Merge pull request #1199 from psavery/hand-picked-indexing

Add hand-picked indexing method

Author: joelvbernier

hexrd/ui/indexing/fiber_pick_utils.py

@@ -0,0 +1,157 @@
+import numpy as np
+
+from hexrd import constants as cnst
+from hexrd.rotations import discreteFiber
+from hexrd.transforms import xfcapi
+
+
+def _pick_to_fiber(pick_coords, eta_ome_maps, map_index, step=0.5,
+                   beam_vec=None, chi=0., as_expmap=True):
+    """
+    Returns the orientations for the specified fiber parameters.
+
+    Parameters
+    ----------
+    pick_coords : array_like
+        The (2, ) list/vector containing the pick coordinates as (eta, omega)
+        in DEGREES.  This corresponds to the (column, row) or (x, y) dimensions
+        on the map.
+    eta_ome_maps : hexrd.xrdutil.utils.EtaOmeMaps
+        The eta-omega maps.
+    map_index : int
+        The index of the current map.
+    step : scalar, optional
+        The step size along the fiber in DEGREES.  The default is 0.5.
+    chi : scalar, optional
+        The chi angle from the associated instrument (specifically,
+        `instr.chi`).  The default is 0.
+    beam_vec : array_like, optional
+        The beam vector of the associated instrument (specifically,
+        `instr.beam_vector`).  The default is None (giving [0, 0, -1]).
+    as_expmap : bool, optional
+        Flag for converting the output from qauternions to exponential map.
+        The default is True.
+
+    Returns
+    -------
+    qfib : numpy.ndarray
+        The array containing the fiber points as quaternions or exponential
+        map parameters, according to the `as_expmap` kwarg.
+
+    """
+    pick_coords = np.atleast_1d(pick_coords).flatten()
+
+    if beam_vec is None:
+        beam_vec = cnst.beam_vec
+
+    ndiv = int(np.round(360./float(step)))
+
+    # grab the planeData instance from the maps
+    # !!! this should have a copy of planeData that has hkls consistent with
+    #     the map data.
+    pd = eta_ome_maps.planeData
+    bmat = pd.latVecOps['B']
+
+    # the crystal direction (plane normal)
+    crys_dir = pd.hkls[:, map_index].reshape(3, 1)
+
+    # the sample direction
+    tth = pd.getTTh()[map_index]  # !!! in radians
+    angs = np.atleast_2d(np.hstack([tth, np.radians(pick_coords)]))
+    samp_dir = xfcapi.anglesToGVec(
+        angs, bHat_l=beam_vec, chi=chi
+    ).reshape(3, 1)
+
+    # make the fiber
+    qfib = discreteFiber(
+        crys_dir, samp_dir,
+        B=bmat, ndiv=ndiv,
+        invert=False,
+        csym=pd.getQSym(), ssym=None
+    )[0]
+
+    if as_expmap:
+        phis = 2.*np.arccos(qfib[0, :])
+        ns = xfcapi.unitRowVector(qfib[1:, :].T)
+        expmaps = phis*ns.T
+        return expmaps.T  # (3, ndiv)
+    else:
+        return qfib.T  # (4, ndiv)
+
+
+def _angles_from_orientation(instr, eta_ome_maps, orientation):
+    """
+    Return the (eta, omega) angles for a specified orientation consistent with
+    input EtaOmeMaps.
+
+    Parameters
+    ----------
+    instr : hexrd.instrument.HEDMInstrument
+        The instrument instance used to generate the EtaOmeMaps.
+    eta_ome_maps : hexrd.xrdutil.utils.EtaOmeMaps
+        The eta-omega maps.
+    orientation : array_like
+        Either a (3, ) or (4, ) element vector specifying an orientation.
+
+    Raises
+    ------
+    RuntimeError
+        If orientation has more than 4 elements.
+
+    Returns
+    -------
+    simulated_angles : list
+        A list with length = len(eta_ome_maps.dataStore) containing the angular
+        coordinates of all valid reflections for each map.  If no valid points
+        exist for a particular map, the entry contains `None`.  Otherwise,
+        the entry is a (2, p) array of the (eta, omega) coordinates in DEGREES
+        for the p valid reflections.
+
+    """
+    plane_data = eta_ome_maps.planeData
+
+    # angle ranges from maps
+    eta_range = (eta_ome_maps.etaEdges[0], eta_ome_maps.etaEdges[-1])
+    ome_range = (eta_ome_maps.omeEdges[0], eta_ome_maps.omeEdges[-1])
+    ome_period = eta_ome_maps.omeEdges[0] + np.r_[0., 2*np.pi]
+
+    # need the hklids
+    hklids = [i['hklID'] for i in plane_data.hklDataList]
+
+    expmap = np.atleast_1d(orientation).flatten()
+    if len(expmap) == 4:
+        # have a quat; convert here
+        phi = 2.*np.arccos(expmap[0])
+        n = xfcapi.unitRowVector(expmap[1:])
+        expmap = phi*n
+    elif len(expmap) > 4:
+        raise RuntimeError(
+            "orientation must be a single exponential map or quaternion"
+        )
+
+    grain_param_list = [np.hstack([expmap, cnst.zeros_3, cnst.identity_6x1]), ]
+    sim_dict = instr.simulate_rotation_series(
+        plane_data, grain_param_list,
+        eta_ranges=[eta_range, ], ome_ranges=[ome_range, ],
+        ome_period=ome_period, wavelength=None
+    )
+
+    rids = []
+    angs = []
+    for sim in sim_dict.values():
+        rids.append(sim[0][0])
+        angs.append(sim[2][0])
+    rids = np.hstack(rids)
+    angs = np.vstack(angs)
+
+    simulated_angles = []
+    for rid in hklids:
+        this_idx = rids == rid
+        if np.any(this_idx):
+            simulated_angles.append(
+                np.degrees(np.atleast_2d(angs[this_idx, 1:]))
+            )
+        else:
+            simulated_angles.append(None)
+
+    return simulated_angles

hexrd/ui/indexing/ome_maps_select_dialog.py

@@ -150,6 +150,7 @@ def update_config(self):
         # Set the new config options on the internal config
         indexing_config = HexrdConfig().indexing_config
         maps_config = indexing_config['find_orientations']['orientation_maps']
+        maps_config['_select_method'] = self.method_name
         maps_config['file'] = self.file_name
         maps_config['threshold'] = self.threshold
         maps_config['bin_frames'] = self.bin_frames
@@ -162,6 +163,8 @@ def update_gui(self):
         indexing_config = HexrdConfig().indexing_config
         maps_config = indexing_config['find_orientations']['orientation_maps']
 
+        self.method_name = maps_config.get('_select_method', 'load')
+
         file_name = maps_config['file'] if maps_config['file'] else ''
 
         self.ui.file_name.setText(file_name)