Merge pull request #566 from OpenCOMPES/ph-peak-for-sector-alignment

rettigl · web-flow · commit 5869eca7c422 · 2025-04-16T23:12:41.000+02:00
Photon peak tutorial for sector alignment
diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt
@@ -127,6 +127,7 @@ figsize
 figsz
 filenotfound
 fixedvertex
+FLACPUPGLASER
 flatidx
 fluence
 fontsize
@@ -158,6 +159,7 @@ imkwds
 imread
 imshow
 imwrite
+incoupl
 incrementation
 inequivalent
 interp
@@ -300,6 +302,7 @@ printfuncs
 psutil
 ptargs
 pullrequest
+PULSEENERGY
 pval
 pyarrow
 pydantic
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -64,5 +64,6 @@ jobs:
           commit-message: Update benchmark targets
           title: "Update benchmark targets"
           branch: "update_benchmark_targets"
+          base: ${{ github.head_ref }}
           body: |
             Generated new benchmark targets.
diff --git a/docs/scripts/build_flash_parquets.py b/docs/scripts/build_flash_parquets.py
@@ -1,5 +1,6 @@
 import os
 from importlib.util import find_spec
+from typing import Any
 
 from sed import SedProcessor
 from sed.dataset import dataset
@@ -12,7 +13,7 @@
 data_path = dataset.dir
 
