Skip to content

Commit

Permalink
added mlpy file check
Browse files Browse the repository at this point in the history
  • Loading branch information
@ludwigc
ludwigc committed Nov 4, 2024
1 parent 0aa363e commit 7ab2828
Show file tree
Hide file tree
Showing 2 changed files with 310 additions and 1 deletion.
2 changes: 1 addition & 1 deletion metabolabpy/__init__.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
__author__ = 'Christian Ludwig (C.Ludwig@bham.ac.uk)'
__credits__ = 'Christian Ludwig (C.Ludwig@bham.ac.uk)'
__version__ = '0.9.62'
__version__ = '0.9.63'
__license__ = 'GPLv3'
309 changes: 309 additions & 0 deletions metabolabpy/nmr/nmrDataSet.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -341,6 +341,30 @@ def bucket_spectra(self):
self.pp.bucket_points = 1
# end bucket_spectra

def check_file(self, data_set_name=''):
if len(data_set_name) == 0:
msg = 'file name empty'
return msg

nda = self.load2(data_set_name)
ds = []
exps = []
for k in range(len(nda)):
exps.append([])
for l in range(len(nda[k])):
if len(nda[k][k].spc[0]) == 0 or len(nda[k][l].fid[0]) == 0:
ds.append(k)
exps[k].append(l)

ds = list(set(ds))
msg = ''
for k in range(len(ds)):
for l in range(len(exps[ds[k]])):
msg += f'File: {data_set_name}, Dataset: {ds[k] + 1}, experiment: {exps[ds[k]][l] + 1} not a valid dataset\n'

return msg
# end check_file

def clear(self):
self.nmrdat = [[]]
self.s = 0
Expand Down Expand Up @@ -1327,6 +1351,291 @@ def load(self, data_set_name):

# end load

def load2(self, data_set_name):
data_sets = np.array([])
l_dir = os.listdir(data_set_name)
cur_data_not_found = True
for k in range(len(l_dir)):
if l_dir[k] == 'curPars.dat':
cur_data_not_found = False

if cur_data_not_found:
return

f_name = os.path.join(data_set_name, 'curPars.dat')
f = open(f_name, 'rb')
cur_pars = pickle.load(f)
f.close()
self.file_format_version = cur_pars[0]
self.s = cur_pars[1]
self.e = cur_pars[2]
# self.pp = cur_pars[3]
c = cur_pars[3]
for k in self.pp.__dict__.keys():
if k != 'cf':
k2 = k
str_idx = k2.find('_')
while str_idx != -1:
str_letter = k2[str_idx + 1]
k2 = k2.replace(k2[str_idx:str_idx + 2], str_letter.upper())
str_idx = k2.find('_')

if hasattr(c, k):
exec('self.pp.' + k + '=c.' + k)

if hasattr(c, k2):
exec('self.pp.' + k + '=c.' + k2)

self.deselect = cur_pars[4]
self.deselect2 = cur_pars[5]
self.cmd_buffer = cur_pars[6]
self.cmd_idx = cur_pars[7]
self.script = cur_pars[8]
self.console = cur_pars[9]
try:
self.tmsp_conc = cur_pars[10]
except:
self.tmsp_conc = 0.5

for k in range(len(l_dir)):
if os.path.isdir(os.path.join(data_set_name, l_dir[k])):
data_sets = np.append(data_sets, l_dir[k])

data_sets = np.sort(data_sets)
data_set_exps = []
for k in range(len(data_sets)):
dir_name = os.listdir(os.path.join(data_set_name, data_sets[k]))
data_exps = np.array([])
for l in range(len(dir_name)):
if os.path.isdir(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l])):
if (os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'titleFile.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'acqusText.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'acqu2sText.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'acqu3sText.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'procsText.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'proc2sText.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'proc3sText.txt')) and
os.path.isfile(
os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), dir_name[l]),
'nmrDataSet.dat'))):
data_exps = np.append(data_exps, dir_name[l])

data_exps2 = []
for k in range(len(data_exps)):
try:
data_exps2.append(int(data_exps[k]))
except:
pass

data_exps2.sort()
data_exps = list(map(str, data_exps2))
data_set_exps.append(data_exps)

nda = []
for k in range(len(data_set_exps)):
nda.append([])
for l in range(len(data_set_exps[k])):
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'nmrDataSet.dat')
f = open(f_name, 'rb')
n = pickle.load(f)
f.close()
if hasattr(n, 'ver'):
vver = ''
else:
vver = '0.1'

nd2 = nd.NmrData()
# nd2.file_version = n.nmrdat[0][0].ver
for kk in nd2.__dict__.keys():
if kk != 'acq' and kk != 'proc' and kk != 'display' and kk != 'apc' and kk != 'hsqc':
kk2 = kk
str_idx = kk2.find('_')
while str_idx != -1:
str_letter = kk2[str_idx + 1]
kk2 = kk2.replace(kk2[str_idx:str_idx + 2], str_letter.upper())
str_idx = kk2.find('_')

