Data processing of spectroscopy data (analytical chemistry)

The data consists of Raman spectra of macrophages. Data treatment is mainly based on the library specio.

In [1]:
from specio import specread # pip install git+https://github.com/paris-saclay-cds/specio.git
from os import path
import glob
from SPARQLWrapper import SPARQLWrapper, JSON
import urllib.request
import os
import errno
import numpy as np

Query data to select spc files in your campaign

In [2]:
sparql = SPARQLWrapper("https://opendata1.opendata.u-psud.fr/sparql/")
sparql.setQuery("""
    prefix daapp: <http://daap.eu/wiki/Data:Project#> 
prefix project:<http://daap.eu/wiki/Data:Analyse_des_macrophages#> 
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select ?spc
where {
        <http://daap.eu/wiki/Analyse_des_macrophages_m├ęthode_1>  daapp:hasCampaign ?campaign .
         ?campaign project:hasSlide ?slide .

        
        ?slide project:hasCell ?cell .
             ?cell project:hasPosition ?position.
             ?position  project:hasMeasure ?spc .
          
} 
""")
sparql.setReturnFormat(JSON)
results = sparql.query().convert()

path = "/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02"
if not os.path.exists(path):
    os.makedirs(path, exist_ok=False)

filenames = []
for result in results["results"]["bindings"]:
    filename = result["spc"]["value"].replace("http://134.158.74.40/", "/home/jupyter/Notebooks/htdocs/")
    if not os.path.exists(filename):
        print('Beginning data file:'+filename)
        urllib.request.urlretrieve(result["spc"]["value"],filename)
                
    filenames.append(filename)
    
filenames
Out[2]:
['/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell01_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell06_n3.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell04_n2.spc']

It is also possible to directly indicate directory and file extension to upload data

In [3]:
# DATA_PATH = ("/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02")
# EXT_FILE = "*.spc"
# filenames = glob.glob(path.join(DATA_PATH, EXT_FILE))
# filenames
In [4]:
filenames
Out[4]:
['/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EDL_L02_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_c2.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell06_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell02_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell06_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell05_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell04_n2.spc']

Read data

In [5]:
# def convert(f):
#     #print(f) 
#     specread(f)

list_raman = [specread(f)
              for f in filenames]
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In [6]:
print(type(list_raman[0]))
<class 'specio.core.util.Spectrum'>

Define the different groups of data (J774 macrophages are prepared in four different growth media)

In [7]:
cell_medium = ["EDL", "LDL", "STD", "EPA"]
dict_raman = {k: [] for k in cell_medium}
In [8]:
for key in dict_raman.keys():
    for f in filenames:
        if key in f:
            dict_raman[key].append(specread(f))
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Define the size of the matrix; create the dataframe and import it to a readable format

In [9]:
spectrum = np.array([sp.amplitudes for sp in list_raman])
print(spectrum.shape)
(504, 1732)
In [10]:
metadata = []
In [11]:
for f in filenames:
    name = os.path.basename(f)
    date, plate, cell, comp = name.split('_')
    date, medium = date[:8], date[8:]
    comp = comp.split('.')[0]
    
    metadata.append({'filename': name,
                     'date': date,
                     'medium': medium,
                     'plate': plate,
                     'cell': cell,
                     'comp': comp[0]})
In [12]:
import pandas as pd
metadata = pd.DataFrame(metadata)
print(metadata.head())
     cell comp      date                       filename medium plate
0  cell01    n  20170413  20170413EPA_L03_cell01_n1.spc    EPA   L03
1  cell06    n  20170413  20170413EPA_L03_cell06_n2.spc    EPA   L03
2  cell07    c  20170413  20170413EPA_L03_cell07_c3.spc    EPA   L03
3  cell03    n  20170413  20170413EPA_L03_cell03_n1.spc    EPA   L03
4  cell04    n  20170413  20170413EPA_L03_cell04_n3.spc    EPA   L03
In [13]:
df_spectrum = pd.DataFrame(spectrum, columns=list_raman[0].wavelength)
In [14]:
df_spectrum = pd.concat([metadata[['filename', 'medium', 'plate', 'comp']],
                         df_spectrum], axis='columns')
In [15]:
from openpyxl import Workbook
df_spectrum.to_excel("/home/jupyter/Notebooks/htdocs/data_RAMAN.xlsx")
In [16]:
df = df_spectrum.set_index(['filename', 'medium', 'plate', 'comp'])
print(df.head)
<bound method NDFrame.head of                                                  400.235413   402.765991   \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      244.555557   261.000000   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      216.666672   226.444443   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      200.444443   210.777771   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      239.333328   252.444427   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      241.777771   258.333344   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      264.777771   275.777771   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      234.222229   259.333344   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      267.222260   273.888885   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      163.222229   181.555557   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      159.888885   173.666656   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      165.000000   173.111115   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      175.777771   193.000000   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      206.000000   211.222214   
20170413EPA_L03_cell02_n2.spc EPA    L03   n      237.111115   247.666672   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      186.000000   205.888885   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      187.111115   202.111115   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      178.555557   188.555557   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      228.999985   239.222229   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      236.555542   232.666672   
20170413EPA_L03_cell05_c3.spc EPA    L03   c      179.888885   198.888885   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      208.444443   215.222229   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      198.555557   209.444427   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      213.222229   229.555557   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      203.777771   218.000000   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      257.555542   266.222229   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      200.000000   212.222214   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      172.111099   179.111115   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      246.444443   268.888885   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      201.111115   206.111115   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      210.000015   217.111115   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      181.333313   188.888885   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      166.888885   178.777771   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      218.888870   227.333328   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      186.333328   199.222229   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      180.000000   185.444443   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      250.888901   268.666656   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      234.222229   251.888885   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      210.333328   222.777771   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      185.888885   186.000000   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      231.111099   240.777786   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      200.333344   215.444443   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      235.000000   237.666687   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      208.222229   220.888885   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      206.888901   217.444443   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      223.666672   240.222229   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      184.222229   199.777771   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      231.111115   235.777771   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      215.555557   228.666687   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      225.777771   238.666672   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      170.555557   177.333328   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      174.222229   186.000000   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      167.888885   177.666672   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      189.888870   207.555557   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      241.111115   262.666656   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      175.000000   193.777771   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      182.777771   189.555557   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      213.333328   230.000000   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      154.777771   171.000000   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      194.888885   212.222229   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      192.333328   210.333328   

