Read Patient Header and Data From the Same File

This snippet is a solution for an Igor user who wanted to use header information to construct the name of a wave to be loaded from a data file. This solution uses the technique of storing the header information in a list of keyword-value pairs and later querying that list for specific fields.

For background information and links to other solutions, see https://www.wavemetrics.com/code-snippet/reading-header-and-data-same-f…

#pragma TextEncoding = "UTF-8"
#pragma rtGlobals=3             // Use modern global access method and strict wave access
#pragma DefaultTab={3,20,4}     // Set default tab width in Igor Pro 9 and later
 
// Reads header information and numeric data from a text file with a format like this:
//      Patient Data
//      Patient Group: 33
//      Subject ID: ABCD 99W
//      Location ID: XYZ 22X
//      Record Number: 55
//
//      Variables
//      Level = 80
//      AudFreq = 4000
//      Fade = 2.5
//      Gain = 1.00
//
//      Data:
//      123.456
//      234.567
//      345.678
 
// The user wanted to use the values of the "Subject ID" field and the Level and AudFreq
// variables to form the name of the resulting wave.
// 
// To understand this file it is best to read it from the bottom (high-level) up.
 
// GetFieldNameAndValueStrFromHeaderLine(headerLine, fieldName, valueStr)
// headerLine is a possible line of header from the file.
// In this example, the header can contain fields and variables. For example:
//      Subject ID: ABCD 99W        // Subject ID is a field
//      Level = 80                  // Level is a variable
// For our purposes, we treat both as header fields and require no conflicts
// between header field names and header variable names.
static Function GetFieldNameAndValueStrFromHeaderLine(headerLine, fieldName, valueStr)
    String headerLine       // Input
    String& fieldName       // Output
    String& valueStr        // Output
    
    int lineLength = strlen(headerLine)
    
    // Header lines start with either "<Field Name>: " or "<Var Name> = "
    int isVarName = 0
    int pos = strsearch(headerLine, ": ", 0)
    if (pos < 0)
        // Did not find <Field Name>: "
        pos = strsearch(headerLine, " = ", 0)
        if (pos < 0)
            // Did not find <Var Name> = "
            return -1           // Failure
        endif
        isVarName = 1
    endif
    
    fieldName = headerLine[0,pos-1]
    if (isVarName)
        valueStr = headerLine[pos+3,lineLength-2]
    else
        valueStr = headerLine[pos+2,lineLength-2]
    endif
 
    return 0                    // Success
End
 
// ReadHeaderInfo(pathName, fileName, maxHeaderLines)
// Returns a list of field names and values as colon-separated keyword-value pairs.
static Function/S ReadHeaderInfo(pathName, fileName, maxHeaderLines)
    String pathName         // Name of symbolic path. Ignored if filePath is full path.
    String fileName         // File name, relative path or full path
    int maxHeaderLines      // Maximum lines of header at start of file
 
    Variable refNum
    Open/R/P=$pathName refNum as fileName
    if (refNum == 0)        // File not opened - bad pathName or fileName
        return ""
    endif
    
    String resultStr = ""
    
    int lineNumber = 0
    do
        String line
        FReadLine refNum, line
        if (strlen(line) == 0)
            break                   // No more text in file
        endif
        
        String fieldName        // e.g., "Subject ID" or "Level"
        String valueStr         // e.g., "ABCD 99W" or "80"
        if (GetFieldNameAndValueStrFromHeaderLine(line, fieldName, valueStr) != 0)
            // No field on this line
            lineNumber += 1
            continue
        endif
        
        resultStr += fieldName + ":" + valueStr + ";"
        
        lineNumber += 1
        if (lineNumber >= maxHeaderLines)
            // There are no more header lines to examine
            break
        endif
    while(1)
    
    Close refNum
    
    return resultStr
End
 
// DemoReadPatientHeaderAndData(pathName, fileName)
// Demonstrates reading header information and data from a file like the "Patient Sample Data.txt" file.
// In this case, the file contains about 30 header lines followed by one column
// of numeric data. The user wants to use certain header fields to form the wave name.
//
// To display an Open File dialog, execute:
//      DemoReadPatientHeaderAndData("", "")
//
// To load a file without an Open File dialog dialog, execute:
//      Create a symbolic path named "PatientData" and then execute
//      DemoReadPatientHeaderAndData("PatientData", "Patient Sample Data.txt")
// If you are not familiar with Igor's "symbolic path" concept, execute this:
//      DisplayHelpTopic "Symbolic Paths"
// 
// If the wave already exists, this routine overwrites it.
Function DemoReadPatientHeaderAndData(pathName, fileName)
    String pathName     // Name of an Igor symbolic path or "" to get an Open File dialog
    String fileName     // Name of file or full path to file or "" to get an Open File dialog
 
    // If necessary, display an Open File dialog to get a valid reference to a file
    if ((strlen(pathName)==0) || (strlen(fileName)==0))
        // Display dialog looking for file
        Variable refNum
        String fileFilters = "Data Files (*.txt,*.dat,*.csv):.txt,.dat,.csv;"
        fileFilters += "All Files:.*;"
        Open /D /R  /F=fileFilters /P=$pathName refNum as fileName
        fileName = S_fileName               // S_fileName is set by Open/D
        if (strlen(fileName) == 0)      // User cancelled?
            return -1
        endif
    endif
    
    // Read header information
    String headerInfo = ReadHeaderInfo(pathName, fileName, 100)
    String subjectIDStr = StringByKey("Subject ID", headerInfo)
    double AudFreq = NumberByKey("AudFreq", headerInfo)
    double Level = NumberByKey("Level", headerInfo)
    // Printf "subjectID=%s, AudFreq=%g, Level=%g\r", subjectIDStr, AudFreq, Level      // For debugging only
    
    // Remove spaces which complicate wave names
    subjectIDStr = ReplaceString(" ", subjectIDStr, "")
    
    // Create a standard name because liberal names create complications
    String name
    sprintf name, "%s_%d_%d", subjectIDStr, AudFreq, Level  // e.g., "ABCD99W_4000_80
    name = CleanupName(name, 0)
    
    // Load wave
    String columnInfoStr = "N=" + name + ";"
    LoadWave/G/P=$pathName/A/O/B=columnInfoStr/Q fileName
    if (V_Flag != 1)        // We expect 1 wave to be created
        return -1               // Failure
    endif
    
    // Create wave reference
    WAVE w = $name
    
    // Store header information in wave note
    String noteText = ReplaceString(";", headerInfo, "\r")  // Each field on separate line
    Note w, noteText
    
    return 0                    // Success
End

 

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