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180 extract functionality from sample in easyreflectometryappproxiesm…
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…odel to lib (#183)

* renaming from item to assembly

* collections are together in folder

* moving responsibilities from model to sample

* rename experiment to model

* test for sample

* ruff

* get classes from module

* add Multilayer assembly if none

* cleaning of sample

* experiment to model and new sample structure

* Update src/easyreflectometry/sample/collections/sample.py

* update jupyter
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@andped10
andped10 authored Sep 20, 2024
1 parent 5d48702 commit 21c958d
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Showing 40 changed files with 687 additions and 393 deletions.
21 changes: 11 additions & 10 deletions docs/src/tutorials/fitting/repeating.ipynb
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "29d5d62d-af4a-416d-bbe2-1338d32b30f5",
"metadata": {},
"outputs": [],
Expand All @@ -45,8 +45,9 @@
"from easyreflectometry.sample import Sample\n",
"from easyreflectometry.sample import Material\n",
"from easyreflectometry.sample import RepeatingMultilayer\n",
"from easyreflectometry.experiment import Model\n",
"from easyreflectometry.experiment import PercentageFhwm\n",
"from easyreflectometry.sample import Multilayer\n",
"from easyreflectometry.model import Model\n",
"from easyreflectometry.model import PercentageFhwm\n",
"from easyreflectometry.calculators import CalculatorFactory\n",
"from easyreflectometry.fitting import Fitter\n",
"from easyreflectometry.plot import plot\n",
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"id": "7121c7e9",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"id": "0f95d620-35b7-4b47-a3b4-9e33d5525b50",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"id": "9a0b37ed-8714-4614-b49f-1e86ac232ac1",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"id": "fed8d60f-a4a7-40f1-8063-eb975bfa6115",
"metadata": {},
"outputs": [],
"source": [
"resolution_function = PercentageFhwm(0)\n",
"sample = Sample(superphase, rep_multilayer, subphase, name='Multilayer Structure')\n",
"sample = Sample(Multilayer(superphase), rep_multilayer, Multilayer(subphase), name='Multilayer Structure')\n",
"model = Model(\n",
" sample=sample,\n",
" scale=1,\n",
Expand All @@ -221,7 +222,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"id": "db1e3df9-d0fa-421a-a959-a8b2fe483310",
"metadata": {},
"outputs": [],
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
"version": "3.12.5"
}
},
"nbformat": 4,
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32 changes: 16 additions & 16 deletions docs/src/tutorials/fitting/simple_fitting.ipynb
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Expand Up @@ -22,7 +22,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "f026d35c-6a4a-4e9d-889c-d23ea6ee7adc",
"metadata": {},
"outputs": [],
Expand All @@ -39,8 +39,8 @@
"from easyreflectometry.sample import Sample\n",
"from easyreflectometry.sample import Material\n",
"from easyreflectometry.sample import Multilayer\n",
"from easyreflectometry.experiment import Model\n",
"from easyreflectometry.experiment import PercentageFhwm\n",
"from easyreflectometry.model import Model\n",
"from easyreflectometry.model import PercentageFhwm\n",
"from easyreflectometry.calculators import CalculatorFactory\n",
"from easyreflectometry.fitting import Fitter\n",
"from easyreflectometry.plot import plot"
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"id": "7d851064-605c-4f80-a510-197bcdbff2ea",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"id": "1fd5d9ba-a912-40f1-96a9-8d8d85c35c18",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"id": "bfd2d8a1-35fe-4a6c-aeee-93f1b4066b61",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 10,
"id": "a6508395-d292-4338-9fbe-77e19b011ae6",
"metadata": {},
"outputs": [],
Expand All @@ -253,12 +253,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 11,
"id": "2a0aee2a-e77e-4558-a8b0-ef2d1cffd4d0",
"metadata": {},
"outputs": [],
"source": [
"sample = Sample(superphase, film_layer, subphase, name='Film Structure')"
"sample = Sample(superphase, Multilayer(film_layer), Multilayer(subphase), name='Film Structure')"
]
},
{
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 13,
"id": "8646c977-28b4-4cd4-adbd-fc263359ca1c",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 18,
"id": "a4d3eae5-ec8d-4a7f-91ef-fcce3cc5a5ed",
"metadata": {},
"outputs": [],
Expand All @@ -373,7 +373,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 19,
"id": "7e2d7b81-7b49-4831-9508-75e0e234f15f",
"metadata": {},
"outputs": [],
Expand All @@ -400,7 +400,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 20,
"id": "cdbe172a-1283-4cdc-8fb2-d3383b8d21b3",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 22,
"id": "3648873e-16bb-449d-b90d-8b1bd4f05eb6",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 23,
"id": "9762fc0b-c4c2-4f92-8560-079ea248dfca",
"metadata": {},
"outputs": [],
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
"version": "3.12.5"
}
},
"nbformat": 4,
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20 changes: 10 additions & 10 deletions docs/src/tutorials/magnetism.ipynb
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "29d5d62d-af4a-416d-bbe2-1338d32b30f5",
"metadata": {},
"outputs": [],
Expand All @@ -38,8 +38,8 @@
"import easyreflectometry\n",
"\n",
"from easyreflectometry.calculators import CalculatorFactory\n",
"from easyreflectometry.experiment import Model\n",
"from easyreflectometry.experiment import PercentageFhwm\n",
"from easyreflectometry.model import Model\n",
"from easyreflectometry.model import PercentageFhwm\n",
"from easyreflectometry.sample import Layer\n",
"from easyreflectometry.sample import Material\n",
"from easyreflectometry.sample import Multilayer\n",
Expand Down Expand Up @@ -91,7 +91,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"id": "0f95d620-35b7-4b47-a3b4-9e33d5525b50",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"id": "2af8c30b",
"metadata": {},
"outputs": [],
"source": [
"two_layers = Multilayer([sld_4_layer, sld_8_layer], name='SLD 4/8 Layer')\n",
"sample = Sample(superphase, two_layers, subphase, name='Two Layer Sample')\n",
"sample = Sample(Multilayer(superphase), two_layers, Multilayer(subphase), name='Two Layer Sample')\n",
"model = Model(\n",
" sample=sample,\n",
" scale=1,\n",
Expand All @@ -144,7 +144,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"id": "b0259cd0",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"id": "f1500603-d85d-4e16-b697-e1bf16502991",
"metadata": {},
"outputs": [],
Expand All @@ -194,7 +194,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"id": "18010202",
"metadata": {},
"outputs": [],
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
"version": "3.12.5"
}
},
"nbformat": 4,
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