class MeasurementItem(object):
+
+  def __init__(self, value):
+    self.value = self.convertNumericToDcmtkFittingString(value)
+
+  def convertNumericToDcmtkFittingString(self, value):
+    if isinstance(value, float) or isinstance(value, int):
+      s = str(value)
+      if (len(s) <= 16):
+        return s
+      elif (s.find(".") >= 0) and (s.find(".") < 15):
+        return s[:16]
+      else:
+        raise ValueError("Value cannot be converted to 16 digits without loosing too much precision!")
+    else:
+      raise TypeError("Value to convert is not of type float or int")
+
+
+class VolumeMeasurementItem(MeasurementItem):
+
+  def __init__(self, value):
+    super().__init__(value)
+    self.quantity = {
+      "CodeValue": "G-D705", 
+      "CodingSchemeDesignator": "SRT", 
+      "CodeMeaning": "Volume"
+    }
+    self.units = {
+      "CodeValue": "cm3",
+      "CodingSchemeDesignator": "UCUM",
+      "CodeMeaning": "cubic centimeter"
+    }
+
+
+class MeanADCMeasurementItem(MeasurementItem):
+  def __init__(self, value):
+    super().__init__(value)
+    self.quantity = {    
+      "CodeValue": "113041",
+      "CodingSchemeDesignator": "DCM",
+      "CodeMeaning": "Apparent Diffusion Coefficient"
+    }
+    self.units = {
+      "CodeValue": "um2/s",
+      "CodingSchemeDesignator": "UCUM",
+      "CodeMeaning": "um2/s"
+    }
+    self.derivationModifier = {
+      "CodeValue": "R-00317",
+      "CodingSchemeDesignator": "SRT",
+      "CodeMeaning": "Mean"
+    }

util/measurementReportUtils/measurementReport.py

@@ -0,0 +1,74 @@
+import json
+
+from .measurementGroup import MeasurementGroup
+from .measurementItem import MeasurementItem
+from .codeSequences import CodeSequence
+
+class MeasurementReport(object):
+  """
+  Data structure plus convenience methods to create measurment reports following
+  the required format to be processed by the DCMQI tid1500writer tool (using the
+  JSON export of this).
+  """
+
+  def __init__(self, seriesNumber, compositeContext, dicomSourceFileList, timePoint, 
+               seriesDescription = "Measurements", procedureReported = None):
+    self.SeriesDescription = str(seriesDescription)
+    self.SeriesNumber = str(seriesNumber)
+    self.InstanceNumber = "1"
+
+    self.compositeContext = [compositeContext]
+
+    self.imageLibrary = dicomSourceFileList
+
+    self.observerContext = {
+      "ObserverType": "PERSON",
+      "PersonObserverName": "Reader01"
+    }
+
+    if procedureReported:
+      self.procedureReported = procedureReported
+
+    self.VerificationFlag = "VERIFIED"
+    self.CompletionFlag = "COMPLETE"
+
+    self.activitySession = "1"
+    self.timePoint = str(timePoint)
+
+    self.Measurements = []
+
+
+  def addMeasurementGroup(self, measurementGroup):
+    self.Measurements.append(measurementGroup)
+
+  
+  def exportToJson(self, fileName):
+    with open(fileName, 'w') as fp:
+      json.dump(self._getAsDict(), fp, indent = 2)
+
+
+  def getJsonStr(self):
+    return json.dumps(self._getAsDict(), indent = 2)
+
+
+  def _getAsDict(self):
+    # This is a bit of a hack to get the "@schema" in there, didn't figure out how to 
+    # do this otherwise with json.dumps. If this wasn't needed I could just dump
+    # the json directly with my custom encoder.
+    jsonStr = json.dumps(self, indent = 2, cls = self._MyJSONEncoder)
+    tempDict = json.loads(jsonStr)
+    outDict = {}
+    outDict["@schema"] = "https://raw.githubusercontent.com/qiicr/dcmqi/master/doc/schemas/sr-tid1500-schema.json#"
+    outDict.update(tempDict)
+    return outDict
+
+  # Inner private class to define a custom JSON encoder for serializing MeasurmentReport
+  class _MyJSONEncoder(json.JSONEncoder):
+    def default(self, obj):
+      if (isinstance(obj, MeasurementReport) or 
+          isinstance(obj, MeasurementGroup) or
+          isinstance(obj, MeasurementItem) or
+          isinstance(obj, CodeSequence)):
+        return obj.__dict__
+      else:
+        return super(MyEncoder, self).default(obj)