ppdmod 2.0.0__tar.gz → 2.0.1__tar.gz

{ppdmod-2.0.0/ppdmod.egg-info → ppdmod-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ppdmod
-Version: 2.0.0
+Version: 2.0.1
 Summary: A package for modelling and model-fitting protoplanetary disks
 Author-email: Marten Scheuck <code@mbscheuck.com>
 License: MIT License
@@ -35,14 +35,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: <3.11,>=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: astropy>=6.1.4
 Requires-Dist: corner>=2.2.2
 Requires-Dist: dynesty>=2.1.4
-Requires-Dist: emcee>=3.1.6
-Requires-Dist: h5py>=3.12.1
 Requires-Dist: matplotlib>=3.9.2
 Requires-Dist: numpy>=2.0.2
 Requires-Dist: openpyxl>=3.1.5

ppdmod-2.0.1/ppdmod/__init__.py

@@ -0,0 +1 @@
+__version__ = "2.0.1"

{ppdmod-2.0.0 → ppdmod-2.0.1}/ppdmod/fitting.py

@@ -241,7 +241,7 @@ def compute_observables(
     return flux_model, vis_model, t3_model
 
 
-def compute_nband_fit_chi_sq(
+def compute_photometry_loglike(
     model_data: NDArray[Any],
     ndim: int,
     reduced: bool = False,
@@ -259,22 +259,67 @@ def compute_nband_fit_chi_sq(
 
     Returns
     -------
-    chi_sq : float
-        The chi square.
+    loglike : float
+        Returns either the loglike or the reduced chi sq.
     """
     # NOTE: The -1 here indicates that one of the parameters is actually fixed
     flux, ndim = OPTIONS.data.flux, ndim - 1
-    val, err = map(lambda x: x.squeeze(), [flux.val, flux.err])
-    chi_sq = compute_loglike(
-        val.compressed(),
-        err.compressed(),
-        model_data.squeeze()[~val.mask],
-    )
+    val, err = map(lambda x: x.squeeze().compressed(), [flux.val, flux.err])
+    model_data = model_data.squeeze()[~flux.val.mask]
 
     if reduced:
+        chi_sq = compute_chi_sq(val, err**2, model_data, "linear")
         return chi_sq / (flux.val.size - ndim)
 
-    return chi_sq
+    return compute_loglike(val, err, model_data)
+
+
+def compute_interferometric_loglike(
+    components: List[Component],
+) -> Tuple:
+    """Calculates the disc model's chi square.
+
+    Parameters
+    ----------
+    components : list of Component
+        The components to be used in the model.
+    method : bool
+        The method used to calculate the chi square.
+        Either "linear" or "logarithmic".
+        Default is "logarithmic".
+
+    Returns
+    -------
+    chi_sq : Tuple of floats
+        The total and the individual chi squares.
+    """
+    observables = ["flux", "vis", "t3"]
+    model_data = dict(zip(observables, compute_observables(components)))
+    wls = OPTIONS.fit.wls.value
+
+    loglikes = []
+    for key in OPTIONS.fit.data:
+        data = getattr(OPTIONS.data, key)
+        key = key if key != "vis2" else "vis"
+
+        loglikes_bands = []
+        for band in OPTIONS.fit.bands:
+            band_indices = get_band_indices(wls, [band])
+            mask = data.val[:, band_indices].mask
+            loglikes_bands.append(
+                compute_loglike(
+                    data.val[:, band_indices].compressed(),
+                    data.err[:, band_indices].compressed(),
+                    model_data[key][:, band_indices][~mask],
+                    kind="linear" if key != "t3" else "periodic",
+                )
+            )
+        loglikes.append(loglikes_bands)
+
+    loglikes = np.array(loglikes).astype(float)
+    weights_general = get_weights(kind="general")
+    weights_bands = get_weights(kind="bands")
+    return np.sum((weights_bands * loglikes).sum(1) * weights_general), loglikes
 
 
 def compute_interferometric_loglike(
@@ -341,7 +386,7 @@ def transform_uniform_prior(theta: NDArray[Any], priors: NDArray[Any]) -> float:
     return priors[:, 0] + (priors[:, 1] - priors[:, 0]) * theta
 
 
-def nband(params: NDArray[Any], labels: List[str], theta: NDArray[Any]) -> NDArray[Any]:
+def photometry(params: NDArray[Any], labels: List[str], theta: NDArray[Any]) -> NDArray[Any]:
     """Transform that soft constrains successive radii to be smaller than the one before."""
     indices = list(map(labels.index, filter(lambda x: "weight" in x, labels)))
     remainder = 100
@@ -406,7 +451,7 @@ def param_transform(theta: List[float]) -> NDArray[Any]:
     """Transform that soft constrains successive radii to be smaller than the one before."""
     params = transform_uniform_prior(theta, get_priors(OPTIONS.model.components))
     if OPTIONS.fit.type == "nband":
-        return nband(params, get_labels(OPTIONS.model.components), theta)
+        return photometry(params, get_labels(OPTIONS.model.components), theta)
 
     components = set_components_from_theta(params, theta)
     for option in OPTIONS.fit.conditions:
@@ -431,7 +476,7 @@ def lnprob(theta: NDArray[Any]) -> float:
     """
     components = set_components_from_theta(theta)
     if OPTIONS.fit.type == "nband":
-        return compute_nband_fit_chi_sq(
+        return compute_photometry_loglike(
             components[0].compute_flux(0, OPTIONS.fit.wls),
             ndim=theta.size,
         )

{ppdmod-2.0.0 → ppdmod-2.0.1/ppdmod.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ppdmod
-Version: 2.0.0
+Version: 2.0.1
 Summary: A package for modelling and model-fitting protoplanetary disks
 Author-email: Marten Scheuck <code@mbscheuck.com>
 License: MIT License
@@ -35,14 +35,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: <3.11,>=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: astropy>=6.1.4
 Requires-Dist: corner>=2.2.2
 Requires-Dist: dynesty>=2.1.4
-Requires-Dist: emcee>=3.1.6
-Requires-Dist: h5py>=3.12.1
 Requires-Dist: matplotlib>=3.9.2
 Requires-Dist: numpy>=2.0.2
 Requires-Dist: openpyxl>=3.1.5

{ppdmod-2.0.0 → ppdmod-2.0.1}/ppdmod.egg-info/requires.txt

@@ -1,8 +1,6 @@
 astropy>=6.1.4
 corner>=2.2.2
 dynesty>=2.1.4
-emcee>=3.1.6
-h5py>=3.12.1
 matplotlib>=3.9.2
 numpy>=2.0.2
 openpyxl>=3.1.5

{ppdmod-2.0.0 → ppdmod-2.0.1}/pyproject.toml

@@ -3,7 +3,7 @@ name = "ppdmod"
 dynamic = ["version"]
 description = "A package for modelling and model-fitting protoplanetary disks"
 readme = "README.md"
-requires-python = ">=3.10,<3.11"
+requires-python = ">=3.11"
 license = {file = "LICENSE"}
 authors = [
 	{name = "Marten Scheuck", email = "code@mbscheuck.com"}
@@ -23,8 +23,6 @@ dependencies = [
     "astropy>=6.1.4",
     "corner>=2.2.2",
     "dynesty>=2.1.4",
-    "emcee>=3.1.6",
-    "h5py>=3.12.1",
     "matplotlib>=3.9.2",
     "numpy>=2.0.2",
     "openpyxl>=3.1.5",

ppdmod-2.0.0/ppdmod/__init__.py

@@ -1 +0,0 @@
-__version__ = "2.0.0"