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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