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How to use _clear method in taiko

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fy.py

Source:fy.py

1#!/usr/bin/env python2# 3#   ___         __                        4# .'  _|.--.--.|  |--..-----..----..-----.5# |   _||  |  ||  _  ||  _  ||   _||  _  |6# |__|  |___  ||_____||_____||__|  |___  |7#       |_____|                    |_____|8#9# THE ULTIMATE SCALAR MAPPING FRAMEWORK FOR TRACKVIS (.TRK) FILES10#11#12#13# (c) 2012 FNNDSC, Children's Hospital Boston 14#15#16import fnmatch17import matplotlib18matplotlib.use( 'Agg' ) # switch to offscreen rendering19import matplotlib.pyplot as plot20from matplotlib.colors import LogNorm21import multiprocessing22import numpy as np23import os24import scipy.io25import shutil26import subprocess27import sys28import time29import fyborg30from FyFilterCortexAction import *31from FyFilterLengthAction import *32from FyLengthAction import *33from FyMapAction import *34from FyRadiusMapAction import *35import colortable36from logger import Logger37from _colors import Colors38from _common import FNNDSCParser39from _common import FNNDSCConsole as c40from _common import FNNDSCFileIO as io41class FyborgLogic:42  def __init( self ):43    '''44    '''45  def intro( self ):46    intro = Colors.CYAN + """47    48                        _.--'''--._49                      .'           `.50                     /               \\51                  .-'                 '-.52                 /                       \\            .----------------.53                / _.--._           _.--._ \\         __i """ + Colors.RED + """*FYBORG POWER*""" + Colors.CYAN + """ |54               / /      `-._   _.-'      \ \\        '-.________________:55              : :      """ + Colors.RED + """.--._""" + Colors.CYAN + """) (""" + Colors.RED + """_.--.""" + Colors.CYAN + """      : :56              | `.    """ + Colors.RED + """/""" + Colors.CYAN + """    / : \    """ + Colors.RED + """\ """ + Colors.CYAN + """   .' |57              :   `-.___.-':/ \:`-.___.-'   :58               \   _       \:_:/       _   /59                `.' "`-.           .-'" '.'60                  :     `-._   _.-'     :61                  |                     |62                  :     _.--._.--._     :63                   \   ^-.__   __.-^   /64                    `-.     '''     .-'65                       \           /66                      /;`-._____.-';\\67                __..-'/             \\'-..__68           __.-'  _.-'               '-._  `-.__69                                             fsc70                          FYBORG71  >> THE ULTIMATE SCALAR MAPPING FRAMEWORK FOR TRACKVIS FILES <<72                73  (c) 2012 FNNDSC / Boston Children's Hospital74  E-Mail us: dev@babyMRI.org75""" + Colors._CLEAR76    print intro77  def outro( self ):78    outro = Colors.CYAN + """79                            .---.--.       .--.   80                          ,(     ),.`.   .'.--.`. 81                          ; \\   / : \\ ;.'.'    \\ ;82\\                         ; """ + Colors.RED + """_""" + Colors.CYAN + """; :""" + Colors.RED + """_""" + Colors.CYAN + """ :""-/ /-.     ;:83 \\                        ;""" + Colors.RED + """'-""" + Colors.CYAN + """;":""" + Colors.RED + """-'""" + Colors.CYAN + """:"-/ /-._^.   ;:84\\ \\                       :  : ;  ; / /  / \\ \\  ;:85\\\\ \\                      :\\  V  / : :  :   ; ;-';86 \\\\ \\                     ; ;._.':,' ;  ;   : :-' 87\\ \\\\ \\                   : : ; : ;o /-._;   : :   88 \\ \\\\ \\                 _;o; : ; '-'.'.-"`. :-^,  89  \\ \\\\ \\            .-.;:_"  _..--"/ /  _  ;y  ;  90   \\ \\\\ \\         .' / '-,; ::    : :  (o) ;   :  91    \\ \\\\ "-.     /  :    ;: ;;    ; ;     /    :  92bug  : \\\\   \\   :   ;    :: ;;  .' ;._..+:     ;  93     :  \\\\   \\  :  _:    ;: :: /   ; ;  ; ;(o):   94"-.   \\  \\\\   \\/ Y' '.  // ^ \\Y   / /  :  '._.;   95\\  \\   \\  ;"-. ;/     7"" / \\ :.-'.' .';  /  /    96\\\\  \\   \\ :   ":_    :"\\ ;..-^'--" .' /  /  /     97 \\\\  \\   "+.;-"" )._..^-""        /  / .' .'      98  ;"+.;_.-" :--=<___)    __..__  /  :-" .'        99\\ :/_. ;  .-" \\ _____.--""__..--""   ;.-"         100 ":  '+'  __..-\\/\\  ''''T__..___..-":             101  :   :\\."      \\/;     ;: () ;  .-" ;            102   "--q/\\        "      :;    :-"    :            103       \\/;              ;:    ;   ..-(            104        "               :-\\__/-+""-. .^.          105                         ; \\  (     \\;  `.        106                        /`. `-/\\ ,=. '.   `.      107                       : \\ \\ :"-:/ .`. \\    \\     108                       ;  ; ;;"-;\\/ .'`."-.  ;    109                      :   : ;"-.: \\/ .' j  "-:    110                      ;   : :"-.;  `: ,' ;    \\   111                     :    : :"-:     "..':     ;  112                     ;    ; ;"-;       `=;  ;  :  113""" + Colors._CLEAR114    print outro115  def run( self, input, output, radius, length, stage, cortex_only, verbose ):116    '''117    '''118    if stage == 0:119      # create output directory120      # but not if we start with a different stage121      os.mkdir( output )122    # activate log file123    self.__debug = verbose124    self.__logger = Logger( os.path.join( output, 'log.txt' ), verbose )125    sys.stdout = self.__logger126    sys.stderr = self.__logger127    # the input data128    _inputs = {'adc':[ '*adc.nii', None],129              'b0':[ '*b0.nii', None],130              'e1':['*e1.nii', None],131              'e2':[ '*e2.nii', None],132              'e3':[ '*e3.nii', None],133              'fa':[ '*fa.nii', None],134              'fibers':['*streamline.trk', '*/final-trackvis/*.trk', None],135              'segmentation': ['*aparc+aseg.mgz', None],136              'T1':['*/mri/brain.mgz', None]137              }138    # the output data139    _outputs = {'T1':os.path.join( output, 'T1.nii' ),140                'segmentation':os.path.join( output, 'aparc+aseg.nii' ),141                'b0_T1_space':os.path.join( output, 'dti_b0_T1_space.nii' ),142                'adc_T1_space':os.path.join( output, 'dti_adc_T1_space.nii' ),143                'fa_T1_space':os.path.join( output, 'dti_fa_T1_space.nii' ),144                'e1_T1_space':os.path.join( output, 'dti_e1_T1_space.nii' ),145                'e2_T1_space':os.path.join( output, 'dti_e2_T1_space.nii' ),146                'e3_T1_space':os.path.join( output, 'dti_e3_T1_space.nii' ),147                'B0toT1matrix':os.path.join( output, 'B0-to-T1.mat' ),148                'fibers':os.path.join( output, 'fybers_T1_space.trk' ),149                'fibers_mapped':os.path.join( output, 'fybers_T1_space_mapped.trk' ),150                'fibers_mapped_length_filtered':os.path.join( output, 'fybers_T1_space_mapped_length_filtered.trk' ),151                'fibers_mapped_length_filtered_cortex_only':os.path.join( output, 'fybers_T1_space_mapped_length_filtered_cortex_only.trk' ),152                'fibers_final':os.path.join( output, 'fybers_final.trk' ),153                'matrix_all': os.path.join( output, 'matrix_all.mat' ),154                'matrix_fibercount': os.path.join( output, 'matrix_fibercount.csv' ),155                'matrix_length': os.path.join( output, 'matrix_length.csv' ),156                'matrix_adc': os.path.join( output, 'matrix_adc.csv' ),157                'matrix_inv_adc': os.path.join( output, 'matrix_inv_adc.csv' ),158                'matrix_fa': os.path.join( output, 'matrix_fa.csv' ),159                'matrix_e1': os.path.join( output, 'matrix_e1.csv' ),160                'matrix_e2': os.path.join( output, 'matrix_e2.csv' ),161                'matrix_e3': os.path.join( output, 'matrix_e3.csv' ),162                'roi':os.path.join( output, 'roi' )163                }164    self.intro()165    # 4 x beep166    print '\a\a\a\a\a\a\a'167    #time.sleep( 3 )168    # stage 1169    c.info( Colors.YELLOW + '>> STAGE [' + Colors.PURPLE + '1' + Colors.YELLOW + ']: ' + Colors.YELLOW + ' ANALYZING INPUT DATA' + Colors._CLEAR )170    if stage <= 2: # we can never skip stage 1 without skipping stage 2171      _inputs = self.analyze_input_data( input, _inputs )172    else:173      c.info( Colors.PURPLE + '  skipping it..' + Colors._CLEAR )174    # stage 2175    c.info( Colors.YELLOW + '>> STAGE [' + Colors.PURPLE + '2' + Colors.YELLOW + ']: ' + Colors.YELLOW + ' PREPROCESSING' + Colors._CLEAR )176    if stage <= 2:177      self.preprocessing( _inputs, _outputs )178    else:179      c.info( Colors.PURPLE + '  skipping it..' + Colors._CLEAR )180    # stage 3181    