essreduce 25.4.1__tar.gz → 25.5.0__tar.gz

{essreduce-25.4.1 → essreduce-25.5.0}/.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: d3d4dc7
+_commit: '2247096'
 _src_path: gh:scipp/copier_template
 description: Common data reduction tools for the ESS facility
 max_python: '3.13'

{essreduce-25.4.1/src/essreduce.egg-info → essreduce-25.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: essreduce
-Version: 25.4.1
+Version: 25.5.0
 Summary: Common data reduction tools for the ESS facility
 Author: Scipp contributors
 License: BSD 3-Clause License
@@ -61,7 +61,7 @@ Requires-Dist: numba; extra == "test"
 Requires-Dist: pooch; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: scipy>=1.7.0; extra == "test"
-Requires-Dist: tof>=25.01.2; extra == "test"
+Requires-Dist: tof>=25.05.0; extra == "test"
 Dynamic: license-file
 
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)

{essreduce-25.4.1 → essreduce-25.5.0}/docs/conf.py

@@ -267,4 +267,7 @@ doctest_default_flags = (
 linkcheck_ignore = [
     # Specific lines in Github blobs cannot be found by linkcheck.
     r'https?://github\.com/.*?/blob/[a-f0-9]+/.+?#',
+    # Linkcheck seems to be denied access by some DOI resolvers.
+    # Since DOIs are supposed to be permanent, we don't need to check them.'
+    r'https://doi\.org/',
 ]

