FileName Class Reference

#include <xmipp_filename.h>

Inheritance diagram for FileName:

Collaboration diagram for FileName:

Public Member Functions
Filename constructors
	FileName ()
	FileName (const String &str)
	FileName (const char *str)
FileName &	operator= (const FileName &op)
	FileName (const FileName &fn)
	FileName (const char *str, int no, const String &ext="")
	FileName (const char *str, const String &ext)
	FileName (const String &str, const String &ext)
Composing/Decomposing the filename
String	getString () const
bool	isEmpty () const
void	compose (const String &str, const size_t no, const String &ext="")
void	compose (const size_t no, const String &str)
void	compose (size_t no, const String &str, const String &ext)
void	compose (const String &blockName, const String &str)
void	composeBlock (const String &blockName, size_t no, const String &str, const String &ext="")
bool	isInStack () const
void	decompose (size_t &no, String &str) const
FileName	getDecomposedFileName () const
FileName	getRoot () const
FileName	getBaseName () const
int	getNumber () const
size_t	getPrefixNumber (size_t pos=0) const
FileName	getDir () const
String	getExtension () const
String	getFileFormat () const
bool	hasImageExtension () const
bool	hasStackExtension () const
bool	hasVolumeExtension () const
bool	hasMetadataExtension () const
size_t	getFileSize () const
String	getBlockName () const
FileName	removePrefixNumber () const
FileName	removeBlockName () const
FileName	removeAllPrefixes () const
void	initRandom (int length)
void	initUniqueName (const char *templateStr="xmippTemp_XXXXXX", const String &fnDir="")
Filename utilities
FileName	toLowercase () const
FileName	toUppercase () const
bool	contains (const String &str) const
FileName	beforeFirstOf (const String &str) const
FileName	beforeLastOf (const String &str) const
FileName	afterFirstOf (const String &str) const
FileName	afterLastOf (const String &str) const
FileName	addPrefix (const String &prefix) const
FileName	addExtension (const String &ext) const
FileName	withoutExtension () const
FileName	withoutRoot () const
FileName	insertBeforeExtension (const String &str) const
FileName	removeExtension (const String &ext) const
FileName	removeLastExtension () const
FileName	removeFilename () const
FileName	removeAllExtensions () const
FileName	removeFileFormat () const
bool	isMetaData (bool failIfNotExists=true) const
bool	isStar1 (bool failIfNotExists) const
FileName	replaceSubstring (const String &subOld, const String &subNew) const
FileName	replaceCharacter (char oldChar, char newChar) const
FileName	replaceExtension (const String &newExt) const
FileName	removeSubstring (const String &sub) const
FileName	removeUntilPrefix (const String &prefix) const
FileName	removeDirectories (int keep=0) const
void	copyFile (const FileName &target) const
bool	exists () const
void	deleteFile () const
bool	existsTrim () const
bool	isDir () const
void	getFiles (std::vector< FileName > &files) const
void	waitUntilStableSize (size_t time_step=250000)
void	createEmptyFile (size_t size, size_t block_size=102400)
void	createEmptyFileWithGivenLength (size_t length=0) const
int	makePath (mode_t mode=0755) const
void	assertExists ()

Detailed Description

Filenames.

This class allows you a lot of usual and common manipulations with filenames. See filename conventions for a detailed explanation of the Filenames dealed here, although most of the functions work with the more general model "name.extension"

Definition at line 65 of file xmipp_filename.h.

Constructor & Destructor Documentation

FileName() [1/7]

FileName::FileName ( )

inline

Empty constructor

The empty constructor is inherited from the string class, so an empty FileName is equal to "".

FileName fn_blobs;

Definition at line 80 of file xmipp_filename.h.

                     : String("")
    {}

FileName() [2/7]

FileName::FileName ( const String &  str )

inline

Constructor from string

The constructor from a string allows building complex expressions based on the string class. Notice that in the following example the type casting to string is very important, if not, the operation is just a pointer movement instead of a string concatenation.

FileName fn_blobs((String) "art00001" + ".blobs");

Definition at line 94 of file xmipp_filename.h.

                               : String(str)
    {}

FileName() [3/7]

FileName::FileName ( const char *  str )

inline

Constructor from char*

Definition at line 99 of file xmipp_filename.h.

                              : String(str)
    {}

FileName() [4/7]

FileName::FileName ( const FileName &  fn )

inline

Copy constructor

Definition at line 111 of file xmipp_filename.h.

                                 : String(fn)
    {}

FileName() [5/7]

FileName::FileName ( const char *  str, int  no, const String &  ext = ""  )

inline

Constructor from root, number and extension

The number and extension are optional.

FileName fn_proj("g1ta000001.xmp"); // fn_proj = "g1ta000001.xmp"
FileName fn_proj("g1ta",1,"xmp"); // fn_proj = "g1ta000001.xmp"
FileName fn_proj("g1ta",1); // fn_proj = "g1ta000001"

Definition at line 124 of file xmipp_filename.h.

    {
        compose(str, no, ext);
    }

FileName() [6/7]

FileName::FileName ( const char *  str, const String &  ext  )

inline

Constructor from root and extension

None of the parameters is optional

FileName fn_proj("g1ta00001", "xmp"); // fn_proj = "g1ta00001.xmp"

Definition at line 137 of file xmipp_filename.h.

