Dev 081

pyproject.toml

@@ -37,6 +37,7 @@ dependencies = [
 	"loguru>=0.7",
 	"typer[all]",
 	"mpire[dill]~=2.10.0",
+	"tomli-w>=1.0.0"
 ]
 
 [project.optional-dependencies]
@@ -89,7 +90,13 @@ addopts = [
     "-ra -q",
     "--cov",
     "--cov-report term-missing html xml annotate",
+	"--strict-markers"
 ]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "serial",
+]
+
 testpaths = [
     "tests",
 ]

src/raman_fitting/config/base_settings.py

@@ -14,7 +14,7 @@
 from raman_fitting.models.deconvolution.spectrum_regions import (
     get_default_regions_from_toml_files,
 )
-from .default_models import load_config_from_toml_files
+from .load_config_from_toml import load_config_from_toml_files
 from .path_settings import create_default_package_dir_or_ask, InternalPathSettings
 from types import MappingProxyType
 

src/raman_fitting/config/default_models/__init__.py

@@ -1,14 +0,0 @@
-from pathlib import Path
-from types import MappingProxyType
-import tomllib
-
-
-def load_config_from_toml_files() -> MappingProxyType:
-    current_parent_dir = Path(__file__).resolve().parent
-    default_peak_settings = {}
-    for i in current_parent_dir.glob("*.toml"):
-        default_peak_settings.update(tomllib.loads(i.read_bytes().decode()))
-    if not default_peak_settings:
-        raise ValueError("default models should not be empty.")
-
-    return MappingProxyType(default_peak_settings)

src/raman_fitting/config/default_models/first_order.toml

@@ -1,16 +1,22 @@
-[first_order]
+[spectrum]
 
-[first_order.models]
+[spectrum.regions.first_order]
+
+[spectrum.regions.first_order.limits]
+min = 900
+max = 2000
+
+[spectrum.regions.first_order.models]
 1peak = "G"
 2peaks = "G+D"
 3peaks = "G+D+D3"
 4peaks = "G+D+D3+D4"
 5peaks = "G+D+D2+D3+D4"
 6peaks = "G+D+D2+D3+D4+D5"
 
-[first_order.peaks]
+[spectrum.regions.first_order.peaks]
 
-[first_order.peaks.G]
+[spectrum.regions.first_order.peaks.G]
 docstring = """
 Graphite belongs to the P63/mmc (D46h) space group. If considering only a graphene plane, at
 the à point of the Brillouin zone, there are six normal modes that possess only one mode (doubly
@@ -23,13 +29,13 @@ Für G: 1580-1590 D5 und D2 weiß ich nicht
 """
 peak_name = "G"
 peak_type = "Lorentzian"
-[first_order.peaks.G.param_hints]
+[spectrum.regions.first_order.peaks.G.param_hints]
 center = {value = 1571, min = 1545, max = 1595}
 sigma = {value = 30, min = 5, max = 150}
 amplitude = {value = 100, min = 1e-05, max = 500}
 
 
-[first_order.peaks.D]
+[spectrum.regions.first_order.peaks.D]
 docstring = """
 D or D1 ; Disordered graphitic lattice (graphene layer edges,A1gsymmetry)
 A defective graphite presents other bands that can be as intense as the G band at D=1350 and D'=1615 cm-1
@@ -38,39 +44,39 @@ Für D1: 1340-1350
 """
 peak_name = "D"
 peak_type = "Lorentzian"
-[first_order.peaks.D.param_hints]
+[spectrum.regions.first_order.peaks.D.param_hints]
 center = {value = 1350, min = 1330, max = 1380}
 sigma = {value = 35, min = 1, max = 150}
 amplitude = {value = 120, min = 1e-05, max = 500}
 
