File: ParseDicts.py

package info (click to toggle)
gdcm 2.4.4-3%2Bdeb8u1
  • links: PTS, VCS
  • area: main
  • in suites: jessie
  • size: 32,912 kB
  • ctags: 52,166
  • sloc: cpp: 188,527; ansic: 124,526; xml: 41,799; sh: 7,162; python: 3,667; cs: 2,128; java: 1,344; lex: 1,290; tcl: 677; php: 128; makefile: 116
file content (401 lines) | stat: -rwxr-xr-x 11,884 bytes parent folder | download | duplicates (9)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
#!/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" )