Merge pull request #135 from scipp/sciline-next2

Refactor for next Sciline (Optional, param tables, and more)
scipp · Jun 17, 2024 · 7d6a037 · 7d6a037
2 parents 4d51289 + e83a965
commit 7d6a037
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diff --git a/docs/api-reference/index.md b/docs/api-reference/index.md
@@ -19,6 +19,10 @@
    :recursive:
 
    providers
+   with_background_runs
+   with_banks
+   with_pixel_mask_filenames
+   with_sample_runs
 ```
 
 ## Submodules

diff --git a/docs/user-guide/common/beam-center-finder.ipynb b/docs/user-guide/common/beam-center-finder.ipynb
@@ -53,7 +53,8 @@
     "workflow = isis.sans2d.Sans2dTutorialWorkflow()\n",
     "# For real data use:\n",
     "# workflow = isis.sans2d.Sans2dWorkflow()\n",
-    "workflow[Filename[SampleRun]] = isis.data.sans2d_tutorial_sample_run()"
+    "workflow[Filename[SampleRun]] = isis.data.sans2d_tutorial_sample_run()\n",
+    "workflow[isis.sans2d.LowCountThreshold] = sc.scalar(-1, unit=\"counts\")"
    ]
   },
   {
@@ -281,7 +282,10 @@
     "workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
     "workflow[sans.beam_center_finder.BeamCenterFinderQBins] = sc.linspace(\n",
     "    'Q', 0.02, 0.25, 71, unit='1/angstrom'\n",
-    ")"
+    ")\n",
+    "workflow[sans.beam_center_finder.BeamCenterFinderMinimizer] = None\n",
+    "workflow[sans.beam_center_finder.BeamCenterFinderTolerance] = None\n",
+    "workflow[DirectBeam] = None"
    ]
   },
   {

diff --git a/docs/user-guide/isis/sans2d.ipynb b/docs/user-guide/isis/sans2d.ipynb
@@ -94,7 +94,7 @@
    "outputs": [],
    "source": [
     "# left-right layout works better for this graph\n",
-    "workflow.visualize(IofQ[SampleRun], graph_attr={'rankdir': 'LR'})"
+    "workflow.visualize(IofQ[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -311,45 +311,6 @@
     "display(sc.plot(iofqs, norm='log'))"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "372b8d4f",
-   "metadata": {},
-   "source": [
-    "### Avoiding duplicate computation with parameter tables\n",
-    "\n",
-    "We have seen above that Sciline can avoid duplicate computation by requesting multiple results.\n",
-    "However, this is not always possible, for example if we want to compute the final result with different parameters.\n",
-    "In this case we can use parameter tables to avoid duplicate computation.\n",
-    "For example, we can compute the final result with different values for handling the uncertainties of the normalization factors.\n",
-    "This will avoid repeating loading files as well as some computation steps:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ceb079ee",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from typing import NewType\n",
-    "\n",
-    "Mode = NewType('Mode', str)\n",
-    "param_table = sciline.ParamTable(\n",
-    "    Mode,\n",
-    "    {\n",
-    "        UncertaintyBroadcastMode: [\n",
-    "            UncertaintyBroadcastMode.upper_bound,\n",
-    "            UncertaintyBroadcastMode.drop,\n",
-    "        ]\n",
-    "    },\n",
-    "    index=[Mode('upper_bound'), Mode('drop')],\n",
-    ")\n",
-    "workflow.set_param_table(param_table)\n",
-    "results = workflow.compute(sciline.Series[Mode, BackgroundSubtractedIofQ])\n",
-    "sc.DataGroup(results).hist().plot(norm='log')"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "94062d33-04cb-4a4d-aef1-e5ec58c228c4",

diff --git a/docs/user-guide/isis/zoom.ipynb b/docs/user-guide/isis/zoom.ipynb
@@ -147,7 +147,7 @@
     "workflow[isis.SampleOffset] = sc.vector([0.0, 0.0, 0.11], unit='m')\n",
