small changes

hexrd/findorientations.py

@@ -74,8 +74,6 @@ def generate_orientation_fibers(eta_ome, threshold, seed_hkl_ids, fiber_ndiv):
     ##    Labeling of spots from seed hkls    ##
     ############################################
 
-    ii       = 0
-    jj       = fiber_ndiv
     qfib     = []
     labels   = []
     numSpots = []
@@ -101,9 +99,9 @@ def generate_orientation_fibers(eta_ome, threshold, seed_hkl_ids, fiber_ndiv):
     ##  Generate discrete fibers from labels  ##
     ############################################
 
-    qfib_tmp = np.empty((4, fiber_ndiv*sum(numSpots)))
-
     for i in range(len(pd_hkl_ids)):
+        ii = 0
+        qfib_tmp = np.empty((4, fiber_ndiv*numSpots[i]))
         for ispot in range(numSpots[i]):
             if not np.isnan(coms[i][ispot][0]):
                 ome_c = eta_ome.omeEdges[0] \
@@ -114,20 +112,22 @@ def generate_orientation_fibers(eta_ome, threshold, seed_hkl_ids, fiber_ndiv):
                 gVec_s = xrdutil.makeMeasuredScatteringVectors(
                     tTh[pd_hkl_ids[i]], eta_c, ome_c
                     )
-
-                qfib_tmp[:, ii:jj] = rot.discreteFiber(
-                    pd.hkls[:, pd_hkl_ids[i]].reshape(3, 1),
-                    gVec_s,
-                    B=bMat,
-                    ndiv=fiber_ndiv,
-                    invert=False,
-                    csym=csym
-                    )[0]
-                ii  = jj
-                jj += fiber_ndiv
+                tmp = mutil.uniqueVectors(
+                    rot.discreteFiber(
+                        pd.hkls[:, pd_hkl_ids[i]].reshape(3, 1),
+                        gVec_s,
+                        B=bMat,
+                        ndiv=fiber_ndiv,
+                        invert=False,
+                        csym=csym
+                        )[0]
+                    )
+                jj = ii + tmp.shape[1]
+                qfib_tmp[:, ii:jj] = tmp
+                ii += tmp.shape[1]
                 pass
             pass
-        qfib.append(mutil.uniqueVectors(qfib_tmp))
+        qfib.append(qfib_tmp[:, :ii])
         pass
     return np.hstack(qfib)
 
@@ -352,4 +352,3 @@ def find_orientations(cfg, hkls=None, profile=False):
     # obselete # if cfg.find_orientations.extract_measured_g_vectors:
     # obselete #     raise NotImplementedError('TODO: implement extract gvecs')
     # obselete #     #extract_measured_g_vectors(cfg)
-

hexrd/xrd/detector.py

@@ -78,6 +78,11 @@
 NCOLS = 2048
 PIXEL = 0.2
 
+# vert
+#NROWS = 2048
+#NCOLS = 2048
+#PIXEL = 0.0045
+
 # pscam
 #NROWS = 2671
 #NCOLS = 4008

hexrd/xrd/transforms.py

@@ -222,7 +222,8 @@ def detectorXYToGvec(xy_det,
                      rMat_d, rMat_s,
                      tVec_d, tVec_s, tVec_c,
                      distortion=(dFunc_ref, dParams_ref),
-                     beamVec=bVec_ref, etaVec=eta_ref):
+                     beamVec=bVec_ref, etaVec=eta_ref,
+                     output_ref=False):
     """
     Takes a list cartesian (x, y) pairs in the detector coordinates and calculates
     the associated reciprocal lattice (G) vectors and (bragg angle, azimuth) pairs
@@ -273,11 +274,19 @@ def detectorXYToGvec(xy_det,
     tTh = np.arccos(np.dot(bHat_l.T, dHat_l)).flatten()
     eta = np.arctan2(dHat_e[1, :], dHat_e[0, :]).flatten()
 
+    # angles for reference frame
+    dHat_ref_l = unitVector(P2_l)
+    dHat_ref_e = np.dot(rMat_e.T, dHat_ref_l)
+    tTh_ref = np.arccos(np.dot(bHat_l.T, unitVector(P2_l))).flatten()
+    eta_ref = np.arctan2(dHat+ref_e[1, :], dHat_ref_e[0, :]).flatten()
+
     # get G-vectors by rotating d by 90-theta about b x d (numpy 'cross' works on row vectors)
     n_g = unitVector(np.cross(bHat_l.T, dHat_l.T).T)
 
     gVec_l = rotate_vecs_about_axis(0.5 * (np.pi - tTh), n_g, dHat_l)
 
+    if output_ref:
+        return (tTh_ref, eta_ref), (tTh, eta), gVec_l
     return (tTh, eta), gVec_l
 
