Add a parameter refinement engine, mythen reduction and sample alignment

.devcontainer/devcontainer.json

@@ -3,7 +3,8 @@
     "name": "Python 3 Developer Container",
     "build": {
         "dockerfile": "../Dockerfile",
-        "target": "developer"
+        "target": "developer",
+        "platform": "linux/amd64"
     },
     "remoteEnv": {
         // Allow X11 apps to run inside the container
@@ -63,7 +64,25 @@
             "source": "devcontainer-shared-cache",
             "target": "/cache",
             "type": "volume"
-        }
+        },
+        {
+            "source": "${localEnv:HOME}${localEnv:USERPROFILE}",
+            "target": "/host-home",
+            "type": "bind"
+        },
+        // Mount facility directories if present on the host (Docker will create
+        // the host directory if it does not exist). These ensure /dls and
+        // /dls_sw are available inside the container when present on the host.
+        // {
+        //     "source": "/dls/i15-1/data",
+        //     "target": "/dls/i15-1/data",
+        //     "type": "bind"
+        // },
+        // {
+        //     "source": "/dls_sw",
+        //     "target": "/dls_sw",
+        //     "type": "bind"
+        // }
     ],
     // Mount the parent as /workspaces so we can pip install peers as editable
     "workspaceMount": "source=${localWorkspaceFolder}/..,target=/workspaces,type=bind",

.gitignore

@@ -5,6 +5,16 @@ __pycache__/
 # C extensions
 *.so
 
+#h5 files, but not hdf5
+*.h5 
+
+# output of running reduction
+*.xye
+**/processed/
+
+#binary files used for ang cal
+*.obj
+
 # Distribution / packaging
 .Python
 env/
@@ -69,3 +79,6 @@ lockfiles/
 
 # ruff cache
 .ruff_cache/
+
+#mac items
+*.DS_Store

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ repos:
     rev: v5.0.0
     hooks:
       - id: check-added-large-files
-        exclude: ^uv.lock
+        exclude: (^uv\.lock$|\.hdf5$)
       - id: check-yaml
       - id: check-merge-conflict
       - id: end-of-file-fixer

.vscode/settings.json

@@ -1,5 +1,6 @@
 {
     "python.testing.unittestEnabled": false,
+    "python.analysis.nodeExecutable": "auto",
     "python.testing.pytestEnabled": true,
     "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {
@@ -9,4 +10,6 @@
     "[python]": {
         "editor.defaultFormatter": "charliermarsh.ruff",
     },
+    "python-envs.defaultEnvManager": "ms-python.python:system",
+    "python-envs.pythonProjects": [],
 }

Dockerfile

@@ -5,7 +5,28 @@ FROM ghcr.io/diamondlightsource/ubuntu-devcontainer:noble AS developer
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
     graphviz \
-    && apt-get dist-clean
+    && apt-get dist-clean 
+
+RUN apt-get update && apt-get install ffmpeg libsm6 libxext6 libgl1 libegl1 -y
+RUN apt-get update && apt-get install -y \
+    libx11-xcb-dev \
+    libglu1-mesa-dev \
+    libxrender-dev \
+    libxi-dev \
+    libxkbcommon-dev \
+    libxkbcommon-x11-dev \
+    libegl1 \
+    libxcb-cursor0 -y
+
+RUN apt-get update && apt-get install -y \
+    libxcb-icccm4 \
+    libxcb-keysyms1 \
+    libxcb-render-util0 \
+    libxcb-xinerama0 \
+    libxcb-xkb1 \
+    libxkbcommon-x11-0
+
+RUN apt-get install fonts-noto-color-emoji -y
 
 # The build stage installs the context into the venv
 FROM developer AS build
@@ -29,7 +50,7 @@ FROM ubuntu:noble AS runtime
 
 # Add apt-get system dependecies for runtime here if needed
 # RUN apt-get update -y && apt-get install -y --no-install-recommends \
-#     some-library \
+#     some-dependecies \
 #     && apt-get dist-clean
 
