TEMP_FILE.write('-Soma_Centroids ' + FILE_GFP_BS_CV_RE_bit +
'_soma_table_centroids.txt' + '\n')
TEMP_FILE.write('-Soma_Montage ' + FILE_GFP_BS_CV_RE_bit + '_soma' +
'\n')
TEMP_FILE.write('-isSmall ' + SMALLIMAGE + '\n')
TEMP_FILE.write('-traceParams ' + LOCAL_DATASET_PATH_PARAMETERS +
'/options_mnt' + '\n')
TEMP_FILE.write('-outPath ' + LOCAL_DATASET_PATH_TRAC_RESULTS + '\n')
TEMP_FILE.write('-outPathDebug ' + LOCAL_DATASET_PATH_TRAC_DEBUG +
'\n')
TEMP_FILE.write('-outPathDebugLevel2 ' +
LOCAL_DATASET_PATH_TRAC_DEBUG_L2 + '\n')
TEMP_FILE.write('-outPathTemp ' + LOCAL_DATASET_PATH_TRAC_TEMP + '\n')
TEMP_FILE.close()
a070_RunTracing.main(FILE_GFP_BS_CV_RE, FARSIGHT_BIN_EXE,
optionsTracing, runTrac_log)
elapsed_1 = (time.clock() - start_1)
print "\t\tTime_1: " + str(elapsed_1)
if (REMOVE_TEMP_TRAC == 1):
shutil.rmtree(LOCAL_DATASET_PATH_TRAC_TEMP)
if runTrac_db == 1:
start_2 = time.clock()
runTrac_db_log = LOCAL_DATASET_PATH_LOG + '/runTrac_db.log'
TEMP_FILE = open(runTrac_db_log, 'w')
TEMP_FILE.write('TracingLog\n')
TEMP_FILE.close()
# Trace editor projection
a024_ProjectFloat.main(LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE,
TEMP_FILE.write('-TRI_Image '+FILE_TRI_BS_RE_bit+'\n')
if haveGFP == 1:
TEMP_FILE.write('-GFP_Image '+FILE_GFP_BS_CV+'\n')
if haveDAP == 1:
TEMP_FILE.write('-DAP_Image '+FILE_DAP_BS_RE_bit+'\n')
TEMP_FILE.write('-Soma_Centroids '+LOCAL_DATASET_PATH_DATA+'/soma_table_centroids.txt'+'\n')
TEMP_FILE.write('-Soma_Montage '+LOCAL_DATASET_PATH_DATA+'/soma'+'\n')
TEMP_FILE.write('-isSmall '+SMALLIMAGE+'\n')
TEMP_FILE.write('-traceParams '+LOCAL_DATASET_PATH_PARAMETERS+'/options_mnt'+'\n')
TEMP_FILE.write('-outPath '+LOCAL_DATASET_PATH_TRAC_RESULTS+'\n')
TEMP_FILE.write('-outPathDebug '+LOCAL_DATASET_PATH_TRAC_DEBUG+'\n')
TEMP_FILE.write('-outPathDebugLevel2 '+LOCAL_DATASET_PATH_TRAC_DEBUG_L2+'\n')
TEMP_FILE.write('-outPathTemp '+LOCAL_DATASET_PATH_TRAC_TEMP+'\n')
TEMP_FILE.close()
a070_RunTracing.main( FARSIGHT_BIN_EXE, optionsTracing, runTrac_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))
if runTrac_db == 1:
start_2 = time.time()
runTrac_db_log = LOCAL_DATASET_PATH_LOG +'/runTrac_db.log'
TEMP_FILE = open(runTrac_db_log, 'w')
TEMP_FILE.write('TracingLog\n')
TEMP_FILE.close()
# Trace editor projection
a024_ProjectFloat.main( LOCAL_DATASET_PATH_LOG, FARSIGHT_BIN_EXE, LOCAL_DATASET_PATH_TRAC_DEBUG, LOCAL_DATASET_PATH_TRAC_TEMP+'/GFP_MNT_PRE', runTrac_db_log, 'ORG', 'NRRD' )
#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("-TRI_Image " + FILE_TRI_BS_RE_bit + "\n")
if haveGFP == 1:
TEMP_FILE.write("-GFP_Image " + FILE_GFP_BS_CV_RE + "\n")
if haveDAP == 1:
TEMP_FILE.write("-DAP_Image " + FILE_DAP_BS_RE_bit + "\n")
TEMP_FILE.write("-Soma_Centroids " + FILE_GFP_BS_CV_RE_bit + "_soma_table_centroids.txt" + "\n")
TEMP_FILE.write("-Soma_Montage " + FILE_GFP_BS_CV_RE_bit + "_soma" + "\n")
TEMP_FILE.write("-isSmall " + SMALLIMAGE + "\n")
TEMP_FILE.write("-traceParams " + LOCAL_DATASET_PATH_PARAMETERS + "/options_mnt" + "\n")
TEMP_FILE.write("-outPath " + LOCAL_DATASET_PATH_TRAC_RESULTS + "\n")
TEMP_FILE.write("-outPathDebug " + LOCAL_DATASET_PATH_TRAC_DEBUG + "\n")
TEMP_FILE.write("-outPathDebugLevel2 " + LOCAL_DATASET_PATH_TRAC_DEBUG_L2 + "\n")
TEMP_FILE.write("-outPathTemp " + LOCAL_DATASET_PATH_TRAC_TEMP + "\n")
TEMP_FILE.close()
a070_RunTracing.main(FILE_GFP_BS_CV_RE, FARSIGHT_BIN_EXE, optionsTracing, runTrac_log)
elapsed_1 = time.clock() - start_1
print "\t\tTime_1: " + str(elapsed_1)
if REMOVE_TEMP_TRAC == 1:
shutil.rmtree(LOCAL_DATASET_PATH_TRAC_TEMP)
if runTrac_db == 1:
start_2 = time.clock()
runTrac_db_log = LOCAL_DATASET_PATH_LOG + "/runTrac_db.log"
TEMP_FILE = open(runTrac_db_log, "w")
TEMP_FILE.write("TracingLog\n")
TEMP_FILE.close()
# Trace editor projection
a024_ProjectFloat.main(
