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Doc for hough indexing with multiple phases #633

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Doc for hough indexing with multiple phases #633

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b9e0c36
Add doc for hough indexing with multiple phases
Erlendos12 Mar 29, 2023
bd5878c
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Erlendos12 Mar 29, 2023
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@Erlendos12
Erlendos12 committed Mar 29, 2023
commit bd5878c4d59b0e8c9f7dbb5d1cf90faded8590c4
66 changes: 34 additions & 32 deletions doc/tutorials/hough_indexing_multiple_phases.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@
"outputs": [],
"source": [
"s = kp.data.sdss_ebsd(allow_download=True)\n",
"s"
"s\n"
]
},
{
Expand All @@ -100,7 +100,7 @@
"outputs": [],
"source": [
"vbse_imager = kp.imaging.VirtualBSEImager(s)\n",
"print(vbse_imager.grid_shape)"
"print(vbse_imager.grid_shape)\n"
]
},
{
Expand All @@ -119,7 +119,7 @@
"outputs": [],
"source": [
"maps_vbse_rgb = vbse_imager.get_rgb_image(r=(2, 1), g=(2, 2), b=(2, 3))\n",
"maps_vbse_rgb"
"maps_vbse_rgb\n"
]
},
{
Expand All @@ -137,7 +137,7 @@
"metadata": {},
"outputs": [],
"source": [
"maps_vbse_rgb.plot()"
"maps_vbse_rgb.plot()\n"
]
},
{
Expand All @@ -157,7 +157,7 @@
"outputs": [],
"source": [
"s.remove_static_background()\n",
"s.remove_dynamic_background()"
"s.remove_dynamic_background()\n"
]
},
{
Expand All @@ -175,7 +175,7 @@
"metadata": {},
"outputs": [],
"source": [
"maps_iq = s.get_image_quality()"
"maps_iq = s.get_image_quality()\n"
]
},
{
Expand All @@ -199,7 +199,7 @@
" colorbar=True,\n",
" colorbar_label=\"Image quality $Q$\",\n",
" remove_padding=True,\n",
")"
")\n"
]
},
{
Expand Down Expand Up @@ -234,7 +234,7 @@
"sig_shape = s.axes_manager.signal_shape[::-1] # (Rows, columns)\n",
"det = kp.detectors.EBSDDetector(sig_shape, sample_tilt=70)\n",
"\n",
"det"
"det\n"
]
},
{
Expand All @@ -254,7 +254,7 @@
"source": [
"grid_shape = (4, 4)\n",
"s_grid, idx = s.extract_grid(grid_shape, return_indices=True)\n",
"s_grid"
"s_grid\n"
]
},
{
Expand All @@ -278,7 +278,7 @@
" rc=idx.reshape(2, -1).T, # Shape (n patterns, 2)\n",
" roi_shape=nav_shape, # Or maps_iq.shape\n",
" roi_image=maps_iq,\n",
")"
")\n"
]
},
{
Expand Down Expand Up @@ -335,7 +335,7 @@
"print(indexer.sampleTilt)\n",
"print(indexer.camElev)\n",
"print(indexer.PC)\n",
"print(indexer.phaselist)"
"print(indexer.phaselist)\n"
]
},
{
Expand All @@ -362,7 +362,7 @@
"\n",
"# Print mean and standard deviation\n",
"print(det.pc_flattened.mean(axis=0))\n",
"print(det.pc_flattened.std(0))"
"print(det.pc_flattened.std(0))\n"
]
},
{
Expand All @@ -380,7 +380,7 @@
"metadata": {},
"outputs": [],
"source": [
"det.plot_pc(\"scatter\", s=50, annotate=True)"
"det.plot_pc(\"scatter\", s=50, annotate=True)\n"
]
},
{
Expand All @@ -401,7 +401,7 @@
"metadata": {},
"outputs": [],
"source": [
"det.pc = det.pc_average"
"det.pc = det.pc_average\n"
]
},
{
Expand All @@ -420,7 +420,7 @@
"metadata": {},
"outputs": [],
"source": [
"det.plot(pattern=s_grid.inav[0, 0].data)"
"det.plot(pattern=s_grid.inav[0, 0].data)\n"
]
},
{
Expand All @@ -443,7 +443,7 @@
"outputs": [],
"source": [
"indexer = det.get_indexer(phase_list)\n",
"indexer.PC"
"indexer.PC\n"
]
},
{
Expand All @@ -466,7 +466,7 @@
"source": [
"xmap, data = s.hough_indexing(\n",
