DiadFit 0.0.54__py3-none-any.whl → 0.0.57__py3-none-any.whl

DiadFit/importing_data_files.py

@@ -19,6 +19,21 @@ encode="ISO-8859-1"
 
 
 def check_for_duplicates(spectra_path, prefix=True, prefix_str=' '):
+    """    This function checks for duplicate filenames in a specified directory and prints the duplicates if found.
+    
+    Parameters:
+    spectra_path (str): 
+        The path of the directory containing the files to be checked for duplicates.
+    prefix (bool):
+        If True, the function will remove the specified prefix string from the filenames before checking for duplicates. Default is True.
+    prefix_str (str: 
+        The prefix string to be removed from filenames if 'prefix' is set to True. Default is a single space ' '.
+    
+    Returns:
+    file_m (numpy.ndarray): A numpy array containing the modified filenames after removing the prefix (if specified).
+    
+    
+    """
 
     All_files_spectra= [f for f in listdir(spectra_path) if isfile(join(spectra_path, f))]
 
@@ -63,7 +78,7 @@ def get_files(path, ID_str=None, file_ext='txt', exclude_str=None, exclude_type=
 
     Returns
     -----------
-    Returns file names as a list.
+    list: file names as a list.
 
     """
 
@@ -118,6 +133,19 @@ def get_all_txt_files(path):
 def get_data(*, path=None, filename=None, Diad_files=None, filetype='Witec_ASCII'):
     """
     Extracts data as a np.array from user file of differen types
+
+    Parameters
+    ---------------
+    path: str
+        path with spectra in
+    filename: str
+        Filename of specific spectra
+    filetype: str
+        choose from 'Witec_ASCII', 'headless_txt', 'headless_csv', 'head_csv', 'Witec_ASCII',
+        'HORIBA_txt', 'Renishaw_txt'
+    Diad_Files: 
+        Name of file, if you dont want to have to specify a path
+        
     """
     if Diad_files is None:
         if filetype == 'headless_txt':
@@ -168,7 +196,7 @@ def get_data(*, path=None, filename=None, Diad_files=None, filetype='Witec_ASCII
 ## Reading different file formats
 def read_HORIBA_to_df(*,  path=None, filename):
     """ This function takes in a HORIBA .txt. file with headers with #, and looks down to the row where Data starts (no #),
-    and saves this to a new file called pandas_.... old file. It exports the data as a pandas dataframe
+    and saves this to a new csv file called pandas_.... old file. It exports the data as a pandas dataframe
 
     Parameters
     -----------
@@ -179,6 +207,11 @@ def read_HORIBA_to_df(*,  path=None, filename):
     filename: str
         Specific file being read
 
+    Returns
+    ------------
+    pd.DataFrame:  
+        Dataframe of x-y data
+
 
     """
     path2=path+'/'+ 'Peak_fits_txt'
@@ -233,6 +266,12 @@ def read_witec_to_df(*,  path=None, filename):
     filename: str
         Specific file being read
 
+
+        Returns
+    ------------
+    pd.DataFrame:  
+        Dataframe of x-y data
+
     """
     if path is None:
         path=os.getcwd()
@@ -286,7 +325,25 @@ def read_witec_to_df(*,  path=None, filename):
 
 
 def convert_datastamp_to_metadata(path, filename, creation=True, modification=False):
-    """ Gets file modification or creation time, outputs as metadata like for WITEC"
+    """ Gets file modification or creation time, outputs as metadata in the same format as for WITEC
+
+    Parameters
+    -------------
+    
+    path: str
+        Path where spectra files are stored
+    filename: str
+        Specific filename
+    creation: bool
+        If True, gets timestamp based on creation date of file
+    modification: bool
+        If True, gets timestamp based on modification date of file
+
+    Returns
+    ----------
+    df of timestamp, and other columns to have the same format as the WITEC metadata output
+
+
     """
     if creation is True and modification is True:
         raise Exception('select either Creation=True or modification=True, not both')
@@ -328,7 +385,25 @@ def convert_datastamp_to_metadata(path, filename, creation=True, modification=Fa
     return Time_Df
 
