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#!/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...
"""
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...
"""
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]+)(.*)$')
m = patt.match(s)
if m:
#print m.groups()
gr = m.group(1)
el_start = m.group(2)
start = '0x00'
end = '0xFF'
for i in range(eval(start), eval(end)):
el = '%02x'% i
l = '('+gr+','+el+el_start+')'+m.group(3)
print l
list.append(l)
return True
return False
def Write(self):
outfile = file(self._OutputFilename, 'w')
outfile.writelines( self._OutLines )
outfile.close()
def Expand(self):
infile = file(self._InputFilename,'r')
for line in infile.readlines():
# ExpandLine also LowerCase the line
self.ExpandLine(line) # l is [1,n] lines
self.Write()
infile.close()
"""
Converter class
Input is of type:
(0008,0001) Length to End UL 1 RET
output should be:
0008 0001 UL 1 Length to End RET
"""
class Converter:
def __init__(self):
self._InputFilename = ''
self._OutputFilename = ''
self._OutLines = []
def SetInputFileName(self,s):
self._InputFilename = s
def SetOutputFileName(self,s):
self._OutputFilename = s
def Open(self):
self._Infile = file(self._InputFilename, 'r')
for line in self._Infile.readlines():
line = line[:-1] # remove '\n'
if (not self.IsAFullLine(line) ):
print "Convert pb:", line
def IsAFullLine(self,s):
patt = re.compile('^\\(([0-9a-fA-Fx]+),([0-9a-fA-F]+)\\)\s+(.*)\s+([A-Z][A-Z])\s+([0-9n-]+)\s*$')
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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