taurex 3.2.2__tar.gz → 3.2.4__tar.gz

{taurex-3.2.2 → taurex-3.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: taurex
-Version: 3.2.2
+Version: 3.2.4
 Summary: TauREx3
 Home-page: https://github.com/ahmed-f-alrefaie/taurex3
 License: BSDv3

{taurex-3.2.2 → taurex-3.2.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "taurex"
-version = "3.2.2"
+version = "3.2.4"
 description = "TauREx3"
 authors = ["Ahmed Faris Al-Refaie <ahmed.al-refaie.12@ucl.ac.uk>"]
 license = "BSDv3"

{taurex-3.2.2 → taurex-3.2.4}/src/taurex/contributions/leemie.py

@@ -143,8 +143,9 @@ class LeeMieContribution(Contribution):
     @fitparam(
         param_name="lee_mie_q",
         param_latex=r"$Q_\mathrm{ext}$",
+        default_mode="log",
         default_fit=False,
-        default_bounds=[-10, 1],
+        default_bounds=[1e-30, 1e6],
     )
     def mieQ(self) -> float:  # noqa: N802
         """Extinction coefficient."""
@@ -159,7 +160,7 @@ class LeeMieContribution(Contribution):
         param_latex=r"$P^{lee}_\mathrm{top}$",
         default_mode="log",
         default_fit=False,
-        default_bounds=[-1, 1],
+        default_bounds=[1e-30, 1e6],
     )
     def mieTopPressure(self) -> float:  # noqa: N802
         """Pressure at top of cloud deck in Pa."""
@@ -175,7 +176,7 @@ class LeeMieContribution(Contribution):
         param_latex=r"$P^{lee}_\mathrm{bottom}$",
         default_mode="log",
         default_fit=False,
-        default_bounds=[-1, 1],
+        default_bounds=[1e-30, 1e6],
     )
     def mieBottomPressure(self) -> float:  # noqa: N802
         """Pressure at bottom of cloud deck in Pa."""
@@ -191,7 +192,7 @@ class LeeMieContribution(Contribution):
         param_latex=r"$\chi^{lee}_\mathrm{mie}$",
         default_mode="log",
         default_fit=False,
-        default_bounds=[-1, 1],
+        default_bounds=[1e-40, 1],
     )
     def mieMixing(self) -> float:  # noqa: N802
         """Mixing ratio in atmosphere."""

{taurex-3.2.2 → taurex-3.2.4}/src/taurex/data/profiles/chemistry/__init__.py

@@ -6,5 +6,7 @@ from .taurexchemistry import TaurexChemistry
 from .gas.constantgas import ConstantGas
 from .gas.twolayergas import TwoLayerGas
 from .gas.powergas import PowerGas
+from .gas.customgas import CustomGas
+from .gas.twopointgas import TwoPointGas
 from .filechemistry import ChemistryFile
 from .autochemistry import AutoChemistry

taurex-3.2.4/src/taurex/data/profiles/chemistry/gas/customgas.py

@@ -0,0 +1,121 @@
+"""Constant gas profile."""
+import typing as t
+
+import numpy as np
+import numpy.typing as npt
+
+from taurex.output import OutputGroup
+from taurex.util import molecule_texlabel
+
+from .gas import Gas
+
+
+class CustomGas(Gas):
+    """Constant gas profile.
+
+    Molecular abundace is constant at each layer of the
+    atmosphere
+
+    """
+
+    def __init__(
+        self,
+        molecule_name: t.Optional[str] = "H2O",
+        mix_ratio: npt.NDArray[np.float64] = None,
+    ) -> None:
+        """Initialize constant gas profile.
+
+        Parameters
+        -----------
+        molecule_name : str
+            Name of molecule
+
+        mix_ratio : float
+            Mixing ratio of the molecule
+
+
+        """
+        super().__init__("CustomGas", molecule_name)
+        self._mix_ratio = mix_ratio
+        self.add_active_gas_param()
+
+    @property
+    def mixProfile(self) -> npt.NDArray[np.float64]:  # noqa: N802
+        """
+
+        Mixing profile
+
+        Returns
+        -------
+        mix: :obj:`array`
+            Mix ratio for molecule at each layer
+
+        """
+
+        return self._mix_array
+
+    def initialize_profile(
+        self,
+        nlayers: t.Optional[int] = None,
+        temperature_profile: t.Optional[npt.NDArray[np.float64]] = None,
+        pressure_profile: t.Optional[npt.NDArray[np.float64]] = None,
+        altitude_profile: t.Optional[npt.NDArray[np.float64]] = None,
+    ) -> None:
+        """Initialize the mixing profile.
+
+        Parameters
+        -----------
+        nlayers: int
+            Number of layers in atmosphere
+        temperature_profile: :obj:`array`
+            Temperature profile of atmosphere
+        pressure_profile: :obj:`array`
+            Pressure profile of atmosphere
+        altitude_profile: :obj:`array`
+            Altitude profile of atmosphere, deprecated
+
+        """
+        self._mix_array = self._mix_ratio
+
+    def add_active_gas_param(self) -> None:
+        """Add the mixing ratio as a fitting parameter.
+
+        Fitting parameter identifier is the molecule name.
+        Generates a fitting parameter on the fly by building
+        getter and setter functions and passing them to
+        :func:`taurex.fitting.fittable.Fittable.add_fittable_param`
+
+        """
+
+        mol_name = self.molecule
+        param_name = self.molecule
+        param_tex = molecule_texlabel(mol_name)
+
+        def read_mol(self):
+            return self._mix_ratio
+
+        def write_mol(self, value):
+            self._mix_ratio = value
+
+        read_mol.__doc__ = f"{mol_name} constant mix ratio (VMR)"
+
+        fget = read_mol
+        fset = write_mol
+
+        bounds = [1.0e-12, 0.1]
+
+        default_fit = False
+        self.add_fittable_param(
+            param_name, param_tex, fget, fset, "log", default_fit, bounds
+        )
+
+    def write(self, output: OutputGroup):
+        """Write constant gas profile to output."""
+        gas_entry = super().write(output)
+        gas_entry.write_scalar("mix_ratio", self._mix_ratio)
+
+        return gas_entry
+
+    @classmethod
+    def input_keywords(cls) -> t.Tuple[str]:
+        return ("custom",)

