Some basic utility functions. More...

#include <string>
#include <typeinfo>
#include <vector>
#include <set>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <sstream>
#include <stdexcept>
#include <iterator>
#include <cmath>
#include <numeric>
#include <memory.h>
#include <map>
#include <random>
#include <iomanip>
#include <limits>

Include dependency graph for cbicaUtilities.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
struct	CSVDict
	A Dictionary structure to for CSV parsing. More...

struct	FileNameParts
	Holds the different parts of a file name (path, base and extension) More...

Functions
std::map< std::string, size_t >	ConfusionMatrix (const std::vector< float > &inputRealLabels, const std::vector< float > &inputPredictedLabels)
	Calculates the Confusion Matrix for a set of real and predicted labels. More...

char *	constCharToChar (const std::string &input)
	Convert const char* to char*. More...

char *	constCharToChar (const char *input)
	Convert const char* to char*. More...

template<typename TConvertType >
TConvertType	convertCharacter (const std::string &input_string)
	Convert first character to integer, double, unsigned int, etc. More...

template<typename TConvertType = int>
std::vector< TConvertType >	convertString (const std::string &input_string)
	Convert entire string to integer, double, unsigned int, etc. More...

bool	copyDir (const std::string &inputFolder, const std::string &destination, bool recursion=true)
	Copy a folder and if recursion enabled, all its contents. More...

bool	copyDirectory (const std::string &inputFolder, const std::string &destination, bool recursion=true)
	Copy a folder and if recursion enabled, all its contents. More...

bool	copyFile (const std::string &inputFile, const std::string &destination)
	Copy a folder and if recursion enabled, all its contents. More...

bool	copyFolder (const std::string &inputFolder, const std::string &destination, bool recursion=true)
	Copy a folder and if recursion enabled, all its contents. More...

bool	createDir (const std::string &dir_name)
	Create a directory. More...

bool	createDirectory (const std::string &dir_name)
	Create a directory. More...

bool	createFolder (const std::string &dir_name)
	Create a directory. More...

std::string	createTemporaryDirectory ()
	Create a temporary directory. More...

std::string	createTmpDir ()
	Create a temporary directory. More...

bool	deleteDir (const std::string &path)
	Delete a folder and contents. More...

bool	deleteEnvironmentVariable (const std::string &variable_name)
	Delete the environment variable. More...

bool	directoryExists (const std::string &dName)
	Check if directory exists. More...

void	dos2unix (const std::string inputFile)
	Ensuring files written using Windows don't mess stuff up. More...

bool	exists (const std::string &path)
	Return True if path exists and false for broken symbolic links. More...

bool	fileExists (const std::string &fName)
	Check if file exists using istream. More...

std::vector< std::string >	filesInDirectory (const std::string &dirName, bool returnFullPath=true)
	Find all files inside a directory. More...

template<typename TContainerType = std::string>
std::pair< bool, int >	findInVector (std::vector< TContainerType > &vector_to_search_in, TContainerType element_to_search_for)
	Searches for an element in a vector and returns true/false and position. More...

std::string	getCurrentGMT ()
	Get current GMT as string delineated as HH:MM:SS.

std::string	getCurrentGMTDate ()
	Get current GMT as string delineated as YYYY:MM:DD.

std::string	getCurrentGMTDateAndTime ()
	Get current GMT as string delineated as YYYY:MM:DD,HH:MM:SS.

std::string	getCurrentLocalDate ()
	Get current local time as string delineated as YYYY:MM:DD.

std::string	getCurrentLocalDateAndTime ()
	Get current local time as string delineated as YYYY:MM:DD,HH:MM:SS.

std::string	getCurrentLocalTime ()
	Get current local time as string delineated as HH:MM:SS.

std::string	getCurrentProcessID ()
	Get the current process ID. More...

std::string	getCurrentYear ()
	Get current Year as string delineated as YYYY.

std::string	getCWD ()
	Get the current working directory. More...

std::vector< std::string >	getCWLFilesInApplicationDir ()

size_t	getDirectorySize (const std::string &rootFolder)
	Get the size of the folder. More...

