Module Expr Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Import alias ImportFrom alias alias alias alias alias Import alias identifier ImportFrom alias ImportFrom alias ImportFrom alias alias Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Num Num Num Num Num Assign NameStore Call AttributeLoad NameLoad attr ListLoad TupleLoad Str NameLoad TupleLoad Str NameLoad FunctionDef arguments args NameParam NameParam defaults NameLoad body Expr Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad If NameLoad body Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults NameLoad body Expr Str Assign NameStore ListLoad For NameStore NameLoad body If BoolOpOr CompareIn Str Call AttributeLoad NameLoad attr CompareIn Str Call AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad If CompareEq Call NameLoad NameLoad Num body If NameLoad body Return NameLoad orelse Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num orelse If CompareGt Call NameLoad NameLoad Num body Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num orelse Return SubscriptLoad NameLoad Index Num decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults Str body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num Return Dict Str Str Str Str Str Str Str NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults Str Num Num NameLoad NameLoad body Expr Str Assign NameStore Dict Assign NameStore Dict Assign NameStore Num If NameLoad body Assign NameStore Call NameLoad NameLoad keyword NameLoad If NameLoad body With Call NameLoad NameLoad NameStore body Assign NameStore ListComp Call AttributeLoad Call AttributeLoad NameLoad attr attr comprehension NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr orelse Assign NameStore NameLoad Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareNotEq Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str For NameStore NameLoad body With Call NameLoad NameLoad NameStore body Assign NameStore ListComp Call AttributeLoad Call AttributeLoad NameLoad attr attr comprehension NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad If CompareIn NameLoad NameLoad body AugAssignAdd NameStore Num If BoolOpAnd NameLoad NameLoad body Raise Call NameLoad BinOpMod Str TupleLoad NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad Call NameLoad SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad Print AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign AttributeStore NameLoad attr Str Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad For NameStore NameLoad body If CompareNotEq NameLoad NameLoad body With Call NameLoad NameLoad NameStore body Assign NameStore ListComp Call AttributeLoad Call AttributeLoad NameLoad attr attr comprehension NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Break Assign NameStore Call NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad Call NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index Num attr Assign TupleStore NameStore NameStore NameStore TupleLoad Call NameLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Call NameLoad SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameStore Call AttributeLoad SubscriptLoad NameLoad Index Num attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Return Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore NameLoad Return Dict Str Str Str Str Str Str Str Str Str Str Str Str SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num Call NameLoad SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num Call NameLoad SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num Call NameLoad SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num Call NameLoad SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Index Num decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad Str body Expr Str Assign NameStore Call AttributeLoad Call NameLoad NameLoad Str attr Assign NameStore ListComp Call AttributeLoad Call AttributeLoad NameLoad attr attr comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr Num Assign NameStore Call NameLoad GeneratorExp TupleLoad Call NameLoad NameLoad SubscriptLoad NameLoad Index Num comprehension NameStore NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str keyword Num Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad NameLoad ExtSlice Slice Slice Num NameLoad SubscriptLoad NameLoad ExtSlice Slice Index Num Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore Call NameLoad GeneratorExp TupleLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num comprehension NameStore NameLoad If NameLoad body Assign NameStore Call NameLoad NameLoad keyword NameLoad If NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad ExtSlice Slice Index NameLoad keyword NameLoad keyword NameLoad Delete SubscriptDel NameLoad Index NameLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Num orelse Assign NameStore NameLoad Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad If NameLoad body Assign AttributeStore NameLoad attr NameLoad For NameStore NameLoad body If CompareEq SubscriptLoad NameLoad Index Num NameLoad body Pass orelse Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Num Break Assign NameStore Call NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Str Expr Call AttributeLoad NameLoad attr keyword Num keyword NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad Str body Expr Str If NameLoad body Assign NameStore Lambda arguments args NameParam defaults Call NameLoad NameLoad keyword NameLoad orelse Assign NameStore Lambda arguments args NameParam defaults NameLoad Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore ListComp Call NameLoad NameLoad keyword Str keyword NameLoad keyword Num keyword Num keyword Str keyword ListLoad Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad NameLoad keyword Num If NameLoad body Assign NameStore Call AttributeLoad NameLoad attr keyword Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Str If NameLoad body Assign AttributeStore NameLoad attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign TupleStore NameStore NameStore NameStore Call AttributeLoad SubscriptLoad NameLoad Index Num attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore TupleLoad Call NameLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Call AttributeLoad SubscriptLoad NameLoad Index Num attr Call NameLoad SubscriptLoad NameLoad Index Num Return Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad Call NameLoad ListLoad Str Str Str Str SubscriptLoad NameLoad Slice Num Assign NameStore TupleLoad Str Str Str Str Str Str Str Str Assign NameStore Call NameLoad GeneratorExp TupleLoad NameLoad NameLoad comprehension NameStore NameLoad Assign SubscriptStore NameLoad Index Str Str Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad NameLoad kwarg body Expr Str Assign NameStore Call NameLoad NameLoad keyword NameLoad If NameLoad body Assign NameStore SubscriptLoad NameLoad Slice Num NameLoad Return Call NameLoad NameLoad NameLoad decorator_list If CompareEq NameLoad Str body Assign NameStore Call NameLoad Str keyword Num keyword NameLoad keyword Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad NameLoad keyword Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad NameLoad keyword Str Print NameLoad Call NameLoad NameLoad SubscriptLoad NameLoad Index SubscriptLoad AttributeLoad NameLoad attr Index Num
N/A N/A  Utilities for converting various file formats to a skspec TimeSpectra.
 To convert a list of raw files, use from_spec_files()
 To convert old-style timefile/spectral data file, use from_timefile_datafile()
 To convert spectral datafiles from Ocean Optics USB2000 and USB650, pas file list in 
 from_spec_files.
 
