From 67811a4c758720169e0a1db0eef0348cd74a16e4 Mon Sep 17 00:00:00 2001
From: quentintanguy <66286557+quentintanguy@users.noreply.github.com>
Date: Thu, 19 Sep 2024 13:39:11 +0200
Subject: [PATCH 1/3] Create accurion.py

Provides a way to import data from Accurion EP4 ellipsometer, similar to woollam, nexus and spetraray.
---
 src/elli/importer/accurion.py | 99 +++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 src/elli/importer/accurion.py

diff --git a/src/elli/importer/accurion.py b/src/elli/importer/accurion.py
new file mode 100644
index 00000000..3ee176a1
--- /dev/null
+++ b/src/elli/importer/accurion.py
@@ -0,0 +1,99 @@
+"""A helper class to load data from Accurion EP4 DAT files.
+Typical files look like: Si3N4_on_4inBF33_W03_20240905-105631.ds.dat
+"""
+
+import pandas as pd
+import chardet
+import numpy as np
+
+def detect_encoding(fname: str):
+	r"""Detects the encoding of file fname. Used in read_accurion_psi_delta only.
+  Args:
+    fname (str): Filename
+  """
+	with open(fname, 'rb') as f:
+		raw_data = f.read()
+	result = chardet.detect(raw_data)
+	return result['encoding']
+
+def read_accurion_psi_delta(fname: str, wrap=True) -> pd.DataFrame:
+	r"""Read a psi/delta Accurion dat file.
+	
+  Args:
+    fname (str): Filename of the measured dat file
+    wrap (bool): Whether delta values should be wrapped; should always be True
+
+  Returns:
+    pd.DataFrame: DataFrame containing the psi/delta data in the pyElli-compatible format.
+  """
+	encoding = detect_encoding(fname)
+	psi_delta_df = pd.read_csv(fname, delimiter="\t", encoding=encoding, skiprows=0, header=0)[1:].astype(float)
+	psi_delta_df = psi_delta_df.reindex(columns=list(["AOI", "Lambda", "Delta", "Psi"]))
+	psi_delta_df = psi_delta_df.rename(columns={
+		"AOI": "Angle of Incidence",
+		"Lambda": "Wavelength",
+		"Delta": "Δ",
+		"Psi": "Ψ"
+		})
+	psi_delta_df = psi_delta_df.groupby(["Angle of Incidence", "Wavelength"]).sum()
+
+	# wrap delta range
+	if wrap:
+		psi_delta_df.loc[:, "Δ"] = psi_delta_df.loc[:, "Δ"].where(
+			psi_delta_df.loc[:, "Δ"] <= 180, psi_delta_df.loc[:, "Δ"] - 360
+		)
+
+	return psi_delta_df
+
+def convert_psi_delta_to_isotropic_mueller_matrix(psi_delta_df) -> pd.DataFrame:
+	r"""Extract aois and wavelengths values from psi_delta pandas.DataFrame and convert it to a Muellermatrix;
+ 	only works for isotropic media.
+
+ 	Args:
+		psi_delta_df (pd.DataFrame): dataFrame returned from data import using 'read_accurion_psi_delta()'
+
+ 	Returns:
+		pd.DataFrame: pyElli-compatible DataFrame of the Mueller matrix
+  """
+	aois = psi_delta_df.index.get_level_values("Angle of Incidence").unique().to_numpy()
+	wavelengths = psi_delta_df.index.get_level_values("Wavelength").unique().to_numpy()
+
+	# create empty Mueller matrix
+	MM = pd.DataFrame(
+		{},
+		columns=["M11", "M12", "M13", "M14", "M21", "M22", "M23", "M24", "M31", "M32", "M33", "M34", "M41", "M42", "M43", "M44"],
+		index=pd.MultiIndex.from_product([aois, wavelengths], names=["Angle of Incidence", "Wavelength"]),
+		dtype=float,
+		)
+
+	# fill in the Mueller matrix coefficients for an isotropic material based equation in https://www.jawoollam.com/resources/ellipsometry-faq#toggle-id-15
+	for aoi in aois:
+		for λ in wavelengths:
+			Δ = psi_delta_df.loc[aoi, λ]["Δ"]
+			Ψ = psi_delta_df.loc[aoi, λ]["Ψ"]
+
+			N = np.cos(2*Ψ)
+			C = np.sin(2*Ψ) * np.cos(2*Δ)
+			S = np.sin(2*Ψ) * np.cos(2*Δ)
+
+			MM.loc[(aoi, λ), "M11"] = 1
+			MM.loc[(aoi, λ), "M12"] = -N
+			MM.loc[(aoi, λ), "M13"] = 0
+			MM.loc[(aoi, λ), "M14"] = 0
+
+			MM.loc[(aoi, λ), "M21"] = -N
+			MM.loc[(aoi, λ), "M22"] = 1
+			MM.loc[(aoi, λ), "M23"] = 0
+			MM.loc[(aoi, λ), "M24"] = 0
+
+			MM.loc[(aoi, λ), "M31"] = 0
+			MM.loc[(aoi, λ), "M32"] = 0
+			MM.loc[(aoi, λ), "M33"] = C
+			MM.loc[(aoi, λ), "M34"] = S
+
+			MM.loc[(aoi, λ), "M41"] = 0
+			MM.loc[(aoi, λ), "M42"] = 0
+			MM.loc[(aoi, λ), "M43"] = -S
+			MM.loc[(aoi, λ), "M44"] = C
+
+	return MM

