def gen_qsub_jobs(neuron_distance_csv, input_dir, output_dir):
df_nd = pd.read_csv(neuron_distance_csv)
images = np.unique( df_nd['image_file_name'])
QMasterV3D = "/data/mat/xiaoxiaol/work/bin/bin_vaa3d_for_clusters/vaa3d"
dfg = df_nd.groupby('image_file_name')
os.system('rm '+data_DIR+'/qsub/*.qsub')
os.system('rm '+data_DIR+'/qsub/*.o*')
#os.system('mkdir ./qsubs')
count = 0
for im in images:
df_image = dfg.get_group(im)
df_image = df_image.sort(['neuron_distance'])
tmp = df_image.iloc[0]['swc_file']
im_id = tmp.split('/')[-2] # 2.v3dpbd
out_dir = output_dir + '/' + im_id.split('.')[0]
input_dir = out_dir
output_eswc_path = out_dir+'/consensus3.eswc'
output_distance_csv = out_dir+"/median_distances3.csv"
if os.path.exists(output_distance_csv):
continue
logfile = output_eswc_path+".log"
line1 = QMasterV3D+" -x consensus_swc -f consensus_swc -i " + input_dir +"/processed/*.swc -o " + output_eswc_path + " -p 3 5 1 > "+logfile
#image_file = image_DIR+ '/'+ im[:-7]+'/'+im
logfile= out_dir+"/median_distances3.csv.log"
line2 = QMasterV3D+" -x consensus_swc -f median_swc -i "+ output_eswc_path +"_SelectedNeurons.ano "+ output_eswc_path +" -o "+ output_distance_csv+" > "+logfile
gold_swc = df_image.iloc[0]['gold_swc_file']
gold_swc = out_dir+'/00_'+gold_swc.split('/')[-1]
distance_log_file = output_eswc_path+".weighted.dist3.log"
# if os.path.exists(distance_log_file):
# continue
line3 = QMasterV3D+" -x neuron_weighted_distance -f neuron_weighted_distance -i "+ output_eswc_path +" "+ gold_swc +" -o "+distance_log_file
lines = line1+";"+line2+";"+line3
#lines = line3
print lines
bn.run_command_lines(lines, 1,data_DIR+"/qsub", count)
count = count +1
return
def gen_qsub_jobs(neuron_distance_csv, input_dir, output_dir):
df_nd = pd.read_csv(neuron_distance_csv)
images = np.unique( df_nd['image_file_name'])
QMasterV3D = "/data/mat/xiaoxiaol/work/bin/bin_vaa3d_for_clusters/vaa3d"
dfg = df_nd.groupby('image_file_name')
os.system('rm -r ./qsubs')
os.system('mkdir ./qsubs')
count = 0
for im in images:
df_image = dfg.get_group(im)
df_image = df_image.sort(['neuron_distance'])
tmp = df_image.iloc[0]['swc_file']
im_id = tmp.split('/')[-2] # 2.v3dpbd
out_dir = output_dir + '/' + im_id.split('.')[0]
input_dir = out_dir
output_eswc_path = out_dir+'/consensus.eswc'
output_distance_csv = out_dir+"/median_distances.csv"
# if os.path.exists(output_distance_csv):
# continue
gold_swc = df_image.iloc[0]['gold_swc_file']
gold_swc = out_dir+'/00_'+gold_swc.split('/')[-1]
distance_log_file = output_eswc_path+".weighted.dist.log"
line = "java -jar /data/mat/xiaoxiaol/data/big_neuron/DiademMetric/DiademMetric.jar -G "+ gold_swc +" -T "+ output_eswc_path +" -D 5 -m true -o "+distance_log_file
#java -jar DiademMetric.jar -G ./Xiao_Xiao_test1_sn.swc -T ./test.swc -D 5 -m true
lines = line1+";"+line2+";"+line3
bn.run_command_lines(lines, 1,"./qsubs", count)
count = count +1
return
def gen_qsub_jobs(neuron_distance_csv, input_dir, output_dir):
df_nd = pd.read_csv(neuron_distance_csv)
images = np.unique(df_nd['image_file_name'])
QMasterV3D = "/data/mat/xiaoxiaol/work/bin/bin_vaa3d_for_clusters/vaa3d"
dfg = df_nd.groupby('image_file_name')
os.system('rm -r ./qsubs')
os.system('mkdir ./qsubs')
count = 0
for im in images:
df_image = dfg.get_group(im)
df_image = df_image.sort(['neuron_distance'])
tmp = df_image.iloc[0]['swc_file']
im_id = tmp.split('/')[-2] # 2.v3dpbd
out_dir = output_dir + '/' + im_id.split('.')[0]
input_dir = out_dir
output_eswc_path = out_dir + '/consensus.eswc'
output_distance_csv = out_dir + "/median_distances.csv"
# if os.path.exists(output_distance_csv):
# continue
gold_swc = df_image.iloc[0]['gold_swc_file']
gold_swc = out_dir + '/00_' + gold_swc.split('/')[-1]
distance_log_file = output_eswc_path + ".weighted.dist.log"
line = "java -jar /data/mat/xiaoxiaol/data/big_neuron/DiademMetric/DiademMetric.jar -G " + gold_swc + " -T " + output_eswc_path + " -D 5 -m true -o " + distance_log_file
#java -jar DiademMetric.jar -G ./Xiao_Xiao_test1_sn.swc -T ./test.swc -D 5 -m true
lines = line1 + ";" + line2 + ";" + line3
bn.run_command_lines(lines, 1, "./qsubs", count)
count = count + 1
return
