Commit 9f1e7931 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

filetype savepoint 2

parent a8fac9db

bin/check_for_tests.sh

0 → 100755
+8 −0
Original line number Diff line number Diff line 
#!/bin/bash



for f in $(find pysen -name '[a-z]*.py'); do 

	tm=$(echo $f | sed -e 's|/|_|g' -e 's|pysen|test|g'); 

	if [ ! -f test/$tm ]; then

		echo "TEST MISSING $f $tm"

	fi

done

pysen/config.py

+1 −1
Original line number Diff line number Diff line
@@ -110,7 +110,7 @@ def get_attenuator_pos(attenuator_angle): 


#

PROTON_CHARGE_RTDL         = 1e-11  # 100 pico Coulomb (RTDL unit)

PROTON_CHARGE_UNIT         = 1e-7   # 0.1 micro Coulomb (NSE control program unit)

PROTON_CHARGE_UNIT         = 1e-07  # 1e-07  # 0.1 micro Coulomb (NSE control program unit)

DEFAULT_ACCELERATOR_FREQ   =   60.0 # Hz

#DEFAULT_ACCELERATOR_POWER  =    1.4 # MW

#DEFAULT_PROTON_ENERGY      = 1000.0 # MeV

pysen/inout/convert2hdf.py

+6 −28
Original line number Diff line number Diff line
@@ -7,40 +7,18 @@ import argparse 
import logging



from pysen import version, setup_logger

from pysen.inout import convert_to_hdf, get_nsefiletype

from pysen.inout import convert_to_hdf #, get_nsefiletype



def convert_file(filenames, outdir, **kwargs):

    """convert magnetic up/down .dat file into an HDF file """

    """convert a TACO/NeXus file into an pysen/HDF file """

    log = logging.getLogger()

    for filename in filenames:

        # get the file extension and the header

        filetype    = get_nsefiletype(filename)

        basename = os.path.basename(filename)

        #filetype = get_nsefiletype(filename)

        try:

            #if file_ext=='.echo':

            if filetype=='application/nse-echo':

                log.debug('reading echo data %s', filename)

                outfile = convert_to_hdf(filename, outdir, data_type='echo', **kwargs)

            elif filetype=='application/nse-xyz':

                log.debug('reading xyz data %s', filename)

                outfile = convert_to_hdf(filename, outdir, data_type='xyz', **kwargs)

            elif filetype=='application/nexus-nse-echo':

                log.debug('reading NeXus echo data %s', filename)

                outfile = convert_to_hdf(filename, outdir, data_type='nexus_echo', **kwargs)

            else:

                _, file_ext = os.path.splitext(basename)

                if file_ext=='.dat':

                    header=''

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

                        header = _fd.readline()

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

                            log.debug('reading magnetic data %s', filename)

                            outfile = convert_to_hdf(filename, outdir, data_type='magnetic', **kwargs)

                        else:

                            raise RuntimeError("Unknown file type (.dat)")

                else:

                    raise RuntimeError("Unknown file type %s" % filetype)

            log.info('written HDF5 file %s', outfile)

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

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

        except RuntimeError as exc:

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

        except OSError as exc:

pysen/inout/utils.py

+43 −26
Original line number Diff line number Diff line
@@ -33,16 +33,25 @@ def get_open_file(filename): 
NSE_FILE_TYPES = {

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

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

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

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

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

"application/nexus-transmission" : '.nxs.h5',

"application/nexus-diffraction"  : '.nxs.h5',

}



def get_mime_filetype(filename):

    "get mime type if all else fails"

    return mimetypes.guess_type(filename)[0]



def get_nexusfiletype(filename):

    "get nexus filetype"

def get_hdf_filetype(filename):

    "get HDF filetype"

    # read /entry/notes to determine the filetype

    base, _   = os.path.splitext(os.path.basename(filename))

    _   , ext = os.path.splitext(base) # get the "second extension"

    if not ext: # no second extension

        return "application/nse-echo-hdf"

    if ext == '.nxs': # .nxs.h5

        with h5py.File(filename, 'r') as nxsfile:

            try:

                notes   = nxsfile['/entry/notes']
@@ -55,18 +64,26 @@ def get_nexusfiletype(filename): 
                    return "application/nexus-nse-echo"

            except KeyError:

                pass

    return mimetypes.guess_type(filename)[0]

    return get_mime_filetype(filename)



def get_dat_filetype(filename):

    "test if old-style magnetic xyz file"

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

        header = fd.readline()

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

            return "application/nse-magnetic"

    return get_mime_filetype(filename)



def get_nsefiletype(filename):

    "get filetype"

    base, ext1 = os.path.splitext(os.path.basename(filename))

    if ext1=='.echo':

        return "application/nse-echo"

    if ext1=='.xyz':

        return "application/nse-xyz"

    if ext1=='.h5':

        base, ext2 = os.path.splitext(base)

        if not ext2:

            return "application/nse-echo-hdf"

        return get_nexusfiletype(filename)

    return mimetypes.guess_type(filename)[0]
 
    _, ext = os.path.splitext(filename)

    filetype =  {

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

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

            '.dat' : get_dat_filetype,

            '.h5'  : get_hdf_filetype,

            }.get(ext, get_mime_filetype)



    if callable(filetype):

        return filetype(filename)

    return filetype