if hasattr(n, kk):
exec('nd2.' + kk + '=n.' + kk)

if hasattr(n, kk2):
exec('nd2.' + kk + '=n.' + kk2)

elif kk == 'acq':
if hasattr(n, kk):
a = n.acq
aq = nd2.acq
for kkk in aq.__dict__.keys():
if kkk != 'reg_ex':
kkk2 = kkk
str_idx = kkk2.find('_')
while str_idx != -1:
str_letter = kkk2[str_idx + 1]
kkk2 = kkk2.replace(kkk2[str_idx:str_idx + 2], str_letter.upper())
str_idx = kkk2.find('_')

if hasattr(a, kkk):
exec('aq.' + kkk + '=a.' + kkk)

if hasattr(a, kkk2):
exec('aq.' + kkk + '=a.' + kkk2)

# else:
# try:
# r = a.reg_ex
# except:
# r = a.regEx
#
# re = aq.reg_ex
# for kkkk in re.__dict__.keys():
# if hasattr(r, kkkk):
# exec('re.' + kkkk + '=r.' + kkkk)
#
# aq.reg_ex = re

nd2.acq = aq

elif kk == 'proc':
if hasattr(n, kk):
p = n.proc
pc = nd2.proc
for kkk in pc.__dict__.keys():
if kkk != 'reg_ex':
kkk2 = kkk
str_idx = kkk2.find('_')
while str_idx != -1:
str_letter = kkk2[str_idx + 1]
kkk2 = kkk2.replace(kkk2[str_idx:str_idx + 2], str_letter.upper())
str_idx = kkk2.find('_')

if hasattr(p, kkk):
exec('pc.' + kkk + '=p.' + kkk)

if hasattr(p, kkk2):
exec('pc.' + kkk + '=p.' + kkk2)

else:
# try:
# r = p.reg_ex
# except:
# r = p.regEx
#
re = pc.reg_ex
# for kkkk in re.__dict__.keys():
# if hasattr(r, kkkk):
# exec('re.' + kkkk + '=r.' + kkkk)
#
# pc.reg_ex = re

nd2.proc = pc

elif kk == 'display':
if hasattr(n, kk):
d = n.display
dp = nd2.display
for kkk in dp.__dict__.keys():
if hasattr(d, kkk):
exec('dp.' + kkk + '=d.' + kkk)

nd2.display = dp

elif kk == 'apc':
if hasattr(n, kk):
ab = n.apc
ac = nd2.apc
for kkk in ac.__dict__.keys():
if hasattr(ab, kkk):
exec('ac.' + kkk + '=ab.' + kkk)

nd2.apc = ac

elif kk == 'hsqc':
if hasattr(n, kk):
h = n.hsqc
hp = nd2.hsqc
for kkk in hp.__dict__.keys():
if hasattr(h, kkk):
# if kkk != 'hsqc_data':
exec('hp.' + kkk + '=h.' + kkk)
#
# else:
# hd = h.hsqc_data
# hdp = hp.hsqc_data
# for kkkk in hdp.__dict__.keys():
# if hasattr(hd, kkkk):
# exec('hdp.' + kkkk + '=hd.' + kkkk)
#
# hp.hsqc_data = hdp

nd2.hsqc = hp

if vver == '0.1':
nd2.ver = '0.1'

nda[k].append(nd2)
nd2 = []
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'titleFile.txt')
f = open(f_name, 'r')
nda[k][l].title = f.read()
f.close()
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'acqusText.txt')
f = open(f_name, 'r')
nda[k][l].acq.acqus_text = f.read()
f.close()
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'acqu2sText.txt')
f = open(f_name, 'r')
nda[k][l].acq.acqu2s_text = f.read()
f.close()
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'acqu3sText.txt')
f = open(f_name, 'r')
nda[k][l].acq.acqu3s_text = f.read()
f.close()
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'procsText.txt')
f = open(f_name, 'r')
nda[k][l].proc.procs_text = f.read()
f.close()
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'proc2sText.txt')
f = open(f_name, 'r')
nda[k][l].proc.proc2s_text = f.read()
f.close()
f_name = os.path.join(os.path.join(os.path.join(data_set_name, data_sets[k]), data_set_exps[k][l]),
'proc3sText.txt')
f = open(f_name, 'r')
nda[k][l].proc.proc3s_text = f.read()
f.close()

#self.cf.current_directory = data_set_name
#self.cf.save_config()
#if len(self.nmrdat) - 1 < self.s:
# self.s = 0
#
#if len(self.nmrdat[self.s]) - 1< self.e:
# self.e = 0

return nda
# end load2

def load_mat(self, file_name=''):
if len(file_name) == 0:
return
Expand Down

0 comments on commit 7ab2828

Please sign in to comment.