I´m assuming you are running an Apache server with PHP as a module:
The php.ini file is read once when the server starts up. Its configuration setting will be shared for all virtual hosts. If you want to change settings for individual virtual hosts use the PHP Apache directives [php.net] whereever you define your virtual hosts.
Then php.ini is read on every invocation of a php script. You cannot use the Apache directives. You might (The User Contributed Notes "nordkynNOSPAMPLZ at tin dot it" [php.net] seems to suggest it might not work, don´t really know) be able to use something like this in your php script:
#!/usr/local/bin/php -c <path>¦<file> //Look for php.ini here <?php SOMETHING ?>