def main():
usage = """usage: %prog [options] programname
Analyze pulse program file <programname> to make suggestions for automated set-up"""
parser = OptionParser(usage)
parser.add_option(
"-a",
"--add_files",
action="store_true",
dest="addfiles",
default=False,
help="look for <programname> in add_files path [default: %default]")
parser.add_option("-v",
"--verboselevel",
type="int",
default=0,
dest="verboselevel",
help="set verbose level [default: %default]")
(options, args) = parser.parse_args()
ut.cd_curd()
# print options
if len(args) == 0:
parser.error("incorrect number of arguments")
return
ppname = args[0]
pp.pp_file = os.path.abspath(ppname)
pp.verbose_level = options.verboselevel
if options.addfiles:
(pp.pp_file, adir) = ut.find_file_dir(ppname, 'PP', addfiles=True)
if not pp.pp_file:
raise Exception('%s not found in add_files path %s' %
(ppname, pp.addfiles_path))
ut.putcomment('Analyzing pulse program file: ' + pp.pp_file,
1,
ornament=False)
if pp.verbose_level > 1:
ut.putcomment('pp.ppGlobals', 1)
ut.show_vars(pp)
parfilename = 'acqus'
analyzepp(pp.pp_file, parfilename)
def printJcamp(j_dc, u_dc):
ut.putcomment('Jcamp variables', 0)
for key in sorted(j_dc):
print('%s:' % key), j_dc[key]
ut.putcomment('User variables', 0)
arrays = u_dc['$ARRAY']
for key in sorted(u_dc):
if key == '$ARRAY':
continue
if key in arrays.keys():
print('%s (%d:%d):' % (key, arrays[key][0], arrays[key][1])),
for (ii, val) in zip(range(arrays[key][0], arrays[key][1] + 1),
u_dc[key]):
print('%s(%d)' % (val, ii)),
print
else:
print('%s:' % key), u_dc[key]
def main():
setopts, args = getopt.gnu_getopt(sys.argv[1:], 'ahv:')
ut.cd_curd()
if len(args) == 0:
printhelp(sys.argv[0])
return
pp.verbose_level = 0
printarraylistflag = False
for opt in setopts:
if opt[0] == '-h':
printhelp(sys.argv[0])
return
elif opt[0] == '-a':
printarraylistflag = True
elif opt[0] == '-v':
pp.verbose_level = int(opt[1])
parname = args[0]
ut.putcomment('Reading Jcamp file: ' + parname, 1, ornament=False)
if pp.verbose_level > 1:
ut.putcomment('pp.ppGlobals', 1)
ut.show_vars(pp)
(j_dc, u_dc) = parseJcamptxt(ut.read_file(parname))
if printarraylistflag:
printarraylist(u_dc)
return
if len(args) == 1:
printJcamp(j_dc, u_dc)
return
if len(args) > 1:
parlist = reduce(lambda x, y: x + ' ' + y, args[1:]).split(',')
for par in parlist:
printpar(par, u_dc)
return
def analyzepp(progfilename, parfilename):
"""Analyze pulse program <progfilename> using acqu file <parfilename>.
Outputs the acquisition parameters and their value.
"""
(pythontext,
nonpythontext) = ut.split_python_text(ut.read_file(progfilename))
nonpythontext = ut.strip_comment(nonpythontext, ';')
(j_dc, u_dc) = sj.parseJcamptxt(ut.read_file(parfilename))
arrays = u_dc['$ARRAY']
usedpars = []
usedpararrays = {}
words = sorted(set(re.split('\W+', nonpythontext)))
ut.putcomment('parsing <%s>' % os.path.basename(progfilename), 1)
for w in words:
m = pp.search_commands_re.match(w)
if m:
if m.group('comarray'):
c = m.group('comarray').upper()
ind = int(m.group('ind'))
p = pp.coms2pars_dict[c][0]
usedpars += [p]
ut.putcomment('%s: %s %d' % (w, pp.coms2pars_dict[c], ind),
1,
ornament=False)
if not p in usedpararrays.keys():
usedpararrays[p] = [ind]
else:
usedpararrays[p] += [ind]
elif m.group('com'):
c = m.group('com').upper()
p = pp.coms2pars_dict[c][0]
ut.putcomment('%s: %s' % (w, pp.coms2pars_dict[c]),
1,
ornament=False)
usedpars += [p]
ut.putcomment('end parsing', 1)
usedpars = sorted(set(usedpars))
for par in usedpars:
conpars = pp.coms2pars_dict[pp.pars2coms_dict[par][0]]
if par in pp.par_array_names:
for ind in sorted(usedpararrays[par]):
for p in conpars:
print('%s %d: %s' % (p, ind, u_dc[p][ind]))
else:
for p in conpars:
print('%s: %s' % (p, u_dc[p]))
def main():
setopts, args = getopt.gnu_getopt(sys.argv[1:], 'ahr:v:')