size_t	getDirSize (const std::string &rootFolder)
	Get the size of the folder. More...

std::string	getEnvironmentVariableValue (const std::string &environmentVariable)
	Gets the value of the specified environment variable.

std::string	getExecutableName ()
	Get the name of the Executable which is calling the function. More...

std::string	getExecutablePath ()
	Get the path of the Executable which is calling the function. More...

std::string	getFilenameBase (const std::string &filename, bool checkFile=true)
	Gets the base of the supplied file name using splitFileName() More...

std::string	getFilenameExtension (const std::string &filename, bool checkFile=true)
	Gets the extension of the supplied file name using splitFileName() More...

std::string	getFilenamePath (const std::string &filename, bool checkFile=true)
	Gets the path of the supplied file name using splitFileName() More...

size_t	getFileSize (const std::string &inputFile)
	Get the size of the file in bytes. More...

size_t	getFolderSize (const std::string &rootFolder)
	Get the size of the folder. More...

std::string	getFullPath ()
	Get the name of the Executable which is calling the function. More...

template<class TDataType = std::string>
std::vector< TDataType >	GetUniqueElements (const std::vector< TDataType > &inputVector)
	Find the unique elements in a vector. More...

std::string	getUserHomeDirectory ()
	Get the home directory of the user. More...

std::string	getUserName ()
	Get the name of the user who is calling the function. More...

bool	IsCompatible (const std::string inputVersionFile)

bool	isDir (const std::string &path)
	Return True if path is an existing directory. More...

bool	isFile (const std::string &path)
	Return True if path is an existing regular file. More...

bool	isLink (const std::string &path)
	Return True if path refers to a directory entry that is a symbolic link. More...

bool	isSymbolicLink (const std::string &path)
	Check if path refers to a symbolic entry. More...

bool	makeDir (const std::string &dir_name)
	Create a directory. More...

bool	makeDirectory (const std::string &dir_name)
	Create a directory. More...

bool	makeFolder (const std::string &dir_name)
	Create a directory. More...

bool	makeSymbolicLink (const std::string &input_fileName, const std::string &ouput_fileName)
	Make a symbolic link from file to another. More...

std::string	makeTempDir ()
	Create a temporary directory. More...

std::string	makeTemporaryDirectory ()
	Create a temporary directory. More...

std::string	normalizePath (const std::string &path)
	Normalize a pathname by collapsing redundant separators and up-level references. More...

std::string	normPath (const std::string &path)
	Normalize a pathname by collapsing redundant separators and up-level references. More...

size_t	numberOfColsInFile (const std::string &csvFileName, const std::string &delim=",")
	Find number of cols in CSV file.

size_t	numberOfRowsInFile (const std::string &csvFileName, const std::string &delim="\n")
	Find number of rows in CSV file.

std::vector< CSVDict >	parseCSVFile (const std::string &csvFileName, const std::string &inputColumns, const std::string &inputLabels, bool checkFile=true, bool pathsRelativeToCSV=false, const std::string &rowsDelimiter="\n", const std::string &colsDelimiter=",", const std::string &optionsDelimiter=",")
	Parse the supplied CSV File and obtain Row and Column information. More...

template<class TDataType = float>
std::vector< TDataType >	randn (const TDataType start, const TDataType end, size_t sizeOfReturn=1)
	A good random number generator using c++11 that gives a random value within a range. More...

template<class TDataType = float>
std::vector< TDataType >	randn (size_t sizeOfReturn=1)
	A good random number generator using c++11 that gives a random value within a range. More...

template<class TDataType = double>
std::vector< std::vector< TDataType > >	readCSVDataFile (const std::string &csvFileName, bool columnMajor=false)
	Read a CSV file which has no header information. More...

std::vector< std::vector< std::string > >	readCSVDataFile (const std::string &csvFileName)
	Read a CSV file which has no header information. More...

std::string	realPath (const std::string &path)
	Return the canonical path of the specified filename. More...

std::string	relativePath (const std::string &path, const std::string &base)
	Return a relative filepath to path. More...

std::string	relPath (const std::string &path, const std::string &base)
	Return a relative filepath to path. More...

