X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Dicts%2FParseDict.py;h=2b3924245ab53897026a32b625fb2b949786f117;hb=97bf5414cdf6800715b7e595aed6c9c25bdde2f5;hp=86409d87c9c5543217b6aef8642037f001e3ce38;hpb=e022c5480089f9fbf2d96523749dc3664bb25d51;p=gdcm.git

diff --git a/Dicts/ParseDict.py b/Dicts/ParseDict.py
index 86409d87..2b392424 100644
--- a/Dicts/ParseDict.py
+++ b/Dicts/ParseDict.py
@@ -182,6 +182,10 @@ class UIDParser(PdfTextParser):
       return PdfTextParser.AddOutputLine(self,s)
     print "Discarding:", s
 
+
+"""
+TransferSyntaxParser
+"""
 class TransferSyntaxParser(UIDParser):
   def IsAFullLine(self,s):
     patt = re.compile('^(.*) Transfer Syntax PS ?[0-9].1?[0-9]$') 
@@ -190,7 +194,203 @@ class TransferSyntaxParser(UIDParser):
     print "Not a TS:", s
     return False
     
-  
+"""
+Papyrus parser
+pdftotext -f 19 -l 41 -raw -nopgbrk /tmp/Papyrus31Specif.pdf /tmp/Papyrus31Specif.txt 
+
+I need to do a second pass for pages:
+#29 since I need to find [0-9.]+
+#40,41 since it start with number in two columns !!
+""" 
+class PapyrusParser(PdfTextParser):
+  def __init__(self):
+    self._PreviousPage = 0
+    self._PreviousNumber = 0
+    PdfTextParser.__init__(self)
+
+  def IsAStartingLine(self,s):
+    patt = re.compile('^[A-Za-z \'\(\)]+ +\\([0-9A-F]+,[0-9A-F]+\\) +(.*)$') 
+    if( patt.match(s) ):
+      return True
+    # After page 39, lines are like:
+    patt = re.compile('^[0-9x]+ [0-9xA-F]+ .*$') 
+    if( patt.match(s) ):
+      #print "PAge 39", s
+      return True
+    return False
+
+  def IsAFullLine(self,s):
+    patt = re.compile('^[A-Za-z \'\(\)]+ +\\([0-9A-F]+,[0-9A-F]+\\) +(.*)$') 
+    if( patt.match(s) ):
+      return True
+    # After page 39, lines are like:
+    patt = re.compile('^[0-9x]+ [0-9xA-F]+ .* [A-Z][A-Z] [0-9].*$') 
+    if( patt.match(s) ):
+      #print "PAge 39", s
+      return True
+    return False
+
+  def IsAComment(self,s):
+    # dummy case:
+    if s == 'Attribute Name Tag Type Attribute Description':
+      #print "Dummy", s
+      return True
+    patt = re.compile('^.*ANNEXE.*$')
+    if patt.match(s):
+      return True
+    # Indicate page #, spaces ending with only one number
+    # Sometime there is a line with only one number, we need to
+    # make sure that page # is strictly increasing
+    patt = re.compile('^[1-9][0-9]+$') 
+    if( patt.match(s) ):
+      p = eval(s)
+      if( p > self._PreviousPage):
+        #print "Page #", p
+        self._PreviousNumber = 0
+        self._PreviousPage = p
+        return True
+#      else:
+#        print "PAGE ERROR:", s
+    # Now within each page there is a comment that start with a #
+    # let's do the page approach wich reset at each page
+    patt = re.compile('^[0-9]+$') 
+    if( patt.match(s) ):
+      if( eval(s) > self._PreviousNumber):
+        #print "Number #", eval(s)
+        self._PreviousNumber = eval(s)
+        return True
+      #else:
+      #  print "ERROR:", s
+    return False
+
+  def AddOutputLine(self,s):
+    assert not self.IsAComment(s)
+    s = s.replace('\n','')
+    #print "REMOVE return:", s
+    patt = re.compile('^([A-Za-z \'\(\)]+) (\\([0-9A-F]+,[0-9A-F]+\\)) ([0-9C]+) (.*)$') 
+    m = patt.match(s)
+    ss = 'dummy (0000,0000) 0'
+    if m:
+      ss = m.group(2) + ' ' + m.group(3) + ' ' + m.group(1)
+    else:
+      patt = re.compile('^([A-Za-z \'\(\)]+) (\\([0-9A-F]+,[0-9A-F]+\\)) (.*)$') 
+      m = patt.match(s)
+      if m:
