Skip to content

Commit

Permalink
Merge pull request #235 from QIICR/measurement-import
Browse files Browse the repository at this point in the history 
ENH: Adds length measurement import
  • Loading branch information
@pieper
pieper authored May 20, 2020
2 parents b3f6cf2 + 9dc1be7 commit 219e887
Showing 1 changed file with 119 additions and 17 deletions.
136 changes: 119 additions & 17 deletions DICOMPlugins/DICOMTID1500Plugin.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,12 @@
import vtk
import datetime
from collections import Counter

import numpy
import random
import pydicom


import slicer
from DICOMLib import DICOMLoadable
from base.DICOMPluginBase import DICOMPluginBase
Expand All @@ -23,6 +27,18 @@ def __init__(self):
DICOMPluginBase.__init__(self)
self.loadType = "DICOM Structured Report TID1500"

self.codings = {
"imagingMeasurementReport": { "scheme": "DCM", "value": "126000" },
"personObserver": { "scheme": "DCM", "value": "121008" },
"imagingMeasuremnts": { "scheme": "DCM", "value": "126010" },
"measurementGroup": { "scheme": "DCM", "value": "125007" },
"trackingIdentifier": { "scheme": "DCM", "value": "112039" },
"trackingUniqueIdentifier": { "scheme": "DCM", "value": "112040" },
"findingSite": { "scheme": "SRT", "value": "G-C0E3" },
"length": { "scheme": "SRT", "value": "G-D7FE" },
}


def examineFiles(self, files):
loadables = []

Expand Down Expand Up @@ -127,11 +143,20 @@ def sortReportsByDateTime(self, uids):
def getDateTime(self, uid):
filename = slicer.dicomDatabase.fileForInstance(uid)
dataset = pydicom.read_file(filename)
seriesDate = dataset.SeriesDate
seriesTime = dataset.SeriesTime
if seriesTime.find("."):
seriesTime = seriesTime.split(".")[0]
return datetime.datetime.strptime(seriesDate+seriesTime, '%Y%m%d%H%M%S')
if hasattr(dataset, 'SeriesDate') and hasattr(dataset, "SeriesTime"):
date = dataset.SeriesDate
time = dataset.SeriesTime
elif hasattr(dataset, 'StudyDate') and hasattr(dataset, "StudyTime"):
date = dataset.StudyDate
time = dataset.StudyDate
else:
date = ""
time = ""
try:
dateTime = datetime.datetime.strptime(date+time, '%Y%m%d%H%M%S')
except ValueError:
dateTime = ""
return dateTime

def load(self, loadable):
logging.debug('DICOM SR TID1500 load()')
Expand Down Expand Up @@ -198,18 +223,22 @@ def load(self, loadable):
table.SetName(srMetadataJSON["SeriesDescription"])

# TODO: think about the following...
segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[-1]
segmentationNodeID = segmentationNode.GetID()
table.SetAttribute("ReferencedSegmentationNodeID", segmentationNodeID)

# TODO: think about a better solution for finding related reports
if idx-1 > -1:
table.SetAttribute("PriorReportUID", sortedUIDs[idx-1])
tables[idx-1].SetAttribute("FollowUpReportUID", uid)
table.SetAttribute("SOPInstanceUID", uid)
self.assignTrackingUniqueIdentifier(outputFile, segmentationNode)
if len(slicer.util.getNodesByClass('vtkMRMLSegmentationNode')) > 0:
segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[-1]
segmentationNodeID = segmentationNode.GetID()
table.SetAttribute("ReferencedSegmentationNodeID", segmentationNodeID)

# TODO: think about a better solution for finding related reports
if idx-1 > -1:
table.SetAttribute("PriorReportUID", sortedUIDs[idx-1])
tables[idx-1].SetAttribute("FollowUpReportUID", uid)
table.SetAttribute("SOPInstanceUID", uid)
self.assignTrackingUniqueIdentifier(outputFile, segmentationNode)

tables.append(table)

self.loadAdditionalMeasurements(uid)

self.cleanup()

return len(tables) > 0
Expand Down Expand Up @@ -276,7 +305,6 @@ def metadata2vtkTableNode(self, metafile):
def addMeasurementsToTable(self, data, table):
for measurement in data["Measurements"]:
name = measurement["TrackingIdentifier"]
value = measurement["ReferencedSegment"]
rowIndex = table.AddEmptyRow()
table.SetCellText(rowIndex, 0, name)
for columnIndex, measurementItem in enumerate(measurement["measurementItems"]):
Expand All @@ -292,7 +320,7 @@ def createAndConfigureTable(self):

def setupTableInformation(self, measurement, table):
col = table.AddColumn()
col.SetName("Segment")
col.SetName("Tracking Identifier")

infoItems = self.enumerateDuplicateNames(self.generateMeasurementInformation(measurement["measurementItems"]))

