R/Rheometer.R

In Ersch001/PhChFo: Collection of functions to import and manipulate data from typical analytical machines found in physical chemistry laboratories

## --------------------------- load data -------------------------
#' Loads the data as exported from the TA instruments rheometer (version ...)
#' and returns them as an data sheet.
#' Please note that there is another function available which does this in a batch mode for a series of excel files.
#' @param RheometerExportFileExcel the url of the excel file as exported from the TA instruments software
#' @param SheetIndexes The index (starting from 1) which sheets should be imported, the equipment typically puts one measurement step in each sheet so in most cases this corresponds to the number of steps as recorded with the equipment
#' @return a dataset with all data and metadata for all steps in the specified excel sheet
#' @export
Rheometer_loadTADataFromFile <- function(RheometerExportFileExcel, SheetIndexes)
{
  library("readxl");
  sampleName <- "NULL"
  measurementDate <- "NULL"
  thisDetail <- read_excel(RheometerExportFileExcel,sheet = 1)
  for(i in 1:length(thisDetail$Filename))
  {
    if(is.na(thisDetail[i,1]))
    {

    } else if(thisDetail[i,1] == "Sample name")
    {
      sampleName <- as.character(thisDetail[[i,2]])
    } else if(thisDetail[i,1] == "rundate")
    {
      if(grepl("-",thisDetail[[i,2]]))
      {
        measurementDate <- as.Date(thisDetail[[i,2]],format = "%d-%m-%Y")
      }
      else
      {
        measurementDate <- as.Date(as.character(as.Date(as.numeric(thisDetail[[i,2]]),origin = "1899-12-30")),format = "%Y-%d-%m")
      }

    }
  }
  combinedSheet <- NULL
  for(s in 1:length(SheetIndexes))
  {
    thisSheet <- read_excel(RheometerExportFileExcel,sheet = SheetIndexes[s])
    colnames(thisSheet) <- NULL
    colnames(thisSheet) <- gsub(" ", "", thisSheet[1,],fixed = TRUE)
    thisSheet <- thisSheet[-1,]
    thisSheet <- thisSheet[-1,]
    for(i in 1:length(thisSheet))
    {
      thisSheet[,i] <- as.double(as.numeric(as.matrix(thisSheet[,i])))
    }
    thisSheet$SampleName = rep(sampleName,length(thisSheet[,1]))
    thisSheet$MeasurementDate = rep(measurementDate,length(thisSheet[,1]))
    thisSheet$StepNumber = rep(SheetIndexes[s],length(thisSheet[,1]))
    combinedSheet <- rbind(combinedSheet,thisSheet)
  }
  return(combinedSheet);
}

#' Loads the data from the excel files as exported from the TA instruments rheometer
#' Expects all excel files to be in one folder without any additional files present
#' @param RheometerExportFolder the folder with the exported files in excel format
#' @param SheetIndexes The index (starting from 1) which sheets should be imported, the equipment typically puts one measurement step in each sheet so in most cases this corresponds to the number of steps as recorded with the equipment
#' @export
Rheometer_loadTADataFromFolder <- function(RheometerExportFolder, SheetIndexes)
{
  RawFlowDataFiles <- list.files(RheometerExportFolder,full.names = TRUE)
  returnData <- data.frame()
  usedSamples <- ""
  for(i in 1:length(RawFlowDataFiles))
  {
    thisFileOutput <- Rheometer_loadTADataFromFile(RawFlowDataFiles[i], SheetIndexes)
    thisFileOutput$DoubleMeasCode <- rep(length(usedSamples[usedSamples == thisFileOutput$SampleName[1]]),length(thisFileOutput[,1]))
    usedSamples <- c(usedSamples,unique(thisFileOutput$SampleName))
    library("plyr")
    returnData <- rbind.fill(returnData,thisFileOutput);
  }
  return(returnData)
}


#' This function loads the data from a text file which contains the
#' data exported from the Anton Paar rheometer and returns a data frame.
#' Multiple samples can be in one file and will be separated in the final data frame.
#' Please make sure that the numbers are exported in a scientific notation with sufficient
#' decimal points to keep the precision of small and large numbers alike. Also please make sure that
#' the decimal separator is set to . (Point) and not to , (Comma). Include all neccesary columns in the
#' Antom Paar software to ensure that the required data is available for possible subsequent data analysis
#' @param ExportedFile the text file containing the raw data as copied from the anton paar software
#' @return returns a dataset containing the data and metadata in column format for all samples
#' @export
Rheometer_loadAntonPaarDataFromFile <- function(ExportedFile)
{
    con  <- file(ExportedFile, open = "r")
    numberOfLines <- 0
    while (length(oneLine <- readLines(con, n = 1, warn = FALSE)) > 0)
    {
        numberOfLines <- numberOfLines+1
    }
    con  <- file(ExportedFile, open = "r")
    returnData <- data.frame()
    savedSamples <- ""
    thisSampleName <- ""
    thisMeasDate <- ""
    numDataPointsNextChunk <- 0
    rownumber <- 1
    thisData <- data.frame()
    StepNumber <- 1
    while (length(oneLine <- readLines(con, n = 1, warn = FALSE)) > 0)
    {
        ColNameSplit <- (strsplit(oneLine, "\t"))
        if(length(ColNameSplit[[1]])<1)
        {
            1+1
        }else if(ColNameSplit[[1]][1] == "Name:")
        {
            thisSampleName <- ColNameSplit[[1]][4]
        } else if(ColNameSplit[[1]][1] == "Measuring Date/Time:")
        {
            thisMeasDate <- ColNameSplit[[1]][4]
        } else if(ColNameSplit[[1]][1] == "Number of Data Points:")
        {
            numDataPointsNextChunk <- as.numeric(ColNameSplit[[1]][4])
        } else if(ColNameSplit[[1]][1] == "Meas. Pts.")
        {
            thisthisData <- read.table(ExportedFile,skip = rownumber+1,sep = "\t", nrows = numDataPointsNextChunk,header = FALSE)
            colnames(thisthisData) <- ColNameSplit[[1]]
            thisthisData$StepNumber <- rep(StepNumber,length(thisthisData[,1]))
            if(length(thisData) >1)
                thisData <- rbind(thisData, thisthisData)
            else
                thisData <-  thisthisData
            rm(thisthisData)
            StepNumber <- StepNumber + 1
        }else if(ColNameSplit[[1]][1] == "Data Series Information" | rownumber >= numberOfLines)
        {
            if( length(thisData)>1)
            {
                thisData$SampleName <- rep(thisSampleName,length(thisData[,1]))
                thisData$MeasurementDate <- rep(thisMeasDate,length(thisData[,1]))
                thisData$DoubleMeasCode <- rep(length(savedSamples[savedSamples == thisSampleName]),length(thisData[,1]))
                if(length(returnData) == 0)
                    returnData <- thisData
                else
                    returnData <- merge(returnData,thisData,all = TRUE)
                thisData <- data.frame()
                thisMeasDate <- ""
                thisSampleName <- ""
                savedSamples <- c(savedSamples,thisSampleName)
            }
            StepNumber <- 1
        }
        rownumber <- rownumber +1
    }
    for(i in 1:11)
    {
        returnData[,i] <- as.numeric(gsub(",",".",returnData[,i]))
    }

    colnames(returnData) <- gsub("\\.","",colnames(returnData))
    colnames(returnData) <- gsub(" ","",colnames(returnData))
    return(returnData)
}


## ------------------- Analyse Data ------------------------