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SOFTWARE FOR SIPM CHARACTERIZATION WITH CAMAC, SCOPE, BIAS VOLTAGE AND TABLE POSITION SUPPORT
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By Gasper Kukec Mezek, April 2015.

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1. Installation:

Pre-requisites for offline and online modes:
a) Offline mode (support for histogramming and analysis):
   - A newer (5.34 or higher) pro version of ROOT (https://root.cern.ch).
b) Online mode (support for histogramming, analysis and data acquisition):
   - Perl developer package libperl-dev for installation of net-snmp (sudo apt-get install libperl-dev).
   - Current version of net-snmp (http://www.net-snmp.org).
   - A newer (5.34 or higher) pro version of ROOT (https://root.cern.ch).
   - USB developer package libusb-dev (sudo apt-get install libusb-dev).

Installation is done through the usual "./configure" and "make" commands to enable the use of this software with 32 bit or 64 bit systems.

Configure takes the following arguments:
- First argument is the configure option (help, nomake, all, clean, compress):
    help = shows configure help
    all = prepares OS dependent files and makes the needed usb daq libraries
    nomake = only prepares OS dependent files
    clean = cleans the installation to the base file structure (keeps the results directory)
    compress = compresses the base installation into a tar-ball
- Second argument is the online/offline configure setting (only used when first argument is nomake or all), that enables the software to work with:
    a connected CAMAC and scope (I)
    only a connected scope (S)
    with no connected devices (O)
- The following arguments set specific computer details and can be entered in any order:
    a) --root-install=/path/to/root/directory -> The ROOT install directory, if it is not installed in a standard location (especially needed when running the program with superuser, since it usually does not have the required environment variables).
    b) --snmp-install=/path/to/snmp/directory -> The NET-SNMP install directory, if it is not installed in a standard location.
    c) --ostype=YYYY -> Optional argument to specifically set the OS type to either 32bit (YYYY = i686) or 64bit (YYYY = x86_64). If argument not supplied, the configure script will try to get this information automatically through uname.

Running "./configure" or "./configure help" will give more information on specific uses.
Example:
   ./configure all I --root-install=/opt/root --snmp-install=/opt/net-snmp --ostype=i686

Makefile:
Once configuration is done, a Makefile will be generated and further installation is done by running "make". Running "make relib" will only recreate the libraries in case something has been edited in them.
Example:
   make

On first run of the program, make sure to copy the ./mpod/WIENER-CRATE-MIB.txt to the MIB directory in your installation of net-snmp. This can be in: 
   ~/.snmp/mibs
or
   [/snmp/install/directory]/share/snmp/mibs

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2. Running the software:

Once installation is performed, use
   ./start.sh
to start the software in offline mode or
   sudo ./start.sh
to start the software in online mode. Once the software starts, it will let you know (in the terminal) if connection to CAMAC was correctly established.

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3. Feature overview:

The main window is divided into 5 subwindows:
a) Settings window:
   - ON/OFF switches for voltage and surface scans.
   - a voltage limiter -> sets the maximum output voltage for safety reasons
   - clean plots toggle switch -> when ON, no additional stats will be displayed on plots/histograms
   - scope IP -> sets the oscilloscope IP address
   - LASER settings info panel -> this will be written to the output file and is used for supplying additional information
   - chamber temperature -> the chamber temperature to be written to the output file
   - incidence angle -> the angle at which the sample is rotated around its axis, relative to the LASER beam (0 degrees is perpendicular to LASER beam)

b) Main measurement window:
   - settings for table position and bias voltage
   - when scans are enabled, additional settings for scans
   - number of events -> setting for the number of events to gather in a measurement
   - time stamp -> informational time (start time of measurement is written to output file)
   - file selector (for scans, the filenames will be appended sequential numbers to distinguish them)
   - start acquisition button -> starts the measurement based on selected settings
   - waveform analysis settings (channel, measurement type)
   - possibility to send custom one-line commands

