Script processes files and combines them into one, but I need the output to maintain separate files

This should work:

<?php
 
/*read configuration file*/
$config_name='cchrc_convert.cfg';
$cchrc_header=array();
$cchrc_data=array();
 
$config=config_fetch($config_name);
$myDir='/home/my_user/my_data';
$csv_file=csv_fetch($myDir);
 
if ($dh = opendir($dir)) {
    while (($csv_file = readdir($myDir)) !== false) {
        if (!is_file($csv_file)) {
            continue;
        }
        csv_convert($csv_file, $cchrc_header, $cchrc_data);
        csv_output($cchrc_header, $cchrc_data, $csv_file);
    }
    closedir($dh);
}
 
function config_fetch($config_name)
{
    $config_file=file($config_name);
    $config=array();
 
    if ($config_file) foreach ($config_file as $line)
    {
        list($key, $value)=explode('=', $line);
        $key=trim($key); $value=trim($value);
        if ($key=='' || $key[0]=='#') continue;
 
        switch ($key)
        {
            default: {
                $config[$key]=$value;
            } break;
            case 'Filter': {
                list($fkey, $fvalue)=explode(',', $value);
                $fkey=trim($fkey); $fvalue=trim($fvalue);
                $config['Filter'][$fkey]=$fvalue;
            } break;
            case 'ColumnKey': {
                $config['ColumnKey']=explode(',', $value);
            } break;
            case 'ColumnValue': {
                $config['ColumnValue']=explode(',', $value);
            } break;
        }
    }
 
    return $config;
}
 
/* read csv data files */
function csv_fetch($myDir)
{
    global $config_name;
 
    echo "Loading files:\n";
 
    if ($dh=opendir($myDir))
    {
        $csv_file=array();
 
        while (($file=readdir($dh))!==false) {
            if ($file==$config_name) continue;
            else if (stristr($file, '.php')) continue;
            else if ($file=='data.csv') continue;
            else if ($file=='.') continue;
            else if ($file=='..') continue;
 
            echo "$file\n";
            $csv_file=array_merge($csv_file, file($file));
        }
 
        if ($csv_file) foreach ($csv_file as $key=>$line) {
            $line=str_replace('"', '', $line);
            $line=str_replace(chr(13).chr(10), '', $line);
            $csv_file[$key]=$line;
        }
 
        closedir($dh);
    }
 
    echo "\n";
 
    return $csv_file;
}
 
/* convert */
function csv_convert($csv_file, &$cchrc_header, &$cchrc_data)
{
    global $config;
 
    echo "Converting data: .";
 
    $element='';
    $count=1;
    $records=count($csv_file);
    if ($csv_file) foreach ($csv_file as $line)
    {
        $csv_datum=explode(',', $line);
 
        /* element */
        if ($csv_datum[0]==$config['HeaderName']) {
            $element=$csv_datum[1];
        }
 
        /* reset element */
        if (count($csv_datum)==0) {
            $element='';
        }
 
        /* filter */
        if ($config['Filter']) foreach ($config['Filter'] as $key=>$value) {
            if ($csv_datum[0]==$key && $csv_datum[1]==$value) {
                $element='';
            }
        }
 
        /* push an item onto an element */
        if ($element!='' && count($csv_datum)==$config['ColumnCount'])
        {
            $key='';
            if ($config['ColumnKey']) foreach ($config['ColumnKey'] as $key_num) {
                if ($key!='') $key.=' '; $key.=$csv_datum[$key_num];
            }
            $value='';
            if ($config['ColumnValue']) foreach ($config['ColumnValue'] as $value_num) {
                if ($value!='') $value.=' '; $value.=$csv_datum[$value_num];
            }
 
            $cchrc_header[$key]=$key;
            $cchrc_data[$element][$key]=$value;
        }
 
        if ($count%1000==0) echo ".";
 
        $count++;
    }
    echo " Done\n";
 
    /* sort data */
    echo "   Sorting data: .";
 
    usort($cchrc_header, sort_date);
    ksort($cchrc_data);
 
    echo " Done\n\n";
    echo "Finished, file saved as 'data.csv'\n";
}
 
function sort_date($a, $b)
{
    // omitted (not an issue)
}
 
function csv_output($cchrc_header, $cchrc_data, $dst)
{
    global $config;
 
