diff --git a/src/geomtools/sfx/report.ipynb b/src/geomtools/sfx/report.ipynb index 5104b492483f97e6bea0bd4ac5601581d7bd152c..a266245165955dba25b1c2c9f13289fbac497f88 100644 --- a/src/geomtools/sfx/report.ipynb +++ b/src/geomtools/sfx/report.ipynb @@ -37,6 +37,7 @@ " read_crystfel_geom, plot_center_shift, plot_cell_parameters,\n", " plot_peakogram, plot_powder, get_peak_position, rmsd_per_group,\n", " avg_pixel_displacement, plot_geoptimiser_errormap,\n", + " plot_data_on_detector, pixels_to_image, badpixels_mask\n", ")" ] }, @@ -188,6 +189,50 @@ "fig, ax = plot_powder(peak_pos, counts=True)" ] }, + { + "cell_type": "markdown", + "id": "c5fb7a10-6ec2-4fc1-93bd-931440c7d0de", + "metadata": {}, + "source": [ + "# Bad pixels" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e5a90585-47e1-4445-a038-e6bed28ec13d", + "metadata": {}, + "outputs": [], + "source": [ + "px = badpixels_mask(pe, panels)\n", + "msk = pixels_to_image((16, 512, 128), px, 'msk')\n", + "fig, ax = plot_data_on_detector(msk, panels, colorbar=False, cmap=plt.cm.copper)" + ] + }, + { + "cell_type": "markdown", + "id": "d13224ba-344a-460d-8a18-ae011e3839e4", + "metadata": {}, + "source": [ + "# Peak distribution (masked)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "aa6706da-0470-4dc1-a88b-428fd209eb89", + "metadata": {}, + "outputs": [], + "source": [ + "flag = ~(\n", + " pe[['panel', 'fs', 'ss', 'intensity']]\n", + " .astype({'fs':int, 'ss':int})\n", + " .join(px.set_index(['panel', 'fs', 'ss']), on=['panel', 'fs', 'ss']).msk\n", + ")\n", + "peak_pos = pe[flag][['intensity']].join(get_peak_position(pe, panels))\n", + "fig, ax = plot_powder(peak_pos, counts=True)" + ] + }, { "cell_type": "markdown", "id": "81b065a7", @@ -237,7 +282,7 @@ "metadata": { "celltoolbar": "Raw Cell Format", "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3.9", "language": "python", "name": "python3" }, @@ -251,7 +296,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.3" + "version": "3.9.16" }, "title": "Detector geometry optimisation report" },