ensemblePLSR/read_settings_file.py at master · pgbrodrick/ensemblePLSR · GitHub

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import configparser
import sys,os,re
import numpy as np


class settings():

  def clean_comments(self,instring):
     orig_instring = instring
     while ('(' in instring):
       start_ind = instring.index('(')
       if (')' not in instring):
         print('unmatched ( in input::::         {}'.format(orig_instring))
         print('terminating')
         quit()
       end_ind = instring.split('=')[0].rindex(')')
       instring = instring.replace(instring[start_ind:end_ind+1],'')
     return instring


  def get_all_settings(self,set_obj):
      out = {}
      for section in set_obj.sections():
        options = set_obj.options(section)
        for option in options:
          read = set_obj.get(section,option)
          option = self.clean_comments(option).lower().strip()
          read = self.clean_comments(read)

          if (',' in read):
            read = re.split(',',read)

          if (read == ''):
            read = None


          out[option] = read
      return out

  def get_setting(self,ref):
    if (ref not in self.settings_dict):
      print('could not locate setting {} in  settings file {}'.format(ref,self.settings_filename))
      print('terminating')
      quit()
    return self.settings_dict[ref]


  def clean_and_check(self):

    if ('csv file' not in self.settings_dict):
      print('no csv input provided.  terminating')
      quit()
    if (self.settings_dict['csv file'] == None):
      print('no csv input provided.  terminating')
      quit()
    if (os.path.isfile(self.settings_dict['csv file']) == False):
      print('csv file: {} is invalid, terminating.'.format(self.settings_dict['csv file']))
      quit()


    ##### bad bands list ( list converted to ints)
    if (self.settings_dict['bad bands'] == None):
      self.settings_dict['bad bands'] = np.array([-1])
    else:
      print('n bad bands {}'.format(len(self.settings_dict['bad bands'])))
      self.settings_dict['bad bands'] = np.array([int(x) for x in self.settings_dict['bad bands']])

    ##### ndvi bands list ( list converted to ints)
    if (self.settings_dict['ndvi bands'] == None):
      self.settings_dict['ndvi bands'] = np.array([34, 46])
    else:
      self.settings_dict['ndvi bands'] = np.array([int(x) for x in self.settings_dict['ndvi bands']])
      assert len(self.settings_dict['ndvi bands']) == 2, 'only 2 NDVI bands available'
      assert self.settings_dict['ndvi bands'][1] > self.settings_dict['ndvi bands'][0], 'only 2 NDVI bands available'


    ###### string lists
    for lk in ['chems','chem transforms','ignore columns']:
      if (self.settings_dict[lk] == None):
        self.settings_dict[lk] = [-1]
      else:
        if (not isinstance(self.settings_dict[lk],str)):
          self.settings_dict[lk] = [x.replace('\'','').replace('\"','').strip() for x in self.settings_dict[lk]]
        else:
          self.settings_dict[lk] = [self.settings_dict[lk].strip()]


    bool_vars = ['brightness normalize','find bad bands','scale response',\
                 'scale features']
    for bool_var in bool_vars:
      if (self.settings_dict[bool_var] == 'false' or self.settings_dict[bool_var] == 'False'):
        self.settings_dict[bool_var] = False
      if (self.settings_dict[bool_var] == 'true' or self.settings_dict[bool_var] == 'True'):
        self.settings_dict[bool_var] = True

    int_vars = ['iterations','samples per crown','max band',\
                'min pixel per crown','max components','test set value']
    for int_var in int_vars:
     if (self.settings_dict[int_var] != None):
      self.settings_dict[int_var] = int(self.settings_dict[int_var].strip())

    float_vars = ['ndvi minimum','ndvi maximum','brightness minimum','brightness maximum','test set holdout fraction',\
                  'iteration holdout fraction','iteration fraction used', 'lowest wavelength','wavelength interval']
    for float_var in float_vars:
     if (self.settings_dict[float_var] != None):
      self.settings_dict[float_var] = float(self.settings_dict[float_var])

    string_vars = ['band preface','crown col','version name']
    for string_var in string_vars:
     if (self.settings_dict[string_var] != None):
      self.settings_dict[string_var] = self.settings_dict[string_var].replace('\'','')
      self.settings_dict[string_var] = self.settings_dict[string_var].replace('\"','')

    if (self.settings_dict['iteration holdout fraction'] in [None,0] and \
        self.settings_dict['iteration fraction used'] != 1):
       print('if iteration fraction used is specified, an iteration holdout fraction greater than 0 must be specified as well')
       quit()


  def __init__(self,filename):
    self.settings_filename = ''
    self.settings_obj = configparser.ConfigParser()
    self.settings_dict = ''
    self.settings_filename = filename
    self.settings_obj.read(filename)
    self.settings_dict = self.get_all_settings(self.settings_obj)