update

NEPMetadataMapping/dicomReader.py

@@ -1,6 +1,7 @@
 import pydicom
 import re
 import logging
+from datetime import datetime
 
 # This class instantiates the class object of a dicom file, which contains the key-value pairs of the fiel metadata.
 class DicomReader:
@@ -15,64 +16,24 @@ def __init__(self, dicomFile, studyName, seriesName):
 
         self.studyName=studyName
         self.seriesName=seriesName
+        self.studyDateTime=None
         self.mainDict={}
-        self.subDict=self.dataset(self.dicomFile)
+        self.subDict=self.pydicomObjects(self.dicomFile)
         self.__dict__.update(self.mainDict)
+        self.studyDateTime =  datetime.strptime(self.studyDateTime, '%Y%m%d %H%M%S').isoformat()
         self.__dict__.pop("mainDict")
         self.__dict__.pop("subDict")
         self.__dict__.pop("dicomFile")
         self.__dict__.pop("pixelData")
-
-    #This method parses the pydicom.Dataset objects created by the pyDicom module to retrieve the primitive data types
+        #print(self.__dict__)
+    #This method parses the pydicom.Dataset and pydicom.Sequence objects created by the pyDicom module to retrieve the primitive data types
     # and separate the attributes.
-    def dataset(self, dataset):
+    def pydicomObjects(self, dataset):
         subDict={}
         subList=[]
         for i in dataset:
             if isinstance(i, pydicom.Dataset):
-                subList.append(self.dataset(i))
-            elif isinstance(i.value, pydicom.Sequence):
-                name=i.name.split()
-                if len(name)==1:
-                    name=name[0].lower()
-                else:
-                    subname=""
-                    for j in name[1:]:
-                        subname+=j.capitalize()
-
-                    name=name[0].lower() + subname
-
-                name=re.sub('[^A-Za-z0-9]+', '', name)
-                subDict[name]=self.sequence(i.value)
-            else:
-                name=i.name.split()
-                if len(name)==1:
-                    name=name[0].lower()
-                else:
-                    subname=""
-                    for j in name[1:]:
-                        subname+=j.capitalize()
-
-                    name=name[0].lower() + subname
-
-                name=re.sub('[^A-Za-z0-9]+', '', name)
-
-                subDict[name]=i.value
-                self.mainDict[name]=i.value
-
-        if len(subList)>0:
-            return subList
-        else:
-            return subDict
-
-    #This method parses the pydicom.Sequence objects created by the pyDicom module to retrieve the primitive data types
-    # and separate the attributes 
-    def sequence(self, sequence):
-        subDict={}
-        subList=[]
-        for i in sequence:
-            if isinstance(i, pydicom.Dataset):
-                subList.append(self.dataset(i))
+                subList.append(self.pydicomObjects(i))
             elif isinstance(i.value, pydicom.Sequence):
                 name=i.name.split()
                 if len(name)==1:
@@ -85,7 +46,7 @@ def sequence(self, sequence):
                     name=name[0].lower() + subname
 
                 name=re.sub('[^A-Za-z0-9]+', '', name)
-                subDict[name]=self.sequence(i.value)
+                subDict[name]=self.pydicomObjects(i.value)
             else:
                 name=i.name.split()
                 if len(name)==1:
@@ -98,6 +59,10 @@ def sequence(self, sequence):
                     name=name[0].lower() + subname
 
                 name=re.sub('[^A-Za-z0-9]+', '', name)
+                if name == "studyDate":
+                    self.studyDateTime=i.value+" "
+                if name == "studyTime":
+                    self.studyDateTime += i.value
                 subDict[name]=i.value
                 self.mainDict[name]=i.value