 # Copy the python installation from the build stage
@@ -42,3 +63,6 @@ ENV PATH=/app/.venv/bin:$PATH
 # change this entrypoint if it is not the same as the repo
 ENTRYPOINT ["XRPD-Toolbox"]
 CMD ["--version"]
+
+ENV MPLCONFIGDIR=/tmp/matplotlib
+RUN export DISPLAY=:0

cifs/CeO2.cif

@@ -0,0 +1,267 @@
+
+#(C) 2026 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
+data_24887-ICSD
+_database_code_ICSD 24887
+_audit_creation_date 2021-08-01
+_chemical_name_common Ceria
+_chemical_formula_structural 'Ce O2'
+_chemical_formula_sum 'Ce1 O2'
+_chemical_name_structure_type CaF2
+_exptl_crystal_density_diffrn 7.19
+_citation_title
+
+;
+Introducing highly redox-active atomic centers into insertion-type electrodes
+for lithium-ion batteries
+;
+loop_
+_citation_id
+_citation_journal_full
+_citation_year
+_citation_journal_volume
+_citation_page_first
+_citation_page_last
+_citation_journal_id_ASTM
+primary 'Advanced Energy Materials' 2020 10 1 14 ADEMBC
+loop_
+_citation_author_citation_id
+_citation_author_name
+primary 'Ma, Yanjiao'
+primary 'Ma, Yuan'
+primary 'Giuli, Gabriele'
+primary 'Euchner, Holger'
+primary 'Gross, Axel'
+primary 'Lepore, Giovanni Orazio'
+primary "d'Acapito, Francesco"
+primary 'Geiger, Dorin'
+primary 'Biskupek, Johannes'
+primary 'Kaiser, Ute'
+primary 'Schütz, Hanno M.'
+primary 'Carlsson, Anna'
+primary 'Diemant, Thomas'
+primary 'Behm, Rolf Jürgen'
+primary 'Kuenzel, Matthias'
+primary 'Passerini, Stef'
+_cell_length_a 5.4178(1)
+_cell_length_b 5.4178(1)
+_cell_length_c 5.4178(1)
+_cell_angle_alpha 90.
+_cell_angle_beta 90.
+_cell_angle_gamma 90.
+_cell_volume 159.03
+_cell_formula_units_Z 4
+_space_group_name_H-M_alt 'F m -3 m'
+_space_group_IT_number 225
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 'z, y, -x'
+2 'y, x, -z'
+3 'x, z, -y'
+4 'z, x, -y'
+5 'y, z, -x'
+6 'x, y, -z'
+7 'z, -y, x'
+8 'y, -x, z'
+9 'x, -z, y'
+10 'z, -x, y'
+11 'y, -z, x'
+12 'x, -y, z'
+13 '-z, y, x'
+14 '-y, x, z'
+15 '-x, z, y'
+16 '-z, x, y'
+17 '-y, z, x'
+18 '-x, y, z'
+19 '-z, -y, -x'
+20 '-y, -x, -z'
+21 '-x, -z, -y'
