Read Patient Header and Data From the Same File
hrodstein
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
#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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Sample patient data file.
September 13, 2021 at 01:30 pm - Permalink