Merge pull request #99 from scipp/update-ess-reduce-nexus

SimonHeybrock · web-flow · commit 90e3a57bab2a · 2024-10-11T12:47:29.000+02:00
Update for restructured NeXus base workflow from `ess.reduce.nexus`
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,7 +31,7 @@ requires-python = ">=3.10"
 # Make sure to list one dependency per line.
 dependencies = [
   "dask",
-  "essreduce>=24.10.0",
+  "essreduce>=24.10.2",
   "graphviz",
   "numpy",
   "plopp",
diff --git a/requirements/base.in b/requirements/base.in
@@ -3,7 +3,7 @@
 # --- END OF CUSTOM SECTION ---
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask
-essreduce>=24.10.0
+essreduce>=24.10.2
 graphviz
 numpy
 plopp
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -1,4 +1,4 @@
-# SHA1:3edca7ef7f02d8df072e91ce62fa7acd26cc0825
+# SHA1:86f9288f7221f3a8506d1cc40db8a4584011b0e0
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -15,15 +15,15 @@ comm==0.2.2
     # via ipywidgets
 contourpy==1.3.0
     # via matplotlib
-cyclebane==24.6.0
+cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
 dask==2024.9.1
     # via -r base.in
 decorator==5.1.1
     # via ipython
-essreduce==24.10.0
+essreduce==24.10.2
     # via -r base.in
 exceptiongroup==1.2.2
     # via ipython
@@ -43,7 +43,7 @@ importlib-metadata==8.5.0
     # via dask
 ipydatawidgets==4.3.5
     # via pythreejs
-ipython==8.27.0
+ipython==8.28.0
     # via ipywidgets
 ipywidgets==8.1.5
     # via
@@ -65,9 +65,9 @@ matplotlib-inline==0.1.7
     # via ipython
 mpltoolbox==24.5.1
     # via scippneutron
-networkx==3.3
+networkx==3.4
     # via cyclebane
-numpy==2.1.1
+numpy==2.1.2
     # via
     #   -r base.in
     #   contourpy
@@ -125,7 +125,7 @@ scipp==24.9.1
     #   scippnexus
 scippneutron==24.9.0
     # via -r base.in
-scippnexus==24.9.1
+scippnexus==24.10.0
     # via
     #   -r base.in
     #   essreduce
@@ -140,7 +140,7 @@ six==1.16.0
     #   python-dateutil
 stack-data==0.6.3
     # via ipython
-toolz==0.12.1
+toolz==1.0.0
     # via
     #   dask
     #   partd
diff --git a/requirements/basetest.txt b/requirements/basetest.txt
@@ -7,15 +7,15 @@
 #
 certifi==2024.8.30
     # via requests
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 exceptiongroup==1.2.2
     # via pytest
 idna==3.10
     # via requests
 iniconfig==2.0.0
     # via pytest
-numpy==2.1.1
+numpy==2.1.2
     # via pandas
 packaging==24.1
     # via
@@ -39,7 +39,7 @@ requests==2.32.3
     # via pooch
 six==1.16.0
     # via python-dateutil
-tomli==2.0.1
+tomli==2.0.2
     # via pytest
 tzdata==2024.2
     # via pandas
diff --git a/requirements/ci.txt b/requirements/ci.txt
@@ -11,11 +11,11 @@ certifi==2024.8.30
     # via requests
 chardet==5.2.0
     # via tox
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 colorama==0.4.6
     # via tox
-distlib==0.3.8
+distlib==0.3.9
     # via virtualenv
 filelock==3.16.1
     # via
@@ -44,11 +44,11 @@ requests==2.32.3
     # via -r ci.in
 smmap==5.0.1
     # via gitdb
-tomli==2.0.1
+tomli==2.0.2
     # via
     #   pyproject-api
     #   tox
-tox==4.21.0
+tox==4.21.2
     # via -r ci.in
 typing-extensions==4.12.2
     # via tox
diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -81,7 +81,7 @@ pip-compile-multi==2.6.4
     # via -r dev.in
 pip-tools==7.4.1
     # via pip-compile-multi