                                                 405.295746   407.824677   \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      259.555542   257.888885   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      221.111115   220.555557   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      214.444443   201.555557   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      249.666672   245.222229   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      249.555542   243.888885   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      277.888885   271.888885   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      259.555573   258.444427   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      286.333344   278.777771   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      178.222229   176.555557   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      171.111115   172.888885   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      168.777771   171.888870   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      184.333328   187.666672   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      215.333328   213.444443   
20170413EPA_L03_cell02_n2.spc EPA    L03   n      245.444443   235.666672   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      193.111115   194.111115   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      196.444458   197.555557   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      185.111115   192.666672   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      237.000000   233.888885   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      241.888885   242.444458   
20170413EPA_L03_cell05_c3.spc EPA    L03   c      186.333328   190.000000   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      215.666672   211.000000   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      205.222229   204.111115   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      222.333328   229.222229   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      214.000000   214.222229   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      260.222229   260.000000   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      215.555557   213.444458   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      170.888901   177.777771   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      257.777771   264.555542   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      209.444443   211.888870   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      211.888901   204.111115   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      196.000000   188.444443   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      169.888885   177.222229   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      229.222229   230.111115   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      198.222229   197.333328   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      184.222229   178.888885   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      261.555542   261.777771   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      244.111115   245.666672   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      221.111130   228.000000   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      191.333328   190.333328   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      240.555542   239.444443   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      212.555573   197.777771   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      235.666672   239.000000   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      216.000000   222.888885   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      214.444443   211.222229   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      238.444443   236.777771   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      204.111115   198.333328   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      238.777771   246.555542   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      231.111115   228.111115   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      242.666672   243.888885   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      178.444443   181.555557   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      183.222229   189.111115   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      181.333328   179.000000   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      202.777771   209.666672   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      262.333313   262.222260   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      183.555557   186.111115   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      190.111099   191.888885   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      225.555557   222.888885   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      168.333344   173.666672   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      206.222229   202.000000   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      211.666672   215.222229   

                                                 410.352783   412.880035   \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      262.777771   259.444458   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      231.111099   223.111115   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      211.444427   205.000015   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      245.444443   247.000000   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      251.555542   254.666672   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      273.777802   267.888885   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      256.666687   258.888885   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      281.222229   269.222229   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      178.000000   171.333344   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      175.111115   171.333328   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      173.777771   169.000000   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      183.444443   184.000000   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      209.666672   210.444443   
20170413EPA_L03_cell02_n2.spc EPA    L03   n      250.333313   239.111115   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      191.888885   190.444443   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      192.444443   200.000000   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      191.444443   194.222229   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      239.111115   237.888885   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      240.444458   244.222229   
20170413EPA_L03_cell05_c3.spc EPA    L03   c      190.222229   188.333328   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      220.555557   217.555557   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      207.444443   203.111115   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      220.888885   229.555557   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      216.555557   214.222229   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      260.666656   256.888855   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      208.333328   215.555557   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      177.111115   176.000000   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      250.333328   269.777771   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      216.222229   213.777771   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      222.777771   224.333328   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      191.999985   190.666672   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      173.444443   170.111115   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      230.111115   223.333328   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      194.666672   193.222229   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      182.777771   187.111115   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      262.777771   265.777771   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      248.222229   245.222229   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      219.888885   224.777771   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      195.444443   190.111115   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      243.666672   244.444443   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      208.333328   207.333328   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      237.111115   240.888885   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      209.777771   217.888885   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      206.333328   205.888885   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      240.888885   236.333328   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      197.555542   197.000000   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      244.222229   235.777771   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      230.555573   229.222229   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      248.888885   240.111115   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      177.777771   170.333328   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      190.444443   188.333328   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      185.000000   173.666672   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      198.222229   204.666687   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      257.777771   259.888855   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      188.666672   181.777771   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      188.888885   185.555557   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      220.222229   227.555557   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      165.000000   171.999985   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      195.666687   204.777771   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      212.777771   201.222229   