if len(args) == 0:
printhelp(sys.argv[0])
return
ppname = args[0]
expname = ppname.split('.')[0]
pp.addfiles_path = pp.addfiles_path.replace('water_nh', expname)
pp.pp_file = os.path.join(pp.addfiles_path, 'pp/user/%s' % ppname)
pplogname = ppname + '.log'
pp.pp_log = os.path.join(pp.addfiles_path, 'pp/user/%s' % pplogname)
pp.verbose_level = 0
pp.run_flag = 'DRY'
for opt in setopts:
if opt[0] == '-h':
printhelp(sys.argv[0])
return
elif opt[0] == '-a':
(pp.pp_file, adir) = ut.find_file_dir(ppname, 'PP', addfiles=True)
if not pp.pp_file:
raise Exception('%s not found in add_files path %s'
% (ppname, pp.addfiles_path))
elif opt[0] == '-r':
pp.run_flag = opt[1]
elif opt[0] == '-v':
pp.verbose_level = int(opt[1])
ut.putcomment('Installing pulse program file: ' + pp.pp_file, 1, ornament=False)
ut.putcomment('Logfile: %s' % os.path.abspath(pp.pp_log), 1, ornament=False)
ut.putcomment('run_flag: %s' % pp.run_flag, 1, ornament=False)
if pp.verbose_level > 1:
ut.putcomment('pp.ppGlobals', 1)
ut.show_vars(pp)
(pythontext, nonpythontext) = ut.split_python_text(ut.read_file(pp.pp_file))
if not pythontext:
raise Exception('%s contains no python text' % pp.pp_file)
pp.pp_log_fd = open(pp.pp_log, 'w')
now = datetime.datetime.now()
pp.pp_log_fd.write('Date and Time: %s \n' % now)
exec pythontext
pp.pp_log_fd.close()
def copy_parfile(ptype, pname, addfilecreatepath):
"""Copy individual parameter file <pname> of type <ptype> to
<addfilecretepath>. <pname> is sought according to the Bruker search path.
The file is copied into a subdirectory of <addfilecretepath> according to
the relative directory in the Bruker lists directory. In case the file comes
from outside of the lists directory (non-standard Bruker path), the file
is put into the first subdirectory entry of lists according to the standard
search path.
"""
(filefullpath, defaultdir) = ut.find_file_dir(pname, ptype)
if not filefullpath:
ut.putcomment('<%s> not found in %s' % (pname, ptype), 0, ornament=False)
return
ut.putcomment('<%s> found in %s as <%s>' % (pname, ptype, filefullpath),
1, ornament=False)
fs = filefullpath.split(pp.lists_path + os.sep + 'lists' + os.sep)
if len(fs) == 2:
d = os.path.dirname(fs[1])
else:
ut.putcomment('<%s> found in %s with unnormal path <%s>'
% (pname, ptype, filefullpath), 1, ornament=False)
(dum, d) = pp.parfile_dirs_default_dict[ptype][0].split('lists' + os.sep)
dd = os.path.join(addfilecreatepath, d)
if not os.path.isdir(dd):
os.makedirs(dd)
shutil.copy2(filefullpath, os.path.join(dd, pname))
def main():
setopts,args = getopt.gnu_getopt(sys.argv[1:], 'ad:hv:')
ut.cd_curd()
pp.verbose_level = 0
addfilesdirname = 'add_files'
for opt in setopts:
if opt[0] == '-h':
printhelp(sys.argv[0])
return
elif opt[0] == '-a':
cds=subprocess.Popen(["curd", "-a"], stdout=subprocess.PIPE).communicate()[0].strip()
os.chdir(cds)
elif opt[0] == '-d':
addfilesdirname = opt[1]
print addfilesdirname
elif opt[0] == '-v':
pp.verbose_level = 1
pp.verbose_level = int(opt[1])
if len(args) == 0:
parname = 'acqus'
else:
parname = args[0]
ut.putcomment('Reading Jcamp file: ' + parname, 1, ornament=True)
if pp.verbose_level > 1:
ut.putcomment('pp.ppGlobals', 1)
ut.show_vars(pp)
(j_dc, u_dc) = sj.parseJcamptxt(ut.read_file(parname))
make_add_files(u_dc, addfilesdirname)
def PP_PUTPAR(name, value):
if pp.run_flag not in pp.run_flags:
raise Exception('unknown run_flag: ' + pp.run_flag)
brukername = name = name.upper()
ut.putcomment('PP_PUTPAR input: %s %s' % (name, value), 2, ornament=False)
m = pp.par_array_names_re.match(name)
if m:
ut.putcomment('detected array ' + m.group('arn') + ' ' + m.group('ind'),
3, ornament=False)
an = m.group('arn')
ind = m.group('ind')
m1 = re.match('(PL|SP)DB', an)
if m1:
an = m1.group(1) + 'W'
value = pow(10.0, -value / 10.)
