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