Update instructions to take runs and scans

The instructions to take a miniDAQ run with a given threshold have been added.

I will proceed in the next days to review the rest

docs/operations/taking-data.md

@@ -2,7 +2,7 @@
 
 The scans and the analyses of the scans need to follow a specific naming convention: 
 
-`<sbit-rate-scan|gbt-phase-scan|latency-scan|dac-scan>-<in|out>-[<comment>-]-<data+revision>`
+`<sbit-rate-scan|gbt-phase-scan|latency-scan|dac-scan>-<in|out>-[<comment>-]-<date+revision>`
 
 Meaningfull scans that are supposed to be stored for future reference are to be stored in the path `/gemdata/data/` with the above naming convention.
 
@@ -10,15 +10,21 @@ Meaningfull scans that are supposed to be stored for future reference are to be
 
 ### Starting the S-bit rate scan
 
-To take a threshold scan, first connect to [RCMS](http://cmsrc-gem.cms:20000/rcms/gui/servlet/FMPilotServlet), then create a miniDAQ3 session or attach to a running session.
+To take an S-bit scan, first connect to [RCMS](http://cmsrc-gem.cms:20000/rcms/gui/servlet/FMPilotServlet), then create a miniDAQ3 session or attach to a running session.
+
+From the RCMS interface, click on "Initialize" and "Connect".
+
+Consider that usually S-bits scans are taken without HV amplification to investigate the noise level in the detector, so you might need to take action with the DCS on the HV settings.
 
-From the RCMS interface, click on "Connect" and then "Configure".
+Open the [xDAQ](http://srv-s2g18-33-01.cms:20400/urn:xdaq-application:service=calibration) calibration suite. In case the calibration suite page was already opened before, reload the page manually.
 
-Open the [xDAQ](http://srv-s2g18-33-01.cms:20100/urn:xdaq-application:service=calibration) calibration suite. In case the calibration suite page was already opened before you clicked on "Connect" in RCMS, reload the page manually.
+From the dropdown menu, select the calibration type "S-bit ARM DAC scan", then  set the number of iterations in the "Iterations" text box to 6 and leave all the other parameters to their default values. Click on "Apply settings".  
 
-From the dropdown menu, select the calibration type "S-bit ARM DAC scan", then  set the number of iterations in the "Iterations" text box to 6 and leave all the other parameters to their default values. Click on "Apply settings" and then "Run".
+move to the RCMS interface leaving the calibration web page open and  click "Configure". Then in the calibration web page, press "Run".
 
-While the scan is ongoing, from any p5 GEM DAQ machine check that the output files are being written in `/gemdata/runs/minidaq/sBitRateScan`.
+While the scan is ongoing, from any p5 GEM DAQ machine check that the output files are being written in `/gemdata/runs/minidaq/sBitRateScan`. You can also check in the logs present in `/gemdata/log/` what the software is doing.
+
+The output files needs to be moved otherwise they will get overwritten by the next scan. 
 
 ### Analyzing the S-bit scan
 
@@ -28,6 +34,18 @@ To analyze an S-bit scan locate first the output in `/gemdata/runs/minidaq/sBitR
 
 At these point analyze the scan using the command `gemos analyze sbit` from the terminal of `gem-locdaq02`: the path of the input file and output directory need to be specified, as well as the options for the plotting and allowed rate for the thresholds settings. 
 
+## Taking a minidaq run with given threshold
+
+To take a threshold scan, first connect to [RCMS](http://cmsrc-gem.cms:20000/rcms/gui/servlet/FMPilotServlet), then create a miniDAQ3 session or attach to a running session.
+
+From the RCMS interface, click on "Initialize" and "Connect". Open the status table by the appropriate button and open the gem calibration interface in the list of running applications. 
+
+**Enable the transfer to tier0 (T0) in the drop down window below the "DAQ" system column, if the data are intended to be saved to disk. It is the case if the data are to be given to the DPG for analysis.**
+
+Select the "Physics" option in the drop down window. The option to use a given threshold for all VFATs instead of the one from the VFAT configuration can be chosen and the threshold can be set. Click on the "Apply settings" button.
+
+Return to the RMCS interface, press on "Configure" and "Start". Once the statistics will be satisfactory, the run should be stopped with the "Stop" button. Then the miniDAQ instance can be destroyed with the "Destroy" button. 
+
 ## Taking a CSC-EMTF-GEM join run on the integration setup in building 904
 
 This paragraph covers the required actions on the GEM side in order to be able to take cosmic data on the GE1/1 integration setup using as triggers the signals from the ME1/1 chamber, available in the setup.
@@ -51,3 +69,4 @@ CMSGEMOS_CONFIG_NAME=b904int-ge11-join-runs CMSGEMOS_PORT=20100 _build/_install/
 ```
 6. The GEM raw data will be stored in the user's temporary folder, `$TMPDIR`, and overwritten at every run.
    Be careful to save the data somewhere if it is important to be kept.
+