Merge pull request #161 from scipp/deprecation_warnings

nvaytet · web-flow · commit f281893f83cf · 2023-01-30T09:56:54.000+01:00
Remove deprecation warnings from docs notebooks
diff --git a/docs/buildconfig/config.yaml b/docs/buildconfig/config.yaml
@@ -0,0 +1,2 @@
+plot:
+  use_plopp: true
diff --git a/docs/conf.py b/docs/conf.py
@@ -3,6 +3,7 @@
 
 import doctest
 import os
+import pathlib
 import sys
 from datetime import date
 from typing import Any, Dict, Optional
@@ -264,3 +265,7 @@ def add_buttons(
     # Specific lines in Github blobs cannot be found by linkcheck.
     r'https?://github\.com/.*?/blob/[a-f0-9]+/.+?#',
 ]
+
+# Set env variable to enable plopp
+docs_dir = pathlib.Path(__file__).parent.absolute()
+os.environ["SCIPPDIR"] = os.path.join(docs_dir, 'buildconfig')
diff --git a/docs/instruments/external/powgen/powgen_reduction.ipynb b/docs/instruments/external/powgen/powgen_reduction.ipynb
@@ -32,6 +32,7 @@
     "%matplotlib widget\n",
     "import scipp as sc\n",
     "import scippneutron as scn\n",
+    "import plopp as pp\n",
     "\n",
     "import ess\n",
     "from ess.diffraction.external import load_calibration\n",
@@ -131,7 +132,7 @@
    },
    "outputs": [],
    "source": [
-    "sample.plot()"
+    "sample.hist(spectrum=500, tof=400).plot()"
    ]
   },
   {
@@ -151,7 +152,7 @@
    },
    "outputs": [],
    "source": [
-    "powgen.instrument_view(sample)"
+    "scn.instrument_view(sample.hist())"
    ]
   },
   {
@@ -486,7 +487,7 @@
    },
    "outputs": [],
    "source": [
-    "sc.histogram(all_spectra, bins=dspacing_edges).plot()"
+    "all_spectra.hist(dspacing=dspacing_edges).plot()"
    ]
   },
   {
@@ -557,7 +558,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized = sc.histogram(normalized, bins=dspacing_edges)"
+    "normalized = normalized.hist(dspacing=dspacing_edges)"
    ]
   },
   {
@@ -623,7 +624,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized.plot(projection='1d')"
+    "pp.superplot(normalized)"
    ]
   }
  ],
diff --git a/docs/instruments/loki/sans2d_reduction.ipynb b/docs/instruments/loki/sans2d_reduction.ipynb
@@ -35,7 +35,8 @@
     "import scipp as sc\n",
     "from ess import loki, sans\n",
     "from ess.logging import configure_workflow\n",
-    "import scippneutron as scn"
+    "import scippneutron as scn\n",
+    "import plopp as pp"
    ]
   },
   {
@@ -233,7 +234,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "scn.instrument_view(ds['sample'], pixel_size=0.0075)"
+    "scn.instrument_view(ds['sample'].hist(), pixel_size=0.0075)"
    ]
   },
   {
@@ -327,7 +328,7 @@
     "    q_bins=q_bins,\n",
     "    gravity=gravity,\n",
     "    monitor_non_background_range=monitor_non_background_range)\n",
-    "sample_q.plot()"
+    "sample_q.hist().plot()"
    ]
   },
   {
@@ -345,7 +346,7 @@
     "    q_bins=q_bins,\n",
     "    gravity=gravity,\n",
     "    monitor_non_background_range=monitor_non_background_range)\n",
-    "background_q.plot()"
+    "background_q.hist().plot()"
    ]