c.info( Colors.YELLOW + '>> STAGE [' + Colors.PURPLE + '3' + Colors.YELLOW + ']: ' + Colors.YELLOW + ' MAPPING' + Colors._CLEAR )182    if stage <= 3:183      self.mapping( _inputs, _outputs, radius )184    else:185      c.info( Colors.PURPLE + '  skipping it..' + Colors._CLEAR )186    c.info( Colors.YELLOW + '>> STAGE [' + Colors.PURPLE + '4' + Colors.YELLOW + ']: ' + Colors.YELLOW + ' FILTERING' + Colors._CLEAR )187    if stage <= 4:188      self.filtering( _inputs, _outputs, length, cortex_only )189    else:190      c.info( Colors.PURPLE + '  skipping it..' + Colors._CLEAR )191    c.info( Colors.YELLOW + '>> STAGE [' + Colors.PURPLE + '5' + Colors.YELLOW + ']: ' + Colors.YELLOW + ' CONNECTIVITY MATRICES' + Colors._CLEAR )192    if stage <= 5:193      self.connectivity( _inputs, _outputs, cortex_only )194    else:195      c.info( Colors.PURPLE + '  skipping it..' + Colors._CLEAR )196    c.info( Colors.YELLOW + '>> STAGE [' + Colors.PURPLE + '6' + Colors.YELLOW + ']: ' + Colors.YELLOW + ' ROI EXTRACTION' + Colors._CLEAR )197    if stage <= 6:198      self.roi_extract( _inputs, _outputs )199    else:200      c.info( Colors.PURPLE + '  skipping it..' + Colors._CLEAR )201    self.outro()202    c.info( '' )203    c.info( 'ALL DONE! SAYONARA..' )204  def preprocessing( self, inputs, outputs ):205    '''206    Co-Register the input files using Flirt.207    '''208    # convert the T1.mgz to T1.nii209    cmd = 'ss;'210    cmd += 'chb-fsstable;'211    cmd += 'mri_convert ' + inputs['T1'][-1] + ' ' + outputs['T1']212    c.info( Colors.YELLOW + '  Converting ' + Colors.PURPLE + 'T1.mgz' + Colors.YELLOW + ' to ' + Colors.PURPLE + 'T1.nii' + Colors.YELLOW + '!' + Colors._CLEAR )213    sp = subprocess.Popen( ["/bin/bash", "-i", "-c", cmd], stdout=sys.stdout )214    sp.communicate()215    # convert the aparc+aseg.mgz to aparc+aseg.nii216    cmd = 'ss;'217    cmd += 'chb-fsstable;'218    cmd += 'mri_convert ' + inputs['segmentation'][-1] + ' ' + outputs['segmentation']219    c.info( Colors.YELLOW + '  Converting ' + Colors.PURPLE + 'aparc+aseg.mgz' + Colors.YELLOW + ' to ' + Colors.PURPLE + 'aparc+aseg.nii' + Colors.YELLOW + '!' + Colors._CLEAR )220    sp = subprocess.Popen( ["/bin/bash", "-i", "-c", cmd], stdout=sys.stdout )221    sp.communicate()222    # register B0 to T1223    cmd = 'ss;'224    cmd += 'chb-fsstable;'225    flirtcmd = 'flirt -in ' + inputs['b0'][-1] + ' -ref ' + outputs['T1'] + ' -usesqform -nosearch -dof 6 -cost mutualinfo -out ' + outputs['b0_T1_space'] + '.gz -omat ' + outputs['B0toT1matrix'] + ';'226    cmd += flirtcmd227    cmd += 'gzip -d -f ' + outputs['b0_T1_space'] + '.gz;'228    self.__logger.debug( flirtcmd )229    c.info( Colors.YELLOW + '  Registering ' + Colors.PURPLE + os.path.split( inputs['b0'][-1] )[1] + Colors.YELLOW + ' to ' + Colors.PURPLE + 'T1.nii' + Colors.YELLOW + ' and storing ' + Colors.PURPLE + os.path.split( outputs['B0toT1matrix'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )230    sp = subprocess.Popen( ["/bin/bash", "-i", "-c", cmd], stdout=sys.stdout )231    sp.communicate()232    # resample all other DTI volumes to T1 space233    for i in inputs:234      if i == 'fibers' or i == 'segmentation' or i == 'T1' or i == 'b0':235        # we do not map these236        continue237      cmd = 'ss;'238      cmd += 'chb-fsstable;'239      flirtcmd = 'flirt -in ' + inputs[i][-1] + ' -ref ' + outputs['T1'] + ' -out ' + outputs[i + '_T1_space'] + '.gz -init ' + outputs['B0toT1matrix'] + ' -applyxfm;'240      cmd += flirtcmd241      cmd += 'gzip -d -f ' + outputs[i + '_T1_space'] + '.gz;'242      self.__logger.debug( flirtcmd )243      c.info( Colors.YELLOW + '  Resampling ' + Colors.PURPLE + os.path.split( inputs[i][-1] )[1] + Colors.YELLOW + ' as ' + Colors.PURPLE + os.path.split( outputs[i + '_T1_space'] )[1] + Colors.YELLOW + ' using ' + Colors.PURPLE + os.path.split( outputs['B0toT1matrix'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )244      sp = subprocess.Popen( ["/bin/bash", "-i", "-c", cmd], stdout=sys.stdout )245      sp.communicate()246    # resample the fibers to T1 space247    cmd = 'ss;'248    cmd += 'chb-fsstable;'249    transformcmd = 'track_transform ' + inputs['fibers'][-1] + ' ' + outputs['fibers'] + ' -src ' + inputs['b0'][-1] + ' -ref ' + outputs['T1'] + ' -reg ' + outputs['B0toT1matrix'] + ';'250    cmd += transformcmd251    self.__logger.debug( transformcmd )252    c.info( Colors.YELLOW + '  Transforming ' + Colors.PURPLE + os.path.split( inputs['fibers'][-1] )[1] + Colors.YELLOW + ' to ' + Colors.PURPLE + os.path.split( outputs['fibers'] )[1] + Colors.YELLOW + ' using ' + Colors.PURPLE + os.path.split( outputs['B0toT1matrix'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )253    sp = subprocess.Popen( ["/bin/bash", "-i", "-c", cmd], stdout=sys.stdout )254    sp.communicate()255  def mapping( self, inputs, outputs, radius ):256    '''257    Map all detected scalar volumes to each fiber.258    '''259    # check if we have all required input data260    # we need at least: 261    #  - outputs['fibers'] == Track file in T1 space262    #  - outputs['segmentation'] == Label Map263    if not os.path.exists( outputs['fibers'] ):264      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + outputs['fibers'] + Colors.RED + ' but we really need it to start with stage 3!!' + Colors._CLEAR )265      sys.exit( 2 )266    if not os.path.exists( outputs['segmentation'] ):267      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + outputs['segmentation'] + Colors.RED + ' but we really need it to start with stage 3!!' + Colors._CLEAR )268      sys.exit( 2 )269    actions = []270    for i in inputs:271      if i == 'fibers' or i == 'segmentation' or i == 'T1' or i == 'b0':272        # we do not map these273        continue274      if not os.path.exists( outputs[i + '_T1_space'] ):275        # we can't map this since we didn't find the file276        continue277      # for normal scalars: append it to the actions278      actions.append( FyMapAction( i, outputs[i + '_T1_space'] ) )279      c.info( Colors.YELLOW + '  Configuring mapping of ' + Colors.PURPLE + os.path.split( outputs[i + '_T1_space'] )[1] + Colors.YELLOW + ' to ' + Colors.PURPLE + os.path.split( outputs['fibers'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )280    # now the segmentation with the lookaround radius281    actions.append( FyRadiusMapAction( 'segmentation', outputs['segmentation'], radius ) )282    c.info( Colors.YELLOW + '  Configuring mapping of ' + Colors.PURPLE + os.path.split( outputs['segmentation'] )[1] + Colors.YELLOW + ' to ' + Colors.PURPLE + os.path.split( outputs['fibers'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )283    # and also the fiber length284    actions.append( FyLengthAction() )285    c.info( Colors.YELLOW + '  Configuring mapping of ' + Colors.PURPLE + 'fiber length' + Colors.YELLOW + ' to ' + Colors.PURPLE + os.path.split( outputs['fibers'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )286    # run, forest, run!!287    c.info( Colors.YELLOW + '  Performing configured mapping for ' + Colors.PURPLE + os.path.split( outputs['fibers'] )[1] + Colors.YELLOW + ' and storing as ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped'] )[1] + Colors.YELLOW + ' (~ 30 minutes)!' + Colors._CLEAR )288    if self.__debug:289      fyborg.fyborg( outputs['fibers'], outputs['fibers_mapped'], actions, 'debug' )290    else:291      fyborg.fyborg( outputs['fibers'], outputs['fibers_mapped'], actions )292  def filtering( self, inputs, outputs, length, cortex_only ):293    '''294    Filter the mapped fibers.295    '''296    # check if we have all required input data297    # we need at least: 298    #  - outputs['fibers_mapped'] == Track file in T1 space with mapped scalars299    if not os.path.exists( outputs['fibers_mapped'] ):300      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + outputs['fibers_mapped'] + Colors.RED + ' but we really need it to start with stage 4!!' + Colors._CLEAR )301      sys.exit( 2 )302    # find the order of the mapped scalars303    header = io.loadTrkHeaderOnly( outputs['fibers_mapped'] )304    scalars = list( header['scalar_name'] )305    # split the length range306    length = length.split( ' ' )307    min_length = int( length[0] )308    max_length = int( length[1] )309    # length filtering310    c.info( Colors.YELLOW + '  Filtering ' + Colors.PURPLE + 'fiber length' + Colors.YELLOW + ' to be ' + Colors.PURPLE + '>' + str( min_length ) + ' and <' + str( max_length ) + Colors.YELLOW + ' for ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped'] )[1] + Colors.YELLOW + ' and