Merge branch 'develop' into rfvc_pr

Author: joelaugustine099

.gitignore

@@ -298,3 +298,4 @@ test.xml
 *_log.txt
 /docs/source/05_reference/_autosummary
 /docs/source/05_reference/_autosummary
+codex.md

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

@@ -149,9 +149,7 @@ Photometrics
 
 .. note::
 
-    **navigate** has been tested with the following versions of the Photometric's
-    drivers:
-
+    **navigate** has been tested with the following versions of the Photometric's drivers:
     - PVCAM: 3.9.13
 
 -----------------
@@ -175,6 +173,32 @@ Iris 15
               settle_down: 0.1 #ms
               flip_x: False
               flip_y: False
+|
+
+-----------------
+
+Ximea
+--------------------------------
+
+MU196MR-ON
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: ximea
+                serial_number: 111
+                camera_connection: PMPCIECam00
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
 
 
 |

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

@@ -15,8 +15,8 @@ frames, and some jitter in timing is anticipated.
 
 .. _hardware_ni:
 
-National Instruments (NI)
--------------------------
+National Instruments
+--------------------
 In principle, most NI-based data acquisition cards should work with the software, so long
 as there are a sufficient number of analog and digital ports, and the sampling rate (typically 100 kHz)
 is high enough per port.

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

@@ -53,21 +53,16 @@ file as follows:
 
 -----------
 
-Sutter Instruments
-------------------
+ASI
+---
 
-Lambda 10-3 & 10-B
-~~~~~~~~~~~~~~~~~~
+FW-1000
+~~~~~~~
 
-We typically communicate with Sutter Lambda 10-3 controllers via serial port. It is
-recommended that you first establish communication with the device using manufacturer
-provided software. Alternatively, one can use MicroManager. For some filter wheel types,
-the filter_wheel_delay is calculated according to the size of the move and model of the
-filter wheel. For other filter wheel types, the filter_wheel_delay is a fixed value, which is specified as
-the ``filter_wheel_delay`` entry in the configuration file. The number of filter wheels
-connected to the controller is specified as ``wheel_number`` in the configuration file.
-Currently, both wheels are moved to the same position, but future implementations will
-enable control of both filter wheels independently.
+The ASI `filter wheel <https://www.asiimaging
+.com/illumination-control/fw-1000-high-speed-filter-wheel/>`_ is controlled by the
+ASI Tiger Controller. Thus, you should provide the same ``comport`` entry as you did
+for the stage. A single communication instance is used for both the stage and filter wheel.
 
 .. collapse:: Configuration File
 
@@ -78,10 +73,10 @@ enable control of both filter wheels independently.
           -
             filter_wheel:
               hardware:
-                type: SutterFilterWheel
+                type: ASI
                 wheel_number: 1
                 port: COM1
-                baudrate: 9600
+                baudrate: 115200
               filter_wheel_delay: 0.03
               available_filters:
                 Empty-Alignment: 0
@@ -91,18 +86,23 @@ enable control of both filter wheels independently.
 
 |
 
--------------
+--------------
 
-ASI
----
+Sutter Instruments
+------------------
 
-FW-1000
-~~~~~~~
+Lambda 10-3 & 10-B
+~~~~~~~~~~~~~~~~~~
 
-The ASI `filter wheel <https://www.asiimaging
-.com/illumination-control/fw-1000-high-speed-filter-wheel/>`_ is controlled by the
-ASI Tiger Controller. Thus, you should provide the same ``comport`` entry as you did
-for the stage. A single communication instance is used for both the stage and filter wheel.
+We typically communicate with Sutter Lambda 10-3 controllers via serial port. It is
+recommended that you first establish communication with the device using manufacturer
+provided software. Alternatively, one can use MicroManager. For some filter wheel types,
+the filter_wheel_delay is calculated according to the size of the move and model of the
+filter wheel. For other filter wheel types, the filter_wheel_delay is a fixed value, which is specified as
+the ``filter_wheel_delay`` entry in the configuration file. The number of filter wheels
+connected to the controller is specified as ``wheel_number`` in the configuration file.
+Currently, both wheels are moved to the same position, but future implementations will
+enable control of both filter wheels independently.
 