   },
   {
@@ -376,8 +377,7 @@
    "source": [
     "fig1, ax1 = plt.subplots(1, 2, figsize=(10, 4))\n",
     "sc.plot(result, ax=ax1[0])\n",
-    "sc.plot(result, norm='log', ax=ax1[1])\n",
-    "fig1"
+    "sc.plot(result, norm='log', ax=ax1[1])"
    ]
   },
   {
@@ -456,8 +456,7 @@
     "\n",
     "fig2, ax2 = plt.subplots(1, 2, figsize=(10, 4))\n",
     "sc.plot(collapsed, ax=ax2[0])\n",
-    "sc.plot(collapsed, norm='log', legend=False, ax=ax2[1])\n",
-    "fig2"
+    "sc.plot(collapsed, norm='log', ax=ax2[1])"
    ]
   },
   {
diff --git a/docs/instruments/loki/sans2d_to_I_of_Q.ipynb b/docs/instruments/loki/sans2d_to_I_of_Q.ipynb
@@ -258,7 +258,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "scn.instrument_view(sample, pixel_size=0.0075)"
+    "scn.instrument_view(sample.hist(), pixel_size=0.0075)"
    ]
   },
   {
@@ -301,7 +301,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sample)"
+    "sc.plot(sample.hist(tof=200).sum('spectrum'))"
    ]
   },
   {
@@ -428,9 +428,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "p = sc.plot(monitors['sample'], norm='log')\n",
-    "sc.plot(monitors['direct'], norm='log', ax=p.ax, color=['C2', 'C3'])\n",
-    "p"
+    "sc.plot({**{f'sample-{key}': val for key, val in monitors['sample'].items()},\n",
+    "         **{f'direct-{key}': val for key, val in monitors['direct'].items()}}\n",
+    "        , norm='log')"
    ]
   },
   {
@@ -646,7 +646,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sample_q, norm='log')"
+    "sc.plot(sample_q.hist(), norm='log')"
    ]
   },
   {
@@ -706,7 +706,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sample_normalized)"
+    "sc.plot(sample_normalized.hist())"
    ]
   },
   {
diff --git a/docs/techniques/wfm/introduction-to-wfm.ipynb b/docs/techniques/wfm/introduction-to-wfm.ipynb
@@ -1056,7 +1056,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "del ax6.texts[3:]\n",
+    "for t in ax6.texts[3:]:\n",
+    "    t.remove()\n",
     "ax6.set_xlim(-1.0e3, 2.0e4)\n",
     "ax6.set_ylim(-1.5, 10.0)\n",
     "fig6.canvas.draw_idle()\n",
@@ -1100,9 +1101,10 @@
     "    ax7.plot([(coords['source_pulse_t_0'] + (0.5 * coords['source_pulse_length'])).value,\n",
     "              arrival_times['wavelength', i].value],\n",
     "             [0.0, sc.norm(coords['position']).value], color='r')\n",
-    "del ax7.texts[3:]\n",
     "ax7.set_xlim(-1.0e3, 2.0e4)\n",
-    "ax7.set_ylim(-1.5, 10.0)"
+    "ax7.set_ylim(-1.5, 10.0)\n",
+    "for t in ax7.texts[3:]:\n",
+    "    t.remove()"
    ]
   },
   {
diff --git a/environment.yml b/environment.yml
@@ -24,6 +24,7 @@ dependencies:
   - pytest=7.2.1
   - python-graphviz=0.20.1
   - pythreejs=2.4.1
+  - scipp==22.11.0
   - scippneutron==22.12.4
   - sphinx=4.5.0
   - sphinx-book-theme=0.3.3
diff --git a/src/ess/diffraction/corrections.py b/src/ess/diffraction/corrections.py
@@ -78,7 +78,7 @@ def normalize_by_vanadium(data: sc.DataArray, *, vanadium: sc.DataArray,
     :
         `data` normalized by `vanadium`.