bool	removeDir (const std::string &path)
	Delete a folder and contents. More...

int	removeDirectoryRecursively (const std::string &dirname, bool bDeleteSubdirectories)
	Recursively delete a folder and contents [internal function]. More...

std::string	replaceString (const std::string &entireString, const std::string &toReplace, const std::string &replaceWith)
	Searches for smaller string in larger string and then replaces it with user-defined input. More...

std::map< std::string, float >	ROC_Values (const std::vector< float > &inputRealLabels, const std::vector< float > &inputPredictedLabels)
	Calculates the ROC Values (see https://en.wikipedia.org/wiki/Receiver_operating_characteristic of all estimates) for a set of real and predicted labels. More...

bool	setEnvironmentVariable (const std::string &variable_name, const std::string &variable_value)
	Sets the environment variable. More...

void	sleep (size_t ms=std::rand() % 1000+1)
	Cross platform sleep. More...

bool	splitFileName (const std::string &dataFile, std::string &path, std::string &baseName, std::string &extension)
	Splits the input file name into its constituents. More...

std::vector< std::string >	stringSplit (const std::string &str, const std::string &delim)
	Splits the string. More...

std::vector< std::string >	subdirectoriesInDirectory (const std::string &dirName, bool recursiveSearch=false, bool returnFullPath=false)
	Find all sub-directories inside a directory. More...

Detailed Description

Some basic utility functions.

This needs c++11 flag enabled in gcc < 5.

https://www.med.upenn.edu/sbia/software///
softw.nosp@m.are@.nosp@m.cbica.nosp@m..upe.nosp@m.nn.ed.nosp@m.u

Copyright (c) 2018 University of Pennsylvania. All rights reserved.
See COPYING file or https://www.med.upenn.edu/cbica/software-agreement.html

Function Documentation

◆ ConfusionMatrix()

std::map< std::string, size_t > cbica::ConfusionMatrix	(	const std::vector< float > &	inputRealLabels,
		const std::vector< float > &	inputPredictedLabels
	)

Calculates the Confusion Matrix for a set of real and predicted labels.

Values returned: True Positive (TP), False Positive (FP), True Negative (TN), False Negative (FN), Real Positive (RP), Preditcted Positive (PP)

Parameters

inputRealLabels	Vector structure containing real labels
inputPredictedLabels	Vector structure containing predicted labels

Returns: std::map< string, size_t > A map of string and corresponding non-negative values

◆ constCharToChar() [1/2]

char* cbica::constCharToChar ( const std::string & input )

Convert const char* to char*.

Parameters

input constant std::string

Returns: character pointer

◆ constCharToChar() [2/2]

char* cbica::constCharToChar ( const char * input )

Convert const char* to char*.

Parameters

input constant character pointer

Returns: character pointer

◆ convertCharacter()

TConvertType cbica::convertCharacter ( const std::string & input_string )

Convert first character to integer, double, unsigned int, etc.

Parameters

input_string Input character to be converted

Returns: Templated to the type of return required

References cbica::convertCharacter().

Referenced by cbica::convertCharacter().

◆ convertString()

std::vector< TConvertType> cbica::convertString ( const std::string & input_string )

Convert entire string to integer, double, unsigned int, etc.

Parameters

input_string Input character to be converted

Returns: Templated vector to the type of return required

References cbica::convertString().

Referenced by cbica::convertString().

◆ copyDir()

bool cbica::copyDir	(	const std::string &	inputFolder,
		const std::string &	destination,
		bool	recursion = `true`
	)

Copy a folder and if recursion enabled, all its contents.

https://msdn.microsoft.com/en-us/library/hh874694.aspx?f=255&MSPPError=-2147217396

Parameters

inputFolder	Folder to copy
destination	Where to copy to
recursion	Do recursion and copy, defaults to true

Returns: true for success

◆ copyDirectory()

bool cbica::copyDirectory	(	const std::string &	inputFolder,
		const std::string &	destination,
		bool	recursion = `true`
	)

Copy a folder and if recursion enabled, all its contents.

https://msdn.microsoft.com/en-us/library/hh874694.aspx?f=255&MSPPError=-2147217396

Parameters

inputFolder	Folder to copy
destination	Where to copy to
recursion	Do recursion and copy, defaults to true

Returns: true for success

◆ copyFile()

bool cbica::copyFile	(	const std::string &	inputFile,
		const std::string &	destination
	)

Copy a folder and if recursion enabled, all its contents.