 def loop_convert_datastamp_to_metadata(path, files, creation=True, modification=False):
-    """ Loops over multiple files to get timestamp the file was created or modified"""
+    """ Loops over multiple files to get timestamp the file was created or modified
+    using the convert_datastamp_to_metadata function.
+
+    path: str
+        Path where spectra files are stored
+    files: list
+        list of filenames
+    creation: bool
+        If True, gets timestamp based on creation date of file
+    modification: bool
+        If True, gets timestamp based on modification date of file
+
+    Returns
+    ----------
+    df of timestamp, and other columns to have the same format as the WITEC metadata output
+
+   
+    
+    """
     df_meta=pd.DataFrame([])
     for file in files:
         df_loop=convert_datastamp_to_metadata(path=path, filename=file,
@@ -343,6 +418,7 @@ creation=creation, modification=modification)
 ## HORIBA acquisition time
 encode="ISO-8859-1"
 def extract_duration_horiba(*, path, filename):
+    """ This function extracts the duration from a HORIBA file by finding the line starting with #Acq. """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -353,7 +429,7 @@ def extract_duration_horiba(*, path, filename):
     return line
 
 def extract_accumulations_horiba(*, path, filename):
-
+    """ This function extracts the accumulations from a HORIBA file by finding the line starting with #Accumu. """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -364,7 +440,7 @@ def extract_accumulations_horiba(*, path, filename):
     return line
 
 def extract_objective_horiba(*, path, filename):
-
+    """ This function extracts the objective used from a HORIBA file by finding the line starting with #Object. """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -375,7 +451,7 @@ def extract_objective_horiba(*, path, filename):
     return line
 
 def extract_date_horiba(*, path, filename):
-
+    """ This function extracts the date used from a HORIBA file by finding the line starting with #Date. """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -386,7 +462,7 @@ def extract_date_horiba(*, path, filename):
     return line
 
 def extract_spectral_center_horiba(*, path, filename):
-
+    """ This function extracts the spectral center used from a HORIBA file by finding the line starting with #Spectro (cm-¹). """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -397,7 +473,7 @@ def extract_spectral_center_horiba(*, path, filename):
     return line
 
 def extract_24hr_time_horiba(*, path, filename):
-
+    """ This function extracts the 24 hr time from a HORIBA file by finding the line starting with #Acquired. """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -406,8 +482,11 @@ def extract_24hr_time_horiba(*, path, filename):
             line=l
             break
     return line
+
 def extract_spectraname_horiba(*, path, filename):
-    """ This function """
+    """
+    This function extracts the spectral name from HORIBA files
+    """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
     while True:
@@ -419,7 +498,7 @@ def extract_spectraname_horiba(*, path, filename):
 
 
 def extract_acq_params_horiba(path, filename):
-    """ Extracts acquisition parameters from HORIBA files
+    """ Extracts all relevant acquisition parameters from a HORIBA file, returns as a dataframe. 
     """
     from datetime import datetime
     # Integration time in seconds
@@ -488,7 +567,18 @@ def extract_acq_params_horiba(path, filename):
 
 def stitch_metadata_in_loop_horiba(AllFiles, path=None):
 
-    """ Stitching all metadata together
+    """ Stitches acquisition parameters together from the function extract_acq_params_horiba for multiple files
+    Parameters
+    -------------
+    AllFiles: list
+        List of all file names
+
+    path: str
+        Path where files are found
+
+    Returns
+    -------------
+    df of aquisitoin parameters
     """
     if path is None:
         path=os.getcwd()
@@ -506,7 +596,7 @@ def stitch_metadata_in_loop_horiba(AllFiles, path=None):
 ## Functions to extract metadata from WITEC files (v instrument specific)
 
 def extract_time_stamp_witec(*, path, filename):
-    """ Extracts time stamps
+    """ Extracts time stamp from a WITEC file
     """
 
     fr = open(path+'/'+filename,  'r', encoding=encode)
@@ -520,7 +610,7 @@ def extract_time_stamp_witec(*, path, filename):
     return line
 
 def extract_laser_power_witec(*, path, filename):
-    """ Extracts laser power
+    """ Extracts laser power from a WITEC file
     """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
@@ -533,7 +623,7 @@ def extract_laser_power_witec(*, path, filename):
     return line
 
 def extract_accumulations_witec(*, path, filename):
-    """ Extracts accumulations
+    """ Extracts accumulations from a WITEC file
     """
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
@@ -547,7 +637,7 @@ def extract_accumulations_witec(*, path, filename):
 
 
 def extract_integration_time_witec(*, path, filename):
-    """ Extracts Integration time
+    """ Extracts Integration time from a WITEC file
     """
 