store as ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped_length_filtered'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )311    fyborg.fyborg( outputs['fibers_mapped'], outputs['fibers_mapped_length_filtered'], [FyFilterLengthAction( scalars.index( 'length' ), min_length, max_length )] )312    header = io.loadTrkHeaderOnly( outputs['fibers_mapped_length_filtered'] )313    new_count = header['n_count']314    c.info( Colors.YELLOW + '  Number of tracks after ' + Colors.PURPLE + 'length filtering' + Colors.YELLOW + ': ' + str( new_count ) + Colors.YELLOW + Colors._CLEAR )315    if cortex_only:316      # special cortex filtering317      c.info( Colors.YELLOW + '  Filtering for ' + Colors.PURPLE + 'valid cortex structures' + Colors.YELLOW + ' in ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped_length_filtered'] )[1] + Colors.YELLOW + ' and store as ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped_length_filtered_cortex_only'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )318      c.info( Colors.PURPLE + '    Conditions for valid fibers:' + Colors._CLEAR )319      c.info( Colors.PURPLE + '    1.' + Colors.YELLOW + ' The fiber track has to pass through the cerebral white matter. (Label values: ' + Colors.PURPLE + '[2, 41]' + Colors.YELLOW + ')' + Colors._CLEAR )320      c.info( Colors.PURPLE + '    2.' + Colors.YELLOW + ' The fiber track shall only touch sub-cortical structures not more than ' + Colors.PURPLE + '5 times' + Colors.YELLOW + '. (Label values: ' + Colors.PURPLE + '[10, 49, 16, 28, 60, 4, 43]' + Colors.YELLOW + ')' + Colors._CLEAR )321      c.info( Colors.PURPLE + '    3.' + Colors.YELLOW + ' The track shall not pass through the corpus callosum (Labels: ' + Colors.PURPLE + '[251, 255]' + Colors.YELLOW + ') and end in the same hemisphere (Labels: ' + Colors.PURPLE + '[1000-1035]' + Colors.YELLOW + ' for left, ' + Colors.PURPLE + '[2000-2035]' + Colors.YELLOW + ' for right).' + Colors._CLEAR )322      fyborg.fyborg( outputs['fibers_mapped_length_filtered'], outputs['fibers_mapped_length_filtered_cortex_only'], [FyFilterCortexAction( scalars.index( 'segmentation' ) )] )323      header = io.loadTrkHeaderOnly( outputs['fibers_mapped_length_filtered_cortex_only'] )324      new_count = header['n_count']325      c.info( Colors.YELLOW + '  Number of tracks after ' + Colors.PURPLE + 'cortex filtering' + Colors.YELLOW + ': ' + str( new_count ) + Colors.YELLOW + Colors._CLEAR )326      c.info( Colors.YELLOW + '  Copied filtered tracks from ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped_length_filtered_cortex_only'] )[1] + Colors.YELLOW + ' to ' + Colors.PURPLE + os.path.split( outputs['fibers_final'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )327      shutil.copyfile( outputs['fibers_mapped_length_filtered_cortex_only'], outputs['fibers_final'] )328    else:329      c.info( Colors.YELLOW + '  Info: ' + Colors.PURPLE + 'Cortical _and_ sub-cortical structures ' + Colors.YELLOW + 'will be included..' + Colors._CLEAR )330      c.info( Colors.YELLOW + '  Copied filtered tracks from ' + Colors.PURPLE + os.path.split( outputs['fibers_mapped_length_filtered'] )[1] + Colors.YELLOW + ' to ' + Colors.PURPLE + os.path.split( outputs['fibers_final'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )331      shutil.copyfile( outputs['fibers_mapped_length_filtered'], outputs['fibers_final'] )332  def connectivity( self, inputs, outputs, cortex_only ):333    '''334    Generate connectivity matrices using mapped values.335    '''336    # check if we have all required input data337    # we need at least: 338    #  - outputs['fibers_mapped'] == Track file in T1 space with mapped scalars339    if not os.path.exists( outputs['fibers_final'] ):340      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + outputs['fibers_final'] + Colors.RED + ' but we really need it to start with stage 5!!' + Colors._CLEAR )341      sys.exit( 2 )342    s = io.loadTrk( outputs['fibers_final'] )343    tracks = s[0]344    header = s[1]345    scalarNames = header['scalar_name'].tolist()346    matrix = {}347    indices = {}348    # check if the segmentation is mapped349    try:350      indices['segmentation'] = scalarNames.index( 'segmentation' )351    except:352      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + 'segmentation' + Colors.RED + ' as a mapped scalar but we really need it!' )353      sys.exit( 2 )354    if cortex_only:355      labels = [2012, 2019, 2032, 2014, 2020, 2018, 2027, 2028, 2003, 2024, 2017, 2026, 2002, 2023, 2010, 2022, 2031, 2029, 2008, 2025, 2005, 2021, 2011, 2013, 2007, 2016, 2006, 2033, 2009, 2015, 2001, 2030, 2034, 2035, 1012, 1019, 1032, 1014, 1020, 1018, 1027, 1028, 1003, 1024, 1017, 1026, 1002, 1023, 1010, 1022, 1031, 1029, 1008, 1025, 1005, 1021, 1011, 1013, 1007, 1016, 1006, 1033, 1009, 1015, 1001, 1030, 1034, 1035]356    else:357      labels = [2012, 2019, 2032, 2014, 2020, 2018, 2027, 2028, 2003, 2024, 2017, 2026, 2002, 2023, 2010, 2022, 2031, 2029, 2008, 2025, 2005, 2021, 2011, 2013, 2007, 2016, 2006, 2033, 2009, 2015, 2001, 2030, 2034, 2035, 49, 50, 51, 52, 58, 53, 54, 1012, 1019, 1032, 1014, 1020, 1018, 1027, 1028, 1003, 1024, 1017, 1026, 1002, 1023, 1010, 1022, 1031, 1029, 1008, 1025, 1005, 1021, 1011, 1013, 1007, 1016, 1006, 1033, 1009, 1015, 1001, 1030, 1034, 1035, 10, 11, 12, 13, 26, 17, 18, 16]358    c.info( Colors.YELLOW + '  Getting ready to create connectivity matrices for the following labels: ' + Colors.PURPLE + str( labels ) + Colors._CLEAR )359    c.info( Colors.YELLOW + '  Note: Mapped scalar values along the points will be averaged for each fiber track.' + Colors._CLEAR )360    # create matrices for the attached scalars361    for i, s in enumerate( scalarNames ):362      if i >= header['n_scalars']:363        break364      if not s or s == 'segmentation':365        continue366      # this is a scalar value for which a matrix will be created367      matrix[s] = np.zeros( [len( labels ), len( labels )] )368      indices[s] = scalarNames.index( s )369      c.info( Colors.YELLOW + '  Preparing matrix (' + Colors.PURPLE + '[' + str( len( labels ) ) + 'x' + str( len( labels ) ) + ']' + Colors.YELLOW + ') for ' + Colors.PURPLE + s + Colors.YELLOW + ' values!' + Colors._CLEAR )370      if s == 'adc':371        s = 'inv_adc'372        matrix[s] = np.zeros( [len( labels ), len( labels )] )373        indices[s] = scalarNames.index( 'adc' )374        c.info( Colors.YELLOW + '  Preparing matrix (' + Colors.PURPLE + '[' + str( len( labels ) ) + 'x' + str( len( labels ) ) + ']' + Colors.YELLOW + ') for ' + Colors.PURPLE + s + Colors.YELLOW + ' values!' + Colors._CLEAR )375    # always create one for the fiber counts376    matrix['fibercount'] = np.zeros( [len( labels ), len( labels )] )377    indices['fibercount'] = 0378    c.info( Colors.YELLOW + '  Preparing matrix (' + Colors.PURPLE + '[' + str( len( labels ) ) + 'x' + str( len( labels ) ) + ']' + Colors.YELLOW + ') for ' + Colors.PURPLE + 'fibercount' + Colors.YELLOW + ' values!' + Colors._CLEAR )379    c.info( Colors.YELLOW + '  Analyzing fibers of ' + Colors.PURPLE + os.path.split( outputs['fibers_final'] )[1] + Colors.YELLOW + '..' + Colors._CLEAR )380    for tCounter, t in enumerate( tracks ):381      tCoordinates = t[0]382      tScalars = t[1]383      # find the segmentation labels for the start and end points384      start_label = tScalars[0, indices['segmentation']]385      end_label = tScalars[-1, indices['segmentation']]386      try:387        # now grab the index of the labels in our label list388        start_index = labels.index( start_label )389        end_index = labels.index( end_label )390      except:391        # this label is not monitored, so ignore this track392        continue393      # loop through all different scalars394      for m in matrix:395        # calculate the mean for each track396        value = np.mean( tScalars[:, indices[m]] )397        if m == 'inv_adc':398          # invert the value since it is 1-ADC399          value = 1 / value400        elif m == 'fibercount':401          # in the case of fibercount, add 1402          value = 1403        # store value in the matrix404        matrix[m][start_index, end_index] += value405        if not start_index == end_index:406          matrix[m][end_index, start_index] += value407    # fiber loop is done, all values are stored408    # now normalize the matrices409    np.seterr( all='ignore' ) # avoid div by 0 warnings410    cbar = None411    for m in matrix:412      if not m == 'fibercount':413        # normalize it414        matrix[m][:] /= matrix['fibercount']415        