Essreduce + Essimaging: tofectomy

packages/essimaging/docs/api-reference/index.md

@@ -10,7 +10,6 @@
    :template: module-template.rst
    :recursive:
 
-   conversion
    data
    tools
    types

packages/essimaging/docs/odin/index.md

@@ -6,5 +6,5 @@ maxdepth: 1
 ---
 
 odin-data-reduction
-odin-make-tof-lookup-table
+odin-make-wavelength-lookup-table
 ```

packages/essimaging/docs/odin/odin-data-reduction.ipynb

@@ -20,7 +20,7 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "from ess.reduce import time_of_flight\n",
+    "from ess.reduce import unwrap\n",
     "from ess import odin\n",
     "import ess.odin.data  # noqa: F401\n",
     "from ess.imaging.types import *"
@@ -45,7 +45,7 @@
     "\n",
     "wf[Filename[SampleRun]] = odin.data.iron_simulation_sample_small()\n",
     "wf[NeXusDetectorName] = \"event_mode_detectors/timepix3\"\n",
-    "wf[time_of_flight.TimeOfFlightLookupTableFilename] = odin.data.odin_tof_lookup_table()"
+    "wf[unwrap.LookupTableFilename] = odin.data.odin_wavelength_lookup_table()"
    ]
   },
   {
@@ -84,9 +84,9 @@
    "id": "7",
    "metadata": {},
    "source": [
-    "## Compute neutron time-of-flight/wavelength\n",
+    "## Compute neutron wavelengths\n",
     "\n",
-    "We will now use the workflow to compute the neutron time-of-flight (equivalent to wavelength) using a lookup table built from the beamline chopper information."
+    "We will now use the workflow to compute the neutron wavelengths using a lookup table built from the beamline chopper information."
    ]
   },
   {
@@ -96,7 +96,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf.visualize(TofDetector[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
+    "wf.visualize(WavelengthDetector[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -106,7 +106,7 @@
    "source": [
     "### Inspect the lookup table\n",
     "\n",
-    "It is always a good idea to quickly plot the TOF lookup table, as a sanity check."
+    "It is always a good idea to quickly plot the wavelength lookup table, as a sanity check."
    ]
   },
   {
@@ -116,7 +116,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = wf.compute(unwrap.LookupTable)\n",
     "table.plot(figsize=(9, 4))"
    ]
   },
@@ -285,7 +285,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

packages/essimaging/docs/odin/odin-make-tof-lookup-table.ipynb → packages/essimaging/docs/odin/odin-make-wavelength-lookup-table.ipynb

@@ -5,7 +5,7 @@
    "id": "0",
    "metadata": {},
    "source": [
-    "# Create a time-of-flight lookup table for ODIN"
+    "# Create a wavelength lookup table for ODIN"
    ]
   },
   {
@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "from ess.reduce import time_of_flight\n",
+    "from ess.reduce import unwrap\n",
     "from ess.reduce.nexus.types import AnyRun\n",
     "from ess.odin.beamline import choppers"
    ]
@@ -39,15 +39,15 @@
     "source_position = sc.vector([0, 0, 0], unit='m')\n",
     "disk_choppers = choppers(source_position)\n",
     "\n",
-    "wf = time_of_flight.TofLookupTableWorkflow()\n",
-    "wf[time_of_flight.DiskChoppers[AnyRun]] = disk_choppers\n",
-    "wf[time_of_flight.SourcePosition] = source_position\n",
-    "wf[time_of_flight.NumberOfSimulatedNeutrons] = 200_000  # Increase this number for more reliable results\n",
-    "wf[time_of_flight.SimulationSeed] = 1234\n",
-    "wf[time_of_flight.PulseStride] = 2\n",
-    "wf[time_of_flight.LtotalRange] = sc.scalar(5.0, unit=\"m\"), sc.scalar(65.0, unit=\"m\")\n",
-    "wf[time_of_flight.DistanceResolution] = sc.scalar(0.1, unit=\"m\")\n",
-    "wf[time_of_flight.TimeResolution] = sc.scalar(250.0, unit='us')"
+    "wf = unwrap.LookupTableWorkflow()\n",
+    "wf[unwrap.DiskChoppers[AnyRun]] = disk_choppers\n",
+    "wf[unwrap.SourcePosition] = source_position\n",
+    "wf[unwrap.NumberOfSimulatedNeutrons] = 200_000  # Increase this number for more reliable results\n",
+    "wf[unwrap.SimulationSeed] = 1234\n",
+    "wf[unwrap.PulseStride] = 2\n",
+    "wf[unwrap.LtotalRange] = sc.scalar(5.0, unit=\"m\"), sc.scalar(65.0, unit=\"m\")\n",
+    "wf[unwrap.DistanceResolution] = sc.scalar(0.1, unit=\"m\")\n",
+    "wf[unwrap.TimeResolution] = sc.scalar(250.0, unit='us')"
    ]
   },
   {
@@ -65,7 +65,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = wf.compute(unwrap.LookupTable)\n",
     "table.array"
    ]
   },
@@ -95,7 +95,7 @@
    "outputs": [],
    "source": [
     "# Write to file\n",
-    "table.save_hdf5('ODIN-tof-lookup-table-5m-65m.h5')"
+    "table.save_hdf5('ODIN-wavelength-lookup-table-5m-65m.h5')"
    ]
   }
  ],

packages/essimaging/docs/tbl/index.md

@@ -7,5 +7,5 @@ maxdepth: 1
 
 tbl-data-reduction
 orca-image-normalization
-tbl-make-tof-lookup-table
+tbl-make-wavelength-lookup-table
 ```

