Formula dispersion (#122)

* Adds draft for formula dispersion init function * Adds working diel-func formula dispersion * Adds FormulaIndex dispersion * Adds formula dispersion represenation test * Adds nexus dispersive material load function * Adds grammar file to manifest * Clean unit check for formula dispersion * Removes unecessary code * Regenerate requirements * Adds nexus dispersive material testing files * Dispersions remodelling * Correctly add dispersions via *args * Adds quoting for fitting install in README * Adds converter functions between index and dielectric dispersions * Adds index based adding and fixes rii * Re-enable index based nexus file * Adds parametrization for adding tests * Adds nexus dispersion tests * Fix parameter order in custom sellmeier (#127) * Update discord link * Update discord badge * Adds absolute delta range * Adds support for 0,360 delta range * Return self in `as_delta_range` * Adds tests * Fix parameter order in custom sellmeier Fixes #126 * Fix documentation --------- Co-authored-by: domna <[email protected]> --------- Co-authored-by: Marius Müller <[email protected]>
PyEllips · Apr 15, 2023 · 5b9d41b · 5b9d41b
1 parent 98b61f4
commit 5b9d41b
Show file tree

Hide file tree

Showing 37 changed files with 1,331 additions and 1,132 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1,2 @@
-recursive-include src/elli/database/refractiveindexinfo-database *.yml
+recursive-include src/elli/database/refractiveindexinfo-database *.yml
+include src/elli/formula_parser/dispersion_function_grammer.lark
diff --git a/README.md b/README.md
@@ -64,7 +64,7 @@ the folder to install it in development mode:
 ```sh
 git clone https://github.com/PyEllips/pyElli
 cd pyElli
-pip install -e .[fitting]
+pip install -e ".[fitting]"
 ```
 
 ## Acknowledgements

diff --git a/pyproject.toml b/pyproject.toml
@@ -28,7 +28,9 @@ dependencies = [
     "h5py",
     "pyyaml",
     "importlib-resources",
-    "rapidfuzz"
+    "rapidfuzz",
+    "lark>=1.1.5",
+    "pint",
 ]
 
 [project.optional-dependencies]