From 20f2bf3ca1e4b6dccf5ded8ed946f1f2dd348648 Mon Sep 17 00:00:00 2001
From: MarJMue <49639740+MarJMue@users.noreply.github.com>
Date: Wed, 2 Oct 2024 12:17:03 +0200
Subject: [PATCH 2/3] Requested changes

---
 src/elli/__init__.py          |   1 +
 src/elli/importer/accurion.py | 127 +++++++++-------------------------
 src/elli/utils.py             |  73 +++++++++++++++++++
 3 files changed, 108 insertions(+), 93 deletions(-)

diff --git a/src/elli/__init__.py b/src/elli/__init__.py
index 984fcedb..c2685d88 100644
--- a/src/elli/__init__.py
+++ b/src/elli/__init__.py
@@ -6,6 +6,7 @@
 from .dispersions import *
 from .dispersions.base_dispersion import *
 from .experiment import Experiment
+from .importer.accurion import read_accurion_psi_delta
 from .importer.nexus import *
 from .importer.spectraray import *
 from .importer.woollam import read_woollam_psi_delta, read_woollam_rho, scale_to_nm
diff --git a/src/elli/importer/accurion.py b/src/elli/importer/accurion.py
index 3ee176a1..87393b9b 100644
--- a/src/elli/importer/accurion.py
+++ b/src/elli/importer/accurion.py
@@ -2,98 +2,39 @@
 Typical files look like: Si3N4_on_4inBF33_W03_20240905-105631.ds.dat
 """
 