     fr = open(path+'/'+filename,  'r', encoding=encode)
@@ -560,7 +650,7 @@ def extract_integration_time_witec(*, path, filename):
     return line
 
 def extract_spectral_center_witec(*, path, filename):
-    """ Extracts Spectral Center
+    """ Extracts Spectral Center from a WITEC file
     """
 
     fr = open(path+'/'+filename,  'r', encoding=encode)
@@ -573,7 +663,7 @@ def extract_spectral_center_witec(*, path, filename):
     return line
 
 def extract_objective_witec(*, path, filename):
-    """ Extracts objective magnification
+    """ Extracts objective magnification from a WITEC file
     """
 
     fr = open(path+'/'+filename,  'r', encoding=encode)
@@ -587,7 +677,7 @@ def extract_objective_witec(*, path, filename):
     return line
 
 def extract_duration_witec(*, path, filename):
-    """ Extracts analysis duration
+    """ Extracts analysis duration from a WITEC file
     """
 
     fr = open(path+'/'+filename,  'r', encoding=encode)
@@ -601,7 +691,7 @@ def extract_duration_witec(*, path, filename):
     return line
 
 def extract_date_witec(*, path, filename):
-    """ Extracts date"""
+    """ Extracts date from a WITEC file"""
 
     fr = open(path+'/'+filename,  'r', encoding=encode)
 
@@ -615,7 +705,7 @@ def extract_date_witec(*, path, filename):
     return line
 
 def checks_if_video_witec(*, path, filename):
-    """ Checks if file is an image (as doesnt have all metadata)
+    """ Checks if a WITEC file is an image (as doesnt have all metadata)
     """
     fr = open(path+'/'+filename,  'r', encoding=encode)
     l1=fr.readline()
@@ -627,7 +717,7 @@ def checks_if_video_witec(*, path, filename):
         return 'not Video'
 
 def checks_if_imagescan_witec(*, path, filename):
-    """ Checks if file is an imagescan (as doesnt have all metadata)
+    """ Checks if a WITEC file is an imagescan (as doesnt have all metadata)
     """
     fr = open(path+'/'+filename,  'r', encoding=encode)
     l1=fr.readline()
@@ -639,7 +729,7 @@ def checks_if_imagescan_witec(*, path, filename):
         return 'not Scan'
 
 def checks_if_general_witec(*, path, filename):
-    """ Checks if file is a spectra file with all the right metadata
+    """ Checks if a WITEC file is a spectra file with all the right metadata
     """
     fr = open(path+'/'+filename,  'r', encoding=encode)
     l1=fr.readline()
@@ -653,7 +743,22 @@ def checks_if_general_witec(*, path, filename):
 
 def extract_acq_params_witec(*, path, filename, trupower=False):
     """ This function checks what type of file you have, and if its a spectra file,
-    uses the functions above to extract various bits of metadata
+    uses the functions above to extract various bits of metadata.
+
+    Parameters
+    --------------
+    path: str
+        Folder where spectra are stored
+    filename: str
+        Specific filename
+
+    Truepower: bool
+        True if your WITEC system has Trupower, else false, as no power in the metadata file
+
+    Returns
+    -------------
+    power, accums, integ, Obj, Dur, dat, spec
+    Values for each acquisition parameters. 
     """
     # Prints what it is, e.g. general if general, video if video
     if path is None:
@@ -722,7 +827,9 @@ def extract_acq_params_witec(*, path, filename, trupower=False):
 
 
 def calculates_time_witec(*, path, filename):
-    """ calculates time for non video files for WITEC files"""
+    """ calculates time as seconds after midnight for non video files for WITEC files
+    
+    """
 
 
 
@@ -776,7 +883,23 @@ def calculates_time_witec(*, path, filename):
     return line3_sec_int, line2
 
 def stitch_metadata_in_loop_witec(*, Allfiles, path, prefix=True, trupower=False):
-    """ Stitches together WITEC metadata for all files in a loop
+    """ Stitches together WITEC metadata for all files in a loop using the function
+    extract_acq_params_witec and calculates_time_witec, exports as a dataframe
+
+    Parameters
+    -----------------
+    Allfiles:list
+        List of files to fit
+    path: str
+        Name of folder with files in
+    prefix: bool
+        If True, removes any characters in the name before the space ' '
+    trupower: bool
+        Can only be True if you have Trupower on your Witec Raman
+
+    Returns
+    -----------
+    DataFrame of metadata parameters with a row for each file. 
     """
     if path is None:
         path=os.getcwd()
@@ -894,17 +1017,20 @@ def extracting_filenames_generic(*, names, prefix=False,
     str_suffix=None,
    file_type=None):
     """
-    Takes filenames from metadata, and makes something consistent with spectra
+    Takes filenames from a panda series (e.g., a column of a dataframe of metadata), outputs a numpy array that is consistent with the same function for 
+    spectra, to allow stitching of spectra and metadata. 
+
 
