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.dsi.universite-paris-saclay.fr/wiki/Data:Project#> 
prefix project:<http://daap.dsi.universite-paris-saclay.fr/wiki/Data:Analyse_des_macrophages#> 
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select ?spc
where {
        <http://daap.dsi.universite-paris-saclay.fr/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_02/20170410LDL_L01_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_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_02/20170413EPA_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell05_c3.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_cell04_c1.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_02/20170413EDL_L03_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell06_c2.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_02/20170413LDL_L03_cell06_c3.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_L01_cell04_n2.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_cell04_c3.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_02/20170413STD_L03_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell01_n2.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_02/20170413STD_L03_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell01_c3.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_cell05_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_cell05_c1.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_cell05_c3.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_cell02_c1.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_02/20170410LDL_L01_cell07_n3.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_02/20170413EDL_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_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_cell03_n3.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_02/20170413EDL_L03_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_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_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_c1.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_02/20170410EDL_L01_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell03_c3.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_cell03_c1.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_02/20170413EPA_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_c3.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_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_c1.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_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_n2.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_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell06_n1.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_cell01_n2.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_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_cell06_n2.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_02/20170411STD_L02_cell06_c1.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_02/20170413EPA_L03_cell05_n1.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_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_c2.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_02/20170413STD_L03_cell04_c1.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_02/20170412LDL_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell02_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_cell07_n2.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_cell07_c2.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_cell06_n1.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_cell06_n3.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_cell06_c3.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_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell05_n3.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_02/20170413STD_L03_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell02_n2.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_02/20170413STD_L03_cell07_n3.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_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell04_c1.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_02/20170411EPA_L01_cell06_c1.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_02/20170410LDL_L01_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell02_c3.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_cell03_c2.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_cell07_c2.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_02/20170413LDL_L03_cell04_n1.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_02/20170412EPA_L02_cell04_c1.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_02/20170412EPA_L02_cell04_c2.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_02/20170412EPA_L02_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell05_c1.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_02/20170412EPA_L02_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell01_n3.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_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_02/20170412EDL_L02_cell02_n1.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_cell02_c2.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_02/20170413EDL_L03_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell05_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell06_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_02/20170413STD_L03_cell06_c1.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_c3.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_02/20170413LDL_L03_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell02_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell02_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell02_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell02_c1.spc',
 '/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_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell01_c1.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_cell01_c3.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_02/20170410EDL_L01_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell04_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell02_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_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell03_c3.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_cell06_c1.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_02/20170413LDL_L03_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_c1.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_02/20170410LDL_L01_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell01_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_02/20170413EPA_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell05_c3.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_cell04_c1.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_02/20170413EDL_L03_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell06_c2.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_02/20170413LDL_L03_cell06_c3.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_L01_cell04_n2.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_cell04_c3.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_02/20170413STD_L03_cell01_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell01_n2.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_02/20170413STD_L03_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell01_c3.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_cell05_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_cell05_c1.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_cell05_c3.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_cell02_c1.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_02/20170410LDL_L01_cell07_n3.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_02/20170413EDL_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell02_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413STD_L03_cell03_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_cell03_n3.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_02/20170413EDL_L03_cell06_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell06_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell06_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EDL_L03_cell06_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412EPA_L02_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_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell05_c1.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_02/20170410EDL_L01_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell03_c3.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_cell03_c1.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_02/20170413EPA_L03_cell03_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_c3.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_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell01_c1.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_cell01_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_n2.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_cell05_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell06_n1.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_cell01_n2.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_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_cell06_n2.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_02/20170411STD_L02_cell06_c1.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_02/20170413EPA_L03_cell05_n1.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_cell05_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell05_c2.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_02/20170413STD_L03_cell04_c1.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_02/20170412LDL_L02_cell02_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell02_c1.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell03_c1.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell01_n3.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell01_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell01_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell01_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell03_c1.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411STD_L02_cell02_n2.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410LDL_L01_cell07_n2.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell04_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell04_c1.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_02/20170412LDL_L02_cell04_n2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell04_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell04_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170412LDL_L02_cell04_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell03_n1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell03_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413EPA_L03_cell03_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_n3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_c2.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170410EDL_L01_cell07_c3.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_c1.spc',
