bdata 5.1.1

BNMR/BNQR MUD file reader and asymmetry calculator

Package Overview

Beta-data package.

Setup

Dependencies needed pre-install:

• python development version: sudo apt-get install python3-dev (on Ubuntu, for example)
• Cython: pip3 install Cython
• numpy: pip3 install numpy

Install

• Install using pip: pip3 install bdata

Optional Configuration

• For bdata: Export the following environment variables to set the local data storage location (add to .bashrc): Set BNMR_ARCHIVE and BNQR_ARCHIVE the following scheme points to the msr files:

     ${BNMR_ARCHIVE}/year/filename.msr
     ${BNQR_ARCHIVE}/year/filename.msr
  

  By default bdata will look for data in $HOME/.bdata/. If the requested run is not found locally, an attempt to downlaod the file from musr.ca will ensue. The file will be written to disk at the appropriate location.

Contents

• mdata [object]: access general MUD files, provides special containers
• bdata [object]: access BNMR MUD files
• bjoined [object]: append bdata objects
• bmerged [object]: combine bdata objects
• life [mdict object]: dictionary of probe lifetimes.
• mudpy [C wrapper]: python access to MUD C functions

mdata

mud-data object. The mdata object is a data container designed for easy reading of any MUD file, regardless of experiment type or mesurement method.

Object Map

Signature:

mdata(filename)

Example: mud = mdata('filename.msr')

Misc Features

Representation

Representation has been nicely formatted so that typing the object name into the interpreter produces nice output.

Operators

mvar, mscaler, and mhist objects allow for arithmatic or logic operators to be used, where the value used in the operation is the mean, count, or data array respectively.

Example: mud.ivar['BNMR:HVBIAS:POS:RDVOL'] + 1 is equivalent to mud.ivar['BNMR:HVBIAS:POS:RDVOL'].mean + 1

Special Rules For Attributes

If an attribute is not found in mdata, it will look for the attribute in the bdict objects in the order: hist, ivar. This second-level attribute search is much slower than regular access.

mdict objects all allow assignment and fetching of dictionary keys as if they were attributes. Note that one can replace + with p, and - with m to allow fetching of histograms.

Example: mud.hist.Bp, mud.hist['B+'], mud.Bp all have the exact same output, with the last being much slower than the others.

bdata

Beta-data object, inherits from mdata. The bdata object is a data container with some basic analysis capabilities, designed to read out MUD data files and to provide user-friendly access to the file headers and provide asymmetry calculations.

Object Map

Signature:

bdata(run_number,year=None,filename='')

Examples:

b = bdata(40001)                     # read run 40001 from the current year. 
b = bdata(40001,year=2017)           # read run 40001 from year 2017.
b = bdata(0,filename='filename.msr') # read file from local memory, run number unused 

Functions:

Signature	Description
asym(option="",omit="",rebin=1,hist_select='',nbm=False)	Calculate asymmetry.
beam_kev(get_error=False)	Get beam implantation energy in keV
get_pulse_s()	Get beam pulse duration in s

Misc Features

In addition to those provided by mdata.

Special Rules For Attributes

If an attribute is not found in bdata, it will look for the attribute in the mdict objects in the order: camp, epics, ppg, hist. This second-level attribute search is much slower than regular access.

bjoined

Object for appending bdata objects. Attribute access works through lists (see examples below). Histogram counts are summed over to emulate data taken within a single run. bdata asymmetry calculations operate on these summed histograms. Additional functionality for proper weighted means of asymmetries of the invididual runs is also given.

Object Map

Signature:

bjoined(bdata_list)

Examples:

blist = [bdata(r,year=2019) for r in range(40010,40013)] # read runs 40010-40012
bjnd = bjoined(blist)                                    # combine these runs

Functions:

In addtion to the bdata functions, bjoined also provides:

Signature	Description
asym_mean(*asym_args,**asym_kwargs)	Take weighted mean of individual asymmetries. Arguments are passed to bdata.asym()

