.. _quickstart-api: .. warning:: This documentation is out of date. The README and the user doc has been updated recently. For now if you need help with API, please contact me at Diamond. -- Rob Walton Quick-Start: Python API ======================= This section describes how to run up only the core in Python or IPython. This provides an API which could be used to integrate Diffcalc into an existing data acquisition system; although the interface described in the README would normally provide a better starting point. For a full description of what Diffcalc does and how to use it please see the 'Diffcalc user manual'. Setup environment ----------------- .. include:: quickstart_setup_environment Start ----- With Python start the sixcircle_api.py example startup script (notice the -i and -m) and call `demo_all()`:: $ python -i -m startup.api.sixcircle >>> demo_all() IPython requires:: $ ipython -i startup/api/sixcircle.py >>> demo_all() Alternatively start Python or IPython and cut and paste lines from the rest of this tutorial. Configure a diffraction calculator ---------------------------------- By default some exceptions are handled in a way to make user interaction friendlier. Switch this off with:: >>> import diffcalc.util >>> diffcalc.util.DEBUG = True To setup a Diffcalc calculator, first configure `diffcalc.settings` module:: >>> from diffcalc import settings >>> from diffcalc.hkl.you.geometry import SixCircle >>> from diffcalc.hardware import DummyHardwareAdapter >>> settings.hardware = DummyHardwareAdapter(('mu', 'delta', 'gam', 'eta', 'chi', 'phi')) >>> settings.geometry = SixCircle() # @UndefinedVariable The hardware adapter is used by Diffcalc to read up the current angle settings, wavelength and axes limits. It is primarily used to simplify commands for end users. It could be dropped for this API use, but it is also used for the important job of checking axes limits while choosing solutions. Geometry plugins are used to adapt the six circle model used internally by Diffcalc to apply to other diffractometers. These contain a dictionary of the 'missing' angles which Diffcalc internally uses to constrain these angles, and a methods to map from external angles to Diffcalc angles and visa versa. Calling the API --------------- The ``diffcalc.dc.dcyou`` module (and others) read the ``diffcalc.settings`` module when first imported. Note that this means that changes to the settings will most likely have no effect unless ``diffcalc.dc.dcyou`` is reloaded:: >>> import diffcalc.dc.dcyou as dc This includes the two critical functions:: def hkl_to_angles(h, k, l, energy=None): """Convert a given hkl vector to a set of diffractometer angles return angle tuple and virtual angles dictionary """ def angles_to_hkl(angle_tuple, energy=None): """Converts a set of diffractometer angles to an hkl position Return hkl tuple and virtual angles dictionary """ ``diffcalc.dc.dcyou`` also brings in all the commands from ``diffcalc.ub.ub``, ``diffcalc.hardware`` and ``diffcalc.hkl.you.hkl``. That is it includes all the commands exposed in the top level namespace when diffcalc is used interactively:: >>> dir(dc) ['__builtins__', '__doc__', '__file__', '__name__', '__package__', '_hardware','_hkl', '_ub', 'addref', 'allhkl', 'angles_to_hkl', 'c2th', 'calcub', 'checkub', 'clearref', 'con', 'constraint_manager', 'delref', 'diffcalc', 'editref', 'energy_to_wavelength', 'hardware', 'hkl_to_angles', 'hklcalc', 'lastub', 'listub', 'loadub', 'newub', 'rmub', 'saveubas', 'setcut', 'setlat', 'setmax', 'setmin', 'settings', 'setu', 