                                                : String(str + ext)
    {}

FileName() [7/7]

FileName::FileName ( const String &  str, const String &  ext  )

inline

Constructor from root and extension

None of the parameters is optional

FileName fn_proj("g1ta00001", "xmp"); // fn_proj = "g1ta00001.xmp"

Definition at line 148 of file xmipp_filename.h.

                                                  : String(str + "." + ext)
    {}

Member Function Documentation

addExtension()

FileName FileName::addExtension

(

const String &

ext

)

const

Add extension at the end.

The "." is added. If the input extension is "" then the same name is returned, with nothing added.

fn_proj = "g1ta00001";
fn_proj.add_extension("xmp"); // fn_proj == "g1ta00001.xmp"

Definition at line 332 of file xmipp_filename.cpp.

{
    if (ext == "")
        return *this;
    else
    {
        FileName retval = *this;
        retval = retval.append((String) "." + ext);
        return retval;
    }
}

addPrefix()

FileName FileName::addPrefix

(

const String &

prefix

)

const

Add string at the beginning

If there is a path then the prefix is added after the path.

fn_proj = "imgs/g1ta00001";
fn_proj.add_prefix("h"); // fn_proj == "imgs/hg1ta00001"

fn_proj = "g1ta00001";
fn_proj.add_prefix("h"); // fn_proj == "hg1ta00001"

Definition at line 324 of file xmipp_filename.cpp.

{
    FileName retval = *this;
    int skip_directories = find_last_of("/") + 1;
    return retval.insert(skip_directories, prefix);
}

afterFirstOf()

FileName FileName::afterFirstOf

(

const String &

str

)

const

Return substring after first instance of argument (as in Bsoft)

FileName fn_proj("g1ta00001.raw#d=f");
fn_proj = fn_proj.after_first_of("#"); // fn_proj = "d=f"

Definition at line 212 of file xmipp_filename.cpp.

{
    size_t point = find_first_of(str);
    return point != npos ? (FileName)substr(point + 1) : *this;
}

afterLastOf()

FileName FileName::afterLastOf

(

const String &

str

)

const

Return substring after last instance of argument (as in Bsoft)

FileName fn_proj("g1ta00001.raw#d=f");
fn_proj = fn_proj.after_last_of("#"); // fn_proj = "d=f"

Definition at line 220 of file xmipp_filename.cpp.

{
    size_t point = find_last_of(str);
    return point != npos ? (FileName)substr(point + 1) : *this;
}

assertExists()

void FileName::assertExists

(

)

This function raised an ERROR if the filename if not empty and if the corresponding file does not exist. This may be useful to have a better (killing) control on (mpi-regulated) jobs

exit_if_not_exists("control_file.txt");

This function is not ported to Python.

Definition at line 840 of file xmipp_filename.cpp.

{
    if (!empty() && !exists())
    {
        std::cerr << "FileName::assertExists: control file" << *this
        << " doesn't exist, exiting..." << std::endl;
        exit(ERR_IO_NOTEXIST);
    }
    //TODO: Maybe change to report error???
    //REPORT_ERROR(ERR_IO_NOTEXIST, (String)"FileName::assertExists: control file" + *this " doesn't exist, exiting...");
}

beforeFirstOf()

FileName FileName::beforeFirstOf

(

const String &

str

)

const

Return substring before first instance of argument (as in Bsoft)

FileName fn_proj("g1ta00001.raw#d=f");
fn_proj = fn_proj.before_first_of("#"); // fn_proj = "g1ta00001.raw"

Definition at line 196 of file xmipp_filename.cpp.

{
    size_t point = find_first_of(str);
    return (point != npos ? (FileName)substr(0, point) : *this);
}

beforeLastOf()

FileName FileName::beforeLastOf

(

const String &

str

)

const

Return substring before last instance of argument (as in Bsoft)

FileName fn_proj("g1ta00001.raw#d=f");
fn_proj = fn_proj.before_last_of("#"); // fn_proj = "g1ta00001.raw"

Definition at line 204 of file xmipp_filename.cpp.

{
    size_t point = find_last_of(str);
    return point != npos ? (FileName)substr(0, point) : *this;
}

compose() [1/4]

void FileName::compose	(	const String &	str,
		const size_t	no,
		const String &	ext = ""
	)

Compose from root, number and extension

fn_proj.compose("g1ta", 1, "xmp");  // fn_proj = "g1ta000001.xmp"

Definition at line 52 of file xmipp_filename.cpp.

{

    if (no == ALL_IMAGES || no == (size_t) -1)
        REPORT_ERROR(ERR_DEBUG_TEST, "Don't compose with 0 or -1 index, now images index start at 1");

    *this = (FileName) str;

    if (no != ALL_IMAGES)
        this->append(formatString("%06lu", no));

    if (!ext.empty())
        *this += (String) "." + ext;
}

compose() [2/4]

void FileName::compose	(	const size_t	no,
		const String &	str
	)

Prefix with number . Mainly for selfiles

fn_proj.compose(1,"g1ta.xmp");  // fn_proj = "000001@g1ta000001.xmp"

Definition at line 68 of file xmipp_filename.cpp.

