NO CODE -- LINT ALL per pre-coomit

.vscode/settings.json

@@ -9,4 +9,4 @@
         "utility": "c",
         "random": "c"
     }
-}
+}

AOloopControl/AOloopControl.c

@@ -64,5 +64,3 @@ static errno_t init_module_CLI()
 
     return RETURN_SUCCESS;
 }
-
-

AOloopControl/examples/KalAO-ttmloop-conf/README.md

@@ -99,7 +99,7 @@ The following files are written to ./conf/DMmodes/ :
 - HpokeC.fits    : Hadamard modes
 - Hmat.fits      : Hadamard matrix (to convert Hadamard-zonal)
 - Hpixindex.fits : Hadamard pixel index
-- SmodesC.fits    : 
+- SmodesC.fits    :
 
 
 
@@ -127,7 +127,7 @@ cacao-aorun-031-RMHdecode
 This should not be used when actually using KalAO as it would overwrite the NCPA reference.
 
 ```bash
-# Acquire reference 
+# Acquire reference
 # cacao-aorun-026-takeref
 ```
 

AOloopControl/examples/MAPS-vispyr-conf/ObsRunNotes.md

@@ -1,12 +1,12 @@
 # Observing Run Notes:
 
-These are notes for running MAPs as of the 2023 May/June run. References to simulations are cut out for ease of use. 
+These are notes for running MAPs as of the 2023 May/June run. References to simulations are cut out for ease of use.
 
 ## Streams
 
 Milk commands for keeping tabs on streams:
 - `milk-streamCTRL`
-    - x => exit the viewer 
+    - x => exit the viewer
 - `milk-fpsCTRL` => "Function Parameter monitor" can set params and run proc from here
     - shift + R => starts a process
     - ctrl + R => ends a process
@@ -36,20 +36,20 @@ connect to hardware
 <br> `./scripts/aorun-setmode-hardw`
 
 
-## CHAI: Setting up 
+## CHAI: Setting up
 (not a part  of this package, MAPs specific)
 
 ```bash
 chai
 > ttmod.enable
-> ttmod.start 
+> ttmod.start
 # these previous two lines have been automated at time of writing
 > viswfs.enable # starting the wfs streams
-> cacao.enable 
+> cacao.enable
 ```
 Once chai has been started, we can look at wfs streams
 ``` bash
-rtimview viswfs_slopes & 
+rtimview viswfs_slopes &
 rtimview viswfs_pupils &
 ```
 
@@ -65,7 +65,7 @@ Start WFS fram aquisition
 
 ### DM to WFS latency
 
-Running from command line: 
+Running from command line:
 ```bash
 # option -w is to wait for completion
 cacao-aorun-020-mlat -w
@@ -167,8 +167,8 @@ cacao-fpsctrl setval mfilt loopON ON
 
 Alternatively, on the fpsCTRL
 - shift + R `wfs2cmodeval`
-- shift + R `mfilt` 
-- shift + R `mvalC2dm` 
+- shift + R `mfilt`
+- shift + R `mvalC2dm`
 - edit values in `mfilt`
    - `mfilt -> loopgain -> 0.1`
    - `mfilt -> loopmult -> 0.98`

AOloopControl/examples/MAPS-vispyr-conf/SimpleStartup.md

@@ -15,15 +15,15 @@ cacao-aorun-025-acqWFS -w start
 ```
 
 Now we are picking a calibration
-``` 
+```
 ls ../maps-calibs
  ```
 find the <calib-dir> from that list that you want to use tonight.
 
 ```
 cacao-calib-apply <calib-dir>
 ```
-^ long term, this needs to shut down all confs and restart them again, this ensures the proper resp mat sizes. 
+^ long term, this needs to shut down all confs and restart them again, this ensures the proper resp mat sizes.
 
