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[ESSIMAGING] Update odin test files and test file generating notebook. #675

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Merged
YooSunYoung merged 2 commits into from
Jul 28, 2026
+64 −34
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[ESSIMAGING] Update odin test files and test file generating notebook. #675

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7e67eff
Update mcstas to nexus notebook.
YooSunYoung Jul 24, 2026
399489a
Histogram with lower resolution for docs build.
YooSunYoung Jul 27, 2026
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32 changes: 22 additions & 10 deletions packages/essimaging/docs/odin/odin-data-reduction.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -207,13 +207,25 @@
"metadata": {},
"outputs": [],
"source": [
"sample_wavs.hist().plot(aspect='equal')"
"# ODIN timepix has 4096x4096 pixels by default, which is too many to visualize without `ignore_size=True` option.\n",
"# we will use 256x256 pixels instead for visualization in the documentation.\n",
"vis_resolution = {\"x_pixel_offset\": 256, \"y_pixel_offset\": 256}"
]
},
{
"cell_type": "markdown",
"cell_type": "code",
"execution_count": null,
"id": "19",
"metadata": {},
"outputs": [],
"source": [
"sample_wavs.hist(vis_resolution).plot(aspect='equal')"
]
},
{
"cell_type": "markdown",
"id": "20",
"metadata": {},
"source": [
"The brighter areas around the edges are regions where neutrons did not travel through the sample.\n",
"We thus want to mask those out using masking rules based on the spatial coordinates of the data:"
Expand All @@ -222,7 +234,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "20",
"id": "21",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -235,18 +247,18 @@
{
"cell_type": "code",
"execution_count": null,
"id": "21",
"id": "22",
"metadata": {},
"outputs": [],
"source": [
"masked = wf.compute(CorrectedDetector[SampleRun])\n",
"\n",
"masked.hist().plot(aspect='equal')"
"masked.hist(vis_resolution).plot(aspect='equal')"
]
},
{
"cell_type": "markdown",
"id": "22",
"id": "23",
"metadata": {},
"source": [
"## Normalize to open beam\n",
Expand All @@ -258,7 +270,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "23",
"id": "24",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -274,7 +286,7 @@
},
{
"cell_type": "markdown",
"id": "24",
"id": "25",
"metadata": {},
"source": [
"## Save the final result"
Expand All @@ -283,7 +295,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "25",
"id": "26",
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -312,7 +324,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.11.15"
}
},
"nbformat": 4,
Expand Down
3 changes: 2 additions & 1 deletion packages/essimaging/src/ess/odin/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

import importlib.metadata

from . import beamline
from . import beamline, data
from .workflows import OdinBraggEdgeWorkflow, OdinOrcaWorkflow, OdinWorkflow

try:
Expand All @@ -18,4 +18,5 @@
"OdinOrcaWorkflow",
"OdinWorkflow",
"beamline",
"data",
]
10 changes: 5 additions & 5 deletions packages/essimaging/src/ess/odin/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,12 @@

_registry = make_registry(
'ess/odin',
version="1",
version="2",
files={
"iron_simulation_ob_large.nxs": "md5:a93517ea2aa167d134ca63671f663f99",
"iron_simulation_ob_small.nxs": "md5:7591ed8f0adec2658fb08190bd530b12",
"iron_simulation_sample_large.nxs": "md5:c162b6abeccb51984880d8d5002bae95",
"iron_simulation_sample_small.nxs": "md5:dda6fb30aa88780c5a3d4cef6ea05278",
"iron_simulation_sample_small.nxs": "md5:80c761ae23afac36385d96db186714b5",
"iron_simulation_ob_small.nxs": "md5:0510ec416526169cea1c1a2d96e32877",
"iron_simulation_sample_large.nxs": "md5:df22835fae4d1e4a3707ce2ee52eaf1d",
"iron_simulation_ob_large.nxs": "md5:a3b3d9b75dd2edada0be0d17ee29b905",
"ODIN-wavelength-lookup-table-5m-65m.h5": "md5:44eef2a2e826cec688aeb1b985eb9f9e", # noqa: E501
"ymir_lego_odin.hdf": "md5:8e8708891e2574046b6f372e5e3516a5",
},
Expand Down
8 changes: 4 additions & 4 deletions packages/essimaging/tests/odin/data_reduction_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ def test_can_compute_tof(run_type, wavelength_mode):
def test_publish_reduced_scitiff(output_folder: Path):
wf = _make_workflow("analytical")
wf[MaskingRules] = {}
new_sizes = {'dim_0': 64, 'dim_1': 64}
new_sizes = {'x_pixel_offset': 64, 'y_pixel_offset': 64}
tbins = sc.linspace('tof', 1.3e4, 1.5e5, 257, unit='us')