 def oscillAnglesOfHKLs(hkls, chi, rMat_c, bMat, wavelength,

share/example_calibration.yml

@@ -1,23 +1,22 @@
 calibration_crystal:
   grain_id: 0
-  inv_stretch: [1.0000059040292837, 0.9999738183256959, 1.0000126480715623, 2.5554636751865275e-05,
-    1.8161682189944448e-05, -4.231458326489244e-07]
-  orientation: [0.6690652732668282, -0.9867626510443996, 0.7368794659890479]
-  position: [0.002789313619905806, -8.48919662546517e-05, 0.0029522147559835]
+  inv_stretch: [1.0, 1.0, 1.0, 0.0, 0.0, 0.0]
+  orientation: [0.6690346914271271, -0.9869288733543594, 0.7369599629623789]
+  position: [0.0004548754772660814, -4.149496451448677e-06, 0.0032386599395495467]
 detector:
   distortion:
     function_name: GE_41RT
-    parameters: [-1.05744106e-05, -7.46544641e-05, -0.000495262465, 2.0, 4.0, 2.0]
+    parameters: [-1.17664823e-05, -7.52004138e-05, -0.000495704535, 2.0, 4.0, 2.0]
   id: GE
   pixels:
     columns: 2048
     rows: 2048
     size: [0.2, 0.2]
   saturation_level: 14000
   transform:
-    t_vec_d: [-1.444787514997142, -3.234136171449198, -1050.676181428589]
-    tilt_angles: [0.000715272463, -0.0031218473, -0.002275628265961305]
+    t_vec_d: [-1.446574406787204, -3.2335905554228175, -1050.6773464083435]
+    tilt_angles: [0.0006399776154511326, -0.0031010546756005974, -0.0022520647676930825]
 oscillation_stage:
-  chi: -0.0008158290648173493
+  chi: -0.0008964328296020562
   t_vec_s: [0.0, 0.0, 0.0]
 

share/example_config.yml

@@ -1,9 +1,9 @@
-analysis_name: sweep0 # defaults to analysis
+analysis_name: RUBY_SWEEP_0 # defaults to analysis
 
 ## working directory defaults to current working directory
 ## all relative paths specified herein are assumed to be in the working_dir
 ## any files not in working_dir should be specified with an absolute path
-#working_dir: 
+#working_dir:
 
 multiprocessing: all # "all", or "half", or -1 means all but one, defaults to -1
 
@@ -13,23 +13,21 @@ material:
 
 image_series:
   file:
-    stem: RUBY_%04d # can include relative or absolute path
-    ids: [4537, 4538] # or can use globs: ["*2[4-9]"]
+    stem: images/RUBY_%04d # can include relative or absolute path
+    ids: [0] # or can use globs: ["*2[4-9]"]
   images:
-    start: 2
-    #stop: 1440
-    #step: 1
+    start: 0
   omega:
     start: -60.0
     step: 0.25
     stop: 60.0
-  dark: RUBY_4537_medianDark
-  flip: v # ~, v, h, hv, vh, cw, ccw
+  #dark: ~
+  #flip: ~ # ~, v, h, hv, vh, cw, ccw
 
 instrument:
-  parameters: ge_detector.yml
+  parameters: example_calibration.yml
   detector: # this section is only needed to convert old files to the new spec
-    parameters_old: ge_rad.par # the old detector spec, produced by the GUI
+    parameters_old: ge_ceo2.par # the old detector spec, produced by the GUI
     pixels: # this section required to convert from old detector spec
       rows: 2048
       columns: 2048
@@ -40,29 +38,29 @@ find_orientations:
     # A file name must be specified. If it doesn't exist, one will be created
     file: eta-omega.cpl
 
-    threshold: 15
-    #bin_frames: 1 # defaults to 1
+    threshold: 1
+    bin_frames: 1 # defaults to 1
 
     ## "all", or a list of hkl orders used to find orientations
     ## defaults to all orders listed in the material definition
     #active_hkls: [0,1,2,3]
 
-  ## either search full quaternian grid, or seed search based on sparse
+  ## either search full quaternion grid, or seed search based on sparse
   ## orientation maps
-  #use_quaternian_grid: some/file/name # defaults to seeded search
-  seed_search: # this section is ignored if use_quaternian_grid is defined
-    hkl_seeds: [0,1] # hkls ids to use, must be defined for seeded search
-  #  fiber_step: 0.5 # degrees, defaults to ome tolerance
+  #use_quaternion_grid: some/file/name # defaults to seeded search
+  seed_search: # this section is ignored if use_quaternion_grid is defined
+    hkl_seeds: [0,1,2] # hkls ids to use, must be defined for seeded search
+    fiber_step: 0.5 # degrees, defaults to ome tolerance
 
   threshold: 5 # defaults to 1
 
   omega:
     tolerance: 1.0 # in degrees, defaults to 2x ome step
 
-  ## specify the branch cut, in degrees. The range must be 360 degrees.
-  ## defaults to ["image_series:omega:start", "image_series:omega:start"+-360]
-  ## depending on sign of "image_series:omega:step"
-  period: [-180, 180] # in degrees, defaults to full 360 starting at "ome start"
+    ## specify the branch cut, in degrees. The range must be 360 degrees.
+    ## defaults to ["image_series:omega:start", "image_series:omega:start"+-360]
+    ## depending on sign of "image_series:omega:step"
+    period: [-180, 180] # in degrees, defaults to full 360 starting at "ome start"
 
   eta:
     tolerance: 1.0 # in degrees, defaults to 2x ome step
@@ -73,22 +71,20 @@ find_orientations:
     completeness: 0.51 # completeness threshold
     #algorithm: fclusterdata # defaults to dbscan
 
-  #extract_measured_g_vectors: true # defaults to false
-
 fit_grains:
   do_fit: true # if false, extracts grains but doesn't fit. defaults to true
 
-  #estimate: multiruby/grains.out # defaults to None
+  estimate: RUBY_SWEEP_0/grains.out # defaults to None
 
-  #npdiv: 1 # number of polar pixel grid subdivisions, defaults to 2
+  npdiv: 3 # number of polar pixel grid subdivisions, defaults to 2
 
   panel_buffer: 10 # don't fit spots within this many pixels from edge
 
-  threshold: 15
+  threshold: 1
 
   tolerance:
     tth: [0.2, 0.1] # tolerance lists must be identical length
-    eta: [2.0, 2.0]
-    omega: [1.0, 1.0]
+    eta: [2.0, 0.5]
+    omega: [1.0, 0.25]
 
-  tth_max: 15 # true, false, or a non-negative value, defaults to true
+  tth_max: 15.25 # true, false, or a non-negative value, defaults to true