{taurex-3.2.2 → taurex-3.2.4}/src/taurex/parameter/classfactory.py

@@ -205,13 +205,12 @@ class ClassFactory(Singleton):
             # Make sure they're unique
             all_files = set(
                 sum(
-                    [p.glob("*.py") for p in paths],
+                    [list(p.glob("*.py")) for p in paths],
                     [],
                 )
             )
-
             for f in all_files:
-                self.info("Loading extensions from %s", f)
+                self.log.info("Loading extensions from %s", f)
                 module_name = f.stem
                 spec = importlib.util.spec_from_file_location(module_name, f)
                 foo = importlib.util.module_from_spec(spec)

{taurex-3.2.2 → taurex-3.2.4}/src/taurex/plot/plotter.py

@@ -39,6 +39,11 @@ class Plotter(object):
 
         if not os.path.exists(self.out_folder):
             os.makedirs(self.out_folder)
+                      
+    def find_nearest(self, array, value):
+        array = np.asarray(array)
+        idx = (np.abs(array - value)).argmin()
+        return idx, array[idx]
 
     @property
     def num_solutions(self,fd_position='Output'):
@@ -775,7 +780,7 @@ class Plotter(object):
         plt.close()
 
 
-    def plot_fitted_tau(self):
+    def plot_fitted_tau(self, wl_min:float=.5, wl_max:float=12.):
         N = self.num_solutions
         for solution_idx, solution_val in self.solution_iter():
 
@@ -784,6 +789,12 @@ class Plotter(object):
 
             pressure = solution_val['Profiles']['pressure_profile'][:]
             wavelength = solution_val['Spectra']['native_wlgrid'][:]
+            
+            wavelength_right = self.find_nearest(wavelength, wl_min)[0]
+            wavelength_left = self.find_nearest(wavelength, wl_max)[0]
+
+            wavelength = wavelength[wavelength_left:wavelength_right+1]
+            contribution = contribution[...,wavelength_left:wavelength_right+1]
 
             self._plot_tau(contribution,pressure,wavelength)
 
@@ -795,7 +806,8 @@ class Plotter(object):
         grid = plt.GridSpec(1, 4, wspace=0.4, hspace=0.3)
         fig = plt.figure('Contribution function')
         ax1 = plt.subplot(grid[0, :3])
-        plt.imshow(contribution, aspect='auto')
+        pos = plt.imshow(contribution, aspect='auto')
+        plt.colorbar(pos, ax=ax1)
 
         ### mapping of the pressure array onto the ticks:
         y_labels = np.array([pow(10., p) for p in np.arange(np.ceil(np.log10(np.max(pressure))), np.floor(np.log10(np.min(pressure)))-1.,step=-1)])
@@ -823,8 +835,8 @@ class Plotter(object):
         plt.xticks(x_ticks, x_labels)
         plt.gca().invert_yaxis()
         plt.gca().invert_xaxis()
-        plt.xlabel(r"Wavelength ($\mu$m)")
-        plt.ylabel("Pressure (Bar)")
+        plt.xlabel(r"Wavelength [$\mu$m]")
+        plt.ylabel("Pressure [bar]")
 
         ax2 = plt.subplot(grid[0, 3])