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#! /usr/bin/env python
"""
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
patt = re.compile('^Page [0-9]+$')
if( patt.match(s) ):
return True
return False
def IsAStartingLine(self,s):
patt = re.compile('^\\([0-9a-fA-Fx]+,[0-9a-fA-F]+\\) (.*)$')
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]$')
if( patt.match(s) ):
return True
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()
"""
subclass
"""
class UIDParser(PdfTextParser):
def IsAStartingLine(self,s):
patt = re.compile('^1.2.840.10008.[0-9.]+ (.*)$')
if( patt.match(s) ):
return True
#print "Is Not:", s
return False
def IsAFullLine(self,s):
patt = re.compile('^1.2.840.10008.[0-9.]+ (.*) PS ?[0-9].1?[0-9]$')
if( patt.match(s) ):
return True
patt = re.compile('^1.2.840.10008.[0-9.]+ (.*) Well-known frame of reference$')
if( patt.match(s) ):
return True
patt = re.compile('^1.2.840.10008.[0-9.]+ (.*) \\(Retired\\)$')
if( patt.match(s) ):
return True
return False
def IsAComment(self,s):
if PdfTextParser.IsAComment(self,s):
return True
# else let's enhance the super class
patt = re.compile('^SPM2 (.*) http(.*)$')
if( patt.match(s) ):
return True
return False
def AddOutputLine(self,s):
if self.IsAFullLine(s):
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]$')
if patt.match(s):
return UIDParser.IsAStartingLine(self,s)
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]+)$')
m = patt.match(s)
if m:
ss = m.group(2).lower() + ' ' + m.group(3).lower() + ' ' + m.group(4) + ' ' + m.group(5) + ' ' + m.group(1)
self._OutLines.append(ss + '\n')
else:
print 'OOOPs', s
"""
This class is meant to expand line like:
- (xxxx,xxxx to xxxx) xxxxxxxxxxxx
or
- (12xx, 3456) comment...
"""
class DicomV3Expander:
def __init__(self):
self._InputFilename = ''
self._OutputFilename = ''
self._OutLines = []
def SetInputFileName(self,s):
self._InputFilename = s
def SetOutputFileName(self,s):
self._OutputFilename = s
# Function to turn into lower case a tag:
# ex: (ABCD, EF01) -> (abcd, ef01)
def LowerCaseTag(self,s):
#print "Before:", s[:-1]
patt = re.compile('^(\\([0-9a-fA-F]+,[0-9a-fA-F]+\\))(.*)$')
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-] .*$')
if patt.match(s):
return s
else:
print "Impossible case:", s
os.sys.exit(1)
def AddOutputLine(self,s):
if s.__class__ == list:
for i in s:
self._OutLines.append(i + '\n')
else:
self._OutLines.append(s + '\n')
# Expand the line approriaetkly and also add it to the
# _OutLines list
def ExpandLine(self, s):
assert s[-1] == '\n'
s = s[:-1] # remove \n
list = []
if self.NeedToExpansion(s, list):
self.AddOutputLine(list) # list != []
elif self.NeedGroupXXExpansion(s, list):
self.AddOutputLine(list) # list != []
elif self.NeedElemXXExpansion(s, list):
self.AddOutputLine(list) # list != []
else:
self.AddOutputLine(self.LowerCaseTag(s))
# If line is like:
# (0020,3100 to 31FF) Source Image Ids RET
def NeedToExpansion(self,s, list):
patt = re.compile('^\\(([0-9a-fA-F]+),([0-9a-fA-F]+) to ([0-9a-fA-F]+)\\)(.*)$')
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]+)(.*)$')
m = patt.match(s)
if m:
#print m.groups()
gr = m.group(1)
el_start = m.group(2)
start = '0x00'
end = '0xFF'
for i in range(eval(start), eval(end)):
el = '%02x'% i
l = '('+gr+','+el+el_start+')'+m.group(3)
print l
list.append(l)
return True
return False
def Write(self):
outfile = file(self._OutputFilename, 'w')
outfile.writelines( self._OutLines )
outfile.close()
def Expand(self):
infile = file(self._InputFilename,'r')
for line in infile.readlines():
# ExpandLine also LowerCase the line
self.ExpandLine(line) # l is [1,n] lines
self.Write()
infile.close()
"""
Parse line from a philips document, line are like this:
Syncra Scan Type 2005,10A1 VR = CS, VM = 1
"""
class InteraParser:
def __init__(self):
self._InputFilename = ''
self._OutputFilename = ''
def Reformat(self,s):
assert self.IsGood(s)
patt = re.compile("^([A-Za-z0-9 -]+) ([0-9A-Z]+),([0-9A-Z]+) VR = ([A-Z][A-Z]), VM = (.*)$")
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 ):
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( outputfilename )
dp.SetOutputFileName( tempfile )
dp.Parse()
exp = DicomV3Expander()
#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" )
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