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fix: dont reread files in sans2d workflow #58

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Jan 30, 2024
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fix: dont reread files in sans2d workflow #58

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119 changes: 49 additions & 70 deletions docs/examples/sans2d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,32 @@
"id": "c21564a8-e742-4183-9edc-2c70c51d5863",
"metadata": {},
"source": [
"## Define reduction parameters\n",
"## Create pipeline using Sciline\n",
"\n",
"We use all providers available in `esssans` as well as the `sans2d`-specific providers, which include I/O and mask setup specific to the [Sans2d](https://www.isis.stfc.ac.uk/Pages/sans2d.aspx) instrument:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "025fca0b-68a7-4d6e-a82a-86713cc3fca7",
"metadata": {},
"outputs": [],
"source": [
"pipeline = sciline.Pipeline(\n",
" sans.providers + sans.sans2d.providers,\n",
" params=sans.sans2d.default_parameters,\n",
")"
]
},
{
"cell_type": "markdown",
"id": "3da2d397-6206-4ed1-a98f-11b3aaf7e5b0",
"metadata": {},
"source": [
"# Define reduction parameters\n",
"\n",
"We define a dictionary containing the reduction parameters, with keys and types given by aliases or types defined in `esssans.types`:"
"We define the reduction parameters, with keys and types given by aliases or types defined in `esssans.types`:"
]
},
{
Expand All @@ -50,55 +73,32 @@
},
"outputs": [],
"source": [
"params = sans.sans2d.default_parameters.copy()\n",
"\n",
"params[FileList[BackgroundRun]] = ['SANS2D00063159.hdf5']\n",
"params[FileList[TransmissionRun[BackgroundRun]]] = params[FileList[BackgroundRun]]\n",
"params[FileList[SampleRun]] = ['SANS2D00063114.hdf5']\n",
"params[FileList[TransmissionRun[SampleRun]]] = params[FileList[SampleRun]]\n",
"params[FileList[EmptyBeamRun]] = ['SANS2D00063091.hdf5']\n",
"params[DirectBeamFilename] = 'DIRECT_SANS2D_REAR_34327_4m_8mm_16Feb16.hdf5'\n",
"params[OutFilename] = 'reduced.nxs'\n",
"pipeline[FileList[BackgroundRun]] = ['SANS2D00063159.hdf5']\n",
"pipeline.insert(sans.transmission_from_background_run)\n",
"pipeline[FileList[SampleRun]] = ['SANS2D00063114.hdf5']\n",
"pipeline.insert(sans.transmission_from_sample_run)\n",
"pipeline[FileList[EmptyBeamRun]] = ['SANS2D00063091.hdf5']\n",
"pipeline[DirectBeamFilename] = 'DIRECT_SANS2D_REAR_34327_4m_8mm_16Feb16.hdf5'\n",
"pipeline[OutFilename] = 'reduced.nxs'\n",
"\n",
"params[WavelengthBins] = sc.linspace(\n",
"pipeline[WavelengthBins] = sc.linspace(\n",
" 'wavelength', start=2.0, stop=16.0, num=141, unit='angstrom'\n",
")\n",
"\n",
"params[sans.sans2d.LowCountThreshold] = sc.scalar(100, unit='counts')\n",
"pipeline[sans.sans2d.LowCountThreshold] = sc.scalar(100, unit='counts')\n",
"\n",
"mask_interval = sc.array(dims=['wavelength'], values=[2.21, 2.59], unit='angstrom')\n",
"params[WavelengthMask] = sc.DataArray(\n",
"pipeline[WavelengthMask] = sc.DataArray(\n",
" sc.array(dims=['wavelength'], values=[True]),\n",
" coords={'wavelength': mask_interval},\n",
")\n",
"\n",
"params[QBins] = sc.linspace(dim='Q', start=0.01, stop=0.6, num=141, unit='1/angstrom')\n",
"params[NonBackgroundWavelengthRange] = sc.array(\n",
"pipeline[QBins] = sc.linspace(dim='Q', start=0.01, stop=0.6, num=141, unit='1/angstrom')\n",
"pipeline[NonBackgroundWavelengthRange] = sc.array(\n",
" dims=['wavelength'], values=[0.7, 17.1], unit='angstrom'\n",
")\n",
"params[CorrectForGravity] = True\n",
"params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound"
]
},
{
"cell_type": "markdown",
"id": "f2c3b542",
"metadata": {},
"source": [
"## Create pipeline using Sciline\n",
"\n",
"We use all providers available in `esssans` as well as the `sans2d`-specific providers, which include I/O and mask setup specific to the [Sans2d](https://www.isis.stfc.ac.uk/Pages/sans2d.aspx) instrument:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "17a01c27",
"metadata": {},
"outputs": [],
"source": [
"providers = sans.providers + sans.sans2d.providers\n",
"pipeline = sciline.Pipeline(providers, params=params)"
"pipeline[CorrectForGravity] = True\n",
"pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound"
]
},
{
Expand Down Expand Up @@ -178,9 +178,10 @@
"metadata": {},
"outputs": [],
"source": [
"params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
"pipeline_drop = sciline.Pipeline(providers, params=params)\n",
"result_drop = pipeline_drop.compute(BackgroundSubtractedIofQ)\n",
"pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
"result_drop = pipeline.compute(BackgroundSubtractedIofQ)\n",
"# Reset the UnsertaintyBroadcastMode to the old value\n",
"pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
"sc.DataGroup(upper_bound=result, dropped=result_drop).plot(norm='log')"
]
},
Expand Down Expand Up @@ -288,10 +289,8 @@
" },\n",
" index=[Mode('upper_bound'), Mode('drop')],\n",
")\n",
"del params[UncertaintyBroadcastMode]\n",
"pl = sciline.Pipeline(providers, params=params)\n",
"pl.set_param_table(param_table)\n",
"results = pl.compute(sciline.Series[Mode, BackgroundSubtractedIofQ])\n",
"pipeline.set_param_table(param_table)\n",
"results = pipeline.compute(sciline.Series[Mode, BackgroundSubtractedIofQ])\n",
"sc.DataGroup(results).plot(norm='log')"
]
},
Expand All @@ -317,40 +316,19 @@
"outputs": [],
"source": [
"band = np.linspace(2.0, 16.0, num=11)\n",
"params[WavelengthBands] = sc.array(\n",
"pipeline[WavelengthBands] = sc.array(\n",
" dims=['band', 'wavelength'],\n",
" values=np.vstack([band[:-1], band[1:]]).T,\n",
" unit='angstrom',\n",
")"
]
},
{
"cell_type": "markdown",
"id": "84bce96e-e1f2-4a77-80ac-a926d3797020",
"metadata": {},
"source": [
"We then need to re-build the pipeline with the updated parameters"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b512a676-4875-47bc-9ac9-afcbf45c631a",
"metadata": {},
"outputs": [],
"source": [
"# Re-add the deleted param\n",
"params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
"\n",
"pipeline = sciline.Pipeline(providers, params=params)"
]
},
{
"cell_type": "markdown",
"id": "cc3cac02-2cb4-4da5-a83d-8e6fb3d2c929",
"metadata": {},
"source": [
"and compute the result"
"Compute the result:"
]
},
{
Expand Down Expand Up @@ -398,7 +376,8 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3"
"pygments_lexer": "ipython3",
"version": "3.10.13"
}
},
"nbformat": 4,
Expand Down
7 changes: 4 additions & 3 deletions docs/examples/zoom.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -129,8 +129,8 @@
"source": [
"providers = sans.providers + sans.isis.providers\n",
"providers = providers + (\n",
" sans.isis.transmission_from_background_run,\n",
" sans.isis.transmission_from_sample_run,\n",
" sans.transmission_from_background_run,\n",
" sans.transmission_from_sample_run,\n",
")\n",
"pipeline = sciline.Pipeline(providers, params=params)\n",
"pipeline.set_param_table(masks)"
Expand Down Expand Up @@ -269,7 +269,8 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3"
"pygments_lexer": "ipython3",
"version": "3.10.13"
}
},
"nbformat": 4,
Expand Down
3 changes: 3 additions & 0 deletions src/esssans/__init__.py
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Expand Up @@ -19,6 +19,7 @@
normalization,
sans2d,
)
from .common import transmission_from_background_run, transmission_from_sample_run
from .direct_beam import direct_beam

