Getting Started
===============

Launching TomoGUI
-----------------

Start TomoGUI from the command line:

.. code-block:: bash

   tomogui

The main window opens ready to load a dataset.

.. figure:: /_static/screenshots/main_window.png
   :alt: TomoGUI main window on launch
   :align: center

   TomoGUI main window with a dataset loaded. Left: controls and the
   parameter tabs. Right: reconstructed image with contrast and slice
   controls.

Basic Workflow
--------------

1. **Select Data Folder** — click *Browse Data Folder* and navigate to your
   tomography data directory. HDF5 projection files in the folder appear in
   the *Projection File* dropdown (and in the Batch tab).
2. **Select Projection File** — pick the ``.h5`` file to reconstruct.
3. **Configure Reconstruction** — reconstruction method, COR method,
   algorithm, binning, nsino-per-chunk, ring-removal, phase retrieval, etc.
4. **Try** — click *Try* to run a quick multi-COR try reconstruction. The
   result appears under ``<folder>_rec/try_center/<dataset>/``.
5. **View Try** — switch to the try-center slice viewer and pick the best
   COR, or let *AI Reco* choose one automatically (see :doc:`ai_reco`).
6. **Full** — click *Full* to run the full reconstruction with the chosen
   COR.

.. figure:: /_static/screenshots/main_tab_overview.png
   :alt: Main tab with parameters filled in
   :align: center

   Main tab with dataset selected and reconstruction parameters filled in.

Your First Reconstruction
--------------------------

.. code-block:: text

   1. Browse Data Folder      → /data2/32ID/2026-04-Allen-0/
   2. Projection File         → sample_0001.h5
   3. Reconstruction method   → recon
   4. COR method              → manual
   5. COR value               → 1024.5
   6. GPU                     → 0
   7. Click Try
   8. Click View Try, pick the best slice
   9. Click Full

After *Try*, the try-center grid can be previewed directly in the image
panel and the COR slider on the right lets you scrub through candidate
centers.

Understanding the Interface
---------------------------

Main Layout
~~~~~~~~~~~

The window is divided into two main panels:

**Left Panel** — controls and parameter tabs:
   - **Main** — Try / Full / AI Reco / TomoLog buttons and common parameters
   - **Reconstruction** — algorithm, nsino-per-chunk, binning, etc.
   - **Hardening** — beam hardening correction
   - **Phase** — phase retrieval parameters
   - **Rings** — ring artifact removal
   - **Geometry** — geometric corrections
   - **Data** — data preprocessing
   - **Performance** — performance tuning
   - **Advanced Config** — full configuration file editing
   - **Batch** — multi-file batch processing (see :doc:`batch_processing`)
   - **HDF5 Viewer** — inspect projections and metadata

**Right Panel** — visualisation:
   - matplotlib image display with toolbar
   - colormap controls
   - contrast (Auto 5–95 % / Reset / Min / Max)
   - slice / COR slider
   - TomoLog integration panel

Log Output
~~~~~~~~~~

The log area shows:
   - command execution status
   - success / failure messages
   - processing progress
   - error information
   - per-file streaming during Batch AI Phase B

Status indicators use coloured text: green ✓ for success, red ✗ for
failure, amber for warnings.

Next Steps
----------

- :doc:`interface_overview` — tour of the full UI
- :doc:`reconstruction` — reconstruction parameters in depth
- :doc:`ai_reco` — automatic COR discovery with DINOv2
- :doc:`batch_processing` — hundreds of datasets with multi-GPU execution
- :doc:`themes` — Light / Dark themes