Disfuse-FORS-Analasis-Functions

Python Module Created for My Masters in Physics Project at Exeter University in Diffuse Fibre Optic Reflectence Spectral Analysis

Dependencies

• numpy
• scipy
• scipy.interpolate
• scipy.misc
• scipy.signal
• matplotlib.pyplot
• glob
• os
• shutil
• math

Functions

• PlotProcessedSpectra
  • Fuction to plot a already genorated FORS spectra
  • Args DataFilePath: File to plot, MatPlotLibColour: Colour for Mat Plot Lib plotts, HeaderSize: Number of lines to skip for header, title: lable at top of graph
• PlotFolderTxt
  • Fuction to plot all text files in a given dirrectory
  • Args Dir: Directory to plot, MatPlotLibColour: Colour for Mat Plot Lib plotts, HeaderSize: Number of lines to skip for header
• SpectralGenAndSave
  • Function to genorate and save a single FORS spectra
  • Args RawDataDir: Full file path for target data, DarkCountDir: Full file path for dark count, ReflectanceStanderdDir: Full file path for ref standard, SaveDir: Directory to save in, SafeFileName: name of resultant file auto adds .txt, HeaderSize: Number of lines to ohmit at top of reading files
• MatchingDatabaseCreator
  • Function to genorate a spectral database from spectra found in a single folder saving calculated spectra into one folder
  • args: Dir: Directory of data, DarkCountFileName: Full file path for dark count, ReflectenceStandardFileName: Full file path for ref standard, SaveDir: Directory to save in, HeaderSize: Number of lines to ohmit at top of reading files
• DiffuseRefelctencePlot
  • Function to plot FORS Spectra between 400 and 900nm
  • Args LegendName: Name of plot for legend, SpreadSheet: Name of google sheet found in gdrive containg data, DarkCountIndex: page index of dark count data found in spesifide google sheet starting at 0, ReflectenceStandardIndex: page index of reflectence standard data found in spesifide google sheet starting at 0, DataIndex: page index of raw data found in spesifide google sheet starting at 0, MatPlotLibColour: optional colour of plot
• SpectralGen
  • Function to Calculate FORS Spectra between 400 and 900nm
  • Args yRawData: y vals for target pigmnent, yDarkCounts: y vals for dark count, yReflectanceStanderd: y vals for reflectence standard
• DiffuseRefelctencePlotFolder
  • Function to plot FORS Spectra between 400 and 900nm, plots all txt files found in a directory skipping the first HeaderSize lines
  • args: Dir: Directory of data, DarkCountFileName: Full file path for dark count, ReflectenceStandardFileName: Full file path for ref standard, MatPlotLibColour: optional colour of plot, HeaderSize: Number of lines to ohmit at top of reading files
• DiffuseRefelctencePlotTxt
  • Function to plot FORS Spectra between 400 and 900nm, plots all txt files found in a directory skipping the first HeaderSize lines
  • args: RawFileName: Full file path for raw data, DarkCountFileName: Full file path for dark count, ReflectenceStandardFileName: Full file path for ref standard, MatPlotLibColour: optional colour of plot, HeaderSize: Number of lines to ohmit at top of reading files
• GeoMixing
  • Fuction to calculate the geometric mean for 2 spectra
  • args ySpectra1: y vals of one spectra, ySpectra2: y vals of second spectra
• MixingAlgorithm
  • Function to plot 2 FORS Spectra between 400 and 900nm and predict the mixed spectra
  • Args arrays 1by4 in order, first spectra, second spectra, mix spectra, prodicted mixed spectra
  • Args LegendName: Name of plot for legend, SpreadSheet: Name of google sheet found in gdrive containg data, DarkCountIndex: page index of dark count data found in spesifide google sheet starting at 0, ReflectenceStandardIndex: page index of reflectence standard data found in spesifide google sheet starting at 0, DataIndex: page index of raw data found in spesifide google sheet starting at 0, MatPlotLibColour: optional colour of plot, ModelUsed: optional picker for mixing algorithm used (defalt Geo)
• MixingFromSpectraSaveing
  • Function to save 2 FORS Spectra between 400 and 900nm and predict the mixed spectra
  • Args SpectraFilePath1: Full file path of first spectra, SpectraFilePath2: Full file path of second spectra, SaveDir: Save data location, MatPlotLibColour: optional colour of plot, ModelUsed: optional picker for mixing algorithm used (defalt Geo), HeaderSize: Number of lines to skip at top of files
• FullMixingSpectratoTXT
  • Function to take raw txt files from a spectrograph and convert them into a mixing peek matching plot
  • Args Raw1, Raw2, Mixed all indicate the 3 pices of recorded data shown below, SaveDir: Save Directory for Prossesed Data, HeaderSize: Number of skip lines in begginging of text file
  • fp: Raw Data, dc: Dark Count, rf: Reflectence Standard
• MixingLinePlotGenorator
  • Function to genorate a plot of the base pigments, the resultent mixed pigments and a estimation of mixing on one plot dividing up lines for prodicted peeks into quadrants
  • args Base1: File path for processed spectra of base pigment, Base2: File path for prossesed Spectra of other base pigment, Mix: File path for prossesed spectra for mixed pigment, Gen: File path for genorated pigment, Legend: legend names for plotting each line
• MixingPlotFullGen
  • Function to tern 3 raw readings of 2 base pigments and one mixed into a plot of pigments and there respective detected peeks
  • Args Raw1, Raw2, Mixed all indicate the 3 pices of recorded data shown below, SaveDir: Save Directory for Prossesed Data, HeaderSize: Number of skip lines in begginging of text file, Legend: Legends for plots
  • fp: Raw Data, dc: Dark Count, rf: Reflectence Standard
• ProssesedFolderPeekToTXT
  • Function to take prossesed data, genorate the values of the detected peeks using PeekFinderTXT and save the results
  • Args Dir: Target Directory containing prossesed data, SaveDir: Directory to save data in, Headersize: Number of skip lines at top of files
• PeekFinderTXT
  • Peek finder for already processed data
  • Args DataPath: Full file path for raw data, HeaderSize: number of lines to skip at top of file
  • Returns: Array of peek locations
• PeekFinder
  • Peek finder for FORS reflectence spectra between 400 and 900nm
  • Args arrSpectralX: X values for spectrum, arrSpectralY, Y values for spectrum, debug: saves a txt file with raw wavelength derivative nad pass test data into a text file in the defalt directory called debug.txt
  • Returns: Array of peek locations
• PeekFinderPlotGenorater
  • Function to genorate plots for all prossesed data found in a directory
  • Args Dir: Directory containting all data, SaveDir: Location to save plots, Headersize: Number of likes to at beggining of reading data, debug: Saves raw wavelength derivative and pass test data into a txt file with the plots