                                                 415.406464   417.932068   \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      263.444458   252.888885   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      228.666672   212.666672   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      204.000000   204.666672   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      236.333328   243.888885   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      258.555542   253.111115   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      270.333344   273.000000   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      257.888885   256.000000   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      271.555542   283.777771   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      175.555557   176.666672   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      171.777771   175.222229   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      172.000000   169.888885   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      190.000000   184.222229   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      217.222229   208.000000   
20170413EPA_L03_cell02_n2.spc EPA    L03   n      238.111115   232.666672   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      198.444443   190.222229   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      199.000000   202.888901   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      186.444443   179.111115   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      233.333328   232.444443   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      236.666672   230.000000   
20170413EPA_L03_cell05_c3.spc EPA    L03   c      191.777771   184.666672   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      221.999985   221.111115   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      203.333328   198.333328   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      229.999985   224.555557   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      215.111115   208.333328   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      262.111115   255.666672   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      215.888885   215.888885   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      178.222229   179.666672   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      259.555542   259.444458   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      207.888885   208.555557   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      222.666687   216.222229   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      194.555557   189.888885   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      176.000000   172.777771   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      229.333328   229.000000   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      191.222214   188.444443   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      183.333328   181.555557   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      257.111115   252.000000   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      248.222229   244.222229   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      221.222229   219.444443   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      190.222229   190.333328   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      241.222229   234.222229   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      212.111115   204.888885   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      235.777771   233.111115   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      212.666672   211.666672   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      204.333313   209.888885   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      233.333328   234.222229   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      199.222229   194.888885   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      248.000015   232.888885   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      225.777771   217.333328   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      235.777771   234.777771   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      173.333328   176.666672   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      185.666672   181.555557   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      184.111115   174.333328   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      202.666672   201.333328   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      260.111115   265.111115   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      185.888885   187.888885   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      189.555557   187.000000   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      217.555557   219.888885   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      174.666672   166.222229   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      209.444443   206.666687   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      210.555557   214.444443   

                                                 420.456848   422.980804   \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      254.333328   251.333328   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      224.333328   217.888885   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      201.222229   210.444427   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      236.222229   240.333328   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      252.666641   247.555542   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      265.555542   268.444458   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      252.555557   241.666656   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      271.888885   269.111115   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      173.222229   176.888885   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      169.555557   171.444443   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      162.333328   173.555557   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      186.888885   181.222229   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      212.000000   209.222229   
20170413EPA_L03_cell02_n2.spc EPA    L03   n      238.777771   236.888885   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      197.555557   200.777771   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      194.000000   198.000015   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      188.888885   188.888885   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      232.000000   229.666672   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      228.000000   231.777771   
20170413EPA_L03_cell05_c3.spc EPA    L03   c      188.222229   186.555557   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      221.111115   212.666672   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      202.888885   197.000000   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      227.666656   226.222229   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      214.777771   209.777771   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      256.000000   254.666672   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      213.999985   215.777771   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      181.000000   179.888885   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      261.111115   262.888885   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      209.555557   204.444443   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      234.222229   240.111115   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      181.333328   187.444427   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      177.555557   169.888885   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      227.888885   225.333328   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      198.222229   190.444443   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      179.888885   178.666656   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      246.777771   253.000000   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      246.888885   248.000000   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      214.000000   211.000000   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      185.222229   192.222229   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      242.222229   223.666672   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      204.222214   202.555557   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      238.000000   232.000000   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      213.333328   217.555557   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      203.666672   202.000000   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      235.444443   229.000000   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      198.333328   197.111130   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      238.555557   228.777771   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      218.888885   217.888885   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      228.888885   240.444443   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      169.444443   178.111099   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      188.222229   182.666672   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      182.111115   179.111115   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      205.000000   196.777771   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      259.333344   254.555557   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      178.555557   182.000000   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      193.000000   189.888885   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      216.888870   216.000000   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      173.555557   163.777786   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      206.777786   205.666672   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      214.333328   217.222229   