-import pandas as pd
-import chardet
 import numpy as np
+import pandas as pd
 
-def detect_encoding(fname: str):
-	r"""Detects the encoding of file fname. Used in read_accurion_psi_delta only.
-  Args:
-    fname (str): Filename
-  """
-	with open(fname, 'rb') as f:
-		raw_data = f.read()
-	result = chardet.detect(raw_data)
-	return result['encoding']
-
-def read_accurion_psi_delta(fname: str, wrap=True) -> pd.DataFrame:
-	r"""Read a psi/delta Accurion dat file.
-	
-  Args:
-    fname (str): Filename of the measured dat file
-    wrap (bool): Whether delta values should be wrapped; should always be True
-
-  Returns:
-    pd.DataFrame: DataFrame containing the psi/delta data in the pyElli-compatible format.
-  """
-	encoding = detect_encoding(fname)
-	psi_delta_df = pd.read_csv(fname, delimiter="\t", encoding=encoding, skiprows=0, header=0)[1:].astype(float)
-	psi_delta_df = psi_delta_df.reindex(columns=list(["AOI", "Lambda", "Delta", "Psi"]))
-	psi_delta_df = psi_delta_df.rename(columns={
-		"AOI": "Angle of Incidence",
-		"Lambda": "Wavelength",
-		"Delta": "Δ",
-		"Psi": "Ψ"
-		})
-	psi_delta_df = psi_delta_df.groupby(["Angle of Incidence", "Wavelength"]).sum()
-
-	# wrap delta range
-	if wrap:
-		psi_delta_df.loc[:, "Δ"] = psi_delta_df.loc[:, "Δ"].where(
-			psi_delta_df.loc[:, "Δ"] <= 180, psi_delta_df.loc[:, "Δ"] - 360
-		)
-
-	return psi_delta_df
-
-def convert_psi_delta_to_isotropic_mueller_matrix(psi_delta_df) -> pd.DataFrame:
-	r"""Extract aois and wavelengths values from psi_delta pandas.DataFrame and convert it to a Muellermatrix;
- 	only works for isotropic media.
-
- 	Args:
-		psi_delta_df (pd.DataFrame): dataFrame returned from data import using 'read_accurion_psi_delta()'
-
- 	Returns:
-		pd.DataFrame: pyElli-compatible DataFrame of the Mueller matrix
-  """
-	aois = psi_delta_df.index.get_level_values("Angle of Incidence").unique().to_numpy()
-	wavelengths = psi_delta_df.index.get_level_values("Wavelength").unique().to_numpy()
-
-	# create empty Mueller matrix
-	MM = pd.DataFrame(
-		{},
-		columns=["M11", "M12", "M13", "M14", "M21", "M22", "M23", "M24", "M31", "M32", "M33", "M34", "M41", "M42", "M43", "M44"],
-		index=pd.MultiIndex.from_product([aois, wavelengths], names=["Angle of Incidence", "Wavelength"]),
-		dtype=float,
-		)
-
-	# fill in the Mueller matrix coefficients for an isotropic material based equation in https://www.jawoollam.com/resources/ellipsometry-faq#toggle-id-15
-	for aoi in aois:
-		for λ in wavelengths:
-			Δ = psi_delta_df.loc[aoi, λ]["Δ"]
-			Ψ = psi_delta_df.loc[aoi, λ]["Ψ"]
-
-			N = np.cos(2*Ψ)
-			C = np.sin(2*Ψ) * np.cos(2*Δ)
-			S = np.sin(2*Ψ) * np.cos(2*Δ)
-
-			MM.loc[(aoi, λ), "M11"] = 1
-			MM.loc[(aoi, λ), "M12"] = -N
-			MM.loc[(aoi, λ), "M13"] = 0
-			MM.loc[(aoi, λ), "M14"] = 0
-
-			MM.loc[(aoi, λ), "M21"] = -N
-			MM.loc[(aoi, λ), "M22"] = 1
-			MM.loc[(aoi, λ), "M23"] = 0
-			MM.loc[(aoi, λ), "M24"] = 0
-
-			MM.loc[(aoi, λ), "M31"] = 0
-			MM.loc[(aoi, λ), "M32"] = 0
-			MM.loc[(aoi, λ), "M33"] = C
-			MM.loc[(aoi, λ), "M34"] = S
-
-			MM.loc[(aoi, λ), "M41"] = 0
-			MM.loc[(aoi, λ), "M42"] = 0
-			MM.loc[(aoi, λ), "M43"] = -S
-			MM.loc[(aoi, λ), "M44"] = C
-
-	return MM
+from . import detect_encoding
+
+
+def read_accurion_psi_delta(fname: str) -> pd.DataFrame:
+    r"""Read a psi/delta Accurion dat file.
+
+    Args:
+      fname (str): Filename of the measured dat file
+
+    Returns:
+      pd.DataFrame: DataFrame containing the psi/delta data in the pyElli-compatible format.
+    """
+    encoding = detect_encoding(fname)
+    psi_delta_df = pd.read_csv(
+        fname, delimiter="\t", encoding=encoding, skiprows=0, header=0
+    )[1:].astype(float)
+    psi_delta_df = psi_delta_df.reindex(columns=list(["AOI", "Lambda", "Delta", "Psi"]))
+    psi_delta_df = psi_delta_df.rename(
+        columns={
+            "AOI": "Angle of Incidence",
+            "Lambda": "Wavelength",
+            "Delta": "Δ",
+            "Psi": "Ψ",
+        }
+    )
+    psi_delta_df = psi_delta_df.groupby(["Angle of Incidence", "Wavelength"]).sum()
+
+    # wrap delta range
+    psi_delta_df.loc[:, "Δ"] = psi_delta_df.loc[:, "Δ"].where(
+        psi_delta_df.loc[:, "Δ"] <= 180, psi_delta_df.loc[:, "Δ"] - 360
+    )
+
+    return psi_delta_df
diff --git a/src/elli/utils.py b/src/elli/utils.py
index 433bc278..4fbde4f5 100644
--- a/src/elli/utils.py
+++ b/src/elli/utils.py
@@ -59,6 +59,79 @@ def calc_rho(psi_delta: pd.DataFrame) -> pd.DataFrame:
     )
 