 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170411EPA_L01_cell05_c2.spc',
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 '/home/jupyter/Notebooks/htdocs/Macrophages_imagerie/Methode_01/Campagne_02/20170413LDL_L03_cell07_c1.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  20170410  20170410LDL_L01_cell01_n1.spc    LDL   L01
1  cell01    n  20170410  20170410LDL_L01_cell01_n2.spc    LDL   L01
2  cell01    c  20170410  20170410LDL_L01_cell01_c1.spc    LDL   L01
3  cell07    n  20170413  20170413EPA_L03_cell07_n2.spc    EPA   L03
4  cell07    n  20170413  20170413EPA_L03_cell07_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 [17]:
from openpyxl import Workbook
df_spectrum.to_excel("/home/jupyter/Notebooks/htdocs/data_RAMAN.xlsx")
In [18]:
df = df_spectrum.set_index(['filename', 'medium', 'plate', 'comp'])
print(df.head)
<bound method NDFrame.head of                                                  400.199219   402.729828   \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n      270.222229   279.777771   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      296.555542   284.000000   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      200.000000   212.222214   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      267.222260   273.888885   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      254.333359   257.888855   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      176.000015   197.555557   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      179.333328   190.666672   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      170.222214   175.555557   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      210.111115   216.555557   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      175.000015   179.111115   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      175.000015   179.111115   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      322.777771   320.777771   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      224.444443   233.000000   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      193.555557   192.111115   
20170413LDL_L03_cell06_n3.spc LDL    L03   n      191.444443   197.111115   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      152.555573   170.444427   
20170413LDL_L03_cell06_c2.spc LDL    L03   c      160.888885   169.333328   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      192.555573   201.222229   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      191.333328   200.555557   
20170411STD_L02_cell07_n1.spc STD    L02   n      219.555557   226.111115   
20170411STD_L01_cell04_n2.spc STD    L01   n      217.777771   227.444443   
20170411STD_L01_cell04_n3.spc STD    L01   n      180.666672   187.777771   
20170411STD_L01_cell04_c3.spc STD    L01   c      156.888885   166.666672   
20170411STD_L02_cell03_n2.spc STD    L02   n      218.333328   225.777771   
20170413STD_L03_cell01_n1.spc STD    L03   n      232.555557   230.777771   
20170413STD_L03_cell01_n2.spc STD    L03   n      259.999969   267.555542   
20170411STD_L02_cell03_c3.spc STD    L02   c      191.888885   198.555557   
20170413STD_L03_cell01_c3.spc STD    L03   c      181.777771   193.777771   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      174.666687   183.333328   
20170411STD_L02_cell05_n1.spc STD    L02   n      245.555557   255.111130   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      285.222229   298.555542   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      228.000015   237.555573   
20170413STD_L03_cell07_c1.spc STD    L03   c      174.888885   179.333328   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      181.555573   194.333344   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      186.555557   198.555573   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      159.555557   166.222229   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      304.888855   305.333344   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      332.333344   332.888885   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      244.555557   261.000000   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      219.111130   222.222229   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      174.777771   182.555557   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      165.000000   173.111115   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      160.888885   173.333328   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      218.333328   230.222229   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      181.000000   210.111115   
20170410EDL_L01_cell04_n3.spc EDL    L01   n      187.666672   204.777771   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      163.999985   180.999985   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      189.111115   197.555573   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      192.444443   194.222229   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      216.666672   226.444443   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      200.444443   201.444443   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      175.999985   178.666672   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      200.000000   208.666672   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      166.222229   174.777771   
20170411STD_L01_cell06_n2.spc STD    L01   n      211.888885   217.222229   
20170411STD_L01_cell06_c1.spc STD    L01   c      162.444443   168.444443   
20170411STD_L01_cell06_c2.spc STD    L01   c      161.222229   168.666672   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      227.333328   235.222229   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      219.555557   235.333313   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      194.888885   212.222229   

                                                 405.259583   407.788513   \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n      276.444458   287.111115   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      282.111115   284.111115   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      215.555557   213.444458   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      286.333344   278.777771   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      273.444427   262.888885   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      195.666687   194.555557   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      191.888885   187.444443   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      182.333328   169.555542   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      222.000000   224.999985   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      178.666672   171.777771   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      178.666672   171.777771   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      341.777771   342.777771   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      231.666672   238.888885   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      199.666672   197.555557   
20170413LDL_L03_cell06_n3.spc LDL    L03   n      206.222229   200.333328   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      166.000000   167.111115   
20170413LDL_L03_cell06_c2.spc LDL    L03   c      168.777771   165.888870   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      205.555557   206.222214   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      204.444427   196.888885   
20170411STD_L02_cell07_n1.spc STD    L02   n      230.666672   221.555557   
20170411STD_L01_cell04_n2.spc STD    L01   n      233.000000   226.888885   
20170411STD_L01_cell04_n3.spc STD    L01   n      181.888885   182.555557   
20170411STD_L01_cell04_c3.spc STD    L01   c      165.666672   162.555573   
20170411STD_L02_cell03_n2.spc STD    L02   n      224.222229   229.888885   
20170413STD_L03_cell01_n1.spc STD    L03   n      231.444443   236.333328   
20170413STD_L03_cell01_n2.spc STD    L03   n      272.666656   272.777771   
20170411STD_L02_cell03_c3.spc STD    L02   c      190.222229   196.222229   
20170413STD_L03_cell01_c3.spc STD    L03   c      193.111115   186.111130   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      176.888885   182.444443   
20170411STD_L02_cell05_n1.spc STD    L02   n      250.444443   251.333328   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      298.777771   290.444458   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      234.777786   238.000000   