    $output=fopen($dst, 'w');
 
    /* Headers */
    fwrite($output, "\"Date\"");
    if ($cchrc_data) foreach ($cchrc_data as $name => $data)
    {
        fwrite($output, ",\"$name\"");
    }
    fwrite($output, "\n");
 
    /*  */
    if ($cchrc_header) foreach ($cchrc_header as $date)
    {
        fwrite($output, "\"$date\"");
        if ($cchrc_data) foreach ($cchrc_data as $name => $data)
        {
            fwrite($output, ",\"".$data[$date]."\"");
        }
        fwrite($output, "\n");
    }
 
    fclose($output);
}
 
function print_array($array, $name='')
{
    echo "$name:";
    print_r($array);
}

Select allOpen in new window

>>and retain the same filenames if possible
So you want to overwrite your original files? If I understand you correctly, the input files have a .csv extension and after processing these files will be overwritten. Make sure you backup your originals first, in case something goes wrong!

Try the attached code. NOTE: I'm prefixing the output files with "sara_" to "preserve" your original files in case something did not work as expected. Once it is working as desired AND you want to overwrite the original csv files, you can just change:
csv_output($cchrc_header, $cchrc_data, 'sara_' . $info['file']);

to:
csv_output($cchrc_header, $cchrc_data, $info['file']);

<?
/*read configuration file*/
$config_name='cchrc_convert.cfg';
$cchrc_header=array();
$cchrc_data=array(); 
$config=config_fetch($config_name);
$myDir='/home/my_user/my_data';
$csv_file=csv_fetch($myDir);
foreach( $csv_file as $info ){ 
		csv_convert($info['data'], $cchrc_header, $cchrc_data);
		csv_output($cchrc_header, $cchrc_data, 'sara_' . $info['file']); 
}
function config_fetch($config_name)
{
        $config_file=file($config_name);
        $config=array(); 
        if ($config_file) foreach ($config_file as $line)
        {
                list($key, $value)=explode('=', $line);
                $key=trim($key); $value=trim($value);
                if ($key=='' || $key[0]=='#') continue; 
                switch ($key)
                {
                        default: {
                                $config[$key]=$value;
                        } break;
                        case 'Filter': {
                                        list($fkey, $fvalue)=explode(',', $value);
                                        $fkey=trim($fkey); $fvalue=trim($fvalue);
                                        $config['Filter'][$fkey]=$fvalue;
                        } break;
                        case 'ColumnKey': {
                                        $config['ColumnKey']=explode(',', $value);
                        } break;
                        case 'ColumnValue': {
                                        $config['ColumnValue']=explode(',', $value);
                        } break;
                }
        } 
        return $config;
} 
/* read csv data files */
function csv_fetch($myDir)
{
        global $config_name; 
        echo "Loading files:\n"; 
        if ($dh=opendir($myDir))
        {
                $csv_file=array(); 
                while (($file=readdir($dh))!==false) {
                        if ($file==$config_name) continue;
                        else if (stristr($file, '.php')) continue;
//                        else if ($file=='data.csv') continue;
                        else if ($file=='.') continue;
                        else if ($file=='..') continue; 
                        echo "$file\n";
					//$csv_file=array_merge($csv_file, file($file));
					$csv_file[]=array('file'=>$file,'data'=>file($file));
                } 
                if ( count($csv_file) > 0 )
			 	foreach ($csv_file as $info) {
					foreach($info as $key=>$line){
                        		$line=str_replace('"', '', $line);
                        		$line=str_replace(chr(13).chr(10), '', $line);
                        		$info[$key]=$line;
					}
                	}
                closedir($dh);
        } 
        echo "\n"; 
        return $csv_file;
} 
/* convert */
function csv_convert($csv_file, &$cchrc_header, &$cchrc_data)
{
        global $config; 
        echo "Converting data: ."; 
        $element='';
        $count=1;
        $records=count($csv_file);
        if ($csv_file) foreach ($csv_file as $line)
        {
                $csv_datum=explode(',', $line); 
                /* element */
                if ($csv_datum[0]==$config['HeaderName']) {
                        $element=$csv_datum[1];
                } 
                /* reset element */
                if (count($csv_datum)==0) {
                        $element='';
                } 
                /* filter */
                if ($config['Filter']) foreach ($config['Filter'] as $key=>$value) {
                        if ($csv_datum[0]==$key && $csv_datum[1]==$value) {
                                $element='';
                        }
                } 
                /* push an item onto an element */
                if ($element!='' && count($csv_datum)==$config['ColumnCount'])
                {
                        $key='';
                        if ($config['ColumnKey']) foreach ($config['ColumnKey'] as $key_num) {
                                if ($key!='') $key.=' '; $key.=$csv_datum[$key_num];
                        }
                        $value='';
                        if ($config['ColumnValue']) foreach ($config['ColumnValue'] as $value_num) {
                                if ($value!='') $value.=' '; $value.=$csv_datum[$value_num];
                        } 
                        $cchrc_header[$key]=$key;
                        $cchrc_data[$element][$key]=$value;
                } 
                if ($count%1000==0) echo "."; 
                $count++;
        }
        echo " Done\n"; 
        /* sort data */
        echo "   Sorting data: ."; 
        usort($cchrc_header, sort_date);
        ksort($cchrc_data); 
        echo " Done\n\n";
        echo "Finished, file saved as 'data.csv'\n";
} 
function sort_date($a, $b)
{
        omitted (not an issue)
} 
function csv_output($cchrc_header, $cchrc_data, $output_file="data.csv")
{
        global $config; 
        $output=fopen($output_file, 'w'); 
        /* Headers */
        fwrite($output, "\"Date\"");
        if ($cchrc_data) foreach ($cchrc_data as $name => $data)
        {
                fwrite($output, ",\"$name\"");
        }
        fwrite($output, "\n"); 
        /*  */
        if ($cchrc_header) foreach ($cchrc_header as $date)
        {
                fwrite($output, "\"$date\"");
                if ($cchrc_data) foreach ($cchrc_data as $name => $data)
                {
                        fwrite($output, ",\"".$data[$date]."\"");
                }
                fwrite($output, "\n");
        } 
        fclose($output);
} 
function print_array($array, $name='')
{
        echo "$name:";
        print_r($array);
} 
?>

