Commit bce09847 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

transmission conversion is working

parent ba2bf344

pysen/inout/__init__.py

+2 −2
Original line number Diff line number Diff line
@@ -5,8 +5,8 @@ from .hdf import HdfConverter, convert_to_hdf # NOQA 
from .reader  import (  read_echo, read_magnetic, read_xyz,         # NOQA

                        read_detimage, read_datfile, read_diffrun,  # NOQA

                        read_datreat , read_transmission )          # NOQA

from .writer  import EchoWriter, DiffractionWriter                  # NOQA

from .scans   import EchoScan, DiffractionScan, XYZScan             # NOQA

from .writer  import EchoWriter, DiffractionWriter, TransmissionWriter    # NOQA

from .scans   import EchoScan, DiffractionScan, TransmissionScan, XYZScan # NOQA

from .utils   import get_nsefiletype

# from .legacy_writer  import write_csv, generate_echo                       # NOQA

# from .legacy_history import extract_data, list_variables, parse_date       # NOQA

pysen/inout/nexus.py

+41 −2
Original line number Diff line number Diff line
@@ -37,7 +37,7 @@ Y0_PIX = 518 
XWID2     =   813//2 # 410 # half-width

YWID2     =   821//2 # 410



LTOT_P2 = Ltot.get('p2')

LTOT_P2 = Ltot.get('p2') # default value if mo_l not found



MOTORS    = ('mophi', 'mopsi', 'mo_z', 'moana', 'mo_l', 'moatt')
@@ -92,6 +92,8 @@ def get_run_info(nxsfile): 
    res['notes']    = nxsfile['/entry/notes'][0].decode('ascii')

    res['duration'] = nxsfile['/entry/duration'][0]

    res['proton_charge'] = nxsfile['/entry/proton_charge'][0]

    res['ipts'] = nxsfile['/entry/experiment_identifier'][0].decode('ascii')

    res['experiment'] = nxsfile['/entry/experiment_title'][0].decode('ascii')



    log.info("%s: %s, duration=%.1f min", base, res['time'], res['duration']/60)

    log.info("%s: %s %s", base, res['title'], res['notes'])
@@ -152,6 +154,20 @@ def get_slice_average(key, val, begin, end=np.inf): 
    return last_val





def process_events(events, pcharge, ltot):

    "process nexus events"

    res = {}

    # get the proton charge for the phase

    res['pcharge'] = np.sum(pcharge[:]['value'])



    # event_time_offset is in usec

    lam = tof2lambda(events['event_time_offset'][:]*MICRO, ltot)/ANGSTROM

    pix = pixel_decompose(events['event_id'][:])

    res['lambda']  = lam

    res['pixel']   = pix

    res['neutron'] = np.vstack((lam,pix))

    return res



def process_scan_point(events, pcharge, ltot, begin=None, end=None, values=None):

    "get data for one phase point"

    ev_t0   = events['event_time_zero']
@@ -180,12 +196,13 @@ def process_scan_point(events, pcharge, ltot, begin=None, end=None, values=None) 
    res['neutron'] = np.vstack((lam,pix))

    return res





def _dummy_callback(*_args, **_kwargs):

    """dummy process scan point (for testing)

    a caller to process scan should override it"""

    return True



# process scan

# process nexus scan

def process_nexus_scan(filename, **kwargs):

    "process nexus file (scan indices)"

    scan_type    = kwargs.pop('scan_type', None)
@@ -247,4 +264,26 @@ def process_nexus_scan(filename, **kwargs): 
                i = k

        k = k + 1

    return info



# process nexus plain

def process_nexus_plain(filename, **kwargs):

    "process nexus file (scan indices)"

    scan_type    = kwargs.pop('scan_type', None)

    data         = kwargs.pop('data', None)

    #

    log     = logging.getLogger('nexus')

    base    = os.path.basename(filename)

    nxsfile = h5py.File(filename, 'r')

    # get file info

    info    = get_run_info(nxsfile)

    if scan_type and scan_type not in info.get('notes','').lower():

        log.warning('not an %s scan (%s)', scan_type, info['notes'])

        return None

    if info['proton_charge']<=0.0:

        log.warning("%s: empty run (pcharge=%g)", base, info['proton_charge'])

        return None

    if data is not None:

        res = process_events(nxsfile['entry/bank1_events'], timevalue_array(nxsfile, 'proton_charge'), info['mo_l'])

        data.update(res)

    return info

# EOF

pysen/inout/nxs2echo.py

+4 −4
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ import os.path 
import logging

import argparse



from pysen.inout import EchoWriter, DiffractionWriter, get_nsefiletype

from pysen.inout import EchoWriter, DiffractionWriter, TransmissionWriter, get_nsefiletype



def main():

