EDCS demo

27/09/19 Basic read + plot for EDCS data.

Basic IO


In [1]:
import sys
import os
import numpy as np

# For module testing, include path to local module code here
modPath = r'/home/femtolab/github/ePSproc/'
sys.path.append(modPath)
import epsproc as ep


* pyevtk not found, VTK export not available. 
* plotly not found, plotly plots not available. 

In [3]:
# Load data from modPath\data\filename
dataPath = os.path.join(modPath, 'data')
fileName = 'test13.inp.out'  # Test with standard ePolyScat test job for N2 EDCS

# Scan file(s)
dataSet = ep.readMatEle(os.path.join(dataPath, fileName), recordType = 'EDCS')


*** ePSproc readMatEle(): scanning files for EDCS segments.

*** Scanning file(s)
['/home/femtolab/github/ePSproc/data/test13.inp.out']

*** Reading ePS output file:  /home/femtolab/github/ePSproc/data/test13.inp.out
Scanning EDCS segments.
Found 4 EDCS segments (sets of scattering results).
Processed 4 sets of EDCS file segments, (0 blank)

In [4]:
dataSet[0].plot()


Out[4]:
<matplotlib.collections.QuadMesh at 0x7f63207caed0>

Low-level function tests


In [5]:
# Load data from modPath\data\filename
dataPath = os.path.join(modPath, 'data')
fileName = 'test13.inp.out'  # Test with standard ePolyScat test job for N2 EDCS

# Run low-level file-scanner for EDCS segments
lines, dumpSegs = ep.EDCSFileParse(os.path.join(dataPath, fileName))


Found 4 EDCS segments (sets of scattering results).

In [6]:
# Inspect one file segment
dumpSegs[0]