20170413STD_L03_cell07_c1.spc STD    L03   c      187.666672   193.555557   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      193.333328   186.333328   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      195.222229   196.000015   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      161.444443   163.000000   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      305.222229   292.777771   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      334.666656   338.888885   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      259.555542   257.888885   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      223.333328   220.111115   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      181.222214   181.777771   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      168.777771   171.888870   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      170.555573   177.777771   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      226.000000   219.111115   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      202.333328   199.333328   
20170410EDL_L01_cell04_n3.spc EDL    L01   n      209.888885   208.000015   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      177.444443   180.555557   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      198.888885   200.888885   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      201.333328   203.777771   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      221.111115   220.555557   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      198.111115   208.777771   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      187.444443   174.111115   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      209.777771   196.333328   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      174.000000   180.999985   
20170411STD_L01_cell06_n2.spc STD    L01   n      230.000000   224.000000   
20170411STD_L01_cell06_c1.spc STD    L01   c      168.888885   165.888870   
20170411STD_L01_cell06_c2.spc STD    L01   c      162.111115   165.888885   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      241.777771   236.222229   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      232.222214   234.888885   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      206.222229   202.000000   

                                                 410.316620   412.843903   \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n      287.666656   283.111115   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      294.000000   312.555542   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      208.333328   215.555557   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      281.222229   269.222229   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      266.666656   269.666656   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      192.666656   186.777771   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      189.444427   188.222229   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      183.666672   172.888885   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      217.777771   214.333328   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      182.333328   177.888885   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      182.333328   177.888885   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      329.777771   335.222229   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      241.000000   241.000000   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      194.444443   199.444443   
20170413LDL_L03_cell06_n3.spc LDL    L03   n      197.111115   191.666672   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      165.333328   166.777771   
20170413LDL_L03_cell06_c2.spc LDL    L03   c      166.111115   171.777771   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      199.666672   203.333328   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      201.222229   199.666687   
20170411STD_L02_cell07_n1.spc STD    L02   n      217.888885   228.666672   
20170411STD_L01_cell04_n2.spc STD    L01   n      225.444443   229.666672   
20170411STD_L01_cell04_n3.spc STD    L01   n      191.111115   178.333328   
20170411STD_L01_cell04_c3.spc STD    L01   c      162.000000   161.222229   
20170411STD_L02_cell03_n2.spc STD    L02   n      235.777771   230.000000   
20170413STD_L03_cell01_n1.spc STD    L03   n      239.333313   234.333328   
20170413STD_L03_cell01_n2.spc STD    L03   n      273.777771   267.888885   
20170411STD_L02_cell03_c3.spc STD    L02   c      205.000000   196.555557   
20170413STD_L03_cell01_c3.spc STD    L03   c      192.777771   194.666672   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      182.777771   181.777771   
20170411STD_L02_cell05_n1.spc STD    L02   n      256.222229   251.333328   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      301.666656   292.555542   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      232.666672   233.444443   
20170413STD_L03_cell07_c1.spc STD    L03   c      185.222229   189.888885   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      191.222229   195.777771   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      197.555557   199.666672   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      166.555557   161.000000   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      304.000000   305.777771   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      342.222229   342.222229   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      262.777771   259.444458   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      228.777771   218.000000   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      182.777771   179.666672   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      173.777771   169.000000   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      172.444443   160.888885   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      225.222229   227.666672   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      194.888885   192.555557   
20170410EDL_L01_cell04_n3.spc EDL    L01   n      203.888901   201.888885   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      186.777771   185.000000   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      192.222229   203.555557   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      205.777771   204.111115   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      231.111099   223.111115   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      204.000015   197.333328   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      186.444427   182.333344   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      207.555557   202.888885   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      173.000000   179.000000   
20170411STD_L01_cell06_n2.spc STD    L01   n      225.000000   218.555557   
20170411STD_L01_cell06_c1.spc STD    L01   c      166.555557   172.555557   
20170411STD_L01_cell06_c2.spc STD    L01   c      165.666672   172.222229   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      227.444443   233.444443   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      231.888885   232.444427   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      195.666687   204.777771   

                                                 415.370331   417.895966   \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n      274.000000   282.777771   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      348.555542   388.111115   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      215.888885   215.888885   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      271.555542   283.777771   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      266.888885   263.666656   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      195.222229   181.777771   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      190.000000   185.555542   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      182.666687   181.555557   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      219.555573   211.888885   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      180.888901   180.888901   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      180.888901   180.888901   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      325.111115   328.444458   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      233.000000   246.333313   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      199.777771   195.777771   
20170413LDL_L03_cell06_n3.spc LDL    L03   n      196.000000   196.555573   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      166.000000   169.333328   
20170413LDL_L03_cell06_c2.spc LDL    L03   c      164.000015   167.333328   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      206.000000   201.333328   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      202.444443   200.888885   
20170411STD_L02_cell07_n1.spc STD    L02   n      222.666687   225.111115   
20170411STD_L01_cell04_n2.spc STD    L01   n      219.777771   222.111115   
20170411STD_L01_cell04_n3.spc STD    L01   n      183.333328   178.555557   
20170411STD_L01_cell04_c3.spc STD    L01   c      161.111115   161.777771   
20170411STD_L02_cell03_n2.spc STD    L02   n      229.555557   225.666672   
20170413STD_L03_cell01_n1.spc STD    L03   n      228.111130   237.000000   
20170413STD_L03_cell01_n2.spc STD    L03   n      270.111115   259.111084   
20170411STD_L02_cell03_c3.spc STD    L02   c      197.222214   193.222229   
20170413STD_L03_cell01_c3.spc STD    L03   c      191.222229   190.666672   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      176.888885   191.222214   
20170411STD_L02_cell05_n1.spc STD    L02   n      255.777771   252.222229   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      288.555542   296.888885   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      229.555557   230.111130   