-[first_order.peaks.D2]
+[spectrum.regions.first_order.peaks.D2]
 docstring = """
 D2 or D' ; Right next to the G peak, sometimes not obvious as G peak split.
 Disordered graphitic lattice (surface graphene layers,E2g-symmetry)
 j.molstruc.2010.12.065
 """
 peak_name = "D2"
 peak_type = "Lorentzian"
-[first_order.peaks.D2.param_hints]
+[spectrum.regions.first_order.peaks.D2.param_hints]
 center = {value = 1606, min = 1592, max = 1635}
 sigma = {value = 30, min = 5, max = 150}
 amplitude = {value = 35, min = 5, max = 500}
 
 
-[first_order.peaks.D3]
+[spectrum.regions.first_order.peaks.D3]
 docstring = """
 D3 or D'' or A or Am ; Between the D and G peak, sometimes too broad.
 For amorphous carbon (Gaussian[26]or Lorentzian[3,18,27]line shape).
 Für D3: 1495-1515
 """
 peak_name = "D3"
 peak_type = "Lorentzian"
-[first_order.peaks.D3.param_hints]
+[spectrum.regions.first_order.peaks.D3.param_hints]
 center = {value = 1480, min = 1450, max = 1525}
 sigma = {value = 25, min = 1, max = 150}
 amplitude = {value = 25, min = 1e-02, max = 500}
 
-[first_order.peaks.D4]
+[spectrum.regions.first_order.peaks.D4]
 docstring = """
 D4 or I ; Below D band, a shoulder sometimes split with D5 band.
 Disordered graphitic lattice (A1gsymmetry)[10],polyenes[3,27], ionic impurities
@@ -80,24 +86,24 @@ Für D4: 1185-1210, but depends on if there is D5 or not.
 """
 peak_name = "D4"
 peak_type = "Lorentzian"
-[first_order.peaks.D4.param_hints]
+[spectrum.regions.first_order.peaks.D4.param_hints]
 center = {value = 1230, min = 1180, max = 1310}
 sigma = {value = 40, min = 1, max = 150}
 amplitude = {value = 20, min = 1e-02, max = 200}
 
-[first_order.peaks.D5]
+[spectrum.regions.first_order.peaks.D5]
 docstring = """
 D5 peak at 1110 cm−1. At lowest should of D peak, below D4.
 Ref: Jurkiewicz, K., Pawlyta, M., Zygadło, D. et al. J Mater Sci (2018) 53: 3509. https://doi.org/10.1007/s10853-017-1753-7
 """
 peak_name = "D5"
 peak_type = "Lorentzian"
-[first_order.peaks.D5.param_hints]
+[spectrum.regions.first_order.peaks.D5.param_hints]
 center = {value = 1110, min = 1080, max = 1150}
 sigma = {value = 40, min = 1, max = 150}
 amplitude = {value = 20, min = 1e-02, max = 200}
 
-[first_order.peaks.Si1]
+[spectrum.regions.first_order.peaks.Si1]
 docstring =  """
 ===== Extra peak at ca. 960 cm-1 presumably from Si substrate 2nd order === not from Nafion...
 => Either cut the Spectra 1000-2000
@@ -106,7 +112,7 @@ docstring =  """
 peak_name = "Si1"
 peak_type = "Gaussian"
 is_substrate = true
-[first_order.peaks.Si1.param_hints]
+[spectrum.regions.first_order.peaks.Si1.param_hints]
 center = {value = 960, min = 900, max = 980}
 sigma = {value = 10, min = 0, max = 150}
 amplitude = {value = 10, min = 0, max = 200}