 
+def convert_psi_delta_to_isotropic_mueller_matrix(psi_delta_df) -> pd.DataFrame:
+    r"""Extract aois and wavelengths values from psi_delta pandas.DataFrame and convert it to a Muellermatrix;
+    only works for isotropic media.
+
+    Args:
+            psi_delta_df (pd.DataFrame): dataFrame returned from data importers'
+
+    Returns:
+            pd.DataFrame: pyElli-compatible DataFrame of the Mueller matrix
+    """
+    aois = psi_delta_df.index.get_level_values("Angle of Incidence").unique().to_numpy()
+    wavelengths = psi_delta_df.index.get_level_values("Wavelength").unique().to_numpy()
+
+    # create empty Mueller matrix
+    MM = pd.DataFrame(
+        {},
+        columns=[
+            "M11",
+            "M12",
+            "M13",
+            "M14",
+            "M21",
+            "M22",
+            "M23",
+            "M24",
+            "M31",
+            "M32",
+            "M33",
+            "M34",
+            "M41",
+            "M42",
+            "M43",
+            "M44",
+        ],
+        index=pd.MultiIndex.from_product(
+            [aois, wavelengths], names=["Angle of Incidence", "Wavelength"]
+        ),
+        dtype=float,
+    )
+
+    # fill in the Mueller matrix coefficients for an isotropic material based equation in https://www.jawoollam.com/resources/ellipsometry-faq#toggle-id-15
+    for aoi in aois:
+        for λ in wavelengths:
+            Δ = psi_delta_df.loc[aoi, λ]["Δ"]
+            Ψ = psi_delta_df.loc[aoi, λ]["Ψ"]
+
+            N = np.cos(2 * Ψ)
+            C = np.sin(2 * Ψ) * np.cos(2 * Δ)
+            S = np.sin(2 * Ψ) * np.cos(2 * Δ)
+
+            MM.loc[(aoi, λ), "M11"] = 1
+            MM.loc[(aoi, λ), "M12"] = -N
+            MM.loc[(aoi, λ), "M13"] = 0
+            MM.loc[(aoi, λ), "M14"] = 0
+
+            MM.loc[(aoi, λ), "M21"] = -N
+            MM.loc[(aoi, λ), "M22"] = 1
+            MM.loc[(aoi, λ), "M23"] = 0
+            MM.loc[(aoi, λ), "M24"] = 0
+
+            MM.loc[(aoi, λ), "M31"] = 0
+            MM.loc[(aoi, λ), "M32"] = 0
+            MM.loc[(aoi, λ), "M33"] = C
+            MM.loc[(aoi, λ), "M34"] = S
+
+            MM.loc[(aoi, λ), "M41"] = 0
+            MM.loc[(aoi, λ), "M42"] = 0
+            MM.loc[(aoi, λ), "M43"] = -S
+            MM.loc[(aoi, λ), "M44"] = C
+
+    return MM
+
+
 def get_qwp_thickness(material: "Material", lbda: float) -> float:
     """Return the thickness of a material in nm for a quarter wave plate at wavelength 'lbda'.
 