{essreduce-25.4.1 → essreduce-25.5.0}/docs/user-guide/tof/dream.ipynb

@@ -23,8 +23,8 @@
    "source": [
     "import plopp as pp\n",
     "import scipp as sc\n",
-    "import sciline as sl\n",
     "from scippneutron.chopper import DiskChopper\n",
+    "from ess.reduce.nexus.types import DetectorData, SampleRun\n",
     "from ess.reduce import time_of_flight"
    ]
   },
@@ -305,17 +305,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow = sl.Pipeline(\n",
-    "    time_of_flight.providers(), params=time_of_flight.default_parameters()\n",
-    ")\n",
-    "workflow[time_of_flight.RawData] = raw_data\n",
-    "workflow[time_of_flight.Ltotal] = Ltotal\n",
-    "workflow[time_of_flight.LtotalRange] = (\n",
+    "wf = time_of_flight.GenericTofWorkflow()\n",
+    "wf[DetectorData[SampleRun]] = raw_data\n",
+    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
+    "wf[time_of_flight.LtotalRange] = (\n",
     "    sc.scalar(75.5, unit=\"m\"),\n",
     "    sc.scalar(78.0, unit=\"m\"),\n",
     ")\n",
     "\n",
-    "workflow.visualize(time_of_flight.TofData)"
+    "wf.visualize(time_of_flight.DetectorTofData[SampleRun])"
    ]
   },
   {
@@ -335,7 +333,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
+    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
     "    choppers=disk_choppers, source_position=source_position, neutrons=2_000_000\n",
     ")"
    ]
@@ -363,7 +361,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim = workflow.compute(time_of_flight.SimulationResults)\n",
+    "sim = wf.compute(time_of_flight.SimulationResults)\n",
     "\n",
     "\n",
     "def to_event_time_offset(sim):\n",
@@ -402,17 +400,35 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = workflow.compute(time_of_flight.TimeOfFlightLookupTable).squeeze()\n",
+    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
     "\n",
     "# Overlay mean on the figure above\n",
     "table[\"distance\", 13].plot(ax=fig2.ax, color=\"C1\", ls=\"-\", marker=None)"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "27",
    "metadata": {},
+   "source": [
+    "The full table covers a range of distances, and looks like"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "28",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "table.plot()"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "29",
+   "metadata": {},
    "source": [
     "### Computing a time-of-flight coordinate\n",
     "\n",
@@ -422,17 +438,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
-    "tofs = workflow.compute(time_of_flight.TofData)\n",
+    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
     "tofs"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "29",
+   "id": "31",
    "metadata": {},
    "source": [
     "Histogramming the data for a plot should show a profile with 6 bumps that correspond to the frames:"
@@ -441,7 +457,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -450,7 +466,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "31",
+   "id": "33",
    "metadata": {},
    "source": [
     "### Converting to wavelength\n",
@@ -461,7 +477,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -481,7 +497,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "33",
+   "id": "35",
    "metadata": {},
    "source": [
     "### Comparing to the ground truth\n",
@@ -493,7 +509,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -510,7 +526,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35",
+   "id": "37",
    "metadata": {},
    "source": [
     "## Multiple detector pixels\n",
@@ -526,7 +542,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "38",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -544,7 +560,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "37",
+   "id": "39",
    "metadata": {},
    "source": [
     "Our raw data has now a `detector_number` dimension of length 2.\n",
@@ -555,7 +571,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38",
+   "id": "40",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -570,7 +586,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "39",
+   "id": "41",
    "metadata": {},
    "source": [
     "Computing time-of-flight is done in the same way as above.\n",
@@ -580,16 +596,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "42",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Update workflow\n",
-    "workflow[time_of_flight.RawData] = raw_data\n",
-    "workflow[time_of_flight.Ltotal] = Ltotal\n",
+    "wf[DetectorData[SampleRun]] = raw_data\n",
+    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
     "\n",
     "# Compute tofs and wavelengths\n",
-    "tofs = workflow.compute(time_of_flight.TofData)\n",
+    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
     "wav_wfm = tofs.transform_coords(\"wavelength\", graph=graph)\n",
     "\n",
     "# Compare in plot\n",
@@ -614,7 +630,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "41",
+   "id": "43",
    "metadata": {},
    "source": [
     "## Handling time overlap between subframes\n",
@@ -634,7 +650,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "44",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -665,7 +681,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "43",
+   "id": "45",
    "metadata": {},
    "source": [
     "We can now see that there is no longer a gap between the two frames at the center of each pulse (green region).\n",
@@ -677,18 +693,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44",
+   "id": "46",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Update workflow\n",
-    "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
+    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
     "    choppers=disk_choppers, source_position=source_position, neutrons=2_000_000\n",
     ")\n",
-    "workflow[time_of_flight.RawData] = ess_beamline.get_monitor(\"detector\")[0]\n",
-    "workflow[time_of_flight.Ltotal] = Ltotal\n",
+    "wf[DetectorData[SampleRun]] = ess_beamline.get_monitor(\"detector\")[0]\n",
+    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
     "\n",
-    "sim = workflow.compute(time_of_flight.SimulationResults)\n",
+    "sim = wf.compute(time_of_flight.SimulationResults)\n",
     "\n",
     "events = to_event_time_offset(sim)\n",
     "events.hist(wavelength=300, event_time_offset=300).plot(norm=\"log\")"
@@ -696,7 +712,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "45",
+   "id": "47",
    "metadata": {},
    "source": [
     "The data in the lookup table contains both the mean time-of-flight for each distance and time-of-arrival bin,\n",
@@ -713,17 +729,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "48",
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = workflow.compute(time_of_flight.TimeOfFlightLookupTable).squeeze()\n",
+    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
     "table.plot() / (sc.stddevs(table) / sc.values(table)).plot(norm=\"log\")"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "47",
+   "id": "49",
    "metadata": {},
    "source": [
     "The workflow has a parameter which is used to mask out regions where the standard deviation is above a certain threshold.\n",
@@ -737,18 +753,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48",
+   "id": "50",
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow[time_of_flight.LookupTableRelativeErrorThreshold] = 0.01\n",
+    "wf[time_of_flight.LookupTableRelativeErrorThreshold] = 0.01\n",
     "\n",
-    "workflow.compute(time_of_flight.TimeOfFlightLookupTable).squeeze().plot()"
+    "wf.compute(time_of_flight.TimeOfFlightLookupTable).plot()"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "49",
+   "id": "51",
    "metadata": {},
    "source": [
     "We can now see that the central region is masked out.\n",
@@ -763,12 +779,12 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "50",
+   "id": "52",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Compute time-of-flight\n",
-    "tofs = workflow.compute(time_of_flight.TofData)\n",
+    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
     "# Compute wavelength\n",
     "wav_wfm = tofs.transform_coords(\"wavelength\", graph=graph)\n",
     "\n",