20170413STD_L03_cell07_c1.spc STD    L03   c      187.222229   185.555557   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      191.444443   191.666672   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      201.222229   195.444443   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      164.555557   168.111115   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      314.000000   316.888855   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      341.888916   348.666656   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      263.444458   252.888885   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      231.666672   225.222229   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      181.000000   181.000000   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      172.000000   169.888885   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      168.222229   165.333328   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      231.666672   222.111099   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      197.222229   196.333328   
20170410EDL_L01_cell04_n3.spc EDL    L01   n      206.444443   205.111115   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      182.777786   180.444443   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      196.444443   200.444443   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      198.444443   198.888870   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      228.666672   212.666672   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      199.222229   203.444458   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      186.555557   180.333328   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      210.666672   204.888885   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      171.777771   172.444443   
20170411STD_L01_cell06_n2.spc STD    L01   n      217.555557   216.777771   
20170411STD_L01_cell06_c1.spc STD    L01   c      171.555557   173.222229   
20170411STD_L01_cell06_c2.spc STD    L01   c      167.444443   164.111115   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      236.555557   232.222229   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      225.333328   233.000000   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      209.444443   206.666687   

                                                 420.420746   422.943268   \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n      272.666656   278.888855   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      458.111115   463.666656   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      213.999985   215.777771   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      271.888885   269.111115   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      261.222229   263.222229   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      191.888885   182.666656   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      189.222229   191.333328   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      172.111115   181.333328   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      216.666672   212.222229   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      176.111115   180.333328   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      176.111115   180.333328   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      322.111115   312.222229   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      237.222229   243.222229   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      204.333344   204.333313   
20170413LDL_L03_cell06_n3.spc LDL    L03   n      204.888885   200.888901   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      170.000000   178.222229   
20170413LDL_L03_cell06_c2.spc LDL    L03   c      170.666672   176.666672   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      204.999985   200.777771   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      208.333328   202.111115   
20170411STD_L02_cell07_n1.spc STD    L02   n      224.333328   221.222229   
20170411STD_L01_cell04_n2.spc STD    L01   n      214.444443   213.222229   
20170411STD_L01_cell04_n3.spc STD    L01   n      184.666672   177.666687   
20170411STD_L01_cell04_c3.spc STD    L01   c      157.444443   159.222229   
20170411STD_L02_cell03_n2.spc STD    L02   n      229.111130   225.333328   
20170413STD_L03_cell01_n1.spc STD    L03   n      229.111115   229.666672   
20170413STD_L03_cell01_n2.spc STD    L03   n      260.222260   261.444458   
20170411STD_L02_cell03_c3.spc STD    L02   c      196.222229   195.888885   
20170413STD_L03_cell01_c3.spc STD    L03   c      192.666656   194.000000   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      187.777771   188.111115   
20170411STD_L02_cell05_n1.spc STD    L02   n      254.222229   250.555557   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      291.777771   301.333313   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      223.666687   226.000000   
20170413STD_L03_cell07_c1.spc STD    L03   c      180.000000   179.333328   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      189.666672   186.888885   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      198.222229   198.222229   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      169.000000   168.333344   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      322.333313   334.888855   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      348.666656   343.000000   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      254.333328   251.333328   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      221.888885   222.111115   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      174.333328   173.777771   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      162.333328   173.555557   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      173.888901   171.222229   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      230.111115   218.555557   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      202.333328   201.888885   
20170410EDL_L01_cell04_n3.spc EDL    L01   n      204.555542   203.888901   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      183.222229   181.777771   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      193.999985   193.000000   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      198.111115   200.222229   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      224.333328   217.888885   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      197.555557   205.777771   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      190.000000   181.555557   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      207.444443   214.222229   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      175.111115   175.888885   
20170411STD_L01_cell06_n2.spc STD    L01   n      217.444443   207.444443   
20170411STD_L01_cell06_c1.spc STD    L01   c      165.888885   165.222214   
20170411STD_L01_cell06_c2.spc STD    L01   c      163.333328   165.222229   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      225.555557   232.111099   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      233.777771   228.666672   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      206.777786   205.666672   

                                                    ...       3784.909668  \
filename                      medium plate comp     ...                     
20170410LDL_L01_cell01_n1.spc LDL    L01   n        ...         98.935760   
20170410LDL_L01_cell01_n2.spc LDL    L01   n        ...        102.091789   
20170410LDL_L01_cell01_c1.spc LDL    L01   c        ...         99.060684   
20170413EPA_L03_cell07_n2.spc EPA    L03   n        ...        104.405922   
20170413EPA_L03_cell07_n3.spc EPA    L03   n        ...        104.529579   
20170413EPA_L03_cell07_c1.spc EPA    L03   c        ...        106.588158   
20170413LDL_L03_cell05_c1.spc LDL    L03   c        ...        105.306328   
20170413LDL_L03_cell05_c3.spc LDL    L03   c        ...        102.970345   
20170412EDL_L02_cell04_n1.spc EDL    L02   n        ...        103.814987   
20170412EDL_L02_cell04_c1.spc EDL    L02   c        ...        102.062042   
20170412EDL_L02_cell04_c2.spc EDL    L02   c        ...        102.062042   
20170413EDL_L03_cell07_n1.spc EDL    L03   n        ...        106.797691   
20170413EDL_L03_cell07_n2.spc EDL    L03   n        ...        108.615822   
20170413EDL_L03_cell07_c1.spc EDL    L03   c        ...        105.457550   
20170413LDL_L03_cell06_n3.spc LDL    L03   n        ...         97.519386   
20170413LDL_L03_cell06_c1.spc LDL    L03   c        ...         98.715446   
20170413LDL_L03_cell06_c2.spc LDL    L03   c        ...         97.983696   
20170412EDL_L02_cell05_n2.spc EDL    L02   n        ...        105.795158   
20170413LDL_L03_cell06_c3.spc LDL    L03   c        ...        105.176163   
20170411STD_L02_cell07_n1.spc STD    L02   n        ...        110.627029   
20170411STD_L01_cell04_n2.spc STD    L01   n        ...        110.940414   
20170411STD_L01_cell04_n3.spc STD    L01   n        ...        106.181938   
20170411STD_L01_cell04_c3.spc STD    L01   c        ...        103.583786   
20170411STD_L02_cell03_n2.spc STD    L02   n        ...        113.090477   
20170413STD_L03_cell01_n1.spc STD    L03   n        ...        104.816444   
20170413STD_L03_cell01_n2.spc STD    L03   n        ...        107.491089   
20170411STD_L02_cell03_c3.spc STD    L02   c        ...        109.139290   
20170413STD_L03_cell01_c3.spc STD    L03   c        ...        105.018341   
20170413LDL_L03_cell01_c3.spc LDL    L03   c        ...        105.028412   
20170411STD_L02_cell05_n1.spc STD    L02   n        ...        109.543045   