Parameters

inputFile	File to copy
destination	Where to copy to

Returns: true for success

◆ copyFolder()

bool cbica::copyFolder	(	const std::string &	inputFolder,
		const std::string &	destination,
		bool	recursion = `true`
	)

Copy a folder and if recursion enabled, all its contents.

https://msdn.microsoft.com/en-us/library/hh874694.aspx?f=255&MSPPError=-2147217396

Parameters

inputFolder	Folder to copy
destination	Where to copy to
recursion	Do recursion and copy, defaults to true

Returns: true for success

◆ createDir()

bool cbica::createDir ( const std::string & dir_name )

Create a directory.

Parameters

dir_name Name of directory to be created with full path

Returns: True if success

Referenced by cbica::WriteDicomImage().

◆ createDirectory()

bool cbica::createDirectory ( const std::string & dir_name )

Create a directory.

Parameters

dir_name Name of directory to be created with full path

Returns: True if success

◆ createFolder()

bool cbica::createFolder ( const std::string & dir_name )

Create a directory.

Parameters

dir_name Name of directory to be created with full path

Returns: True if success

◆ createTemporaryDirectory()

std::string cbica::createTemporaryDirectory ( )

Create a temporary directory.

Wrap for createTmpDir()

Returns: True if success

◆ createTmpDir()

std::string cbica::createTmpDir ( )

Create a temporary directory.

Creates a user-writable file using the following format: USER_HOME_DIR + EXE_NAME + tmp_ + processID;

If this file is existing, for whatever reason, then a new is created which has the time stamp appended.

Returns: Path of temporary directory

◆ deleteDir()

bool cbica::deleteDir ( const std::string & path )

Delete a folder and contents.

Parameters

path	Folder to delete

Returns: true for success

◆ deleteEnvironmentVariable()

bool cbica::deleteEnvironmentVariable ( const std::string & variable_name )

Delete the environment variable.

Parameters

variable_name Name of the Variable

Returns: True if successful

◆ directoryExists()

bool cbica::directoryExists ( const std::string & dName )

Check if directory exists.

Parameters

dName String to check

Returns: True if directory exists

◆ dos2unix()

void cbica::dos2unix ( const std::string inputFile )

Ensuring files written using Windows don't mess stuff up.

Base implementation from https://www.digitalpeer.com/blog/simple-text-processing-with-cpp-dos2unix-example

◆ exists()

bool cbica::exists ( const std::string & path )

Return True if path exists and false for broken symbolic links.

Reimplementation of python's "os.path.exists": On some platforms, this function may return False if permission is not granted to execute os.stat() on the requested file, even if the path physically exists.

Parameters

path	Path to check

Returns: True if path is valid and false for broken symbolic links

◆ fileExists()

bool cbica::fileExists ( const std::string & fName )

Check if file exists using istream.

Parameters

fName Filename to check

Returns: True if file exists

◆ filesInDirectory()

std::vector< std::string > cbica::filesInDirectory	(	const std::string &	dirName,
		bool	returnFullPath = `true`
	)

Find all files inside a directory.

Parameters

dirName The directory to do the search in

Referenced by cbica::GetImageReader().

◆ findInVector()

std::pair<bool, int> cbica::findInVector	(	std::vector< TContainerType > &	vector_to_search_in,
		TContainerType	element_to_search_for
	)

Searches for an element in a vector and returns true/false and position.

Templated function to take in any kind of vector and element.

Parameters

vector_to_search_in	Vector to do the search in
element_to_search_for	Element to search for
position	Last position of found element in vector (-1) if not found

Returns: True if found; Position if found (-1) if not

References cbica::findInVector().

Referenced by cbica::findInVector().

◆ getCurrentProcessID()

std::string cbica::getCurrentProcessID ( )

Get the current process ID.