providers = (
Expand Down Expand Up @@ -50,4 +51,6 @@
'normalization',
'providers',
'sans2d',
'transmission_from_sample_run',
'transmission_from_background_run',
]
20 changes: 20 additions & 0 deletions src/esssans/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@
import scipp as sc
from scipp.constants import g

from .types import BackgroundRun, LoadedFileContents, SampleRun, TransmissionRun


def gravity_vector() -> sc.Variable:
"""
Expand Down Expand Up @@ -80,3 +82,21 @@ def mask_range(
else:
out.masks[name] = mask_values
return out


def transmission_from_sample_run(
data: LoadedFileContents[SampleRun],
) -> LoadedFileContents[TransmissionRun[SampleRun]]:
"""
Use transmission from a sample run, instead of dedicated run.
"""
return LoadedFileContents[TransmissionRun[SampleRun]](data)


def transmission_from_background_run(
data: LoadedFileContents[BackgroundRun],
) -> LoadedFileContents[TransmissionRun[BackgroundRun]]:
"""
Use transmission from a background run, instead of dedicated run.
"""
return LoadedFileContents[TransmissionRun[BackgroundRun]](data)
3 changes: 0 additions & 3 deletions src/esssans/isis/__init__.py
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Expand Up @@ -9,7 +9,6 @@
sans2d_tube_detector_pixel_shape,
)
from . import io, masking
from .common import transmission_from_background_run, transmission_from_sample_run
from .io import CalibrationFilename, DataFolder, Filename, PixelMaskFilename
from .masking import PixelMask
from .visualization import plot_flat_detector_xy
Expand Down Expand Up @@ -39,7 +38,5 @@
'PixelMask',
'PixelMaskFilename',
'providers',
'transmission_from_background_run',
'transmission_from_sample_run',
'plot_flat_detector_xy',
]
24 changes: 0 additions & 24 deletions src/esssans/isis/common.py
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