 Returns a skspec TimeSpectra with custom attributes "metadata", "filedict", "baseline".
  N/A __author__ Adam Hughes, Zhaowen Liu N/A __copyright__ Copyright 2012, GWU Physics N/A __license__ Free BSD N/A __maintainer__ Adam Hughes N/A __email__ hugadams@gwmail.gwu.edu N/A __status__ Development N/A os pandas DataFrame Series datetime read_csv concat N/A numpy np skspec.core.timespectra TimeSpectra skspec.core.specindex SpecIndex skspec.core.file_utils get_files_in_dir get_shortname N/A logging N/A logger N/A N/A logging getLogger __name__ N/A spec_suite_months N/A jan feb mar apr may jun jul aug sep oct nov dec 1 2 3 4 5 6 7 8 9 10 11 12 N/A spec_dtype N/A N/A np dtype N/A N/A wavelength float N/A intensity float get_shortname N/A N/A filepath cut_extension N/A False N/A N/A  simply get the filename of fullpath.  Cut extension will remove file extension N/A shortname N/A N/A N/A os path basename filepath N/A cut_extension N/A N/A shortname N/A N/A N/A N/A os path splitext shortname N/A 0 N/A shortname N/A extract_darkfile N/A N/A filelist return_null N/A True N/A N/A  Attempts to pick out a dark file from a list using string matching.  Handling of darkfile
    is done by other functions.  Opted to raise errors and warnings here, instead of downstream.

    If return_null: it will return none if no dark file is found.  Otherwise it will raise an error. N/A darkfiles N/A N/A infile filelist N/A N/A N/A N/A dark N/A N/A infile lower N/A drk N/A N/A infile lower N/A N/A N/A N/A darkfiles append infile N/A N/A N/A len darkfiles 0 N/A N/A return_null N/A N/A None N/A N/A N/A Warning N/A WARNING: Darkfile not found in filelist:           startfile %s - endfile %s N/A N/A filelist N/A 0 N/A filelist N/A -1 N/A N/A N/A N/A len darkfiles 1 N/A N/A N/A Warning N/A Multiple darkfiles founds in filelist:        startfile %s - endfile %s N/A N/A filelist N/A 0 N/A filelist N/A -1 N/A N/A N/A darkfiles N/A 0 N/A get_headermetadata_dataframe N/A N/A dataframe time_file_dict name N/A N/A N/A  After creation of the dataframe and datetime-to-file dic, various metadata attributes 
    come together like filecount, filestart, filend etc...
    **run title becomes name of dataframe and can be adopted by plots N/A filecount N/A len N/A dataframe columns N/A N/A timestart timeend N/A N/A N/A dataframe columns N/A 0 N/A N/A dataframe columns N/A -1 N/A N/A filestart fileend N/A N/A time_file_dict N/A timestart N/A time_file_dict N/A timeend N/A N/A specstart specend N/A N/A N/A dataframe index N/A 0 N/A N/A dataframe index N/A -1 N/A N/A filecount timestart timeend filestart fileend specstart specend filecount timestart timeend filestart fileend specstart specend N/A from_spec_files N/A N/A file_list name skiphead skipfoot check_for_overlapping_time extract_dark N/A 17 1 True True N/A N/A  Takes in raw files directly from Ocean optics USB2000 and USB650 spectrometers and returns a
    skspec TimeSpectra. If spectral data stored without header, can be called with skiphead=0.