matrix[m] = np.nan_to_num( matrix[m] )416      # store the matrix417      c.info( Colors.YELLOW + '  Storing ' + Colors.PURPLE + m + Colors.YELLOW + ' connectivity matrix as ' + Colors.PURPLE + os.path.split( outputs['matrix_' + m] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )418      np.savetxt( outputs['matrix_' + m], matrix[m], delimiter='\t' )419      # store a picture420      picture_path = os.path.splitext( os.path.split( outputs['matrix_' + m] )[1] )[0] + '.png'421      c.info( Colors.YELLOW + '  Generating ' + Colors.PURPLE + m + ' image' + Colors.YELLOW + ' as ' + Colors.PURPLE + picture_path + Colors.YELLOW + '!' + Colors._CLEAR )422      img = plot.imshow( matrix[m], interpolation='nearest' )423      img.set_cmap( 'jet' )424      img.set_norm( LogNorm() )425      img.axes.get_xaxis().set_visible( False )426      img.axes.get_yaxis().set_visible( False )427      if not cbar:428        cbar = plot.colorbar()429      cbar.set_label( m )430      cbar.set_ticks( [] )431      plot.savefig( os.path.join( os.path.split( outputs['matrix_' + m] )[0], picture_path ) )432    np.seterr( all='warn' ) # reactivate div by 0 warnings433    # now store the matlab version as well434    c.info( Colors.YELLOW + '  Storing ' + Colors.PURPLE + 'matlab data bundle' + Colors.YELLOW + ' containing ' + Colors.PURPLE + 'all matrices' + Colors.YELLOW + ' as ' + Colors.PURPLE + os.path.split( outputs['matrix_all'] )[1] + Colors.YELLOW + '!' + Colors._CLEAR )435    scipy.io.savemat( outputs['matrix_all'], matrix, oned_as='row' )436  def roi_extract( self, inputs, outputs ):437    '''438    '''439    # check if we have all required input data440    # we need at least: 441    #  - outputs['fibers_mapped'] == Track file in T1 space with mapped scalars442    if not os.path.exists( outputs['fibers_final'] ):443      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + outputs['fibers_final'] + Colors.RED + ' but we really need it to start with stage 6!!' + Colors._CLEAR )444      sys.exit( 2 )445    s = io.loadTrk( outputs['fibers_final'] )446    tracks = s[0]447    header = s[1]448    scalarNames = header['scalar_name'].tolist()449    labels = {}450    # check if the segmentation is mapped451    try:452      seg_index = scalarNames.index( 'segmentation' )453    except:454      c.error( Colors.RED + 'Could not find ' + Colors.YELLOW + 'segmentation' + Colors.RED + ' as a mapped scalar but we really need it!' )455      sys.exit( 2 )456    # create the roi subfolder457    if not os.path.exists( outputs['roi'] ):458      os.mkdir( outputs['roi'] )459    # parse the color table460    lut = colortable.freesurfer.split( '\n' )461    colors = {}462    for color in lut:463      if not color or color[0] == '#':464        continue465      splitted_line = color.split( ' ' )466      splitted_line = filter( None, splitted_line )467      colors[splitted_line[0]] = splitted_line[1]468    # loop through tracks469    for i, t in enumerate( tracks ):470      tCoordinates = t[0]471      tScalars = t[1]472      # grab the scalars for each point473      for scalar in tScalars:474        # but only the label value475        label_value = str( int( scalar[seg_index] ) )476        if not label_value in labels:477          labels[label_value] = []478        if not i in labels[label_value]:479          # store the unique fiber id for this label480          labels[label_value].append( i )481    # now loop through all detected labels482    for l in labels:483      new_tracks = []484      for t_id in labels[l]:485        # grab the fiber + scalars486        current_fiber = tracks[t_id]487        new_tracks.append( current_fiber )488      # now store the trk file489      trk_outputfile = l + '_' + colors[l] + '.trk'490      nii_outputfile = l + '_' + colors[l] + '.nii'491      c.info( Colors.YELLOW + '  Creating fiber ROI ' + Colors.PURPLE + trk_outputfile + Colors.YELLOW + '!' + Colors._CLEAR )492      io.saveTrk( os.path.join( outputs['roi'], trk_outputfile ), new_tracks, header, None, True )493      # also create a roi label volume for this label value494      c.info( Colors.YELLOW + '  Creating NII ROI ' + Colors.PURPLE + nii_outputfile + Colors.YELLOW + '!' + Colors._CLEAR )495      cmd = 'ss;'496      cmd += 'chb-fsstable;'497      cmd += 'mri_binarize --i ' + outputs['segmentation'] + ' --o ' + os.path.join( outputs['roi'], nii_outputfile ) + ' --match ' + l + ' --binval ' + l + ';'498      self.__logger.debug( cmd )499      sp = subprocess.Popen( ["/bin/bash", "-i", "-c", cmd], stdout=sys.stdout )500      sp.communicate()501  def analyze_input_data( self, input_directory, inputs ):502    '''503    Scan an input directory for all kind of inputs. Connectome Pipeline output has 504    higher priority than Tractography Pipeline output since the Connectome pipeline 505    also includes the Tractography output.506    507    Returns a dictionary of found files.508    '''509    for root, dirs, files in os.walk( input_directory ):510      dirs.sort()511      for f in files:512        fullpath = os.path.join( root, f )513        # try to find the files514        for _f in inputs:515          # don't check if we already found this one516          if inputs[_f][-1] != None:517            continue518          for _mask in inputs[_f][:-1]:519            if fnmatch.fnmatch( fullpath, _mask ):520              # this matches our regex521              c.info( Colors.YELLOW + '  Found ' + Colors.PURPLE + f + Colors.YELLOW + '!' + Colors._CLEAR )522              self.__logger.debug( 'Full path: ' + fullpath )523              inputs[_f][-1] = fullpath524              #time.sleep( 1 )525              # don't consider any other option526              break527    return inputs528# ENTRYPOINT529if __name__ == "__main__":530  # 1) scan input directory531  # 2) preform preprocessing 532  # 3) perform mapping533  # 4) perform filtering534  # 5) create connectivity matrices535  parser = FNNDSCParser( description='fyborg - THE ULTIMATE SCALAR MAPPING FRAMEWORK FOR TRACKVIS (.TRK) FILES' )536  parser.add_argument( '-i', '--input', action='store', dest='input', required=True, help='The input folder which gets scanned automatically for usable volume- and track-files.' )537  parser.add_argument( '-o', '--output', action='store', dest='output', required=True, help='The output folder which gets created if it does not exit' )538  parser.add_argument( '-r', '--radius', action='store', dest='radius', default=3, type=int, help='The look-a-round radius in voxels. E.g. --radius 10, DEFAULT: 3' )539  parser.add_argument( '-l', '--length', action='store', dest='length', default="20 200", help='The lower and upper borders for length thresholding in mm. E.g. --length "60 100", DEFAULT "20 200" ' )540  parser.add_argument( '-co', '--cortex_only', action='store_true', dest='cortex_only', help='Perform filtering for cortex specific analysis and skip sub-cortical structures.' )541  parser.add_argument( '-s', '--stage', action='store', dest='stage', default=0, type=int, help='Start with a specific stage while skipping the ones before. E.g. --stage 3 directly starts the mapping without preprocessing, --stage 4 starts with the filtering' )542  parser.add_argument( '-overwrite', '--overwrite', action='store_true', dest='overwrite', help='Overwrite any existing output. DANGER!!' )543  parser.add_argument( '-v', '--verbose', action='store_true', dest='verbose', help='Show verbose output' )544  # always show the help if no arguments were specified545  if len( sys.argv ) == 1:546    parser.print_help()547    sys.exit( 1 )548  options = parser.parse_args()549  # validate the inputs here550  if not os.path.isdir( options.input ):551    c.error( Colors.RED + 'Could not find the input directory! Specify a valid directory using -i $PATH.' + Colors._CLEAR )552    sys.exit( 2 )553  if os.path.exists( options.output ) and int( options.stage ) == 0:554    if not options.overwrite:555      c.error( Colors.RED + 'The output directory exists! Add --overwrite to erase previous content!' + Colors._CLEAR )556      c.error( Colors.RED + 'Or use --stage > 2 to start with a specific stage which re-uses the previous content..' + Colors._CLEAR )557      sys.exit( 2 )558    else:559      # silently delete the existing output560      shutil.rmtree( options.output )561  if options.stage > 0 and not os.path.exists( options.output ):562    # we start with a specific stage so we need the output stuff563    c.error( Colors.RED + 'The output directory does not exist! We need it when using -s/--stage to resume the process!' + Colors._CLEAR )564    sys.exit( 2 )565  logic = FyborgLogic()...