     Parameters
     -----------
-    names: Pandas.Series of sample names from 'filename' column of metadata output
+    names: Pandas.Series 
+        Series of sample names, e.g., from 'filename' column of metadata output
 
     prefix: bool
         if True, has a number before the file name
 
     str_prefix: str
-        The string separating the prefix from the file name
+        The string separating the prefix from the file name (e.g. if file is 01 test, str_prefix=" ")
 
     suffix: bool
         if True, has a number or name after the filename
@@ -915,6 +1041,10 @@ def extracting_filenames_generic(*, names, prefix=False,
     file_type: str
         The file extension, e.g., '.csv'
 
+    Returns
+    -----------------
+    np.array of names, with prefix, suffix and filetype stripped away
+
     """
     if isinstance(names, list):
         names_df=pd.DataFrame(data={'name': names})
@@ -957,6 +1087,7 @@ def extracting_filenames_generic(*, names, prefix=False,
 
     return file_m
 
+# These are largely redundant.  
 def extract_temp_Aranet(df):
     """ Extracts temperature data from the aranet
     """

DiadFit/ne_lines.py

@@ -23,6 +23,22 @@ encode="ISO-8859-1"
 
 ## Plotting Ne lines, returns peak position
 def find_closest(df, line1_shift):
+    """ 
+   This function finds the closest Raman shift value in the inputted dataframe to the inputted line position
+
+   Parameters
+   -------------
+    df: pd.DataFrame
+        Dataframe of Ne line positions based on laser wavelength from the function calculate_Ne_line_positions
+    
+    line1_shift: int, float
+        input line position
+
+   Returns
+   -------------
+   Closest theoretical line position
+
+    """
     dist = (df['Raman_shift (cm-1)'] - line1_shift).abs()
     return df.loc[dist.idxmin()]
 
@@ -30,7 +46,25 @@ def find_closest(df, line1_shift):
 
 def calculate_Ne_splitting(wavelength=532.05, line1_shift=1117, line2_shift=1447, cut_off_intensity=2000):
     """
-    Calculates ideal splitting in air between lines closest to user-specified line shift
+    Calculates ideal splitting in air between lines closest to user-specified line shift. E.g. if user enters
+    1117 and 1447 line, it looks for the nearest theoretical Ne line position based on your wavelength, 
+    and calculates the ideal splitting between these theoretical line positions. This is used to calculate the 
+    ideal Ne line splitting for doing the Ne correction routine of Lamadrid et al. (2017)
+
+    Parameters
+    -------------
+    Wavelength: int
+        Wavelength of your laser
+    line1_shift: int, float
+        Estimate of position of line 1
+    line2_shift: int, float
+        Estimate of position of line 2
+    cut_off_intensity: int, float
+        only searches through lines with a theoretical intensity from NIST grater than this value 
+
+    Returns
+    ----------
+    df of theoretical splitting, line positions used for this, and entered Ne line positions
     """
 
     df_Ne=calculate_Ne_line_positions(wavelength=wavelength, cut_off_intensity=cut_off_intensity)
@@ -51,7 +85,22 @@ def calculate_Ne_splitting(wavelength=532.05, line1_shift=1117, line2_shift=1447
 
 def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
     """
-    Calculates Ne line positions using the theoretical lines from NIST for the user inputted wavelenth
+    Calculates Raman shift for a given laser wavelength of Ne lines, using the datatable from NIST of Ne line
+    emissoin in air and the intensity of each line.
+
+    Parameters
+    ---------------
+    Wavelength: float
+        Wavelength of laser
+    cut_off_intensity: float
+        Only chooses lines with intensities greater than this
+
+    Returns
+    ------------
+    pd.DataFrame
+        df wih Raman shift, intensity, and emission line position in air. 
+    
+
     """
 
     Ne_emission_line_air=np.array([
@@ -163,10 +212,24 @@ Ne_array=None):
 