 ```
 cacao-aorun-050-wfs2cmval start
@@ -32,9 +32,8 @@ cacao-aorun-070-cmval2dm start
 ```
 
 To start the 2D DM viewing stream:
-``` 
+```
 tmux new -s remap
-./scripts/maps-remapdm10disp 
+./scripts/maps-remapdm10disp
 ctrl-b d
 ```
-

AOloopControl/examples/MAPS-vispyr-conf/cacaovars.bash

@@ -74,7 +74,7 @@ export CACAO_FPSPROC_MLAT="ON"
 #
 export CACAO_FPSPROC_ACQUWFS="ON"
 
-# Acquire linear RM 
+# Acquire linear RM
 #
 export CACAO_FPSPROC_MEASURELINRESP="ON"
 

AOloopControl/examples/MAPS-vispyr-conf/data/mk2Dmapping

@@ -21,4 +21,3 @@ saveFITS actmap mapping.fits
 listim
 exitCLI
 EOF
-

AOloopControl/examples/MAPS-vispyr-conf/data/mkMapping.sh

@@ -26,4 +26,3 @@ saveFITS actmap mapping.fits
 listim
 exitCLI
 EOF
-

AOloopControl/examples/MAPS-vispyr-conf/fpssetup.setval.conf

@@ -14,4 +14,3 @@ setval acquWFS-LOOPNUMBER.procinfo.RTprio 49
 setval acquWFS-LOOPNUMBER.procinfo.cset aol0RT
 setval acquWFS-LOOPNUMBER.procinfo.loopcntMax -1
 setval acquWFS-LOOPNUMBER.WFSnormfloor 1.0
-

AOloopControl/examples/MAPS-vispyr-conf/scripts/aorun-setmode-sim

@@ -48,7 +48,7 @@ ln -sf ${MILK_SHM_DIR}/${CACAO_WFSSTREAMSIM}.im.shm ${MILK_SHM_DIR}/aol${CACAO_L
 
 # DM
 echo "Linking DM ${CACAO_DMSIMINDEX}"
- 
+
 ln -sf ${MILK_SHM_DIR}/dm${CACAO_DMSIMINDEX}disp03.im.shm ${MILK_SHM_DIR}/aol${CACAO_LOOPNUMBER}_dmC.im.shm
 
 ln -sf ${MILK_SHM_DIR}/dm${CACAO_DMSIMINDEX}disp00.im.shm ${MILK_SHM_DIR}/aol${CACAO_LOOPNUMBER}_dmO.im.shm

AOloopControl/examples/MAPS-vispyr-conf/scripts/maps-remapdm10disp

@@ -1,4 +1,3 @@
 #!/usr/bin/env bash
 
 ./scripts/maps-remapshmim dm10disp dm10disp2D
-

AOloopControl/examples/MAPS-vispyr-conf/scripts/maps-start-remaps

@@ -24,7 +24,7 @@ tmux send-keys -t dm00disp2D Enter
 ##########################################
 #
 # Setup aol2_dmC2D
-# 
+#
 ##########################################
 
 # Check if the session exists, discarding output
@@ -46,7 +46,7 @@ tmux send-keys -t aol2_dmC2D Enter
 ##########################################
 #
 # Setup aol2_dmRM2D
-# 
+#
 ##########################################
 
 # Check if the session exists, discarding output
@@ -62,5 +62,3 @@ tmux send-keys -t aol2_dmRM2D Enter
 tmux send-keys -t aol2_dmRM2D C-c
 tmux send-keys -t aol2_dmRM2D "./scripts/maps-remapshmim aol2_dmRM aol2_dmRM2D"
 tmux send-keys -t aol2_dmRM2D Enter
-
-

AOloopControl/examples/MAPS-vispyr-conf/scripts/maps-startturb

@@ -16,4 +16,3 @@ sendFPScmd  "runstart DMatmturb-2"
 
 
 ./scripts/maps-unmapturb
-

AOloopControl/examples/MAPS-vispyr-conf/scripts/maps-unmapturb

@@ -1,4 +1,3 @@
 #!/usr/bin/env bash
 
 ./scripts/maps-unmapshmim mapsturb2D dm10disp10
-

AOloopControl/examples/ao3k-apd188-conf/cacaovars.bash

@@ -139,4 +139,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-apd188-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-apd3k-conf/cacaovars.bash