Provides wraps to _getpid() in OS-specific ways

◆ getCWD()

std::string cbica::getCWD ( )

Get the current working directory.

[Wrap for cbica::getcwd()]

Returns: Current working directory

◆ getDirectorySize()

size_t cbica::getDirectorySize ( const std::string & rootFolder )

Get the size of the folder.

Parameters

rootFolder The input folder

◆ getDirSize()

size_t cbica::getDirSize ( const std::string & rootFolder )

Get the size of the folder.

Parameters

rootFolder The input folder

◆ getExecutableName()

std::string cbica::getExecutableName ( )

Get the name of the Executable which is calling the function.

Returns: exe name

◆ getExecutablePath()

std::string cbica::getExecutablePath ( )

Get the path of the Executable which is calling the function.

returns the path after calling splitFileName on getFullPath

Returns: exe name

◆ getFilenameBase()

std::string cbica::getFilenameBase	(	const std::string &	filename,
		bool	checkFile = `true`
	)

Gets the base of the supplied file name using splitFileName()

Prefer to use "/" as file path delimiter.

Parameters

filename	The input filename
checkFile	Checks existence of file using fileExists

Returns: std::string which has the file extension

◆ getFilenameExtension()

std::string cbica::getFilenameExtension	(	const std::string &	filename,
		bool	checkFile = `true`
	)

Gets the extension of the supplied file name using splitFileName()

Prefer to use "/" as file path delimiter.

Parameters

filename	The input filename
checkFile	Checks existence of file using fileExists

Returns: std::string which has the file extension

Referenced by cbica::GetImageReader(), cbica::ReadImageWithOrientFix(), and cbica::WriteImage().

◆ getFilenamePath()

std::string cbica::getFilenamePath	(	const std::string &	filename,
		bool	checkFile = `true`
	)

Gets the path of the supplied file name using splitFileName()

Prefer to use "/" as file path delimiter.

Parameters

filename	The input filename
checkFile	Checks existence of file using fileExists

Returns: std::string which has the file extension

Referenced by cbica::GetDicomImageReader(), and cbica::GetImageReader().

◆ getFileSize()

size_t cbica::getFileSize ( const std::string & inputFile )

Get the size of the file in bytes.

Parameters

inputFile The input file

◆ getFolderSize()

size_t cbica::getFolderSize ( const std::string & rootFolder )

Get the size of the folder.

Parameters

rootFolder The input folder

◆ getFullPath()

std::string cbica::getFullPath ( )

Get the name of the Executable which is calling the function.

Returns: exe name

◆ GetUniqueElements()

std::vector< TDataType > cbica::GetUniqueElements ( const std::vector< TDataType > & inputVector )

Find the unique elements in a vector.

Implementation incorporated from the SO answer in https://stackoverflow.com/a/1041939/1228757

Parameters

inputVector The vector on which to search for unique elements

Returns: An std::vector with unique elements

References cbica::GetUniqueElements().

Referenced by cbica::GetDicomImageReader(), and cbica::GetUniqueElements().

◆ getUserHomeDirectory()

std::string cbica::getUserHomeDirectory ( )

Get the home directory of the user.

Windows - C:/Users/XYZ Linux - /home/XYZ

Returns: user directory

◆ getUserName()

std::string cbica::getUserName ( )

Get the name of the user who is calling the function.

Returns: user name

◆ isDir()

bool cbica::isDir ( const std::string & path )

Return True if path is an existing directory.

Reimplementation of python's "os.path.isdir": This follows symbolic links, so both islink() and isdir() can be true for the same path.

[Wrap of cbica::directoryExists()]

Parameters

path	Directory name to check

Returns: True of path is an existing directory

Referenced by cbica::GetDicomImageReader(), and cbica::WriteDicomImage().

◆ isFile()

bool cbica::isFile ( const std::string & path )

Return True if path is an existing regular file.

Reimplementation for python's "os.path.isfile": This follows symbolic links, so both islink() and isfile() can be true for the same path.

[Wrap of cbica::fileExists()]

Parameters

path	Filename of file to check

Returns: True if path is an existing regular file

Referenced by cbica::readCSVDataFile().

