Merge pull request #283 from jadball/master

Add Astra support
FABLE-3DXRD · May 21, 2024 · 8e87e16 · 8e87e16
2 parents dd2c425 + 07a0f01
commit 8e87e16
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Showing 7 changed files with 2,192 additions and 21 deletions.
diff --git a/ImageD11/nbGui/3DXRD/1_3DXRD_refine_parameters.ipynb b/ImageD11/nbGui/3DXRD/1_3DXRD_refine_parameters.ipynb
@@ -75,7 +75,8 @@
     "import ImageD11.columnfile\n",
     "from ImageD11.sinograms import properties, dataset\n",
     "\n",
-    "from ImageD11.blobcorrector import eiger_spatial"
+    "from ImageD11.blobcorrector import eiger_spatial\n",
+    "from ImageD11.peakselect import select_ring_peaks_by_intensity"
    ]
   },
   {
@@ -198,7 +199,7 @@
     "# this indicates the fractional intensity cutoff we will select\n",
     "# if the blue line does not look elbow-shaped in the logscale plot, try changing the \"doplot\" parameter (the y scale of the logscale plot) until it does\n",
     "\n",
-    "cf_strong = utils.selectpeaks(cf_3d, frac=0.985, dsmax=1.04, doplot=0.8, dstol=0.01)\n",
+    "cf_strong = select_ring_peaks_by_intensity(cf_3d, frac=0.985, dsmax=1.04, doplot=0.8, dstol=0.01)\n",
     "print(f\"Got {cf_strong.nrows} strong peaks for indexing\")\n",
     "cf_strong.writefile(f'{sample}_{dataset}_3d_peaks_strong.flt')"
    ]
@@ -214,7 +215,7 @@
     "# we will also export some additional strong peaks across all rings\n",
     "# this will be useful for grain refinement later (using makemap)\n",
     "\n",
-    "cf_strong_allrings = utils.selectpeaks(cf_3d, frac=0.95, dsmax=cf_3d.ds.max(), doplot=0.05, dstol=0.01)\n",
+    "cf_strong_allrings = select_ring_peaks_by_intensity(cf_3d, frac=0.95, dsmax=cf_3d.ds.max(), doplot=0.05, dstol=0.01)\n",
     "print(f\"Got {cf_strong_allrings.nrows} strong peaks for makemap\")\n",
     "cf_strong_allrings_path = f'{sample}_{dataset}_3d_peaks_strong_all_rings.flt'\n",
     "cf_strong_allrings.writefile(cf_strong_allrings_path)"
@@ -307,6 +308,25 @@
     "ImageD11.indexing.loglevel = 3"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# let's plot the assigned peaks\n",
+    "\n",
+    "fig, ax = plt.subplots()\n",
+    "\n",
+    "# indexer.ra is the ring assignments\n",
+    "\n",
+    "ax.scatter(cf_strong.ds, cf_strong.eta, c=indexer.ra, cmap='tab20', s=1)\n",
+    "ax.set_xlabel(\"d-star\")\n",
+    "ax.set_ylabel(\"eta\")\n",
+    "\n",
+    "plt.show()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -396,7 +416,8 @@
    "outputs": [],
    "source": [
     "omegas_sorted = np.sort(ds.omega)[0]\n",
-    "omega_slop = np.round(np.diff(omegas_sorted).mean(), 3)\n",
+    "omega_step = np.round(np.diff(omegas_sorted).mean(), 3)\n",
+    "omega_slop = omega_step/2\n",
     "\n",
     "makemap_hkl_tol_seq = [0.05, 0.025, 0.01]"
    ]
@@ -409,12 +430,14 @@
    },
    "outputs": [],
    "source": [
+    "symmetry = \"cubic\"\n",
+    "\n",
     "for inc, makemap_tol in enumerate(makemap_hkl_tol_seq):\n",
     "    print(f\"Running makemap {inc+1}/{len(makemap_hkl_tol_seq)}\")\n",
     "    if inc == 0:  # ubi into map\n",
-    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_ubi_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s cubic -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort\n",
+    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_ubi_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s {symmetry} -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort\n",
     "    else:  # map into map\n",
-    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_map_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s cubic -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort"
