This module defines classes, objects and routines for reading SPEC datafiles into python classes. There are three main classes for the data, SpecDataFile, SpecScan and SpecData and are arranged as follows:
SpecDataFile, contains a single data file. The datafile is indexed upon initializing the class to allow for fast searching of large data files.
To retrieve a scan from the datafile, an item is requested from the object. For example:
>>>sd = SpecDataFile('data.01')
>>>scan = sd[100]
The construct sd[100] will return scan 100 as a SpecScan object. By passing a range of integers, for example:
>>>scans = sd[[100, 101]]
these data will be concatenated into a single object. This is useful, for example, when two scans are used to take the data (one wide, one close) and you need to fit the data.
The SpecScan object contains members for all motors and counters for the scan in question. These can be accessed in two main ways. For example, to obtain the detector counts for the scan as an array:
>>>Det = sd[1000].Detector
or:
>>>scan = sd[1000]
>>>Det = scan.Detector
can be used. For situations where you need machine adjustable code, the construct:
>>>Det = scan.values['Detector']
can be used, where the member ‘values’ is a python dictionary of all scan variables. In addition to the counters and motors, values defined in the header are also included. See the SpecScan class documentation for further information.
For example, to plot (using matplotlib) the theta values against the detector normalized to the monitor one could run the code:
>>>sd = SpecDataFile('data.01')
>>>scan = sd[100]
>>>plot(scan.Theta, scan.Detector / scan.Monitor)
and error-bars can be plotted using:
>>>x = scan.Theta
>>>y = scan.Detector / scan.Monitor
>>>e = sqrt(scan.Detetor) / scan.Monitor
>>>errorbar(x, y, yerr = e)
One can easily perform calculations on the data with this setup. For example, if measurements are taken with a photodiode, often the x-ray flux is the required value. The pyspec.utils contains the function itophotons() which can be used to calculate the flux. For example:
>>>from pyspec.utils import itophotons
>>>x = scan.Theta
>>>y = itophotons(scan.pdiode, scan.energy)
>>>plot(x, y, 'ro')
Finally, the SpecScan class defines some helper routines for plotting, fitting etc. which can be used to help in data analysis. See the documentation on the SpecScan class for more information. These classes form the basis for the SPEC datafile handling. There are three objects, the SpecDataFile the SpecScan and the SpecData.
There are a number of helper routines which allow for quick plotting of scans. These try to guess the best they can what the last scan was viewing. This is done like CPLOT [1] where the first column in the data file is assumed to be the scan axis and the last column the counter. Data is normalized by a beam intensity monitor which is assumed to be the second from last column. To plot a scan from a spec file:
>>>sd = SpecDataFile('data.01')
>>>scan = sd[100]
>>>scan.plot()
The default behavior can be overridden by a number of keyword arguments passed to the plot function. These allow for the user to easily plot different counters, or to normalize to a different monitor. This is accomplished by the use of the xcol, ycol and mcol keyword arguments. These arguments can be either a column number (negative numbers count from the last column) or a column (counter) name. For example, to plot the Theta axis against mdet1 with Ring as the monitor:
>>>scan.plot(xcol='Theta', ycol='mdet1', mcol = 'Ring')
The scan.plot() function is really the overloaded SpecPlot.show() function, and returns a SpecPlot instance. The possible keyword arguments are defined by this function and are listed below:
Plot and display the scan
‘xcol’, ‘ycol’ and ‘mcol’ can be either numbers (negative count from end) or string values for the motor names
for 2D plots ‘xcol’ can be a list or array e.g. [0, 1]