test_protectclass.py

Source:test_protectclass.py

...16import unittest17class Test_protectName(unittest.TestCase):18    def setUp(self):19        from zope.security.checker import _clear20        _clear()21    def tearDown(self):22        from zope.security.checker import _clear23        _clear()24    def _callFUT(self, class_, name, permission):25        from zope.security.protectclass import protectName26        return protectName(class_, name, permission)27    def test_wo_existing_checker_w_zope_Public(self):28        from zope.security.checker import CheckerPublic29        from zope.security.checker import _checkers30        self._callFUT(Foo, 'bar', 'zope.Public')31        self.assertTrue(_checkers[Foo].get_permissions['bar'] is CheckerPublic)32    def test_w_existing_checker(self):33        from zope.security.checker import Checker34        from zope.security.checker import _checkers35        checker = _checkers[Foo] = Checker({})36        permission = object()37        self._callFUT(Foo, 'bar', permission)38        self.assertTrue(_checkers[Foo] is checker)39        self.assertTrue(checker.get_permissions['bar'] is permission)40class Test_protectSetAttribute(unittest.TestCase):41    def setUp(self):42        from zope.security.checker import _clear43        _clear()44    def tearDown(self):45        from zope.security.checker import _clear46        _clear()47    def _callFUT(self, class_, name, permission):48        from zope.security.protectclass import protectSetAttribute49        return protectSetAttribute(class_, name, permission)50    def test_wo_existing_checker_w_zope_Public(self):51        from zope.security.checker import CheckerPublic52        from zope.security.checker import _checkers53        self._callFUT(Foo, 'bar', 'zope.Public')54        self.assertTrue(_checkers[Foo].set_permissions['bar'] is CheckerPublic)55    def test_w_existing_checker(self):56        from zope.security.checker import Checker57        from zope.security.checker import _checkers58        checker = _checkers[Foo] = Checker({})59        permission = object()60        self._callFUT(Foo, 'bar', permission)61        self.assertTrue(_checkers[Foo] is checker)62        self.assertTrue(checker.set_permissions['bar'] is permission)63class Test_protectLikeUnto(unittest.TestCase):64    def setUp(self):65        from zope.security.checker import _clear66        _clear()67    def tearDown(self):68        from zope.security.checker import _clear69        _clear()70    def _callFUT(self, class_, like_unto):71        from zope.security.protectclass import protectLikeUnto72        return protectLikeUnto(class_, like_unto)73    def test_wo_existing_like_unto_checker(self):74        from zope.security.checker import _checkers75        self.assertFalse(Foo in _checkers)76        self._callFUT(Bar, Foo)77        self.assertFalse(Foo in _checkers)78        self.assertFalse(Bar in _checkers)79    def test_w_existing_like_unto_checker_wo_existing_checker(self):80        from zope.security.checker import Checker81        from zope.security.checker import CheckerPublic82        from zope.security.checker import defineChecker83        from zope.security.checker import _checkers...