     """
-    norm = sc.lookup(sc.histogram(vanadium, bins=edges), dim=edges.dim)
+    norm = sc.lookup(vanadium.hist({edges.dim: edges}), dim=edges.dim)
     # Converting to unit 'one' because the division might produce a unit
     # with a large scale if the proton charges in data and vanadium were
     # measured with different units.
diff --git a/src/ess/diffraction/grouping.py b/src/ess/diffraction/grouping.py
@@ -4,10 +4,7 @@
 from scippneutron.conversion.graph import beamline
 
 
-def group_by_two_theta(data: sc.DataArray,
-                       *,
-                       edges: sc.Variable,
-                       replace_dim: str = 'spectrum') -> sc.DataArray:
+def group_by_two_theta(data: sc.DataArray, *, edges: sc.Variable) -> sc.DataArray:
     """
     Group data into two_theta bins.
 
@@ -18,17 +15,11 @@ def group_by_two_theta(data: sc.DataArray,
         or coords or attrs that can be used to compute it.
     edges:
         Bin edges in two_theta. `data` is grouped into those bins.
-    replace_dim:
-        Dimension that is replaced by two_theta.
-        All events are concatenated along this dimension.
 
     Returns
     -------
     :
         `data` grouped into two_theta bins.
     """
-    data = data.transform_coords('two_theta', graph=beamline.beamline(scatter=True))
-    return sc.groupby(data,
-                      'two_theta',
-                      bins=edges.to(unit=data.coords['two_theta'].unit,
-                                    copy=False)).bins.concat(replace_dim)
+    out = data.transform_coords('two_theta', graph=beamline.beamline(scatter=True))
+    return out.bin(two_theta=edges.to(unit=out.coords['two_theta'].unit, copy=False))
diff --git a/src/ess/external/powgen/instrument_view.py b/src/ess/external/powgen/instrument_view.py
@@ -28,12 +28,14 @@ def instrument_view(da: sc.DataArray,
     kwargs:
         See :func:`scippneutron.instrument_view`
     """
-    if 'camera' not in kwargs:
-        kwargs = {
-            **kwargs, 'camera': {
-                'position': sc.vector(value=[-3, 3, 3], unit=da.coords[positions].unit)
-            }
-        }
+    # TODO: the camera argument does not work with the Plopp instrument view
+    # if 'camera' not in kwargs:
+    #     kwargs = {
+    #         **kwargs, 'camera': {
+    #             'position': sc.vector(value=[-3, 3, 3],
+    #                                   unit=da.coords[positions].unit)
+    #         }
+    #     }
     return scn.instrument_view(da,
                                positions=positions,
                                components=components,
diff --git a/src/ess/sans/i_of_q.py b/src/ess/sans/i_of_q.py
@@ -169,7 +169,7 @@ def _convert_dense_to_q_and_merge_spectra(
     data_q.coords['wavelength'] = data_q.attrs.pop('wavelength')
     for i in range(wavelength_bands.sizes['wavelength'] - 1):
         band = data_q['wavelength', wavelength_bands[i]:wavelength_bands[i + 1]]