                                                    ...       3784.897461  \
filename                      medium plate comp     ...                     
20170413EPA_L03_cell01_n1.spc EPA    L03   n        ...        107.803780   
20170413EPA_L03_cell06_n2.spc EPA    L03   n        ...        105.323906   
20170413EPA_L03_cell07_c3.spc EPA    L03   c        ...        104.057602   
20170413EPA_L03_cell03_n1.spc EPA    L03   n        ...        101.181686   
20170413EPA_L03_cell04_n3.spc EPA    L03   n        ...        107.905670   
20170413EPA_L03_cell05_n3.spc EPA    L03   n        ...        107.819817   
20170413EPA_L03_cell05_n2.spc EPA    L03   n        ...         99.747490   
20170413EPA_L03_cell07_n2.spc EPA    L03   n        ...        104.405922   
20170413EPA_L03_cell02_c1.spc EPA    L03   c        ...        106.241249   
20170413EPA_L03_cell02_c2.spc EPA    L03   c        ...        105.281425   
20170413EPA_L03_cell01_c2.spc EPA    L03   c        ...        101.214073   
20170413EPA_L03_cell04_c1.spc EPA    L03   c        ...        108.430092   
20170413EPA_L03_cell06_c3.spc EPA    L03   c        ...        100.749077   
20170413EPA_L03_cell02_n2.spc EPA    L03   n        ...        105.974602   
20170413EPA_L03_cell02_n3.spc EPA    L03   n        ...        103.740952   
20170413EPA_L03_cell02_c3.spc EPA    L03   c        ...        109.509911   
20170413EPA_L03_cell07_c2.spc EPA    L03   c        ...        105.053139   
20170413EPA_L03_cell03_n2.spc EPA    L03   n        ...        105.926376   
20170413EPA_L03_cell06_n1.spc EPA    L03   n        ...        103.691757   
20170413EPA_L03_cell05_c3.spc EPA    L03   c        ...        101.551018   
20170410LDL_L01_cell03_c1.spc LDL    L01   c        ...        103.302399   
20170410LDL_L01_cell06_n3.spc LDL    L01   n        ...        101.403625   
20170410LDL_L01_cell01_c3.spc LDL    L01   c        ...        107.055176   
20170410LDL_L01_cell07_c2.spc LDL    L01   c        ...        103.149399   
20170410LDL_L01_cell05_n2.spc LDL    L01   n        ...         95.248787   
20170410LDL_L01_cell01_c1.spc LDL    L01   c        ...         99.060684   
20170410LDL_L01_cell05_c3.spc LDL    L01   c        ...        103.288635   
20170410LDL_L01_cell03_n2.spc LDL    L01   n        ...         97.081703   
20170410LDL_L01_cell07_n3.spc LDL    L01   n        ...        101.930550   
20170410LDL_L01_cell04_c3.spc LDL    L01   c        ...        110.154610   
...                                                 ...               ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n        ...        108.821846   
20170411EPA_L01_cell05_c3.spc EPA    L01   c        ...        107.978958   
20170411EPA_L01_cell07_n2.spc EPA    L01   n        ...        104.223953   
20170411EPA_L01_cell02_c1.spc EPA    L01   c        ...        107.001724   
20170412EPA_L02_cell02_c3.spc EPA    L02   c        ...        104.553741   
20170412EPA_L02_cell05_n2.spc EPA    L02   n        ...        106.257927   
20170412EPA_L02_cell07_n1.spc EPA    L02   n        ...        105.549995   
20170412EPA_L02_cell03_c2.spc EPA    L02   c        ...        101.219933   
20170412EPA_L02_cell01_c2.spc EPA    L02   c        ...        104.488876   
20170412EPA_L02_cell06_n1.spc EPA    L02   n        ...         99.712906   
20170412EPA_L02_cell03_n3.spc EPA    L02   n        ...        108.546577   
20170412EPA_L02_cell07_n3.spc EPA    L02   n        ...         99.684410   
20170412EPA_L02_cell02_c1.spc EPA    L02   c        ...        105.040794   
20170412EPA_L02_cell04_n2.spc EPA    L02   n        ...        104.837234   
20170412EPA_L02_cell01_n2.spc EPA    L02   n        ...        103.417458   
20170412EPA_L02_cell05_c1.spc EPA    L02   c        ...        113.989868   
20170412EPA_L02_cell03_n1.spc EPA    L02   n        ...        104.138885   
20170412EPA_L02_cell07_n2.spc EPA    L02   n        ...        109.810371   
20170412EPA_L02_cell02_n3.spc EPA    L02   n        ...        101.967140   
20170412EPA_L02_cell03_c3.spc EPA    L02   c        ...        107.223633   
20170412EPA_L02_cell07_c3.spc EPA    L02   c        ...        109.842712   
20170412EPA_L02_cell02_c2.spc EPA    L02   c        ...        103.461540   
20170412EPA_L02_cell04_n3.spc EPA    L02   n        ...        107.083313   
20170412EPA_L02_cell01_n3.spc EPA    L02   n        ...         99.939034   
20170412EPA_L02_cell03_c1.spc EPA    L02   c        ...        105.745827   
20170412EPA_L02_cell06_c2.spc EPA    L02   c        ...        108.798813   
20170413LDL_L03_cell05_n2.spc LDL    L03   n        ...         97.850304   
20170413LDL_L03_cell07_c3.spc LDL    L03   c        ...        111.915665   
20170413LDL_L03_cell07_c1.spc LDL    L03   c        ...        110.397018   
20170413EDL_L03_cell04_n2.spc EDL    L03   n        ...        105.793419   