src/raman_fitting/config/default_models/low_first_order.toml

@@ -0,0 +1,87 @@
+[spectrum]
+
+[spectrum.regions.low_first_order]
+
+[spectrum.regions.low_first_order.limits]
+min = 220
+max = 500
+extra_margin = 10
+
+[spectrum.regions.low_first_order.models]
+low1peak = "A"
+low2peaks = "B+C"
+low3peaks = "A+B+C"
+low4peaks = "A+B+C+C2"
+low5peaks = "A+B+C+C2+F"
+
+[spectrum.regions.low_first_order.peaks]
+
+[spectrum.regions.low_first_order.peaks.A]
+docstring = """
+A, around 290
+"""
+peak_name = "A"
+peak_type = "Lorentzian"
+[spectrum.regions.low_first_order.peaks.A.param_hints]
+center = {value = 290, min = 220, max = 300}
+sigma = {value = 30, min = 2, max = 70}
+amplitude = {value = 50, min = 1e-05, max = 500}
+
+
+[spectrum.regions.low_first_order.peaks.B]
+docstring = """
+around 320
+"""
+peak_name = "B"
+peak_type = "Lorentzian"
+[spectrum.regions.low_first_order.peaks.B.param_hints]
+center = {value = 315, min = 300, max = 340}
+sigma = {value = 35, min = 1, max = 150}
+amplitude = {value = 120, min = 1e-05, max = 500}
+
+[spectrum.regions.low_first_order.peaks.C]
+docstring = """
+around 340
+"""
+peak_name = "C"
+peak_type = "Lorentzian"
+[spectrum.regions.low_first_order.peaks.C.param_hints]
+center = {value = 340, min = 325, max = 355}
+sigma = {value = 30, min = 5, max = 150}
+amplitude = {value = 70, min = 5, max = 500}
+
+
+[spectrum.regions.low_first_order.peaks.C2]
+docstring = """
+should of c, around 370
+"""
+peak_name = "C2"
+peak_type = "Lorentzian"
+[spectrum.regions.low_first_order.peaks.C2.param_hints]
+center = {value = 360, min = 355, max = 375}
+sigma = {value = 25, min = 5, max = 150}
+amplitude = {value = 25, min = 1e-02, max = 500}
+
+[spectrum.regions.low_first_order.peaks.F]
+docstring = """
+F, around 475
+"""
+peak_name = "F"
+peak_type = "Lorentzian"
+[spectrum.regions.low_first_order.peaks.F.param_hints]
+center = {value = 475, min = 450, max = 500}
+sigma = {value = 40, min = 1, max = 150}
+amplitude = {value = 20, min = 1e-02, max = 200}
+
+
+[spectrum.regions.low_first_order.peaks.Si2]
+docstring =  """
+Extra band at 670
+"""
+peak_name = "Si2"
+peak_type = "Gaussian"
+is_substrate = true
+[spectrum.regions.low_first_order.peaks.Si2.param_hints]
+center = {value = 670, min = 600, max = 710}
+sigma = {value = 40, min = 0, max = 150}
+amplitude = {value = 10, min = 0, max = 200}

src/raman_fitting/config/default_models/normalization.toml

@@ -1,30 +1,35 @@
-[normalization]
+[spectrum]
 
-[normalization.models]
+[spectrum.regions.normalization.limits]
+min = 1500
+max = 1675
+extra_margin = 10
+
+[spectrum.regions.normalization.models]
 norm = "norm_G+norm_D"
 
-[normalization.peaks]
+[spectrum.regions.normalization.peaks]
 
-[normalization.peaks.norm_G]
+[spectrum.regions.normalization.peaks.norm_G]
 docstring = """
 G_peak used for normalization
 """
 peak_name = "norm_G"
 peak_type = "Lorentzian"
 is_for_normalization = true
-[normalization.peaks.norm_G.param_hints]
+[spectrum.regions.normalization.peaks.norm_G.param_hints]
 center = {"value" = 1581, "min" = 1500, "max" = 1600}
 sigma = {"value" = 40, "min" = 1e-05, "max" = 1e3}
 amplitude = {"value" = 8e4, "min" = 1e2}
 