‘norm = False’ will suppress normalization of the data ‘doplot = False’ will suppress the plotting of the figure ‘errors = False’ will suppress the plotting of errorbars ‘check_errorbars = True’ will suppress errorbar checking ‘fmt’ is the format string passed onto the plot command ‘new = True’ will create a new figure ‘xint = 200’ will set the x size of the 2D grid to 200 pts ‘yint = 200’ will set the y size of the 2D grid to 200 pts ‘log = True’ will set the y axis to logscale ‘twodtype = ‘contout’‘
You can obtain data on the scan, to find out which variables are defined in the class for a give scan. This is accomplished using the str method. Whenever a string is requested of the class, a string containing a formatted output of the information is provided. For example:
>>>print sd[100]
Scan:
500
Datafile:
/home/tardis/swilkins/Dropbox/Data/CDI_2011_02_01/CDI_2011_02_01
Scan Command:
round_roi_scan npbx -0.0075 0.0075 npbz -0.0075 0.0075 0.0012 5 0.5
Scan Constants:
ccdAcquireTime Lattice RLattice ccdAcquirePeriod
scandatum energy or0 or1
ccdNumExposures or1Lambda or1Angles wavelength
scan_command comments scan_type or0Angles
UB header data ccdNumImages
alphabeta Qvec scanno scan
or0Lambda ccdNumAcquisitions omega azimuth
Motors:
Chi MIR_ROLL ExitSlit NPBY
XDiff1 Theta YS XDiff2
EXSyh XDiff MuT Phi
AZS MuR ZDiff NPTX
EXSh TMM NPTZ RDiff
NPTY SGM Gamma Delta
ExitSlitY PDiff BPM_Y BPM_X
Mu DiffSlitVert MIR_X XS
EntSlit YDiff AYS ZS
SExitSlit MIR_YAW NIX ZDiff3
ZDiff2 ZDiff1
Scan Variables:
kpts Detector DELPos Current
NPBX Epoch CCPres NPBZ
Monitor SGME ccdnet3 Seconds
cnptx sdet2 IONPress ccdtot2
Monitor2 K ccdnet2 mdet1
mdet2 H L Treg
Tsam ccdnet5 Ring sdet1
SGMENC Shutter ccdnet1 ccdnet4
THPos ccdtot3 ccdtot1 ccdtot4
ccdtot5
DataFile class for handling spec data files
Read all scans into the object
Get a scan from the data file
This routine gets a scan from the data file and loads it into the list of SpecData instances.
setting ‘setkeys = True’ will set attributes to the specdata item of all the motors and counters
The mask can be used to detete bad points. This should be a list of datum (data point numbers) which should be excluded. If the “item” is a list of scans (that will be concatenated or binned together) this should be a list containing either None for no removal of data points or a list of points to remove
Returns the ScanData object corresponding to the scan requested.
Returns string with statistics on specfile.
Index the datafile
This routine indexes and sorts the byte-offests for all the scans (Lines beginning with ‘#S’)
Read the spec header from the datafile.
Reload the data file
This routine reloads (reindexes) the datafile
Reset the specfile class
This routine resets the SpecDataFile, as if no scans had been read.
Set the modee to deal with multiple scans
Class defining a SPEC scan
This class defines a single spec scan, or a collection of scans either binned or concatenated. The class has members for the data and variables contained in the scan. If the optional ‘setkeys’ is defined (see __init__) then the motor positions and variables will be set as class members. For example, in a typical scan the motor position TTH can be accessed as a class member by SpecScan.TTH
This object has some standard members:
header : [string] Header of spec scan values : [dict] All scan data variables (Motors and Counters) data : [array] All scan data (cols = variables, rows = datum) comments : [string] Comments inserted in scan scandate : [time] Date of start of scan
There are a number of special members. Wherever possible the following members are added to the class:
Qvec : [array] Q Vector alphabeta : [array] array([alpha, beta]) wavelength : [float] incident wavelength omega : [float] omega ((TTH / 2) - TH) azimuth : [float] azimuthal angle
Bin the scans together adding the column values
a is a SpecScan object of the file to bin.
Note: This routine only bins the “data” portion of the scan. It returns the origional scans motors etc.
Overloaded function which calls the current scanplot with scanplot.fit(...)
This function returns the SIXC angles for the scan as a Nx6 array
Return an tuple of two arrays of y and e
Plot the SpecScan using matplotlib
Plot the SpecScan CCD images using matplotlib
Return string of statistics on SpecScan
Footnotes
| [1] | CPLOT Certified Scientific Software <http://www.certif.com/>. |