@@ -144,4 +144,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-apd3k-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-bimdm3kpt-conf/cacaovars.bash

@@ -139,4 +139,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-bimdm3kpt-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-lowfs188-conf/cacaovars.bash

@@ -138,4 +138,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-lowfs188-conf/fpssetup.setval.conf

@@ -23,4 +23,4 @@ setval mfilt-LOOPNUMBER.procinfo.triggersname aolLOOPNUMBER_modevalWFS
 
 setval mvalC2dm-LOOPNUMBER.procinfo.RTprio 48
 setval mvalC2dm-LOOPNUMBER.procinfo.cset aolrt
-setval mvalC2dm-LOOPNUMBER.GPUindex 99
+setval mvalC2dm-LOOPNUMBER.GPUindex 99

AOloopControl/examples/ao3k-lowfs188-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-lowfs3k-conf/cacaovars.bash

@@ -138,4 +138,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-lowfs3k-conf/fpssetup.setval.conf

@@ -23,4 +23,4 @@ setval mfilt-LOOPNUMBER.procinfo.triggersname aolLOOPNUMBER_modevalWFS
 
 setval mvalC2dm-LOOPNUMBER.procinfo.RTprio 48
 setval mvalC2dm-LOOPNUMBER.procinfo.cset aolrt
-setval mvalC2dm-LOOPNUMBER.GPUindex 99
+setval mvalC2dm-LOOPNUMBER.GPUindex 99

AOloopControl/examples/ao3k-lowfs3k-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-nirpyr188-conf/aolooptest

@@ -1,4 +1,3 @@
 #!/usr/bin/env bash
 
 # Full deployment test
-

AOloopControl/examples/ao3k-nirpyr188-conf/cacaovars.bash

@@ -138,4 +138,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-nirpyr188-conf/fpssetup.setval.conf

@@ -56,4 +56,3 @@ setval wfscamsim-LOOPNUMBER.wfscamim iiwisim
 setval wfscamsim-LOOPNUMBER.fluxtotal 30000.0
 setval wfscamsim-LOOPNUMBER.camgain 0.01
 setval wfscamsim-LOOPNUMBER.compphnoise OFF
-

AOloopControl/examples/ao3k-nirpyr188-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-nirpyr3k-conf/aolooptest

@@ -1,4 +1,3 @@
 #!/usr/bin/env bash
 
 # Full deployment test
-

AOloopControl/examples/ao3k-nirpyr3k-conf/cacaovars.bash

@@ -138,4 +138,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-nirpyr3k-conf/fpssetup.setval.conf

@@ -57,4 +57,3 @@ setval wfscamsim-LOOPNUMBER.wfscamim iiwisim
 setval wfscamsim-LOOPNUMBER.fluxtotal 30000.0
 setval wfscamsim-LOOPNUMBER.camgain 0.01
 setval wfscamsim-LOOPNUMBER.compphnoise OFF
-

AOloopControl/examples/ao3k-nirpyr3k-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-ttoff188-conf/aolooptest

@@ -1,4 +1,3 @@
 #!/usr/bin/env bash
 
 # Full deployment test
-

AOloopControl/examples/ao3k-ttoff188-conf/cacaovars.bash

@@ -141,4 +141,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-ttoff188-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/ao3k-ttoff3k-conf/aolooptest

@@ -1,4 +1,3 @@
 #!/usr/bin/env bash
 
 # Full deployment test
-

AOloopControl/examples/ao3k-ttoff3k-conf/cacaovars.bash

@@ -141,4 +141,3 @@ echo "Processing cacaovars file ${cvarf}"
 . ./${cvarf}
 done
 shopt -u nullglob #revert nullglob back to it's normal default state
-

AOloopControl/examples/ao3k-ttoff3k-conf/runexample

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-

AOloopControl/examples/scexao-NIRPL-conf/README.md

@@ -1,5 +1,5 @@
 # Overview
-## Near-IR Photonic Lantern - photometric 
+## Near-IR Photonic Lantern - photometric
 (scroll down for dispersed PL instructions!)
 
