Python Group.i0方法代码示例

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import i0 [as 别名]
def parse_jsonathena(text, filename):
    """parse a JSON-style athena file"""
    jsdict = json.loads(text)

    out = Group()
    out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)

    header = []
    athena_names = []
    for key, val in jsdict.items():
        if key.startswith('_____head'):
            header.append(val)
        elif key.startswith('_____journ'):
            journal = val
        elif key.startswith('_____order'):
            athena_names = val

    out.journal = journal
    out.header = '\n'.join(header)
    out.group_names  = []
    for name in athena_names:
        label = name
        dat = jsdict[name]
        x = np.array(dat['x'], dtype='float64')
        y = np.array(dat['y'], dtype='float64')
        this = Group(athena_id=name, energy=x, mu=y,
                     bkg_params=Group(), fft_params=Group(),
                     athena_params=Group())
        if 'i0' in dat:
            this.i0 = np.array(dat['i0'], dtype='float64')
        if 'signal' in dat:
            this.signal = np.array(dat['signal'], dtype='float64')
        if 'stddev' in dat:
            this.stddev = np.array(dat['stddev'], dtype='float64')
        if 'args' in dat:
            for key, val in dat['args'].items():
                if key.startswith('bkg_'):
                    setattr(this.bkg_params, key[4:], asfloat(val))
                elif key.startswith('fft_'):
                    setattr(this.fft_params, key[4:], asfloat(val))
                elif key == 'label':
                    label = this.label = val
                else:
                    setattr(this.athena_params, key, asfloat(val))
        this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, name)
        name = fix_varname(label)
        if name.startswith('_'):
            name = 'd' + name
        setattr(out, name, this)
        out.group_names.append(name)
    return out

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import i0 [as 别名]
def read_athena(filename, match=None, do_preedge=True, do_bkg=True, do_fft=True, use_hashkey=False, _larch=None):
    """read athena project file
    returns a Group of Groups, one for each Athena Group in the project file

    Arguments:
        filename (string): name of Athena Project file
        match (sring): pattern to use to limit imported groups (see Note 1)
        do_preedge (bool): whether to do pre-edge subtraction [True]
        do_bkg (bool): whether to do XAFS background subtraction [True]
        do_fft (bool): whether to do XAFS Fast Fourier transform [True]
        use_hashkey (bool): whether to use Athena's hash key as the
                       group name instead of the Athena label [False]

    Returns:
        group of groups each named according the label used by Athena.

    Notes:
        1. To limit the imported groups, use the pattern in `match`,
           using '*' to match 'all' '?' to match any single character,
           or [sequence] to match any of a sequence of letters.  The match
           will always be insensitive to case.
        3. do_preedge,  do_bkg, and do_fft will attempt to reproduce the
           pre-edge, background subtraction, and FFT from Athena by using
           the parameters saved in the project file.
        2. use_hashkey=True will name groups from the internal 5 character
           string used by Athena, instead of the group label.

    Example:
        1. read in all groups from a project file:
           cr_data = read_athena('My Cr Project.prj')

        2. read in only the "merged" data from a Project, and don't do FFT:
           zn_data = read_athena('Zn on Stuff.prj', match='*merge*', do_fft=False)

    """

    from larch_plugins.xafs import pre_edge, autobk, xftf

    if not os.path.exists(filename):
        raise IOError("%s '%s': cannot find file" % (ERR_MSG, filename))

    try:
        fh = GzipFile(filename)
        lines = [bytes2str(t) for t in fh.readlines()]
        fh.close()
    except:
        raise ValueError("%s '%s': invalid gzip file" % (ERR_MSG, filename))

    athenagroups = []
    dat = {"name": ""}
    Athena_version = None
    vline = lines.pop(0)
    if "Athena project file -- Demeter version" not in vline:
        raise ValueError("%s '%s': invalid Athena File" % (ERR_MSG, filename))

    major, minor, fix = "0", "0", "0"
    try:
        vs = vline.split("Athena project file -- Demeter version")[1]
        major, minor, fix = vs.split(".")
    except:
        raise ValueError("%s '%s': cannot read version" % (ERR_MSG, filename))
    if int(minor) < 9 or int(fix[:2]) < 21:
        raise ValueError("%s '%s': file is too old to read" % (ERR_MSG, filename))

    for t in lines:
        if t.startswith("#") or len(t) < 2:
            continue
        key = t.split(" ")[0].strip()
        key = key.replace("$", "").replace("@", "")
        if key == "old_group":
            dat["name"] = perl2json(t)
        elif key == "[record]":
            athenagroups.append(dat)
            dat = {"name": ""}
        elif key == "args":
            dat["args"] = perl2json(t)
        elif key in ("x", "y", "i0"):
            dat[key] = np.array([float(x) for x in perl2json(t)])

    if match is not None:
        match = match.lower()

    out = Group()
    out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
    for dat in athenagroups:
        label = dat["name"]
        this = Group(
            athena_id=label, energy=dat["x"], mu=dat["y"], bkg_params=Group(), fft_params=Group(), athena_params=Group()
        )
        if "i0" in dat:
            this.i0 = dat["i0"]
        if "args" in dat:
            for i in range(len(dat["args"]) // 2):
                key = dat["args"][2 * i]
                val = dat["args"][2 * i + 1]
                if key.startswith("bkg_"):
                    setattr(this.bkg_params, key[4:], val)
                elif key.startswith("fft_"):
                    setattr(this.fft_params, key[4:], val)
                elif key == "label":
#.........这里部分代码省略.........