diff --git a/requirements/dev-requirements.txt b/requirements/dev-requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
+# This file is autogenerated by pip-compile with python 3.9
+# To update, run:
 #
 #    pip-compile --extra=fitting --extra=testing --generate-hashes --output-file=requirements/dev-requirements.txt pyproject.toml requirements/fitting-requirements.txt
 #
@@ -292,6 +292,12 @@ h5py==3.7.0 \
     # via
     #   -r requirements/fitting-requirements.txt
     #   pyElli (pyproject.toml)
+importlib-metadata==6.0.0 \
+    --hash=sha256:7efb448ec9a5e313a57655d35aa54cd3e01b7e1fbcf72dce1bf06119420f5bad \
+    --hash=sha256:e354bedeb60efa6affdcc8ae121b73544a7aa74156d047311948f6d711cd378d
+    # via
+    #   -r requirements/fitting-requirements.txt
+    #   nbconvert
 importlib-resources==5.10.0 \
     --hash=sha256:c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668 \
     --hash=sha256:ee17ec648f85480d523596ce49eae8ead87d5631ae1551f913c0100b5edd3437
@@ -451,6 +457,12 @@ kiwisolver==1.4.4 \
     # via
     #   -r requirements/fitting-requirements.txt
     #   matplotlib
+lark==1.1.5 \
+    --hash=sha256:4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d \
+    --hash=sha256:8476f9903e93fbde4f6c327f74d79e9b4bd0ed9294c5dfa3164ab8c581b5de2a
+    # via
+    #   -r requirements/fitting-requirements.txt
+    #   pyElli (pyproject.toml)
 lmfit==1.0.3 \
     --hash=sha256:d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2
     # via
@@ -828,6 +840,12 @@ pillow==9.3.0 \
     # via
     #   -r requirements/fitting-requirements.txt
     #   matplotlib
+pint==0.20.1 \
+    --hash=sha256:387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067 \
+    --hash=sha256:68afe65665542ee3ec99f69f043b1d39bfe7c6d61b786940157138fd08b838fb
+    # via
+    #   -r requirements/fitting-requirements.txt
+    #   pyElli (pyproject.toml)
 plotly==5.10.0 \
     --hash=sha256:4d36d9859b7a153b273562deeed8c292587a472eb1fd57cd4158ec89d9defadb \
     --hash=sha256:989b13825cc974390aa0169479485d9257d37848a47bc63957251f8e1a7046ba
@@ -1382,3 +1400,10 @@ widgetsnbextension==3.6.1 \
     # via
     #   -r requirements/fitting-requirements.txt
     #   ipywidgets
+zipp==3.15.0 \
+    --hash=sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b \
+    --hash=sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556
+    # via
+    #   -r requirements/fitting-requirements.txt
+    #   importlib-metadata
+    #   importlib-resources
diff --git a/requirements/fitting-requirements.txt b/requirements/fitting-requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
+# This file is autogenerated by pip-compile with python 3.9
+# To update, run:
 #
 #    pip-compile --extra=fitting --generate-hashes --output-file=requirements/fitting-requirements.txt pyproject.toml requirements/requirements.txt
 #
@@ -202,6 +202,10 @@ h5py==3.7.0 \
     # via
     #   -r requirements/requirements.txt
     #   pyElli (pyproject.toml)
+importlib-metadata==6.0.0 \
+    --hash=sha256:7efb448ec9a5e313a57655d35aa54cd3e01b7e1fbcf72dce1bf06119420f5bad \
+    --hash=sha256:e354bedeb60efa6affdcc8ae121b73544a7aa74156d047311948f6d711cd378d
+    # via nbconvert
 importlib-resources==5.10.0 \
     --hash=sha256:c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668 \
     --hash=sha256:ee17ec648f85480d523596ce49eae8ead87d5631ae1551f913c0100b5edd3437
@@ -338,6 +342,12 @@ kiwisolver==1.4.4 \
     --hash=sha256:f8ad8285b01b0d4695102546b342b493b3ccc6781fc28c8c6a1bb63e95d22f09 \
     --hash=sha256:f9f39e2f049db33a908319cf46624a569b36983c7c78318e9726a4cb8923b26c
     # via matplotlib
+lark==1.1.5 \
+    --hash=sha256:4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d \
+    --hash=sha256:8476f9903e93fbde4f6c327f74d79e9b4bd0ed9294c5dfa3164ab8c581b5de2a
+    # via
+    #   -r requirements/requirements.txt
+    #   pyElli (pyproject.toml)
 lmfit==1.0.3 \
     --hash=sha256:d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2
     # via pyElli (pyproject.toml)
@@ -679,6 +689,12 @@ pillow==9.3.0 \
     --hash=sha256:ebf2029c1f464c59b8bdbe5143c79fa2045a581ac53679733d3a91d400ff9efb \
     --hash=sha256:f1ff2ee69f10f13a9596480335f406dd1f70c3650349e2be67ca3139280cade0
     # via matplotlib
+pint==0.20.1 \
+    --hash=sha256:387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067 \
+    --hash=sha256:68afe65665542ee3ec99f69f043b1d39bfe7c6d61b786940157138fd08b838fb
+    # via
+    #   -r requirements/requirements.txt
+    #   pyElli (pyproject.toml)
 plotly==5.10.0 \
     --hash=sha256:4d36d9859b7a153b273562deeed8c292587a472eb1fd57cd4158ec89d9defadb \
     --hash=sha256:989b13825cc974390aa0169479485d9257d37848a47bc63957251f8e1a7046ba
@@ -1126,3 +1142,10 @@ widgetsnbextension==3.6.1 \
     --hash=sha256:954e0faefdd414e4e013f17dbc7fd86f24cf1d243a3ac85d5f0fc2c2d2b50c66 \
     --hash=sha256:9c84ae64c2893c7cbe2eaafc7505221a795c27d68938454034ac487319a75b10
     # via ipywidgets
+zipp==3.15.0 \
+    --hash=sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b \
+    --hash=sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556
+    # via
+    #   -r requirements/requirements.txt
+    #   importlib-metadata
+    #   importlib-resources
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
+# This file is autogenerated by pip-compile with python 3.9
+# To update, run:
 #
 #    pip-compile --generate-hashes --output-file=requirements/requirements.txt pyproject.toml
 #
@@ -30,6 +30,10 @@ importlib-resources==5.10.0 \
     --hash=sha256:c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668 \
     --hash=sha256:ee17ec648f85480d523596ce49eae8ead87d5631ae1551f913c0100b5edd3437
     # via pyElli (pyproject.toml)
+lark==1.1.5 \
+    --hash=sha256:4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d \
+    --hash=sha256:8476f9903e93fbde4f6c327f74d79e9b4bd0ed9294c5dfa3164ab8c581b5de2a
+    # via pyElli (pyproject.toml)
 numpy==1.23.2 \
     --hash=sha256:17e5226674f6ea79e14e3b91bfbc153fdf3ac13f5cc54ee7bc8fdbe820a32da0 \
     --hash=sha256:2bd879d3ca4b6f39b7770829f73278b7c5e248c91d538aab1e506c628353e47f \
@@ -87,6 +91,10 @@ pandas==1.4.4 \
     --hash=sha256:e7cc960959be28d064faefc0cb2aef854d46b827c004ebea7e79b5497ed83e7d \
     --hash=sha256:ee6f1848148ed3204235967613b0a32be2d77f214e9623f554511047705c1e04
     # via pyElli (pyproject.toml)
+pint==0.20.1 \
+    --hash=sha256:387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067 \
+    --hash=sha256:68afe65665542ee3ec99f69f043b1d39bfe7c6d61b786940157138fd08b838fb
+    # via pyElli (pyproject.toml)
 python-dateutil==2.8.2 \
     --hash=sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86 \
     --hash=sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9
@@ -270,3 +278,7 @@ six==1.16.0 \
     --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \
     --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
     # via python-dateutil
+zipp==3.15.0 \
+    --hash=sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b \
+    --hash=sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556
+    # via importlib-resources
diff --git a/src/elli/database/refractive_index_info.py b/src/elli/database/refractive_index_info.py
@@ -21,7 +21,12 @@
     SellmeierCustomExponent,
     Table,
 )
-from ..dispersions.base_dispersion import Dispersion, DispersionSum
+from ..dispersions.base_dispersion import (
+    Dispersion,
+    DispersionSum,
+    IndexDispersion,
+    IndexDispersionSum,
+)
 from ..materials import IsotropicMaterial
 
