Commit 3e122264 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

first revision to plot .nxs.h5 files directly 

for now we will implicitly convert
a) scan=echo         -> s*.echo      -> .h5
b) scan=diffraction  -> diffrun*.dat
c) scan=transmisison -> trasmission*.dat
parent 5af40a98

pyproject.toml

+1 −1
Original line number Diff line number Diff line
@@ -11,7 +11,7 @@ authors = [ 


description = "Python tools for the SNS-NSE instrument"

readme = "README.md"

requires-python = ">=3.7"

requires-python = ">=3.9"



classifiers = [

    "Programming Language :: Python :: 3",

pysen/config.py

+3 −9
Original line number Diff line number Diff line
@@ -33,12 +33,6 @@ MIN_PHI = 3.0 # degrees 
MAX_PHI = dict(zip(INST_POSITIONS,[29.0,42.0,56.0,79.5])) # degrees

PHI_LIMS = (3.0, 79.5)



# wavelenth bandwitdh

# now computed based on Ltot

#DLAMBDA =  {'p1': 3.6, # lambda in Angstroms

#            'p2': 3.1,

#            'p3': 2.7,

#            'p4': 2.4}



# 3. The Detector

XDET = 0.300 # [m] detector width
@@ -145,8 +139,8 @@ def phi_limits(pos='p2'): 
    """ get instrument scattering angle limits in degrees"""

    return MIN_PHI, MAX_PHI.get(pos, MIN_PHI)



def wavelength_bandwitdh(pos='p2', freq=DEFAULT_ACCELERATOR_FREQ):

    """ get instrument wavelength bandwitdh limits in Angstroms"""

def wavelength_bandwidth(pos='p2', freq=DEFAULT_ACCELERATOR_FREQ):

    """ get instrument wavelength bandwidth limits in Angstroems"""

    return HMN/(Ltot.get(pos)*freq*ANGSTROM)
@@ -332,7 +326,7 @@ def coverage(lmax, qmin, **kwargs): 
    tbins    = kwargs.pop('tbins', None)

    ntbin    = kwargs.pop('ntbin', 42  )

    detpos   = kwargs.pop('pos',  'p2' )

    dlam     = kwargs.pop('dlam', wavelength_bandwitdh(detpos))

    dlam     = kwargs.pop('dlam', wavelength_bandwidth(detpos))

    rpixel   = kwargs.pop('rpixel', (NXCHAN//2))

    check_limits  = kwargs.pop('limits', True) # check limits

pysen/inout/hdf.py

+5 −2
Original line number Diff line number Diff line
@@ -211,8 +211,8 @@ def convert_to_hdf(filename, outdir, **kwargs): 
                    'magnetic'   : read_magnetic,

                    'nexus_echo' : read_nexus_echo,

                    #

                    'application/nse-echo'       : read_echo,

                    'application/nse-xyz'        : read_xyz,

                    'application/taco-nse-echo'  : read_echo,

                    'application/taco-nse-xyz'   : read_xyz,

                    'application/nexus-nse-echo' : read_nexus_echo,

                    }
@@ -268,12 +268,15 @@ def convert_files(filenames, outdir, **kwargs): 
    """convert *.nxs.h5 file to/from old TACO style files"""

    log = logging.getLogger()

    converter = ConverterType.get(kwargs.pop('converter', 'from_taco'))

    results = []

    for filename in filenames:

        try:

            basename = os.path.basename(filename)

            outfile = converter(filename, outdir, **kwargs)

            log.info('converted %s to %s', basename, outfile)

            results.append(outfile)

        except RuntimeError as exc:

            log.warning("error converting %s: (%s)", basename, exc)

        except OSError as exc:

            log.warning("error converting %s: (%s)", basename, exc.strerror)

    return results

pysen/inout/reader.py

+43 −38
Original line number Diff line number Diff line
@@ -772,10 +772,12 @@ def read_magnetic(filename): 
def read_transmission(filename):

    "read transmission file"

    result = OrderedDict()

    #transtab = { '"' : None,

    #             '\n': None, }

    try:

        with open(filename, mode='r', encoding='ascii') as _fdesc:

        lines = iter(_fdesc.readlines())

            lines = _fdesc.readlines()

    except TypeError:

        lines = filename

    lines = iter(lines)

    prevline = None

    while True:

        line = next(lines)
@@ -788,9 +790,9 @@ def read_transmission(filename): 
    result['proposal'  ] = header[0]

    result['sample'    ] = header[1].split()[-1]

    result['wavelength'] = _evaluate(header[2].split()[-1])

        thead = remove_chars(line, delchars='"\n').split()

        tdata = remove_chars(next(lines), delchars='"\n').split()

        for k,v in zip(thead, tdata):

    t_head = remove_chars(line, delchars='"\n').split()

    t_data = remove_chars(next(lines), delchars='"\n').split()

    for k,v in zip(t_head, t_data):

        result[k] = _evaluate(v)

    tmpkey = None

    tmparr = []
@@ -824,10 +826,13 @@ def read_diffrun(filename, att_table=None): 
    wlendata  = []

    wlen_list = None

    attenuator = 1

    try:

        with open(filename, mode='r', encoding='ascii') as _fdesc:

        lines = iter(_fdesc.readlines())

            lines = _fdesc.readlines()

    except TypeError:

        lines = filename

    #

    for line in lines:

    for line in iter(lines):

        line   = line.strip()

        tokens = line.split()

        if not tokens:

pysen/inout/utils.py

+26 −7
Original line number Diff line number Diff line
@@ -31,10 +31,14 @@ def get_open_file(filename): 




NSE_FILE_TYPES = {

"application/nse-echo"           : '.echo'  ,

"application/nse-xyz"            : '.xyz'   ,

"application/nse-magnetic"       : '.dat'   ,

"application/taco-nse-echo"           : '.echo'  ,

"application/taco-nse-transmission"   : '.dat'   ,

"application/taco-nse-diffraction"    : '.dat'   ,

"application/taco-nse-xyz"            : '.xyz'   ,

"application/taco-nse-magnetic"       : '.dat'   ,

#

"application/nse-echo-hdf"       : '.h5'    ,

#

"application/nexus-nse-echo"     : '.nxs.h5',

"application/nexus-nse-xyz"      : '.nxs.h5',

"application/nexus-nse-transmission" : '.nxs.h5',
@@ -71,18 +75,33 @@ def get_hdf_filetype(filename): 


def get_dat_filetype(filename):

    "test if old-style magnetic xyz file"

    def find_first_line(fdesc):

        "find first non-empty line"

        while True:

            line = fdesc.readline()

            if line.strip():

                return line.lower()

        return None



    with open(filename, 'r', encoding='ascii') as fd:

        header = fd.readline()

        header = find_first_line(fd)

        if header.startswith('-------------- physics parameters'):

            return "application/nse-magnetic"

            return "application/taco-nse-magnetic"

        if header.startswith('"transmission'):

            return "application/taco-nse-transmission"

        if header.startswith('"##############'):

            #get next line to see if difraction scan

            header = fd.readline()

            if "diffraction" in header:

                return "application/taco-nse-diffraction"

    return get_mime_filetype(filename)



def get_nsefiletype(filename):

    "get filetype"

    _, ext = os.path.splitext(filename)

    filetype =  {

            '.echo': "application/nse-echo",

            '.xyz' : "application/nse-xyz",

            '.echo': "application/taco-nse-echo",

            '.xyz' : "application/taco-nse-xyz",

            '.dat' : get_dat_filetype,

            '.h5'  : get_hdf_filetype,

            }.get(ext, get_mime_filetype)