Correct g-vector origin in point-by-point indexing

ImageD11/sinograms/geometry.py

@@ -67,6 +67,17 @@
 from skimage.feature import blob_log
 
 
+def sample_to_lab_sincos(sx, sy, y0, dty, sinomega, cosomega):
+    """Same as sample_to_lab but using sinomega and cosomega"""
+    sxr = sx * cosomega - sy * sinomega
+    syr = sx * sinomega + sy * cosomega
+
+    lx = sxr
+    ly = syr - y0 + dty
+
+    return lx, ly
+
+
 def sample_to_lab(sx, sy, y0, dty, omega):
     """Converts sample (sx, sy) position to the lab frame (lx, ly)
     The sample reference frame could be rotated by an angle omega (degrees) CCW about the rotation axis
@@ -219,6 +230,12 @@ def dty_to_dtyi(dty, ystep):
     return dtyi
 
 
+def dtyi_to_dty(dtyi, ystep):
+    """Converts dtyi value (step space) to dty value (lab frame)"""
+    _, sy = step_to_sample(0, dtyi, ystep)
+    return sy
+
+
 def dty_to_dtyi_for_sinogram(dty, ystep, ymin):
     """Converts dty value (lab frame) to something like scan number"""
     dtyi = np.round((dty - ymin) / ystep).astype(int)

ImageD11/sinograms/point_by_point.py

@@ -4,6 +4,9 @@
 # Try to build the point-by-point mapping code ...
 from __future__ import print_function, division
 import os
+
+from matplotlib import pyplot as plt
+
 os.environ["OMP_NUM_THREADS"] = "1"
 import sys
 from ImageD11 import cImageD11
@@ -21,7 +24,8 @@
 import ImageD11.sinograms.dataset
 import ImageD11.indexing
 import ImageD11.columnfile
-from ImageD11.sinograms.geometry import dty_to_dtyi, dtyimask_from_sincos
+from ImageD11.sinograms.geometry import dty_to_dtyi, dtyimask_from_sincos, step_to_sample, sample_to_lab_sincos, \
+    dtyi_to_dty
 
 
 # GOTO - find somewhere!
@@ -139,13 +143,12 @@ def idxpoint(
     i,
     j,
     isel,
+    omega,
     sinomega,
     cosomega,
     dtyi,
-    gx,
-    gy,
-    gz,
-    eta,
+    sc,
+    fc,
     ystep=2.00,
     y0=0.0,
     minpks=1000,
@@ -189,13 +192,35 @@ def idxpoint(
     mr = isel
     # select the peaks using the geometry module
     m = dtyimask_from_sincos(i, j, sinomega, cosomega, dtyi, y0, ystep)
-    # the arrays to use for indexing (this point in space)
-    # TODO: Correct these for origin point
+    # now we correct g-vectors for origin point
+
+    # compute the sample coordinates for this pixel
+    sx, sy = step_to_sample(i, j, ystep)
+    dty = dtyi_to_dty(dtyi, ystep)
+
+    # compute x distance offset for this pixel
+    lx, _ = sample_to_lab_sincos(sx, sy, y0, dty, sinomega, cosomega)
+    parlocal = parglobal.get_parameters().copy()
+    parlocal['distance'] = parlocal['distance'] - lx
+
+    # compute tth eta for all peaks with corrected distance at this pixel
+    tth, eta = ImageD11.transform.compute_tth_eta((sc, fc), **parlocal)
+
+    # compute gvectors for all peaks with corrected distance at this pixel
+    gx, gy, gz = ImageD11.transform.compute_g_vectors(tth, eta,
+                                               omega,
+                                               parlocal['wavelength'],
+                                               wedge=parlocal['wedge'],
+                                               chi=parlocal['chi'])
+
+    # mask g-vectors to this pixel for indexing
     inds = np.mgrid[0 : len(gx)][m & mr]
     gv = np.empty((len(inds), 3), "d")
     gv[:, 0] = gx[inds]
     gv[:, 1] = gy[inds]
     gv[:, 2] = gz[inds]
+
+    # index with masked g-vectors
     ind = ImageD11.indexing.indexer(
         unitcell=ucglobal,
         wavelength=parglobal.get("wavelength"),
@@ -255,13 +280,12 @@ def proxy(args):
         i,
         j,
         sm["isel"],
+        sm["omega"],
         sm["sinomega"],
         sm["cosomega"],
         sm["dtyi"],
-        sm["gx"],
-        sm["gy"],
-        sm["gz"],
-        sm["eta"],
+        sm["sc"],
+        sm["fc"],
         **idxopts
     )
     return i, j, g