+        ss = m.group(2) + ' 0 ' + m.group(1)
+      else:
+        ss = s
+        # There is two case one that end with all capital letter
+        # explaining the 'DEFINED TERMS'
+        patt = re.compile('^[0-9x]+ [0-9xA-F]+ .* [A-Z][A-Z] [0-9] [A-Z, ]$') 
+        #patt = re.compile('^[0-9x]+ [0-9xA-F]+ .* [A-Z][A-Z] [0-9]|1\\-n [A-Z, |3.0]+$') 
+        #patt = re.compile('^[0-9x]+ [0-9xA-F]+ .* [A-Z][A-Z] [01n-] [A-Z, |3.0]+$') 
+        if patt.match(s):
+          print "Match", s
+          ss = ''
+    self._OutLines.append(ss + '\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.IsAFullLine(previousbuffer):
+            self.AddOutputLine(previousbuffer)
+          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
+          # just to be safe remove any white space at begining of string
+          assert not self.IsAComment(line)
+          self._PreviousBuffers.append(line.strip())
+        else:
+          #print "Not a line",line
+          assert not self.IsAComment(line)
+          # just to be safe remove any white space at begining of string
+          self._PreviousBuffers.append(line.strip())
+      else:
+        #print "Previous buffer:",self._PreviousBuffers
+        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()
+
+"""
+Parser for:
+GE Medical Systems HISPEED ADVANTAGE CT/i CONFORMANCE STATEMENT
+pdftotext -f 81 -l 90 -raw -nopgbrk 2162114_100r5.pdf 2162114_100r5.txt
+"""
+class GEMSParser(PdfTextParser):
+#  def __init__(self):
+#    PdfTextParser.__init__(self)
+
+  def IsAStartingLine(self,s):
+    #patt = re.compile('^[A-Za-z \'\(\)]+ +\\([0-9A-F]+,[0-9A-F]+\\) +(.*)$') 
+    patt = re.compile('^[A-Za-z0-9 .#(),_/-]+ +\\([0-9A-F]+, ?[0-9A-F]+\\) +(.*)$')
+    if( patt.match(s) ):
+      return True
+    return False
+
+  def IsAFullLine(self,s):
+    #patt = re.compile('^[A-Za-z \'\(\)]+ +\\([0-9A-F]+,[0-9A-F]+\\) +(.*)$') 
+    patt = re.compile('^[A-Za-z0-9 .#(),_/-]+ +\\([0-9A-F]+, ?[0-9A-F]+\\) [A-Z][A-Z] [0-9]+$') 
+    if( patt.match(s) ):
+      return True
+    print "Not full:", s
+    return False
+
+  def IsAComment(self,s):
+    if PdfTextParser.IsAComment(self,s):
+      return True
+    #patt = re.compile('^.*GE Medical Systems LightSpeed QX/i CONFORMANCE STATEMENT REV 2.2 sm 2288567-100.*$')
+    #if patt.match(s):
+    #  return True
+    patt = re.compile('^.*GE Medical Systems HISPEED ADVANTAGE CT/i CONFORMANCE STATEMENT.*$') 
+    if patt.match(s):
+      return True
+    patt = re.compile('^GE Medical Systems LightSpeed QX/i CONFORMANCE STATEMENT.*$')
+    if patt.match(s):
+      return True
+    patt = re.compile('^Attribute Name Tag VR VM$')
+    if patt.match(s):
+      return True
+    patt = re.compile('^B.[1-9].*Private .*$')
+    if patt.match(s):
+      return True
+    patt = re.compile('^Table B.1.? .* Private .*$')
+    if patt.match(s):
+      return True
+    patt = re.compile('^Note :.*$')
+    if patt.match(s):
+      return True
+    patt = re.compile('^7.11.1$')
+    if patt.match(s):
+      return True
+    return False
+
+  def AddOutputLine(self,s):
+    #print s
+    assert not self.IsAComment(s)
+    patt = re.compile('^([A-Za-z0-9 .#(),_/-]+) +\\(([0-9A-F]+), ?([0-9A-F]+)\\) ([A-Z][A-Z]) ([0-9]+)$') 
+    m = patt.match(s)
+    if m:
+      ss = m.group(2).lower() + ' ' + m.group(3).lower() + ' ' + m.group(4) + ' ' + m.group(5) + ' ' + m.group(1)
+      self._OutLines.append(ss + '\n')
+    else:
+      print 'OOOPs', s
+
 
