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
