Merge pull request #13 from khelm/add-missing-vr

added missing vr values to owl file and cleaned up errors .  Added codes used to generate owl file to repo.

check_add_vr.py

@@ -0,0 +1,188 @@
+'''
+  This code checks each entry in the dicom_ontology.owl file for an
+  explicit VR assignment.  The issue is that the "new" entries - 
+  the entries/tags not in the original set that were scraped from
+  the NEMA website and instantiated in Neurolex - do not have
+  VR values attached. The reason for this is that in the DICOM 
+  standard documentation a listing of all of the tags are in Parts
+  06 and 07, but these lists do not include the definitions. The
+  definitions are given in tables in other Parts, so have to 
+  be extracted from those tables.
+
+  This code checks to see if an entry specifies the VR value and 
+  if not, retrieves it from the file 
+  /home/karl/Work/INCF/XML_code/dicom_dict_vr.py
+  which was created by the code: 
+  /home/karl/Work/INCF/XML_code/vr_generate_dict.py
+
+  This code skips reads lines until it finds 
+  a line containing "Datatype Properties" and continues to read lines 
+  until is finds a line that contains "dicom#dicom".  It collects 
+  lines in the variable "entry" until it encounters a line containing 
+  " ." which is the ending character for an entry. If it finds
+  a line containing "dicom:VR" then it writes the entry after removing 
+  an extra blank line that was written into the original owl file as
+  the line previous to the line containing the VR info. The code then 
+  writes that entry to the output file and then reads on, collecting the 
+  next entry. If the entry does not contain VR line, it queries the 
+  dicom_dict_vr.py file to find the VR value and writes a line 
+  containing the VR value in the correct format.
+
+  Note that since the code starts collecting entries with the "Datatype
+  Properties" section, everything above that needs to be pasted into 
+  the resulting file to make a complete owl file.  Also, the Class section
+  will be unchanged since there are no VR values for these terms
+  (since they are not official DICOM tags, but terms I extracted from the 
+  official Part documents). The code checks for the presence of "xxxx" in 
+  the dicom tag. If that string is in the tag then just write the entry 
+  unchanged into the output file.
+
+
+Sample Complete Entry
+------------------------------------------------
+###  http://purl.org/nidash/dicom#dicom_00280011
+
+dicom:dicom_00280011 rdf:type owl:DatatypeProperty ;
+
+        rdfs:label "Columns"^^xsd:string ;
+
+        obo:IAO_0000114  obo:IAO_0000428 ;
+
+        obo:IAO_0000115 "Number of columns in the image."^^xsd:string ;
+
+        dicom:dicom_xxxx0065 "(0028,0011)"^^xsd:string ;
+
+        dicom:VR "US"^^xsd:string ;
+
+        rdfs:subClassOf dc:identifier .
+
+
+2018-09-04 - started
+2018-09-14 - ran on full owl file and checked result into GitHub repo 
+
+Karl Helmer
+Athinoula A. Martinos Center for Biomedical Imaging
+Massachusetts General Hospital, 2018
+
+'''
+
+import os, sys
+import re
+import ast
+
+#************************************************
+#input parameters
+inDir = '/home/karl/Work/INCF/dicom-ontology/'
+inFilename = 'dicom_ontology.owl'
+outDir = '/home/karl/Work/INCF/dicom-ontology/'
+outFilename = 'dicom_ontology_new.owl'
+vrDir = '/home/karl/Work/INCF/XML_code/'
+vrFilename = 'dicom_dict_vr.dict'
+startEntry = 'dicom#dicom'
+endEntry = ' .'
+startPlace = 'Datatype Properties'
+#************************************************
+
+def search_vr(entry):
+    #make 1 string rather than searching in each string individually
+    #this is faster than using some version of "any"
+    combined = ' '.join(entry) 
+    test = 'dicom:VR' in combined
+
+    return test
+
+
+def get_tag(entry):
+
+    # check each line in entry for the dicom tag
+    for e in entry:
+        if 'rdf:type' in e:
+            t = re.search('dicom_(.+?) ', e)
+            tag = t.group(1)
+            if tag:
+                #print "The DICOM tag is: ", tag
+                return tag
+            else:
+                #this will crash the program since no tag value is returned
+                print "no dicom tag value found in: ", entry 
+
+
+def get_vr(vrDir, vrFilename, tag):
+    if tag:
+        vrF = open(vrDir+vrFilename, 'r').read()
+        dicomDict = ast.literal_eval(vrF)
+        if tag:
+            vr = dicomDict.get(tag,'')[0]
+            #print "vr value is = ", vr    
+            return vr
+    else:
+        print "vr value not found for tag = ", tag
+        return None
+
+
+def add_vr_to_entry(vr, entry):
+    vrLine = '        dicom:VR "{}"^^xsd:string   ;\n'.format(vr)
+    entry.insert(4,vrLine)
+    entry.insert(5,'\n')
+
+    return entry
+
+
+def write_entry(entry, outFile):
+    for line in entry:
+        outFile.write(line)
+    outFile.write('\n\n')
+
+
+def remove_sequential_blanks_in_entry(entry):
+    for i in range(len(entry)-1):
+        if entry[i] == entry[i+1]:
+            del entry[i]
+            break
+
+    return entry
+
+
+
+def main():
+
+    # open the dicom ontology file and start reading
+    with open(inDir+inFilename, 'r') as inFile, open(outDir+outFilename, 'w') as outFile:
+        entry = []
+        copy = False 
+        dt = False
+        for line in inFile: 
+            if startPlace in line: #find "Datatype Properties" line and start here
+                dt = True
+                print "starting place is:", startPlace
+
+            if dt == True: #start check after Datatype Prop line
+                if startEntry in line:
+                    copy = True
+                    #print 'start of entry'
+                if endEntry in line:
+                    copy = False
+                    entry.append(line)        #append the last line of entry
+                    #print 'end of entry'
+
+                    #now check the entry list as a whole
+                    vrFlag = search_vr(entry) #see if the entry has a VR line
+                    tag = get_tag(entry)  #extract the tag from entry
+                    print tag, vrFlag
+                    if vrFlag == False and ("xxxx" not in tag):
+                        vr = get_vr(vrDir, vrFilename, tag)      #get vr value from the dict
+                        entry1 = add_vr_to_entry(vr, entry)
+                        write_entry(entry1, outFile)    #write entry with added vr to outfile
+                        entry = []            #clear entry list when finished
+                    else:
+                        entry2 = remove_sequential_blanks_in_entry(entry)
+                        write_entry(entry2, outFile)    #write unchanged entry to outfile
+                        entry = []
+                elif copy:
+                    entry.append(line)
+
+
+
+##############################################################
+if __name__ == "__main__":
+    main()