Misc Features

Special Rules For Attributes and Lists

Attribute access passes through list objects. For example, if we have created the bjnd object from the previous example, we run

bjnd.camp

we get a list of mdict objects. We can access the magnetic field strength as follows:

bjnd.camp.b_field

or a list of the mean values:

bjnd.camp.b_field.mean

despite the fact that at each stage a list is returned. Attribute lookup is treated the same as in bdata so that the above could be shortened to

 bjnd.b_field.mean

with some small penalty to run time.

bmerged

Object for combining bdata objects. Unlike bjoined, bmerged should look and behave more or less identically to the bdata object. In this way, runs can be combined and replaced in existing code with little modification. Histograms are combined in the same was as bjoined: counts are summed over to emulate data taken within a single run. bdata asymmetry calculations operate on these summed histograms.

Object Map

Signature:

bmerged(bdata_list)

Examples:

blist = [bdata(r,year=2019) for r in range(40010,40013)] # read runs 40010-40012
bjnd = bmerged(blist)                                    # combine these runs

life

Probe lifetimes. Example:

import bdata as bd
lifeitme = bd.life.Li8
error = bd.life.Li8_err

Probes implemented are keyed by Li8, Li9, Be11, F20, Mg31, Ac230, Ac234.

mudpy

Wrap the mud_friendly.c functions using Cython. Gives low-level access to mud files.

Functions:

File IO

Cython Function (python-accessible)	C Function (wrapped)
open_read(file_name)	int MUD_openRead(char* file_name, unsigned int* pType)
close_read(file_handle)	void MUD_closeRead(int file_handle)

Headers

Cython Function (python-accessible)	C Function (wrapped)
get_description(file_handle)	int MUD_getRunDesc(int fh, unsigned int* pType)
get_exp_number(file_handle)	int MUD_getExptNumber(int fh, unsigned int* pExpNumber)
get_run_number(file_handle)	int MUD_getRunNumber(int fh, unsigned int* pRunNumber)
get_elapsed_seconds(file_handle)	int MUD_getElapsedSec(int fh, unsigned int* pElapsedSec)
get_start_time(file_handle)	int MUD_getTimeBegin(int fh, unsigned int* pTimeBegin)
get_end_time(file_handle)	int MUD_getTimeEnd(int fh, unsigned int* pTimeEnd)
get_title(file_handle)	int MUD_getTitle(int fh, char* string, int strdim)
get_lab(file_handle)	int MUD_getLab(int fh, char* string, int strdim)
get_area(file_handle)	int MUD_getArea(int fh, char* string, int strdim)
get_method(file_handle)	int MUD_getMethod(int fh, char* string, int strdim)
get_apparatus(file_handle)	int MUD_getApparatus(int fh, char* string, int strdim)
get_insert(file_handle)	int MUD_getInsert(int fh, char* string, int strdim)
get_sample(file_handle)	int MUD_getSample(int fh, char* string, int strdim)
get_orientation(file_handle)	int MUD_getOrient(int fh, char* string, int strdim)
get_das(file_handle)	int MUD_getDas(int fh, char* string, int strdim)
get_experimenter(file_handle)	int MUD_getExperimenter(int fh, char* string, int strdim)
get_temperature(file_handle)	int MUD_getTemperature(int fh, char* string, int strdim )
get_field(file_handle)	int MUD_getField(int fh, char* string, int strdim )

Comments

Cython Function (python-accessible)	C Function (wrapped)
get_comments(file_handle)	int MUD_getComments(int fh, unsigned int* pType, unsigned int* number_of_comments)
get_comment_prev(file_handle,comment_id_number)	int MUD_getCommentPrev(int fh, int num, unsigned int* pPrev )
get_comment_next(file_handle,comment_id_number)	int MUD_getCommentNext(int fh, int num, unsigned int* pNext )
get_comment_time(file_handle,comment_id_number)	int MUD_getCommentTime(int fh, int num, unsigned int* pTime )
get_comment_author(file_handle,comment_id_number)	int MUD_getCommentAuthor(int fh, int num, char* author, int strdim )
get_comment_title(file_handle,comment_id_number)	int MUD_getCommentTitle(int fh, int num, char* title, int strdim )
get_comment_body(file_handle,comment_id_number)	int MUD_getCommentBody(int fh, int num, char* body, int strdim )

