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New tutorials for hextof #518

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merged 4 commits into from
Nov 21, 2024
Merged

New tutorials for hextof #518

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4556c83
add review suggestions
rettigl Nov 21, 2024
4d4000b
integrate into docs
rettigl Nov 21, 2024
643a615
Two new tutorials for HEXTOF at FLASH as an example of trXPS and trXP…
kutnyakhov Aug 12, 2024
fbbf129
fix headings
rettigl Nov 20, 2024
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5 changes: 5 additions & 0 deletions .cspell/custom-dictionary.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,7 @@ levelname
linalg
linekwds
linesegkwds
linestyles
linewidth
linspace
literalinclude
Expand Down Expand Up @@ -325,6 +326,7 @@ scandir
scatt
scatterkwds
scicat
scipy
SDIAG
sdir
segs
Expand All @@ -341,6 +343,7 @@ stepsize
subdir
subdirs
subfolders
suptitle
symscores
targcenter
termorder
Expand All @@ -367,6 +370,7 @@ TZCYXS
tzoffset
ubid
UDLD
ufunc
unbinned
uncategorised
undoc
Expand All @@ -375,6 +379,7 @@ varnames
venv
verts
viewcode
vlines
vmax
voxels
VTOF
Expand Down
22 changes: 22 additions & 0 deletions docs/scripts/build_flash_parquets.py
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Expand Up @@ -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,
)
1 change: 1 addition & 0 deletions docs/scripts/download_data.py
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Expand Up @@ -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)
2 changes: 2 additions & 0 deletions docs/user_guide/advanced_topics.md
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Expand Up @@ -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
```
3 changes: 2 additions & 1 deletion docs/workflows/index.md
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Expand Up @@ -8,5 +8,6 @@ myst:

```{toctree}
../tutorial/4_hextof_workflow
../tutorial/5_sxp_workflow.ipynb
../tutorial/5_sxp_workflow
../tutorial/9_hextof_workflow_trXPD
```
17 changes: 9 additions & 8 deletions sed/core/processor.py
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Expand Up @@ -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, :],
Expand Down
8 changes: 8 additions & 0 deletions sed/dataset/datasets.json
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Expand Up @@ -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": [
Expand Down
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