{essreduce-25.4.1 → essreduce-25.5.0}/docs/user-guide/tof/frame-unwrapping.ipynb

@@ -31,8 +31,8 @@
    "source": [
     "import plopp as pp\n",
     "import scipp as sc\n",
-    "import sciline as sl\n",
     "from scippneutron.chopper import DiskChopper\n",
+    "from ess.reduce.nexus.types import DetectorData, SampleRun\n",
     "from ess.reduce import time_of_flight\n",
     "import tof\n",
     "\n",
@@ -159,14 +159,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow = sl.Pipeline(\n",
-    "    time_of_flight.providers(), params=time_of_flight.default_parameters()\n",
-    ")\n",
+    "wf = time_of_flight.GenericTofWorkflow()\n",
     "\n",
-    "workflow[time_of_flight.RawData] = nxevent_data\n",
-    "workflow[time_of_flight.Ltotal] = nxevent_data.coords[\"Ltotal\"]\n",
-    "workflow[time_of_flight.LtotalRange] = detectors[0].distance, detectors[-1].distance\n",
-    "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
+    "wf[DetectorData[SampleRun]] = nxevent_data\n",
+    "wf[time_of_flight.DetectorLtotal[SampleRun]] = nxevent_data.coords[\"Ltotal\"]\n",
+    "wf[time_of_flight.LtotalRange] = detectors[0].distance, detectors[-1].distance\n",
+    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
     "    choppers={\n",
     "        \"chopper\": DiskChopper(\n",
     "            frequency=-chopper.frequency,\n",
@@ -184,7 +182,7 @@
     "    source_position=sc.vector([0, 0, 0], unit=chopper.distance.unit),\n",
     ")\n",
     "\n",
-    "workflow.visualize(time_of_flight.TofData)"
+    "wf.visualize(time_of_flight.DetectorTofData[SampleRun])"
    ]
   },
   {
@@ -225,7 +223,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = workflow.compute(time_of_flight.TimeOfFlightLookupTable).squeeze()\n",
+    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
     "table.plot()"
    ]
   },
@@ -246,7 +244,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tofs = workflow.compute(time_of_flight.TofData)\n",
+    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
     "\n",
     "tof_hist = tofs.hist(tof=sc.scalar(500.0, unit=\"us\"))\n",
     "pp.plot({det.name: tof_hist[\"detector_number\", i] for i, det in enumerate(detectors)})"
@@ -370,17 +368,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow = sl.Pipeline(\n",
-    "    time_of_flight.providers(), params=time_of_flight.default_parameters()\n",
-    ")\n",
+    "wf = time_of_flight.GenericTofWorkflow()\n",
     "\n",
     "nxevent_data = results.to_nxevent_data()\n",
     "\n",
-    "workflow[time_of_flight.PulseStride] = 2\n",
-    "workflow[time_of_flight.RawData] = nxevent_data\n",
-    "workflow[time_of_flight.Ltotal] = nxevent_data.coords[\"Ltotal\"]\n",
-    "workflow[time_of_flight.LtotalRange] = detectors[0].distance, detectors[-1].distance\n",
-    "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
+    "wf[time_of_flight.PulseStride] = 2\n",
+    "wf[DetectorData[SampleRun]] = nxevent_data\n",
+    "wf[time_of_flight.DetectorLtotal[SampleRun]] = nxevent_data.coords[\"Ltotal\"]\n",
+    "wf[time_of_flight.LtotalRange] = detectors[0].distance, detectors[-1].distance\n",
+    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
     "    choppers={\n",
     "        ch.name: DiskChopper(\n",
     "            frequency=-ch.frequency,\n",
@@ -399,8 +395,8 @@
     "    source_position=sc.vector([0, 0, 0], unit=chopper.distance.unit),\n",
     ")\n",
     "\n",
-    "workflow[time_of_flight.DistanceResolution] = sc.scalar(0.5, unit=\"m\")\n",
-    "workflow[time_of_flight.LookupTableRelativeErrorThreshold] = 0.1"
+    "wf[time_of_flight.DistanceResolution] = sc.scalar(0.5, unit=\"m\")\n",
+    "wf[time_of_flight.LookupTableRelativeErrorThreshold] = 0.1"
    ]
   },
   {
@@ -418,9 +414,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = workflow.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
     "\n",
-    "table[\"pulse\", 0].plot(title=\"Pulse-0\") + table[\"pulse\", 1].plot(title=\"Pulse-1\")"
+    "table.plot()"
    ]
   },
   {
@@ -438,7 +434,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tofs = workflow.compute(time_of_flight.TofData)\n",
+    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
     "\n",
     "tof_hist = tofs.hist(tof=sc.scalar(500.0, unit=\"us\"))\n",
     "pp.plot({det.name: tof_hist[\"detector_number\", i] for i, det in enumerate(detectors)})"

