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ParseDicts.py

#! /usr/bin/env python
"""
WARNING: This script has no meaning today (post 2008).
Since the standard is now available as .doc. If we assume
that the .doc is valid (according to standard only pdf should)
then there is not point in using this parser anymore today.

Let's write our own python parser to clean up the pdf (after 
pdftotext of course). 
Instructions: run pdftotext like this:

$ pdftotext -f 9 -l 81 -raw -nopgbrk 04_06PU.PDF 04_06PU-3.txt

then run the python parser like this:

$ python ParseDict.py 04_06PU.txt dicomV3.dic
"""
import re,os

"""
PdfTextParser takes as input a text file (produced by pdftotext)
and create as output a clean file (ready to be processed) by
DicomV3Expander
Warning: PdfTextParser does not expand:
- (xxxx,xxxx to xxxx) xxxxxxxxxxxx
or
- (12xx, 3456) comment...

"""
00030 class PdfTextParser:
  # Cstor
  def __init__(self):
    self._InputFilename = ''
    self._OutputFilename = ''
    self._Infile = 0
    self._OutLines = []
    self._PreviousBuffers = []

  def SetInputFileName(self,s):
    self._InputFilename = s

  def SetOutputFileName(self,s):
    self._OutputFilename = s
  
  # Function returning if s is a comment for sure
  def IsAComment(self,s):
    #print s,  len(s)
    if s == "Tag Name VR VM":
      return True
    elif s == "PS 3.6-2003":
      return True
    elif s == "PS 3.6-2004":
      return True
    elif s == "PS 3.6-2006":
      return True
    elif s == "PS 3.6-2007":
      return True
    patt = re.compile('^Page [0-9]+$') 
    if( patt.match(s) ):
      return True
    patt = re.compile('^(.*)PS 3.6-2007(.*)$') 
    if( patt.match(s) ):
      return True
    patt = re.compile('^\s*(- Standard -)\s*')
    if( patt.match(s) ):
      return True
    patt = re.compile('^\s*Tag\s+Name\s+VR\s+VM\s*$')
    if( patt.match(s) ):
      return True
    return False

  def IsAStartingLine(self,s):
    patt = re.compile('^\\([0-9a-fA-Fx]+,[0-9a-fA-F]+\\) (.*)$') 
    if( patt.match(s) ):
      return True
    return False

  def IsAFullLine(self,s):
    #patt = re.compile('^\\([0-9a-fA-Fx]+,[0-9a-fA-F]+\\) (.*) [A-Z][A-Z] [0-9]$')
    patt = re.compile('^\\([0-9a-fA-Fx]+,[0-9a-fA-F]+\\)\s+(.*)\s+[A-Z][A-Z]\s+([0-9n-]+)\s*$')
    if( patt.match(s) ):
      return True
    patt = re.compile('^\\([0-9a-fA-Fx]+,[0-9a-fA-F]+\\)\s+(.*)\s+[A-Z][A-Z]\s+([0-9n-]+)\s+RET\s*$')
    if( patt.match(s) ):
      return True
    print "IsAFullLine failed on", s
    return False

  # FIXME this function could be avoided...
  def IsSuspicious(self,s):
    l = len(s)
    if l > 80:
      return True
    return False

  def AddOutputLine(self,s):
    assert not self.IsAComment(s)
    self._OutLines.append(s + '\n')

  def Open(self):
    self._Infile = file(self._InputFilename, 'r')
    for line in self._Infile.readlines():
      line = line[:-1] # remove '\n'
      if not self.IsAComment( line ):
        if self.IsAStartingLine(line):
          #print "Previous buffer:",self._PreviousBuffers
          previousbuffer = ' '.join(self._PreviousBuffers)
          if self.IsAStartingLine(previousbuffer):
            if not self.IsSuspicious(previousbuffer):
              self.AddOutputLine(previousbuffer)
            else:
              # this case should not happen if I were to rewrite the
              # thing I should be able to clean that
              #print "Suspicious:", previousbuffer
              #print "List is:", self._PreviousBuffers
              s = self._PreviousBuffers[0]
              if self.IsAFullLine(s):
                # That means we have a weird line that does not start
                # as usual (xxxx,xxxx) therefore we tried constructing
                # a buffer using a the complete previous line...
                #print "Full line:", s
                self.AddOutputLine(s)
                s2 = ' '.join(self._PreviousBuffers[1:])
                #print "Other Full line:", s2
                self.AddOutputLine(s2)
              else:
                # we have a suspicioulsy long line, so what that could
                # happen, let's check:
                if self.IsAFullLine(previousbuffer):
                  self.AddOutputLine(previousbuffer)
                else:
                  # This is the only case where we do not add
                  # previousbuffer to the _OutLines
                  print "Suspicious and Not a full line:", s
          else:
            if previousbuffer:
              print "Not a buffer:", previousbuffer
          # We can clean buffer, since only the case 'suspicious' +
          # 'Not a full line' has not added buffer to the list
          self._PreviousBuffers = []
          # In all cases save the line for potentially growing this line
          assert not self.IsAComment(line)
          self._PreviousBuffers.append(line)
        else:
          #print "Not a line",line
          assert not self.IsAComment(line)
          self._PreviousBuffers.append(line)
      else:
        #print "Comment:",line
        previousbuffer = ' '.join(self._PreviousBuffers)
        if previousbuffer and self.IsAStartingLine(previousbuffer):
          #print "This line is added:", previousbuffer
          self.AddOutputLine( previousbuffer )
        else:
          #print "Line is comment:", line
          print "Buffer is:", previousbuffer
        # Ok this is a comment we can safely clean the buffer:
        self._PreviousBuffers = []
    self.Write()