{
    if (no == ALL_IMAGES || no == (size_t) -1)
        REPORT_ERROR(ERR_DEBUG_TEST, "Don't compose with 0 or -1 index, now images index start at 1");

    if (no != ALL_IMAGES)
    {
        size_t first = str.rfind(AT);
        if (first != npos)
        {
            std::vector<String> prefixes;
            int nPref = splitString(str.substr(0, first),",",prefixes, false);

            if (isalpha(prefixes[nPref-1].at(0)))
                formatStringFast(*this, "%06lu,%s", no, str.c_str());
        }
        else
            formatStringFast(*this, "%06lu@%s", no, str.c_str());
    }
    else
        *this = str;
}

compose() [3/4]

void FileName::compose	(	size_t	no,
		const String &	str,
		const String &	ext
	)

Prefix with number and extension .

fn_proj.compose(1, "g1ta", "xmp");  // fn_proj = "000001@g1ta000001.xmp"

Definition at line 92 of file xmipp_filename.cpp.

{
    if (no == ALL_IMAGES || no == (size_t) -1)
        REPORT_ERROR(ERR_DEBUG_TEST, "Don't compose with 0 or -1 index, now images index start at 1");

    if (no != ALL_IMAGES)
        formatStringFast(*this, "%06lu@%s.%s", no,
                         str.c_str(), ext.c_str());
    else
        *this = str;
}

compose() [4/4]

void FileName::compose	(	const String &	blockName,
		const String &	str
	)

Prefix with string (blockname) .

fn_proj.compose(b00001, "g1ta.xmp");  // fn_proj = "b000001@g1ta.xmp"

Definition at line 105 of file xmipp_filename.cpp.

{
    if (blockName.empty())
        *this = str;
    else
        formatStringFast(*this, "%s@%s", blockName.c_str(), str.c_str());
}

composeBlock()

void FileName::composeBlock	(	const String &	blockName,
		size_t	no,
		const String &	str,
		const String &	ext = ""
	)

Constructor: string, number, rootfilename and extension: mainly for numered metadata blocks..

fn_proj.composeBlock("bb",5, "g1ta","xmp");  // fn_proj = "bb000005@g1ta.xmp"
fn_proj.composeBlock("bb",5, "g1ta.xmp");    // fn_proj = "bb000005@g1ta.xmp"

Definition at line 114 of file xmipp_filename.cpp.

{
    formatStringFast(*this, "%s%06lu@%s", blockName.c_str(), no, root.c_str());
    if (ext != "")
        *this += (String) "." + ext;
}

contains()

bool FileName::contains

(

const String &

str

)

const

Check whether the filename contains the argument substring

FileName fn_proj("g1ta00001.raw#d=f");
if (fn_proj.contains("raw) )  // true

Definition at line 189 of file xmipp_filename.cpp.

{
    return find(str) != npos;
}

copyFile()

void FileName::copyFile

(

const FileName &

target

)

const

copy one file

Definition at line 656 of file xmipp_filename.cpp.

{
    std::ifstream f1(this->c_str(), std::fstream::binary);
    std::ofstream
    f2(target.c_str(), std::fstream::trunc | std::fstream::binary);
    f2 << f1.rdbuf();
}

createEmptyFile()

void FileName::createEmptyFile	(	size_t	size,
		size_t	block_size = 102400
	)

Write a zero filled file with the desired size.

The file is written by blocks to speed up, you can modify the block size. An exception is thrown if any error happens

Definition at line 752 of file xmipp_filename.cpp.

{
    unsigned char * buffer = (unsigned char*) calloc(sizeof(unsigned char),
                             block_size);
    if (buffer == NULL)
        REPORT_ERROR(ERR_MEM_NOTENOUGH, "create_empty_file: No memory left");
    FILE * fd = fopen(c_str(), "w");
    if (fd == NULL)
        REPORT_ERROR(ERR_IO_NOTOPEN, (String)"FileName::createEmptyFile: Cannot open file" + *this);
    for (size_t i = 0; i < size / block_size; i++)
        fwrite(buffer, sizeof(unsigned char), block_size, fd);
    fwrite(buffer, sizeof(unsigned char), size % block_size, fd);
    fclose(fd);
    free(buffer);
}

createEmptyFileWithGivenLength()

void FileName::createEmptyFileWithGivenLength

(

size_t

length = 0

)

const

Create empty file with a given length.

Definition at line 768 of file xmipp_filename.cpp.

{
    FILE* fMap = fopen(c_str(),"wb");
    if (!fMap)
        REPORT_ERROR(ERR_IO_NOWRITE, *this);
    if (length>0)
    {
        char c=0;
        if ((fseek(fMap, length-1, SEEK_SET) == -1) || (fwrite(&c,1,1,fMap) != 1))
            REPORT_ERROR(ERR_IO_NOWRITE,"FileName::createEmptyFileWithGivenLength: Cannot create empty file");
    }
    fclose(fMap);
}

decompose()

void FileName::decompose	(	size_t &	no,
		String &	str
	)		const

Decompose filenames with . Mainly from selfiles

fn_proj.decompose(no,filename);  // fn_proj = "000001@g1ta000001.xmp"
                                 // no=1
                                 // filename = "g1ta000001.xmp"

Definition at line 128 of file xmipp_filename.cpp.