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import i0 [as 别名]
def parse_perlathena(text, filename):
    """
    parse old athena file format to Group of Groups
    """
    lines = text.split('\n')
    athenagroups = []
    raw = {'name':''}
    vline = lines.pop(0)
    if  "Athena project file -- Demeter version" not in vline:
        raise ValueError("%s '%s': invalid Athena File" % (ERR_MSG, filename))

    major, minor, fix = '0', '0', '0'
    try:
        vs = vline.split("Athena project file -- Demeter version")[1]
        major, minor, fix = vs.split('.')
    except:
        raise ValueError("%s '%s': cannot read version" % (ERR_MSG, filename))
    if int(minor) < 9 or int(fix[:2]) < 21:
        raise ValueError("%s '%s': file is too old to read" % (ERR_MSG, filename))

    header = [vline]
    journal = {}
    is_header = True
    for t in lines:
        if t.startswith('#') or len(t) < 2 or 'undef' in t:
            if is_header:
                header.append(t)
            continue
        is_header = False
        key = t.split(' ')[0].strip()
        key = key.replace('$', '').replace('@', '')
        if key == 'old_group':
            raw['name'] = plarray2json(t)
        elif key == '[record]':
            athenagroups.append(raw)
            raw = {'name':''}
        elif key == 'journal':
            journal = plarray2json(t)
        elif key == 'args':
            raw['args'] = plarray2json(t)
        elif key == 'xdi':
            raw['xdi'] = t
        elif key in ('x', 'y', 'i0', 'signal', 'stddev'):
            raw[key] = np.array([float(x) for x in plarray2json(t)])
        elif key == '1;': # end of list
            pass
        else:
            print(" do not know what to do with key ", key, raw['name'])

    out = Group()
    out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
    out.journal = journal
    out.group_names = []
    out.header = '\n'.join(header)
    for dat in athenagroups:
        label = dat.get('name', 'unknown')
        this = Group(athena_id=label, energy=dat['x'], mu=dat['y'],
                     bkg_params=Group(), fft_params=Group(),
                     athena_params=Group())
        if 'i0' in dat:
            this.i0 = dat['i0']
        if 'signal' in dat:
            this.signal = dat['signal']
        if 'stddev' in dat:
            this.stddev = dat['stddev']
        if 'args' in dat:
            for i in range(len(dat['args'])//2):
                key = dat['args'][2*i]
                val = dat['args'][2*i+1]
                if key.startswith('bkg_'):
                    setattr(this.bkg_params, key[4:], asfloat(val))
                elif key.startswith('fft_'):
                    setattr(this.fft_params, key[4:], asfloat(val))
                elif key == 'label':
                    label = this.label = val
                elif key in ('valence', 'lasso_yvalue',
                             'epsk', 'epsr', 'importance'):
                    setattr(this, key, asfloat(val))
                elif key in ('atsym', 'edge', 'provenance'):
                    setattr(this, key, val)
                else:
                    setattr(this.athena_params, key, asfloat(val))
        this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, dat['name'])
        name = fix_varname(label)
        if name.startswith('_'):
            name = 'd' + name
        setattr(out, name, this)
        out.group_names.append(name)

    return out

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import i0 [as 别名]
# now import larch-specific Python code
from larch_plugins.xafs import autobk, xftf

# create a larch interpreter, passed to most functions
my_larch = Interpreter(with_plugins=False)

# create an empty Group
xafsdat = Group()

# read data (here using np.loadtxt), stick into Group
# using "expected names" for XAFS data
rawdata = np.loadtxt('../xafsdata/fe2o3_rt1.xmu')

xafsdat.energy = rawdata[:, 0]
xafsdat.mu     = rawdata[:, 1]
xafsdat.i0     = rawdata[:, 1]

# run autobk on the xafsdat Group, including a larch Interpreter....
# note that this expects 'energy' and 'mu' to be in xafsdat, and will
# write data for 'k', 'chi', 'kwin', 'e0', ... into xafsdat
autobk(xafsdat, rbkg=1.0, kweight=2, _larch=my_larch)

# Fourier transform to R space, again passing in a Group (here,
# 'k' and 'chi' are expected, and writitng out 'r', 'chir_mag',
# and so on
xftf(xafsdat, kmin=2, kmax=15, dk=3, kweight=2, _larch=my_larch)

#
# plot grid of results:
# mu + bkg
pylab.subplot(2, 2, 1)