 
-config_override = {
+config_override: dict[str, Any] = {
     "core": {
         "paths": {
             "raw": data_path,
@@ -51,3 +52,66 @@
         system_config=config_file,
         collect_metadata=False,
     )
+
+dataset.get("Photon_peak", root_dir="./tutorial")
+data_path = dataset.dir
+
+config_override = {
+    "core": {
+        "paths": {
+            "raw": data_path,
+            "processed": data_path + "/processed/",
+        },
+    },
+    "dataframe": {
+        "ubid_offset": 0,
+        "channels": {
+            "timeStamp": {
+                "index_key": "/zraw/TIMINGINFO/TIME1.BUNCH_FIRST_INDEX.1/dGroup/index",
+                "dataset_key": "/zraw/TIMINGINFO/TIME1.BUNCH_FIRST_INDEX.1/dGroup/time",
+            },
+            "pulseId": {
+                "index_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/index",
+                "dataset_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/value",
+            },
+            "dldPosX": {
+                "index_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/index",
+                "dataset_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/value",
+            },
+            "dldPosY": {
+                "index_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/index",
+                "dataset_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/value",
+            },
+            "dldTimeSteps": {
+                "index_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/index",
+                "dataset_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/value",
+            },
+            "dldAux": {
+                "index_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/index",
+                "dataset_key": "/zraw/FLASH.FEL/HEXTOF.DAQ/DLD1/dGroup/value",
+            },
+            "bam": {
+                "index_key": "/zraw/FLASH.SDIAG/BAM.DAQ/4DBC3.HIGH_CHARGE_ARRIVAL_TIME/dGroup/index",
+                "dataset_key": "/zraw/FLASH.SDIAG/BAM.DAQ/4DBC3.HIGH_CHARGE_ARRIVAL_TIME/dGroup/value",
+            },
+            "delayStage": {
+                "index_key": "/zraw/FLASH.SYNC/LASER.LOCK.EXP/FLASH1.MOD1.PG.OSC/FMC0.MD22.1.ENCODER_POSITION.RD/dGroup/index",
+                "dataset_key": "/zraw/FLASH.SYNC/LASER.LOCK.EXP/FLASH1.MOD1.PG.OSC/FMC0.MD22.1.ENCODER_POSITION.RD/dGroup/value",
+            },
+            "opticalDiode": {
+                "format": "per_train",
+                "index_key": "/uncategorised/FLASH.LASER/FLACPUPGLASER1.PULSEENERGY/PG2_incoupl/PULSEENERGY.MEAN/index",
+                "dataset_key": "/uncategorised/FLASH.LASER/FLACPUPGLASER1.PULSEENERGY/PG2_incoupl/PULSEENERGY.MEAN/value",
+            },
+        },
+    },
+}
+
+runs = ["40887"]
+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
@@ -7,3 +7,4 @@
 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)
+dataset.get("Photon_peak", remove_zip=True, root_dir=root_dir)
diff --git a/docs/workflows/index.md b/docs/workflows/index.md
@@ -11,4 +11,5 @@ myst:
 ../tutorial/5_sxp_workflow
 ../tutorial/9_hextof_workflow_trXPD
 ../tutorial/12_momentum_correction_of_binned_data
+../tutorial/13_hextof_dld_sector_alignment_with_photon_peak
 ```
diff --git a/src/sed/config/datasets.json b/src/sed/config/datasets.json
@@ -22,6 +22,13 @@
         ],
         "rearrange_files": true
     },
+    "Photon_peak": {
+        "url": "https://zenodo.org/records/15011781/files/single_event_data.zip",
+        "subdirs": [
+            "analysis_data"
+        ],
+        "rearrange_files": true
+    },
     "TaS2": {
         "url": "https://zenodo.org/records/10160182/files/TaS2.zip",
         "subdirs": [
diff --git a/src/sed/config/flash_example_config.yaml b/src/sed/config/flash_example_config.yaml
@@ -51,7 +51,7 @@ dataframe:
   forward_fill_iterations: 2                      # Number of iterations to fill the pulseId forward
   split_sector_id_from_dld_time: True             # Remove reserved bits for dldSectorID from dldTimeSteps column
   sector_id_reserved_bits: 3                      # Bits reserved for dldSectorID in the dldTimeSteps column
-  sector_delays: [0., 0., 0., 0., 0., 0., 0., 0.] # Sector delays
+  sector_delays: [0., 0., 0., 0., 0., 0., 0., 0.] # Sector delays in 'step' units applied to dldTimeSteps column
 
   # Time and binning settings
   tof_binwidth: 2.0576131995767355E-11            # Base time-of-flight bin width in seconds
@@ -177,10 +177,11 @@ dataframe:
           slice: 15
 
     # ADC containing the pulser sign (1: value approx. 35000, 0: 33000)
-    pulserSignAdc:
-      format: per_pulse
-      index_key: "/FL1/Experiment/PG/SIS8300 100MHz ADC/CH6/TD/index"
-      dataset_key: "/FL1/Experiment/PG/SIS8300 100MHz ADC/CH6/TD/value"
+    # enable if needed
+    # pulserSignAdc:
+    #   format: per_pulse
+    #   index_key: "/FL1/Experiment/PG/SIS8300 100MHz ADC/CH6/TD/index"
+    #   dataset_key: "/FL1/Experiment/PG/SIS8300 100MHz ADC/CH6/TD/value"
 
     # the energy of the monochromatized beam. This is a quasi-static value.
     # there is a better channel which still needs implementation.
diff --git a/tutorial/12_momentum_correction_of_binned_data.ipynb b/tutorial/12_momentum_correction_of_binned_data.ipynb
@@ -194,7 +194,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig,ax = plt.subplots(1,2,figsize=(8,3), layout='constrained')\n",
+    "fig,ax = plt.subplots(1,2,figsize=(6,2.5), layout='constrained')\n",
     "binned_data.isel(t=40).T.plot(ax=ax[0], cmap=\"terrain_r\")\n",
     "ax[0].set_title('corrected data')\n",
     "difference_data.isel(t=40).T.plot(ax=ax[1])\n",
@@ -212,9 +212,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "sed_kernel_v1",
+   "display_name": ".venv",
    "language": "python",
-   "name": "sed_kernel_v1"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
diff --git a/tutorial/13_hextof_dld_sector_alignment_with_photon_peak.ipynb b/tutorial/13_hextof_dld_sector_alignment_with_photon_peak.ipynb
