openspi.core¶
Functions¶
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Processes .csv files to match the required format for OpenSpecy processing. |
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Processes a batch of .csv files in the given folder by calling |
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Processes spectra through the OpenSpecy R package and returns a dataframe |
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Sorts the dataframe exported from the R script and rearranges it into a |
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A complete function for spectral pre-processing, processing through the |
Module Contents¶
- openspi.core.process_csv(file_path, range_min, range_max)¶
Processes .csv files to match the required format for OpenSpecy processing. (The required format is two columns named
'wavenumber'and'intensity')- Parameters:
file_path (str) – The complete path to the .csv file to be processed. This function only accepts .csv files, and any other file types will cause the function to stop.
range_min (int) – The minimum wavenumber of the desired spectral range. Note that this value can be greater than the actual minimum if cropping is desired.
range_max (int) – The maximum wavenumber of the desired spectral range. Note that this value can be less than the actual maximum if cropping is desired.
- Returns:
file_path – The complete path to the processed .csv file.
- Return type:
str
- openspi.core.process_csv_folder(folder_path, range_min, range_max)¶
Processes a batch of .csv files in the given folder by calling process_csv, then zips the processed files to send to OpenSpecy.
- Parameters:
folder_path (str) – The complete path to the folder containing .csv files to be processed. This function only accepts .csv files, and any other file types will cause the function to stop.
range_min (int) – The minimum wavenumber of the desired spectral range. Note that this value can be greater than the actual minimum if cropping is desired.
range_max (int) – The maximum wavenumber of the desired spectral range. Note that this value can be less than the actual maximum if cropping is desired.
- Returns:
zipped_file_path – The complete path to a zipped folder containing the processed .csv files. This will be located in the same directory as the original folder path.
- Return type:
str
- openspi.core.r_script(file_path, range_min, range_max, adj_intens: bool = False, adj_intens_type: str = 'none', subtract_baseline: bool = False, top_n: int = 5)¶
Processes spectra through the OpenSpecy R package and returns a dataframe with the library matches and other data https://github.com/wincowgerDEV/OpenSpecy-package
- Parameters:
file_path (str) – Path to the zipped folder containing the processed .csv files OR the path to a single .csv file.
range_min (int) – The minimum wavenumber of the desired spectral range. Note that this value can be greater than the actual minimum if cropping is desired.
range_max (int) – The maximum wavenumber of the desired spectral range. Note that this value can be less than the actual maximum if cropping is desired.
top_n (int) – The top n highest matches desired. Recommended values: 1 <= n >= 10 (Not yet supported)
adj_intens (bool) – If True, the function will adjust the intensity of the spectra using the OpenSpecy package.
adj_intens_type (str) – The type of intensity adjustment to be made. Options are ‘none’, ‘transmittance’, or ‘absorbance’
subtract_baseline (bool) – If True, the function will subtract the baseline from the spectra using IModPolyFit from the OpenSpecy package.
- Returns:
df_top_matches – A Pandas dataframe containing the library match data for the files.
- Return type:
dataframe
- openspi.core.sort_export(df, excel_path, top_n, nrel=False)¶
Sorts the dataframe exported from the R script and rearranges it into a more presentable format. Exports an Excel file.
- Parameters:
df (df) – The dataframe exported from the R script.
excel_path (str) – The full path to an .xlsx file.
top_n (int) – The number of top matches for each file. Equal to top_n in openspi_main. Default is 5.
nrel (Bool) – Adds an extra row regarding first well information to the “Matches Checked sheet.”
- Return type:
None.
- openspi.core.openspi_main(source_path, range_min, range_max, export_xlsx=None, export_dir=None, nrel_version=False, adj_intens=False, adj_intens_type='none', subtr_baseline=False)¶
A complete function for spectral pre-processing, processing through the OpenSpecy library in R, and configuring/processing the outputted data into an Excel spreadsheet.
- Parameters:
source_path (str) – The complete path to the folder containing .csv files to be processed OR the path to a single .csv file. This function only accepts .csv files, and any other file types will cause the function to stop.
range_min (int) – The minimum wavenumber of the desired spectral range. Note that this value can be greater than the actual minimum if cropping is desired.
range_max (int) – The maximum wavenumber of the desired spectral range. Note that this value can be less than the actual maximum if cropping is desired.
export_xlsx (str) – The desired name of the outputted .xlsx file. If the file name does not contain the file extention .xlsx, it will be added. Optional; if not specified, the outputted file will be named according to the source file/folder.
export_dir (str) – The desired location of the outputted .xlsx file. Optional; if not specified, the file will be saved in the parent directory of the source file/folder.
nrel_version (bool) – If True, the function will use the NREL version of OpenSpecy, which has two differences: 1) all .sp files present in the folder will be deleted, and 2) the outputted file will be named in a specific way according to the files contained within.
top_n (int) – The top n highest matches desired. Recommended values: 1 <= n >= 10. Not yet supported.
adj_intens (bool) – If True, the function will adjust the intensity of the spectra using the OpenSpecy package.
adj_intens_type (str) – The type of intensity adjustment to be made. Options are ‘none’, ‘transmittance’, or ‘absorbance’
subtr_baseline (bool) – If True, the function will subtract the baseline from the spectra using IModPolyFit from the OpenSpecy package.
- Return type:
None.