packages/essimaging/docs/tbl/tbl-data-reduction.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "import plopp as pp\n",
-    "from ess.reduce import time_of_flight\n",
+    "from ess.reduce import unwrap\n",
     "from ess import tbl\n",
     "import ess.tbl.data  # noqa: F401\n",
     "from ess.imaging.types import *"
@@ -40,7 +40,7 @@
     "wf = tbl.TblWorkflow()\n",
     "\n",
     "wf[Filename[SampleRun]] = tbl.data.tutorial_sample_data()\n",
-    "wf[TimeOfFlightLookupTableFilename] = tbl.data.tbl_tof_lookup_table_no_choppers()"
+    "wf[LookupTableFilename] = tbl.data.tbl_wavelength_lookup_table_no_choppers()"
    ]
   },
   {
@@ -89,7 +89,7 @@
    "id": "8",
    "metadata": {},
    "source": [
-    "### Time-of-flight"
+    "### Neutron wavelengths"
    ]
   },
   {
@@ -99,15 +99,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf.visualize(TofDetector[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
+    "wf.visualize(WavelengthDetector[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "10",
    "metadata": {},
    "source": [
-    "#### Visualize the time-of-flight lookup table"
+    "#### Visualize the wavelength lookup table"
    ]
   },
   {
@@ -117,7 +117,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = wf.compute(unwrap.LookupTable)\n",
     "table.plot()"
    ]
   },
@@ -136,10 +136,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ngem_tofs = wf.compute(TofDetector[SampleRun])\n",
     "ngem_wavs = wf.compute(WavelengthDetector[SampleRun])\n",
     "\n",
-    "ngem_tofs.bins.concat().hist(tof=100).plot() + ngem_wavs.bins.concat().hist(wavelength=100).plot()"
+    "ngem_wavs.bins.concat().hist(wavelength=100).plot()"
    ]
   },
   {
@@ -182,7 +181,7 @@
    "id": "17",
    "metadata": {},
    "source": [
-    "### Time-of-flight"
+    "### Neutron wavelengths"
    ]
   },
   {
@@ -192,15 +191,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "he3_tofs = {}\n",
     "he3_wavs = {}\n",
     "\n",
     "for bank in ('he3_detector_bank0', 'he3_detector_bank1'):\n",
     "    he3_wf[NeXusDetectorName] = bank\n",
-    "    he3_tofs[bank] = he3_wf.compute(TofDetector[SampleRun]).bins.concat().hist(tof=100)\n",
     "    he3_wavs[bank] = he3_wf.compute(WavelengthDetector[SampleRun]).bins.concat().hist(wavelength=100)\n",
     "\n",
-    "pp.plot(he3_tofs) + pp.plot(he3_wavs)"
+    "pp.plot(he3_wavs)"
    ]
   }
  ],
@@ -219,7 +216,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

packages/essimaging/docs/tbl/tbl-make-tof-lookup-table.ipynb → packages/essimaging/docs/tbl/tbl-make-wavelength-lookup-table.ipynb

@@ -5,7 +5,7 @@
    "id": "0",
    "metadata": {},
    "source": [
-    "# Create a time-of-flight lookup table for TBL"
+    "# Create a wavelength lookup table for TBL"
    ]
   },
   {
@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "from ess.reduce import time_of_flight\n",
+    "from ess.reduce import unwrap\n",
     "from ess.reduce.nexus.types import AnyRun"
    ]
   },
@@ -37,15 +37,15 @@
    "source": [
     "source_position = sc.vector([0, 0, 0], unit='m')\n",
     "\n",
-    "wf = time_of_flight.TofLookupTableWorkflow()\n",
-    "wf[time_of_flight.DiskChoppers[AnyRun]] = {}\n",
-    "wf[time_of_flight.SourcePosition] = source_position\n",
-    "wf[time_of_flight.NumberOfSimulatedNeutrons] = 200_000  # Increase this number for more reliable results\n",
-    "wf[time_of_flight.SimulationSeed] = 1234\n",
-    "wf[time_of_flight.PulseStride] = 1\n",
-    "wf[time_of_flight.LtotalRange] = sc.scalar(5.0, unit=\"m\"), sc.scalar(35.0, unit=\"m\")\n",
-    "wf[time_of_flight.DistanceResolution] = sc.scalar(0.1, unit=\"m\")\n",
-    "wf[time_of_flight.TimeResolution] = sc.scalar(250.0, unit='us')"
+    "wf = unwrap.LookupTableWorkflow()\n",
+    "wf[unwrap.DiskChoppers[AnyRun]] = {}\n",
+    "wf[unwrap.SourcePosition] = source_position\n",
+    "wf[unwrap.NumberOfSimulatedNeutrons] = 200_000  # Increase this number for more reliable results\n",
+    "wf[unwrap.SimulationSeed] = 1234\n",
+    "wf[unwrap.PulseStride] = 1\n",
+    "wf[unwrap.LtotalRange] = sc.scalar(5.0, unit=\"m\"), sc.scalar(35.0, unit=\"m\")\n",
+    "wf[unwrap.DistanceResolution] = sc.scalar(0.1, unit=\"m\")\n",
+    "wf[unwrap.TimeResolution] = sc.scalar(250.0, unit='us')"
    ]
   },
   {
@@ -63,7 +63,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = wf.compute(unwrap.LookupTable)\n",
     "table.array"
    ]
   },
@@ -94,7 +94,7 @@
    "source": [
     "# Save chopper metadata\n",
     "# Write to file\n",
-    "table.save_hdf5('TBL-tof-lookup-table-no-choppers-5m-35m.h5')"
+    "table.save_hdf5('TBL-wavelength-lookup-table-no-choppers-5m-35m.h5')"
    ]
   }
  ],