test_logger.py

Source:test_logger.py

...47        with self.assertRaises(ValueError):48            CoreLog.debug("hey")49        CoreLog("debug")50        CoreLog.info("hey")51        CoreLog()._clear()52    def test_mylogger_verbose(self):53        """verbose setting54        """55        print()56        CoreLog("debug")57        CoreLog.verbose("hey")58        CoreLog()._clear()59    def test_mylogger_notime(self):60        """without time61        """62        print()63        CoreLog("debug", time=False)64        CoreLog.verbose("hey")65        CoreLog()._clear()66    def test_mylogger_noname(self):67        """without name68        """69        print()70        CoreLog("debug", name="")71        CoreLog.verbose("hey")72        CoreLog()._clear()73        CoreLog("debug", name=None)74        CoreLog.verbose("hey")75        CoreLog()._clear()76    def test_mylogger_noname_notime(self):77        """without time and name78        """79        print()80        CoreLog("debug", name="", time=False)81        CoreLog.verbose("hey")82        CoreLog()._clear()83    def test_mylogger_debug(self):84        """debug setting85        """86        print()87        CoreLog("debug")88        CoreLog.debug("hey")89        CoreLog.verbose("hey")90        CoreLog.info("hey")91        CoreLog.warning("hey")92        CoreLog.error("hey")93        CoreLog.critical("hey")94        CoreLog.fatal("hey")95        CoreLog()._clear()96    def test_mylogger_verbose(self):97        """debug setting98        """99        print()100        CoreLog("verbose")101        CoreLog.debug("hey")102        CoreLog.verbose("hey")103        CoreLog.info("hey")104        CoreLog.warning("hey")105        CoreLog.error("hey")106        CoreLog.critical("hey")107        CoreLog()._clear()108    def test_mylogger_info(self):109        """debug setting110        """111        print()112        CoreLog("info")113        CoreLog.debug("hey")114        CoreLog.verbose("hey")115        CoreLog.info("hey")116        CoreLog.warning("hey")117        CoreLog.error("hey")118        CoreLog.critical("hey")119        CoreLog()._clear()120    def test_mylogger_warning(self):121        """debug setting122        """123        print()124        CoreLog("warning")125        CoreLog.debug("hey")126        CoreLog.verbose("hey")127        CoreLog.info("hey")128        CoreLog.warning("hey")129        CoreLog.error("hey")130        CoreLog.critical("hey")131        CoreLog()._clear()132    def test_mylogger_error(self):133        """debug setting134        """135        print()136        CoreLog("error")137        CoreLog.debug("hey")138        CoreLog.verbose("hey")139        CoreLog.info("hey")140        CoreLog.warning("hey")141        CoreLog.error("hey")142        CoreLog.critical("hey")143        CoreLog()._clear()144    def test_mylogger_critical(self):145        """debug setting146        """147        print()148        CoreLog("critical")149        CoreLog.debug("hey")150        CoreLog.verbose("hey")151        CoreLog.info("hey")152        CoreLog.warning("hey")153        CoreLog.error("hey")154        CoreLog.critical("hey")155        CoreLog()._clear()156    def test_mylogger_quiet(self):157        """debug setting158        """159        print()160        CoreLog("quiet")161        CoreLog.debug("hey")162        CoreLog.verbose("hey")163        CoreLog.info("hey")164        CoreLog.warning("hey")165        CoreLog.error("hey")166        CoreLog.critical("hey")167        CoreLog()._clear()168    def test_mylogger_fatal(self):169        """debug setting170        """171        print()172        CoreLog("fatal")173        CoreLog.debug("hey")174        CoreLog.verbose("hey")175        CoreLog.info("hey")176        CoreLog.warning("hey")177        CoreLog.error("hey")178        CoreLog.critical("hey")179        CoreLog()._clear()180if __name__ == '__main__':...

Credentials.py

Source:Credentials.py

1#!/usr/bin/python2# coding:utf-83from Global import default4def _clear(number):5        result = []6        while number:7            result.append(chr(number % 128))8            number >>= 79        return ''.join(reversed(result))10def Credentials(auth_type='db', city=default['city']):    11    credentials = {'BJ': {}, 'WX': {}, 'XM': {}, 'LA': {}, 'DC': {}, 'KL': {}}12    credentials['BJ']['linux-simple'] = ('root', _clear(55599684644640946))13    credentials['BJ']['ple-tools-db'] = ('ple', _clear(675655278160864618085))14    credentials['BJ']['ldap'] = ('uid=root,cn=users,dc=xserver,dc=base-fx,dc=com', _clear(142739024786090804172849))15    credentials['BJ']['ad'] = ('cn=Administrator,cn=users,dc=ad,dc=base-fx,dc=com', _clear(938724368017542699568))16    credentials['BJ']['snmp'] = ('basenet')17    credentials['BJ']['localhost'] = ('root', _clear(55599684644640946))18    credentials['XM']['localhost'] = ('root', _clear(55599684644640946))19    credentials['WX']['localhost'] = ('root', _clear(55599684644640946))20    credentials['BJ']['switches'] = ('basefx', _clear(55599684644640946))21    credentials['qubedb'] = ('qube_admin',_clear(65753674419924920))22    credentials['BJ']['qube.base-fx.com'] = credentials['qubedb']23    credentials['BJ']['qube.bj.base-fx.com'] = credentials['qubedb']24    credentials['WX']['qube.wx.base-fx.com'] = credentials['qubedb']25    credentials['XM']['qube.xm.base-fx.com'] = credentials['qubedb']26    credentials['XM']['qube.kl.base-fx.com'] = credentials['qubedb']27    credentials['XM']['qube.dc.base-fx.com'] = credentials['qubedb']28    credentials['BJ']['xen-master.base-fx.com'] = ('itd', _clear(434545571551329))29    credentials['WX']['xen-master.base-fx.com'] = ('itd', _clear(434545571551329))30    credentials['XM']['xen-master.base-fx.com'] = ('itd', _clear(434545571551329))31    credentials['LA']['xen-master.base-fx.com'] = ('itd', _clear(434545571551329))32    credentials['DC']['xen-master.base-fx.com'] = ('itd', _clear(434545571551329))33    credentials['KL']['xen-master.base-fx.com'] = ('itd', _clear(434545571551329))34    credentials['BJ']['xen22.base-fx.com'] = ('itd', _clear(434545571551329))35    credentials['db'] = ('itd',_clear(63840988175379178))36    credentials['BJ']['db.base-fx.com'] = credentials['db']37    credentials['KL']['db.base-fx.com'] = credentials['db']38    credentials['DC']['db.base-fx.com'] = credentials['db']39    credentials['WX']['db.base-fx.com'] = credentials['db']40    credentials['XM']['db.base-fx.com'] = credentials['db']41    credentials['BJ']['dbd.base-fx.com'] = credentials['db']42    credentials['KL']['dbd.base-fx.com'] = credentials['db']43    credentials['DC']['dbd.base-fx.com'] = credentials['db']44    credentials['WX']['dbd.base-fx.com'] = credentials['db']45    credentials['XM']['dbd.base-fx.com'] = credentials['db']46    try:47        return credentials[city.upper()][auth_type]48    except:49        return credentials['BJ']['linux-simple']...

comment.py

Source:comment.py

...25        self.id = '{0}/{1}'.format(m.group('t').lower(), m.group('r'))26class RTNoMatch(Exception):27    """No Match Exception"""28    pass29def _clear(section, lineno=0):30    return section[lineno].lstrip('# ').rstrip('.')31def _pass(section, lineno=0):32    return section[lineno]33def check(section):34    """Parse and Dispatch Errors35    .. seealso:: The :py:mod:`rtkit.errors` module36    .. doctest::37        >>> check(['# Unknown object type: spam'])38        Traceback (most recent call last):39                ...40        RTUnknownTypeError: Unknown object type: spam41        >>> check(["# Invalid object specification: 'spam'"])42        Traceback (most recent call last):43                ......

