Investigator Project Manager

project manager proejct manager overview the project manager provides hierarchical organization and file management for amics investigator projects, specimens, and measurements it reflects both the logical acquisition structure and the physical file structure on disk, enabling direct control over execution order, data organization, and result access the project manager operates as a folder backed system its tree view is generated by reading the directory structure of the configured project manager (pm) location changes in the project manager modify project metadata and file placement but do not alter acquisition parameters unless explicitly edited purpose the project manager is used to create and organize projects and specimens manage measurement execution order import, edit, and remove measurements control project level file destinations access result files and storage locations synchronize acquisition outputs with the project manager data store project manager data model the project manager represents data using the following hierarchy project logical container corresponding to a project folder specimen subfolder representing a physical specimen and its associated measurements measurement individual acquisition definition and its result files each node corresponds directly to a folder or file structure on disk within the configured pm location context menu operations context menus are available by right clicking on project manager nodes available actions depend on the selected level project context menu when a project node is selected, the following options are available new project… creates a new project folder within the pm location and initializes project metadata edit opens project properties for renaming or metadata updates remove removes the project from the project manager files are not deleted unless explicitly removed from disk move up / move down changes the display and execution order of projects in the project manager open folder location opens the project folder in the operating system file explorer specimen context menu when a specimen node is selected, the following options are available new project… creates a new project and associates the current specimen context with it import a measurement… imports a single measurement result into the selected specimen import measurements… imports multiple measurements into the selected specimen edit opens specimen properties, including naming templates and destination settings remove removes the specimen from the project manager without deleting underlying files move up / move down reorders specimens within the project open folder location opens the specimen folder in the file system measurement context menu when a measurement node is selected, the following options are available open in process… opens the measurement in the processing or results environment edit opens measurement properties editable fields are limited by acquisition state and parameter locks remove removes the measurement from the project manager result files remain on disk unless manually deleted move up / move down reorders the measurement within the specimen execution sequence open folder location opens the measurement result directory project manager location and file handling the project manager location defines the root directory used to build the project manager tree this location is configured in common settings key behaviors the pm system monitors folder structure to populate the project manager tree each project, specimen, and measurement corresponds to a folder or file entry the pm location is independent of the active invest project file location measurement file storage and copy behavior during acquisition, measurement result files are handled as follows all result data is first written to the directory associated with the active invest project file upon completion, a copy of the measurement results is written to the configured project manager location the project manager tree reflects the copied result set this ensures that acquisition is completed locally and reliably before file synchronization to the project manager structure clean up source option when enabled, the clean up source option removes the original measurement files from the invest project directory after successful copy to the project manager location this option frees local storage in the invest project directory retains a single authoritative copy in the pm location does not affect project manager indexing or result availability clean up source operates only after successful file copy and does not delete data from the pm location constraints and notes active or running measurements cannot be removed or reordered file system permissions must allow read/write access to both the invest location and the pm location the project manager does not modify acquisition parameters or classification workflows deleting nodes from the project manager does not automatically delete files from disk the project manager provides deterministic, folder based control of amics data organization while maintaining a clear separation between acquisition execution and long term data storage data managment specimen level project control the project manager destination can be overridden at the specimen level during run setup when a specimen level pm location is defined all measurements for that specimen are copied to the specified destination project level pm settings are ignored for that specimen the project manager tree reflects the specimen specific folder structure this enables flexible data routing for multi specimen runs, shared storage environments, or downstream processing workflows automatic backup amics investigator includes an automatic backup mechanism that creates a secondary copy of project and measurement data during normal operation automatic backup is designed to protect against data loss caused by system interruption, storage failure, or unintended file removal automatic backup operates independently of the project manager copy mechanism and applies to all projects unless explicitly disabled purpose and scope of automatic backup automatic backup ensures that a recoverable copy of critical project data exists throughout acquisition and processing it is intended as a safety mechanism and does not replace structured data management through the project manager automatic backup applies to the following data types invest project files experiment and specimen metadata measurement configuration files intermediate acquisition data written during active runs final project manager copies and externally imported result files are not modified by the backup process backup location the backup destination is defined in common settings use backup enables or disables automatic backup backup location defines the root directory where backup copies are written backup data is stored using a mirrored folder structure that reflects the active invest project organization understanding at the time of backup backup behavior backup files are written automatically during normal save and acquisition operations backups are created incrementally as project state changes backup operations do not interrupt acquisition or processing workflows backup files are not indexed by the project manager and do not appear in the project manager tree the backup mechanism operates in the background and does not require user interaction once enabled relationship to project manager storage automatic backup and project manager storage serve different roles automatic backup provides recovery protection for active and intermediate project data project manager storage provides structured, long term organization of completed measurement results automatic backup always references the invest project context and does not replace or modify project manager copies constraints and notes backup storage requires sufficient disk space and write permissions backup files are not automatically purged or versioned restoring data from backup requires manual file replacement backup data is not synchronized across multiple systems automatic backup provides a non intrusive safeguard that complements, but does not replace, disciplined project manager data handling and storage practices