From 9f757cf411592dcdeee3930156b0a9851c34e484 Mon Sep 17 00:00:00 2001
From: MarJMue <49639740+MarJMue@users.noreply.github.com>
Date: Wed, 2 Oct 2024 12:24:02 +0200
Subject: [PATCH 3/3] Add test

---
 tests/test_accurion.py                        |  16 +++
 ...i3N4_on_4inBF33_W02_20240903-150451.ds.dat | 116 ++++++++++++++++++
 2 files changed, 132 insertions(+)
 create mode 100644 tests/test_accurion.py
 create mode 100644 tests/test_accurion/Si3N4_on_4inBF33_W02_20240903-150451.ds.dat

diff --git a/tests/test_accurion.py b/tests/test_accurion.py
new file mode 100644
index 00000000..8e10b965
--- /dev/null
+++ b/tests/test_accurion.py
@@ -0,0 +1,16 @@
+"""Tests for reading accurion files"""
+
+import pytest
+from fixtures import datadir  # pylint: disable=unused-import
+
+import elli
+
+
+# pylint: disable=redefined-outer-name
+def test_reading_of_psi_delta_woollam(datadir):
+    """Psi/delta Accurion file is read w/o errors"""
+    data = elli.read_accurion_psi_delta(
+        datadir / "Si3N4_on_4inBF33_W02_20240903-150451.ds.dat"
+    )
+
+    assert data.shape == (114, 2)
diff --git a/tests/test_accurion/Si3N4_on_4inBF33_W02_20240903-150451.ds.dat b/tests/test_accurion/Si3N4_on_4inBF33_W02_20240903-150451.ds.dat
new file mode 100644
index 00000000..5eaa8b03
--- /dev/null
+++ b/tests/test_accurion/Si3N4_on_4inBF33_W02_20240903-150451.ds.dat
@@ -0,0 +1,116 @@
+#ROIidx	AOI	Lambda	Bandwidth	ExposureTime	ROI_x	ROI_y	Delta	Psi
+#-	deg	nm	nm	us	µm	µm	deg	deg
+0	40.000	365.0	6.1	115908	417.6	409.8	179.785156	32.535931
+0	40.000	370.0	6.3	113546	417.6	409.8	179.815674	32.514015
+0	40.000	375.1	5.1	108872	417.6	409.8	179.887863	32.167427
+0	40.000	380.4	6.3	128641	417.7	409.9	179.846115	32.424763
+0	40.000	385.9	6.1	116358	417.7	409.9	179.964935	32.358204
+0	40.000	391.4	6.3	107241	417.7	409.9	180.198441	32.235497
+0	40.000	397.2	5.3	106364	417.8	410.0	180.418350	32.211399
+0	40.000	403.1	4.3	71897	417.9	410.1	180.286850	32.482040
+0	40.000	409.2	4.4	65173	418.0	410.2	179.812210	32.669853
+0	40.000	415.5	4.3	54421	418.0	410.2	179.373871	32.483944
+0	40.000	422.0	4.3	53257	418.0	410.2	179.641830	31.710491
+0	40.000	428.7	4.3	50623	418.0	410.2	181.694778	30.964096
+0	40.000	435.6	4.2	36828	418.0	410.2	182.461807	31.806063
+0	40.000	442.8	4.2	26359	418.0	410.2	180.825607	33.171253
+0	40.000	450.2	4.2	19839	417.8	410.0	179.336304	33.702694
+0	40.000	457.8	4.2	21279	417.7	409.9	177.524414	32.973022
