Commit c8e3f3a5 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

fixed issue #4 (incorrect i00 assignment) 

the problem was that i00 (main SC current) is slowly changing and not all
echo phases had a i00 entered in the /entry/DASlogs/BL15:Bruker:ReadOutCurrent)

So, if empty 'slice' pick the last known value.

Also run pylint police in test subdirectory.
parent 3ffdcd27

misc/plot_daslog2.py

0 → 100755
+28 −0
Original line number Diff line number Diff line 
#!/usr/bin/env python3



import sys

import os

import subprocess

import h5py



import numpy as np

import matplotlib.pyplot as plt





filename=sys.argv[1]

skip=4



nxsfile = h5py.File(filename)



for var in sys.argv[2:]:

    times  = nxsfile[f"/entry/DASlogs/{var}/time"]

    values = nxsfile[f"/entry/DASlogs/{var}/value"]

    times  = np.asarray(times)

    values = np.asarray(values)

    plt.plot(times, values, 'o--', ms=2, label=var)

plt.legend()

plt.show()

pysen/inout/nexus.py

+23 −18
Original line number Diff line number Diff line
@@ -26,6 +26,7 @@ import numpy as np 
import h5py



from pysen import MICRO, ANGSTROM, tof2lambda

from pysen.config import Ltot



TDC_SHIFT =    10

TDC_MAXCH = 0x3FF
@@ -36,6 +37,8 @@ Y0_PIX = 518 
XWID2     =   813//2 # 410 # half-width

YWID2     =   821//2 # 410



LTOT_P2 = Ltot.get('p2')



MOTORS    = ('mophi', 'mopsi', 'mo_z', 'moana', 'mo_l', 'moatt')



B_SENSORS = {'b_sample': 'sample'  ,
@@ -69,17 +72,6 @@ def timevalue_array(nexus_file, vname, prefix="/entry/DASlogs", dtype=TimeFloatV 
    v_value = nexus_file[f"{prefix}/{vname}/value"][:]

    return np.array(list(zip(v_time,v_value)), dtype=dtype)



def get_average(val, begin, end):

    """

    calculate average between two time stamps

    """

    sel = np.logical_and(begin<val['time'],   val['time']<end)

    sel = val[sel]

    if sel.size:

        avg = np.average(sel['value'])

    else:

        avg = np.average(val['value'])

    return avg



def time_format(ctime, fmt='%c'):

    "convert 'nexus' time to 'echo' time format"
@@ -117,8 +109,9 @@ def get_run_info(nxsfile): 
            value = default_value

        return value

    # FIXME: put these in some confg list

    res['mo_l']  = get_average_value('/entry/DASlogs/BL15:Mot:mo_l',  21.3)

    res['mophi'] = get_average_value('/entry/DASlogs/BL15:Mot:mophi', None)

    for motor in ('mophi', 'mopsi', 'mo_z', 'moana', 'mo_l', 'moatt'):

        default_value = LTOT_P2 if motor=='mo_l' else None

        res[motor] = get_average_value(f"/entry/DASlogs/BL15:Mot:{motor}", default_value)

    res['qmin' ] = get_average_value('/entry/DASlogs/BL15:Mot:Qmin', 0.1)

    res['lmin' ] = get_average_value('/entry/DASlogs/BL15:Chop:Skf1:WavelengthSet', None)

    res['lmax' ] = get_average_value('/entry/DASlogs/BL15:Chop:Skf4:WavelengthSet', None)
@@ -145,6 +138,20 @@ def print_nexus_info(runinfo): 
            res = res + f"\n{k:16}: {v}"

    return res



def get_slice_average(key, val, begin, end=np.inf):

    """ calculate average between two time stamps """

    sel = np.logical_and(begin<val['time'],   val['time']<end)

    sel = val[sel]

    if sel.size:

        return np.average(sel['value'])

    # empty slice

    # FIXME: assuming there will be data before

    last_time = val['time']<=end

    last_val  = val[last_time]['value'][-1]

    logging.getLogger('nexus').warning("key '%s': empty slice, last known value: %s", key, last_val)

    return last_val





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']
@@ -158,7 +165,7 @@ def process_scan_point(events, pcharge, ltot, begin=None, end=None, values=None) 


    # other stuff

    for key, val in values.items():

        res[key] = get_average(val, begin, end)

        res[key] = get_slice_average(key, val, begin, end)



    # events selection

    ev_sel = np.logical_and(begin<ev_t0,ev_t0<end)
@@ -212,8 +219,6 @@ def process_nexus(filename, **kwargs): 
        'i00'  : timevalue_array(nxsfile, 'BL15:Bruker:ReadOutCurrent'),

        'phase': timevalue_array(nxsfile, 'BL15:CAENELS5:ActualCurrent'),

    }

    for motor in ('mophi', 'mopsi', 'mo_z', 'moana', 'mo_l', 'moatt'):

        values[motor] = timevalue_array(nxsfile, f"BL15:Mot:{motor}")

    for bsens in ('sample', 'encl1', 'encl2', 'ext1','ext2', 'ext3','ext4','ext5'):

        values['b_'+bsens] = timevalue_array(nxsfile, f"BL15:PLC:Mag:{bsens}")
@@ -227,7 +232,7 @@ def process_nexus(filename, **kwargs): 
                res = process_scan_point(events, pcharge, ltot=info['mo_l'],