                                                 3786.424805  3787.952637  \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      104.691223   106.356422   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      106.766785   112.320786   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      105.610222   108.162849   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      101.616798   101.718567   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      108.235565   108.898811   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      103.701691   107.250244   
20170413EPA_L03_cell05_n2.spc EPA    L03   n       99.845268    97.831932   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      104.624397   101.731773   
20170413EPA_L03_cell02_c1.spc EPA    L03   c       99.905365   107.791718   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      104.612656   104.610565   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      110.543266   105.316917   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      108.759712   106.422668   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      105.622856   101.274429   
20170413EPA_L03_cell02_n2.spc EPA    L03   n       99.297104   104.064056   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      101.738739   102.847641   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      102.060249   105.055023   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      105.162827   106.716919   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      104.036255   108.368355   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      105.132622   107.462364   
20170413EPA_L03_cell05_c3.spc EPA    L03   c      103.533875   101.961189   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      100.520729   101.294609   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      104.954720   101.283592   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      107.166183   107.499397   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      104.144676   101.028839   
20170410LDL_L01_cell05_n2.spc LDL    L01   n       99.792099   101.113190   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      105.055145    98.716270   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      102.843773   102.065582   
20170410LDL_L01_cell03_n2.spc LDL    L01   n       98.403374    94.836182   
20170410LDL_L01_cell07_n3.spc LDL    L01   n       98.148987   104.811867   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      109.271599   103.944145   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      104.152870   108.039474   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      102.640915   101.969536   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      106.329384   104.879242   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      105.663826   105.548149   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      107.439369   106.436111   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      105.920731   106.139099   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      100.988434   106.093544   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      106.098816   102.422134   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      107.264664   109.707115   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      102.375534   100.593719   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      105.985542   103.424500   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      110.233711   108.338562   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      107.143333   102.468109   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      109.946594   102.055931   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      103.409615   104.290672   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      113.099823   111.098671   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      107.353821   106.457642   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      108.696320   113.026726   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      106.296516   104.514801   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      105.557182   105.112968   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      111.284492   109.948479   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      102.454323   104.780434   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      104.079689   108.631622   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      101.817024   105.139458   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      105.518753   104.847237   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      103.907700   108.349937   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      105.067566   100.395950   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      105.359856   109.359596   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      106.725052   107.275299   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      101.900284   101.229393   

                                                 3789.479492  3791.005615  \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      110.243858   107.464630   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      105.652557   107.095436   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      108.937698   109.712540   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      102.042572    96.477684   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      106.117592   110.225273   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      103.909912   107.791786   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      100.374153   101.694145   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      105.061371   106.390961   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      106.011383   105.564407   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      105.052910   105.495247   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      106.312790   105.975319   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      106.752281   109.859695   
20170413EPA_L03_cell06_c3.spc EPA    L03   c      102.814888   105.577560   
20170413EPA_L03_cell02_n2.spc EPA    L03   n       95.942108   102.709068   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      105.512100   103.954338   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      102.827560   108.822357   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      101.493263   104.936256   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      103.367119   106.699226   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      105.236565   103.232971   
20170413EPA_L03_cell05_c3.spc EPA    L03   c       96.166267   101.482460   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      100.401817   100.842361   
20170410LDL_L01_cell06_n3.spc LDL    L01   n      102.834679    99.274643   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      107.499290   109.165863   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      105.024117   102.686058   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      100.323174    98.755379   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      104.044067    98.705200   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      101.176285   104.064758   
20170410LDL_L01_cell03_n2.spc LDL    L01   n       98.157867    96.368446   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      101.474754   100.804306   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      103.283340   106.622559   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      105.814949   112.701530   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      105.742607   107.849014   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      105.318008   106.090096   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      104.321358   103.872353   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      103.210632   107.096275   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      104.468575   105.686935   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      104.198662   106.081535   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      104.189903   101.957672   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      103.371780   108.369774   
20170412EPA_L02_cell06_n1.spc EPA    L02   n       98.811905   101.918976   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      106.085678   101.746864   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      107.332306   108.770500   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      103.570648   101.006531   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      107.498619   108.163513   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      103.060608   103.608337   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      109.097519   111.540810   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      101.228127   107.998611   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      103.912666   108.354187   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      101.955307   106.840248   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      109.335411   104.557838   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      108.056923   106.943146   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      100.328773   102.321571   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      110.627991   107.402145   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      102.017456   104.673218   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      106.509048   107.615303   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      107.569931   106.012169   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      105.391006   101.052727   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      103.470451   112.581314   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      106.269989   107.820244   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      106.780708   102.220924   

                                                 3792.531494  3794.057861  \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      105.796509   106.461723   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      106.760559   106.759003   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      110.598518   107.262253   
20170413EPA_L03_cell03_n1.spc EPA    L03   n       99.690575   100.236809   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      109.110733   108.107307   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      108.562561   104.666672   
20170413EPA_L03_cell05_n2.spc EPA    L03   n      101.347488    96.778580   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      101.165016   101.494591   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      107.006310    97.670418   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      105.493156   109.713287   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      106.748970   104.078163   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      110.855972   112.296715   
20170413EPA_L03_cell06_c3.spc EPA    L03   c       99.895813   104.880714   
20170413EPA_L03_cell02_n2.spc EPA    L03   n      101.142685    98.798531   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      103.618790   105.394348   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      106.261551   107.922997   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      104.601486   105.488922   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      101.586876   106.474541   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      105.896065   104.114700   
20170413EPA_L03_cell05_c3.spc EPA    L03   c       98.576431   103.003738   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      102.838455   102.390106   
20170410LDL_L01_cell06_n3.spc LDL    L01   n       98.270164   101.821251   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      109.499084   110.498985   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      103.459122    99.898834   
20170410LDL_L01_cell05_n2.spc LDL    L01   n      101.076469    98.175346   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      102.255219   102.471909   
20170410LDL_L01_cell05_c3.spc LDL    L01   c      101.508804   102.952835   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      101.579010    95.678482   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      104.244957   100.463417   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      108.072868   108.412079   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      108.032570   111.919159   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      104.622086   104.728500   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      104.639977   103.523193   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      106.090004   102.085449   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      110.759689   109.423111   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      108.349739   103.679207   
20170412EPA_L02_cell07_n1.spc EPA    L02   n       99.853310   104.402870   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      105.169868   105.382095   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      111.145561   107.365776   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      103.359390   103.355347   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      100.519157   103.180336   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      108.542030   105.202431   
20170412EPA_L02_cell02_c1.spc EPA    L02   c      103.220192   106.544960   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      107.272873   107.715546   
20170412EPA_L02_cell01_n2.spc EPA    L02   n       98.822723   105.592667   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      106.984100   112.316284   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      101.769104   107.428474   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      106.684578   104.126083   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      109.947418   104.610138   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      111.669174   109.447182   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      109.940475   110.382271   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      103.647682   102.640457   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      104.176292   108.617104   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      105.328979   103.651413   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      102.943794   107.383392   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      106.343277   102.341064   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      102.603333   105.820602   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      105.914391   107.469688   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      112.037163   110.142960   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      107.327797   103.768005   