" phase_list=phase_list, indexer=indexer, verbose=2, return_index_data=True\n",
")"
")\n"
]
},
{
Expand All @@ -476,7 +476,7 @@
"metadata": {},
"outputs": [],
"source": [
"xmap"
"xmap\n"
]
},
{
Expand Down Expand Up @@ -510,7 +510,7 @@
" im = a.imshow(xmap.get_map_data(to_plot))\n",
" fig.colorbar(im, ax=a, label=to_plot)\n",
" a.axis(\"off\")\n",
"fig.subplots_adjust(wspace=0, hspace=0.05)"
"fig.subplots_adjust(wspace=0, hspace=0.05)\n"
]
},
{
Expand All @@ -534,7 +534,7 @@
"metadata": {},
"outputs": [],
"source": [
"xmap.plot(remove_padding=True)"
"xmap.plot(remove_padding=True)\n"
]
},
{
Expand All @@ -556,7 +556,7 @@
"sym = xmap.phases[0].point_group\n",
"\n",
"ckey = plot.IPFColorKeyTSL(sym, v_ipf)\n",
"ckey"
"ckey\n"
]
},
{
Expand Down Expand Up @@ -588,7 +588,7 @@
"# Place color key in bottom right corner, coordinates are [left, bottom, width, height]\n",
"ax_ckey = fig.add_axes([0.63, 0.08, 0.2, 0.2], projection=\"ipf\", symmetry=sym)\n",
"ax_ckey.plot_ipf_color_key(show_title=False)\n",
"ax_ckey.patch.set_facecolor(\"None\")"
"ax_ckey.patch.set_facecolor(\"None\")\n"
]
},
{
Expand Down Expand Up @@ -619,7 +619,7 @@
" ax[i].imshow(rgb.reshape(xmap.shape + (3,)))\n",
" ax[i].set_title(f\"IPF-{title}\")\n",
" ax[i].axis(\"off\")\n",
"fig.subplots_adjust(wspace=0.02)"
"fig.subplots_adjust(wspace=0.02)\n"
]
},
{
Expand All @@ -645,7 +645,7 @@
")\n",
"rlv = rlv.symmetrise()\n",
"simulator = kp.simulations.KikuchiPatternSimulator(rlv)\n",
"sim = simulator.on_detector(det, xmap.rotations.reshape(*xmap.shape))"
"sim = simulator.on_detector(det, xmap.rotations.reshape(*xmap.shape))\n"
]
},
{
Expand All @@ -667,7 +667,7 @@
"s.add_marker(markers, plot_marker=False, permanent=True)\n",
"\n",
"# To remove existing markers\n",
"# del s.metadata.Markers"
"# del s.metadata.Markers\n"
]
},
{
Expand All @@ -685,7 +685,7 @@
"metadata": {},
"outputs": [],
"source": [
"maps_nav_rgb = kp.draw.get_rgb_navigator(rgb_x.reshape(xmap.shape + (3,)))"
"maps_nav_rgb = kp.draw.get_rgb_navigator(rgb_x.reshape(xmap.shape + (3,)))\n"
]
},
{
Expand All @@ -695,7 +695,7 @@
"metadata": {},
"outputs": [],
"source": [
"s.plot(maps_nav_rgb)"
"s.plot(maps_nav_rgb)\n"
]
},
{
Expand Down Expand Up @@ -733,7 +733,7 @@
" scan_unit=\"um\",\n",
")\n",
"print(xmap_austenite, \"\\n\")\n",
"print(xmap_ferrite)"
"print(xmap_ferrite)\n"
]
},
{
Expand All @@ -756,7 +756,7 @@
"nav_mask_austenite = nav_mask_austenite.reshape(xmap.shape)\n",
"\n",
"nav_mask_ferrite = ~(xmap_ferrite.phase_id == xmap.phases.id_from_name(\"ferrite\"))\n",
"nav_mask_ferrite = nav_mask_ferrite.reshape(xmap.shape)"
"nav_mask_ferrite = nav_mask_ferrite.reshape(xmap.shape)\n"
]
},
{
Expand Down Expand Up @@ -801,7 +801,7 @@
" method=\"minimize\",\n",
" method_kwargs=dict(method=\"Nelder-Mead\", tol=1e-4),\n",
" compute=True,\n",
")"
")\n"
]
},
{
Expand All @@ -810,7 +810,9 @@
"metadata": {},
"outputs": [],
"source": [
"refined_xmap = kp.indexing.merge_crystal_maps([refined_xmap_austenite, refined_xmap_ferrite])"
"refined_xmap = kp.indexing.merge_crystal_maps(\n",
" [refined_xmap_austenite, refined_xmap_ferrite]\n",
")"
]
},
{
Expand Down Expand Up @@ -846,7 +848,7 @@
" rgb = ckey.orientation2color(map.rotations)\n",
" cell.imshow(rgb.reshape(map.shape + (3,)))\n",
" else:\n",
" cell.plot_map(map)"
" cell.plot_map(map)\n"
]
},
{
Expand Down