    Parameters
    ----------
       name: Set name of returned TimeSpectra.
       
       check_for_overlapping_time: will raise errors if any files have identical times. Otherwise, time
                                   is overwritten.  Really only useful for testing or otherwise cornercase instances.
       
       extract_dark: Attempt to find a filename with caseinsenstive string match to "dark".  If dark spectrum
                     not found, will print warning.  If multiple darks found, will raise error.
      
       skiphead/skipfoot: Mostly for reminder that this filetype has a 17 line header and a 1 line footer.
       
    Notes
    -----
        Built to work with 2-column data only!!!

        Dataframe is constructed from a list of dictionaries.
        Each dataframe gets an appended headerdata attribute (dataframe.headerdata) which is a dictionary,
        keyed by columns and stores (infile, header, footer) data so no info is lost between files.

        Constructed to work for non-equally spaced datafiles, or non-identical data (aka wavelengths can have nans).
     N/A dict_of_series N/A N/A time_file_dict N/A N/A _overlap_count 0 N/A extract_dark N/A N/A darkfile N/A extract_darkfile file_list return_null True N/A darkfile N/A N/A N/A open darkfile f N/A N/A header N/A N/A N/A N/A N/A f next strip N/A x N/A xrange skiphead N/A wavedata N/A N/A np genfromtxt darkfile dtype spec_dtype skip_header skiphead skip_footer skipfoot N/A darktime N/A _get_datetime_specsuite header N/A baseline N/A Series N/A wavedata N/A intensity index N/A wavedata N/A wavelength name darkfile N/A N/A N/A file_list remove darkfile N/A N/A N/A f close N/A N/A baseline None N/A file_list N/A f N/A f file_list N/A N/A N/A N/A os path basename f .gitignore N/A infile file_list N/A N/A N/A open infile f N/A N/A header N/A N/A N/A N/A N/A f next strip N/A x N/A xrange skiphead N/A wavedata N/A N/A np genfromtxt infile dtype spec_dtype skip_header skiphead skip_footer skipfoot N/A datetime N/A _get_datetime_specsuite header N/A N/A datetime time_file_dict N/A N/A _overlap_count 1 N/A N/A check_for_overlapping_time _overlap_count N/A N/A N/A IOError N/A Duplicate time %s found in between files %s, %s. To overwrite, set check_for_overlapping_time = False. N/A datetime infile N/A time_file_dict N/A datetime N/A N/A time_file_dict N/A datetime infile N/A N/A dict_of_series N/A datetime N/A Series N/A wavedata N/A intensity index N/A wavedata N/A wavelength N/A N/A N/A f close N/A df N/A DataFrame dict_of_series N/A N/A df columns N/A timespec N/A TimeSpectra df name name N/A N/A timespec specunit nm N/A N/A timespec filedict time_file_dict N/A N/A timespec baseline baseline N/A infile file_list N/A N/A N/A infile darkfile N/A N/A N/A open infile f N/A N/A header N/A N/A N/A N/A N/A f next strip N/A x N/A xrange skiphead N/A meta_partial N/A _get_metadata_fromheader header N/A N/A meta_general N/A get_headermetadata_dataframe timespec time_file_dict N/A N/A N/A meta_general update meta_partial N/A N/A timespec metadata meta_general N/A _overlap_count N/A N/A N/A N/A logger warn N/A Time duplication found in %s of %s files.  Duplicates were removed! N/A _overlap_count N/A len file_list N/A timespec N/A _get_datetime_specsuite N/A N/A specsuiteheader N/A N/A N/A  Special, Ocean-optics specific function to get date information from a their customized header. N/A dateline N/A N/A N/A specsuiteheader N/A 2 split N/A N/A year month day N/A N/A int N/A dateline N/A 6 N/A dateline N/A 2 N/A int N/A dateline N/A 3 N/A month N/A spec_suite_months N/A N/A N/A month lower N/A N/A hrs mins secs N/A N/A N/A dateline N/A 4 split : N/A hrs N/A int hrs N/A mins N/A int mins N/A secs N/A int secs N/A N/A datetime year month day hrs mins secs N/A _get_metadata_fromheader N/A N/A specsuiteheader N/A N/A N/A  Populates metadata attributes from the speactrasuite datafile header N/A sh specsuiteheader N/A N/A dark_spec_pres spectrometer int_unit int_time spec_avg boxcar ref_spec_pres electric_dark_correct strobe_lamp detector_nonlin_correct stray_light_correct pix_in_spec N/A N/A N/A N/A sh N/A 4 split N/A 3 N/A N/A N/A N/A sh N/A 7 split N/A 1 N/A N/A N/A N/A sh N/A 8 split N/A 2 N/A int N/A N/A N/A N/A sh N/A 8 split N/A 3 N/A int N/A N/A N/A N/A sh N/A 9 split N/A 2 N/A int N/A N/A N/A N/A sh N/A 10 split N/A 2 N/A N/A N/A N/A sh N/A 5 split N/A 3 N/A N/A N/A N/A sh N/A 11 split N/A 4 N/A N/A N/A N/A sh N/A 12 split N/A 2 N/A N/A N/A N/A sh N/A 13 split N/A 4 N/A N/A N/A N/A sh N/A 14 split N/A 4 N/A int N/A N/A N/A N/A sh N/A 15 split N/A 6 N/A from_timefile_datafile N/A N/A datafile timefile extract_dark name N/A True N/A N/A  Converts old-style spectral data from GWU phys lab into  
    a dataframe with timestamp column index and wavelength row indicies.