...                                                 ...               ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n        ...        105.800438   
20170411EPA_L01_cell07_n3.spc EPA    L01   n        ...        103.724518   
20170413STD_L03_cell07_c1.spc STD    L03   c        ...         97.945137   
20170413LDL_L03_cell02_c2.spc LDL    L03   c        ...        101.454880   
20170413LDL_L03_cell02_c3.spc LDL    L03   c        ...        106.495506   
20170410LDL_L01_cell06_c3.spc LDL    L01   c        ...        104.168037   
20170410LDL_L01_cell02_n1.spc LDL    L01   n        ...        106.980110   
20170410LDL_L01_cell02_c1.spc LDL    L01   c        ...        105.599625   
20170413EPA_L03_cell01_n1.spc EPA    L03   n        ...        107.803780   
20170413EPA_L03_cell01_n2.spc EPA    L03   n        ...        108.526428   
20170413EPA_L03_cell01_c1.spc EPA    L03   c        ...        105.956154   
20170413EPA_L03_cell01_c2.spc EPA    L03   c        ...        101.214073   
20170413EPA_L03_cell01_c3.spc EPA    L03   c        ...        102.472000   
20170410LDL_L01_cell03_n3.spc LDL    L01   n        ...        101.530716   
20170410EDL_L01_cell04_n1.spc EDL    L01   n        ...        105.884605   
20170410EDL_L01_cell04_n3.spc EDL    L01   n        ...         92.602135   
20170410EDL_L01_cell04_c1.spc EDL    L01   c        ...        100.366028   
20170410EDL_L01_cell04_c2.spc EDL    L01   c        ...        101.604950   
20170413EPA_L03_cell02_n1.spc EPA    L03   n        ...        101.196892   
20170413EPA_L03_cell06_n2.spc EPA    L03   n        ...        105.323906   
20170413EPA_L03_cell06_n3.spc EPA    L03   n        ...        105.444519   
20170411EPA_L01_cell03_c1.spc EPA    L01   c        ...        108.875954   
20170411EPA_L01_cell03_c2.spc EPA    L01   c        ...        107.302834   
20170411EPA_L01_cell03_c3.spc EPA    L01   c        ...        111.274254   
20170411STD_L01_cell06_n2.spc STD    L01   n        ...        107.752464   
20170411STD_L01_cell06_c1.spc STD    L01   c        ...        107.919830   
20170411STD_L01_cell06_c2.spc STD    L01   c        ...        106.474442   
20170413LDL_L03_cell07_n1.spc LDL    L03   n        ...        107.447830   
20170413LDL_L03_cell07_n3.spc LDL    L03   n        ...        110.121773   
20170413LDL_L03_cell07_c1.spc LDL    L03   c        ...        110.397018   

                                                 3786.437256  3787.964111  \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n       97.370834    96.694794   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      104.197861    99.637276   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      105.055145    98.716270   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      104.624397   101.731773   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      107.747925   105.410721   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      110.256302   107.368904   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      102.519356   107.065704   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      104.852715   103.623962   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      104.364807   102.914612   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      106.169197   106.720779   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      106.169197   106.720779   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      105.683098   103.568481   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      114.504448   110.504196   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      103.008034   104.780746   
20170413LDL_L03_cell06_n3.spc LDL    L03   n      100.842964    96.944321   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      102.713333   101.822342   
20170413LDL_L03_cell06_c2.spc LDL    L03   c       96.307922    98.076584   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      104.797844   108.467194   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      104.836159   103.496147   
20170411STD_L02_cell07_n1.spc STD    L02   n      108.966408   112.083565   
20170411STD_L01_cell04_n2.spc STD    L01   n      109.377213   111.036232   
20170411STD_L01_cell04_n3.spc STD    L01   n      105.066833   104.840614   
20170411STD_L01_cell04_c3.spc STD    L01   c      102.357147   103.352730   
20170411STD_L02_cell03_n2.spc STD    L02   n      106.756157   114.755180   
20170413STD_L03_cell01_n1.spc STD    L03   n      104.476692   106.248039   
20170413STD_L03_cell01_n2.spc STD    L03   n      110.708511   110.703697   
20170411STD_L02_cell03_c3.spc STD    L02   c      107.249786   106.138062   
20170413STD_L03_cell01_c3.spc STD    L03   c      103.236855   103.455360   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      103.910583   103.348297   
20170411STD_L02_cell05_n1.spc STD    L02   n      107.102615   112.217751   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      102.572540   104.455772   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      101.384628   103.933632   
20170413STD_L03_cell07_c1.spc STD    L03   c       99.603455    98.261772   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      103.669205   101.550201   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      104.821945   101.815041   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      103.057091   100.279457   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      101.302765   104.403191   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      105.253181   107.573395   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      104.691223   106.356422   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      106.079147   109.742973   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      106.839714   101.056610   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      110.543266   105.316917   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      103.467613   102.129890   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      100.746498    95.740044   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      105.775375   104.999504   
20170410EDL_L01_cell04_n3.spc EDL    L01   n       92.810089    94.018051   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      104.805298    97.689011   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      105.489159   104.373337   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      103.525589   105.187622   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      106.766785   112.320786   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      101.880959   102.095184   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      106.986618   109.875084   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      111.624107   109.834244   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      111.940483   109.717834   
20170411STD_L01_cell06_n2.spc STD    L01   n      109.530716   109.420059   
20170411STD_L01_cell06_c1.spc STD    L01   c      104.473976   103.917007   
20170411STD_L01_cell06_c2.spc STD    L01   c      106.806175   106.360138   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      110.563965   107.346741   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      108.454147   107.342072   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      106.725052   107.275299   

                                                 3789.490967  3791.018066  \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n       96.129852    95.453812   
20170410LDL_L01_cell01_n2.spc LDL    L01   n       99.743355   101.849426   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      104.044067    98.705200   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      105.061371   106.390961   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      103.962425   105.847450   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      108.592606   109.816307   
20170413LDL_L03_cell05_c1.spc LDL    L03   c       99.500969   104.158447   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      104.395218    99.610909   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      102.464432    96.903145   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      103.494583   104.379509   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      103.494583   104.379509   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      100.787224   108.672615   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      110.948387   106.059227   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      104.220116   101.548370   
20170413LDL_L03_cell06_n3.spc LDL    L03   n       96.379021    96.369278   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      106.375801   102.484802   
20170413LDL_L03_cell06_c2.spc LDL    L03   c       95.845245    97.725021   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      107.469879   107.694778   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      103.600586   100.482796   
20170411STD_L02_cell07_n1.spc STD    L02   n      110.756271   112.651199   
20170411STD_L01_cell04_n2.spc STD    L01   n      105.361938   109.909851   
20170411STD_L01_cell04_n3.spc STD    L01   n      101.836632   103.610397   
20170411STD_L01_cell04_c3.spc STD    L01   c      105.126076   103.788322   
20170411STD_L02_cell03_n2.spc STD    L02   n      108.531998   110.086571   
20170413STD_L03_cell01_n1.spc STD    L03   n      103.797188   104.124100   
20170413STD_L03_cell01_n2.spc STD    L03   n      114.698906   105.249664   
20170411STD_L02_cell03_c3.spc STD    L02   c      106.470772   104.914604   
20170413STD_L03_cell01_c3.spc STD    L03   c      104.673866   101.447945   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      100.563805   103.223732   
20170411STD_L02_cell05_n1.spc STD    L02   n      109.999557   111.892456   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      107.116783   101.555565   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      100.815964   105.698303   