     """
     Loads Ne line, uses scipy find peaks to identify peaks, overlays these,
-    and returns peak positions to feed into fitting algorithms
+    and returns approximate peak positions, prominences etc to feed into fitting algorithms
 
     Parameters
     -----------
+    config: from Neon_id_config
+        This is used to identify peaks using Scipy find peaks. Parameters that can be tweaked
+        exclude_range_1: None, or Tuple[float, float]
+            Range to exclude (e.g, cosmic ray, instrument noise)
+        exclude_range_2: None, or Tuple[float, float]
+            Range to exclude (e.g, cosmic ray, instrument noise)
+        height, distance, prominence, width, threshold: float
+            Scipy find peak parameters you can tweak
+        peak1_cent: float
+            Estimate of location of Ne line 1
+        peak2_cent: float
+            Estimate of location of Ne line 2
+        n_peaks: float
+            Looks through the largest N peaks of scipy in the entire spectra and identifies them on the plot
 
     path: str
         Folder user wishes to read data from
@@ -175,33 +238,23 @@ Ne_array=None):
         Specific file being read
 
     filetype: str
-        Identifies type of file
-        Witec_ASCII: Datafile from WITEC with metadata for first few lines
-        headless_txt: Txt file with no headers, just data with wavenumber in 1st col, int 2nd
-        HORIBA_txt: Datafile from newer HORIBA machines with metadata in first rows
-        Renishaw_txt: Datafile from renishaw with column headings.
-
-    n_peaks: int
-        Number of peaks to return values for
+        choose from 'Witec_ASCII', 'headless_txt', 'headless_csv', 'head_csv', 'Witec_ASCII',
+        'HORIBA_txt', 'Renishaw_txt'
 
-    peak1_cent: int or float, default 1118
-        Position to look for 1st peak in, finds peaks within +/- 5 of this
-
-    peak2_cent: int or float, default 1447
-        Position to look for 2nd peak in, finds peaks within +/- 5 of this
-
-
-    height, threshold, distance, prominence, width: int
-         parameters for scipy find peaks
+    plot_figure: bool
+        If True, plots a figure highlighting the identified peaks
 
-    exclude_range_1: None or list
-        users can enter a range (e.g [1100, 1112]) to exclude a part of their spectrum,
-        perhaps to remove cosmic rays
+    print_df: bool
+        if True, prints the positions of the N biggest peaks it found
 
-    exclude_range_2: None or list
-        users can enter a range (e.g [1100, 1112]) to exclude a part of their spectrum,
-        perhaps to remove cosmic rays
+    Ne_array: np.array
+        Can also enter data as a numpy array, rather than as a filename, filepath and filetype
 
+    Returns
+    --------------
+    Ne, df_fit_params
+    Ne: np.array of spectral data (with ranges excluded)
+    df_fit_params: DataFrame of approximate peak positions, prominences etc. 
 
 
     """
@@ -259,7 +312,7 @@ Ne_array=None):
     df_sort_Ne_trim=df_sort_Ne[0:n_peaks]
 
     if print_df is True:
-        print('Biggest 6 peaks:')
+        print('Biggest N peaks:')
         display(df_sort_Ne_trim)
 
     # Get peak within +-5
@@ -338,9 +391,12 @@ Ne_array=None):
         nearest_pk1=peak1_cent
 
 
-        ax1.annotate('peak=' + pos_pk1, xy=(df_fit_params['Peak1_cent'].iloc[0]+3,
-        Baseline_Neon1*1.5+700), xycoords="data", fontsize=10, rotation=90)
+        #ax1.annotate('peak=' + pos_pk1, xy=(df_fit_params['Peak1_cent'].iloc[0]+3,
+        #Baseline_Neon1*1.5+700), xycoords="data", fontsize=10, rotation=90)
 
+        ax1.annotate('peak=' + pos_pk1, xy=(0.8, 0.3),xycoords="axes fraction", fontsize=10, rotation=90)
+
+       
 
         ax1.plot(df_fit_params['Peak1_cent'], df_fit_params['Peak1_height'], '*k', mfc='yellow', ms=8, label='selected peak')
 
@@ -350,8 +406,9 @@ Ne_array=None):
         pos_pk2=str(np.round(df_fit_params['Peak2_cent'].iloc[0], 2))
         ax2.plot([peak2_cent-20, peak2_cent+20], [Baseline_Neon2, Baseline_Neon2], '-g')
 