Out[6]:
[[0, 10830, 'EDCS - differential cross section program\n'],
 [0,
  10831,
  '----------------------------------------------------------------------\n'],
 [0, 10832, '\n'],
 [0,
  10833,
  ' Title -                                                                       \n'],
 [0, 10834, ' Maximum l to use from k matrices (lmax) =   10\n'],
 [0,
  10835,
  'Minimum l to compute in the expansion of the DCS (lbigl) =    0\n'],
 [0, 10836, 'Maximum l to use in the expansion of the DCS (lbig) =   20\n'],
 [0, 10837, 'Unit to write DCS in plot format (iuplt) =    0\n'],
 [0, 10838, 'Number of angles at which to compute the DCS (nang) =  181\n'],
 [0, 10839, 'Print flag (iprint) =    0\n'],
 [0, 10840, 'Energy to compute the EDCS at (eV) =      3.00000000\n'],
 [0, 10841, '\n'],
 [0, 10842, '\n'],
 [0,
  10843,
  '  Energy (eV)= 3.0000      Energy (ryd)=0.2204960  xk=0.4695700\n'],
 [0, 10844, '\n'],
 [0, 10845, '\n'],
 [0, 10846, ' AL coefficients\n'],
 [0, 10847, '        -1     0.30000000000000E+01\n'],
 [0, 10848, '         0     0.54024139702667E+01\n'],
 [0, 10849, '         1     0.20001650397665E+01\n'],
 [0, 10850, '         2     0.16217303863025E+01\n'],
 [0, 10851, '         3    -0.23809592325903E+01\n'],
 [0, 10852, '         4     0.13484180228387E+01\n'],
 [0, 10853, '         5     0.18365857453963E-01\n'],
 [0, 10854, '         6    -0.54365471200529E-02\n'],
 [0, 10855, '         7    -0.93590163431004E-02\n'],
 [0, 10856, '         8    -0.11746922380453E-01\n'],
 [0, 10857, '         9    -0.12283287440712E-01\n'],
 [0, 10858, '        10    -0.23835235245853E-02\n'],
 [0, 10859, '        11    -0.76078219515096E-02\n'],
 [0, 10860, '        12    -0.75374221031280E-02\n'],
 [0, 10861, '        13     0.33432420523306E-02\n'],
 [0, 10862, '        14     0.30033210974078E-02\n'],
 [0, 10863, '        15     0.26056309951987E-02\n'],
 [0, 10864, '        16     0.20828132795496E-02\n'],
 [0, 10865, '        17     0.16250251678011E-02\n'],
 [0, 10866, '        18     0.10940533236128E-02\n'],
 [0, 10867, '        19     0.64990710983458E-03\n'],
 [0, 10868, '        20     0.29032054309118E-03\n'],
 [0, 10869, '\n'],
 [0, 10870, 'For comparison\n'],
 [0, 10871, '        -1        3.00000     alcoef\n'],
 [0, 10872, '         0        5.40241     alcoef\n'],
 [0, 10873, '         1        2.00017     alcoef\n'],
 [0, 10874, '         2        1.62173     alcoef\n'],
 [0, 10875, '         3       -2.38096     alcoef\n'],
 [0, 10876, '         4        1.34842     alcoef\n'],
 [0, 10877, '         5        0.01837     alcoef\n'],
 [0, 10878, '         6       -0.00544     alcoef\n'],
 [0, 10879, '         7       -0.00936     alcoef\n'],
 [0, 10880, '         8       -0.01175     alcoef\n'],
 [0, 10881, '         9       -0.01228     alcoef\n'],
 [0, 10882, '        10       -0.00238     alcoef\n'],
 [0, 10883, '        11       -0.00761     alcoef\n'],
 [0, 10884, '        12       -0.00754     alcoef\n'],
 [0, 10885, '        13        0.00334     alcoef\n'],
 [0, 10886, '        14        0.00300     alcoef\n'],
 [0, 10887, '        15        0.00261     alcoef\n'],
 [0, 10888, '        16        0.00208     alcoef\n'],
 [0, 10889, '        17        0.00163     alcoef\n'],
 [0, 10890, '        18        0.00109     alcoef\n'],
 [0, 10891, '        19        0.00065     alcoef\n'],
 [0, 10892, '        20        0.00029     alcoef\n'],
 [0, 10893, ' Total Cross Section (Angstrom^2) =  0.1901078216E+02\n'],
 [0,
  10894,
  ' Momentum Transfer Cross Section (Angstrom^2) =  0.1666462715E+02\n'],
 [0, 10895, ' Differential Cross Section \n'],
 [0, 10896, '   Ang   Cross Section (Angstrom^2)\n'],
 [0, 10897, '     0.0    0.2231399912E+01\n'],
 [0, 10898, '     1.0    0.2231161267E+01\n'],
 [0, 10899, '     2.0    0.2230448701E+01\n'],
 [0, 10900, '     3.0    0.2229272059E+01\n'],
 [0, 10901, '     4.0    0.2227646904E+01\n'],
 [0, 10902, '     5.0    0.2225593337E+01\n'],
 [0, 10903, '     6.0    0.2223134480E+01\n'],
 [0, 10904, '     7.0    0.2220294785E+01\n'],