20170413STD_L03_cell07_c1.spc STD    L03   c       99.475662    98.800659   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      102.431198   104.756645   
20170413LDL_L03_cell02_c3.spc LDL    L03   c       94.808151   102.356812   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      108.168495    99.946442   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      104.948059   106.381828   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      106.893600   109.436035   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      110.243858   107.464630   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      106.740150   107.959534   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      101.162392   107.268173   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      106.312790   105.975319   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      108.569946   107.898895   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      101.289146    98.616035   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      107.668060   106.781067   
20170410EDL_L01_cell04_n3.spc EDL    L01   n       93.448227    95.322845   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      107.128288   102.012001   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      105.368660   106.586174   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      101.071877   107.845024   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      105.652557   107.095436   
20170413EPA_L03_cell06_n3.spc EPA    L03   n       99.642738   100.412514   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      108.652420   107.540886   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      112.155502   110.254532   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      106.050728   108.939194   
20170411STD_L01_cell06_n2.spc STD    L01   n      106.087204   113.643234   
20170411STD_L01_cell06_c1.spc STD    L01   c      108.248924   103.025284   
20170411STD_L01_cell06_c2.spc STD    L01   c      109.025215   104.468063   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      108.018410   110.467865   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      111.118889   109.340141   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      106.269989   107.820244   

                                                 3792.543945  3794.069336  \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n       97.222229    97.323952   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      101.955498   101.172699   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      102.255219   102.471909   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      101.165016   101.494591   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      106.621361   105.061943   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      106.262245   106.597061   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      100.704796   106.028938   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      103.937721    99.264519   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      103.675179   105.558334   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      102.486641   105.038231   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      102.486641   105.038231   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      106.891342   103.221191   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      112.947868   107.058731   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      100.876625   102.982674   
20170413LDL_L03_cell06_n3.spc LDL    L03   n       98.692863    99.349770   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      102.149361   100.369476   
20170413LDL_L03_cell06_c2.spc LDL    L03   c      100.604797   100.817902   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      105.808578   108.255714   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      102.809456   104.469452   
20170411STD_L02_cell07_n1.spc STD    L02   n      107.101692   109.663300   
20170411STD_L01_cell04_n2.spc STD    L01   n      104.568871   109.227898   
20170411STD_L01_cell04_n3.spc STD    L01   n      101.828651   104.491310   
20170411STD_L01_cell04_c3.spc STD    L01   c      106.561684   103.779488   
20170411STD_L02_cell03_n2.spc STD    L02   n      110.530037   112.751282   
20170413STD_L03_cell01_n1.spc STD    L03   n      106.562126   104.777924   
20170413STD_L03_cell01_n2.spc STD    L03   n      112.244873   114.017830   
20170411STD_L02_cell03_c3.spc STD    L02   c      110.358437   106.913391   
20170413STD_L03_cell01_c3.spc STD    L03   c      102.333138   102.662750   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      103.772568   104.099182   
20170411STD_L02_cell05_n1.spc STD    L02   n      110.340919   112.678284   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      105.438789   108.433128   
20170411EPA_L01_cell07_n3.spc EPA    L01   n       99.691750   104.796295   
20170413STD_L03_cell07_c1.spc STD    L03   c      101.014542    99.561745   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      100.415421   105.740860   
20170413LDL_L03_cell02_c3.spc LDL    L03   c       97.238800   101.454124   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      101.724373   101.835625   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      107.371147   103.582687   
20170410LDL_L01_cell02_c1.spc LDL    L01   c      108.978477   103.520920   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      105.796509   106.461723   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      106.734467   107.176071   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      106.596184   101.146400   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      106.748970   104.078163   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      102.450066   102.334557   
20170410LDL_L01_cell03_n3.spc LDL    L01   n       97.831802   102.047577   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      105.227402   105.007072   
20170410EDL_L01_cell04_n3.spc EDL    L01   n       94.308586    97.849861   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      101.340149   106.446083   
20170410EDL_L01_cell04_c2.spc EDL    L01   c      105.248154   108.243469   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      100.507065   100.502434   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      106.760559   106.759003   
20170413EPA_L03_cell06_n3.spc EPA    L03   n      102.515633   101.952072   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      106.873772   106.984444   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      110.353577   111.119270   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      109.716522   106.382767   
20170411STD_L01_cell06_n2.spc STD    L01   n      110.532593   109.310844   
20170411STD_L01_cell06_c1.spc STD    L01   c      104.912750   102.689117   
20170411STD_L01_cell06_c2.spc STD    L01   c      105.577576   107.909325   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      106.361763   108.366768   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      109.116959   106.338219   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      112.037163   110.142960   

                                                 3795.594482  3797.119141  \
filename                      medium plate comp                             
20170410LDL_L01_cell01_n1.spc LDL    L01   n       93.425697    95.749657   
20170410LDL_L01_cell01_n2.spc LDL    L01   n      101.612099   104.051521   
20170410LDL_L01_cell01_c1.spc LDL    L01   c      100.910805   103.683052   
20170413EPA_L03_cell07_n2.spc EPA    L03   n      107.157532   105.042671   
20170413EPA_L03_cell07_n3.spc EPA    L03   n      106.280304   103.832001   
20170413EPA_L03_cell07_c1.spc EPA    L03   c      102.820763   108.155586   
20170413LDL_L03_cell05_c1.spc LDL    L03   c      101.019737   101.232758   
20170413LDL_L03_cell05_c3.spc LDL    L03   c      102.258003   104.584793   
20170412EDL_L02_cell04_n1.spc EDL    L02   n      107.774826   103.102417   
20170412EDL_L02_cell04_c1.spc EDL    L02   c      102.478714   105.252525   
20170412EDL_L02_cell04_c2.spc EDL    L02   c      102.478714   105.252525   
20170413EDL_L03_cell07_n1.spc EDL    L03   n      103.884354   104.436424   
20170413EDL_L03_cell07_n2.spc EDL    L03   n      107.058464   110.169312   
20170413EDL_L03_cell07_c1.spc EDL    L03   c      103.533142   102.305855   
20170413LDL_L03_cell06_n3.spc LDL    L03   n       98.673355    97.996948   
20170413LDL_L03_cell06_c1.spc LDL    L03   c      102.478485   103.143044   
20170413LDL_L03_cell06_c2.spc LDL    L03   c       98.586555   100.133018   
20170412EDL_L02_cell05_n2.spc EDL    L02   n      107.258392   106.149971   
20170413LDL_L03_cell06_c3.spc LDL    L03   c      100.685005   102.233887   
20170411STD_L02_cell07_n1.spc STD    L02   n      110.113785   114.786491   
20170411STD_L01_cell04_n2.spc STD    L01   n      107.220268   104.657066   
20170411STD_L01_cell04_n3.spc STD    L01   n      105.820656   104.038895   
20170411STD_L01_cell04_c3.spc STD    L01   c      103.330620   100.659546   
20170411STD_L02_cell03_n2.spc STD    L02   n      107.639206   111.527115   
20170413STD_L03_cell01_n1.spc STD    L03   n      100.882622   104.320648   
20170413STD_L03_cell01_n2.spc STD    L03   n      112.235252   106.563789   
20170411STD_L02_cell03_c3.spc STD    L02   c      107.468323   106.467712   
20170413STD_L03_cell01_c3.spc STD    L03   c      105.214600   105.877548   
20170413LDL_L03_cell01_c3.spc LDL    L03   c      104.648018   102.863518   
20170411STD_L02_cell05_n1.spc STD    L02   n      108.571198   110.130760   
...                                                      ...          ...   