+    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_map_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s {symmetry} -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort"
    ]
   },
   {

diff --git a/ImageD11/nbGui/3DXRD/2_3DXRD_index.ipynb b/ImageD11/nbGui/3DXRD/2_3DXRD_index.ipynb
@@ -305,6 +305,25 @@
     "ImageD11.indexing.loglevel = 3"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# let's plot the assigned peaks\n",
+    "\n",
+    "fig, ax = plt.subplots()\n",
+    "\n",
+    "# indexer.ra is the ring assignments\n",
+    "\n",
+    "ax.scatter(cf_strong.ds, cf_strong.eta, c=indexer.ra, cmap='tab20', s=1)\n",
+    "ax.set_xlabel(\"d-star\")\n",
+    "ax.set_ylabel(\"eta\")\n",
+    "\n",
+    "plt.show()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -424,7 +443,8 @@
    "outputs": [],
    "source": [
     "omegas_sorted = np.sort(ds.omega)[0]\n",
-    "omega_slop = np.round(np.diff(omegas_sorted).mean(), 3)\n",
+    "omega_step = np.round(np.diff(omegas_sorted).mean(), 3)\n",
+    "omega_slop = omega_step/2\n",
     "\n",
     "makemap_hkl_tol_seq = [0.05, 0.025, 0.01]"
    ]
@@ -437,12 +457,14 @@
    },
    "outputs": [],
    "source": [
+    "symmetry = \"cubic\"\n",
+    "\n",
     "for inc, makemap_tol in enumerate(makemap_hkl_tol_seq):\n",
     "    print(f\"Running makemap {inc+1}/{len(makemap_hkl_tol_seq)}\")\n",
     "    if inc == 0:  # ubi into map\n",
-    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_ubi_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s cubic -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort\n",
+    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_ubi_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s {symmetry} -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort\n",
     "    else:  # map into map\n",
-    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_map_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s cubic -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort"
+    "        makemap_output = !makemap.py -p {ds.parfile} -u {tmp_map_path} -U {tmp_map_path} -f {cf_strong_allrings_path} -F {unindexed_flt_path} -s {symmetry} -t {makemap_hkl_tol_seq[inc]} --omega_slop={omega_slop} --no_sort"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/2_S3DXRD_sinograms_map.ipynb b/ImageD11/nbGui/S3DXRD/2_S3DXRD_sinograms_map.ipynb
@@ -630,8 +630,8 @@
    "outputs": [],
    "source": [
     "fig, a = plt.subplots(1,2,figsize=(10,5))\n",
-    "rec = a[0].imshow(grainsinos[8].recons[\"iradon\"], vmin=0, origin=\"lower\")\n",
-    "sin = a[1].imshow(grainsinos[8].ssino, aspect='auto')\n",
+    "rec = a[0].imshow(grainsinos[0].recons[\"iradon\"], vmin=0, origin=\"lower\")\n",
+    "sin = a[1].imshow(grainsinos[0].ssino, aspect='auto')\n",
     "\n",
     "# Function to update the displayed image based on the selected frame\n",
     "def update_frame(i):\n",
@@ -1044,6 +1044,9 @@
     "        print(\"Whole sample mask recon\")\n",
     "        whole_sample_sino, xedges, yedges = np.histogram2d(cf_4d.dty, cf_4d.omega, bins=[ds.ybinedges, ds.obinedges])\n",
     "        whole_sample_recon = run_iradon(whole_sample_sino, ds.obincens, pad, shift, workers=nthreads, apply_halfmask=is_half_scan, mask_central_zingers=is_half_scan)\n",
+    "        \n",
+    "        recon_man_mask = apply_manual_mask(whole_sample_recon)\n",
+    "        \n",
     "        if manual_threshold is None:\n",
     "            thresh = threshold_otsu(recon_man_mask)\n",
     "        else:\n",