From 09f4c70c6a08a246cad8db044ef85fbb5da5089f Mon Sep 17 00:00:00 2001
From: James Ball <jadball@gmail.com>
Date: Thu, 21 Nov 2024 17:04:33 +0100
Subject: [PATCH] Fix y0 bug, a bit of cleanup

---
 .../S3DXRD/select_for_index_unknown.ipynb     | 39 ++++++++++++-------
 1 file changed, 25 insertions(+), 14 deletions(-)

diff --git a/ImageD11/nbGui/S3DXRD/select_for_index_unknown.ipynb b/ImageD11/nbGui/S3DXRD/select_for_index_unknown.ipynb
index 9e11d6cc..a356754d 100644
--- a/ImageD11/nbGui/S3DXRD/select_for_index_unknown.ipynb
+++ b/ImageD11/nbGui/S3DXRD/select_for_index_unknown.ipynb
@@ -90,7 +90,7 @@
    },
    "outputs": [],
    "source": [
-    "ds.parfile = aroot + \"/LMGO_pseudo_cubic.par\"\n",
+    "# ds.parfile = aroot + \"/LMGO_pseudo_cubic.par\"\n",
     "cf_4d = ds.get_cf_4d()\n",
     "ds.update_colfile_pars( cf_4d )"
    ]
@@ -98,12 +98,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "\" \".join(cf_4d.titles)"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "major_phase_str = 'Al'"
    ]
   },
   {
@@ -129,9 +137,8 @@
    },
    "outputs": [],
    "source": [
-    "# fixme - removing the main phase - could skip this part if there is no main phase\n",
-    "a = 3.90725\n",
-    "ucell = ImageD11.unitcell.unitcell( [2*a, 2*a, 2*a, 90, 90, 90], \"P\")\n",
+    "ucell = ds.phases.unitcells[major_phase_str]\n",
+    "\n",
     "ucell.makerings( dsbinedges[-1] )\n",
     "ucell.lattice_parameters"
    ]
@@ -269,7 +276,8 @@
     "    return pair\n",
     "\n",
     "om = np.linspace( cring.omega.min(), cring.omega.max(), 90 )\n",
-    "fitline, = ax[1].plot( om, np.zeros_like(om), '-')\n",
+    "fitlinel, = ax[0].plot( om, np.zeros_like(om), '-')\n",
+    "fitliner, = ax[1].plot( om, np.zeros_like(om), '-')\n",
     "\n",
     "### GLOBALS, also y0\n",
     "p1 = None   # index of first peak in cring\n",
@@ -305,7 +313,8 @@
     "                    [ -sj, -cj] ] )\n",
     "    xy = x, y = np.linalg.inv(R).dot( [ yi, yj ] )\n",
     "    ycalc = ImageD11.sinograms.geometry.x_y_y0_omega_to_dty(om, x, y, y0)\n",
-    "    fitline.set_ydata( ycalc )\n",
+    "    fitlinel.set_ydata( ycalc )\n",
+    "    fitliner.set_ydata( ycalc )\n",
     "    peak_ycalc = ImageD11.sinograms.geometry.x_y_y0_omega_to_dty(cring.omega, x, y, y0)\n",
     "    \n",
     "def onpick( evt ):\n",
@@ -523,8 +532,8 @@
     "sino, obinedge, ybinedge = np.histogram2d( cring.omega, cring.dty, weights = np.log(cring.sum_intensity),\n",
     "                      bins = (np.linspace(ds.obinedges.min(), ds.obinedges.max(), nbins_angle), ds.ybinedges) )\n",
     "obincen = 0.5*(obinedge[:-1] + obinedge[1:])\n",
-    "recon = ImageD11.sinograms.roi_iradon.iradon( sino.T, obincen, filter_name='shepp-logan', \n",
-    "                                             workers=ImageD11.cImageD11.cores_available())"
+    "recon = ImageD11.sinograms.roi_iradon.run_iradon(sino.T, obincen, filter_name='shepp-logan', \n",
+    "                                             workers=ImageD11.cImageD11.cores_available(), shift=-y0/ds.ystep, pad=0)"
    ]
   },
   {
@@ -557,10 +566,10 @@
     "    if evt.inaxes == ax[1]:\n",
     "        y = evt.xdata\n",
     "        x = evt.ydata\n",
-    "        ycalc = ImageD11.sinograms.geometry.dtycalc( om, x, y, 0 )\n",
+    "        ycalc = ImageD11.sinograms.geometry.dtycalc( om, x, y, y0 )\n",
     "        global ycalcall, pos\n",
     "        pos = y,x\n",
-    "        ycalcall = ImageD11.sinograms.geometry.dtycalc( cring.omega, x, y, 0 )\n",
+    "        ycalcall = ImageD11.sinograms.geometry.dtycalc( cring.omega, x, y, y0 )\n",
     "        fitline1.set_ydata( ycalc + 1 )\n",
     "        fitline2.set_ydata( ycalc - 1 )\n",
     "        location.set_xdata( [y,] )\n",
@@ -664,6 +673,8 @@
     "for c in cells:\n",
     "    plt.plot( c.ringds, np.full( len(c.ringds), o) ,\"|\", ms=10, lw =.1, label=(\"%.4f \"*6)%tuple(c.lattice_parameters) )\n",
     "    o *= 2\n",
+    "o *= 2\n",
+    "plt.plot( ucell.ringds, np.full( len(ucell.ringds), o) ,\"|\", ms=10, lw =.1, label=(\"%.4f \"*6)%tuple(ucell.lattice_parameters) )\n",
     "plt.semilogy()\n",
     "plt.xlim(0.1,0.6)\n",
     "plt.legend(loc='upper left');"