20170413LDL_L03_cell02_n1.spc LDL    L03   n      102.094124   107.310699   
20170411EPA_L01_cell07_n3.spc EPA    L01   n      103.234184   105.005417   
20170413STD_L03_cell07_c1.spc STD    L03   c      100.108963    96.211731   
20170413LDL_L03_cell02_c2.spc LDL    L03   c      100.399628   101.169518   
20170413LDL_L03_cell02_c3.spc LDL    L03   c      105.113892   100.218109   
20170410LDL_L01_cell06_c3.spc LDL    L01   c      101.502441   100.058151   
20170410LDL_L01_cell02_n1.spc LDL    L01   n      102.794228   102.339104   
20170410LDL_L01_cell02_c1.spc LDL    L01   c       99.730019   104.828003   
20170413EPA_L03_cell01_n1.spc EPA    L03   n      106.571388   106.903259   
20170413EPA_L03_cell01_n2.spc EPA    L03   n      104.284355   110.614853   
20170413EPA_L03_cell01_c1.spc EPA    L03   c      109.474411   100.691315   
20170413EPA_L03_cell01_c2.spc EPA    L03   c      107.074028   108.625458   
20170413EPA_L03_cell01_c3.spc EPA    L03   c      103.219063   101.992455   
20170410LDL_L01_cell03_n3.spc LDL    L01   n      100.818901   100.145782   
20170410EDL_L01_cell04_n1.spc EDL    L01   n      105.897850   104.899742   
20170410EDL_L01_cell04_n3.spc EDL    L01   n       95.946716    97.154671   
20170410EDL_L01_cell04_c1.spc EDL    L01   c      100.885353   102.991280   
20170410EDL_L01_cell04_c2.spc EDL    L01   c       99.460999   103.567421   
20170413EPA_L03_cell02_n1.spc EPA    L03   n      105.720016   104.604271   
20170413EPA_L03_cell06_n2.spc EPA    L03   n      108.090759   109.978104   
20170413EPA_L03_cell06_n3.spc EPA    L03   n       96.944077    99.602745   
20170411EPA_L01_cell03_c1.spc EPA    L01   c      105.206245   108.094688   
20170411EPA_L01_cell03_c2.spc EPA    L01   c      106.551628   110.428452   
20170411EPA_L01_cell03_c3.spc EPA    L01   c      109.160118   106.048569   
20170411STD_L01_cell06_n2.spc STD    L01   n      106.644661   110.311798   
20170411STD_L01_cell06_c1.spc STD    L01   c      104.243263   107.908501   
20170411STD_L01_cell06_c2.spc STD    L01   c      106.463287   105.683914   
20170413LDL_L03_cell07_n1.spc LDL    L03   n      106.927330   109.932335   
20170413LDL_L03_cell07_n3.spc LDL    L03   n      108.781700   106.225166   
20170413LDL_L03_cell07_c1.spc LDL    L03   c      111.359879   104.354584   

                                                 3798.643555  
filename                      medium plate comp               
20170410LDL_L01_cell01_n1.spc LDL    L01   n       96.740280  
20170410LDL_L01_cell01_n2.spc LDL    L01   n      103.046486  
20170410LDL_L01_cell01_c1.spc LDL    L01   c       96.344177  
20170413EPA_L03_cell07_n2.spc EPA    L03   n      105.816727  
20170413EPA_L03_cell07_n3.spc EPA    L03   n      106.717010  
20170413EPA_L03_cell07_c1.spc EPA    L03   c      106.045967  
20170413LDL_L03_cell05_c1.spc LDL    L03   c       99.334679  
20170413LDL_L03_cell05_c3.spc LDL    L03   c      101.800484  
20170412EDL_L02_cell04_n1.spc EDL    L02   n      103.652229  
20170412EDL_L02_cell04_c1.spc EDL    L02   c      105.915222  
20170412EDL_L02_cell04_c2.spc EDL    L02   c      105.915222  
20170413EDL_L03_cell07_n1.spc EDL    L03   n      105.321831  
20170413EDL_L03_cell07_n2.spc EDL    L03   n      108.502388  
20170413EDL_L03_cell07_c1.spc EDL    L03   c      102.189667  
20170413LDL_L03_cell06_n3.spc LDL    L03   n       98.431641  
20170413LDL_L03_cell06_c1.spc LDL    L03   c      101.585381  
20170413LDL_L03_cell06_c2.spc LDL    L03   c       96.457222  
20170412EDL_L02_cell05_n2.spc EDL    L02   n      103.819313  
20170413LDL_L03_cell06_c3.spc LDL    L03   c      101.338341  
20170411STD_L02_cell07_n1.spc STD    L02   n      107.903648  
20170411STD_L01_cell04_n2.spc STD    L01   n      108.538307  
20170411STD_L01_cell04_n3.spc STD    L01   n      106.368233  
20170411STD_L01_cell04_c3.spc STD    L01   c      104.321785  
20170411STD_L02_cell03_n2.spc STD    L02   n      110.192810  
20170413STD_L03_cell01_n1.spc STD    L03   n      105.314232  
20170413STD_L03_cell01_n2.spc STD    L03   n      110.781212  
20170411STD_L02_cell03_c3.spc STD    L02   c      107.244873  
20170413STD_L03_cell01_c3.spc STD    L03   c       98.540520  
20170413LDL_L03_cell01_c3.spc LDL    L03   c      104.856796  
20170411STD_L02_cell05_n1.spc STD    L02   n      109.245895  
...                                                      ...  
