Using EMHealth
==============

Dashboards
----------

Once you login into Grafana at http://localhost:3000, you may want to adjust the default preferences.
Navigate to `Administration > General > Default preferences` where you can set the interface theme, week start etc.
We recommend to set Home Dashboard to **TEM/Fleet overview**.

At the moment, all dashboards are grouped into TEM, SEM and DB performance folders.

TEM dashboards
~~~~~~~~~~~~~~

Overviews
^^^^^^^^^

Fleet overview
``````````````

This is the main dashboard, which can display multiple instruments simultaneously. Key metrics include:

- Beam Time Pie Chart: Shows the daily average vacuum status of an instrument, including time spent with column valves open or closed, or during cryo-cycling.
- Utilization Gauge: Indicates the daily average time the instrument spent actively acquiring data on EPU/Tomo.
- Last Cryo Cycle: Occurred X days ago.
- Specimen Throughput: Tracks the number of cartridges and cassettes loaded over time.
- Data Throughput: Displays the number of offloaded movies and total data volume (Falcon cameras only).

.. image:: /_static/dash-overview.png

Productivity
````````````

This view shows per-instrument counters for autoloader cartridges/cassettes, acquired images, and EPU/Tomo sessions.
The utilization and beam time bar charts provide alternative representations of running acquisition time from the main dashboard.

For each EPU session, we track:

- Session ID
- Start and End Time
- Actual Acquisition Time
- Total Number of Images Acquired
- Skipped Images Counter
- Acquisition Speed
- Error Status (whether the session ended with an error)

For each Tomo session, we track:

- Session ID
- Start and End Time
- Actual Acquisition Time
- Total Number of Images, Tilt Series, and Search Maps Acquired
- Acquisition Speed
- Error Status (whether the session ended with an error)

.. image:: /_static/dash-prod.png

Alerts
``````

Provides instrument summary and recent alerts for each microscope module

.. image:: /_static/dash-alerts.png

Modules
^^^^^^^

Autoloader
``````````

Pressure, axis movements, temperatures, and LN levels are continuously monitored. This view helps you:

- Estimate the baseline pressure of the autoloader
- Verify the reproducibility of arm movements
- Track LN refilling frequency
- Monitor temperature recovery of the CRT and docker after cassette loading

.. image:: /_static/dash-al.png

Column
``````

This view displays:

- Buffer cycle status
- Cryo cycle frequency and duration
- Lens temperatures
- IGP vacuum levels and lifetime
- Optics board errors

.. image:: /_static/dash-column.png

Detectors
`````````

Projection vacuum, overall status and sensor temperature for detectors and energy filter are provided

.. image:: /_static/dash-detectors.png

Motion
``````

Tracks motion errors for stage axes and all apertures

.. image:: /_static/dash-motion.png

PC Health
`````````

Microscope PC statistics

.. image:: /_static/dash-pc.png

Source
``````

Various parameters for FEG and HT are being monitored

.. image:: /_static/dash-source.png

For developers
^^^^^^^^^^^^^^

Data browser
````````````

Mostly used for visualizing raw data from the database

.. image:: /_static/dash-browser.png

Import Alarms
-------------

.. note:: This functionality is currently under development

Universal Error Codes (UECs) or Alarms from an instrument are stored in a database separate from Health Monitor events and
can be typically displayed with UEC Viewer on the MPC. You could also install *FEI UEC Notifications Exporter* and save UECs to XML,
but this is not supported by ``EMHealth``. If you have the credentials to access the MSSQL server on MPC,
you can import UECs from MSSQL into ``EMHealth`` database. To make it work, MSSQL_USER and MSSQL_PASSWORD (in the `docker/.env`) have to be defined,
as well as the *server* field for each instrument in the `instruments.json`.

.. code-block::

    emhealth db -d tem import-uec

Alerting
--------

This functionality is currently under development.

Export data and reporting
-------------------------

You have several options available here:

1. To export raw data from a panel to CSV/Excel format, select `Inspect > Data`. The new window allows you to configure export options and download CSV

.. image:: /_static/export-csv.png

2. To render PNG image of a panel, select `Share > Share link`. In the new window you can customize the image size, then Generate and Download image.

.. image:: /_static/export-png.png