Select allOpen in new window

Thanks very much hielo, the script runs and produces a bunch of sara_files.  Unfortunately, all they contain is the word "Date" so I should have included that function, which I copy below.  

I had hoped to address the date issue separately, since when I ran the original script, I got an error:  Sorting data: .PHP Notice:  Use of undefined constant sort_date - assumed 'sort_date' in /home/my_user/my_data/cchrc_convert.php on line 139.  I think the script made an assumption because the output in the original data.csv was sorted by date - the problem was that a) it was only one file and b) it overwrote all the data from the first dates processed, leaving only 8 and 9 July.

I also have this error when running the original script: PHP Notice:  Undefined offset:  1 in /home/my_user/my_data/cchrc_convert.php on line 21.  Again, since the script ran and produced a data file in the correct format, I saw it as a non-critical error.

I see the above as separate questions, but I have to be able to get to some level of output in the sara files before asking them.  Thanks again.

function sort_date($a, $b)
{
        list($a_date, $a_time)=explode(' ', $a);
        $a_date=explode('/', $a_date);
        if ($a_date[0]<9) $a_date[0]='0'.$a_date[0];
        if ($a_date[1]<9) $a_date[1]='0'.$a_date[1];
        $a_test=$a_date[2].$a_date[1].$a_date[0].$a_time;
 
        list($b_date, $b_time)=explode(' ', $b);
        $b_date=explode('/', $b_date);
        if ($b_date[0]<9) $b_date[0]='0'.$b_date[0];
        if ($b_date[1]<9) $b_date[1]='0'.$b_date[1];
        $b_test=$b_date[2].$b_date[1].$b_date[0].$b_time;
 
        if ($a_test==$b_test) return 0;
        return ($a_test>$b_test)?1:-1;
}

Select allOpen in new window

If you need nee files just change the line
csv_output($cchrc_header, $cchrc_data, $csv_file);
to
csv_output($cchrc_header, $cchrc_data, 'new_' . $csv_file);
in my code.

It worked!!  Thanks very much.  For reasons which I don't yet understand, hernst42's solution didn't work for me.  I will now endeavor to understand how you fixed this :)