c) Histogram file selection window:
   - open past measurements for analysis
   - if using multiple files, use multiple file select or select all listed files
   - files will be used in order displayed on the list
   - to clear the complete list, use the clear list button
   - to edit the header information of currently selected files, use the edit header button
   - any opened measurement has an info display of its header at the bottom for easier navigation

d) Histogram window:
   - displays the currently selected histogram in the histogram file selection window

e) Histogram controls window:
   - directly linked to the histogram window, it enables plotting options
   - can set ranges on histogram plots
   - can change between different histogram types (ADC, TDC, ADC vs. TDC, 2D surface plot)
   - for the 2D surface plot, the relevant files need to be selected in the histogram file selection window
   - toggle for logarithmic Y scale
   - the currently selected histogram can be manually exported with the export button
   - fit settings used when running "Fit spectrum" and "Fit all selected" options in the Analysis menu

On the top, there are 4 menus:
a) File:
   - New Measurement -> not working
   - Exit -> exit the software (shortkey x)

b) Analysis:
   - Histogram type -> change between histogram types (same as in histogram controls window)
   - Fit spectrum -> fit the currently open spectrum for peaks
   - Fit all selected -> fit all the selected ADC spectra selected in the histogram file selection window for peaks and display the breakdown voltage plots
   - Integrate spectrum (X, Y) -> integrate the ADC spectrum for multiple files with an X or Y scan (used for edge scans)
   - Relative PDE -> calculation of the relative PDE for the currently selected files

c) Tools:
   - Fieldpoint temperature sensor -> direct graphing of the fieldpoint temperature sensor (with settings for fieldpoint channel, start time and end time), output is a graph (if exporting) and a comma separated list saved to folder ./fieldpoint. Updating the graph can cause unstable behavior. If possible, use ~/sipmscan/fieldpoint_standalone instead.

d) Windows:
   - Specific window tiling
   - Switch between active windows

e) Help information

Important!
When using any analysis method (surface 2D plot, fitting, integration, ADC spectra display) only events inside the selected TDC window will be used so set the TDC range accordingly.

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4. Change log:

17.7.2015 (Current Rev):
a) Fixed a problem with ADC peak fitting (peak fitting returning a segmentation fault).
b) Added support to edit file headers (in case, some were created at an older date and did not include some header information or there was a mistake in writing them).
c) Temperature data can only be retrieved when connected to the IJS network (IP = 178.172.43.xxx) and is disabled otherwise.
d) The relative PDE measurement now takes the incidence angle value directly from input files.
e) Currently, data acquisition only works on 32bit computers.
f) Fixed issue with program not correctly writting multiple channels.

5.5.2015 (Rev 128):
a) Added a header display for opened files in the histogram file selection window. This enables a quicker view of the measurement information.
b) Added an incidence angle input to be able to save sample rotation angle to headers of files.
c) Added support for the fieldpoint temperature sensor (FP RTD 122). Can now plot and export data from the sensor for a specific channel and specific time range. For now, this option only works if the PC you are using this program on is connected to an internet/ethernet connection at IJS.
d) Added a limited relative PDE analysis option. At this time, it takes the selected files and calculates the PDE, relative to the first selected file. The first file should be measured at incidence angle 0, with others having an incidence angle shift of +15 (1st file -> 0, 2nd file -> 15, 3rd file -> 30,...).

9.4.2015 (Rev 127):
a) Added communications panel for connecting to a Tektronix scope.
b) Added limited support for waveform analysis with a Tektronix scope. For now, it only works when linking it to CAMAC acquisition.
c) Added a manual chamber temperature entry field.

16.3.2015 (Rev 117):
a) First version of sipmscan.
b) Added support for CAMAC, bias voltage settings and table position settings.
c) Added support for opening measured histograms.
d) Added support for analysis:
   - making surface plots
   - fitting the ADC spectrum
   - creating breakdown voltage plots
   - integrating the ADC spectrum with changing X or Y direction (edge scans)