diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb index 0da8927940511bc6d4ff66db89f4624bbb4ca632..7ca70a974be7c05d321b7e5f994567414c28590b 100644 --- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb +++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb @@ -911,7 +911,7 @@ "metadata": {}, "outputs": [], "source": [ - "def do_2d_plot(data, edges, y_axis, x_axis):\n", + "def do_2d_plot(data, edges, y_axis, x_axis, title=\"\"):\n", " fig = plt.figure(figsize=(10, 10))\n", " ax = fig.add_subplot(111)\n", " extent = [np.min(edges[1]), np.max(edges[1]),\n", @@ -920,6 +920,7 @@ " norm=LogNorm(vmin=1, vmax=max(10, np.max(data))))\n", " ax.set_xlabel(x_axis)\n", " ax.set_ylabel(y_axis)\n", + " ax.set_title(title)\n", " cb = fig.colorbar(im)\n", " cb.set_label(\"Counts\")" ] @@ -1105,7 +1106,8 @@ " bins=(100, int(pulse_range[1])),\n", " range=[[clamp(vmin, -50, -0.2), min(vmax, 1000)], pulse_range],\n", ")\n", - "do_2d_plot(hist, (bins_x, bins_y), \"Signal (ADU)\", \"Pulse id\")\n", + "do_2d_plot(hist, (bins_x, bins_y), \"Signal (ADU)\", \"Pulse id\", title=\"Signal-Pulse ID\")\n", + "\n", "if vmax > 1000: # a zoom out plot.\n", " hist, bins_x, bins_y = calgs.histogram2d(\n", " mean_data.flatten().astype(np.float32),\n", @@ -1113,7 +1115,7 @@ " bins=(100, int(pulse_range[1])),\n", " range=[[clamp(vmin, -50, -0.2), min(vmax, 20000)], pulse_range]\n", " )\n", - " do_2d_plot(hist, (bins_x, bins_y), \"Signal (ADU)\", \"Pulse id\")" + " do_2d_plot(hist, (bins_x, bins_y), \"Signal (ADU)\", \"Pulse id\", title=\"Signal-Pulse ID (Extended View)\")" ] }, { @@ -1216,9 +1218,9 @@ " display(Markdown(f'A mean across train: {tid}\\n'))\n", " fig = plt.figure(figsize=(20, 10))\n", " ax = fig.add_subplot(111)\n", - " data = np.nanmean(corrected, axis=0)\n", - " vmin, vmax = np.nanpercentile(data, [5, 99.9])\n", - " ax = geom.plot_data_fast(data, ax=ax, vmin=vmin, vmax=vmax, cmap=cmap)\n", + " data = np.mean(corrected, axis=0)\n", + " vmax = np.nanpercentile(data, 99.8)\n", + " ax = geom.plot_data_fast(data, ax=ax, vmin=max(-50, np.nanmin(data)), vmax=vmax, cmap=cmap)\n", " pass\n", "else:\n", " print(\"Skipping mean CORRECTED preview for single memory cell, \"\n", @@ -1234,9 +1236,14 @@ "display(Markdown(f'A single shot of the CORRECTED image from cell {cell_id_preview} \\n'))\n", "fig = plt.figure(figsize=(20, 10))\n", "ax = fig.add_subplot(111)\n", - "vmin, vmax = np.nanpercentile(corrected[cell_idx_preview], [5, 99.9])\n", + "vmax = np.nanpercentile(corrected[cell_idx_preview], 99.8)\n", "ax = geom.plot_data_fast(\n", - " corrected[cell_idx_preview], ax=ax, vmin=vmin, vmax=vmax, cmap=cmap)\n", + " corrected[cell_idx_preview],\n", + " ax=ax,\n", + " vmin=max(-50, np.nanmin(corrected[cell_idx_preview])),\n", + " vmax=vmax,\n", + " cmap=cmap,\n", + ")\n", "pass" ] },