first start

Author: damskii9992

.gitignore

@@ -41,6 +41,12 @@ docs/_build
 # VSCode
 .vscode
 
+# Large files
+*.hdf
+*normalized.tiff
+*sample.tiff
+*open_beam.tiff
+
 # Misc
 ..*
 *.log

pyproject.toml

@@ -31,6 +31,7 @@ requires-python = ">=3.9,<3.12"
 dependencies = [
     "easyscience>=0.6.0",
     "scipp>=23.12.0",
+    "easycrystallography",
 ]
 
 [project.optional-dependencies]

src/easyimaging/project/sample_model/crystal_structure/crystal_structure.py

@@ -0,0 +1,60 @@
+import numbers
+from typing import List
+from typing import Tuple
+from typing import Union
+
+from easycrystallography.Structures.Phase import Phase
+from easycrystallography.Structures.Phase import Phases
+
+
+class CrystalAlloy(Phases):
+
+    def __init__(self, name: str, phases: list[Phase], fractions: list[numbers.Number]):
+        super().__init__(name=name)
+
+        if not isinstance(phases, list[Phase]):
+            raise TypeError(f"phases should be a list of Phase objects, got {type(phases)}") 
+        if not isinstance(fractions, list[numbers.Number]):
+            raise TypeError(f"fractions should be a list of numbers, got {type(fractions)}")
+        if len(phases) != len(fractions):
+            raise ValueError(f"phases and fractions should have the same length, got {len(phases)} and {len(fractions)}")
+        if sum(fractions) > 1:
+            raise ValueError(f"fractions should sum to 1 or less, got {sum(fractions)}")
+        if any(fraction < 0 for fraction in fractions):
+            raise ValueError(f"fractions should be non-negative, got {fractions}")
+        
+        self._phases = phases
+        self._fractions = fractions
+
+    def __getitem__(self, idx) -> List[Tuple[Phase, numbers.Number]]:
+        if isinstance(idx, int):
+            return self._phases[idx], self._fractions[idx]
+        elif isinstance(idx, slice):
+            return [(self._phases[i], self._fractions[i]) for i in range(len(self._phases))][idx]
+        else:
+            raise TypeError(f"Invalid index type: {type(idx)}. Expected int or slice.")
+        
+    def __setitem__(self, idx, value) -> None:
+        
+    def __len__(self) -> int:
+        return len(self._phases)
+
+    def __delitem__(self, idx) -> None:
+        if isinstance(idx, int):
+            del self._phases[idx]
+            del self._fractions[idx]
+        elif isinstance(idx, slice):
+            del self._phases[idx]
+            del self._fractions[idx]
+        else:
+            raise TypeError(f"Invalid index type: {type(idx)}. Expected int or slice.")
+
+    @property
+    def phases(self) -> List[Tuple[Phase, numbers.Number]]:
+        """Get the phases and their corresponding fractions."""
+        return [(phase, fraction) for phase, fraction in zip(self._phases, self._fractions)]
+    
+    @phases.setter
+    def phases(self):
+        raise AttributeError("phases is read-only, use set_phases() to overwrite it")
+    

src/easyimaging/project/sample_model/crystal_structure/phase.py

@@ -0,0 +1,136 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import easycrystallography as ec\n",
+    "from easycrystallography.Structures.Phase import Phase"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase = Phase(name='Iron')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase.space_group.name_hm_alt = 'P4/mmm'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase.cell.length_a = 2.866"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase.atoms.append(label='Fe', type_symbol='Fe', fract_x=0.0, fract_y=0.0, fract_z=0.0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase.add_atom(label='Fe', type_symbol='Fe', fract_x=0.5, fract_y=0.5, fract_z=0.5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Atom Fe (Fe) @ (0.5, 0.5, 0.5)"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "phase.atoms[1]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "phase.remove_atom('Fe')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Collection of 0 sites."
+      ]
+     },
+     "execution_count": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "phase.atoms"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "easyimaging",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}