    "the main"
@@ -29,7 +29,6 @@ def main(): 
                        const=logging.WARNING, help='suppress info messages')

    args = parser.parse_args()





    logging.basicConfig(format='%(levelname)s %(message)s', level=args.loglevel)

    log = logging.getLogger()
@@ -40,6 +39,7 @@ def main(): 
        file_type = get_nsefiletype(file_name)

        writer_class = { 'application/nexus-nse-echo'     : EchoWriter,

                         'application/nexus-diffraction'  : DiffractionWriter,

                         'application/nexus-transmission' : TransmissionWriter,

                        }.get(file_type, None)

        if not isinstance(writer_class, type):

            log.warning("file '%s' unknown file type %s", file_name, file_type)

pysen/inout/scans.py

+4 −10
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ import logging 
import numpy as np



from ..config import NXCHAN as NPIX, NTCHAN as NTOF

from .nexus   import process_nexus_scan, print_nexus_info, X0_PIX, Y0_PIX, XWID2, YWID2

from .nexus   import process_nexus_scan, process_nexus_plain, print_nexus_info, X0_PIX, Y0_PIX, XWID2, YWID2



# BUNCH OF HARD CODED CONSTANTS
@@ -61,14 +61,9 @@ class BaseScan: 
        self.log.debug("nexus info: %s", print_nexus_info(self.info))

        return True



class TransmissionScan:

class TransmissionScan(BaseScan):

    """Read SNS-NSE EPICS/NeXus transmission scan file

    """

    def __init__(self):

        "the constructor"

        self.log  = logging.getLogger()

        self.data = {}

        self.info = None



    def read_nexus(self, nxsfile, **kwargs):

        """read nexus file"""
@@ -76,10 +71,9 @@ class TransmissionScan: 
        #

        kwargs.setdefault('npix', NPIX)

        kwargs.setdefault('ntof', NTOF)

        scan_type = kwargs.setdefault('scan_type', None)

        kwargs.setdefault('scan_type', None)

        #

        self.info = process_nexus_scan(nxsfile, scanpoint_cb=self.phasepoint_callback,

                                  scan_type=scan_type)

        self.info = process_nexus_plain(nxsfile, data=self.data)

        if self.info is None:

            return False

        self.info.update(**kwargs)

pysen/inout/writer.py

+53 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ from ..config import ( XDET, YDET, DEFAULT_PROTON_ENERGY as PROTON_ENERGY, 
            PROTON_CHARGE_UNIT, get_attenuator_pos)

from ..constants import PICO, NANO, MICRO, ANGSTROM, GAUSS

from .nexus import MOTORS, B_SENSORS

from .scans import EchoScan, DiffractionScan

from .scans import EchoScan, DiffractionScan, TransmissionScan



# BUNCH OF HARD CODED CONSTANTS

# TO DO: some of this is repeated in nexus.py file (merge!)
@@ -33,6 +33,58 @@ def get_phase_index(scan_index, offset=0): 






class TransmissionWriter(TransmissionScan):

    "Convert EPICS/ADARA/NeXus file to transmission .dat file"



    @staticmethod

    def make_filename(base):

        "make diffraction filename"

        root, _ = os.path.splitext(os.path.basename(base)) # remove h5

        root, _ = os.path.splitext(root)                   # remove nxs

        numor = int(root.split('_')[-1])

        return f"transmission_{numor}.dat"



    def save(self, outdir='.'):

        "convert read nexus file to diffrun .dat file"

        transmission_run = self.make_filename(self.info['base'])

        with open(os.path.join(outdir, transmission_run), 'wt', encoding='ascii') as fd:

            #

            self.log.info("%s: creating transmission .dat file", transmission_run)

            lmax = self.info.get('lmax', 8.0)*ANGSTROM

            ipts = self.info.get('ipts',' ').lower().replace('ipts-','')

            fd.write(f"\n\"Transmission for IPTS \" {ipts}")

            fd.write(f"  \", sample \" {self.info.get('title','')}")

            fd.write(f"  \", wavelength \" {lmax} \n")



            # detector data

            res = self.data

            #qmin    = res.get('qmin')

            pcharge  = res['pcharge']*PICO/PROTON_CHARGE_UNIT #  convert to echo units

            neutrons = res['neutron']

            xbin = self.info['xbin']

            ybin = self.info['ybin']

            tbin = self.info['tbin']

            h3,_  = np.histogramdd((neutrons[0], neutrons[1], neutrons[2]),

                                  bins=(tbin, ybin, xbin))

            detsum  = neutrons.shape[-1]

            tofdet  = h3.sum(axis=(1,2))



            fd.write( "\"detector.sum anode strobe mon1 mon2 proton_charge det.sum/proton_charge\"\n")

            fd.write(f"{detsum} {detsum} {detsum} 0 0 {pcharge:.0f} {detsum/pcharge}\n")

            fd.write( "\n\"detector array\"\n")

            fd.write("\n".join([f"{val:.0f}" for val in tofdet]))

            fd.write( "\n\"mon1 array\"\n")

            fd.write("\n".join(["0" for _ in tofdet]))

            fd.write( "\n\"mon2 array\"\n")

            fd.write("\n".join(["0" for _ in tofdet]))

            fd.write( "\n")

#

            #fd.write(f"\"Det sum/proton charge\"  {detsum/pcharge:g}  ")

            #fd.write(f"\"Det win/proton charge\"  {detwin/pcharge:g}  ")

            #fd.write( "\n")



            self.log.info("%s: done", transmission_run)

        return transmission_run



class DiffractionWriter(DiffractionScan):

    "Convert EPICS/ADARA/NeXus file to diffrun .dat file"