Module: xrd.experiment

Module for wrapping the main functionality of the xrd package.

The Experiment class is the primary interface. Other classes are helpers.

9 Classes

class hexrd.xrd.experiment.FitModes

Bases: object

Indicators for single-frame or multiframe data files

class hexrd.xrd.experiment.ImageModes

Bases: object

Indicators for single-frame or multiframe data files

class hexrd.xrd.experiment.Experiment(cfgFile='/home/docs/checkouts/readthedocs.org/user_builds/hexrd/envs/0.2.x/local/lib/python2.7/site-packages/hexrd/data/materials.cfg', matFile='/home/docs/checkouts/readthedocs.org/user_builds/hexrd/envs/0.2.x/local/lib/python2.7/site-packages/hexrd/data/all_materials.cfg')

Bases: object

Wrapper for xrd functionality

__init__(cfgFile='/home/docs/checkouts/readthedocs.org/user_builds/hexrd/envs/0.2.x/local/lib/python2.7/site-packages/hexrd/data/materials.cfg', matFile='/home/docs/checkouts/readthedocs.org/user_builds/hexrd/envs/0.2.x/local/lib/python2.7/site-packages/hexrd/data/all_materials.cfg')

Constructor for Experiment

INPUTS

cfgFile – name of the config file to use for initialization;

an empty string indicates that default values for options are used

matFile – name of the materials data file; a real file name

is required here

activeImage

Active image

activeMaterial

Active Material

Can be set by number (index in material list) or by name.

On output, it is always a material instance.

activeReader

Get method for activeReader

Reader is set by using index in reader list or by name.

active_img

Current image

add_to_img_list(name)

Append the active image to the image list

calInput

(read only) Calibration input data

calibrate(log=None)

Calibrate the detector

Currently, uses polar rebin only.

clear_reader()

Close current reader

clear_spots()

Reset the list of spots

curFrameNumber

Current frame number

detector

(read only) detector

dump_grainList(f)

dump grainList to cPickle

export_grainList(f, dspTol=None, etaTol=None, omeTol=None, doFit=False, sort=True)

export method for grainList

find_raw_spots()

find spots using current reader and options

fitRMats

(get-only) Rotation matrices from indexing

getSavedReader(which)

Get a specified reader

get_spots_ind()

Select spots for indexing

hydra

(read only) hydra image class

img_list

(get only) List of saved images (get only)

img_names

(get-only) List of names for saved images

index_opts

(get-only) Options for indexing

loadDetector(fname)

Load the detector information from a file

INPUTS fname – the name of the file to load from

loadMaterialList(fname)

Load the pickled material list from a file

INPUTS fname – the name of the file to load from

loadRawSpots(fname)

Load the detector information from a file

INPUTS fname – the name of the file to load from

loadReaderList(fname)

Load the reader list from a file

INPUTS fname – the name of the file to load from

matDict

(read only) Dictionary mapping material names to material

matList

List of materials

matNames

(read only) List of material names

newDetector(gp, dp)

Create a new detector with given geometry and distortion parameters

gp - initial geometric parameters dp - initial distortion parameters

newMaterial()

Create a new material and add it to the list

newReader()

Add new reader to the list and make it active

Changes name if necessary.

numFramesTotal

Number of frames available for reading

raw_spots

(get-only) spots from image before culling and association with rings

readImage(frameNum=1)

Read and return an image

DESCRIPTION

This reads an image according to the active reader specification, saving it in the activeImage attribute.

readerListAddCurrent()

Add current list to list of saved readers

readerNames

Return list of saved readers

refineFlags

(read only) refinement flags for calibration

refine_grains(minCompl, nSubIter=3, doFit=False, etaTol=valWUnit("etaTol", "ANGLE", 1.0, "degrees"), omeTol=valWUnit("etaTol", "ANGLE", 1.0, "degrees"), fineDspTol=0.005, fineEtaTol=valWUnit("etaTol", "ANGLE", 0.5, "degrees"), fineOmeTol=valWUnit("etaTol", "ANGLE", 0.5, "degrees"))

refine a grain list

run_indexer()