 [0, 10905, '     8.0    0.2217098289E+01\n'],
 [0, 10906, '     9.0    0.2213566999E+01\n'],
 [0, 10907, '    10.0    0.2209719526E+01\n'],
 [0, 10908, '    11.0    0.2205570102E+01\n'],
 [0, 10909, '    12.0    0.2201128070E+01\n'],
 [0, 10910, '    13.0    0.2196397884E+01\n'],
 [0, 10911, '    14.0    0.2191379628E+01\n'],
 [0, 10912, '    15.0    0.2186070008E+01\n'],
 [0, 10913, '    16.0    0.2180463739E+01\n'],
 [0, 10914, '    17.0    0.2174555207E+01\n'],
 [0, 10915, '    18.0    0.2168340271E+01\n'],
 [0, 10916, '    19.0    0.2161818054E+01\n'],
 [0, 10917, '    20.0    0.2154992580E+01\n'],
 [0, 10918, '    21.0    0.2147874123E+01\n'],
 [0, 10919, '    22.0    0.2140480157E+01\n'],
 [0, 10920, '    23.0    0.2132835839E+01\n'],
 [0, 10921, '    24.0    0.2124973983E+01\n'],
 [0, 10922, '    25.0    0.2116934525E+01\n'],
 [0, 10923, '    26.0    0.2108763531E+01\n'],
 [0, 10924, '    27.0    0.2100511802E+01\n'],
 [0, 10925, '    28.0    0.2092233193E+01\n'],
 [0, 10926, '    29.0    0.2083982757E+01\n'],
 [0, 10927, '    30.0    0.2075814825E+01\n'],
 [0, 10928, '    31.0    0.2067781155E+01\n'],
 [0, 10929, '    32.0    0.2059929256E+01\n'],
 [0, 10930, '    33.0    0.2052300959E+01\n'],
 [0, 10931, '    34.0    0.2044931317E+01\n'],
 [0, 10932, '    35.0    0.2037847862E+01\n'],
 [0, 10933, '    36.0    0.2031070210E+01\n'],
 [0, 10934, '    37.0    0.2024610033E+01\n'],
 [0, 10935, '    38.0    0.2018471314E+01\n'],
 [0, 10936, '    39.0    0.2012650862E+01\n'],
 [0, 10937, '    40.0    0.2007139010E+01\n'],
 [0, 10938, '    41.0    0.2001920423E+01\n'],
 [0, 10939, '    42.0    0.1996974958E+01\n'],
 [0, 10940, '    43.0    0.1992278511E+01\n'],
 [0, 10941, '    44.0    0.1987803808E+01\n'],
 [0, 10942, '    45.0    0.1983521101E+01\n'],
 [0, 10943, '    46.0    0.1979398758E+01\n'],
 [0, 10944, '    47.0    0.1975403726E+01\n'],
 [0, 10945, '    48.0    0.1971501885E+01\n'],
 [0, 10946, '    49.0    0.1967658294E+01\n'],
 [0, 10947, '    50.0    0.1963837354E+01\n'],
 [0, 10948, '    51.0    0.1960002908E+01\n'],
 [0, 10949, '    52.0    0.1956118290E+01\n'],
 [0, 10950, '    53.0    0.1952146349E+01\n'],
 [0, 10951, '    54.0    0.1948049463E+01\n'],
 [0, 10952, '    55.0    0.1943789537E+01\n'],
 [0, 10953, '    56.0    0.1939328011E+01\n'],
 [0, 10954, '    57.0    0.1934625872E+01\n'],
 [0, 10955, '    58.0    0.1929643662E+01\n'],
 [0, 10956, '    59.0    0.1924341505E+01\n'],
 [0, 10957, '    60.0    0.1918679131E+01\n'],
 [0, 10958, '    61.0    0.1912615920E+01\n'],
 [0, 10959, '    62.0    0.1906110960E+01\n'],
 [0, 10960, '    63.0    0.1899123136E+01\n'],
 [0, 10961, '    64.0    0.1891611254E+01\n'],
 [0, 10962, '    65.0    0.1883534212E+01\n'],
 [0, 10963, '    66.0    0.1874851234E+01\n'],
 [0, 10964, '    67.0    0.1865522168E+01\n'],
 [0, 10965, '    68.0    0.1855507848E+01\n'],
 [0, 10966, '    69.0    0.1844770534E+01\n'],
 [0, 10967, '    70.0    0.1833274408E+01\n'],
 [0, 10968, '    71.0    0.1820986122E+01\n'],
 [0, 10969, '    72.0    0.1807875382E+01\n'],
 [0, 10970, '    73.0    0.1793915537E+01\n'],
 [0, 10971, '    74.0    0.1779084163E+01\n'],
 [0, 10972, '    75.0    0.1763363609E+01\n'],
 [0, 10973, '    76.0    0.1746741483E+01\n'],
 [0, 10974, '    77.0    0.1729211056E+01\n'],
 [0, 10975, '    78.0    0.1710771570E+01\n'],
 [0, 10976, '    79.0    0.1691428440E+01\n'],
 [0, 10977, '    80.0    0.1671193339E+01\n'],
 [0, 10978, '    81.0    0.1650084181E+01\n'],
 [0, 10979, '    82.0    0.1628124987E+01\n'],
 [0, 10980, '    83.0    0.1605345675E+01\n'],
 [0, 10981, '    84.0    0.1581781762E+01\n'],
 [0, 10982, '    85.0    0.1557474020E+01\n'],
 [0, 10983, '    86.0    0.1532468089E+01\n'],
 [0, 10984, '    87.0    0.1506814073E+01\n'],
 [0, 10985, '    88.0    0.1480566138E+01\n'],
 [0, 10986, '    89.0    0.1453782124E+01\n'],
 [0, 10987, '    90.0    0.1426523177E+01\n'],
 [0, 10988, '    91.0    0.1398853426E+01\n'],
 [0, 10989, '    92.0    0.1370839690E+01\n'],
 [0, 10990, '    93.0    0.1342551233E+01\n'],
 [0, 10991, '    94.0    0.1314059559E+01\n'],