m1 = re.match('(D|IN|P|INP)', an)
if m1 and (type(value) == str):
m2 = pp.time_units_re.match(value)
if m2:
val = m2.group('val')
un = m2.group('unit')
value = float(val) * pp.time_units[un]
if re.match('(P|INP)', an):
value = value * 1e6
brukername = an + ' ' + ind
pp.pp_log_fd.write('%s: %s\n' % (brukername, str(value)))
ut.putcomment('PP_PUTPAR: %s %s' % (brukername, str(value)), ornament=False)
if pp.run_flag == 'DRY':
# print top.Cmd.putPar(brukername, str(value))
return None
elif pp.run_flag in ['FORCE', 'NORMAL', 'INTERACTIVE']:
return TC.PUTPAR(brukername, str(value))
return None
def write_bruker_search_path(ftype, destfile, sourcefile=None, sourcetext=None):
"""Will copy a file from sourcefile (out of the add_files directory) or
text to destfile in first directory of Bruker search path for
ftype = cpd, f1, gp, ... with checks for overwrite, identity, etc.
"""
if pp.run_flag not in pp.run_flags:
raise Exception('unknown run_flag: ' + pp.run_flag)
destfile = destfile + pp.name_tag
ut.putcomment('write_bruker_search_path: start', 2)
ut.putcomment('ftype: %s, destfile: %s' % (ftype, destfile), 2, ornament=False)
if sourcetext and sourcefile:
raise Exception('both sourcefile and sourcetext defined')
if sourcetext:
source = sourcetext
sourcestring = 'sourcetext'
ut.putcomment('input is from sourcetext', 2, ornament=False)
ut.putcomment(source, 2, ornament=False)
else:
ut.putcomment('input is from sourcefile: ' + pp.addfiles_path + '/' + sourcefile,
2, ornament=False)
sourcestring = 'sourcefile <%s>' % sourcefile
f = open(os.path.join(pp.addfiles_path, sourcefile))
source = f.read()
f.close()
ut.putcomment(source, 3, ornament=False)
(destfilefullpath, destdir) = ut.find_file_dir(destfile, ftype)
if destfilefullpath:
ut.putcomment('destination file exists: ' + destfilefullpath, 2, ornament=False)
if not ut.cmp_text_file(source, destfilefullpath):
outstring = ('PP_FILE NO_ACTION: %s equals destfile <%s>'
% (sourcestring, destfilefullpath))
ut.putcomment(outstring, 1, ornament=False)
pp.pp_log_fd.write('%s\n' % outstring)
else:
outstring = ('PP_FILE CONFLICT: %s is not equal to destfile <%s>'
% (sourcestring, destfilefullpath))
ut.putcomment(outstring, 0, ornament=False)
pp.pp_log_fd.write('%s\n' % outstring)
if pp.run_flag == 'DRY':
outstring = ('PP_FILE OVERWRITE: %s will overwrite destfile <%s>'
% (sourcestring, destfilefullpath))
pp.pp_log_fd.write('%s\n' % outstring)
elif pp.run_flag == 'NORMAL':
raise Exception('%s\nPP_FILE NO_OVERWRITE: run_flag is %s\n'
% (outstring, pp.run_flag))
elif pp.run_flag == 'FORCE':
outstring = ('PP_FILE OVERWRITE: %s overwrites destfile <%s>'
% (sourcestring, destfilefullpath))
ut.putcomment(outstring, 0, ornament=False)
pp.pp_log_fd.write('%s\n' % outstring)
ut.write_text_file(source, destfilefullpath)
elif pp.run_flag == 'INTERACTIVE':
raise Exception('%s\nPP_FILE NO_OVERWRITE: run_flag is %s\n'
% (outstring, pp.run_flag))
else:
df1 = os.path.join(destdir, destfile)
outstring = ('PP_FILE CREATE: destfile <%s> from %s'
% (df1, sourcestring))
ut.putcomment(outstring, 1, ornament=False)
pp.pp_log_fd.write('%s\n' % outstring)
if pp.run_flag == 'DRY':
pass
elif pp.run_flag in ['FORCE', 'NORMAL', 'INTERACTIVE']:
ut.write_text_file(source, df1)
else:
raise Exception('unknown run_flag: ' + pp.run_flag)
ut.putcomment('write_bruker_search_path: end', 2)
return destfile
def printarraylist(u_dc):
arrays = u_dc['$ARRAY']
ut.putcomment('User variable arrays', 0)
for key in sorted(arrays):
print('%s:' % key), arrays[key]