                                                 3795.583008  3797.107666  \
filename                      medium plate comp                             
20170413EPA_L03_cell01_n1.spc EPA    L03   n      106.571388   106.903259   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      108.090759   109.978104   
20170413EPA_L03_cell07_c3.spc EPA    L03   c      104.481537   106.367500   
20170413EPA_L03_cell03_n1.spc EPA    L03   n      104.005249    96.662590   
20170413EPA_L03_cell04_n3.spc EPA    L03   n      109.103867   105.433769   
20170413EPA_L03_cell05_n3.spc EPA    L03   n      109.770775   102.874870   
20170413EPA_L03_cell05_n2.spc EPA    L03   n       99.209709    97.529716   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      107.157532   105.042671   
20170413EPA_L03_cell02_c1.spc EPA    L03   c      106.445656   104.443108   
20170413EPA_L03_cell02_c2.spc EPA    L03   c      108.044525   108.042419   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      107.074028   108.625458   
20170413EPA_L03_cell04_c1.spc EPA    L03   c      109.848549   108.622604   
20170413EPA_L03_cell06_c3.spc EPA    L03   c       99.421165   104.628296   
20170413EPA_L03_cell02_n2.spc EPA    L03   n       96.009933    98.665756   
20170413EPA_L03_cell02_n3.spc EPA    L03   n      105.058815   103.945488   
20170413EPA_L03_cell02_c3.spc EPA    L03   c      105.584442   105.579201   
20170413EPA_L03_cell07_c2.spc EPA    L03   c      109.043037   105.819374   
20170413EPA_L03_cell03_n2.spc EPA    L03   n      106.362190   103.694283   
20170413EPA_L03_cell06_n1.spc EPA    L03   n      105.000008   107.218643   
20170413EPA_L03_cell05_c3.spc EPA    L03   c       96.542152   101.858345   
20170410LDL_L01_cell03_c1.spc LDL    L01   c      104.052887    97.493423   
20170410LDL_L01_cell06_n3.spc LDL    L01   n       99.594551    96.590080   
20170410LDL_L01_cell01_c3.spc LDL    L01   c      104.498878   103.498772   
20170410LDL_L01_cell07_c2.spc LDL    L01   c      103.005226   102.333839   
20170410LDL_L01_cell05_n2.spc LDL    L01   n       99.718651    96.817528   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      100.910805   103.683052   
20170410LDL_L01_cell05_c3.spc LDL    L01   c       98.730209   101.396454   
20170410LDL_L01_cell03_n2.spc LDL    L01   n      104.444603    96.655174   
20170410LDL_L01_cell07_n3.spc LDL    L01   n      104.570732   102.455841   
20170410LDL_L01_cell04_c3.spc LDL    L01   c      107.973526   107.090500   
...                                                      ...          ...   
20170411EPA_L01_cell01_n2.spc EPA    L01   n      106.361305   106.247894   
20170411EPA_L01_cell05_c3.spc EPA    L01   c      104.612671   107.607964   
20170411EPA_L01_cell07_n2.spc EPA    L01   n      104.295280   106.956261   
20170411EPA_L01_cell02_c1.spc EPA    L01   c      105.636429   106.409645   
20170412EPA_L02_cell02_c3.spc EPA    L02   c      103.419853   109.083260   
20170412EPA_L02_cell05_n2.spc EPA    L02   n      105.119797   103.893707   
20170412EPA_L02_cell07_n1.spc EPA    L02   n      104.619087   100.501984   
20170412EPA_L02_cell03_c2.spc EPA    L02   c      104.927628   103.250954   
20170412EPA_L02_cell01_c2.spc EPA    L02   c      108.141563   109.917336   
20170412EPA_L02_cell06_n1.spc EPA    L02   n      101.795753   104.569496   
20170412EPA_L02_cell03_n3.spc EPA    L02   n      101.619293   104.280472   
20170412EPA_L02_cell07_n3.spc EPA    L02   n      107.862854   109.189941   
20170412EPA_L02_cell02_c1.spc EPA    L02   c       97.203056   103.638931   
20170412EPA_L02_cell04_n2.spc EPA    L02   n      106.936012   110.489807   
20170412EPA_L02_cell01_n2.spc EPA    L02   n      103.473717    97.132545   
20170412EPA_L02_cell05_c1.spc EPA    L02   c      113.648468   116.313972   
20170412EPA_L02_cell03_n1.spc EPA    L02   n      104.976738   107.858330   
20170412EPA_L02_cell07_n2.spc EPA    L02   n      108.456482   105.342430   
20170412EPA_L02_cell02_n3.spc EPA    L02   n      105.161743   105.380020   
20170412EPA_L02_cell03_c3.spc EPA    L02   c      111.336296   109.558723   
20170412EPA_L02_cell07_c3.spc EPA    L02   c      108.824020   112.932465   
20170412EPA_L02_cell02_c2.spc EPA    L02   c      100.411026   100.181595   
20170412EPA_L02_cell04_n3.spc EPA    L02   n      103.835701   108.943192   
20170412EPA_L02_cell01_n3.spc EPA    L02   n      103.640511   102.296272   
20170412EPA_L02_cell03_c1.spc EPA    L02   c      102.267433   107.262581   
20170412EPA_L02_cell06_c2.spc EPA    L02   c      104.561058   109.336617   
20170413LDL_L03_cell05_n2.spc LDL    L03   n      101.593430   103.588486   
20170413LDL_L03_cell07_c3.spc LDL    L03   c      108.136108   104.802521   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      111.359879   104.354584   
20170413EDL_L03_cell04_n2.spc EDL    L03   n      104.541542   102.981750   