{
    char buffer[1024];
    unsigned long int auxNo;
    int ok = sscanf(c_str(), "%lu@%s", &auxNo, buffer);
    no=auxNo;
    if (ok != 2)
    {
        no = ALL_IMAGES;
        str = *this;
        return;
    }
    else if (no == 0)
        REPORT_ERROR(ERR_INDEX_OUTOFBOUNDS, formatString("FileName::decompose: Incorrect index number at filename %s; It must start at %lu",c_str(),FIRST_IMAGE));

    str = buffer;
}

deleteFile()

void FileName::deleteFile

(

)

const

Delete the file if exists

Definition at line 670 of file xmipp_filename.cpp.

{
    FileName temp = this->removeFileFormat().removeAllPrefixes();
    if (temp.exists())
        unlink(temp.c_str());
}

exists()

bool FileName::exists

(

)

const

True if the filename exists, check from current directory if is relative

FileName fn("g1ta0001");
if (fn.exists())
    std::cout << "The file exists" << std::endl;

Definition at line 665 of file xmipp_filename.cpp.

{
    return fileExists(getDecomposedFileName().removeFileFormat());
}

existsTrim()

bool FileName::existsTrim

(

)

const

True if the file exists in the current directory Remove leading xx@ and tailing :xx

if (exists("g1ta00001"))
    std::cout << "The file exists" << std::endl;

Definition at line 677 of file xmipp_filename.cpp.

{
    FileName auxF(*this);
    size_t found = find_first_of(AT);

    if (found != String::npos)
        auxF =  substr(found+1);

    found = auxF.find_first_of(NUM);

    if ( found != String::npos)
        auxF = auxF.substr(0, found);
    found = auxF.find_first_of(COLON);

    if (found != String::npos)
        auxF = auxF.substr(0, found);
    return fileExists(auxF.c_str());
}

getBaseName()

FileName FileName::getBaseName

(

)

const

Get the base name from a filename

Definition at line 227 of file xmipp_filename.cpp.

{
    FileName baseName = removeLastExtension();
    return baseName.afterLastOf("/");
}

getBlockName()

String FileName::getBlockName

(

)

const

Get blockName from filename

fn_meta="block1@md1.doc"
String blockName;
blockName=fn_meta.getblockName();//blockName="block1"

Definition at line 485 of file xmipp_filename.cpp.

{
    size_t first = rfind(AT);
    String result = "";
    if (first != npos)
    {
        result = substr(0, first);
        if ((first = result.find(COMMA)) != npos) // Assign and compare at the same time
          result = result.substr(first+1);

        /* using isdigit instead of isalpha allows to
         * detect as blockname rootnames starting by "/"
         */
        if (result.empty() || isdigit(result[0]))
            result = "";
    }
    return result;

}

getDecomposedFileName()

FileName FileName::getDecomposedFileName

(

)

const

Get decomposed filename from filenames with . Mainly from selfiles

filename = fn_proj.decomposedFileName();  // fn_proj = "000001@g1ta000001.xmp"
                                         // no=1
                                         // filename = "g1ta000001.xmp"

Definition at line 147 of file xmipp_filename.cpp.

{
    String str;
    size_t no;
    decompose(no, str);
    return str;
}

getDir()

FileName FileName::getDir

(

)

const

Definition at line 235 of file xmipp_filename.cpp.

{
    size_t pos = find_last_of("/");
    return (FileName)( pos != npos ? substr(0, pos+1) : "");
}

getExtension()

String FileName::getExtension

(

)

const

Get the last extension from filename

The extension is returned without the dot. If there is no extension "" is returned.

String ext = fn_proj.get_extension();

Definition at line 242 of file xmipp_filename.cpp.

{
    size_t posA = find_last_of("/");
    size_t posB = find_last_of(".");
    if (posB==npos)
        return "";
    if (posA==npos)
        return substr(posB+1);
    if (posB>posA)
        return substr(posB+1);
    return "";
}

getFileFormat()

String FileName::getFileFormat

(

)

const

Get image format identifier

fn_proj = "g1ta00001.xmp";
fn_proj = fn_proj.get_file_format(); // fn_proj == "xmp"
fn_proj = "g1ta00001.nor:spi";
fn_proj = fn_proj.get_file_format(); // fn_proj == "spi"
fn_proj = "input.file#120,120,55,1024,float";
fn_proj = fn_proj.get_file_format(); // fn_proj == "raw"

Definition at line 396 of file xmipp_filename.cpp.

{
    size_t first;
    FileName result;
    if ((first = rfind(COLON)) != npos)
        result = substr(first + 1);
    else if ((first = rfind(".")) != npos)
    {
        // Get everything from the '.' to the end of the filename
        // If there is a '#', only keep whatever is between the '.' and the '#'
        result = substr(first + 1);
        result = result.substr(0, result.find(NUM));
    }
    else if (find(NUM) != npos)
        return "raw";
    return result.toLowercase();
}

getFiles()

void FileName::getFiles

(

std::vector< FileName > &

files

)

const

Return the list of files if this filename is a directory

Definition at line 697 of file xmipp_filename.cpp.

{
    files.clear();

    DIR *dp;
    struct dirent *dirp;
    if ((dp  = opendir(c_str())) == NULL)
        REPORT_ERROR(ERR_IO_NOTEXIST,*this);

    while ((dirp = readdir(dp)) != NULL)
        if (strcmp(dirp->d_name,".")!=0 && strcmp(dirp->d_name,"..")!=0)
            files.push_back(FileName(dirp->d_name));
    closedir(dp);
    std::sort(files.begin(),files.end());
}

getFileSize()

size_t FileName::getFileSize

(

)

const

Get the size of the file.