    Creates the DataFrame from a dictionary of Series, keyed by datetime.
    **name becomes name of dataframe N/A tlines N/A N/A N/A open timefile r readlines N/A tlines N/A N/A N/A N/A N/A line strip split N/A line tlines N/A N/A N/A tlines pop 0 N/A time_file_dict N/A dict N/A N/A N/A _get_datetime_timefile tline N/A tline N/A 0 N/A tline tlines N/A wavedata N/A N/A np genfromtxt datafile dtype float skip_header 1 N/A N/A data wavelengths N/A N/A wavedata N/A N/A N/A 1 None N/A wavedata N/A N/A N/A 0 N/A sorted_tfd N/A sorted N/A N/A time_file_dict items N/A N/A sorted_times sorted_files N/A zip N/A N/A N/A i N/A 0 N/A i N/A 1 N/A i sorted_tfd N/A extract_dark N/A N/A darkfile N/A extract_darkfile sorted_files return_null True N/A darkfile N/A N/A darkindex N/A N/A sorted_files index darkfile N/A darktime N/A sorted_times N/A darkindex N/A baseline N/A Series N/A data N/A N/A N/A darkindex index wavelengths name darkfile N/A N/A time_file_dict N/A darktime N/A sorted_times N/A list sorted_times N/A N/A N/A sorted_times remove darktime N/A data N/A N/A np delete data darkindex 1 N/A N/A baseline None N/A dataframe N/A TimeSpectra data columns sorted_times index wavelengths N/A N/A dataframe baseline baseline N/A N/A dataframe filedict time_file_dict N/A name N/A N/A N/A dataframe name name N/A line tlines N/A N/A N/A N/A line N/A 0 darkfile N/A N/A N/A N/A meta_partial N/A _get_headermetadata_timefile N/A line N/A 0 N/A N/A meta_general N/A get_headermetadata_dataframe dataframe time_file_dict N/A N/A N/A meta_general update meta_partial N/A N/A dataframe metadata meta_general N/A N/A dataframe specunit nm N/A N/A N/A dataframe sort axis 1 inplace True N/A dataframe N/A from_gwu_chem_UVVIS N/A N/A filelist sortnames shortname cut_extension name N/A False True False N/A N/A  Format for comma delimited two column data from GWU chemistry's UVVis.  These have no useful metadata
    or dark data and so it is important that users either pass in a correctly sorted filelist.  Once the 
    dataframe is created, on can do df=df.reindex(columns=[correct order]).  
    