-[normalization.peaks.norm_D]
+[spectrum.regions.normalization.peaks.norm_D]
 docstring = """
 D_peak for normalization
 """
 peak_name = "norm_D"
 peak_type = "Lorentzian"
 is_for_normalization = true
-[normalization.peaks.norm_D.param_hints]
+[spectrum.regions.normalization.peaks.norm_D.param_hints]
 center = {"value" = 1350, "min" = 1300, "max" = 1400}
 sigma = {"value" = 90, "min" = 1e-05}
 amplitude = {"value" = 10e5, "min" = 1e2}

src/raman_fitting/config/default_models/second_order.toml

@@ -1,38 +1,44 @@
-[second_order]
+[spectrum]
 
-[second_order.models]
+[spectrum.regions.second_order]
+
+[spectrum.regions.second_order.limits]
+min = 2150
+max = 3380
+
+[spectrum.regions.second_order.models]
 2nd_4peaks = "D4D4+D1D1+GD1+D2D2"
 
-[second_order.peaks]
+[spectrum.regions.second_order.peaks]
 
-[second_order.peaks.D4D4]
+[spectrum.regions.second_order.peaks.D4D4]
 peak_name = "D4D4"
 peak_type = "Lorentzian"
-[second_order.peaks.D4D4.param_hints]
+[spectrum.regions.second_order.peaks.D4D4.param_hints]
 center = {value = 2435, min = 2400, max = 2550}
 sigma = {value = 30, min = 1, max = 200}
 amplitude = {value = 2, min = 1e-03, max = 100}
 
-[second_order.peaks.D1D1]
+[spectrum.regions.second_order.peaks.D1D1]
 peak_name = "D1D1"
 peak_type = "Lorentzian"
-[second_order.peaks.D1D1.param_hints]
+[spectrum.regions.second_order.peaks.D1D1.param_hints]
 center = {value = 2650, min = 2600, max = 2750}
 sigma = {value = 60, min = 1, max = 200}
 amplitude = {value = 14, min = 1e-03, max = 100}
 
-[second_order.peaks.GD1]
+[spectrum.regions.second_order.peaks.GD1]
 peak_name = "GD1"
 peak_type = "Lorentzian"
-[second_order.peaks.GD1.param_hints]
+[spectrum.regions.second_order.peaks.GD1.param_hints]
 center = {value = 2900, min = 2800, max = 2950}
 sigma = {value = 50, min = 1, max = 200}
 amplitude = {value = 10, min = 1e-03, max = 100}
 
-[second_order.peaks.D2D2]
+[spectrum.regions.second_order.peaks.D2D2]
 peak_type = "Lorentzian"
 peak_name = "D2D2"
-[second_order.peaks.D2D2.param_hints]
+[spectrum.regions.second_order.peaks.D2D2.param_hints]
 center = {value = 3250, min = 3000, max = 3400}
 sigma = {value = 60, min = 20, max = 200}
 amplitude = {value = 1, min = 1e-03, max = 100}

src/raman_fitting/config/default_models/spectrum_regions.toml

@@ -1,10 +1,15 @@
 [spectrum]
 
 [spectrum.regions]
-full = {"min" = 200, "max" = 3600}
-full_first_and_second = {"min" = 800, "max" = 3500}
-low = {"min" = 150, "max" = 850, "extra_margin" = 10}
-first_order = {"min" = 900, "max" = 2000}
-mid = {"min" = 1850, "max" = 2150, "extra_margin" = 10}
-normalization = {"min" = 1500, "max" = 1675, "extra_margin" = 10}
-second_order = {"min" = 2150, "max" = 3380}
+
+[spectrum.regions.full]
+limits = {"min" = 200, "max" = 3600}
+
+[spectrum.regions.full_first_and_second]
+limits = {"min" = 800, "max" = 3500}
+
+[spectrum.regions.low]
+limits = {"min" = 150, "max" = 850, "extra_margin" = 10}
+
+[spectrum.regions.mid]
+limits = {"min" = 1850, "max" = 2150, "extra_margin" = 10}