Using-the-Peary-software-:-pearycli-and-ATLASPixServer.md

@@ -202,36 +202,36 @@ The next sections will detail each of these commands and their purposes
 * `version <ID>` : Returns the FW and SW version for device with ID `<ID>`
 
 # ATLASPix specific commands 
-* setOutputDirectory
-* SetMatrix
-* setOutput
-* LoadConfig
-* WriteConfig
-* powerStatusLog
-* lock
-* unlock
-* LoadTDAC
-* setAllTDAC
-* FindHotPixels
-* MaskPixel
-* ReapplyMask
-* MaskColumn
-* setThreshold
-* setVMinus
-* SetPixelInjection
-* SetInjectionOff
-* pulse
-* doSCurvesPixel
-* doSCurves
-* MeasureTOT
-* VerifyTuning
-* NoiseRun
-* TDACScan
-* getTriggerCount
-* MonitorPower
-* StopMonitorPower
-* resetFIFO
-* isLocked
+* `setOutputDirectory <directory path> <ID>` : Set the directory where all data and configuration files will be saved
+* `SetMatrix <type> <ID>` : Required after add_device. Tells the ATLASPix software which ATLASPix Matrix is wirebonded on the PCB. Choices are : M1,M1ISO,M2. Mostly M1 is used. 
+* `setOutput <type> <ID>` : Set the type of data output used when starting data acquisition. Choices are : test or binary
+* `LoadConfig <config file path> <ID>` : Load the register value from the config file specified and write the values to the ATLASPix chip
+* `WriteConfig <config file suffix>` : Write the current configuration of the ATLASPix and DAQ to a config file in the output directory specified by the setOutputDirectory command. The suffix is provided by the command and two files are written two disk : suffix.cfg containing registers values, suffix_TDAC.cfg containing trim DAC and mask values for each pixels.
+* `powerStatusLog <ID>` : Outputs on screen the power consumption of the ATLASPix board
+* `lock <ID>` : Configure the ATLASPix to locked mode. All matrix functionality are shut down and power consumption is reduced to minimum.
+* `unlock <ID>` : Configure the ATLASPix to unlocked mode.Matrix functionality are turned on and chip is fully functional
+* 'LoadTDAC <TDAC File> <ID>' : Load into the matrix TDAC registers the TDAC and Mask values written in the TDAC file
+* `setAllTDAC <value> <ID>` : Set all pixel TDAC registers to value.  
+* `FindHotPixels <frequency> <ID>` : DAQ must be stopped when using this command. The command will perform a one second data acquisition, count the firing rate of the pixels that fires and mask the pixels with a rate higher that frequency (in Hz)
+* `MaskPixel <column> <row> <ID>` : Mask the pixel (col,row)
+* 'ReapplyMask <ID>' : Re-apply the mask to all the pixel masked. To be used after setAllTDAC, for example, that erase the mask registers from the pixels
+* `MaskColumn <column> <ID>` : Mask a whole column of the MAtrix
+* `setThreshold <threshold value> <ID>` : Set the threshold of the matrix, in V. Keep in mind the threshold has to be larger than bias BLPix, the amplifier baseline (default value 0.8V). Therefore, setting a threshold of 0.875V corresponds to a threshold of th = (ThPix - BLPix) = 0.875-0.8 = 0.075V. A typical operation threshold is 0.9V.
+* `setVMinus <value> <ID>` : Set the VMinusPD bias voltage (typical 0.65V). The VMinusPD voltage set the strength of the output stage of the pixel discriminator. Too low value lead to cross-talk and noise. Too high value prevent the output stage from working. To be adjusted device per device , if necessary. 
+* `SetPixelInjection <column> <row> <amplifier output state> <discriminator output state> <injection> <ID>` : Set the output and injection register for pixel (col,row). The first bit, amplifier output state,when set to 1, route the output of the amplifier for pixel (col,row) to the lemo on PCB (only for column 0, unused for others). The second bit, discriminator output state, when set to 1, routes the discriminator output of the selected column to the lemo on PCB. The third bit, injection, activate the injection from pulser in the selected row when set to 1.  
+* `SetInjectionOff <ID>` : Set all injection bit for all row to 0 
+* `pulse <number of pulse> <number of clock cycle low> <number of clock cycle high> <pulse height> <ID>` : Sends a number of pulses with a given amplitude to the ATLASPix. The time the pulser is low (0V) and high (pulse height) is set by providing the duration in number of clock cycle for each state. The clock period is 12.5ns unless otherwise notified. This command is also used to program the pulser when using he trigger_injection register to send pulses each time a trigger is received. 
+* `doSCurvesPixel <column> <row> <vmin> <vmax> <npulses> <npoints> <ID>` : Perform a SCurve measurement on pixel (col,row) from vmin to vmax V with npulses pulses per pulse height, for npoints pulse heights.
+* `doSCurves <vmin> <vmax> <npulses> <npoints> <ID>` : Perform a SCurve measurement on all pixels from vmin to vmax V with npulses pulses per pulse height, for npoints pulse heights.
+* `MeasureTOT <vmin> <vmax> <npulses> <npoints> <ID>` : Perform a measurement of average TOT vs pulse height on all pixels from vmin to vmax V with npulses pulses per pulse height, for npoints pulse heights.
+* `VerifyTuning<vmin> <vmax> <npulses> <npoints> <ID>`: After loading a TDAC map, perform SCurves of all pixels to measure the threshold dispertion. Write a file named SCurve_TDAC_verification.txt containing the SCurves data. 
+* `NoiseRun <time> <ID>` : Perform a data acquisition for X seconds. 
+* `TDACScan <VNDAC> <vmin> <vmax> <npulses> <npoints> <ID>` : Perform a Scurve measurements on all pixels, for a given VNDAC, for all TDAC values (0 to 7). Files containing the SCurve data, names SCurves_VNDACX_TDACX.txt are saved to disk.
+* `getTriggerCount <ID>` : Print on screen the number of trigger received and accepted by the DAQ
+* `MonitorPower <ID>` : Starts a thread where power consumption of the ATLASPix is read and written to file every minute
+* `StopMonitorPower <ID>` : Stop the MonitorPower thread.
+* `resetFIFO <ID>` : reset the FIFO holding the ATLASPix data. 
+