docs: some fixes after comments from celine (#137)

Author: jokasimr

docs/user-guide/dream/dream-visualize-absorption.ipynb

@@ -37,9 +37,11 @@
    "id": "2",
    "metadata": {},
    "source": [
-    "## Load the data\n",
+    "## Load the detector geometry\n",
     "\n",
-    "We load a dataset from a Geant4 simulation only to get access to the detector geometry."
+    "We load a dataset from a Geant4 simulation **only** to get access to the detector geometry.\n",
+    "The neutron intensity distribution is not used in this visualization.\n",
+    "This visualization only displays the absorption correction at each pixel in the detector."
    ]
   },
   {
@@ -69,7 +71,7 @@
    "id": "5",
    "metadata": {},
    "source": [
-    "### Rod-like sample oriented along x-axis"
+    "### Rod-like sample oriented along y-axis"
    ]
   },
   {
@@ -87,9 +89,9 @@
     "# The shape determines the shape and the orientation of the sample\n",
     "rod_shape = Cylinder(\n",
     "    radius=sc.scalar(1, unit='cm'),\n",
-    "    height=(height := sc.scalar(5., unit='cm')),\n",
-    "    # Cylinder is oriented along the x-axis\n",
-    "    symmetry_line=(symmetry_line := sc.vector([1, 0, 0])),\n",
+    "    height=(height := sc.scalar(10., unit='cm')),\n",
+    "    # Cylinder is oriented along the y-axis\n",
+    "    symmetry_line=(symmetry_line := sc.vector([0, 1, 0])),\n",
     "    center_of_base=-height * symmetry_line / 2,\n",
     ")"
    ]
@@ -105,13 +107,13 @@
     "    rod_shape,\n",
     "    vanadium,\n",
     "    beam_direction=sc.vector([0, 0, 1]),\n",
-    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
+    "    wavelength=sc.geomspace('wavelength', 0.5, 4, 20, unit='angstrom'),\n",
     "    # To make it faster, don't compute the transmission fraction for every detector pixel, it's not necessary for the visualization.\n",
     "    detector_position=dg['mantle'].coords['position']['strip', ::4]['wire', ::2].copy(),\n",
     "    quadrature_kind='cheap',\n",
     ")\n",
     "\n",
-    "# The visualization expects the `position` coord to denote detector positions, and `wavelength` to be the last dimension.\n",
+    "# The visualization expects the `position` coord to denote detector positions\n",
     "transmission_fraction_mantle.coords['position'] = transmission_fraction_mantle.coords.pop('detector_position')\n",
     "dream.instrument_view(transmission_fraction_mantle, dim='wavelength', pixel_size=20.0)"
    ]
@@ -130,75 +132,29 @@
    "cell_type": "markdown",
    "id": "9",
    "metadata": {},
-   "source": [
-    "## Disk-like sample oriented along x-axis"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "10",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "disk_shape = Cylinder(\n",
-    "    radius=sc.scalar(5, unit='cm'),\n",
-    "    height=(height := sc.scalar(1., unit='cm')),\n",
-    "    # Cylinder is oriented along the x-axis\n",
-    "    symmetry_line=(symmetry_line := sc.vector([1, 0, 0])),\n",
-    "    center_of_base=-height * symmetry_line / 2,\n",
-    ")\n",
-    "\n",
-    "transmission_fraction_mantle = compute_transmission_map(\n",
-    "    disk_shape,\n",
-    "    vanadium,\n",
-    "    beam_direction=sc.vector([0, 0, 1]),\n",
-    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
-    "    # To make it faster, don't compute the transmission fraction for every detector pixel, it's not necessary for the visualization.\n",
-    "    detector_position=dg['mantle'].coords['position']['strip', ::4]['wire', ::2].copy(),\n",
-    "    quadrature_kind='cheap',\n",
-    ")\n",
-    "\n",
-    "# The visualization expects the `position` coord to denote detector positions, and `wavelength` to be the last dimension.\n",
-    "transmission_fraction_mantle.coords['position'] = transmission_fraction_mantle.coords.pop('detector_position')\n",
-    "dream.instrument_view(transmission_fraction_mantle, dim='wavelength', pixel_size=20.0)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "11",
-   "metadata": {},
    "source": [
     "## Does absorption influence the intensity in the endcap detector?"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
     "transmission_fraction_endcap = compute_transmission_map(\n",
     "    rod_shape,\n",
     "    vanadium,\n",
     "    beam_direction=sc.vector([0, 0, 1]),\n",
-    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
+    "    wavelength=sc.geomspace('wavelength', 0.5, 4, 20, unit='angstrom'),\n",
     "    detector_position=dg['endcap_backward'].coords['position']['strip', 0].copy(),\n",
     "    quadrature_kind='cheap',\n",
     ")\n",
     "\n",
     "transmission_fraction_endcap.coords['position'] = transmission_fraction_endcap.coords.pop('detector_position')\n",
     "dream.instrument_view(transmission_fraction_endcap, dim='wavelength', pixel_size=20.0)"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "13",
-   "metadata": {},
-   "source": [
-    "As expected the impact of absorption on on the intensity in the endcap detector is close to uniform."
-   ]
   }
  ],
  "metadata": {

src/ess/dream/instrument_view.py

@@ -49,6 +49,15 @@ def instrument_view(
     """
     from plopp.widgets import Box
 
+    if dim and isinstance(data, sc.DataArray) and dim in data.dims[:-1]:
+        data = data.transpose([d for d in data.dims if d != dim] + [dim])
+
+    if dim and isinstance(data, sc.DataGroup):
+        data = data.copy(deep=False)
+        for k, v in data.items():
+            if dim in v.dims[:-1]:
+                data[k] = v.transpose([d for d in v.dims if d != dim] + [dim])
+
     view = InstrumentView(
         data, dim=dim, pixel_size=pixel_size, autoscale=autoscale, **kwargs
     )

tests/dream/instrument_view_test.py

@@ -48,6 +48,23 @@ def test_instrument_view_one_module(fake_instrument_data):
     assert hasattr(view, 'slider')
 
 
+def test_instrument_view_slider_not_last_dim_dataarray(fake_instrument_data):
+    da = fake_instrument_data['bank1']
+    da = da.transpose(('tof', *(set(da.dims) - {'tof'})))
+    InstrumentView(da, dim='tof')
+
+
+def test_instrument_view_slider_not_last_dim_datagroup(fake_instrument_data):
+    da = fake_instrument_data
+    # Add extra dim so that not all entries in the group have the same set of dimensions
+    da['bank2'] = da['bank2'].broadcast(
+        dims=[*da['bank2'].dims, 'extra_dimension'], shape=[*da['bank2'].shape, 1]
+    )
+    for k, v in da.items():
+        da[k] = v.transpose(('tof', *(set(v.dims) - {'tof'})))
+    InstrumentView(da, dim='tof')
+
+
 def test_instrument_view_no_tof_slider(fake_instrument_data):
     view = InstrumentView(fake_instrument_data.sum('tof'))
     assert hasattr(view, 'checkboxes')