'setub', 'showref', 'swapref', 'trialub', 'ub', 'ub_commands_for_help', 'ubcalc', 'uncon'] This doesn't form the best API to program against though, so it is best to use the four modules more directly. The example below assumes you have also imported:: >>> from diffcalc.ub import ub >>> from diffcalc import hardware >>> from diffcalc.hkl.you import hkl Getting help ------------ To get help for the diffcalc angle calculations, the orientation phase, the angle calculation phase, and the dummy hardware adapter commands:: >>> help(dc) >>> help(ub) >>> help(hkl) >>> help(hardware) Orientation ----------- To orient the crystal for example (see the user manual for a fuller tutorial) first find some reflections:: # Create a new ub calculation and set lattice parameters ub.newub('test') ub.setlat('cubic', 1, 1, 1, 90, 90, 90) # Add 1st reflection (demonstrating the hardware adapter) hardware.settings.hardware.wavelength = 1 ub.c2th([1, 0, 0]) # energy from hardware settings.hardware.position = 0, 60, 0, 30, 0, 0 # mu del nu eta chi ph ub.addref([1, 0, 0]) # energy & pos from hardware # Add 2nd reflection (this time without the hardware adapter) ub.c2th([0, 1, 0], 12.39842) ub.addref([0, 1, 0], [0, 60, 0, 30, 0, 90], 12.39842) To check the state of the current UB calculation:: >>> ub.ub() UBCALC name: test n_phi: 0.00000 0.00000 1.00000 <- set n_hkl: -0.00000 0.00000 1.00000 miscut: None CRYSTAL name: cubic a, b, c: 1.00000 1.00000 1.00000 90.00000 90.00000 90.00000 B matrix: 6.28319 0.00000 0.00000 0.00000 6.28319 0.00000 0.00000 0.00000 6.28319 UB MATRIX U matrix: 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.00000 U angle: 0 UB matrix: 6.28319 0.00000 0.00000 0.00000 6.28319 0.00000 0.00000 0.00000 6.28319 REFLECTIONS ENERGY H K L MU DELTA GAM ETA CHI PHI TAG 1 12.398 1.00 0.00 0.00 0.0000 60.0000 0.0000 30.0000 0.0000 0.0000 2 12.398 0.00 1.00 0.00 0.0000 60.0000 0.0000 30.0000 0.0000 90.0000 And finally to check the reflections were specified acurately:: >>> dc.checkub() ENERGY H K L H_COMP K_COMP L_COMP TAG 1 12.3984 1.00 0.00 0.00 1.0000 0.0000 0.0000 2 12.3984 0.00 1.00 0.00 -0.0000 1.0000 0.0000 Motion ------ Hkl positions and virtual angles can now be read up from angle settings (the easy direction!):: >>> dc.angles_to_hkl((0., 60., 0., 30., 0., 0.)) # energy from hardware ((1.0, 5.5511151231257827e-17, 0.0), {'alpha': -0.0, 'beta': 3.5083546492674376e-15, 'naz': 0.0, 'psi': 90.0, 'qaz': 90.0, 'tau': 90.0, 'theta': 29.999999999999996}) Before calculating the settings to reach an hkl position (the trickier direction) hardware limits must be set and combination of constraints chosen. The constraints here result in a four circle like mode with a vertical scattering plane and incident angle 'alpha' equal to the exit angle 'beta':: >>> hkl.con('qaz', 90) ! 2 more constraints required qaz: 90.0000 >>> hkl.con('a_eq_b') ! 1 more constraint required qaz: 90.0000 a_eq_b >>> hkl.con('mu', 0) qaz: 90.0000 a_eq_b mu: 0.0000 To check the constraints:: >>> hkl.con() DET REF SAMP ====== ====== ====== delta --> a_eq_b --> mu alpha eta --> qaz beta chi naz psi phi mu_is_nu qaz: 90.0000 a_eq_b mu: 0.0000 Type 'help con' for instructions Limits can be set to help Diffcalc choose a solution:: >>> hardware.setmin('delta', 0) # used when choosing solution Angles and virtual angles are then easily determined for a given hkl reflection:: >>> dc.hkl_to_angles(1, 0, 0) # energy from hardware ((0.0, 60.0, 0.0, 30.0, 0.0, 0.0), {'alpha': -0.0, 'beta': 0.0, 'naz': 0.0, 'psi': 90.0, 'qaz': 90.0, 'tau': 90.0, 'theta': 30.0} )