Small quality of life improvements

FABLE-3DXRD · Nov 6, 2024 · f159837 · f159837
1 parent 223d754
commit f159837
Show file tree

Hide file tree

Showing 7 changed files with 56 additions and 13 deletions.
diff --git a/ImageD11/nbGui/S3DXRD/4_visualise.ipynb b/ImageD11/nbGui/S3DXRD/4_visualise.ipynb
@@ -92,7 +92,8 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "ds.phases = ds.get_phases_from_disk()"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/5_combine_phases.ipynb b/ImageD11/nbGui/S3DXRD/5_combine_phases.ipynb
@@ -86,8 +86,7 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "phases = ds.get_phases_from_disk()\n",
-    "ds.phases = phases\n",
+    "ds.phases = ds.get_phases_from_disk()\n",
     "ds.phases.unitcells"
    ]
   },

diff --git a/ImageD11/nbGui/S3DXRD/6_stack_layers.ipynb b/ImageD11/nbGui/S3DXRD/6_stack_layers.ipynb
@@ -83,6 +83,19 @@
     "print(ds.shape)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8ea038db-b86c-4ce3-9117-83060f68351e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# load phases from parameter file\n",
+    "\n",
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -95,12 +108,12 @@
     "samples_dict = {}\n",
     "\n",
     "skips_dict = {\n",
-    "    \"FeAu_0p5_tR_nscope\": [\"top_100um\", \"top_-100um\"]\n",
+    "    ds.sample: []\n",
     "}\n",
     "\n",
     "dset_prefix = \"top\"\n",
     "\n",
-    "sample_list = [\"FeAu_0p5_tR_nscope\"]\n",
+    "sample_list = [ds.sample]\n",
     "\n",
     "for sample in sample_list:\n",
     "    all_dset_folders_for_sample = os.listdir(os.path.join(rawdata_path, sample))\n",
@@ -114,8 +127,7 @@
     "    samples_dict[sample] = dsets_list\n",
     "    \n",
     "# manually override:\n",
-    "\n",
-    "samples_dict = {\"FeAu_0p5_tR_nscope\": [\"top_150um\", \"top_200um\", \"top_250um\"]}"
+    "# samples_dict = {\"FeAu_0p5_tR_nscope\": [\"top_150um\", \"top_200um\", \"top_250um\"]}"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/pbp_2_visualise.ipynb b/ImageD11/nbGui/S3DXRD/pbp_2_visualise.ipynb
@@ -88,7 +88,8 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "ds.phases = ds.get_phases_from_disk()"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb b/ImageD11/nbGui/S3DXRD/pbp_3_refinement.ipynb
@@ -100,7 +100,8 @@
    "source": [
     "# load phases from parameter file\n",
     "\n",
-    "ds.phases = ds.get_phases_from_disk()"
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
    ]
   },
   {

diff --git a/ImageD11/nbGui/S3DXRD/tomo_1_index.ipynb b/ImageD11/nbGui/S3DXRD/tomo_1_index.ipynb
@@ -260,10 +260,10 @@
     "\n",
     "fig, ax = plt.subplots(figsize=(16, 9), constrained_layout=True)\n",
     "\n",
-    "ax.plot( ucell.ringds, [1e4,]*len(ucell.ringds), '|', ms=90, c=\"red\")\n",
-    "\n",
     "ax.plot(cf_4d.ds, cf_4d.sum_intensity,',', label='cf_4d')\n",
     "ax.plot(cf_strong.ds, cf_strong.sum_intensity,',', label='cf_strong')\n",
+    "ax.plot( ucell.ringds, [1e4,]*len(ucell.ringds), '|', ms=90, c=\"red\")\n",
+    "\n",
     "ax.semilogy()\n",
     "\n",
     "ax.set_xlabel(\"Dstar\")\n",

diff --git a/ImageD11/nbGui/TDXRD/4_3DXRD_merge_slices.ipynb b/ImageD11/nbGui/TDXRD/4_3DXRD_merge_slices.ipynb
@@ -76,6 +76,30 @@
     "processed_data_root_dir = ds.analysisroot"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ds.phases = ds.get_phases_from_disk()\n",
+    "ds.phases.unitcells"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# now let's select a phase to index from our parameters json\n",
+    "phase_str = 'Fe'\n",
+    "\n",
+    "ucell = ds.phases.unitcells[phase_str]\n",
+    "\n",
+    "print(ucell.lattice_parameters, ucell.spacegroup)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -159,7 +183,7 @@
    "source": [
     "# load grains for each dataset and tie them to the dataset objects\n",
     "for ds in ds_dict.values():\n",
-    "    ds.grains = ds.get_grains_from_disk()"
+    "    ds.grains = ds.get_grains_from_disk(phase_str)"
    ]
   },
   {
@@ -276,8 +300,13 @@
     "\n",
     "from xfab.symmetry import Umis\n",
     "\n",
+    "# USER: Check the symmetry here\n",
+    "# crystal_system number must be one of 1: Triclinic, 2: Monoclinic, 3: Orthorhombic, 4: Tetragonal, 5: Trigonal, 6: Hexagonal, 7: Cubic\n",
+    "\n",
+    "crystal_system_number = 7  # cubic\n",
+    "\n",
     "def misorien_deg(U1, U2):\n",
-    "    return np.min(Umis(U1, U2, 7), axis=0)[1]  # 7 == cubic\n",
+    "    return np.min(Umis(U1, U2, crystal_system_number), axis=0)[1]  # 7 == cubic\n",
     "\n",
     "matches = []\n",
     "\n",