+0	40.000	465.7	4.2	31348	417.7	409.9	175.019714	29.624680
+0	40.000	473.8	4.1	38385	417.7	409.9	184.791260	25.209936
+0	40.000	482.3	4.2	19254	417.6	409.8	184.419479	30.734592
+0	40.000	491.1	4.1	10388	417.6	409.8	180.833572	33.546158
+0	40.000	500.2	4.1	8430	417.6	409.8	179.733200	34.397530
+0	40.000	509.6	4.1	8864	417.5	409.8	178.651398	33.714882
+0	40.000	519.4	4.1	11995	417.6	409.8	175.087067	30.998163
+0	40.000	529.6	4.0	23893	417.6	409.8	173.824173	23.673731
+0	40.000	540.2	4.1	21080	417.6	409.8	186.372284	26.547739
+0	40.000	551.2	4.0	10855	417.5	409.7	182.173080	31.793457
+0	40.000	562.7	4.0	7704	417.5	409.7	180.295517	33.912464
+0	40.000	574.6	4.0	6862	417.5	409.7	179.983643	34.416878
+0	40.000	587.1	4.0	7236	417.5	409.7	179.309082	33.597958
+0	40.000	600.2	4.0	10360	417.5	409.8	176.537186	31.162548
+0	40.000	613.8	4.0	19510	417.5	409.7	173.198044	25.677353
+0	40.000	628.1	4.0	23063	417.6	409.8	184.833145	24.293219
+0	40.000	643.0	4.0	14486	417.5	409.7	183.686890	30.058107
+0	40.000	658.7	4.0	9899	417.5	409.7	180.956879	32.944775
+0	40.000	675.2	3.9	9021	417.5	409.7	180.208603	34.125999
+0	40.000	692.5	4.0	10334	417.5	409.7	180.069046	34.137150
+0	40.000	710.7	3.9	14555	417.5	409.7	179.159897	33.001068
+0	40.000	729.9	3.9	24887	417.5	409.7	176.283844	30.347702
+0	40.000	750.2	3.9	48739	417.4	409.6	174.189240	25.170830
+0	40.000	771.6	3.9	70770	417.4	409.6	184.720505	24.475565
+0	40.000	794.3	3.9	55938	417.3	409.5	183.936996	29.644312
+0	40.000	818.4	3.9	32599	417.1	409.3	181.270737	32.460072
+0	40.000	843.9	3.8	31036	417.0	409.2	180.351196	33.767361
+0	40.000	871.1	3.9	36529	416.9	409.1	180.189163	34.017212
+0	40.000	900.2	4.0	37733	416.7	409.0	179.688858	33.218037
+0	40.000	931.2	4.0	86622	416.6	408.8	177.657486	31.222305
+0	40.000	964.5	4.1	10000	415.7	407.9	174.415024	27.342821
+0	40.000	1000.2	4.0	10000	415.4	407.7	179.864182	23.185122
+0	40.000	1038.6	16.2	2000	415.3	407.5	185.227509	27.188955
+0	40.000	1080.1	15.2	1000	414.7	406.9	182.442734	30.897955
+0	40.000	1125.1	15.8	500	414.4	406.7	180.780197	32.758415
+0	40.000	1174.0	15.5	500	414.0	406.3	180.278580	33.568390
+0	40.000	1227.4	15.7	500	413.6	405.8	180.096664	33.390888
+0	40.000	1285.8	15.5	500	413.0	405.3	179.265884	32.347992
+0	40.000	1350.1	15.3	1000	412.4	404.7	176.933167	30.021086
+0	40.000	1421.1	15.2	2000	411.6	403.9	174.649048	25.813662
+0	40.000	1500.0	15.2	5000	410.8	403.1	182.420883	23.373127
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