if haveGFP == 1:
TEMP_FILE.write('-GFP_Image '+FILE_GFP_BS_CV_RE_bit+'\n')
if haveDAP == 1:
TEMP_FILE.write('-DAP_Image '+FILE_DAP_BS_RE_bit+'\n')
TEMP_FILE.write('-isSmall '+SMALLIMAGE+'\n')
TEMP_FILE.write('-segParams '+LOCAL_DATASET_PATH_PARAMETERS+'/Seg_Params.ini'+'\n')
TEMP_FILE.write('-projectDefinition '+LOCAL_DATASET_PATH_PARAMETERS+'/ProjectDefinition.xml'+'\n')
TEMP_FILE.write('-optionsMNT '+LOCAL_DATASET_PATH_PARAMETERS+'/options_mnt'+'\n')
TEMP_FILE.write('-outPath '+LOCAL_DATASET_PATH_SEGM+'\n')
TEMP_FILE.write('-outPathDebug '+LOCAL_DATASET_PATH_SEGM_DEBUG+'\n')
TEMP_FILE.write('-outPathDebugLevel2 '+LOCAL_DATASET_PATH_SEGM_DEBUG_L2+'\n')
TEMP_FILE.write('-outPathTemp '+LOCAL_DATASET_PATH_SEGM_TEMP+'\n')
TEMP_FILE.close()
#FILE_Cy5_BS_RE_bit = FILE_Cy5_BS+'_RE_bit'
a060_RunSegmentation.main( FILE_GFP_BS_CV_RE_bit, FARSIGHT_BIN_EXE, optionsSegm, runSegm_log )
shutil.rmtree(LOCAL_DATASET_PATH_SEGM_TEMP)
elapsed_1 = (time.clock() - start_1)
print "\t\tTime_1: "+str(elapsed_1)
if runSegm_db == 1:
start_2 = time.clock()
runSegm_db_log = LOCAL_DATASET_PATH_LOG +'/runSegm_db.log'
TEMP_FILE = open(runSegm_db_log, 'w')
TEMP_FILE.write('SegmentLog\n')
TEMP_FILE.close()
a021_Project.main( LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE, LOCAL_DATASET_PATH_SEGM_DEBUG, FILE_GFP_BS_CV_RE_bit+'_soma', runSegm_db_log, 'ORG_RES_BIN' )
a021_Project.main( LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE, LOCAL_DATASET_PATH_SEGM_DEBUG, FILE_GFP_BS_CV_RE_bit+'_label', runSegm_db_log, 'ORG_RES_BIN' )
a023_ProjectRGB.main( LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE, LOCAL_DATASET_PATH_SEGM_DEBUG, FILE_GFP_BS_CV_RE_bit, FILE_GFP_BS_CV_RE_bit+'_soma', '_GFP_SOMA_', runSegm_db_log )
a023_ProjectRGB.main( LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE, LOCAL_DATASET_PATH_SEGM_DEBUG, FILE_DAP_BS_RE_bit, FILE_GFP_BS_CV_RE_bit+'_label', '_DAPI_LABEL_', runSegm_db_log )
TEMP_FILE.write('-segParams ' + LOCAL_DATASET_PATH_PARAMETERS +
'/Seg_Params.ini' + '\n')
TEMP_FILE.write('-projectDefinition ' + LOCAL_DATASET_PATH_PARAMETERS +
'/ProjectDefinition.xml' + '\n')
TEMP_FILE.write('-optionsMNT ' + LOCAL_DATASET_PATH_PARAMETERS +
'/options_mnt' + '\n')
TEMP_FILE.write('-outPath ' + LOCAL_DATASET_PATH_SEGM + '\n')
TEMP_FILE.write('-outPathDebug ' + LOCAL_DATASET_PATH_SEGM_DEBUG +
'\n')
TEMP_FILE.write('-outPathDebugLevel2 ' +
LOCAL_DATASET_PATH_SEGM_DEBUG_L2 + '\n')
TEMP_FILE.write('-outPathTemp ' + LOCAL_DATASET_PATH_SEGM_TEMP + '\n')
TEMP_FILE.close()
#FILE_Cy5_BS_RE_bit = FILE_Cy5_BS+'_RE_bit'
a060_RunSegmentation.main(FILE_GFP_BS_CV_RE_bit, FARSIGHT_BIN_EXE,
optionsSegm, runSegm_log)
shutil.rmtree(LOCAL_DATASET_PATH_SEGM_TEMP)
elapsed_1 = (time.clock() - start_1)
print "\t\tTime_1: " + str(elapsed_1)
if runSegm_db == 1:
start_2 = time.clock()
runSegm_db_log = LOCAL_DATASET_PATH_LOG + '/runSegm_db.log'
TEMP_FILE = open(runSegm_db_log, 'w')
TEMP_FILE.write('SegmentLog\n')
TEMP_FILE.close()
a021_Project.main(LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE,
LOCAL_DATASET_PATH_SEGM_DEBUG,
FILE_GFP_BS_CV_RE_bit + '_soma', runSegm_db_log,
'ORG_RES_BIN')
if haveDAP == 1:
TEMP_FILE.write('-DAP_Image '+FILE_DAP_BS_RE_bit+'\n')
TEMP_FILE.write('-isSmall '+SMALLIMAGE+'\n')
TEMP_FILE.write('-segParams '+LOCAL_DATASET_PATH_PARAMETERS+'/Seg_Params.ini'+'\n')
TEMP_FILE.write('-projectDefinition '+LOCAL_DATASET_PATH_PARAMETERS+'/ProjectDefinition.xml'+'\n')
TEMP_FILE.write('-optionsMNT '+LOCAL_DATASET_PATH_PARAMETERS+'/options_mnt'+'\n')
TEMP_FILE.write('-outPath '+LOCAL_DATASET_PATH_SEGM+'\n')
TEMP_FILE.write('-outPathDebug '+LOCAL_DATASET_PATH_SEGM_DEBUG+'\n')
TEMP_FILE.write('-outPathDebugLevel2 '+LOCAL_DATASET_PATH_SEGM_DEBUG_L2+'\n')
TEMP_FILE.write('-outPathTemp '+LOCAL_DATASET_PATH_SEGM_TEMP+'\n')
TEMP_FILE.write('-outPathData '+LOCAL_DATASET_PATH_DATA+'\n')
TEMP_FILE.close()
#FILE_Cy5_BS_RE_bit = FILE_Cy5_BS+'_RE_bit'
a060_RunSegmentation.main( FILE_GFP_BS_CV_RE_bit, FARSIGHT_BIN_EXE, optionsSegm, runSegm_log, LOCAL_DATASET_PATH_DATA )
elapsed_1 = (time.time() - start_1)
print "\t\tTime_1: hm: "+str(round(elapsed_1/3600))+":"+str(round(elapsed_1/60))
FILE_LABEL = LOCAL_DATASET_PATH_DATA+'\label'
FILE_SOMA = LOCAL_DATASET_PATH_DATA+'\soma'
FILE_SOMA_CEN = LOCAL_DATASET_PATH_DATA+'\soma_centrois.txt'
if( REMOVE_TEMP_SEGM == 1 ):
shutil.rmtree(LOCAL_DATASET_PATH_SEGM_TEMP)
#os.makedirs(LOCAL_DATASET_PATH_SEGM_TEMP)
if runSegm_db == 1:
start_2 = time.time()
runSegm_db_log = LOCAL_DATASET_PATH_LOG +'/runSegm_db.log'
TEMP_FILE = open(runSegm_db_log, 'w')