-plumbum==1.8.3
+plumbum==1.9.0
     # via copier
 prometheus-client==0.21.0
     # via jupyter-server
@@ -115,7 +115,7 @@ terminado==0.18.1
     #   jupyter-server-terminals
 toposort==1.10
     # via pip-compile-multi
-types-python-dateutil==2.9.0.20240906
+types-python-dateutil==2.9.0.20241003
     # via arrow
 uri-template==1.3.0
     # via jsonschema
diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -26,9 +26,9 @@ bleach==6.1.0
     # via nbconvert
 certifi==2024.8.30
     # via requests
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
-debugpy==1.8.6
+debugpy==1.8.7
     # via ipykernel
 defusedxml==0.7.1
     # via nbconvert
@@ -60,7 +60,7 @@ jinja2==3.1.4
     #   sphinx
 jsonschema==4.23.0
     # via nbformat
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
 jupyter-client==8.6.3
     # via
@@ -81,7 +81,7 @@ markdown-it-py==3.0.0
     # via
     #   mdit-py-plugins
     #   myst-parser
-markupsafe==2.1.5
+markupsafe==3.0.1
     # via
     #   jinja2
     #   nbconvert
@@ -150,7 +150,7 @@ snowballstemmer==2.2.0
     # via sphinx
 soupsieve==2.6
     # via beautifulsoup4
-sphinx==8.0.2
+sphinx==8.1.0
     # via
     #   -r docs.in
     #   myst-parser
@@ -160,7 +160,7 @@ sphinx==8.0.2
     #   sphinx-copybutton
     #   sphinx-design
     #   sphinxcontrib-bibtex
-sphinx-autodoc-typehints==2.4.4
+sphinx-autodoc-typehints==2.5.0
     # via -r docs.in
 sphinx-copybutton==0.5.2
     # via -r docs.in
@@ -182,7 +182,7 @@ sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 tinycss2==1.3.0
     # via nbconvert
-tomli==2.0.1
+tomli==2.0.2
     # via sphinx
 tornado==6.4.1
     # via
diff --git a/requirements/nightly.txt b/requirements/nightly.txt
@@ -16,7 +16,7 @@ comm==0.2.2
     # via ipywidgets
 contourpy==1.3.0
     # via matplotlib
-cyclebane==24.6.0
+cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
@@ -42,7 +42,7 @@ importlib-metadata==8.5.0
     # via dask
 ipydatawidgets==4.3.5
     # via pythreejs
-ipython==8.27.0
+ipython==8.28.0
     # via ipywidgets
 ipywidgets==8.1.5
     # via
@@ -64,7 +64,7 @@ matplotlib-inline==0.1.7
     # via ipython
 mpltoolbox==24.5.1
     # via scippneutron
-networkx==3.3
+networkx==3.4
     # via cyclebane
 parso==0.8.4
     # via jedi
@@ -115,7 +115,7 @@ scipy==1.14.1
     #   scippnexus
 stack-data==0.6.3
     # via ipython
-toolz==0.12.1
+toolz==1.0.0
     # via
     #   dask
     #   partd
diff --git a/requirements/static.txt b/requirements/static.txt
@@ -7,7 +7,7 @@
 #
 cfgv==3.4.0
     # via pre-commit
-distlib==0.3.8
+distlib==0.3.9
     # via virtualenv
 filelock==3.16.1
     # via virtualenv
@@ -17,7 +17,7 @@ nodeenv==1.9.1
     # via pre-commit
 platformdirs==4.3.6
     # via virtualenv
-pre-commit==3.8.0
+pre-commit==4.0.1
     # via -r static.in
 pyyaml==6.0.2
     # via pre-commit
diff --git a/requirements/wheels.txt b/requirements/wheels.txt
@@ -5,11 +5,11 @@
 #
 #    pip-compile-multi
 #
-build==1.2.2
+build==1.2.2.post1
     # via -r wheels.in
 packaging==24.1
     # via build
 pyproject-hooks==1.2.0
     # via build
-tomli==2.0.1
+tomli==2.0.2
     # via build
diff --git a/src/ess/dream/io/geant4.py b/src/ess/dream/io/geant4.py
@@ -4,19 +4,20 @@
 import numpy as np
 import sciline
 import scipp as sc
+import scippnexus as snx
 