◆ isLink()

bool cbica::isLink ( const std::string & path )

Return True if path refers to a directory entry that is a symbolic link.

Reimplementation of python's "os.path.islink": Always False if symbolic links are not supported by the python runtime.

Parameters

path	Path to check

Returns: True if path is symbolic link

◆ isSymbolicLink()

bool cbica::isSymbolicLink ( const std::string & path )

Check if path refers to a symbolic entry.

[Wrap of cbica::isLink()]

Parameters

path	Path to check

Returns: True if path is symbolic link

◆ makeDir()

bool cbica::makeDir ( const std::string & dir_name )

Create a directory.

Parameters

dir_name Name of directory to be created with full path

◆ makeDirectory()

bool cbica::makeDirectory ( const std::string & dir_name )

Create a directory.

Parameters

dir_name Name of directory to be created with full path

◆ makeFolder()

bool cbica::makeFolder ( const std::string & dir_name )

Create a directory.

Parameters

dir_name Name of directory to be created with full path

◆ makeSymbolicLink()

bool cbica::makeSymbolicLink	(	const std::string &	input_fileName,
		const std::string &	ouput_fileName
	)

Make a symbolic link from file to another.

Parameters

input_fileName	Input file name for which symbolic link needs to be created
output_fileName	Output file name which is the symbolic link for input_fileName

Returns: True if symbolic link successfully created

◆ makeTempDir()

std::string cbica::makeTempDir ( )

Create a temporary directory.

Wrap for createTmpDir()

Returns: True if success

◆ makeTemporaryDirectory()

std::string cbica::makeTemporaryDirectory ( )

Create a temporary directory.

Wrap for createTmpDir()

Returns: True if success

◆ normalizePath()

std::string cbica::normalizePath ( const std::string & path )

Normalize a pathname by collapsing redundant separators and up-level references.

[Wrap for cbica::normPath()]

Parameters

path	Path to normalize

Returns: std::string Normalized path

◆ normPath()

std::string cbica::normPath ( const std::string & path )

Normalize a pathname by collapsing redundant separators and up-level references.

Reimplementation of python's "os.path.normpath": Normalize a pathname by collapsing redundant separators and up-level references so that A//B, A/B/, A/./B and A/foo/../B all become A/B. This string manipulation may change the meaning of a path that contains symbolic links. On Windows, it converts forward slashes to backward slashes.

Parameters

path	Path to normalize

Returns: std::string Normalized path

Referenced by cbica::GetDicomImageReader(), and cbica::GetImageReader().

◆ parseCSVFile()

std::vector< CSVDict > cbica::parseCSVFile	(	const std::string &	csvFileName,
		const std::string &	inputColumns,
		const std::string &	inputLabels,
		bool	checkFile = `true`,
		bool	pathsRelativeToCSV = `false`,
		const std::string &	rowsDelimiter = `"\n"`,
		const std::string &	colsDelimiter = `","`,
		const std::string &	optionsDelimiter = `","`
	)

Parse the supplied CSV File and obtain Row and Column information.

Assumptions:

Header information is in first row
Full paths of images are given
Image paths are either absolute (default behaviour) OR relative to the location of CSV file OR relative to CWD

Parameters

csvFileName	The full path of the file to parse, all paths are absolute or relative to current working directory
inputColumns	The string of input columns which contain the data to be used for further processing
inputLabels	The string of input labels per subject based on which further processing is to be done; if this is empty, it is initialized as 1 for all subjects
checkFile	Check the validity of the file; defaults to true
pathsRelativeToCSV	The paths in the CSV file are relative to the location of CSV file otherwise, they are checked relative to the CWD
rowsDelimiter	The delimiters used to distinguish rows in the file
colsDelimiter	The delimiters used to distinguish cols in the file
optionsDelimiter	The delimiters used in inputColumns and inputLabel

Returns: Vector of CSV Dictionary items: Collection of input images are respective labels

◆ randn() [1/2]

std::vector< TDataType > cbica::randn	(	const TDataType	start,
		const TDataType	end,
		size_t	sizeOfReturn = `1`
	)

A good random number generator using c++11 that gives a random value within a range.