sample = wf.compute(TofDetector[SampleRun]).drop_coords('detector_number')
Expand All @@ -98,9 +98,9 @@ def test_publish_reduced_scitiff(output_folder: Path):

normed = num / den

to_scitiff = normed.rename_dims(dim_0='y', dim_1='x', tof='t').drop_coords(
'position'
)
to_scitiff = normed.rename_dims(
y_pixel_offset='y', x_pixel_offset='x', tof='t'
).drop_coords('position')

assert "tof" in to_scitiff.coords
assert "Ltotal" in to_scitiff.coords
Expand Down
45 changes: 31 additions & 14 deletions packages/essimaging/tools/mcstas_to_nexus.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -133,11 +133,13 @@
" \"\"\"\n",
" # Find shape of detector panel\n",
" with h5.File(template_nexus_file, \"r\") as f:\n",
" shape = f[f\"{detector_entry_path}/x_pixel_offset\"].shape\n",
" x_shape = f[f\"{detector_entry_path}/x_pixel_offset\"].shape[0]\n",
" y_shape = f[f\"{detector_entry_path}/y_pixel_offset\"].shape[0]\n",
" det_numbers = f[f\"{detector_entry_path}/detector_number\"][()]\n",
"\n",
" da = load_mcstas_simulation_data(mcstas_data_file, nevents=int(nevents))\n",
" binned = da.bin(y=shape[0], x=shape[1]).rename_dims(y=\"dim_0\", x=\"dim_1\")\n",
" binned = da.bin(y=y_shape, x=x_shape).rename_dims(y=\"dim_0\", x=\"dim_1\")\n",
" display(\"Binned data:\", binned)\n",
"\n",
" toa = binned.bins.coords[\"time_of_arrival\"].bins.concat().value\n",
"\n",
Expand Down Expand Up @@ -173,9 +175,10 @@
"\n",
" # Now edit the template file\n",
" print(f\"Writing {outfile} file\")\n",
" shutil.copyfile(template_nexus_file, outfile)\n",
" tmp_output = \"tmp.output.nxs\"\n",
" shutil.copyfile(template_nexus_file, tmp_output)\n",
"\n",
" with h5.File(outfile, \"r+\") as f:\n",
" with h5.File(tmp_output, \"r+\") as f:\n",
"\n",
" # Detector data\n",
" if detector_entry_path is not None:\n",
Expand Down Expand Up @@ -222,7 +225,18 @@
" values=event_index.coords[\"event_time_zero\"]\n",
" .to(unit=monitor_data[\"event_time_zero\"].attrs[\"units\"], copy=False)\n",
" .values.astype(int),\n",
" )"
" )\n",
"\n",
" # Remove user info\n",
" for subgroup in f['entry']:\n",
" if f[f'entry/{subgroup}'].attrs.get('NX_class') == 'NXuser':\n",
" del f[f'entry/{subgroup}']\n",
"\n",
" with h5.File(tmp_output, \"r\") as f:\n",
" with h5.File(outfile, \"w\") as outf:\n",
" for key in f:\n",
" outf.copy(f[key], key)\n",
" outf.attrs.update(f.attrs)"
]
},
{
Expand All @@ -232,20 +246,23 @@
"metadata": {},
"outputs": [],
"source": [
"directory_path = \"/dmsc/scipp/odin/\"\n",
"files = [\n",
" \"small_mcstas_sample_images.h5\",\n",
" \"small_mcstas_ob_images.h5\",\n",
" \"iron_simulation_sample.h5\",\n",
" \"iron_simulation_ob.h5\",\n",
"]\n",
"\n",
"suffixes = {'_small.nxs': 1e6, '_large.nxs': 1e7, '_extra_large.nxs': 1e8}\n",
"\n",
"for file in files:\n",
" mcstas_to_nexus(\n",
" mcstas_data_file=file,\n",
" template_nexus_file=\"977695_00072982.hdf\",\n",
" outfile=file.replace(\".h5\", \".nxs\"),\n",
" nevents=1e6,\n",
" )"
" for suffix, nevents in suffixes.items():\n",
" mcstas_to_nexus(\n",
" mcstas_data_file=directory_path+\"/\"+file,\n",
" template_nexus_file=\"/ess/raw/coda/999999/raw/coda_odin_999999_00013934.hdf\",\n",
" monitor_entry_path=None,\n",
" outfile=file.replace(\".h5\", suffix),\n",
" nevents=nevents,\n",
" )"
]
}
],
Expand All @@ -265,7 +282,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.11.15"
}
},
"nbformat": 4,
Expand Down