OrchidReader Simple Setup

A python script intended to be an easy way to prepare runs of OrchidReader, the first step in the analysis chain for background data from HFIR.

Overview

This program reads the contents of the given input directory and produces the files (OrchidReader configuration files and qsub batch files) necessary to run OrchidReader on the data. In that process it determines if it needs to break the data into several batches based on time gap between files, or if different files in the same folder belong to different array positions or detector configurations. It then outputs the appropriate sets of configuration files and qsub files in the output directory it was given (or the default output directory) and produces a script where it was run that will submit those batch processing files.

Invocation

OrchidReaderSimpleSetup is invoked as follows:

orchid_reader_simple_setup.py <Path-To-Input-File-Directory> [Path-To-Output-File-Directory]

python orchid_reader_simple_setup.py <Path-To-Input-File-Directory> [Path-To-Output-File-Directory]

Here, Path-To-Input-File-Directory is the path to the directory containing the set of input files to be processed by OrchidReader. Path-To-Output-File-Directory is the path to the directory that individual batch outputs are to be placed in. It defaults to: /data1/prospect/ProcessedData/OrchidAnalysis/TimeSeries_2017, this default can be changed easily by modifying orchid_reader_simple_setup.py (the default is stored in the global variable: DEFAULT_OUTDIR).

Adding New Configurations

Over the course of operation it is to be expected that the detector setup or array position can change, temporarily or otherwise, new detector configurations, array times, etc can be produced quite easily by editting serveral files.

Adding a Detector Configuration Exception

For to add a detector configuration change for a small set of runs using a to a pre-existing configuration one need only edit orsslib/setup_changes.py.

Step 1: Add a new variable containing the patterns found in the file names from the runs for which the change applies. The example below describes runs for which only the moderated 3He detector was part of the setup.

  MOD_HE_RUN_PATTERNS = ["Jun05_2017_0001.dat", "Jun06_2017_0000.dat"]

Step 2: Add the relevant detector setup to the end of the EXCEPTION_DATA list.

  EXCEPTION_DATA = [ds.DEFAULT_SETUP, ds.CEBR_SETUP, ds.NO_HE_SETUP, ds.MOD_HE_SETUP]

Step 3: Add the name of the detector setup to the EXCEPTION_NAME list.

  EXCEPTION_NAME = ["Default", "CeBr3", "No_3He", "Mod_3He"]

Step 4: Add the new list of file name patterns to the EXCEPTION_PATTERN variable.

  EXCEPTION_PATTERN = [CEBR_RUN_PATTERNS, NO_HE_RUN_PATTERNS, MOD_HE_RUN_PATTERNS]

With these steps complete, any file names containing the patterns given in the variable in step 1, will have the detector setup set to the one given in EXCEPTION_DATA.

Changing the Default Detector Configuration

To change the default detector configuration, simply change the first element of the EXCEPTION_DATA list to the new default detector configuration.

Adding an Array Position Exception

To change the position that the array was in for a set of runs, follow a procedure similar to that for Adding a detector Configuration Exception with the following differences:

Edit orsslib/position_changes.py instead of orsslib/setup_changes.py
The entry in the EXCEPTION_DATA list is a tuple containing the x and y position of the array instead of a detector configuration class.

Adding a New Detector Configuration

To add a new detector configuration, you need to edit orsslib/detector_setups.py.

First, create an array setup class and assign it to a new variable

 NEW_SETUP = ArraySetup()

Second, create a detector setup class with the appropriate parameters. electronic_config is a tuple containing two tuples, the first tuple contains the digitizer module and channel number, the second tuple contains the MPOD HV system module and channel number. position is a tuple containing the x, y, and z offsets relative to the array position. det_type is a string containing the detector type, current options are: "NaI", "LS", "CeBr3", "HeMod", "HeUnmod". thresholds is a tuple containing energy and psd cutoff thresholds that should be applied to projections of that detectors spectra.

  TMP = DetectorSetup(electronic_config, position, det_type, thresholds)

Third, add the detector to the array configuration. detector_number is the unique identifier for that particular detector.

  NEW_SETUP.add_detector(detector_number, copy.deepcopy(TMP))

Fourth, repeat steps 2 and 3 for every detector in the array (copy, paste modify helps a lot).

jmatta1/OrchidReaderSimpleSetup