from __future__ import division
import sys
import brukerIO
import numpy as n
import argparse
parser = argparse.ArgumentParser(description='Calculate (S0-S)/S0 spectrum from 1D REDOR or RESPDOR with interleaved acquisition')
parser.add_argument('inputs', help='Full path of the dataset to process')
parser.add_argument('--threshold', '-t', required=True, help='threshold signal below which S0 is not significant')
parser.add_argument('--order', '-o', required=False, default='0', help='Order in 2D 0: S0-S / 1: S-S0')
args = parser.parse_args()
infile = args.inputs
threshold = float(args.threshold)
order = args.order
dat =brukerIO.dataset(brukerIO.splitprocpath(infile))
spect = dat.readspect1d()
# print("spectrum shape is ",spect.shape)
(si2,) = spect.shape
# print("si2=%d" % (si2,))
spect = spect.reshape(si2//2, 2)
if order == '0':
S0 = spect[:, 0]
S = spect[:, 1]
elif order == '1':
S = spect[:, 0]
S0 = spect[:, 1]
else: raise("order should be 0 (S0-S) or 1 (S-S0)")
for i in range(si2//2):
if S0[i] < threshold :
import brukerIO
from shutil import copyfile
sample = "../data/qcpmg/4/pdata/1/"
fresh = "../data/qcpmg/4/" + 'acqu'
backup = "../data/qcpmg/4/" + 'acqu.bak'
copyfile(backup, fresh)
dat = brukerIO.dataset(brukerIO.splitprocpath(sample))
P = [
"P 1",
"L 31",
"SPNAM 8",
"BF1",
"NS",
"AUNM",
"LOCKED",
"L 64",
"TOTO",
]
values = [
1.5,
5,
"test_shape",
180.2,
23,
"toto",
True,
7,
'bidule',
#SF
# autres parameters pour interpreter correctement un processed file
#BYTORDP
#NC_proc
#PPARMOD : dimension 0=1D 1=2D 2=3D...
infile = sys.argv[1]
infile1D = sys.argv[2]
# create 1D processed dataset :
# - copy 2D into 1D and adapt proc and procs to 1D
#translate filename into bruker dataset components
data = brukerIO.splitprocpath(infile)
data1D = brukerIO.splitprocpath(infile1D)
#initialize dataset
dat = brukerIO.dataset(data)
dat1D = brukerIO.dataset(data1D)
# 2rr is the main file
# 2ri or 2ir or 2ii could be the imaginary part depending on MC2 and PH_mod
# typically MC2 is QF for popt (hence 2ii file is generated unless PH_mod is ps or mc meaning no imaginary part exists)
# for now I only try to read 2ii imaginary file, and don't attempt to read other files (2ri or 2ir)
#read 2D 2rr data
Fr = "2rr"
Fi = "2ii"
spect = dat.readspect2d(Fr)
try:
specti = dat.readspect2d(Fi)
except IOError:
print("reading 2ii file failed")
specti = np.zeros_like(spect)
required=False,
type=int,
default=0,
help='last FID point of refocused echo')
parser.add_argument('--tdeff',
required=False,
type=int,
help='only keep tdeff points',
default=0)
parser.add_argument('infile', help='Full path of the dataset to process')
args = parser.parse_args()
data = brukerIO.splitprocpath(args.infile)
#initialize dataset
dat = brukerIO.dataset(data)
#read 1D fid file and remove digital filter
spect = dat.readfidc(rmGRPDLY=False)
digfilt = int(round(dat.getdigfilt()))
(td_spectrum, ) = spect.shape
# calculate the theoretical td from pulse sequence parameters unless td is provided as argument
if args.td:
print("limit fid to " + str(args.td), digfilt)
td = args.td // 2 - digfilt
else:
"p13+3.5+d6*2+de*2+d3*2" # delays to consider
p13 = dat.readacqpar("P 13")
d3 = dat.readacqpar("D 3") * 1e6
d6 = dat.readacqpar("D 6") * 1e6