+22 '-z, -x, -y'
+23 '-y, -z, -x'
+24 '-x, -y, -z'
+25 '-z, -y, x'
+26 '-y, -x, z'
+27 '-x, -z, y'
+28 '-z, -x, y'
+29 '-y, -z, x'
+30 '-x, -y, z'
+31 '-z, y, -x'
+32 '-y, x, -z'
+33 '-x, z, -y'
+34 '-z, x, -y'
+35 '-y, z, -x'
+36 '-x, y, -z'
+37 'z, -y, -x'
+38 'y, -x, -z'
+39 'x, -z, -y'
+40 'z, -x, -y'
+41 'y, -z, -x'
+42 'x, -y, -z'
+43 'z, y, x'
+44 'y, x, z'
+45 'x, z, y'
+46 'z, x, y'
+47 'y, z, x'
+48 'x, y, z'
+49 'z, y+1/2, -x+1/2'
+50 'y, x+1/2, -z+1/2'
+51 'x, z+1/2, -y+1/2'
+52 'z, x+1/2, -y+1/2'
+53 'y, z+1/2, -x+1/2'
+54 'x, y+1/2, -z+1/2'
+55 'z, -y+1/2, x+1/2'
+56 'y, -x+1/2, z+1/2'
+57 'x, -z+1/2, y+1/2'
+58 'z, -x+1/2, y+1/2'
+59 'y, -z+1/2, x+1/2'
+60 'x, -y+1/2, z+1/2'
+61 '-z, y+1/2, x+1/2'
+62 '-y, x+1/2, z+1/2'
+63 '-x, z+1/2, y+1/2'
+64 '-z, x+1/2, y+1/2'
+65 '-y, z+1/2, x+1/2'
+66 '-x, y+1/2, z+1/2'
+67 '-z, -y+1/2, -x+1/2'
+68 '-y, -x+1/2, -z+1/2'
+69 '-x, -z+1/2, -y+1/2'
+70 '-z, -x+1/2, -y+1/2'
+71 '-y, -z+1/2, -x+1/2'
+72 '-x, -y+1/2, -z+1/2'
+73 '-z, -y+1/2, x+1/2'
+74 '-y, -x+1/2, z+1/2'
+75 '-x, -z+1/2, y+1/2'
+76 '-z, -x+1/2, y+1/2'
+77 '-y, -z+1/2, x+1/2'
+78 '-x, -y+1/2, z+1/2'
+79 '-z, y+1/2, -x+1/2'
+80 '-y, x+1/2, -z+1/2'
+81 '-x, z+1/2, -y+1/2'
+82 '-z, x+1/2, -y+1/2'
+83 '-y, z+1/2, -x+1/2'
+84 '-x, y+1/2, -z+1/2'
+85 'z, -y+1/2, -x+1/2'
+86 'y, -x+1/2, -z+1/2'
+87 'x, -z+1/2, -y+1/2'
+88 'z, -x+1/2, -y+1/2'
+89 'y, -z+1/2, -x+1/2'
+90 'x, -y+1/2, -z+1/2'
+91 'z, y+1/2, x+1/2'
+92 'y, x+1/2, z+1/2'
+93 'x, z+1/2, y+1/2'
+94 'z, x+1/2, y+1/2'
+95 'y, z+1/2, x+1/2'
+96 'x, y+1/2, z+1/2'
+97 'z+1/2, y, -x+1/2'
+98 'y+1/2, x, -z+1/2'
+99 'x+1/2, z, -y+1/2'
+100 'z+1/2, x, -y+1/2'
+101 'y+1/2, z, -x+1/2'
+102 'x+1/2, y, -z+1/2'
+103 'z+1/2, -y, x+1/2'
+104 'y+1/2, -x, z+1/2'
+105 'x+1/2, -z, y+1/2'
+106 'z+1/2, -x, y+1/2'
+107 'y+1/2, -z, x+1/2'
+108 'x+1/2, -y, z+1/2'
+109 '-z+1/2, y, x+1/2'
+110 '-y+1/2, x, z+1/2'
+111 '-x+1/2, z, y+1/2'
+112 '-z+1/2, x, y+1/2'
+113 '-y+1/2, z, x+1/2'
+114 '-x+1/2, y, z+1/2'
+115 '-z+1/2, -y, -x+1/2'
+116 '-y+1/2, -x, -z+1/2'
+117 '-x+1/2, -z, -y+1/2'
+118 '-z+1/2, -x, -y+1/2'