Parameters

start	Start value of range; defaults to 0
end	End value of range; defaults to 1
sizeOfReturn	Size of the returned vector

References cbica::randn().

Referenced by cbica::randn().

◆ randn() [2/2]

std::vector< TDataType > cbica::randn ( size_t sizeOfReturn = 1 )

A good random number generator using c++11 that gives a random value within a range.

Parameters

sizeOfReturn Size of the returned vector

References cbica::randn().

◆ readCSVDataFile() [1/2]

std::vector< std::vector< TDataType > > cbica::readCSVDataFile	(	const std::string &	csvFileName,
		bool	columnMajor = `false`
	)

Read a CSV file which has no header information.

To read CSV file with header information, check parseCSVFile() function. This should not be used for obtaining strings

Parameters

csvFileName	The full path of the file to parse, all paths are absolute or relative to current working directory
columnMajor	If true, then return is a vector of all the columns; otherwise it is a vector of the rows

References cbica::isFile(), cbica::numberOfColsInFile(), cbica::numberOfRowsInFile(), and cbica::readCSVDataFile().

Referenced by cbica::readCSVDataFile().

◆ readCSVDataFile() [2/2]

std::vector< std::vector< std::string > > cbica::readCSVDataFile ( const std::string & csvFileName )

Read a CSV file which has no header information.

To read CSV file with header information, check parseCSVFile() function. This should be used for obtaining strings

Parameters

csvFileName The full path of the file to parse, all paths are absolute or relative to current working directory

◆ realPath()

std::string cbica::realPath ( const std::string & path )

Return the canonical path of the specified filename.

Reimplementation of python's "os.path.realpath": Return the canonical path of the specified filename, eliminating any symbolic links encountered in the path (if they are supported by the operating system).

Parameters

path	Filename to check

Returns: canonical path of path

◆ relativePath()

std::string cbica::relativePath	(	const std::string &	path,
		const std::string &	base
	)

Return a relative filepath to path.

Wrap of cbica::relPath()

Parameters

path	Path to check
base	Base file name

Returns: Relative filepath to path either from current directory or from an optional start dir

◆ relPath()

std::string cbica::relPath	(	const std::string &	path,
		const std::string &	base
	)

Return a relative filepath to path.

Reimplementation for python's "os.path.relpath": Return a relative filepath to path either from the current directory or from an optional start directory. This is a path computation: the filesystem is not accessed to confirm the existence or nature of path or start.

Parameters

path	Path to check
base	Base file name

Returns: Relative filepath to path either from current directory or from an optional start dir

◆ removeDir()

bool cbica::removeDir ( const std::string & path )

Delete a folder and contents.

Parameters

path	Folder to delete

Returns: true for success

◆ removeDirectoryRecursively()

int cbica::removeDirectoryRecursively	(	const std::string &	dirname,
		bool	bDeleteSubdirectories
	)

Recursively delete a folder and contents [internal function].

Parameters

dirname Folder to delete

Returns: true for success

◆ replaceString()

std::string cbica::replaceString	(	const std::string &	entireString,
		const std::string &	toReplace,
		const std::string &	replaceWith
	)

Searches for smaller string in larger string and then replaces it with user-defined input.

Parameters

entireString	String to search
toReplace	String to replace
replaceWith	String to replace toReplace with

Returns: std::string of result

◆ ROC_Values()

std::map< std::string, float > cbica::ROC_Values	(	const std::vector< float > &	inputRealLabels,
		const std::vector< float > &	inputPredictedLabels
	)

Calculates the ROC Values (see https://en.wikipedia.org/wiki/Receiver_operating_characteristic of all estimates) for a set of real and predicted labels.