Definition at line 414 of file xmipp_filename.cpp.

{
    Stat info;
    if (stat(c_str(), &info))
    {
        char cCurrentPath[FILENAME_MAX];
        char *success=getcwd(cCurrentPath, sizeof(cCurrentPath));
        if (success==NULL)
            cCurrentPath[0]='\0';
        REPORT_ERROR(ERR_UNCLASSIFIED,formatString("FileName::getFileSize: Cannot get size of file %s/%s",cCurrentPath,this->c_str()));
    }
    return info.st_size;

//    int fd = open(c_str(), O_RDONLY);
//    size_t size = lseek(fd, 0, SEEK_END); // seek to end of file
//    close(fd);
//
//    return size;

}

getNumber()

int FileName::getNumber

(

)

const

Get the number from a filename

If there is no number a -1 is returned.

FileName proj("g1ta00001");
int num = proj.getNumber();

Definition at line 447 of file xmipp_filename.cpp.

{
    size_t skip_directories = find_last_of("/") + 1;
    size_t point = find_first_of(".", skip_directories);
    if (point == npos)
        point = length();
    size_t root_end = find_last_not_of("0123456789", point - 1);
    if (root_end + 1 != point)
    {
        if (point - root_end > FILENAMENUMBERLENGTH)
            root_end = point - FILENAMENUMBERLENGTH - 1;
        String aux = substr(root_end + 1, point - root_end + 1);
        return atoi(aux.c_str());
    }
    else
        return -1;
}

getPrefixNumber()

size_t FileName::getPrefixNumber

(

size_t

pos = 0

)

const

Get the number from a stack filename

If there is no number a 0 is returned.

FileName proj("24@images.stk");
size_t num = proj.getStackNumber();

Definition at line 466 of file xmipp_filename.cpp.

{
    size_t first = rfind(AT);
    size_t result = ALL_IMAGES;
    if (first != npos)
    {
        std::vector<String> prefixes;
        size_t nPref = splitString(substr(0, first),",",prefixes, false);

        if (pos > nPref-1)
            REPORT_ERROR(ERR_ARG_INCORRECT, formatString("getPrefixNumber: Selected %lu position greater than %lu positions \n"
                         " detected in %s filename.",pos+1, nPref, this->c_str()));

        if (isdigit(prefixes[pos].at(0)))
            result = textToSizeT(prefixes[pos].c_str());
    }
    return result;
}

getRoot()

FileName FileName::getRoot

(

)

const

Get the root from a filename

FileName fn_root, fn_proj("g1ta00001");
fn_root = fn_proj.get_root();

Definition at line 157 of file xmipp_filename.cpp.

{
    size_t skip_directories = find_last_of("/") + 1;
    size_t point = find_first_of(".", skip_directories);
    if (point == npos)
        point = length();
    size_t root_end = find_last_not_of("0123456789", point - 1);
    if (root_end + 1 != point)
        if (point - root_end > FILENAMENUMBERLENGTH)
            root_end = point - FILENAMENUMBERLENGTH - 1;
    return substr(0, root_end + 1);
}

getString()

String FileName::getString ( ) const

inline

Convert to String

Definition at line 158 of file xmipp_filename.h.

    {
        return (String)(*this);
    }

hasImageExtension()

bool FileName::hasImageExtension

(

)

const

True if the extension of this filename is of an image type

Definition at line 256 of file xmipp_filename.cpp.

{
    String ext = getFileFormat();
    return (ext=="img" || ext=="hed" || ext=="inf" || ext=="raw" || ext=="mrc" ||
            ext=="map" || ext=="spi" || ext=="xmp" || ext=="tif" || ext=="dm3" ||
            ext=="spe" || ext=="em"  || ext=="pif" || ext=="ser" || ext=="stk" ||
            ext=="mrcs"|| ext=="jpg" || ext=="dm4");
}

hasMetadataExtension()

bool FileName::hasMetadataExtension

(

)

const

True if the extension of this filename is of a metadata file

Definition at line 283 of file xmipp_filename.cpp.

{
    String ext = getFileFormat();
    return (ext == "sel"    || ext == "xmd" || ext == "doc" ||
            ext == "ctfdat" || ext == "ctfparam" || ext == "pos" ||
            ext == "sqlite" || ext == "xml" || ext == "star");
}

hasStackExtension()

bool FileName::hasStackExtension

(

)

const

True if the extension of this filename is of a stack type

Definition at line 266 of file xmipp_filename.cpp.

{
    String ext = getFileFormat();
    return (ext=="stk" || ext=="spi" || ext=="xmp" || ext=="mrcs" || ext=="mrc" ||
            ext=="img" || ext=="hed" || ext=="pif" || ext=="tif"  || ext=="dm3" ||
            ext=="ser" || ext=="st"  || ext=="dm4");
}

hasVolumeExtension()

bool FileName::hasVolumeExtension

(

)

const

True if the extension of this filename is of a stack type

Definition at line 275 of file xmipp_filename.cpp.

