Quick start: Assembly file

This section provides quickstart instructions for using commie, many aspects can be fine-tuned by additional keywords in the assembly file, as is explained in more detail in Sec. 3.3.5.

Below is an example of an assembly file that provides commie with only the minimum amount of information it needs, the motor positions and where the files are located:

high,    bsx=0.01252,bsy=0.015048,dnx=-0.00785,dny=0.009153
top_low, bsx=0.01254,bsy=0.0136078,dnx=-0.007848,dny=0.009 
top_int, bsx=0.01254,bsy=0.014328,dnx=-0.007852,dny=0.009025
bot_low, bsx=0.01249,bsy=0.0163141,dnx=-0.007855,dny=0.009282
bot_int, bsx=0.012555,bsy=0.0153369,dnx=-0.007851,dny=0.009185
bs_moved,bsx=0.01252,bsy=0.0153480,dnx=-0.007850,dny=0.009183
;
topdir, /common/Users/jsteinbr/data/
sample, dt_2007_03_09/dt_2007_03_09: 168-287
no_sample, dt_2007_03_09/dt_2007_03_09: 408-527
dark_current, dt_2007_03_06/dark_current/dt_2007_02_28:116-225

This is simple enough to write, but a few words are in order on how it is meant to be interpreted:

• One starts with a list of positions (they go on until you hit the character ;. These can be named anything you want; the end result will be to produce a string array of
  position_names=['a_low','a_high','b_low']
  These will be used for grouping together files in what follows.

• Following the first position name, a series of motor names are specified, along with the settings of these motors. The above example will produce a string array of
  motor_names=['dnx','dny','bsx','bsy']
  and for this, the first position name, one will produce floating point array entries of
  motor_values[0,0]=30., motor_values[1,0]=500., and so on. That is, motor_values will be an array with a number of columns equal to the number of motor_names and a number of rows equal to the number of position_names.

• When subsequent files are read in, they will be assigned to position_names by looking for the greatest number of closest matches to one position. This should normally correspond to the number of specified motors.

• By specifying the topdir you provide info on where all data, including masks and dark_current files are sitting.

• One then specifies the sequence of files for both the sample-in recordings (sample) the no_sample recordings of the scattering background, and the dark current exposures (dark_current). There is also the possibility to specify subdirectories to the top directory given in topdir. This is illustrated in the sample scriptfile above and keeps the program flexible to accomodate for all sorts of data-sorting preferences.

• There's a subtlety on sequences: it's possible that a data collection run will start late one evening and end the next morning so that the date of the files change. For that reason, it is required that the user always indicates the header of the file right after the subdirectory, as illustrated in the sample scriptfile. The advantage of this over an automated date-rollover routine is that you might have data that is not from subsequent days. Note that the header is separated from the indices by the character :.

• Specify the dark current files in a similar manner to the sample and no_sample files with the tag dark_current.

If all information is correct, you can start commie with

commie, '/path/to/assembly-file'

There are some command line arguments that can influence commie's behaviour, see Sec. 3.3.3.