def copyBySpecimenId(df): ids = df['specimen__id'] for i in range(len(ids)): swc_filename, swc_path = lu.get_swc_from_lims(str(ids[i])) cmd = 'cp ' + swc_path + ' ' + save_data_dir + '/' print cmd os.system(cmd)
def copyBySpecimenId(df): ids = df['specimen__id'] for i in range(len(ids)): swc_filename, swc_path = lu.get_swc_from_lims(str(ids[i])) cmd = 'cp '+swc_path +' '+ save_data_dir+'/' print cmd os.system(cmd)
parser.add_argument("-p", dest="plot", action="store_true") parser.add_argument("-o", dest="outputDir", default="./result") parser.add_argument("-i", "-local_path", dest="local_path", default=None) args = parser.parse_args() outputDir = args.outputDir up_data = np.loadtxt(outputDir + "/data/" + args.specimen_id + "_upbase.dat") down_data = np.loadtxt(outputDir + "/data/" + args.specimen_id + "_downbase.dat") specimen_id = args.specimen_id specimen_name, ephys_roi_result_id = lims_orca_utils.get_ephys_id_from_lims(args.specimen_id) # specimen_name, ephys_roi_result_id, specimen_id = get_specimen_info_from_lims(args.specimen_id) swc_filename, swc_path = lims_orca_utils.get_swc_from_lims(specimen_id) local_path = args.local_path if local_path: swc_path = local_path + "/" + swc_filename print "using:", swc_path h.load_file("stdgui.hoc") h.load_file("import3d.hoc") load_morphology(swc_path) for sec in h.allsec(): sec.insert("pas") for seg in sec: seg.pas.e = 0
args = parser.parse_args() outputDir = args.outputDir up_data = np.loadtxt(outputDir + "/data/" + args.specimen_id + '_upbase.dat') down_data = np.loadtxt(outputDir + "/data/" + args.specimen_id + '_downbase.dat') specimen_id = args.specimen_id specimen_name, ephys_roi_result_id = lims_orca_utils.get_ephys_id_from_lims( args.specimen_id) #specimen_name, ephys_roi_result_id, specimen_id = get_specimen_info_from_lims(args.specimen_id) swc_filename, swc_path = lims_orca_utils.get_swc_from_lims(specimen_id) local_path = args.local_path if (local_path): swc_path = local_path + '/' + swc_filename print "using:", swc_path h.load_file("stdgui.hoc") h.load_file("import3d.hoc") load_morphology(swc_path) for sec in h.allsec(): sec.insert('pas') for seg in sec: seg.pas.e = 0