 [0, 10992, '    95.0    0.1285438246E+01\n'],
 [0, 10993, '    96.0    0.1256762821E+01\n'],
 [0, 10994, '    97.0    0.1228110658E+01\n'],
 [0, 10995, '    98.0    0.1199560913E+01\n'],
 [0, 10996, '    99.0    0.1171194468E+01\n'],
 [0, 10997, '   100.0    0.1143093899E+01\n'],
 [0, 10998, '   101.0    0.1115343434E+01\n'],
 [0, 10999, '   102.0    0.1088028925E+01\n'],
 [0, 11000, '   103.0    0.1061237787E+01\n'],
 [0, 11001, '   104.0    0.1035058925E+01\n'],
 [0, 11002, '   105.0    0.1009582622E+01\n'],
 [0, 11003, '   106.0    0.9849003793E+00\n'],
 [0, 11004, '   107.0    0.9611047016E+00\n'],
 [0, 11005, '   108.0    0.9382888154E+00\n'],
 [0, 11006, '   109.0    0.9165463176E+00\n'],
 [0, 11007, '   110.0    0.8959707480E+00\n'],
 [0, 11008, '   111.0    0.8766550862E+00\n'],
 [0, 11009, '   112.0    0.8586911788E+00\n'],
 [0, 11010, '   113.0    0.8421691032E+00\n'],
 [0, 11011, '   114.0    0.8271764821E+00\n'],
 [0, 11012, '   115.0    0.8137977627E+00\n'],
 [0, 11013, '   116.0    0.8021134817E+00\n'],
 [0, 11014, '   117.0    0.7921995331E+00\n'],
 [0, 11015, '   118.0    0.7841264631E+00\n'],
 [0, 11016, '   119.0    0.7779588080E+00\n'],
 [0, 11017, '   120.0    0.7737544974E+00\n'],
 [0, 11018, '   121.0    0.7715643332E+00\n'],
 [0, 11019, '   122.0    0.7714315594E+00\n'],
 [0, 11020, '   123.0    0.7733915269E+00\n'],
 [0, 11021, '   124.0    0.7774714578E+00\n'],
 [0, 11022, '   125.0    0.7836903058E+00\n'],
 [0, 11023, '   126.0    0.7920587092E+00\n'],
 [0, 11024, '   127.0    0.8025790262E+00\n'],
 [0, 11025, '   128.0    0.8152454435E+00\n'],
 [0, 11026, '   129.0    0.8300441450E+00\n'],
 [0, 11027, '   130.0    0.8469535295E+00\n'],
 [0, 11028, '   131.0    0.8659444632E+00\n'],
 [0, 11029, '   132.0    0.8869805584E+00\n'],
 [0, 11030, '   133.0    0.9100184654E+00\n'],
 [0, 11031, '   134.0    0.9350081706E+00\n'],
 [0, 11032, '   135.0    0.9618932935E+00\n'],
 [0, 11033, '   136.0    0.9906113749E+00\n'],
 [0, 11034, '   137.0    0.1021094154E+01\n'],
 [0, 11035, '   138.0    0.1053267827E+01\n'],
 [0, 11036, '   139.0    0.1087053289E+01\n'],
 [0, 11037, '   140.0    0.1122366354E+01\n'],
 [0, 11038, '   141.0    0.1159117950E+01\n'],
 [0, 11039, '   142.0    0.1197214296E+01\n'],
 [0, 11040, '   143.0    0.1236557054E+01\n'],
 [0, 11041, '   144.0    0.1277043465E+01\n'],
 [0, 11042, '   145.0    0.1318566473E+01\n'],
 [0, 11043, '   146.0    0.1361014837E+01\n'],
 [0, 11044, '   147.0    0.1404273253E+01\n'],
 [0, 11045, '   148.0    0.1448222477E+01\n'],
 [0, 11046, '   149.0    0.1492739477E+01\n'],
 [0, 11047, '   150.0    0.1537697623E+01\n'],
 [0, 11048, '   151.0    0.1582966907E+01\n'],
 [0, 11049, '   152.0    0.1628414240E+01\n'],
 [0, 11050, '   153.0    0.1673903793E+01\n'],
 [0, 11051, '   154.0    0.1719297420E+01\n'],
 [0, 11052, '   155.0    0.1764455149E+01\n'],
 [0, 11053, '   156.0    0.1809235736E+01\n'],
 [0, 11054, '   157.0    0.1853497295E+01\n'],
 [0, 11055, '   158.0    0.1897097971E+01\n'],
 [0, 11056, '   159.0    0.1939896657E+01\n'],
 [0, 11057, '   160.0    0.1981753739E+01\n'],
 [0, 11058, '   161.0    0.2022531848E+01\n'],
 [0, 11059, '   162.0    0.2062096600E+01\n'],
 [0, 11060, '   163.0    0.2100317316E+01\n'],
 [0, 11061, '   164.0    0.2137067696E+01\n'],
 [0, 11062, '   165.0    0.2172226439E+01\n'],
 [0, 11063, '   166.0    0.2205677806E+01\n'],
 [0, 11064, '   167.0    0.2237312108E+01\n'],
 [0, 11065, '   168.0    0.2267026126E+01\n'],
 [0, 11066, '   169.0    0.2294723463E+01\n'],
 [0, 11067, '   170.0    0.2320314823E+01\n'],
 [0, 11068, '   171.0    0.2343718241E+01\n'],
 [0, 11069, '   172.0    0.2364859253E+01\n'],
 [0, 11070, '   173.0    0.2383671025E+01\n'],
 [0, 11071, '   174.0    0.2400094450E+01\n'],
 [0, 11072, '   175.0    0.2414078212E+01\n'],
 [0, 11073, '   176.0    0.2425578838E+01\n'],
 [0, 11074, '   177.0    0.2434560723E+01\n'],
 [0, 11075, '   178.0    0.2440996157E+01\n'],
 [0, 11076, '   179.0    0.2444865341E+01\n'],
 [0, 11077, '   180.0    0.2446156390E+01\n']]

