Library Spectra Export process results

Read spectra files exported from the Bruker Spectra Library. All spectra files shall end with ".spectrum" and be located in one folder. Only one spectrum per file.

Please, specify the folder containing *.spectrum files and the name for the results file:



In [1]:

    
folder  = 'D:\data\Libraries\Example_Xpec'
archive = 'all_spectra.json'

Load modules and define functions.



In [2]:

    
import sys
import os.path
import codecs
import json

def dpstr2dict(filename, data_points_string, meta_count):
    data_points = {} # using a dict to store the spectrum
                     # TODO: maybe use numpy ndarray instead
    points = data_points_string.strip().split()
    count = len(points)
    if (count / 2) != int(meta_count):
        print "Could not convert string to dict! Data point mismatch in spectrum: " + filename
        return data_points_string # preserve original data
    for i in xrange(0, count, 2):
        data_points[float(points[i])] = int(points[i + 1])
    #print (meta_count)
    #print len(data_points)
    return data_points

def readspectrum(filename, filecontent):
    spectrum = {'SpecFile': filename}
    values = ""
    for line in filecontent.splitlines():
        contents = line.split(':')
        if len(contents) == 2:
            key, value = contents
            spectrum[key.strip()] = value.strip()
        # 'Date', 'AnalName' and probably comments have multiple ':'
        elif len(contents) > 2:
            key = contents[0]
            value = ':'.join(contents[1:])
            spectrum[key.strip()] = value.strip()
        # spectra do not contain ":"
        else:
            values += contents[0]
    values = dpstr2dict(filename, values, spectrum['Num Peaks'])
    spectrum['Values'] = values
    return spectrum

Run the main script, which uses the functions above to collect all spectra in a list of dicts.



In [3]:

    
folder = os.path.abspath(folder)

if not os.path.exists(folder) or not os.path.isdir(folder):
    print "Folder not found!"
    sys.exit(0)

library = []

for spectrum in os.listdir(folder):
    if not spectrum.endswith('.spectrum'):
        print "Skipped file: " + spectrum
        continue
    spectrum = os.path.join(folder, spectrum)
    #print spectrum
    with codecs.open(spectrum, 'r', 'cp1252') as s:
        data = readspectrum(spectrum, s.read())
        library.append(data)

print 'The library contains ' + str(len(library)) + ' spectra.'









    



The library contains 352 spectra.

Store all spectra in a single JSON file.



In [4]:

    
archive = os.path.join(folder, archive)

with open(archive, 'w') as out:
    json.dump(library, out, indent = 4, sort_keys = True)