                                                 3798.632080  
filename                      medium plate comp               
20170413EPA_L03_cell01_n1.spc EPA    L03   n      105.679573  
20170413EPA_L03_cell06_n2.spc EPA    L03   n      108.198776  
20170413EPA_L03_cell07_c3.spc EPA    L03   c      107.031242  
20170413EPA_L03_cell03_n1.spc EPA    L03   n      103.764359  
20170413EPA_L03_cell04_n3.spc EPA    L03   n      105.097008  
20170413EPA_L03_cell05_n3.spc EPA    L03   n      107.756760  
20170413EPA_L03_cell05_n2.spc EPA    L03   n       99.294159  
20170413EPA_L03_cell07_n2.spc EPA    L03   n      105.816727  
20170413EPA_L03_cell02_c1.spc EPA    L03   c      107.551682  
20170413EPA_L03_cell02_c2.spc EPA    L03   c      104.151428  
20170413EPA_L03_cell01_c2.spc EPA    L03   c      104.732430  
20170413EPA_L03_cell04_c1.spc EPA    L03   c      106.952232  
20170413EPA_L03_cell06_c3.spc EPA    L03   c      100.724304  
20170413EPA_L03_cell02_n2.spc EPA    L03   n       99.543823  
20170413EPA_L03_cell02_n3.spc EPA    L03   n      105.498833  
20170413EPA_L03_cell02_c3.spc EPA    L03   c      106.796204  
20170413EPA_L03_cell07_c2.spc EPA    L03   c      106.929031  
20170413EPA_L03_cell03_n2.spc EPA    L03   n      106.804176  
20170413EPA_L03_cell06_n1.spc EPA    L03   n      103.770607  
20170413EPA_L03_cell05_c3.spc EPA    L03   c       95.618980  
20170410LDL_L01_cell03_c1.spc LDL    L01   c      103.045090  
20170410LDL_L01_cell06_n3.spc LDL    L01   n      102.252281  
20170410LDL_L01_cell01_c3.spc LDL    L01   c      106.276428  
20170410LDL_L01_cell07_c2.spc LDL    L01   c      101.662445  
20170410LDL_L01_cell05_n2.spc LDL    L01   n       99.694168  
20170410LDL_L01_cell01_c1.spc LDL    L01   c       96.344177  
20170410LDL_L01_cell05_c3.spc LDL    L01   c       99.951614  
20170410LDL_L01_cell03_n2.spc LDL    L01   n      100.087990  
20170410LDL_L01_cell07_n3.spc LDL    L01   n       99.340950  
20170410LDL_L01_cell04_c3.spc LDL    L01   c      111.985260  
...                                                      ...  
20170411EPA_L01_cell01_n2.spc EPA    L01   n      103.912270  
20170411EPA_L01_cell05_c3.spc EPA    L01   c      101.603256  
20170411EPA_L01_cell07_n2.spc EPA    L01   n      103.506134  
20170411EPA_L01_cell02_c1.spc EPA    L01   c      110.071747  
20170412EPA_L02_cell02_c3.spc EPA    L02   c      106.968910  
20170412EPA_L02_cell05_n2.spc EPA    L02   n      106.445412  
20170412EPA_L02_cell07_n1.spc EPA    L02   n      103.051537  
20170412EPA_L02_cell03_c2.spc EPA    L02   c      105.018723  
20170412EPA_L02_cell01_c2.spc EPA    L02   c      104.804230  
20170412EPA_L02_cell06_n1.spc EPA    L02   n      104.898796  
20170412EPA_L02_cell03_n3.spc EPA    L02   n      101.163879  
20170412EPA_L02_cell07_n3.spc EPA    L02   n      107.628120  
20170412EPA_L02_cell02_c1.spc EPA    L02   c      101.630379  
20170412EPA_L02_cell04_n2.spc EPA    L02   n      106.488052  
20170412EPA_L02_cell01_n2.spc EPA    L02   n      106.346924  
20170412EPA_L02_cell05_c1.spc EPA    L02   c      106.646164  
20170412EPA_L02_cell03_n1.spc EPA    L02   n      103.739929  
20170412EPA_L02_cell07_n2.spc EPA    L02   n      108.228386  
20170412EPA_L02_cell02_n3.spc EPA    L02   n      105.709412  
20170412EPA_L02_cell03_c3.spc EPA    L02   c      107.225624  
20170412EPA_L02_cell07_c3.spc EPA    L02   c      108.707588  
20170412EPA_L02_cell02_c2.spc EPA    L02   c      104.174385  
20170412EPA_L02_cell04_n3.spc EPA    L02   n      109.606232  
20170412EPA_L02_cell01_n3.spc EPA    L02   n      104.618698  
20170412EPA_L02_cell03_c1.spc EPA    L02   c      103.591064  
20170412EPA_L02_cell06_c2.spc EPA    L02   c      108.778847  
20170413LDL_L03_cell05_n2.spc LDL    L03   n      103.027985  
20170413LDL_L03_cell07_c3.spc LDL    L03   c      106.135582  
20170413LDL_L03_cell07_c1.spc LDL    L03   c      109.015938  
20170413EDL_L03_cell04_n2.spc EDL    L03   n      102.755302  

