Example #1
0
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)
Example #2
0
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]
Example #3
0
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
Example #4
0
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]))
Example #5
0
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()
Example #6
0
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))
Example #7
0
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)
Example #8
0
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
Example #9
0
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
Example #10
0
def printarraylist(u_dc):
    arrays = u_dc['$ARRAY']

    ut.putcomment('User variable arrays', 0)
    for key in sorted(arrays):
        print('%s:' % key), arrays[key]