Merge pull request #518 from OpenCOMPES/new-tutorials-for-hextof

New tutorials for hextof
OpenCOMPES · Nov 21, 2024 · bd69746 · bd69746
2 parents 42c8d18 + 4d4000b
commit bd69746
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Showing 10 changed files with 1,676 additions and 9 deletions.
diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt
@@ -172,6 +172,7 @@ levelname
 linalg
 linekwds
 linesegkwds
+linestyles
 linewidth
 linspace
 literalinclude
@@ -325,6 +326,7 @@ scandir
 scatt
 scatterkwds
 scicat
+scipy
 SDIAG
 sdir
 segs
@@ -341,6 +343,7 @@ stepsize
 subdir
 subdirs
 subfolders
+suptitle
 symscores
 targcenter
 termorder
@@ -367,6 +370,7 @@ TZCYXS
 tzoffset
 ubid
 UDLD
+ufunc
 unbinned
 uncategorised
 undoc
@@ -375,6 +379,7 @@ varnames
 venv
 verts
 viewcode
+vlines
 vmax
 voxels
 VTOF

diff --git a/docs/scripts/build_flash_parquets.py b/docs/scripts/build_flash_parquets.py
@@ -27,3 +27,25 @@
         system_config=config_file,
         collect_metadata=False,
     )
+
+dataset.get("W110", root_dir="./tutorial")
+data_path = dataset.dir
+
+
+config_override = {
+    "core": {
+        "paths": {
+            "data_raw_dir": data_path,
+            "data_parquet_dir": data_path + "/processed/",
+        },
+    },
+}
+
+runs = ["44498", "44455"]
+for run in runs:
+    sp = SedProcessor(
+        runs=run,
+        config=config_override,
+        system_config=config_file,
+        collect_metadata=False,
+    )
diff --git a/docs/scripts/download_data.py b/docs/scripts/download_data.py
@@ -6,3 +6,4 @@
 dataset.get("Gd_W110", remove_zip=True, root_dir=root_dir)
 dataset.get("TaS2", remove_zip=True, root_dir=root_dir)
 dataset.get("Au_Mica", remove_zip=True, root_dir=root_dir)
+dataset.get("W110", remove_zip=True, root_dir=root_dir)
diff --git a/docs/user_guide/advanced_topics.md b/docs/user_guide/advanced_topics.md
@@ -3,4 +3,6 @@
 ../tutorial/6_binning_with_time-stamped_data
 ../tutorial/7_correcting_orthorhombic_symmetry
 ../tutorial/8_jittering_tutorial
+../tutorial/10_hextof_workflow_trXPS_bam_correction
+../tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB
 ```
diff --git a/docs/workflows/index.md b/docs/workflows/index.md
@@ -8,5 +8,6 @@ myst:
 
 ```{toctree}
 ../tutorial/4_hextof_workflow
-../tutorial/5_sxp_workflow.ipynb
+../tutorial/5_sxp_workflow
+../tutorial/9_hextof_workflow_trXPD
 ```
diff --git a/sed/core/processor.py b/sed/core/processor.py
@@ -1343,14 +1343,15 @@ def calibrate_energy_axis(
             **kwds,
         )
         if verbose:
-            print("Quality of Calibration:")
-            self.ec.view(
-                traces=self.ec.traces_normed,
-                xaxis=self.ec.calibration["axis"],
-                align=True,
-                energy_scale=energy_scale,
-                backend="bokeh",
-            )
+            if self.ec.traces_normed is not None:
+                print("Quality of Calibration:")
+                self.ec.view(
+                    traces=self.ec.traces_normed,
+                    xaxis=self.ec.calibration["axis"],
+                    align=True,
+                    energy_scale=energy_scale,
+                    backend="bokeh",
+                )
             print("E/TOF relationship:")
             self.ec.view(
                 traces=self.ec.calibration["axis"][None, :],

diff --git a/sed/dataset/datasets.json b/sed/dataset/datasets.json
@@ -14,6 +14,14 @@
         ],
         "rearrange_files": true
     },
+    "W110": {
+        "url": "https://zenodo.org/records/12609441/files/single_event_data.zip",
+        "subdirs": [
+            "analysis_data",
+            "calibration_data"
+        ],
+        "rearrange_files": true
+    },
     "TaS2": {
         "url": "https://zenodo.org/records/10160182/files/TaS2.zip",
         "subdirs": [