[504 rows x 1732 columns]>

Calculate the mean spectrum by group according to cell culture medium

In [17]:
import matplotlib.pyplot as plt
%matplotlib inline
plt.plot(df.groupby('medium').mean().T)
plt.show()

Principle Component Analysis, illustration of loading plots, of screeplot and score plots

In [18]:
from sklearn.decomposition import PCA
In [19]:
pca = PCA()
pca.fit(spectrum)
Out[19]:
PCA(copy=True, iterated_power='auto', n_components=None, random_state=None,
  svd_solver='auto', tol=0.0, whiten=False)
In [20]:
wavelength=list_raman[0].wavelength
plt.plot(wavelength,pca.components_[:2].T)
plt.show()
In [21]:
plt.plot(pca.explained_variance_ratio_[0:5])
plt.show()
In [22]:
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import make_pipeline
In [23]:
pca_norm = make_pipeline(StandardScaler(), PCA(n_components=6, whiten=True))
pca = PCA(n_components=6, whiten=True)
X_r = pca.fit_transform(spectrum)
X_r = pca_norm.fit_transform(spectrum)
In [24]:
print(X_r.shape)
(504, 6)
In [25]:
plt.plot(wavelength,pca.components_[0].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [26]:
plt.plot(wavelength,pca.components_[1].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [27]:
plt.plot(wavelength,pca.components_[2].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [28]:
plt.plot(wavelength,pca.components_[3].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [29]:
plt.plot(wavelength,pca.components_[4].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.axvspan(1350, 1400, alpha=0.2, color='grey')
plt.show()
In [30]:
plt.plot(wavelength,pca.components_[5].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [31]:
for medium in metadata['medium'].unique() :
    mask = metadata['medium'] == medium
    plt.scatter(X_r[mask, 0], X_r[mask, 1],
                label=medium, s=5, alpha=0.7)
plt.legend()
plt.show()
In [32]:
plt.scatter(X_r[:, 0], X_r[:, 1])
plt.show()
In [33]:
from specio.core.util import Spectrum

Create a matrix with the spectra of a specific cell culture medium (one group) and plot the spectra, than calculate the second derivative and plot it

In [34]:
wavelength = dict_raman["EDL"][0].wavelength
spectrum = np.array([sp.amplitudes for sp in dict_raman["EDL"]])
inst_spect = Spectrum(amplitudes=spectrum, wavelength=wavelength, meta=None)
print(inst_spect)
Spectrum: 
wavelength:
 [ 400.20645142  402.73706055  405.26681519 ... 3795.69213867 3797.21679688
 3798.74194336] 
amplitudes: 
 [[210.1111145  216.55555725 222.         ... 107.77482605 103.10241699
  103.65222931]
 [167.44444275 176.         178.55555725 ... 102.1860733  102.73604584
  104.84156799]
 [183.         192.66668701 198.33332825 ... 101.46784973 102.01954651
  100.90455627]
 ...
 [166.1111145  172.33332825 173.777771   ... 104.17563629 101.50362396
  103.05383301]
 [174.33332825 183.777771   189.222229   ... 100.08542633 104.41386414
  102.29785156]
 [192.33332825 210.33332825 211.66667175 ... 104.54154205 102.98175049
  102.75530243]] 
metadata: 
 {} 

In [35]:
plt.plot(inst_spect.wavelength, inst_spect.amplitudes.T)
plt.show()
In [36]:
from scipy.misc import derivative
In [37]:
f=lambda x : np.exp(-x)*np.sin(x)
In [38]:
second=derivative(f,spectrum[0,:],n=2)
In [39]:
plt.plot(wavelength,second)
Out[39]:
[<matplotlib.lines.Line2D at 0x7f7c09ca42e8>]