  def Write(self):
    outfile = file(self._OutputFilename, 'w')
    outfile.writelines( self._OutLines )
    outfile.close()
    self._Infile.close()
    
  # Main function to call for parsing
  def Parse(self):
    self.Open()



"""
This class is meant to expand line like:
- (xxxx,xxxx to xxxx) xxxxxxxxxxxx
or
- (12xx, 3456) comment...

"""
00180 class DicomV3Expander:
  def __init__(self):
    self._InputFilename = ''
    self._OutputFilename = ''
    self._OutLines = []

  def SetInputFileName(self,s):
    self._InputFilename = s

  def SetOutputFileName(self,s):
    self._OutputFilename = s
 
  # Function to turn into lower case a tag:
  # ex: (ABCD, EF01) -> (abcd, ef01)
  def LowerCaseTag(self,s):
    #print "Before:", s[:-1]
    patt = re.compile('^(\\([0-9a-fA-F]+,[0-9a-fA-F]+\\))(.*)$')
    m = patt.match(s)
    if m:
      s1 = m.group(1)
      s2 = m.group(2)
      return s1.lower() + s2
    else:
      patt = re.compile('^[0-9a-fA-F]+ [0-9a-fA-F]+ [A-Z][A-Z] [0-9n-] .*$')
      if patt.match(s):
        return s
      else:
        print "Impossible case:", s
        #os.sys.exit(1)
        return ""

  def AddOutputLine(self,s):
    if s.__class__ == list:
      for i in s:
        self._OutLines.append(i + '\n')
    else:
      self._OutLines.append(s + '\n')

  # Expand the line approriaetkly and also add it to the
  # _OutLines list
  def ExpandLine(self, s):
    assert s[-1] == '\n'
    s = s[:-1]  # remove \n
    list = []
    if self.NeedToExpansion(s, list):
      self.AddOutputLine(list) # list != []
    elif self.NeedGroupXXExpansion(s, list):
      self.AddOutputLine(list) # list != []
    elif self.NeedElemXXExpansion(s, list):
      self.AddOutputLine(list) # list != []
    else:
      self.AddOutputLine(self.LowerCaseTag(s))

  # If line is like:
  # (0020,3100 to 31FF) Source Image Ids RET
  def NeedToExpansion(self,s, list):
    patt = re.compile('^\\(([0-9a-fA-F]+),([0-9a-fA-F]+) to ([0-9a-fA-F]+)\\)(.*)$')
    m = patt.match(s)
    if m:
      #print m.groups()
      gr = m.group(1)
      el_start = '0x'+m.group(2)
      el_end = '0x'+m.group(3)
      for i in range(eval(el_start), eval(el_end)):
        el = hex(i)[2:]
        l = '('+gr+','+el+')'+m.group(4)
        list.append(l)
      return True
    return False

  # If line is like:
  # (50xx,1200) Number of Patient Related Studies IS 1
  def NeedGroupXXExpansion(self,s,list):
    patt = re.compile('^\\(([0-9a-fA-F]+)xx,([0-9a-fA-F]+)\\)(.*)$')
    m = patt.match(s)
    if m:
      #print m.groups()
      gr_start = m.group(1)
      el = m.group(2)
      #el_start = '0x'+m.group(2)
      #el_end = '0x'+m.group(3)
      start = '0x'+gr_start+'00'
      end   = '0x'+gr_start+'FF'
      for i in range(eval(start), eval(end)):
        gr = hex(i)[2:]
        l = '('+gr+','+el+')'+m.group(3)
        #print l
        list.append(l)
      return True
    return False