    It uses read_csv() to and creates a list of dataframes.  Afterwards, concat() merges these.
    
    Kwds:
       sortnames- Will attempt to autosort the filelist. Otherwise, order of files passed in is
                  directly used as columns.
       shortname- If false, full file path is used as the column name.  If true, only the filename is used. 
       
       cut_extension- If using the shortname, this will determine if the file extension is saved or cut from the data. N/A shortname N/A N/A fget N/A N/A N/A x N/A N/A get_shortname x cut_extension cut_extension N/A N/A fget N/A N/A N/A x N/A x N/A working_names N/A N/A fget afile N/A afile filelist N/A dflist N/A N/A read_csv afile sep , header None index_col 0 skiprows 2 na_values names N/A N/A fget afile N/A afile filelist N/A dataframe N/A concat dflist axis 1 N/A sortnames N/A N/A dataframe N/A N/A dataframe reindex columns N/A sorted working_names N/A dataframe N/A TimeSpectra dataframe N/A N/A dataframe metadata None N/A N/A dataframe filedict None N/A N/A dataframe baseline None N/A N/A dataframe specunit nm N/A name N/A N/A N/A dataframe name name N/A dataframe N/A _get_datetime_timefile N/A N/A splitline N/A N/A N/A  Takes in SPLIT line of timefile (aka a list), returns datetime object  N/A N/A hrs mins secs N/A N/A N/A splitline N/A 4 split : N/A hrs N/A int hrs N/A mins N/A int mins N/A secs N/A int secs N/A N/A day month year N/A N/A int N/A splitline N/A 3 N/A spec_suite_months N/A N/A N/A N/A splitline N/A 2 lower N/A int N/A splitline N/A 1 N/A N/A datetime year month day hrs mins secs N/A _get_headermetadata_timefile N/A N/A splitline N/A N/A N/A  Return the reduced, available components of headermetadata from timefile (missing data). N/A filldic N/A dict N/A zip N/A int_time int_unit spec_avg boxcar N/A splitline N/A 5 N/A missing N/A spectrometer dark_spec_pres ref_spec_pres electric_dark_correct strobe_lamp detector_nonlin_correct stray_light_correct pix_in_spec N/A missingdic N/A dict N/A N/A item None N/A item missing N/A N/A missingdic N/A spectrometer USB2E7196 N/A missingdic N/A from_oceanoptics N/A N/A directory sample_by sort N/A None True from_spec_files_kwds N/A N/A  Wrapper to from_spec_files to both generate a file list from a directory and read files into time spectra.
        
        Parameters:
        -----------
            directory: directory with raw spectral files.
            sample_by: Sample every X files.  (Useful for reducing large datsets prior to readin)
            **from_spec_files_kwds: All kwds passed to from_spec_files().
            
        Notes:
        ------
            Slice works by taking the 0 file every time and counting from there.  So if you enter sample_by=3,
            expect to get files 0, 3, 6 etc... but if sample_by_10, you get files 0,10,20
     N/A files N/A get_files_in_dir directory sort sort N/A sample_by N/A N/A files N/A files N/A 0 sample_by N/A N/A from_spec_files files from_spec_files_kwds N/A N/A N/A __name__ __main__ N/A N/A ts N/A from_oceanoptics ../data/gwuspecdata/fiber1 sample_by 10 sort True name oceanopticstest N/A files N/A get_files_in_dir ../data/gwuspecdata/fiber1 N/A ts N/A from_spec_files files name Test Spectra N/A files N/A get_files_in_dir ../data/gwuspecdata/IRData N/A ts3 N/A from_gwu_chem_UVVIS files name IR Spec N/A ts3 N/A type ts3 N/A ts3 N/A N/A N/A ts3 columns N/A 0