_uploader.py

Source:_uploader.py

1#2# The XBUILD uploader.3#4# (c) 2012 The XTK Developers <dev@goXTK.com>5#6import os7import sys8import subprocess9import config10from _cdash import CDash11from _colors import Colors12#13#14#15class Uploader( object ):16  '''17  '''18  def run( self, options=None ):19    '''20    Performs the action.21    '''22    print 'Uploading results for ' + config.SOFTWARE_SHORT + '...'23    # check which submission type24    submissiontype = 'Experimental'25    if options.continuous:26      submissiontype = 'Continuous'27    elif options.nightly:28      submissiontype = 'Nightly'29    # now we create a dashboard submission file30    cdasher = CDash()31    #32    # build33    #34    print Colors.CYAN + 'Loading Build Report..' + Colors._CLEAR35    buildReport = os.path.join( config.TEMP_PATH, config.SOFTWARE_SHORT + '_Build.xml' )36    if os.path.isfile( buildReport ):37      # found a build report38      print Colors.ORANGE + 'Found Build Report!' + Colors._CLEAR39      with open( buildReport, 'r' ) as f:40        cdasher.submit( f.read(), submissiontype )41      print Colors.ORANGE + '..Successfully uploaded as ' + Colors.CYAN + submissiontype + Colors.ORANGE + '.' + Colors._CLEAR42    else:43      # not found44      print Colors.ORANGE + 'Not Found!' + Colors._CLEAR45      buildReport = None46    #47    # test48    #49    print Colors.CYAN + 'Loading Testing Report..' + Colors._CLEAR50    testReport = os.path.join( config.TEMP_PATH, config.SOFTWARE_SHORT + '_Test.xml' )51    if os.path.isfile( testReport ):52      # found a build report53      print Colors.ORANGE + 'Found Testing Report!' + Colors._CLEAR54      with open( testReport, 'r' ) as f:55        cdasher.submit( f.read(), submissiontype )56      print Colors.ORANGE + '..Successfully uploaded as ' + Colors.CYAN + submissiontype + Colors.ORANGE + '.' + Colors._CLEAR57    else:58      # not found59      print Colors.ORANGE + 'Not Found!' + Colors._CLEAR60      testReport = None61    #62    # coverage summary63    # 64    print Colors.CYAN + 'Loading Coverage Summary..' + Colors._CLEAR65    coverageReport = os.path.join( config.TEMP_PATH, config.SOFTWARE_SHORT + '_Coverage.xml' )66    if os.path.isfile( coverageReport ):67      # found a build report68      print Colors.ORANGE + 'Found Coverage Summary!' + Colors._CLEAR69      with open( coverageReport, 'r' ) as f:70        cdasher.submit( f.read(), submissiontype )71      print Colors.ORANGE + '..Successfully uploaded as ' + Colors.CYAN + submissiontype + Colors.ORANGE + '.' + Colors._CLEAR72    else:73      # not found74      print Colors.ORANGE + 'Not Found!' + Colors._CLEAR75      coverageReport = None76    #77    # coverage log78    # 79    print Colors.CYAN + 'Loading Coverage Log..' + Colors._CLEAR80    coverageLog = os.path.join( config.TEMP_PATH, config.SOFTWARE_SHORT + '_CoverageLog.xml' )81    if os.path.isfile( coverageLog ):82      # found a build report83      print Colors.ORANGE + 'Found Coverage Log!' + Colors._CLEAR84      with open( coverageLog, 'r' ) as f:85        cdasher.submit( f.read(), submissiontype )86      print Colors.ORANGE + '..Successfully uploaded as ' + Colors.CYAN + submissiontype + Colors.ORANGE + '.' + Colors._CLEAR87    else:88      # not found89      print Colors.ORANGE + 'Not Found!' + Colors._CLEAR90      coverageLog = None91    # delete old reports92    if buildReport:93      os.unlink( buildReport )94    if testReport:95      os.unlink( testReport )96    if coverageReport:97      os.unlink( coverageReport )98    if coverageLog:...

test.py

Source:test.py

1#!/usr/bin/env python2import subprocess, time3import _test_functions as tf4from time import time, gmtime, strftime, sleep5# import the xbuild system6import sys7sys.path.append( './xbuild/' )8from _core import *9TESTS = ['test_mapping', 'test_mapping_2_2_2', 'test_mapping_real', 'test_mapping_neighbors', 'test_mapping_neighbors_real', 'test_mapping_real_outside_vol']10# ENTRYPOINT11if __name__ == "__main__":12  print 'Testing now...'13  print14  sleep( 1 )15  results = []16  for t in TESTS:17    for tool in ['_fyborg.py', '_matlab.py']:18      fullname = t + tool19      command = './' + fullname20      log = ''21      status = 'failed'22      start_time = time()23      process = subprocess.Popen( command, bufsize=0, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )24      for line in process.stdout:25        line = line.strip( '\n' )26        if line.find( 'ALL OK' ) != -1:27          # test ran through28          status = 'passed'29        log += line + '\n'30        print line31      end_time = time()32      execution_time = end_time - start_time33      # we need to also strip the bell and backspace chars from matlab errors34      results.append( [fullname, status, tf.Colors.strip( log.replace( '\a', '' ).replace( '\b', '' ) ) , execution_time, None, None] )35  print36  print37  print 'All done!!'38  print39  print tf.Colors.PURPLE + '================================' + tf.Colors._CLEAR40  print tf.Colors.ORANGE + '         R E S U L T S' + tf.Colors._CLEAR41  print tf.Colors.PURPLE + '================================' + tf.Colors._CLEAR42  for r in results:43    if r[1] == 'passed':44      result = tf.Colors.GREEN + 'PASSED'45    else:46      result = tf.Colors.RED + 'FAILED'47    print tf.Colors.CYAN + 'Test: ' + tf.Colors.PURPLE + r[0] + ' ' + result48  print49  # now we create a dashboard submission file50  cdasher = CDash()51  xmlfile = cdasher.run( ['Testing', results] )52  with open( os.path.join( config.TEMP_PATH, config.SOFTWARE_SHORT + '_Test.xml' ), 'w' ) as f:53    f.write( xmlfile )54  print tf.Colors.PURPLE + 'Uploading to CDash..' + tf.Colors._CLEAR55  # check which submission type56  submissiontype = 'Experimental'57  if len( sys.argv ) > 1 and sys.argv[1] == '-n':58    submissiontype = 'Nightly'59  print Colors.CYAN + 'Loading Testing Report..' + Colors._CLEAR60  testReport = os.path.join( config.TEMP_PATH, config.SOFTWARE_SHORT + '_Test.xml' )61  if os.path.isfile( testReport ):62    # found a build report63    print Colors.ORANGE + 'Found Testing Report!' + Colors._CLEAR64    with open( testReport, 'r' ) as f:65      cdasher.submit( f.read(), submissiontype )66    print Colors.ORANGE + '..Successfully uploaded as ' + Colors.CYAN + submissiontype + Colors.ORANGE + '.' + Colors._CLEAR67  else:68    # not found69    print Colors.ORANGE + 'Not Found!' + Colors._CLEAR70    testReport = None71  if testReport:...

_depsgenerator.py

Source:_depsgenerator.py

1#2# The XBUILD depenceny generator.3#4# (c) 2012 The XTK Developers <dev@goXTK.com>5#6import os7import sys8import subprocess9import config10from _cdash import CDash11from _colors import Colors12from _jsfilefinder import JSFileFinder13#14#15#16class DepsGenerator( object ):17  '''18  '''19  def run( self, options=None ):20    '''21    Performs the action.22    '''23    print 'Generating dependency file for ' + config.SOFTWARE_SHORT + '...'24    # grab all js files25    filefinder = JSFileFinder()26    jsfiles = filefinder.run( ['USE_INCLUDES'] )27    arguments = []28    # closure base path29    basepath = os.path.dirname( os.path.dirname( config.CLOSUREDEPSWRITER_PATH ) )30    # set the output file31    arguments.extend( ['--output_file=' + config.DEPS_OUTPUT_PATH] )32    # add js files33    for j in jsfiles:34      arguments.extend( ['--path_with_depspath=' + j + ' ' + os.path.relpath( j, basepath )] )35    #36    # call the closure depswriter37    #38    command = [config.CLOSUREDEPSWRITER_PATH]39    command.extend( arguments )40    process = subprocess.Popen( command, bufsize=0, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )41    # no output is good42    noOutput = True43    # print any output in red since it probably indicates an error44    for line in process.stdout:45      line = line.strip( '\n' )46      print Colors.RED + line + Colors._CLEAR47      noOutput = False48    if noOutput:49      # all good and done50      print Colors.ORANGE + 'Dependency file ' + Colors.PURPLE + config.DEPS_OUTPUT_PATH + Colors.ORANGE + ' generated. ' + Colors._CLEAR51      print Colors.ORANGE + 'Usage:' + Colors._CLEAR52      print Colors.CYAN + '  <script type="text/javascript" src="' + os.path.relpath( config.CLOSUREGOOGBASE_PATH, os.path.join( config.SOFTWARE_PATH, '../' ) ) + '"></script>' + Colors._CLEAR53      print Colors.CYAN + '  <script type="text/javascript" src="' + os.path.relpath( config.DEPS_OUTPUT_PATH, os.path.join( config.SOFTWARE_PATH, '../' ) ) + '"></script>' + Colors._CLEAR54    else:55      # maybe an error...