 .. collapse:: Configuration File
 
@@ -113,10 +113,10 @@ for the stage. A single communication instance is used for both the stage and fi
           -
             filter_wheel:
               hardware:
-                type: ASI
+                type: SutterFilterWheel
                 wheel_number: 1
                 port: COM1
-                baudrate: 115200
+                baudrate: 9600
               filter_wheel_delay: 0.03
               available_filters:
                 Empty-Alignment: 0
@@ -126,7 +126,7 @@ for the stage. A single communication instance is used for both the stage and fi
 
 |
 
---------------
+-------------
 
 LUDL Electronic Products
 ------------------------
@@ -164,13 +164,10 @@ MAC6000
 
 -------------
 
-Analog/Digital Devices
-----------------------
+National Instruments
+--------------------
 
-Some manufacturers provide filter wheels that are controlled by analog or digital signals.
-Here, each digital signal corresponds to a filter position. The user must specify the
-number of filters in the filter wheel and the digital signal that corresponds to each
-filter position.
+Some manufacturers provide filter wheels that are controlled by analog or digital signals. Here, each digital signal corresponds to a filter position. The user must specify the number of filters in the filter wheel and the digital signal that corresponds to each filter position.
 
 .. collapse:: Configuration File
 

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

@@ -7,13 +7,10 @@ Galvo mirrors are used for fast scanning, shadow reduction, and occasionally as
 
 ------------
 
-Analog-Controlled Galvo
------------------------
+National Instruments
+--------------------
 
-Multiple types of galvanometers have been used, including Cambridge
-Technologies/Novanta, Thorlabs, and ScannerMAX. Each of these devices
-are externally controlled via analog signals delivered from a data
-acquisition card.
+Multiple types of galvanometers have been used, including Cambridge Technologies/Novanta, Thorlabs, and ScannerMAX. Each of these devices are externally controlled via analog signals delivered from an NI-based data acquisition card.
 
 .. collapse:: Configuration File
 

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

@@ -1,36 +1,74 @@
 ======
 Lasers
 ======
-We currently support laser control via voltage signals. In the near-future, we will consider implementing
-laser control via serial communication for power control, but digital modulation will still be controlled via
-voltage signals.
+We currently support laser control via voltage signals. In the near-future, we will consider implementing laser control via serial communication for power control, but digital modulation will still be controlled via voltage signals. The ``onoff`` entry is for digital modulation. The ``power`` entry is for analog modulation.
 
 ---------------------
 
-Analog/Digital-Controlled Lasers
+Applied Scientific Instrumentation
+----------------------------------
+
+
+Tiger Controller
+~~~~~~~~~~~~~~~~~~
+
+The Tiger Controller from ASI can also be used to perform analog, digital, and mixed modulation of lasers. Digital modulation is controlled with a `TGPLC <https://asiimaging.com/docs/tiger_programmable_logic_card>`_ or `TGGALVO <https://asiimaging.com/docs/tggalvo>`_ control cards, while analog modulation is controlled with a TGGALVO control card.
+
 --------------------------------
 
-Most lasers are controlled externally via mixed analog and digital modulation.
-The ``onoff`` entry is for digital modulation. The ``power`` entry is for analog
-modulation.
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            lasers:
+               -
+                wavelength: 488
+                onoff:
+                  hardware:
+                    type: ASI
+                    axis: [2-8]
+                    min: 0.0
+                    max: 5.0
+                power:
+                  hardware:
+                    type: ASI
+                    axis: A
+                    min: 0.0
+                    max: 5.0
+               -
+                wavelength: 561
+                onoff:
+                  hardware:
+                    type: ASI
+                    axis: [2-8]
+                    min: 0.0
+                    max: 5.0
+                power:
+                  hardware:
+                    type: ASI
+                    axis: B
+                    min: 0.0
+                    max: 5.0
+
+
+-------------------
+
+
+National Instruments
+--------------------
+
+Most lasers are controlled externally via mixed analog and digital modulation. Thus, a NI data acquisition card may be used to control the laser. In general, an analog output can be used to control both the digital and analog modulation of the laser, whereas a digital output can only be used to control the digital modulation of the laser.
 