{
    String ext = getFileFormat();
    return (ext=="vol" || ext=="spi" || ext=="xmp" || ext=="mrc" || ext=="map" ||
            ext=="em"  || ext=="pif" || ext=="inf" || ext=="raw");
}

initRandom()

void FileName::initRandom

(

int

length

)

Random name

Generate a random name of the desired length.

Definition at line 292 of file xmipp_filename.cpp.

{
    randomize_random_generator();
    *this = "";
    for (int i = 0; i < length; i++)
        *this += 'a' + FLOOR(rnd_unif(0, 26));
}

initUniqueName()

void FileName::initUniqueName	(	const char *	templateStr = "xmippTemp_XXXXXX",
		const String &	fnDir = ""
	)

Unique name

Generate a unique name replacing each 'X' with a character from the portable filename character set. The characters are chosen such that the resulting name does not duplicate the name of an existing file.

Definition at line 301 of file xmipp_filename.cpp.

{
#ifndef __MINGW32__
    int fd;
    const int len=512;
    char filename[len];
    if (fnDir!="")
        strcpy(filename,(fnDir+"/").c_str());
    else
        filename[0]=0;
    strcat(filename, templateStr);
    filename[len - 1] = 0;
    if ((fd = mkstemp(filename)) == -1)
    {
        perror("FileName::Error generating tmp lock file");
        exit(1);
    }
    close(fd);
    *this = filename;
#endif
}

insertBeforeExtension()

FileName FileName::insertBeforeExtension

(

const String &

str

)

const

Insert before first extension

If there is no extension, the insertion is performed at the end.

fn_proj = "g1ta00001.xmp";
fn_proj = fn_proj.insert_before_extension("pp");
// fn_proj == "g1ta00001pp.xmp"

fn_proj = "g1ta00001";
fn_proj = fn_proj.insert_before_extension("pp");
// fn_proj=="g1ta00001pp"

Definition at line 358 of file xmipp_filename.cpp.

{
    FileName retval = *this;
    size_t pos = find_last_of('.');
    return  pos != npos ? retval.insert(pos, str) : retval.append(str);
}

isDir()

bool FileName::isDir

(

)

const

True if the path is a directory

Definition at line 714 of file xmipp_filename.cpp.

{
    Stat st_buf;
    if (stat (c_str(), &st_buf) != 0)
        REPORT_ERROR(ERR_UNCLASSIFIED,(String)"Cannot determine status of filename "+ *this);
    return (S_ISDIR (st_buf.st_mode));
}

isEmpty()

bool FileName::isEmpty ( ) const

inline

True if the FileName has an empty value ""

Definition at line 165 of file xmipp_filename.h.

    {
        return *this == "";
    }

isInStack()

bool FileName::isInStack

(

)

const

True if this filename belongs to a stack

Definition at line 122 of file xmipp_filename.cpp.

{
    return find(AT) != String::npos;
}

isMetaData()

bool FileName::isMetaData

(

bool

failIfNotExists = true

)

const

Is this file a MetaData file? Returns true if the get_file_format extension == "sel", "doc" or "xmd" Otherwise, the file is opened and checked for the occurrence of "XMIPP_3 *" in its first line

Definition at line 556 of file xmipp_filename.cpp.

{
    //check empty string
    if (empty())
        REPORT_ERROR(ERR_ARG_INCORRECT, "FileName::isMetaData: Empty string is not a MetaData");
    //file names containing : or % are not metadatas
    //size_t found = this->find('@');
    if (find_first_of(":#") != npos)
        return false;

    //check if file exists
    if (failIfNotExists && !existsTrim())
        REPORT_ERROR(ERR_IO_NOTFILE, formatString("FileName::isMetaData: File: '%s' does not exist", c_str()));
    //This is dangerous and should be removed
    //in next version. only star1 files should be OK
    //ROB
    //FIXME
    return (hasMetadataExtension() || isStar1(failIfNotExists));
}

isStar1()

bool FileName::isStar1

(

bool

failIfNotExists

)

const

True if it is a Star 1 file.

Definition at line 576 of file xmipp_filename.cpp.

{
    std::ifstream infile( this->removeAllPrefixes().c_str(), std::ios_base::in);
    String line;

    if (infile.fail())
    {
        if (failIfNotExists)
            REPORT_ERROR( ERR_IO_NOTEXIST, formatString("File '%s' does not exist.", this->removeAllPrefixes().c_str()));
        else
            return false;
    }

    // Search for xmipp_3,
    char cline[128];
    infile.getline(cline, 128);
    infile.close();
    line = cline;
    size_t pos = line.find(METADATA_XMIPP_STAR);
    return (pos != npos); // xmipp_star_1 token found
}

makePath()

int FileName::makePath

(

mode_t

mode = 0755

)

const

makePath - ensure all directories in path exist Algorithm takes the pessimistic view and works top-down to ensure each directory in path exists, rather than optimistically creating the last element and working backwards. Return null if fails

Definition at line 811 of file xmipp_filename.cpp.