-        bands.append(sc.histogram(band, bins=q_bins).sum('spectrum'))
+        bands.append(band.hist({q_bins.dim: q_bins}).sum('spectrum'))
     q_summed = sc.concat(bands, 'wavelength')
     return q_summed
 

Original file line number	Diff line number	Diff line change
`@@ -32,6 +32,7 @@`
`32`	`32`	`"%matplotlib widget\n",`
`33`	`33`	`"import scipp as sc\n",`
`34`	`34`	`"import scippneutron as scn\n",`
	`35`	`+ "import plopp as pp\n",`
`35`	`36`	`"\n",`
`36`	`37`	`"import ess\n",`
`37`	`38`	`"from ess.diffraction.external import load_calibration\n",`
`@@ -131,7 +132,7 @@`
`131`	`132`	`},`
`132`	`133`	`"outputs": [],`
`133`	`134`	`"source": [`
`134`		`- "sample.plot()"`
	`135`	`+ "sample.hist(spectrum=500, tof=400).plot()"`
`135`	`136`	`]`
`136`	`137`	`},`
`137`	`138`	`{`
`@@ -151,7 +152,7 @@`
`151`	`152`	`},`
`152`	`153`	`"outputs": [],`
`153`	`154`	`"source": [`
`154`		`- "powgen.instrument_view(sample)"`
	`155`	`+ "scn.instrument_view(sample.hist())"`
`155`	`156`	`]`
`156`	`157`	`},`
`157`	`158`	`{`
`@@ -486,7 +487,7 @@`
`486`	`487`	`},`
`487`	`488`	`"outputs": [],`
`488`	`489`	`"source": [`
`489`		`- "sc.histogram(all_spectra, bins=dspacing_edges).plot()"`
	`490`	`+ "all_spectra.hist(dspacing=dspacing_edges).plot()"`
`490`	`491`	`]`
`491`	`492`	`},`
`492`	`493`	`{`
`@@ -557,7 +558,7 @@`
`557`	`558`	`},`
`558`	`559`	`"outputs": [],`
`559`	`560`	`"source": [`
`560`		`- "normalized = sc.histogram(normalized, bins=dspacing_edges)"`
	`561`	`+ "normalized = normalized.hist(dspacing=dspacing_edges)"`
`561`	`562`	`]`
`562`	`563`	`},`
`563`	`564`	`{`
`@@ -623,7 +624,7 @@`
`623`	`624`	`},`
`624`	`625`	`"outputs": [],`
`625`	`626`	`"source": [`
`626`		`- "normalized.plot(projection='1d')"`
	`627`	`+ "pp.superplot(normalized)"`
`627`	`628`	`]`
`628`	`629`	`}`
`629`	`630`	`],`
Original file line number	Diff line number	Diff line change
`@@ -35,7 +35,8 @@`
`35`	`35`	`"import scipp as sc\n",`
`36`	`36`	`"from ess import loki, sans\n",`
`37`	`37`	`"from ess.logging import configure_workflow\n",`
`38`		`- "import scippneutron as scn"`
	`38`	`+ "import scippneutron as scn\n",`
	`39`	`+ "import plopp as pp"`
`39`	`40`	`]`
`40`	`41`	`},`
`41`	`42`	`{`
`@@ -233,7 +234,7 @@`
`233`	`234`	`"metadata": {},`
`234`	`235`	`"outputs": [],`
`235`	`236`	`"source": [`
`236`		`- "scn.instrument_view(ds['sample'], pixel_size=0.0075)"`
	`237`	`+ "scn.instrument_view(ds['sample'].hist(), pixel_size=0.0075)"`
`237`	`238`	`]`
`238`	`239`	`},`
`239`	`240`	`{`
`@@ -327,7 +328,7 @@`
`327`	`328`	`" q_bins=q_bins,\n",`
`328`	`329`	`" gravity=gravity,\n",`
`329`	`330`	`" monitor_non_background_range=monitor_non_background_range)\n",`
`330`		`- "sample_q.plot()"`
	`331`	`+ "sample_q.hist().plot()"`
`331`	`332`	`]`
`332`	`333`	`},`
`333`	`334`	`{`
`@@ -345,7 +346,7 @@`
`345`	`346`	`" q_bins=q_bins,\n",`
`346`	`347`	`" gravity=gravity,\n",`
`347`	`348`	`" monitor_non_background_range=monitor_non_background_range)\n",`
`348`		`- "background_q.plot()"`