 """
 This class is meant to expand line like:
@@ -222,8 +422,12 @@ class DicomV3Expander:
       s2 = m.group(2)
       return s1.lower() + s2
     else:
-      print "Impossible case:", s
-      os.sys.exit(1)
+      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)
 
   def AddOutputLine(self,s):
     if s.__class__ == list:
@@ -240,7 +444,9 @@ class DicomV3Expander:
     list = []
     if self.NeedToExpansion(s, list):
       self.AddOutputLine(list) # list != []
-    elif self.NeedXXExpansion(s, 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))
@@ -264,7 +470,7 @@ class DicomV3Expander:
 
   # If line is like:
   # (50xx,1200) Number of Patient Related Studies IS 1
-  def NeedXXExpansion(self,s,list):
+  def NeedGroupXXExpansion(self,s,list):
     patt = re.compile('^\\(([0-9a-fA-F]+)xx,([0-9a-fA-F]+)\\)(.*)$')
     m = patt.match(s)
     if m:
@@ -283,6 +489,40 @@ class DicomV3Expander:
       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 )
@@ -296,6 +536,149 @@ class DicomV3Expander:
     self.Write()
     infile.close()
 
+"""
+Parse line from a philips document, line are like this:
+
+Syncra Scan Type 2005,10A1 VR = CS, VM = 1
+"""
+class InteraParser:
+  def __init__(self):
+    self._InputFilename = ''
+    self._OutputFilename = ''
+
+  def Reformat(self,s):
+    assert self.IsGood(s)
+    patt = re.compile("^([A-Za-z0-9 -]+) ([0-9A-Z]+),([0-9A-Z]+) VR = ([A-Z][A-Z]), VM = (.*)$")
+    m = patt.match(s)
+    if m:
+      dicom = m.group(2) + ' ' + m.group(3) + ' ' + m.group(4) + ' ' + m.group(5) + ' ' + m.group(1)
+      return dicom
+    else:
+      print "oops"
+
+  def IsGood(self,s):
+    patt = re.compile("^[A-Za-z0-9 -]+ [0-9A-Z]+,[0-9A-Z]+ VR = [A-Z][A-Z], VM = .*$")
+    if patt.match(s):
+      return True
+    print "Not good:", s
+    return False
+
+  def SetInputFileName(self,s):
+    self._InputFilename = s
+
+  def SetOutputFileName(self,s):
+    self._OutputFilename = s
+  
+  def Parse(self):
+    infile = file(self._InputFilename, 'r')
+    outLines = []
+    for line in infile.readlines():
+      print self.Reformat(line)
+      outLines.append( self.Reformat(line) + '\n' )
+    outfile = file(self._OutputFilename, 'w')
+    outfile.writelines( outLines )
+    outfile.close()
+ 
+"""
+Parse line from a dicom3tools document, line are like this:
+
+(0003,0008) VERS="SSPI" VR="US"   VM="1"        Owner="SIEMENS ISI"             Keyword="ISICommandField"                       Name="ISI Command Field"
+"""
+class Dicom3ToolsParser:
+  def __init__(self):
+    self._InputFilename = ''
+    self._OutputFilename = ''
+
+  def Reformat(self,s):
+    assert self.IsGood(s)
+    patt = re.compile("^\(([0-9a-f]+),([0-9a-f]+)\)\s+VERS=\".*\"\s+VR=\"([A-Z][A-Z])\"\s+VM=\"(.*)\"\s+Owner=\".*\"\s+Keyword=\".*\"\s+Name=\"(.*)\"$")
+    m = patt.match(s)
+    dicom = ''
+    if m:
+      # Apparently some have Name == '?', skip those
+      name = m.group(5)
+      if name != '?' and name != '? ':
+        dicom = m.group(1) + ' ' + m.group(2) + ' ' + m.group(3) + ' ' + m.group(4) + ' ' + m.group(5)
+      else:
+        print "oops"
+    else:
+      print "oops"
+    return dicom
+
+  def IsGood(self,s):
+    #patt = re.compile("^\([0-9a-f]+,[0-9a-f]+\) VERS=\".*\" VR=\"[A-Z][A-Z]\" VM=\".*\" Owner=\".*\" Keyword=\".*\" Name=\".*\"$")
+    patt = re.compile("^\([0-9a-f]+,[0-9a-f]+\)\s+VERS=\".*\"\s+VR=\"[A-Z][A-Z]\"\s+VM=\".*\"\s+Owner=\".*\"\s+Keyword=\".*\"\s+Name=\".*\".*$")