                        begin=scan_index[i]['time'], end=scan_index[k]['time'],

                        values=values)

                # FIXME: get tau ....

                # FIXME: get tau, j1, j2

                for key in ('tau', 'j1', 'j2'):

                    it =  info[key]['time']<=scan_index[i]['time']   # tau set before scan

                    res[key] = info[key][it]['value'][-1]

pysen/inout/utils.py

+33 −2
Original line number Diff line number Diff line
@@ -2,16 +2,22 @@ 
pysen I/O utils module

"""



# based recipe on stack overflow http://bit.ly/2cv5wpk

#

import os.path

import bz2

import gzip

import mimetypes



import h5py



# based recipe on stack overflow http://bit.ly/2cv5wpk

magic_dict = {

    #"\x50\x4b\x03\x04": "zip"

    b"\x1f\x8b\x08"    : gzip.open, # GZIP

    b"\x42\x5a\x68"    : bz2.open , # BZIP2

}







max_len = max(len(x) for x in magic_dict)



def get_open_file(filename):
@@ -22,3 +28,28 @@ def get_open_file(filename): 
        if file_start == magic:

            return magic_dict.get(magic, open)

    return open





def get_nsefiletype(filename):

    "get filetype"

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

    if ext=='.echo':

        return "application/nse-echo"

    if ext=='.h5':

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

        if not ext2:

            return "application/nse-echo-hdf"

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

        try:

            notes   = nxsfile['/entry/notes']

            notes   = bytes(notes[0]).decode('ascii').lower()

            if 'scan=transmission' in notes:

                return "application/nexus-transmission"

            if 'scan=diffraction' in notes:

                return "application/nexus-diffraction"

            if 'scan=echo' in notes:

                return "application/nexus-nse-echo"



        except KeyError:

            pass

    return mimetypes.guess_type(filename)[0]

pysen/inout/writer.py

+10 −8
Original line number Diff line number Diff line
@@ -166,10 +166,12 @@ class EchoWriter(EchoScan): 
            phasesens   = self.info.get('phasesens')

            for it,tau in enumerate(self.data):

                self.log.info("%s: writing tau=%2d", self.echofile, tau)

                res    = self.data[tau][-1] # last phase

                ftau   = res['tau']*NANO

                j1, j2 = res['j1'],  res['j2']

                i0, i5 = res['i00'], res['phase']

                #res1   = self.data[tau][ 0] # first phase

                res2   = self.data[tau][-1] # last phase

                ftau   = res2['tau']*NANO

                j1, j2 = res2['j1'],  res2['j2']

                i5     = res2['phase']

                i0     = res2['i00'] # FIXME - bug here, often i00 is missig per phase point



                fd.write(f"c p{it}\n")

                #
@@ -180,12 +182,12 @@ class EchoWriter(EchoScan): 
                #

                fd.write( "c bsensors (x,y,z) aimed | actual\n")

                for bsens in B_SENSORS:

                    bfld = res[bsens]*MICRO/GAUSS

                    bfld = res2[bsens]*MICRO/GAUSS

                    fd.write(f"* {bsens:8s} 7.7 7.7 7.7 {bfld:14.6f} 0.0 0.0\n")

                #

                fd.write( "c motors\n")

                for mot in MOTORS:

                    pos = res[mot]

                    pos = self.info[mot]

                    if mot=='mo_l': # mo_l => convert to mm from m

                        pos = pos*1000.0

                    fd.write(f"* {mot:8s} {pos:9.3f} {pos:9.3f}\n")
@@ -208,8 +210,8 @@ class EchoWriter(EchoScan): 
                fd.write( "lambdaTable = \n")

                for lam in lambda_tab:

                    fd.write(f"   {lam:g}\n")

                phi = res['mophi']

                psi = res['mopsi']

                phi = self.info['mophi']

                psi = self.info['mopsi']

                sx = +np.sin(np.radians(phi))

                cx = -np.cos(np.radians(phi))

                fd.write(f"phi =    {phi:g} \n")

pysen/plot/nseplotlib.py

+3 −3
Original line number Diff line number Diff line
@@ -275,15 +275,15 @@ def plot_atari(hdfile, iecho=None, **kwargs): 
        minud, maxud = None, None

        try:

            tmp = np.hstack((pha,up,dn))

            minud = 10**np.floor(np.log10(min(tmp)))

            maxud = 10**np.ceil (np.log10(max(tmp)))

            #minud = min(0.0,0.8*min(tmp)) # 10**np.floor(np.log10(min(tmp)))

            #maxud = max(0.0,1.2*max(tmp)) # 10**np.ceil (np.log10(max(tmp)))

        except ValueError as exc:

            log.warning("cannot determine echo min/max: %s",exc)

            only_echo =True



        if only_echo:

            _txt = r'$A(Q,t)$=%.3g$\pm$%.3g' % res['amplitude']

            minud, maxud = None, None

            #minud, maxud = None, None

            log.info("Phase=%.4g(%.4g) Amp=%.4g(%.4g) Average=%.4g(%.4g)",

                phase_ef, phase_err,

                res['amplitude'][0], res['amplitude'][1],