	`349`	`+ "background_q.hist().plot()"`
`349`	`350`	`]`
`350`	`351`	`},`
`351`	`352`	`{`
`@@ -376,8 +377,7 @@`
`376`	`377`	`"source": [`
`377`	`378`	`"fig1, ax1 = plt.subplots(1, 2, figsize=(10, 4))\n",`
`378`	`379`	`"sc.plot(result, ax=ax1[0])\n",`
`379`		`- "sc.plot(result, norm='log', ax=ax1[1])\n",`
`380`		`- "fig1"`
	`380`	`+ "sc.plot(result, norm='log', ax=ax1[1])"`
`381`	`381`	`]`
`382`	`382`	`},`
`383`	`383`	`{`
`@@ -456,8 +456,7 @@`
`456`	`456`	`"\n",`
`457`	`457`	`"fig2, ax2 = plt.subplots(1, 2, figsize=(10, 4))\n",`
`458`	`458`	`"sc.plot(collapsed, ax=ax2[0])\n",`
`459`		`- "sc.plot(collapsed, norm='log', legend=False, ax=ax2[1])\n",`
`460`		`- "fig2"`
	`459`	`+ "sc.plot(collapsed, norm='log', ax=ax2[1])"`
`461`	`460`	`]`
`462`	`461`	`},`
`463`	`462`	`{`
Original file line number	Diff line number	Diff line change
`@@ -258,7 +258,7 @@`
`258`	`258`	`"metadata": {},`
`259`	`259`	`"outputs": [],`
`260`	`260`	`"source": [`
`261`		`- "scn.instrument_view(sample, pixel_size=0.0075)"`
	`261`	`+ "scn.instrument_view(sample.hist(), pixel_size=0.0075)"`
`262`	`262`	`]`
`263`	`263`	`},`
`264`	`264`	`{`
`@@ -301,7 +301,7 @@`
`301`	`301`	`"metadata": {},`
`302`	`302`	`"outputs": [],`
`303`	`303`	`"source": [`
`304`		`- "sc.plot(sample)"`
	`304`	`+ "sc.plot(sample.hist(tof=200).sum('spectrum'))"`
`305`	`305`	`]`
`306`	`306`	`},`
`307`	`307`	`{`
`@@ -428,9 +428,9 @@`
`428`	`428`	`"metadata": {},`
`429`	`429`	`"outputs": [],`
`430`	`430`	`"source": [`
`431`		`- "p = sc.plot(monitors['sample'], norm='log')\n",`
`432`		`- "sc.plot(monitors['direct'], norm='log', ax=p.ax, color=['C2', 'C3'])\n",`
`433`		`- "p"`
	`431`	`+ "sc.plot({**{f'sample-{key}': val for key, val in monitors['sample'].items()},\n",`
	`432`	`+ " **{f'direct-{key}': val for key, val in monitors['direct'].items()}}\n",`
	`433`	`+ " , norm='log')"`
`434`	`434`	`]`
`435`	`435`	`},`
`436`	`436`	`{`
`@@ -646,7 +646,7 @@`
`646`	`646`	`"metadata": {},`
`647`	`647`	`"outputs": [],`
`648`	`648`	`"source": [`
`649`		`- "sc.plot(sample_q, norm='log')"`
	`649`	`+ "sc.plot(sample_q.hist(), norm='log')"`
`650`	`650`	`]`
`651`	`651`	`},`
`652`	`652`	`{`
`@@ -706,7 +706,7 @@`
`706`	`706`	`"metadata": {},`
`707`	`707`	`"outputs": [],`
`708`	`708`	`"source": [`
`709`		`- "sc.plot(sample_normalized)"`
	`709`	`+ "sc.plot(sample_normalized.hist())"`
`710`	`710`	`]`
`711`	`711`	`},`
`712`	`712`	`{`
Original file line number	Diff line number	Diff line change
`@@ -78,7 +78,7 @@ def normalize_by_vanadium(data: sc.DataArray, *, vanadium: sc.DataArray,`
`78`	`78`	`:`
`79`	`79`	`data` normalized by `vanadium`.
`80`	`80`	`"""`
`81`		`- norm = sc.lookup(sc.histogram(vanadium, bins=edges), dim=edges.dim)`
	`81`	`+ norm = sc.lookup(vanadium.hist({edges.dim: edges}), dim=edges.dim)`
`82`	`82`	`# Converting to unit 'one' because the division might produce a unit`
`83`	`83`	`# with a large scale if the proton charges in data and vanadium were`
`84`	`84`	`# measured with different units.`