Run indexer

saveDetector(fname)

Save the detector information to a file

INPUTS fname – the name of the file to save in

saveRMats(f)

save rMats to npy file

saveRawSpots(fname)

Save the detector information to a file

INPUTS fname – the name of the file to save in

saveReaderList(fname)

Save the reader list to a file

INPUTS fname – the name of the file to save in

savedReaders

Return list of saved readers

Experiment.simulateGrain(rMat=array([[ 1., 0., 0.],

[ 0., 1., 0.],

[ 0., 0., 1.]]), vMat=array([ 1., 1., 1., 0., 0., 0.]), planeData=None, detector=None, omegaRanges=[(-3.141592653589793, 3.141592653589793)], output=None)

Simulate a grain with choice of active material

spotOpts

(get-only) spot finding options

spot_readers

(get-only) list of readers used to generate spots

spots_for_indexing

(get-only) spots associated with rings

class hexrd.xrd.experiment.ReaderInput(name='reader', desc='no description')

Bases: object

ReaderInput

This class is for holding input required to instantiate a reader object. Currently, only GE reader is supported.

__init__(name='reader', desc='no description')

Constructor for ReaderInput

INPUT name – [optional] (str) name desc – [optional] (str) description

NOTES * currently only GE reader is supported

RC

alias of ReadGE

aggMode

Mode identifier for frame aggregation

aggModeOp

(read only) option to pass to GE reader instances for aggregation mode

darkFile

Full pathname of dark file

getNumberOfFrames()

Return number of frames available in data files

hasImages

(get only) true if list of images has been set

imageNames

Get method for imageNames

makeReader()

Return a reader instance based on self

setOmegaInfo(imgName, omin, omax, odel)

Set omega info for the specified image

class hexrd.xrd.experiment.CalibrationInput(mat, xtol=1e-06)

Bases: object

CalibrationInput

__init__(mat, xtol=1e-06)

Constructor for CalibrationInput

cakeArgs

(get only) Keyword arguments for polar rebinning

calData

(get only) Lattice parameter data for calibrant

This provides a deepcopy with wavelength, strain magnitude and two-theta width set.

calMat

Calibration material (calibrant)

fitType

fit type: direct or caked

class hexrd.xrd.experiment.DetectorInfo(gParms=, []dParms=[])

Bases: object

Class for detector and associated data

__init__(gParms=, []dParms=[])

Constructor for detectorInfo

calibrate(calInp, rdrInp, mat, log=None)

Calibrate this detector using specified reader and options

class hexrd.xrd.experiment.PolarRebinOpts

Bases: object

Options for polar rebinning

__init__()

Constructor for PolarRebinOpts

This routine sets default values for caking options.

The following attributes (with initial values) can be modified directly.

etaMin = 0 etaMax = 360 rhoMin = 100 rhoMax = 1000 numEta = 36 numRho = 500 correct = True

kwArgs

(get only) Return keyword args to pass to polarRebin

class hexrd.xrd.experiment.SpotOptions

Bases: object

Manage options available for spot finding and analysis

Mainly, this manages the keyword options to the findSpotsOmegaStack() static method in the Spots class.

__init__()

SpotOptions Constructor

class hexrd.xrd.experiment.IndexOptions

Bases: object

indexOptions

__init__()

Constructor for indexOptions

5 Functions

hexrd.xrd.experiment.newName(name, nlist)

return a name not in the list, but based on name input

hexrd.xrd.experiment.saveExp(e, f)

save experiment to file

hexrd.xrd.experiment.loadExp(inpFile, matFile='/home/docs/checkouts/readthedocs.org/user_builds/hexrd/envs/0.2.x/local/lib/python2.7/site-packages/hexrd/data/materials.cfg')

Load an experiment from a config file or from a saved exp file

inpFile – the name of either the config file or the saved exp file;

empty string means start new experiment

matFile – name of the materials file

hexrd.xrd.experiment.refineDetector(grainList, scl=None, gtol=1e-06)

hexrd.xrd.experiment.objFunc(x, grainList, scl)