Using AI Code Generation

1const { openBrowser, goto, closeBrowser, _clear } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await goto("google.com");6        await _clear("Search");7    } catch (e) {8        console.error(e);9    } finally {10        await closeBrowser();11    }12})();13### _clear(options)14const { openBrowser, goto, closeBrowser, _clear } = require('taiko');15(async () => {16    try {17        await openBrowser();18        await goto("google.com");19        await _clear({id: "lst-ib"});20    } catch (e) {21        console.error(e);22    } finally {23        await closeBrowser();24    }25})();26### _close()27const { openBrowser, goto, closeBrowser, _close } = require('taiko');28(async () => {29    try {30        await openBrowser();31        await goto("google.com");32        await _close();33    } catch (e) {34        console.error(e);35    } finally {36        await closeBrowser();37    }38})();39### _click()40const { openBrowser, goto, closeBrowser, _click } = require('taiko');41(async () => {42    try {43        await openBrowser();44        await goto("google.com");45        await _click("Search");46    } catch (e) {47        console.error(e);48    } finally {49        await closeBrowser();50    }51})();52### _click(options)53const { openBrowser, goto, closeBrowser, _click } = require('taiko');54(async () => {55    try {56        await openBrowser();

Using AI Code Generation

1const { openBrowser, goto, button, closeBrowser } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await goto("google.com");6        await button("I'm Feeling Lucky").click();7        await button("I'm Feeling Lucky")._clear();8    } catch (e) {9        console.error(e);10    } finally {11        await closeBrowser();12    }13})();

Using AI Code Generation

1const { openBrowser, goto, _clear, textBox, write, closeBrowser } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await write("Taiko", into(textBox("Search")));6        await _clear(textBox("Search"));7        await write("Taiko", into(textBox("Search")));8    } catch (error) {9        console.error(error);10    } finally {11        await closeBrowser();12    }13})();14_setCookie(cookieData);15const { openBrowser, goto, _setCookie, closeBrowser } = require('taiko');16(async () => {17    try {18        await openBrowser();19        await _setCookie({name: 'cookie_name', value: 'cookie_value', domain: 'google.com', path: '/', expires: (new Date()).getTime() + (1000 * 60 * 60)});20    } catch (error) {21        console.error(error);22    } finally {23        await closeBrowser();24    }25})();26_deleteCookie(name, domain, path);27const { openBrowser, goto, _deleteCookie, closeBrowser } = require('taiko');28(async () => {29    try {30        await openBrowser();31        await _deleteCookie('cookie_name', 'google.com', '/');32    } catch (error) {

Using AI Code Generation

1const { openBrowser, goto, closeBrowser, _clear } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await _clear("Search");6    } catch (e) {7        console.error(e);8    } finally {9        await closeBrowser();10    }11})();12const { openBrowser, goto, closeBrowser, _click, _text } = require('taiko');13(async () => {14    try {15        await openBrowser();16        await _click(_text("Search"));17    } catch (e) {18        console.error(e);19    } finally {20        await closeBrowser();21    }22})();23const { openBrowser, goto, closeBrowser, _closeTab } = require('taiko');24(async () => {25    try {26        await openBrowser();27        await _closeTab();28    } catch (e) {29        console.error(e);30    } finally {31        await closeBrowser();32    }33})();34const { openBrowser, goto, closeBrowser, _doubleClick, _text } = require('taiko');35(async () => {36    try {37        await openBrowser();38        await _doubleClick(_text("Search"));39    } catch (e) {40        console.error(e);41    } finally {42        await closeBrowser();43    }44})();45const { openBrowser, goto, closeBrowser, _dragAndDrop, _text } = require('taiko');46(async () => {47    try {48        await openBrowser();

Using AI Code Generation

1const { openBrowser, goto, write, closeBrowser, _clear } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await write("Hello World");6        await _clear();7        await closeBrowser();8    } catch (e) {9        console.error(e);10    } finally {11    }12})();

Using AI Code Generation

1const { openBrowser, goto, _clear, write, closeBrowser, textBox } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await goto("google.com");6        await write("Taiko", into(textBox({"id":"lst-ib"})));7        await _clear(textBox({"id":"lst-ib"}));8    } catch (e) {9        console.error(e);10    } finally {11        await closeBrowser();12    }13})();14-   `element` **[ElementWrapper](#elementwrapper)** 15const { openBrowser, goto, _click, link, closeBrowser } = require('taiko');16(async () => {17    try {18        await openBrowser();19        await goto("google.com");20        await _click(link("Gmail"));21    } catch (e) {22        console.error(e);23    } finally {24        await closeBrowser();25    }26})();27const { openBrowser, goto, _closeBrowser } = require('taiko');28(async () => {29    try {30        await openBrowser();31        await goto("google.com");32        await _closeBrowser();33    } catch (e) {34        console.error(e);35    }36})();37const { openBrowser, goto, _count, link, closeBrowser } = require('taiko');38(async () => {39    try {40        await openBrowser();41        await goto("google.com");42        let count = await _count(link());43        console.log(count);44    } catch (e) {45        console.error(e);46    } finally {47        await closeBrowser();48    }49})();

Using AI Code Generation

1const { openBrowser, goto, textBox, _clear, closeBrowser } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await goto("google.com");6        await textBox().type("hello world");7        await _clear(textBox());8        await textBox().type("hello world");9    } catch (e) {10        console.error(e);11    } finally {12        await closeBrowser();13    }14})();15const { openBrowser, goto, _getBrowserInfo, closeBrowser } = require('taiko');16(async () => {17    try {18        await openBrowser();19        await goto("google.com");20        let info = await _getBrowserInfo();21        console.log(info);22    } catch (e) {23        console.error(e);24    } finally {25        await closeBrowser();26    }27})();28const { openBrowser, goto, _getElements, closeBrowser } = require('taiko');29(async () => {30    try {31        await openBrowser();32        await goto("google.com");33        let elements = await _getElements("input[type='text']");34        console.log(elements);35    } catch (e) {36        console.error(e);37    } finally {38        await closeBrowser();39    }40})();41const { openBrowser, goto, _getPlugins, closeBrowser } = require('taiko');42(async () => {43    try {44        await openBrowser();45        await goto("google.com");46        let plugins = await _getPlugins();47        console.log(plugins);48    } catch (e) {49        console.error(e);50    } finally {51        await closeBrowser();52    }53})();54const { openBrowser, goto, _getCookies, closeBrowser } = require('taiko');

Using AI Code Generation

1(async () => {2    try {3        await openBrowser({headless:false});4        await goto("google.com");5        await write("Taiko");6        await press("Enter");7        await click("Taiko - Google Search");8        await _clear();9    } catch (e) {10        console.error(e);11    } finally {12        await closeBrowser();13    }14})();

Using AI Code Generation

1const { openBrowser, closeBrowser, goto, click, button, _clear, write, text, link, image, toRightOf, toLeftOf, below } = require('taiko');2(async () => {3    try {4        await openBrowser();5        await _clear(textBox(toRightOf("Google Search")));6        await write("Taiko", into(textBox(toRightOf("Google Search"))));7        await click("Google Search");8        await click(link("Taiko - The Browser Automation Framework", below(image("Taiko - The Browser Automation Framework"))));9        await click("Docs");10        await click("API");11        await click("clear");12        await click("clear");13        await click("clear");

Using AI Code Generation

1await _clear();2await closeBrowser();3await closeTab();4await count({ id: 'myId' });5await currentURL();6await $(link('Click me'));7await $$(link('Click me'));8await dragAndDrop($('[id="drag"]'), { x: 100, y: 100 });9await evaluate(() => {10    return document.title;11});12await focus(textBox('Enter your name'));

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.