+119 '-y+1/2, -z, -x+1/2'
+120 '-x+1/2, -y, -z+1/2'
+121 '-z+1/2, -y, x+1/2'
+122 '-y+1/2, -x, z+1/2'
+123 '-x+1/2, -z, y+1/2'
+124 '-z+1/2, -x, y+1/2'
+125 '-y+1/2, -z, x+1/2'
+126 '-x+1/2, -y, z+1/2'
+127 '-z+1/2, y, -x+1/2'
+128 '-y+1/2, x, -z+1/2'
+129 '-x+1/2, z, -y+1/2'
+130 '-z+1/2, x, -y+1/2'
+131 '-y+1/2, z, -x+1/2'
+132 '-x+1/2, y, -z+1/2'
+133 'z+1/2, -y, -x+1/2'
+134 'y+1/2, -x, -z+1/2'
+135 'x+1/2, -z, -y+1/2'
+136 'z+1/2, -x, -y+1/2'
+137 'y+1/2, -z, -x+1/2'
+138 'x+1/2, -y, -z+1/2'
+139 'z+1/2, y, x+1/2'
+140 'y+1/2, x, z+1/2'
+141 'x+1/2, z, y+1/2'
+142 'z+1/2, x, y+1/2'
+143 'y+1/2, z, x+1/2'
+144 'x+1/2, y, z+1/2'
+145 'z+1/2, y+1/2, -x'
+146 'y+1/2, x+1/2, -z'
+147 'x+1/2, z+1/2, -y'
+148 'z+1/2, x+1/2, -y'
+149 'y+1/2, z+1/2, -x'
+150 'x+1/2, y+1/2, -z'
+151 'z+1/2, -y+1/2, x'
+152 'y+1/2, -x+1/2, z'
+153 'x+1/2, -z+1/2, y'
+154 'z+1/2, -x+1/2, y'
+155 'y+1/2, -z+1/2, x'
+156 'x+1/2, -y+1/2, z'
+157 '-z+1/2, y+1/2, x'
+158 '-y+1/2, x+1/2, z'
+159 '-x+1/2, z+1/2, y'
+160 '-z+1/2, x+1/2, y'
+161 '-y+1/2, z+1/2, x'
+162 '-x+1/2, y+1/2, z'
+163 '-z+1/2, -y+1/2, -x'
+164 '-y+1/2, -x+1/2, -z'
+165 '-x+1/2, -z+1/2, -y'
+166 '-z+1/2, -x+1/2, -y'
+167 '-y+1/2, -z+1/2, -x'
+168 '-x+1/2, -y+1/2, -z'
+169 '-z+1/2, -y+1/2, x'
+170 '-y+1/2, -x+1/2, z'
+171 '-x+1/2, -z+1/2, y'
+172 '-z+1/2, -x+1/2, y'
+173 '-y+1/2, -z+1/2, x'
+174 '-x+1/2, -y+1/2, z'
+175 '-z+1/2, y+1/2, -x'
+176 '-y+1/2, x+1/2, -z'
+177 '-x+1/2, z+1/2, -y'
+178 '-z+1/2, x+1/2, -y'
+179 '-y+1/2, z+1/2, -x'
+180 '-x+1/2, y+1/2, -z'
+181 'z+1/2, -y+1/2, -x'
+182 'y+1/2, -x+1/2, -z'
+183 'x+1/2, -z+1/2, -y'
+184 'z+1/2, -x+1/2, -y'
+185 'y+1/2, -z+1/2, -x'
+186 'x+1/2, -y+1/2, -z'
+187 'z+1/2, y+1/2, x'
+188 'y+1/2, x+1/2, z'
+189 'x+1/2, z+1/2, y'
+190 'z+1/2, x+1/2, y'
+191 'y+1/2, z+1/2, x'
+192 'x+1/2, y+1/2, z'
+loop_
+_atom_type_symbol
+_atom_type_oxidation_number
+Ce4+ 4
+O2- -2
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_U_iso_or_equiv
+_atom_site_occupancy
+Ce1 Ce4+ 4 a 0 0 0 0.00078 1.
+O1 O2- 8 c 0.25 0.25 0.25 0.005 1.
+#End of TTdata_24887-ICSD