Histograms

Cython Function (python-accessible)	C Function (wrapped)
get_hists(file_handle)	int MUD_getHists( int fh, unsigned int* pType, unsigned int* pNum )
get_hist_type(file_handle,hist_id_number)	int MUD_getHistType( int fh, int num, unsigned int* pType )
get_hist_n_bytes(file_handle,hist_id_number)	int MUD_getHistNumBytes( int fh, int num, unsigned int* pNumBytes )
get_hist_n_bins(file_handle,hist_id_number)	int MUD_getHistNumBins( int fh, int num, unsigned int* pNumBins )
get_hist_bytes_per_bin(file_handle,hist_id_number)	int MUD_getHistBytesPerBin( int fh, int num, unsigned int* pBytesPerBin )
get_hist_fs_per_bin(file_handle,hist_id_number)	int MUD_getHistFsPerBin( int fh, int num, unsigned int* pFsPerBin )
get_hist_t0_ps(file_handle,hist_id_number)	int MUD_getHistT0_Ps( int fh, int num, unsigned int* pT0_ps )
get_hist_t0_bin(file_handle,hist_id_number)	int MUD_getHistT0_Bin( int fh, int num, unsigned int* pT0_bin )
get_hist_good_bin1(file_handle,hist_id_number)	int MUD_getHistGoodBin1( int fh, int num, unsigned int* pGoodBin1 )
get_hist_good_bin2(file_handle,hist_id_number)	int MUD_getHistGoodBin2( int fh, int num, unsigned int* pGoodBin2 )
get_hist_background1(file_handle,hist_id_number)	int MUD_getHistBkgd1( int fh, int num, unsigned int* pBkgd1 )
get_hist_background2(file_handle,hist_id_number)	int MUD_getHistBkgd2( int fh, int num, unsigned int* pBkgd2 )
get_hist_n_events(file_handle,hist_id_number)	int MUD_getHistNumEvents( int fh, int num, unsigned int* pNumEvents )
get_hist_title(file_handle,hist_id_number)	int MUD_getHistTitle( int fh, int num, char* title, int strdim )
get_hist_sec_per_bin(file_handle,hist_id_number)	int MUD_getHistSecondsPerBin( int fh, int num, double* pSecondsPerBin )
get_hist_data(file_handle,hist_id_number)	int MUD_getHistData( int fh, int num, void* pData )
get_hist_data_pointer(file_handle,hist_id_number)	int MUD_getHistpData( int fh, int num, void** ppData )

Scalers

Cython Function (python-accessible)	C Function (wrapped)
get_scalers(file_handle)	int MUD_getScalers( int fh, unsigned int* pType, unsigned int* pNum )
get_scaler_label(file_handle,scalar_id_number)	int MUD_getScalerLabel( int fh, int num, char* label, int strdim )
get_scaler_counts(file_handle,scalar_id_number)	int MUD_getScalerCounts( int fh, int num, unsigned int* pCounts )

Independent Variables

Cython Function (python-accessible)	C Function (wrapped)
get_ivars(file_handle)	int MUD_getIndVars(int fh, unsigned int* pType, unsigned int* number_of_variables)
get_ivar_low(file_handle,variable_id_number)	int MUD_getIndVarLow( int fh, int num, double* pLow )
get_ivar_high(file_handle,variable_id_number)	int MUD_getIndVarHigh( int fh, int num, double* pHigh )
get_ivar_mean(file_handle,variable_id_number)	int MUD_getIndVarMean( int fh, int num, double* pMean )
get_ivar_std(file_handle,variable_id_number)	int MUD_getIndVarStddev( int fh, int num, double* pStddev )
get_ivar_skewness(file_handle,variable_id_number)	int MUD_getIndVarSkewness( int fh, int num, double* pSkewness )
get_ivar_name(file_handle,variable_id_number)	int MUD_getIndVarName( int fh, int num, char* name, int strdim )
get_ivar_description(file_handle,variable_id_number)	int MUD_getIndVarDescription( int fh, int num, char* description,int strdim)
get_ivar_units(file_handle,variable_id_number)	int MUD_getIndVarUnits( int fh, int num, char* units, int strdim )