-        ax2.annotate('peak=' + pos_pk2, xy=(df_fit_params['Peak2_cent'].iloc[0]-5,
-        Baseline_Neon1*2+700), xycoords="data", fontsize=10, rotation=90)
+        # ax2.annotate('peak=' + pos_pk2, xy=(df_fit_params['Peak2_cent'].iloc[0]-5,
+        # Baseline_Neon1*2+700), xycoords="data", fontsize=10, rotation=90)
+        ax2.annotate('peak=' + pos_pk2,xy=(0.8, 0.3),xycoords="axes fraction", fontsize=10, rotation=90)
 
 
 
@@ -385,7 +442,7 @@ Ne_array=None):
 def remove_Ne_baseline_pk1(Ne, N_poly_pk1_baseline=None, Ne_center_1=None,
 lower_bck=None, upper_bck1=None, upper_bck2=None, sigma_baseline=None):
     """ This function uses a defined range of values to fit a baseline of Nth degree polynomial to the baseline
-    around the 1117 peak
+    around a specified peak
 
     Parameters
     -----------
@@ -410,6 +467,18 @@ lower_bck=None, upper_bck1=None, upper_bck2=None, sigma_baseline=None):
     upper_bck2: list (length 2). default [30, 50]
         position used for 2nd upper background relative to peak, so =[30, 50] takes a
         background +30 and +50 from the peak center
+
+    Returns
+    -----------
+    y_corr, Py_base, x,  Ne_short, Py_base, Baseline_y, Baseline_x
+    
+    y_corr (numpy.ndarray): The corrected y-values after subtracting the fitted polynomial baseline from the original data.
+    Py_base (numpy.ndarray): The y-values of the fitted polynomial baseline.
+    x (numpy.ndarray): The x-values of the trimmed data within the specified range.
+    Ne_short (numpy.ndarray): The trimmed data within the specified range.
+    Baseline_y (numpy.ndarray): The y-values of the baseline data points.
+    Baseline_x (numpy.ndarray): The x-values of the baseline data points
+
     """
 
     lower_0baseline_pk1=Ne_center_1+lower_bck[0]
@@ -456,7 +525,7 @@ def remove_Ne_baseline_pk2(Ne, N_poly_pk2_baseline=None, Ne_center_2=None, sigma
 lower_bck=None, upper_bck1=None, upper_bck2=None):
 
     """ This function uses a defined range of values to fit a baseline of Nth degree polynomial to the baseline
-    around the 1447 peak
+    around a second selected peak
 
     Parameters
     -----------
@@ -481,6 +550,19 @@ lower_bck=None, upper_bck1=None, upper_bck2=None):
     upper_bck2: list (length 2) Default [50, 51]
         position used for 2nd upper background relative to peak, so =[30, 50] takes a
         background +30 and +50 from the peak center
+
+    Returns
+    -----------
+    y_corr, Py_base, x,  Ne_short, Py_base, Baseline_y, Baseline_x
+
+    y_corr (numpy.ndarray): The corrected y-values after subtracting the fitted polynomial baseline from the original data.
+    Py_base (numpy.ndarray): The y-values of the fitted polynomial baseline.
+    x (numpy.ndarray): The x-values of the trimmed data within the specified range.
+    Ne_short (numpy.ndarray): The trimmed data within the specified range.
+    Baseline_y (numpy.ndarray): The y-values of the baseline data points.
+    Baseline_x (numpy.ndarray): The x-values of the baseline data points.
+
+    
     """
 
 
@@ -930,11 +1012,8 @@ plot_figure=True, loop=True,
         used to save filename in datatable, and to make a new folder.
 
     filetype: str
-        Identifies type of file
-        Witec_ASCII: Datafile from WITEC with metadata for first few lines
-        headless_txt: Txt file with no headers, just data with wavenumber in 1st col, int 2nd
-        HORIBA_txt: Datafile from newer HORIBA machines with metadata in first rows
-        Renishaw_txt: Datafile from renishaw with column headings.
+        choose from 'Witec_ASCII', 'headless_txt', 'headless_csv', 'head_csv', 'Witec_ASCII',
+        'HORIBA_txt', 'Renishaw_txt'
 
     amplitude: int or float
         first guess of peak amplitude

{DiadFit-0.0.54.dist-info → DiadFit-0.0.57.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 0.0.54
+Version: 0.0.57
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser