Labels.py

#!/usr/bin/env python3
#*********************************************************************
#                                                          24 Sep 2015
#               Andrew J. Worth
#               andy@neuromorphometrics.com
#
#               Neuromorphometrics
#               22 Westminster Street
#               Somerville, MA  02144-1630  USA
#
#               http://neuromorphometrics.com
#
#*********************************************************************
#*                                                                   *
#*  (c) Copyright 2015 Neuromorphometrics      All rights reserved   *
#*                                                                   *
#*********************************************************************
#-------------------------------------------------------------------------------
# Usage String:
"""
SYNOPSIS
 
    Labels.py 
 

DESCRIPTION
 
    Reads and writes NVM label files
 
EXAMPLES
 
    Import to set things up, 
    then Read() to read in all labels
    Should eventually add a Write() function

AUTHOR
 
    Andrew J. Worth
    andy@neuromorphometrics.com
     
    Neuromorphometrics, Inc.
    22 Westminster Street
    Somerville, MA  02144-1630  USA
     
    http://Neuromorphometrics.com
 
LICENSE
    (c) Copyright 2015 Neuromorphometrics, Inc.   All rights reserved.
 
VERSION
"""
import sys
import os
import xml.etree.ElementTree as ET
import json

whoIam = os.path.basename(__file__)
#print(whoIam)
#print('Exiting Early.')
#sys.exit()

DefaultLabelFiles = [ \
  'defaultLabel', \
  'parcLabels', \
  'sulciLabels' ]

Columns = [
  'Name', \
  'Number', \
  'RGBColor', \
  'Type', \
]

# Label files be like:
# 
# <?xml version="1.0"?>
# <LabelList>
# <Label>
#   <Name>3rd Ventricle</Name>
#   <Number>4</Number>
#   <Kind>GeneralLabel</Kind>
#   <RGBColor>204 182 142</RGBColor>
# </Label>
# ...
# </LabelList>
#
# Where 'Kind' can be: (MUST BE SAME as in nvm_LabelXML.cxx)
#  <Kind>ExtractableContour</Kind>
#  <Kind>SulciLine</Kind>
#  <Kind>CerebralParcUnit</Kind>
#  <Kind>CerebellarParcUnit</Kind>
#  <Kind>GeneralLabel</Kind> 
#  <Kind>UnknownLabel</Kind>

numLabels = 0
maxLabelNumber = 0

Labels = [ ]

#-------------------------------------------------------------------------------
# Read the given label xml file and append to list
def readFile(fullLabelFileName,VerboseLevel):

  global numLabels, maxLabelNumber, Labels

  tree = ET.parse(fullLabelFileName)
  root = tree.getroot()
  #print('root', root)
  labellist = root.findall('Label')
  #print('labellist ', labellist)
  names = [ e.find('Name').text for e in labellist]
  #print('names ', names)
  numbers = [ int(e.find('Number').text) for e in labellist]
  #print('numbers', numbers)
  colors = [ e.find('RGBColor').text for e in labellist]
  #print('colors ', colors)
  kinds = [ e.find('Kind').text for e in labellist]

  for ii, name in enumerate(names):
    if VerboseLevel >= 2:
      print(ii,name,numbers[ii],colors[ii],kinds[ii])
    if numbers[ii] > maxLabelNumber:
      maxLabelNumber = numbers[ii] 
    Labels.append([name,numbers[ii],colors[ii],kinds[ii]])

  #print('Exiting Early.')
  #sys.exit()
  # End for fName

#-------------------------------------------------------------------------------
# Read all default label files and sort resulting Labels
def Read(VerboseLevel):

  global numLabels, maxLabelNumber, Labels

  for fName in DefaultLabelFiles:
    fullLabelFileName = './Labels/'+fName+'.xml'
    if VerboseLevel >= 0:
      print(whoIam,': Reading Label file', fullLabelFileName)

    if os.access(fullLabelFileName,os.F_OK) == False:
      print(whoIam,'ERROR: missing default label file: '+fullLabelFileName)
      continue

    readFile(fullLabelFileName)

  Labels.sort(key=lambda tup: tup[1])

  numLabels = len(Labels)

  if VerboseLevel >= 1:
    print(whoIam,': All Sorted Labels...')
    sys.stdout.write('#')
    for ii in range(len(Columns)):
      sys.stdout.write(', {}'.format(Columns[ii]))
    print('')
    for ii in range(len(Labels)):
      print(ii,Labels[ii])

  if VerboseLevel >= 0:
    print(whoIam,': maxLabelNumber',maxLabelNumber)
    print(whoIam,': numLabels', numLabels)

  #print('Exiting Early.')
  #sys.exit()
  # End Read()

#-------------------------------------------------------------------------------
def Write(FileName,VerboseLevel):

  f = open(FileName,'w')

  # Print first part of result XML file
  f.write("<?xml version=\"1.0\"?>\n")
  f.write("<LabelList>\n")

  for ll in Labels:
    if ll[1] != 0:
      f.write('<Label>\n')
      f.write('  <Name>'+ll[0]+'</Name>\n')
      f.write('  <Number>'+str(ll[1])+'</Number>\n')
      f.write('  <RGBColor>'+ll[2]+'</RGBColor>\n')
      f.write('  <Kind>'+ll[3]+'</Kind>\n')
      f.write('</Label>\n')

  f.write("</LabelList>\n")

  f.close()

  if VerboseLevel >= 1:
    print("All done.")

  #print('Exiting Early.')
  #sys.exit()
  # End Write()

#-------------------------------------------------------------------------------
# Write the labels as a dictionary mapping label numbers to the other info
def Writejson(FileName,VerboseLevel):

  dictLabels = dict()

  for ll in Labels:
    if ll[1] != 0:
      thisLabel = {
      'Name':     ll[0],
      'RGBColor': ll[2],
      'Kind':     ll[3]
      }
      dictLabels[str(ll[1])] = thisLabel

  outstr = json.dumps(dictLabels, indent=2)

  if VerboseLevel >= 1:
    print(outstr)

  f = open(FileName,'w')
  f.write(outstr)
  f.close()

  #print('Exiting Early.')
  #sys.exit()
  # End Write()


# vi:set autoindent ts=2 sw=2 expandtab : See Vim, :help 'modeline'