{
    char *pp;
    char *sp;
    int status;
    char *copypath = strdup(c_str());
    if (copypath == NULL)
        REPORT_ERROR(ERR_MEM_BADREQUEST,"FileName::makePath: Canot alloc memory");

    status = 0;
    pp = copypath;
    while (status == 0 && (sp = strchr(pp, '/')) != 0)
    {
        if (sp != pp)
        {
            /* Neither root nor double slash in path */
            *sp = '\0';
            status = do_mkdir(copypath, mode);
            *sp = '/';
        }
        pp = sp + 1;
    }
    if (status == 0)
        status = do_mkdir(c_str(), mode);
    free(copypath);
    return status;
}

operator=()

FileName& FileName::operator= ( const FileName &  op )

inline

Assignment constructor

Definition at line 104 of file xmipp_filename.h.

    {
        return (FileName&) std::string::operator=(op);
    }

removeAllExtensions()

FileName FileName::removeAllExtensions

(

)

const

Remove all extensions

Definition at line 382 of file xmipp_filename.cpp.

{
    FileName retval = *this;
    size_t first = find_last_of('/');
    first = find_first_of('.', first + 1);
    return (first == npos) ? retval: retval.substr(0, first);
}

removeAllPrefixes()

FileName FileName::removeAllPrefixes

(

)

const

Remove blockName or slice number from filename

fn_meta="block1@md1.doc"
String blockName;
filename=removeBlockNameOrSliceNumber();//filename="md1.doc"

Definition at line 548 of file xmipp_filename.cpp.

{
    size_t first = rfind(AT);
    if (first != npos)
        return substr(first + 1);
    return *this;
}

removeBlockName()

FileName FileName::removeBlockName

(

)

const

Remove blockName from filename

fn_meta="block1@md1.doc"
String blockName;
filename=fn_meta.getblockName();//filename="md1.doc"

Definition at line 505 of file xmipp_filename.cpp.

{
    size_t first = rfind(AT);

    if (first != npos)
    {
        String block = substr(0, first);
        size_t second = block.find(COMMA);

        if (second == npos)
        {
          if (!isdigit(block[0])){
            return substr(first + 1);
          }
        }
        else
        {
          String prefix = block.substr(0, second);
          block = block.substr(second + 1);
          if (!isdigit(block[0]))
            return prefix + substr(first);
        }
    }
    return *this;
}

removeDirectories()

FileName FileName::removeDirectories

(

int

keep = 0

)

const

Remove all directories

Or if keep>0, then keep the lowest keep directories

Definition at line 641 of file xmipp_filename.cpp.

{
    size_t last_slash = rfind("/");
    int tokeep = keep;
    while (tokeep > 0)
    {
        last_slash = rfind("/", last_slash - 1);
        tokeep--;
    }
    if (last_slash == npos)
        return *this;
    else
        return substr(last_slash + 1, length() - last_slash);
}

removeExtension()

FileName FileName::removeExtension

(

const String &

ext

)

const

Remove a certain extension

It doesn't matter if there are several extensions and the one to be removed is in the middle. If the given extension is not present in the filename nothing is done.

fn_proj = "g1ta00001.xmp.bak";
fn_proj = fn_proj.remove_extension("xmp");
// fn_proj == "g1ta00001.bak"

Definition at line 366 of file xmipp_filename.cpp.

{
    FileName retval = *this;
    size_t first = find((String) "." + ext);
    return (first == npos) ? retval: retval.erase(first, 1 + ext.length());
}

removeFileFormat()

FileName FileName::removeFileFormat

(

)

const

Remove file format

fn_proj = "g1ta00001.xmp";
fn_proj = fn_proj.get_file_format(); // fn_proj == "xmp"
fn_proj = "g1ta00001.nor:spi";
fn_proj = fn_proj.get_file_format(); // fn_proj == "spi"
fn_proj = "input.file#d=f#x=120,120,55#h=1024";
fn_proj = fn_proj.get_file_format(); // fn_proj == "raw"

Definition at line 435 of file xmipp_filename.cpp.

{
    size_t found = rfind(NUM);
    if (found != String::npos)
        return substr(0, found);
    found = rfind(COLON);
    if (found != String::npos)
        return substr(0, found);
    return *this;
}

removeFilename()

FileName FileName::removeFilename

(

)

const

Extract the directory portion from a filename string (e.g. /foo/bar.txt -> /foo).

Definition at line 390 of file xmipp_filename.cpp.

{
    size_t first = find_last_of('/');
    return (first == npos) ? "" : substr(0, first);
}

removeLastExtension()

FileName FileName::removeLastExtension

(

)

const

Definition at line 374 of file xmipp_filename.cpp.

{
    FileName retval = *this;
    size_t first = find_last_of('.');
    return (first == npos) ? retval : retval.substr(0, first);
}

removePrefixNumber()

FileName FileName::removePrefixNumber

(

)

const

Remove leading number from filename

fn_meta="1@md1.doc"
String blockName;
filename=fn_meta.removeSliceNumber();//filename="md1.doc"

Definition at line 531 of file xmipp_filename.cpp.

{
    size_t first = rfind(AT);

    if (first != npos)
    {
        std::vector<String> prefixes;
        int nPref = splitString(substr(0, first),",",prefixes, false);

        if (isdigit(prefixes[nPref-1].at(0)))
            return substr(first + 1);
        else if (nPref > 1) // isalpha and we remove the ","
            return substr(first - prefixes[nPref-1].size());
    }
    return *this;
}

removeSubstring()

FileName FileName::removeSubstring

(

const String &

sub

)

const

Remove a substring from the filename

If the substring is not present the same FileName is returned, if it is there the substring is removed. It is equivalent to replaceSubstring(sub, "");

Definition at line 625 of file xmipp_filename.cpp.