 cacao-task-manager tasks for this example :
@@ -223,12 +223,12 @@ cacao-fpsctrl setval mfilt loopON ON
 
 ```
 ## NIRPL - dispersed mode
-In this section we set up and test the simulator mode for the dispersed 3-port PL. This involves new `cacao` functions. Work in progress! Currently testing on my laptop (WSL2). 
+In this section we set up and test the simulator mode for the dispersed 3-port PL. This involves new `cacao` functions. Work in progress! Currently testing on my laptop (WSL2).
 
 ### Simulator mode
 To run simulator mode you will need to two things: an N x M reference wfs image and an N x M x 2500 zonal response matrix.
-These files need to be named `wfsref.fits` and `respM.fits`, and put in (or replaced in) `scexao-NIRPL-conf/simLHS`. Currently, 
-the simulator is configured to pull old files corresponding to a non-dispersed 19-port PL, imaged on `glint`, from some google drive link, and I don't know how to change that. 
+These files need to be named `wfsref.fits` and `respM.fits`, and put in (or replaced in) `scexao-NIRPL-conf/simLHS`. Currently,
+the simulator is configured to pull old files corresponding to a non-dispersed 19-port PL, imaged on `glint`, from some google drive link, and I don't know how to change that.
 
 ### Loop deployment
 As usual, run
@@ -237,7 +237,7 @@ As usual, run
 cacao-loop-deploy scexao-NIRPL
 ```
 
-to deploy the loop. Then, to start the simulator, run 
+to deploy the loop. Then, to start the simulator, run
 
 ```bash
 ./scripts/aorun-setmode-sim
@@ -272,23 +272,23 @@ To make this shared memory, use
 which will call a Python function in `scripts/utility.py`. To edit the behavior of this script, you can add new functions to this file.
 
 ### Take dark
-First we take a raw (full-frame) dark with 
+First we take a raw (full-frame) dark with
 ```bash
 cacao-aorun-005-takedark
 ```
 which copies the dark to the shared memory `aol6_wfsdarkraw`.
 
-Then we remap this dark using 
+Then we remap this dark using
 ```bash
 ./scripts/scexao-NIRPL-mapdark-spec
 ```
 (which, again, you might need to run twice. The first run will initialize some needed shared memories - I need to automate this better). This rewrites `aol6_wfsdark` so it has a shape of N x Z.
 
 ### WFS image acquisition
 
-Finally, we can start the `acquire_spectra-6` function through `fpsCTRL`. In `comp`, there are toggles for dark subtraction, normalization. Note that the normalization is different than what is done in `acqu_WFS-6`; normalization is done per-wavelength, as opposed to dividing the entire WFS image by the flux total. After running, the processed WFS image is written to the shared memory `aol6_imWFS2` as usual. 
+Finally, we can start the `acquire_spectra-6` function through `fpsCTRL`. In `comp`, there are toggles for dark subtraction, normalization. Note that the normalization is different than what is done in `acqu_WFS-6`; normalization is done per-wavelength, as opposed to dividing the entire WFS image by the flux total. After running, the processed WFS image is written to the shared memory `aol6_imWFS2` as usual.
 
-You can also take a reference using 
+You can also take a reference using
 ```bash
 cacao-aorun-026-takeref
 ```
@@ -299,7 +299,7 @@ Finally, you can average the traces horizontally by `x` pixels using the `binnin
 
 ## how to install and uninstall
 ### installation
-In your $MILK_ROOT folder, do 
+In your $MILK_ROOT folder, do
 ```bash
 cd plugins/cacao-src
 git pull
@@ -322,8 +322,6 @@ rm -r .NIRPL*
 tmux kill-server
 rm -r /milk/shm/*
 ```
-Maybe don't run this if you have other shared memories you don't want to nuke. 
+Maybe don't run this if you have other shared memories you don't want to nuke.
 
 THE END (for now)
-
-