 from ess.powder.types import (
     CalibratedDetector,
     CalibrationData,
     CalibrationFilename,
     DetectorData,
     Filename,
-    NeXusDetector,
+    NeXusComponent,
     NeXusDetectorName,
-    NeXusSample,
-    NeXusSource,
+    Position,
     RunType,
 )
+from ess.reduce.nexus.types import CalibratedBeamline
 from ess.reduce.nexus.workflow import GenericNeXusWorkflow
 
 MANTLE_DETECTOR_ID = sc.index(7)
@@ -60,9 +61,23 @@ def load_geant4_csv(file_path: Filename[RunType]) -> AllRawDetectors[RunType]:
 
 def extract_geant4_detector(
     detectors: AllRawDetectors[RunType], detector_name: NeXusDetectorName
-) -> NeXusDetector[RunType]:
+) -> NeXusComponent[snx.NXdetector, RunType]:
     """Extract a single detector from a loaded GEANT4 simulation."""
-    return NeXusDetector[RunType](detectors["instrument"][detector_name])
+    return NeXusComponent[snx.NXdetector, RunType](
+        detectors["instrument"][detector_name]
+    )
+
+
+def get_calibrated_geant4_detector(
+    detector: NeXusComponent[snx.NXdetector, RunType],
+) -> CalibratedDetector[RunType]:
+    """
+    Replacement for :py:func:`ess.reduce.nexus.workflow.get_calibrated_detector`.
+
+    Since the Geant4 detectors already have computed positions as well as logical shape,
+    this just extracts the relevant event data.
+    """
+    return detector['events'].copy(deep=False)
 
 
 def _load_raw_events(file_path: str) -> sc.DataArray:
@@ -171,21 +186,21 @@ def geant4_load_calibration(filename: CalibrationFilename) -> CalibrationData:
 
 
 def dummy_assemble_detector_data(
-    detector: CalibratedDetector[RunType],
+    detector: CalibratedBeamline[RunType],
 ) -> DetectorData[RunType]:
     """Dummy assembly of detector data, detector already contains neutron data."""
     return DetectorData[RunType](detector)
 
 
-def dummy_source() -> NeXusSource[RunType]:
-    return NeXusSource[RunType](
-        sc.DataGroup(position=sc.vector([np.nan, np.nan, np.nan], unit="mm"))
+def dummy_source_position() -> Position[snx.NXsource, RunType]:
+    return Position[snx.NXsource, RunType](
+        sc.vector([np.nan, np.nan, np.nan], unit="mm")
     )
 
 
-def dummy_sample() -> NeXusSample[RunType]:
-    return NeXusSample[RunType](
-        sc.DataGroup(position=sc.vector([np.nan, np.nan, np.nan], unit="mm"))
+def dummy_sample_position() -> Position[snx.NXsample, RunType]:
+    return Position[snx.NXsample, RunType](
+        sc.vector([np.nan, np.nan, np.nan], unit="mm")
     )
 
 
@@ -197,7 +212,8 @@ def LoadGeant4Workflow() -> sciline.Pipeline:
     wf.insert(extract_geant4_detector)
     wf.insert(load_geant4_csv)
     wf.insert(geant4_load_calibration)
+    wf.insert(get_calibrated_geant4_detector)
     wf.insert(dummy_assemble_detector_data)
-    wf.insert(dummy_source)
-    wf.insert(dummy_sample)
+    wf.insert(dummy_source_position)
+    wf.insert(dummy_sample_position)
     return wf
diff --git a/src/ess/dream/workflow.py b/src/ess/dream/workflow.py
diff --git a/src/ess/powder/types.py b/src/ess/powder/types.py
diff --git a/tests/dream/geant4_reduction_test.py b/tests/dream/geant4_reduction_test.py
diff --git a/tests/dream/io/geant4_test.py b/tests/dream/io/geant4_test.py
diff --git a/tests/dream/io/nexus_test.py b/tests/dream/io/nexus_test.py

Original file line number	Diff line number	Diff line change
`@@ -5,11 +5,11 @@`
`5`	`5`	`#`
`6`	`6`	`# pip-compile-multi`
`7`	`7`	`#`
`8`		`-build==1.2.2`
	`8`	`+build==1.2.2.post1`
`9`	`9`	`# via -r wheels.in`
`10`	`10`	`packaging==24.1`
`11`	`11`	`# via build`
`12`	`12`	`pyproject-hooks==1.2.0`
`13`	`13`	`# via build`
`14`		`-tomli==2.0.1`
	`14`	`+tomli==2.0.2`
`15`	`15`	`# via build`