 .. note::
-    Omicron LightHUB Ultra laser launches include both Coherent- and LuxX lasers,
-    which vary according to wavelength. LuxX lasers should be operated in an ACC
-    operating mode with the analog modulation option enabled. The Coherent Obis lasers
-    should be set in the mixed modulation mode.
+    Omicron LightHUB Ultra laser launches include both Coherent- and LuxX lasers, which vary according to wavelength. LuxX lasers should be operated in an ACC operating mode with the analog modulation option enabled. The Coherent Obis lasers should be set in the mixed modulation mode.
 
 .. note::
-    Coherent Obis lasers should be set in the mixed modulation mode. It is not uncommon
-    for the slew rate from the data acquisition card to be insufficient to drive the modulation
-    of the laser if the laser is set to an analog modulation mode.
+    Coherent Obis lasers should be set in the mixed modulation mode. It is not uncommon for the slew rate from the data acquisition card to be insufficient to drive the modulation of the laser if the laser is set to an analog modulation mode.
 
 .. note::
-    Users have reported intermittent connection issues at random intervals arising
-    from USB-based communication instance with Coherent Obis controllers. Specifically,
-    these errors were observed as a conflict over COM port assignments between the
-    Coherent OBIS laser and the ASI Tiger controller. These issues are discussed in
-    depth in the :ref:`communication challenges <obis_tiger_connection>` section.
+    Users have reported intermittent connection issues at random intervals arising from USB-based communication instance with Coherent Obis controllers. Specifically, these errors were observed as a conflict over COM port assignments between the Coherent OBIS laser and the ASI Tiger controller. These issues are discussed in depth in the :ref:`communication challenges <obis_tiger_connection>` section.
 
 
 .. collapse:: Configuration File
@@ -68,12 +106,10 @@ modulation.
                     channel: PXI6733/ao1
                     min: 0.0
                     max: 5.0
-
 |
 
 -------------------
 
-
 Synthetic Lasers
 --------------------------------
 
@@ -113,5 +149,4 @@ Synthetic Lasers
                     channel: PXI6733/ao1
                     min: 0.0
                     max: 5.0
-
 |

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

@@ -57,13 +57,10 @@ operating range.
 
 -------------
 
-Analog Controlled Voice Coils and Tunable Lenses
-------------------------------------------------
+National Instruments
+--------------------
 
-In principle, this hardware type can support any analog-controlled voice coil or tunable lens.
-The `BLINK <https://www.thorlabs.com/thorproduct.cfm?partnumber=BLINK>`_ and the
-`Optotune Focus Tunable Lens <https://www.optotune.com/tunable-lenses>`_ are
-controlled with an analog signal from the DAQ.
+In principle, this hardware type can support any analog-controlled voice coil or tunable lens. The `BLINK <https://www.thorlabs.com/thorproduct.cfm?partnumber=BLINK>`_ and the `Optotune Focus Tunable Lens <https://www.optotune.com/tunable-lenses>`_ are controlled with an analog signal from the DAQ.
 
 -----------------
 

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

@@ -15,11 +15,40 @@ is closed.
 
 ------------
 
-National Instruments (NI)
-----------------------------
 
-We can control these shutters using a digital output from a National
-Instruments (NI) data acquisition card.
+Applied Scientific Instrumentation
+----------------------------------
+
+Tiger Controller
+~~~~~~~~~~~~~~~~~~
+
+-----------------
+
+The `tgplc <https://asiimaging.com/docs/tiger_programmable_logic_card>`_ control card from ASI can be used to trigger shutter operation.
+
+-----------------
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            shutter:
+              hardware:
+                type: ASI
+                axis: [1-8]
+                min: 0.0
+                max: 5.0
+
+|
+
+-----------------
+
+National Instruments
+--------------------
+
+We can control these shutters using a digital output from a National Instruments (NI) data acquisition card.
 
 .. Note::
 
@@ -68,4 +97,4 @@ shutter.
                 min: 0.0
                 max: 5.0
 
-|
+------------------

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

@@ -519,8 +519,8 @@ KST101
 
 .. _galvo_stage:
 
-Analog-Controlled Galvo/Piezo
------------------------------
+National Instruments
+--------------------
 
 We sometimes control position via a galvo or piezo with no software API.
 In this case, we treat a standard galvo mirror or piezo as a stage axis. We control the