Add bad pixels to sfx geometry report

758e874c · Egor Sobolev · 5101b754 · 758e874c
Commit 758e874c authored 9 months ago by Egor Sobolev
--- 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"
 },

 %% Cell type:code id:3852d9ec-1143-4846-9f48-11751729d547 tags:parameters

 ``` python
 xwiz_dir = ""
 stream_file = ""
 summary_file = ""
 prefix=prefix = ""
 output_dir = ""
 geometry_file = ""
 connected_groups = ""
 ```

 %% Cell type:code id:19d522a3-26f5-4ac6-a4af-ee2139deafa2 tags:

 ``` python
 import os
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 from cfelpyutils.geometry import load_crystfel_geometry
 from geomtools import (
    read_crystfel_streamfile, extract_geometry, parse_xwiz_summary,
    read_crystfel_geom, plot_center_shift, plot_cell_parameters,
    plot_peakogram, plot_powder, get_peak_position, rmsd_per_group,
    avg_pixel_displacement, plot_geoptimiser_errormap,
+    plot_data_on_detector, pixels_to_image, badpixels_mask
 )
 ```

 %% Cell type:code id:776ff0aa tags:

 ``` python
 xwiz_conf, summary = parse_xwiz_summary(summary_file)
 propno = int(xwiz_conf['data']['proposal'])
 runs = eval(xwiz_conf['data']['runs'])

 panels, beam = read_crystfel_geom(geometry_file, indexes={'modno': 1})

 panel_columns = panels.columns.tolist() + ['panel']
 if connected_groups not in panel_columns:
    raise ValueError(
        f"Connected groups '{connected_groups}' are not defined")

 photon_energy = beam['photon_energy']
 clen = panels.clen.unique()
 if len(clen) == 1:
    clen = clen[0]

 fr, pe, la, re, ma = read_crystfel_streamfile(
    stream_file, panels, connected_groups, disp=False)
 ```

 %% Cell type:markdown id:046f728b tags:

 # EXtra-xwiz summary

 %% Cell type:code id:7c2a58aa tags:

 ``` python
 print(f"Proposal: {propno}")
 print(f"Runs: {runs}")
 print()
 print(f"Photon energy: {photon_energy} eV")
 print(f"Distance to sample: {clen} m")
 print()
 print(summary)
 print()
 print("From Crystfel stream file")
 print(f"read: {len(fr):9d} chunks, {len(la):9d} crystalls")
 ```

 %% Cell type:markdown id:3978ac22 tags:

 # Cell parameters

 %% Cell type:code id:2050288b-6bbd-4e5a-9854-04cde094ff6b tags:

 ``` python
 fig, axs = plot_cell_parameters(la)
 plt.show()
 ```

 %% Cell type:markdown id:59980ed1 tags:

 # Center shift

 %% Cell type:code id:c4265f40-f0c4-4ad6-bfbd-21796fb1354c tags:

 ``` python
 fig, ax = plot_center_shift(la)
 plt.show()
 ```

 %% Cell type:markdown id:d772ce42 tags:

 # Peakogram

 %% Cell type:code id:5ce7abee-fd09-48d3-85ef-cacc7b3a3468 tags:

 ``` python
 fig, ax = plot_peakogram(re)
 plt.show()
 ```

 %% Cell type:markdown id:7f05317e tags:

 # Pseudo-powder diffraction

 %% Cell type:code id:3cdf4100 tags:

 ``` python
 peak_pos = pe[['intensity']].join(get_peak_position(pe, panels))
 fig, ax = plot_powder(peak_pos, counts=False)
 ```

 %% Cell type:markdown id:c407096a tags:

 # Peak distribution

 %% Cell type:code id:aa673412 tags:

 ``` python
 fig, ax = plot_powder(peak_pos, counts=True)
 ```

+%% Cell type:markdown id:c5fb7a10-6ec2-4fc1-93bd-931440c7d0de tags:
+
+# Bad pixels
+
+%% Cell type:code id:e5a90585-47e1-4445-a038-e6bed28ec13d tags:
+
+``` python
+px = badpixels_mask(pe, panels)
+msk = pixels_to_image((16, 512, 128), px, 'msk')
+fig, ax = plot_data_on_detector(msk, panels, colorbar=False, cmap=plt.cm.copper)
+```
+
+%% Cell type:markdown id:d13224ba-344a-460d-8a18-ae011e3839e4 tags:
+
+# Peak distribution (masked)
+
+%% Cell type:code id:aa6706da-0470-4dc1-a88b-428fd209eb89 tags:
+
+``` python
+flag = ~(
+    pe[['panel', 'fs', 'ss', 'intensity']]
+    .astype({'fs':int, 'ss':int})
+    .join(px.set_index(['panel', 'fs', 'ss']), on=['panel', 'fs', 'ss']).msk
+)
+peak_pos = pe[flag][['intensity']].join(get_peak_position(pe, panels))
+fig, ax = plot_powder(peak_pos, counts=True)
+```
+
 %% Cell type:markdown id:81b065a7 tags:

 # Geoptimiser error map

 %% Cell type:code id:0d829343 tags:

 ``` python
 pxdispl = avg_pixel_displacement(ma, panels)
 fig, ax = plot_geoptimiser_errormap(pxdispl, panels)
 ```

 %% Cell type:markdown id:5cbe54a5 tags:

 \newpage

 %% Cell type:code id:d4041551 tags:

 ``` python
 rmsd_detector = np.sqrt((pxdispl.r_avg * pxdispl.r_avg).mean())
 print(f"Detector-wide error: RMSD = {rmsd_detector:.4f} pixels.")

 rmsd = rmsd_per_group(pxdispl, panels, connected_groups)
 rmsd = rmsd.sort_index(key=np.vectorize(lambda x: int(x[1:])))
 print("Error per module:")
 display(rmsd)
 ```