  # If line is like:
  # (2001,xx00) Number of Patient Related Studies IS 1
  def NeedElemXXExpansion(self,s,list):
    patt = re.compile('^([0-9a-fA-F]+) ([0-9a-fA-F]+)xx(.*)$')
    m = patt.match(s)
    if m:
      #print m.groups()
      gr = m.group(1)
      el_start = m.group(2)
      start = '0x00'
      end   = '0xFF'
      for i in range(eval(start), eval(end)):
        el = '%02x'% i
        l = '('+gr+','+el_start+el+')'+m.group(3)
        print l
        list.append(l)
      return True
    else:
      patt = re.compile('^([0-9a-fA-F]+) xx([0-9a-fA-F]+)(.*)$')
      m = patt.match(s)
      if m:
        #print m.groups()
        gr = m.group(1)
        el_start = m.group(2)
        start = '0x00'
        end   = '0xFF'
        for i in range(eval(start), eval(end)):
          el = '%02x'% i
          l = '('+gr+','+el+el_start+')'+m.group(3)
          print l
          list.append(l)
        return True
    return False

  def Write(self):
    outfile = file(self._OutputFilename, 'w')
    outfile.writelines( self._OutLines )
    outfile.close()

  def Expand(self):
    infile = file(self._InputFilename,'r')
    for line in infile.readlines():
      # ExpandLine also LowerCase the line
      self.ExpandLine(line) # l is [1,n] lines
    self.Write()
    infile.close()

"""
Converter class
Input is of type:

(0008,0001) Length to End UL 1 RET

output should be:

0008 0001 UL 1 Length to End RET
"""
00328 class Converter:
  def __init__(self):
    self._InputFilename = ''
    self._OutputFilename = ''
    self._OutLines = []
  def SetInputFileName(self,s):
    self._InputFilename = s

  def SetOutputFileName(self,s):
    self._OutputFilename = s

  def Open(self):
    self._Infile = file(self._InputFilename, 'r')
    for line in self._Infile.readlines():
      line = line[:-1] # remove '\n'
      if (not self.IsAFullLine(line) ):
        print "Convert pb:", line

  def IsAFullLine(self,s):
    patt = re.compile('^\\(([0-9a-fA-Fx]+),([0-9a-fA-F]+)\\)\s+(.*)\s+([A-Z][A-Z])\s+([0-9n-]+)\s*$')
    m = patt.match(s)
    if( m ):
      output = ''
      output = m.group(1).lower() + ' ' + m.group(2).lower() + ' ' + m.group(4) + ' ' + m.group(5) + ' ' + m.group(3).strip()
      self.AddOutputLine( output )
      return True
    patt_ret = re.compile('^\\(([0-9a-fA-Fx]+),([0-9a-fA-F]+)\\)\s+(.*)\s+([A-Z][A-Z])\s+([0-9n-]+)\s+(RET)\s*$')
    m = patt_ret.match(s)
    if( m ):
      output = ''
      output = m.group(1).lower() + ' ' + m.group(2).lower() + ' ' + m.group(4) + ' ' + m.group(5) + ' ' + m.group(3).strip() + ' (' + m.group(6) + ')'
      self.AddOutputLine( output )
      return True
    return False
 
  def AddOutputLine(self,s):
    self._OutLines.append(s + '\n')

  def Write(self):
    outfile = file(self._OutputFilename, 'w')
    outfile.writelines( self._OutLines )
    outfile.close()
    self._Infile.close()

  def Convert(self):
     self.Open()
     self.Write()
 
if __name__ == "__main__":
  argc = len(os.sys.argv )
  if ( argc < 3 ):
    print "Sorry, wrong list of args"
    os.sys.exit(1) #error

  inputfilename = os.sys.argv[1]
  outputfilename = os.sys.argv[2]
  tempfile = "/tmp/mytemp"

  dp = PdfTextParser()
  dp.SetInputFileName( inputfilename )
  dp.SetOutputFileName( tempfile )
  dp.Parse()

  exp = DicomV3Expander()
  exp.SetInputFileName( tempfile )
  exp.SetOutputFileName( outputfilename )
  exp.Expand()

  conv = Converter()
  conv.SetInputFileName( tempfile )
  conv.SetOutputFileName( '/tmp/myconv' )
  conv.Convert()

  #print dp.IsAStartingLine( "(0004,1212) File-set Consistency Flag US 1\n" )

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