{
    return replaceSubstring(sub, "");
}

removeUntilPrefix()

FileName FileName::removeUntilPrefix

(

const String &

prefix

)

const

Remove until prefix

Remove the starting string until the given prefix, inclusively. For instance /usr/local/data/ctf-image00001.fft with ctf- yields image00001.fft. If the prefix is not found nothing is done.

Definition at line 631 of file xmipp_filename.cpp.

{
    size_t pos = find(prefix);
    if (pos == npos)
        return *this;
    FileName result = *this;
    return result.erase(0, pos + prefix.length());
}

replaceCharacter()

FileName FileName::replaceCharacter	(	char	oldChar,
		char	newChar
	)		const

Replace all occurrences of a character by another character

Definition at line 611 of file xmipp_filename.cpp.

{
    FileName result = *this;
    std::replace(result.begin(), result.end(), oldChar, newChar);
    return result;
}

replaceExtension()

FileName FileName::replaceExtension

(

const String &

newExt

)

const

Substitute last extension by a new one

fn_proj = "g1ta00001.xmp.bak";
fn_proj = fn_proj.replaceExtension("bor");
// fn_proj == "g1ta00001.xmp.bor"

Definition at line 619 of file xmipp_filename.cpp.

{
    return removeLastExtension() + "." + newExt;
}

replaceSubstring()

FileName FileName::replaceSubstring	(	const String &	subOld,
		const String &	subNew
	)		const

Replace a the first occurrence of substring 'subOld' by 'subNew' If 'subOld' not present, not changes are done. The search is done from left to right

fn_proj = "g1ta00001.xmp.bak";
fn_proj = fn_proj.replace(".xmp", ".bor");
// fn_proj == "g1ta00001.bor.bak"

fn_proj = "g1ta00001.xmp.bak";
fn_proj = fn_proj.replace(".bor", "");
// fn_proj == "g1ta00001.bak"

Definition at line 599 of file xmipp_filename.cpp.

{
    size_t pos = find(subOld);
    if (pos == npos)
        return *this;

    FileName result = *this;
    result.replace(pos, subOld.length(), subNew);
    return result;
}

toLowercase()

FileName FileName::toLowercase

(

)

const

Change all characters for lowercases

FileName fn_proj("g1tA00001");
fn_proj = fn_proj.to_lowercase(); // fn_proj = "g1ta00001"

Definition at line 171 of file xmipp_filename.cpp.

{
    FileName result = *this;
    for (size_t i = 0; i < result.length(); i++)
        result[i] = tolower(result[i]);
    return result;
}

toUppercase()

FileName FileName::toUppercase

(

)

const

Change all characters for uppercases

FileName fn_proj("g1tA00001");
fn_proj = fn_proj.to_uppercase(); // fn_proj = "G1Ta00001"

Definition at line 180 of file xmipp_filename.cpp.

{
    FileName result = *this;
    for (size_t i = 0; i < result.length(); i++)
        result[i] = toupper(result[i]);
    return result;
}

waitUntilStableSize()

void FileName::waitUntilStableSize

(

size_t

time_step = 250000

)

Waits until the given filename has a stable size

The stable size is defined as having the same size within two samples separated by time_step (microsecs).

An exception is throw if the file exists but its size cannot be stated.

Definition at line 723 of file xmipp_filename.cpp.

{
    size_t idx;
    FileName basicName;
    decompose(idx, basicName);

    if (!exists())
        return;
    Stat info1, info2;
    if (stat(basicName.c_str(), &info1))
        REPORT_ERROR(ERR_UNCLASSIFIED,
                     (String)"FileName::waitUntilStableSize: Cannot get size of file " + *this);
    off_t size1 = info1.st_size;
    do
    {
        usleep(time_step);
        if (stat(basicName.c_str(), &info2))
            REPORT_ERROR(ERR_UNCLASSIFIED,
                         (String)"FileName::waitUntilStableSize: Cannot get size of file " + *this);
        off_t size2 = info2.st_size;
        if (size1 == size2)
            break;
        size1 = size2;
    }
    while (true);
    return;
}

withoutExtension()

FileName FileName::withoutExtension

(

)

const

Remove last extension, if any

fn_proj = "g1ta00001.xmp";
fn_proj = fn_proj.without_extension(); // fn_proj == "g1ta00001"

fn_proj = "g1ta00001";
fn_proj = fn_proj.without_extension(); // fn_proj == "g1ta00001"

Definition at line 345 of file xmipp_filename.cpp.

{
    FileName retval = *this;
    return retval.substr(0, rfind("."));
}

withoutRoot()

FileName FileName::withoutRoot

(

)

const

Remove the root

fn_proj = "g1ta00001.xmp";
fn_proj = fn_proj.without_root(); // fn_proj == "00001.xmp"

fn_proj = "g1ta00001";
fn_proj = fn_proj.without_root(); // fn_proj == "00001"

Definition at line 352 of file xmipp_filename.cpp.

{
    return removeSubstring(getRoot());
}

---

The documentation for this class was generated from the following files:

• xmippCore/core/xmipp_filename.h
• xmippCore/core/xmipp_filename.cpp