 WavelengthFilterType = Union[
@@ -282,7 +287,9 @@ def get_mat(self, book: str, page: str) -> IsotropicMaterial:
         """
         return IsotropicMaterial(self.load_dispersion(book, page))
 
-    def load_dispersion(self, book: str, page: str) -> Dispersion:
+    def load_dispersion(
+        self, book: str, page: str
+    ) -> Union[Dispersion, IndexDispersion]:
         """Load a dispersion from the refractive index database.
         Selection by material and source identifiers.
 
@@ -307,6 +314,7 @@ def load_dispersion(self, book: str, page: str) -> Dispersion:
         )
 
         dispersion_list = []
+        contains_index_dispersion = False
 
         for dispersion_relation in yml_file["DATA"]:
             if dispersion_relation["type"] == "tabulated nk":
@@ -319,6 +327,7 @@ def load_dispersion(self, book: str, page: str) -> Dispersion:
                 df.set_index("Wavelength", inplace=True)
 
                 dispersion = Table(lbda=df.index, n=df["n"] + 1j * df["k"])
+                contains_index_dispersion = True
 
             elif dispersion_relation["type"] == "tabulated n":
                 df = pd.read_table(
@@ -330,6 +339,7 @@ def load_dispersion(self, book: str, page: str) -> Dispersion:
                 df.set_index("Wavelength", inplace=True)
 
                 dispersion = Table(lbda=df.index, n=df["n"])
+                contains_index_dispersion = True
 
             elif dispersion_relation["type"] == "tabulated k":
                 df = pd.read_table(
@@ -341,6 +351,7 @@ def load_dispersion(self, book: str, page: str) -> Dispersion:
                 df.set_index("Wavelength", inplace=True)
 
                 dispersion = Table(lbda=df.index, n=0 + 1j * df["k"])
+                contains_index_dispersion = True
 
             elif dispersion_relation["type"] == "formula 1":
                 coeffs = list(
@@ -415,6 +426,7 @@ def load_dispersion(self, book: str, page: str) -> Dispersion:
                     cauchy.add(f_i / 1e3**e_i, e_i)
 
                 dispersion = cauchy
+                contains_index_dispersion = True
 
             else:
                 raise ValueError("Unimplemented Format.")
@@ -423,6 +435,13 @@ def load_dispersion(self, book: str, page: str) -> Dispersion:
 
         if len(dispersion_list) == 1:
             return dispersion_list[0]
+
+        if contains_index_dispersion:
+            for i, dispersion in enumerate(dispersion_list):
+                if not isinstance(dispersion, IndexDispersion):
+                    dispersion_list[i] = dispersion.as_index()
+
+            return IndexDispersionSum(*dispersion_list)
         return DispersionSum(*dispersion_list)
 
     def get_reference(self, book: str, page: str) -> str:

diff --git a/src/elli/dispersions/__init__.py b/src/elli/dispersions/__init__.py
@@ -20,3 +20,4 @@
 from .tauc_lorentz import TaucLorentz
 from .cody_lorentz import CodyLorentz
 from .pseudo_dielectric import PseudoDielectricFunction
+from .formula import Formula, FormulaIndex