Values returned: True Positive (TP), False Positive (FP), True Negative (TN), False Negative (FN), Real Positive (RP), Preditcted Positive (PP) [all from ConfusionMatrix()], Accuracy, Positive Predictive Value (PPV) [aka Precision], False Discovery Rate (FDR), False Omission Rate (FOR), Negative Predictive Value (NPV), Prevalence, True Positive Rate (TPR) [aka Sensitivity, Recall, Probability of Detection (POD)], False Positive Rate (FPR) [aka Fall-out], False Negative Rate (FNR) [aka Miss Rate (MR)], True Negative Rate (TNR) [aka Specificity], Positive Likelihood Ratio (LR+), Negative Likelihood Ratio (LR−), Diagnostic Odds Ratio (DOR), Dice Score (Dice), Jaccard ratio/index (JR)

Parameters

inputRealLabels	Vector structure containing real labels
inputPredictedLabels	Vector structure containing predicted labels

Returns: std::map< string, size_t > A map of string and corresponding float values

◆ setEnvironmentVariable()

bool cbica::setEnvironmentVariable	(	const std::string &	variable_name,
		const std::string &	variable_value
	)

Sets the environment variable.

Parameters

variable_name	Name of the Variable
variable_value	Value of variable_name

Returns: True if successful

◆ sleep()

void cbica::sleep ( size_t ms = std::rand() % 1000+1 )

Cross platform sleep.

Defaults to "std::rand() % 1000 + 1"

◆ splitFileName()

bool cbica::splitFileName	(	const std::string &	dataFile,
		std::string &	path,
		std::string &	baseName,
		std::string &	extension
	)

Splits the input file name into its constituents.

Parameters

dataFile	The full file name which is the input
baseName	Overwritten with file name without extension
extension	Overwritten with extension without '.'
path	Overwritten with path to file

Returns: True if successful

◆ stringSplit()

std::vector<std::string> cbica::stringSplit	(	const std::string &	str,
		const std::string &	delim
	)

Splits the string.

Parameters

str	String to split
delim	Delimiter on the basis of which splitting is to be done

Returns: results Output in the form of vector of strings

Referenced by cbica::ChangeImageValues(), and cbica::GetImageReader().

◆ subdirectoriesInDirectory()

std::vector<std::string> cbica::subdirectoriesInDirectory	(	const std::string &	dirName,
		bool	recursiveSearch = `false`,
		bool	returnFullPath = `false`
	)

Find all sub-directories inside a directory.

Parameters

dirName	The directory to do the search in
recursiveSearch	Whether to do a recursive search or on a single level

Classes

Functions

Detailed Description

Function Documentation

◆ ConfusionMatrix()

◆ constCharToChar() [1/2]

◆ constCharToChar() [2/2]

◆ convertCharacter()

◆ convertString()

◆ copyDir()

◆ copyDirectory()

◆ copyFile()

◆ copyFolder()

◆ createDir()

◆ createDirectory()

◆ createFolder()

◆ createTemporaryDirectory()

◆ createTmpDir()

◆ deleteDir()

◆ deleteEnvironmentVariable()

◆ directoryExists()

◆ dos2unix()

◆ exists()

◆ fileExists()

◆ filesInDirectory()

◆ findInVector()

◆ getCurrentProcessID()

◆ getCWD()

◆ getDirectorySize()

◆ getDirSize()

◆ getExecutableName()

◆ getExecutablePath()

◆ getFilenameBase()

◆ getFilenameExtension()

◆ getFilenamePath()

◆ getFileSize()

◆ getFolderSize()

◆ getFullPath()

◆ GetUniqueElements()

◆ getUserHomeDirectory()

◆ getUserName()

◆ isDir()

◆ isFile()

◆ isLink()

◆ isSymbolicLink()

◆ makeDir()

◆ makeDirectory()

◆ makeFolder()

◆ makeSymbolicLink()

◆ makeTempDir()

◆ makeTemporaryDirectory()

◆ normalizePath()

◆ normPath()

◆ parseCSVFile()

◆ randn() [1/2]

◆ randn() [2/2]

◆ readCSVDataFile() [1/2]

◆ readCSVDataFile() [2/2]

◆ realPath()

◆ relativePath()

◆ relPath()

◆ removeDir()

◆ removeDirectoryRecursively()

◆ replaceString()

◆ ROC_Values()

◆ setEnvironmentVariable()

◆ sleep()

◆ splitFileName()

◆ stringSplit()

◆ subdirectoriesInDirectory()