     "workflow[isis.DetectorBankOffset] = sc.vector([0.0, 0.0, 0.5], unit='m')\n",
     "masks = isis.data.zoom_tutorial_mask_filenames()\n",
-    "workflow.set_param_series(PixelMaskFilename, masks)"
+    "workflow = sans.with_pixel_mask_filenames(workflow, masks)"
    ]
   },
   {

diff --git a/docs/user-guide/loki/loki-direct-beam.ipynb b/docs/user-guide/loki/loki-direct-beam.ipynb
@@ -86,11 +86,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "masks = loki.data.loki_tutorial_mask_filenames()\n",
-    "banks = ['larmor_detector']\n",
-    "workflow.insert(sans.merge_banks)\n",
-    "workflow.set_param_series(PixelMaskFilename, masks)\n",
-    "workflow.set_param_series(NeXusDetectorName, banks)"
+    "workflow = sans.with_pixel_mask_filenames(\n",
+    "    workflow, masks=loki.data.loki_tutorial_mask_filenames()\n",
+    ")\n",
+    "workflow[NeXusDetectorName] = 'larmor_detector'"
    ]
   },
   {
@@ -206,8 +205,6 @@
    "outputs": [],
    "source": [
     "bc_workflow = workflow.copy()\n",
-    "bc_workflow.del_param_table(NeXusDetectorName)\n",
-    "bc_workflow[NeXusDetectorName] = 'larmor_detector'\n",
     "bc_workflow.insert(sans.beam_center_from_center_of_mass)"
    ]
   },
@@ -544,7 +541,7 @@
    "id": "c3e2ff3d-2b3d-4ba7-b4ca-f0a5617d22dc",
    "metadata": {},
    "source": [
-    "We update the workflow, inserting parameter series and merging providers:"
+    "We modify the workflow, setting multiple background and sample runs:"
    ]
   },
   {
@@ -557,12 +554,9 @@
     "# Reset workflow\n",
     "workflow[DimsToKeep] = []\n",
     "\n",
-    "# Set parameter series for file names\n",
-    "workflow.set_param_series(Filename[SampleRun], sample_runs)\n",
-    "workflow.set_param_series(Filename[BackgroundRun], background_runs)\n",
-    "\n",
-    "# Add event merging provider\n",
-    "workflow.insert(sans.merge_runs)"
+    "# Transform base workflow to use multiple sample and background runs\n",
+    "workflow = sans.with_background_runs(workflow, runs=background_runs)\n",
+    "workflow = sans.with_sample_runs(workflow, runs=sample_runs)"
    ]
   },
   {
@@ -571,8 +565,8 @@
    "metadata": {},
    "source": [
     "If we now visualize the workflow,\n",
-    "we can see that every step for the `SampleRun` and `BackgroundRun` branches are now series of types (3D-looking boxes instead of flat rectangles).\n",
-    "There is also the new `merge_multiple_runs` step that combines the events from the two runs,\n",
+    "we can see that every step for the `SampleRun` and `BackgroundRun` branches are now replicated (drawn as 3D-looking boxes instead of flat rectangles, set `compact=False` to show flattened version).\n",
+    "There is also the new `merge_contributions` step that combines the events from the two runs,\n",
     "just before the normalization."
    ]
   },

diff --git a/pyproject.toml b/pyproject.toml
@@ -33,9 +33,11 @@ dependencies = [
   "dask",
   "graphviz",
   "essreduce",
+  "numpy<2.0.0",
+  "pandas",
   "plopp",
   "pythreejs",
-  "sciline>=24.4.1",
+  "sciline>=24.06.0",
   "scipp>=23.8.0",
   "scippneutron>=23.9.0",
   "scippnexus>=23.12.1",  # 23.12.0 and below deadlock in threaded use

diff --git a/requirements/base.in b/requirements/base.in
@@ -5,9 +5,11 @@
 dask
 graphviz
 essreduce
+numpy<2.0.0
+pandas
 plopp
 pythreejs
-sciline>=24.4.1
+sciline>=24.06.0
 scipp>=23.8.0
 scippneutron>=23.9.0
 scippnexus>=23.12.1
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -1,4 +1,4 @@
-# SHA1:a7107dcab866c4c7fe8573b3c5cbaf22e7b1f587
+# SHA1:397546fc6b5f1262c66d9da45a959b3f1266e092
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -7,9 +7,7 @@