In [7]:
# Parse results - basic manual version
# Now implemented in ep.EDCSSegParse()
# from io import StringIO
# EDCSlist = []
# Elist = []
# for dumpSeg in dumpSegs:
#     # E = dumpSeg[13][2].split()
#     E = np.float(ep.parseLineDigits(dumpSeg[13][2])[0])
#     Elist.append(E)
    
#     # For each line convert to float - bit ugly, but works
#     tmp = []
#     for testLine in dumpSeg[67:]:
#         tmp.append(np.genfromtxt(StringIO(testLine[2])))
    
#     # Stack with E
#     EDCSlist.append(np.asarray(tmp))
    
# np.asarray(Elist)
# # print(np.asarray(EDCSlist))

# With functions

# Single energy
EDCS, attribs = ep.EDCSSegParse(dumpSegs[0])

EDCS[0:10,:]


Out[7]:
array([[0.        , 2.23139991],
       [1.        , 2.23116127],
       [2.        , 2.2304487 ],
       [3.        , 2.22927206],
       [4.        , 2.2276469 ],
       [5.        , 2.22559334],
       [6.        , 2.22313448],
       [7.        , 2.22029479],
       [8.        , 2.21709829],
       [9.        , 2.213567  ]])

In [8]:
# Test code - now functionalised in ep.EDCSSegsParseX
import xarray as xr
dataList = []
dataArray = []
ekeList = []
blankSegs = 0

# Loop over DumpIdy segments, extract data & reformat
# If blank, skip parser and append blankSegs.
for dumpSeg in dumpSegs:
    if len(dumpSeg)>4:
        segBlock, attribs = ep.EDCSSegParse(dumpSeg)
        dataArray.append(segBlock[:,1])         # For brevity, just stack XS data here - will save Xarray sorting later.
        dataList.append([segBlock[:,0], segBlock[:,1], attribs])
        ekeList.append(attribs[0][1])

    else:
        blankSegs += 1
        ekeList.append(np.nan)

# Dump lists into Xarray - will work provided same theta over all records.
daOut = xr.DataArray(np.asarray(dataArray), coords={'E':ekeList, 'Theta':segBlock[:,0]}, dims = ['E','Theta'])

daOut


Out[8]:
<xarray.DataArray (E: 4, Theta: 181)>
array([[ 2.23139991,  2.23116127,  2.2304487 ,  2.22927206,  2.2276469 ,
         2.22559334,  2.22313448,  2.22029479,  2.21709829,  2.213567  ,
         2.20971953,  2.2055701 ,  2.20112807,  2.19639788,  2.19137963,
         2.18607001,  2.18046374,  2.17455521,  2.16834027,  2.16181805,
         2.15499258,  2.14787412,  2.14048016,  2.13283584,  2.12497398,
         2.11693453,  2.10876353,  2.1005118 ,  2.09223319,  2.08398276,
         2.07581483,  2.06778116,  2.05992926,  2.05230096,  2.04493132,
         2.03784786,  2.03107021,  2.02461003,  2.01847131,  2.01265086,
         2.00713901,  2.00192042,  1.99697496,  1.99227851,  1.98780381,
         1.9835211 ,  1.97939876,  1.97540373,  1.97150188,  1.96765829,
         1.96383735,  1.96000291,  1.95611829,  1.95214635,  1.94804946,
         1.94378954,  1.93932801,  1.93462587,  1.92964366,  1.9243415 ,
         1.91867913,  1.91261592,  1.90611096,  1.89912314,  1.89161125,
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Coordinates:
  * E        (E) float64 3.0 4.0 5.0 6.0
  * Theta    (Theta) float64 0.0 1.0 2.0 3.0 4.0 ... 177.0 178.0 179.0 180.0

In [9]:
# Plot from Xarray
daOut.plot()


Out[9]:
<matplotlib.collections.QuadMesh at 0x7f63207fff90>