+    if patt.match(s):
+      return True
+    print "Not good:", s
+    return False
+
+  def SetInputFileName(self,s):
+    self._InputFilename = s
+
+  def SetOutputFileName(self,s):
+    self._OutputFilename = s
+  
+  def Parse(self):
+    infile = file(self._InputFilename, 'r')
+    outLines = []
+    for line in infile.readlines():
+      newline = self.Reformat(line)
+      print newline
+      if newline:
+        outLines.append( newline + '\n' )
+    outfile = file(self._OutputFilename, 'w')
+    outfile.writelines( outLines )
+    outfile.close()
+ 
+"""
+Parse line from a PhilipsAdvance document, line are like this:
+
+GE Advance Implementation Version Name (0009,1001) 3 LO 2 n/a
+"""
+class GEAdvanceParser:
+  def __init__(self):
+    self._InputFilename = ''
+    self._OutputFilename = ''
+
+  def Reformat(self,s):
+    assert self.IsGood(s)
+    #patt = re.compile("^\(([0-9a-f]+),([0-9a-f]+)\)\s+VERS=\".*\"\s+VR=\"([A-Z][A-Z])\"\s+VM=\"(.*)\"\s+Owner=\".*\"\s+Keyword=\".*\"\s+Name=\"(.*)\"$")
+    patt = re.compile("^([A-Za-z0-9 ._>]+) \\(([0-9A-F]+),([0-9A-F]+)\\) [0-9] ([A-Z][A-Z]) ([0-9]) .*$")
+    m = patt.match(s)
+    dicom = ''
+    if m:
+      dicom = m.group(2) + ' ' + m.group(3).lower() + ' ' + m.group(4) + ' ' + m.group(5) + ' ' + m.group(1)
+    else:
+      print "oops"
+    return dicom
+
+  def IsGood(self,s):
+    #patt = re.compile("^\([0-9a-f]+,[0-9a-f]+\)\s+VERS=\".*\"\s+VR=\"[A-Z][A-Z]\"\s+VM=\".*\"\s+Owner=\".*\"\s+Keyword=\".*\"\s+Name=\".*\".*$")
+    patt = re.compile("^[A-Za-z0-9 ._>]+ \\([0-9A-F]+,[0-9A-F]+\\) [0-9] [A-Z][A-Z] [0-9] .*$")
+    if patt.match(s):
+      return True
+    print "Not good:", s
+    return False
+
+  def SetInputFileName(self,s):
+    self._InputFilename = s
+
+  def SetOutputFileName(self,s):
+    self._OutputFilename = s
+  
+  def Parse(self):
+    infile = file(self._InputFilename, 'r')
+    outLines = []
+    for line in infile.readlines():
+      newline = self.Reformat(line)
+      #print newline
+      if newline:
+        outLines.append( newline + '\n' )
+    outfile = file(self._OutputFilename, 'w')
+    outfile.writelines( outLines )
+    outfile.close()
+ 
 if __name__ == "__main__":
   argc = len(os.sys.argv )
   if ( argc < 3 ):
@@ -311,15 +694,42 @@ if __name__ == "__main__":
   #dp.SetOutputFileName( outputfilename )
   dp.SetOutputFileName( tempfile )
   dp.Parse()
-
   exp = DicomV3Expander()
-  exp.SetInputFileName( tempfile )
+  #exp.SetInputFileName( tempfile )
+  exp.SetInputFileName( inputfilename )
   exp.SetOutputFileName( outputfilename )
   exp.Expand()
-  """
+
   dp = TransferSyntaxParser()
   dp.SetInputFileName( inputfilename )
   dp.SetOutputFileName( outputfilename )
   dp.Parse()
 
+  dp = PapyrusParser()
+  dp.SetInputFileName( inputfilename )
+  dp.SetOutputFileName( outputfilename )
+  dp.Parse()
+
+  dp = InteraParser()
+  dp.SetInputFileName( inputfilename )
+  dp.SetOutputFileName( outputfilename )
+  dp.Parse()
+  dp = GEMSParser()
+  dp.SetInputFileName( inputfilename )
+  dp.SetOutputFileName( outputfilename )
+  dp.Parse()
+
+  """
+  dp = Dicom3ToolsParser()
+  dp.SetInputFileName( inputfilename )
+  dp.SetOutputFileName( outputfilename )
+  dp.Parse()
+
+  """
+  dp = GEAdvanceParser()
+  dp.SetInputFileName( inputfilename )
+  dp.SetOutputFileName( outputfilename )
+  dp.Parse()
+  """
+
   #print dp.IsAStartingLine( "(0004,1212) File-set Consistency Flag US 1\n" )