 #
 asttokens==2.4.1
     # via stack-data
-backcall==0.2.0
-    # via ipython
-certifi==2024.2.2
+certifi==2024.6.2
     # via requests
 charset-normalizer==3.3.2
     # via requests
@@ -21,115 +19,130 @@ comm==0.2.2
     # via ipywidgets
 contourpy==1.2.1
     # via matplotlib
+cyclebane==24.6.0
+    # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2024.4.1
+dask==2024.6.0
     # via -r base.in
 decorator==5.1.1
     # via ipython
 essreduce==24.3.11
     # via -r base.in
+exceptiongroup==1.2.1
+    # via ipython
 executing==2.0.1
     # via stack-data
-fonttools==4.50.0
+fonttools==4.53.0
     # via matplotlib
-fsspec==2024.3.1
+fsspec==2024.6.0
     # via dask
 graphviz==0.20.3
     # via -r base.in
-h5py==3.10.0
+h5py==3.11.0
     # via
     #   scippneutron
     #   scippnexus
-idna==3.6
+idna==3.7
     # via requests
+importlib-metadata==7.1.0
+    # via dask
 ipydatawidgets==4.3.5
     # via pythreejs
-ipython==8.9.0
+ipython==8.25.0
     # via ipywidgets
-ipywidgets==8.1.2
+ipywidgets==8.1.3
     # via
     #   ipydatawidgets
     #   pythreejs
 jedi==0.19.1
     # via ipython
-jupyterlab-widgets==3.0.10
+jupyterlab-widgets==3.0.11
     # via ipywidgets
 kiwisolver==1.4.5
     # via matplotlib
 locket==1.0.0
     # via partd
-matplotlib==3.8.4
+matplotlib==3.9.0
     # via plopp
-matplotlib-inline==0.1.6
+matplotlib-inline==0.1.7
     # via ipython
+networkx==3.3
+    # via cyclebane
 numpy==1.26.4
     # via
+    #   -r base.in
     #   contourpy
     #   h5py
     #   ipydatawidgets
     #   matplotlib
+    #   pandas
     #   pythreejs
     #   scipp
     #   scippneutron
     #   scipy
-packaging==24.0
+packaging==24.1
     # via
     #   dask
     #   matplotlib
     #   pooch
-parso==0.8.3
+pandas==2.2.2
+    # via -r base.in
+parso==0.8.4
     # via jedi
-partd==1.4.1
+partd==1.4.2
     # via dask
 pexpect==4.9.0
     # via ipython
-pickleshare==0.7.5
-    # via ipython
 pillow==10.3.0
     # via matplotlib
-platformdirs==4.2.0
+platformdirs==4.2.2
     # via pooch
-plopp==24.2.0
-    # via -r base.in
-pooch==1.8.1
+plopp==24.5.0
+    # via
+    #   -r base.in
+    #   scippneutron
+pooch==1.8.2
     # via scippneutron
-prompt-toolkit==3.0.36
+prompt-toolkit==3.0.47
     # via ipython
 ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.2
     # via stack-data
-pygments==2.17.2
+pygments==2.18.0
     # via ipython
 pyparsing==3.1.2
     # via matplotlib
 python-dateutil==2.9.0.post0
     # via
     #   matplotlib
+    #   pandas
     #   scippnexus
 pythreejs==2.4.2
     # via -r base.in
+pytz==2024.1
+    # via pandas
 pyyaml==6.0.1
     # via dask
-requests==2.31.0
+requests==2.32.3
     # via pooch
-sciline==24.4.1
+sciline==24.6.0
     # via -r base.in
 scipp==24.5.1
     # via
     #   -r base.in
     #   essreduce
     #   scippneutron
     #   scippnexus
-scippneutron==24.3.0
+scippneutron==24.5.0
     # via -r base.in
 scippnexus==24.3.1
     # via
     #   -r base.in
     #   essreduce
     #   scippneutron
-scipy==1.13.0
+scipy==1.13.1
     # via
     #   scippneutron
     #   scippnexus
@@ -143,7 +156,7 @@ toolz==0.12.1
     # via
     #   dask
     #   partd
-traitlets==5.14.2
+traitlets==5.14.3
     # via
     #   comm
     #   ipython
@@ -153,9 +166,15 @@ traitlets==5.14.2
     #   traittypes
 traittypes==0.2.1
     # via ipydatawidgets
+typing-extensions==4.12.2
+    # via ipython
+tzdata==2024.1
+    # via pandas
 urllib3==2.2.1
     # via requests
 wcwidth==0.2.13
     # via prompt-toolkit
-widgetsnbextension==4.0.10
+widgetsnbextension==4.0.11
     # via ipywidgets
+zipp==3.19.2
+    # via importlib-metadata