Expand Down Expand Up @@ -338,6 +366,80 @@ def enumerateDuplicateNames(self, items):
items[idx]["name"] = item
return items

def isConcept(self, item, coding):
code = item.ConceptNameCodeSequence[0]
return code.CodingSchemeDesignator == self.codings[coding]["scheme"] and code.CodeValue == self.codings[coding]["value"]

def loadAdditionalMeasurements(self, srUID):
"""
Loads length measements as annotation rulers
TODO: need to generalize to other report contents
"""

srFilePath = slicer.dicomDatabase.fileForInstance(srUID)
sr = dicom.read_file(srFilePath)

if not self.isConcept(sr, "imagingMeasurementReport"):
return sr

contents = {}
measurements = []
contents['measurements'] = measurements
for item in sr.ContentSequence:
if self.isConcept(item, "personObserver"):
contents['personObserver'] = item.PersonName
if self.isConcept(item, "imagingMeasuremnts"):
for contentItem in item.ContentSequence:
if self.isConcept(contentItem, "measurementGroup"):
measurement = {}
for measurementItem in contentItem.ContentSequence:
if self.isConcept(measurementItem, "trackingIdentifier"):
measurement['trackingIdentifier'] = measurementItem.TextValue
if self.isConcept(measurementItem, "trackingUniqueIdentifier"):
measurement['trackingUniqueIdentifier'] = measurementItem.UID
if self.isConcept(measurementItem, "findingSite"):
measurement['findingSite'] = measurementItem.ConceptCodeSequence[0].CodeMeaning
if self.isConcept(measurementItem, "length"):
for lengthItem in measurementItem.ContentSequence:
measurement['polyline'] = lengthItem.GraphicData
for selectionItem in lengthItem.ContentSequence:
if selectionItem.RelationshipType == "SELECTED FROM":
for reference in selectionItem.ReferencedSOPSequence:
measurement['referencedSOPInstanceUID'] = reference.ReferencedSOPInstanceUID
if hasattr(reference, "ReferencedFrameNumber") and reference.ReferencedFrameNumber != "1":
print('Error - only single frame references supported')
measurements.append(measurement)

for measurement in contents['measurements']:
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetLocked(True)
rulerNode.SetName(contents['personObserver'])

referenceFilePath = slicer.dicomDatabase.fileForInstance(measurement['referencedSOPInstanceUID'])
reference = dicom.read_file(referenceFilePath)
origin = numpy.array(reference.ImagePositionPatient)
alongColumnVector = numpy.array(reference.ImageOrientationPatient[:3])
alongRowVector = numpy.array(reference.ImageOrientationPatient[3:])
alongColumnVector *= reference.PixelSpacing[1]
alongRowVector *= reference.PixelSpacing[0]
col1,row1,col2,row2 = measurement['polyline']
lpsToRAS = numpy.array([-1,-1,1])
p1 = (origin + col1 * alongColumnVector + row1 * alongRowVector) * lpsToRAS
p2 = (origin + col2 * alongColumnVector + row2 * alongRowVector) * lpsToRAS
rulerNode.SetPosition1(*p1)
rulerNode.SetPosition2(*p2)

rulerNode.Initialize(slicer.mrmlScene)
colorIndex = 1 + len(slicer.util.getNodesByClass('vtkMRMLAnnotationRulerNode'))
colorNode = slicer.util.getNode("GenericAnatomyColors")
color = [0,]*4
colorNode.GetColor(colorIndex, color)
rulerNode.GetDisplayNode().SetColor(*color[:3])
rulerNode.GetAnnotationTextDisplayNode().SetColor(*color[:3])
rulerNode.GetAnnotationPointDisplayNode().SetColor(*color[:3])
rulerNode.GetAnnotationPointDisplayNode().SetGlyphScale(2)
rulerNode.GetAnnotationLineDisplayNode().SetLabelPosition(random.random())


class DICOMLongitudinalTID1500PluginClass(DICOMTID1500PluginClass):

Expand Down

0 comments on commit 219e887

Please sign in to comment.