{essreduce-25.4.1 → essreduce-25.5.0}/docs/user-guide/tof/wfm.ipynb

@@ -24,8 +24,8 @@
     "import numpy as np\n",
     "import plopp as pp\n",
     "import scipp as sc\n",
-    "import sciline as sl\n",
     "from scippneutron.chopper import DiskChopper\n",
+    "from ess.reduce.nexus.types import DetectorData, SampleRun\n",
     "from ess.reduce import time_of_flight"
    ]
   },
@@ -326,15 +326,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow = sl.Pipeline(\n",
-    "    time_of_flight.providers(), params=time_of_flight.default_parameters()\n",
-    ")\n",
-    "workflow[time_of_flight.RawData] = raw_data\n",
-    "workflow[time_of_flight.Ltotal] = Ltotal\n",
-    "workflow[time_of_flight.LtotalRange] = Ltotal, Ltotal\n",
-    "workflow[time_of_flight.LookupTableRelativeErrorThreshold] = 0.1\n",
+    "wf = time_of_flight.GenericTofWorkflow()\n",
+    "wf[DetectorData[SampleRun]] = raw_data\n",
+    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
+    "wf[time_of_flight.LtotalRange] = Ltotal, Ltotal\n",
+    "wf[time_of_flight.LookupTableRelativeErrorThreshold] = 0.1\n",
     "\n",
-    "workflow.visualize(time_of_flight.TofData)"
+    "wf.visualize(time_of_flight.DetectorTofData[SampleRun])"
    ]
   },
   {
@@ -354,7 +352,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
+    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
     "    choppers=disk_choppers,\n",
     "    source_position=source_position,\n",
     "    neutrons=3_000_000\n",
@@ -384,7 +382,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim = workflow.compute(time_of_flight.SimulationResults)\n",
+    "sim = wf.compute(time_of_flight.SimulationResults)\n",
     "# Compute time-of-arrival at the detector\n",
     "tarrival = sim.time_of_arrival + ((Ltotal - sim.distance) / sim.speed).to(unit=\"us\")\n",
     "# Compute time-of-flight at the detector\n",
@@ -416,7 +414,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = workflow.compute(time_of_flight.TimeOfFlightLookupTable).squeeze()\n",
+    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
     "\n",
     "# Overlay mean on the figure above\n",
     "table[\"distance\", 1].plot(ax=fig2.ax, color=\"C1\", ls=\"-\", marker=None)\n",
@@ -450,7 +448,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tofs = workflow.compute(time_of_flight.TofData)\n",
+    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
     "tofs"
    ]
   },

{essreduce-25.4.1 → essreduce-25.5.0}/pyproject.toml

@@ -46,7 +46,7 @@ test = [
     "pooch",
     "pytest",
     "scipy>=1.7.0",
-    "tof>=25.01.2",
+    "tof>=25.05.0",
 ]
 
 [project.scripts]

{essreduce-25.4.1 → essreduce-25.5.0}/requirements/base.txt

@@ -1,13 +1,13 @@
 # SHA1:082d6bf55d8a06cdc1dd3a0a78dd31c318c26424
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 annotated-types==0.7.0
     # via pydantic
-contourpy==1.3.1
+contourpy==1.3.2
     # via matplotlib
 cyclebane==24.10.0
     # via sciline
@@ -35,30 +35,29 @@ matplotlib==3.10.1
     # via
     #   mpltoolbox
     #   plopp
-mpltoolbox==24.5.1
+mpltoolbox==25.4.0
     # via scippneutron
 networkx==3.4.2
     # via cyclebane
-numpy==2.2.4
+numpy==2.2.5
     # via
     #   contourpy
     #   h5py
     #   matplotlib
-    #   mpltoolbox
     #   scipp
     #   scippneutron
     #   scipy
-packaging==24.2
+packaging==25.0
     # via
     #   lazy-loader
     #   matplotlib
-pillow==11.1.0
+pillow==11.2.1
     # via matplotlib
-plopp==25.3.0
+plopp==25.4.1
     # via scippneutron
-pydantic==2.11.3
+pydantic==2.11.4
     # via scippneutron
-pydantic-core==2.33.1
+pydantic-core==2.33.2
     # via pydantic
 pyparsing==3.2.3
     # via matplotlib
@@ -69,7 +68,7 @@ python-dateutil==2.9.0.post0
     #   scippnexus
 sciline==25.4.1
     # via -r base.in
-scipp==25.4.0
+scipp==25.5.0
     # via
     #   -r base.in
     #   scippneutron
@@ -86,7 +85,7 @@ scipy==1.15.2
     #   scippnexus
 six==1.17.0
     # via python-dateutil
-typing-extensions==4.13.1
+typing-extensions==4.13.2
     # via
     #   pydantic
     #   pydantic-core

{essreduce-25.4.1 → essreduce-25.5.0}/requirements/basetest.in

@@ -12,4 +12,4 @@ numba
 pooch
 pytest
 scipy>=1.7.0
-tof>=25.01.2
+tof>=25.05.0