update Nexus config file

OpenCOMPES · Feb 28, 2024 · a510154 · a510154
1 parent 5f903a6
commit a510154
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Showing 2 changed files with 29 additions and 30 deletions.
diff --git a/specsscan/config/NXmpes_arpes_config.json b/specsscan/config/NXmpes_arpes_config.json
@@ -107,7 +107,7 @@
       "analyzer_elevation/@units": "degrees",
       "analyzer_elevation/@vector": [0, 1, 0],
       "analyzer_rotation/@depends_on": "rot_y",
-      "analyzer_rotation": 90,
+      "analyzer_rotation": 0,
       "analyzer_rotation/@transformation_type": "rotation",
       "analyzer_rotation/@units": "degrees",
       "analyzer_rotation/@vector": [0, 0, 1],
@@ -271,33 +271,38 @@
     "drain_current": {
       "amperemeter": "@link:/entry/instrument/manipulator/drain_current_amperemeter"
     },
-    "depends_on": "/entry/sample/transformations/bz_offset",
+    "depends_on": "/entry/sample/transformations/offset_azimuth",
     "transformations": {
-      "AXISNAME[bz_offset]/@depends_on": "sample_azimuth",
-      "AXISNAME[bz_offset]": 0,
-      "AXISNAME[bz_offset]/@units": "degrees",
-      "AXISNAME[bz_offset]/@transformation_type": "rotation",
-      "AXISNAME[bz_offset]/@vector": [0, 0, 1],
-      "sample_azimuth/@depends_on": "sample_tilt",
+      "offset_azimuth/@depends_on": "sample_azimuth",
+      "offset_azimuth": 0,
+      "offset_azimuth/@units": "degrees",
+      "offset_azimuth/@transformation_type": "rotation",
+      "offset_azimuth/@vector": [0, 0, 1],
+      "sample_azimuth/@depends_on": "offset_tilt",
       "sample_azimuth": "@attrs:metadata/scan_info/trARPES:Carving:OMG.RBV",
       "sample_azimuth/@units": "degrees",
       "sample_azimuth/@transformation_type": "rotation",
       "sample_azimuth/@vector": [0, 0, 1],
-      "sample_tilt/@depends_on": "sample_polar",
+      "offset_tilt/@depends_on": "sample_tilt",
+      "offset_tilt": 0,
+      "offset_tilt/@units": "degrees",
+      "offset_tilt/@transformation_type": "rotation",
+      "offset_tilt/@vector": [1, 0, 0],
+      "sample_tilt/@depends_on": "offset_polar",
       "sample_tilt": "@attrs:metadata/scan_info/trARPES:Carving:PHI.RBV",
       "sample_tilt/@units": "degrees",
       "sample_tilt/@transformation_type": "rotation",
       "sample_tilt/@vector": [1, 0, 0],
-      "sample_polar/@depends_on": "polar_offset",
+      "offset_polar/@depends_on": "sample_polar",
+      "offset_polar": -321,
+      "offset_polar/@units": "degrees",
+      "offset_polar/@transformation_type": "rotation",
+      "offset_polar/@vector": [0, 1, 0],
+      "sample_polar/@depends_on": "yz_flip",
       "sample_polar": "@attrs:metadata/scan_info/trARPES:Carving:THT.RBV",
       "sample_polar/@units": "degrees",
       "sample_polar/@transformation_type": "rotation",
       "sample_polar/@vector": [0, 1, 0],
-      "polar_offset/@depends_on": "yz_flip",
-      "polar_offset": -321,
-      "polar_offset/@units": "degrees",
-      "polar_offset/@transformation_type": "rotation",
-      "polar_offset/@vector": [0, 1, 0],
       "AXISNAME[yz_flip]/@depends_on": "xy_adjust",
       "AXISNAME[yz_flip]": 90.0,
       "AXISNAME[yz_flip]/@units": "degrees",

diff --git a/tutorial/specscan_conversion_to_NXmpes.ipynb b/tutorial/specscan_conversion_to_NXmpes.ipynb
@@ -26,7 +26,8 @@
     "%load_ext autoreload\n",
     "%autoreload 2\n",
     "from specsscan import SpecsScan\n",
-    "from pathlib import Path"
+    "from pathlib import Path\n",
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -123,12 +124,10 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "config = {\"nexus\":{\"definition\": \"NXmpes_arpes\"}, \"spa_params\":{\"crop\":True, \"ek_min\":20.2, \"ek_max\":22.5, \"ang_min\":-13.5, \"ang_max\":13.5}}"
+    "config = {\"nexus\":{\"definition\": \"NXmpes_arpes\"}, \"spa_params\":{\"crop\":True, \"ek_range_min\":0.07597844332538181, \"ek_range_max\":0.9117413199045858, \"ang_range_min\":0.16453159041394336, \"ang_range_max\":0.8840087145969499,}}"
    ]
   },
   {
@@ -147,7 +146,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The load_scan method loads the scan as an xarray along with the metadata needed for nexus conversion. The progress bars can be activated by changing the config parameter, enable_nested_progress_bar, to true in config.yaml "
+    "The load_scan method loads the scan as an xarray along with the metadata needed for nexus conversion."
    ]
   },
   {
@@ -173,7 +172,8 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "res_xarray[:,29,:].plot()"
+    "res_xarray[:,29,:].plot()\n",
+    "plt.show()"
    ]
   },
   {
@@ -185,7 +185,8 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "res_xarray.loc[{\"energy\":slice(21.6, 21.8)}].sum(axis=2).plot()"
+    "res_xarray.loc[{\"energy\":slice(21.6, 21.8)}].sum(axis=2).plot()\n",
+    "plt.show()"
    ]
   },
   {
@@ -199,13 +200,6 @@
     "sps.save(\"FS_map_CsV3Sb5.h5\")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The data may be visualised as a 2D plot by slicing the xarray in 2 dimensions keeping the third fixed. In the plot below, the Angle vs Ekin data is plotted for a fixed mirrorX value."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,