20170413LDL_L03_cell02_n1.spc LDL    L03   n      105.860580  
20170411EPA_L01_cell07_n3.spc EPA    L01   n      103.776634  
20170413STD_L03_cell07_c1.spc STD    L03   c      102.536720  
20170413LDL_L03_cell02_c2.spc LDL    L03   c       97.939407  
20170413LDL_L03_cell02_c3.spc LDL    L03   c      103.988991  
20170410LDL_L01_cell06_c3.spc LDL    L01   c      106.724968  
20170410LDL_L01_cell02_n1.spc LDL    L01   n      103.550636  
20170410LDL_L01_cell02_c1.spc LDL    L01   c      104.148216  
20170413EPA_L03_cell01_n1.spc EPA    L03   n      105.679573  
20170413EPA_L03_cell01_n2.spc EPA    L03   n      106.389786  
20170413EPA_L03_cell01_c1.spc EPA    L03   c      104.352638  
20170413EPA_L03_cell01_c2.spc EPA    L03   c      104.732430  
20170413EPA_L03_cell01_c3.spc EPA    L03   c      104.988060  
20170410LDL_L01_cell03_n3.spc LDL    L01   n       99.583786  
20170410EDL_L01_cell04_n1.spc EDL    L01   n      109.901634  
20170410EDL_L01_cell04_n3.spc EDL    L01   n       92.029289  
20170410EDL_L01_cell04_c1.spc EDL    L01   c       98.875000  
20170410EDL_L01_cell04_c2.spc EDL    L01   c      104.784950  
20170413EPA_L03_cell02_n1.spc EPA    L03   n      104.155212  
20170413EPA_L03_cell06_n2.spc EPA    L03   n      108.198776  
20170413EPA_L03_cell06_n3.spc EPA    L03   n       95.816971  
20170411EPA_L01_cell03_c1.spc EPA    L01   c      107.205368  
20170411EPA_L01_cell03_c2.spc EPA    L01   c      110.749710  
20170411EPA_L01_cell03_c3.spc EPA    L01   c      107.937019  
20170411STD_L01_cell06_n2.spc STD    L01   n      107.312279  
20170411STD_L01_cell06_c1.spc STD    L01   c      105.351532  
20170411STD_L01_cell06_c2.spc STD    L01   c      103.015663  
20170413LDL_L03_cell07_n1.spc LDL    L03   n      107.937340  
20170413LDL_L03_cell07_n3.spc LDL    L03   n      111.335320  
20170413LDL_L03_cell07_c1.spc LDL    L03   c      109.015938  

[504 rows x 1732 columns]>

Calculate the mean spectrum by group according to cell culture medium

In [19]:
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 [20]:
from sklearn.decomposition import PCA
In [21]:
pca = PCA()
pca.fit(spectrum)
Out[21]:
PCA(copy=True, iterated_power='auto', n_components=None, random_state=None,
  svd_solver='auto', tol=0.0, whiten=False)
In [22]:
wavelength=list_raman[0].wavelength
plt.plot(wavelength,pca.components_[:2].T)
plt.show()
In [23]:
plt.plot(pca.explained_variance_ratio_[0:5])
plt.show()
In [24]:
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import make_pipeline
In [25]:
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 [26]:
print(X_r.shape)
(504, 6)
In [27]:
plt.plot(wavelength,pca.components_[0].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [28]:
plt.plot(wavelength,pca.components_[1].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [29]:
plt.plot(wavelength,pca.components_[2].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [30]:
plt.plot(wavelength,pca.components_[3].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [31]:
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 [32]:
plt.plot(wavelength,pca.components_[5].T)
plt.axvspan(1000, 1200, alpha=0.2, color='grey')
plt.show()
In [33]:
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 [34]:
plt.scatter(X_r[:, 0], X_r[:, 1])
plt.show()
In [35]:
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 [36]:
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]
 [175.00001526 179.1111145  178.66667175 ... 102.47871399 105.25252533
  105.91522217]
 [175.00001526 179.1111145  178.66667175 ... 102.47871399 105.25252533
  105.91522217]
 ...
 [187.66667175 204.777771   209.8888855  ...  95.94671631  97.15467072
   92.02928925]
 [163.99998474 180.99998474 177.44444275 ... 100.88535309 102.9912796
   98.875     ]
 [189.1111145  197.55557251 198.8888855  ...  99.46099854 103.56742096
  104.78495026]] 
metadata: 
 {} 

In [37]:
plt.plot(inst_spect.wavelength, inst_spect.amplitudes.T)
plt.show()
In [38]:
from scipy.misc import derivative
In [39]:
f=lambda x : np.exp(-x)*np.sin(x)
In [40]:
second=derivative(f,spectrum[0,:],n=2)
In [41]:
plt.plot(wavelength,second)
Out[41]:
[<matplotlib.lines.Line2D at 0x7f51d4a745c0>]