Add ASI PLC control logic docs and images

docs/source/02_user_guide/01_supported_hardware/asi_logic.rst

@@ -0,0 +1,75 @@
+.. _asi_logic:
+
+
+=================
+ASI Control Logic
+=================
+
+Z-Stack Acquisition
+-------------------
+
+The diagrams in this section describe the ASI Tiger PLC logic only. They show how
+the logic card sequences triggers between the backplane and the front connectors
+during acquisition; waveform generation itself remains on the TGDAQ.
+
+In the standard Z-stack workflow shown below, the sequence is:
+
+1. Software asserts cell 1 (``Starting Trigger``), which starts the stack cycle.
+2. Cell 2 (``First Galvo Trigger``) issues the first galvo trigger through the
+   backplane. Cell 9 adds the programmed phase offset, and cell 10 issues the
+   second galvo trigger. Together, these cells align the galvo timing with the
+   upcoming exposure.
+3. In parallel, cell 3 (``Start Delay``) inserts the common startup delay, while
+   cell 4 (``One Shot``) emits ``numZSteps`` clock pulses, one pulse for each
+   axial position in the stack.
+4. Cell 5 gates the cell 4 pulse train with the inverted stage-sync input. A
+   trigger is released only when the stage indicates that the next exposure can
+   proceed.
+5. In the default configuration, cell 6 drives the camera and lasers through the
+   Tiger front connectors. The same event also feeds cells 11 and 12, which
+   apply the camera-to-remote-focus delay before sending the remote-focus trigger
+   through the backplane.
+6. Cell 7 waits for the configured ``Sweep Time`` and then issues the next stage
+   trigger through the front connectors, advancing to the next Z position.
+
+This loop repeats until cell 4 has emitted all ``numZSteps`` pulses. At that
+point, the PLC sequence completes and software regains control. Because the PLC
+owns the timing within the stack, inter-frame timing remains deterministic and
+software intervention is limited to stack boundaries or an operator stop command.
+
+All backplane triggers are received by the TGDAQ. The TGDAQ can be configured to
+emit one waveform per trigger or to begin continuous waveform output on the first
+trigger and continue until software stops it.
+
+
+.. image:: ../../images/plc_control_loop.png
+   :align: center
+   :alt: ASI Tiger PLC control logic for standard Z-stack acquisition.
+
+The second Z-stack workflow is used when the remote-focus waveform must be issued
+before the camera exposure. In this version, cell 6 triggers remote focus first,
+cell 11 inserts the required camera-delay offset, and cell 12 then drives the
+camera and lasers. The galvo timing path, the ``numZSteps`` counter, the
+stage-ready gate, and the ``Sweep Time`` stage advance are otherwise unchanged.
+
+.. image:: ../../images/plc_control_loop_2.png
+   :align: center
+   :alt: ASI Tiger PLC control logic for Z-stack acquisition with remote focus preceding camera trigger.
+
+
+Continuous Acquisition
+----------------------
+
+Continuous acquisition uses a related PLC pattern, but replaces the finite
+``numZSteps`` stack counter with a free-running loop. Cell 1 starts the sequence,
+cells 2, 9, and 10 generate the paired galvo triggers, and cell 3 provides time
+for serial-command processing before cell 4 latches the continuous state. Cells
+5, 6, and 7 then form the repeating RFVC loop: cell 5 enables the next RFVC
+trigger while cell 7 is inactive, cell 6 issues that trigger, and cell 7 delays
+the next loop iteration. From cell 6, cells 11 and 12 apply the camera delay and
+then assert the camera trigger output. The loop continues until software clears
+the continuous-acquisition state.
+
+.. image:: ../../images/plc_continuous.png
+   :align: center
+   :alt: ASI Tiger PLC control logic for continuous acquisition.

docs/source/02_user_guide/01_supported_hardware/daq.rst

@@ -53,7 +53,7 @@ but also the software implementation within **navigate**.
 
 Information on setting up one particular ASI setup can be found in the
 `Altair getting started guide <https://thedeanlab.github.io/altair/getting_started/getting_started.html>`_.
-This is the recommended setup for `Altair <https://thedeanlab.github.io/altair/index.html>`_, a microscope designed by the Dean Lab for dissemination purposes.
+This is the recommended setup for `Altair <https://thedeanlab.github.io/altair/index.html>`_, a microscope designed by the Dean Lab for dissemination purposes. A diagram and discussion on how the logic is implemented in **navigate** can be found :ref:`here <asi_logic>` .
 
 
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