distclassipy 0.1.5__tar.gz → 0.2.0a0__tar.gz

{distclassipy-0.1.5 → distclassipy-0.2.0a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: distclassipy
-Version: 0.1.5
+Version: 0.2.0a0
 Summary: A python package for a distance-based classifier which can use several different distance metrics.
 Author-email: Siddharth Chaini <sidchaini@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -694,7 +694,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: joblib>=1.3.2
-Requires-Dist: numpy<2,>=1.25.2
+Requires-Dist: numpy>=1.25.2
 Requires-Dist: pandas>=2.0.3
 Requires-Dist: scikit-learn>=1.2.2
 
@@ -740,9 +740,9 @@ X, y = make_classification(
     random_state=0,
     shuffle=False,
 )
-clf = dcpy.DistanceMetricClassifier(metric="canberra")
+clf = dcpy.DistanceMetricClassifier()
 clf.fit(X, y)
-print(clf.predict([[0, 0, 0, 0]]))
+print(clf.predict([[0, 0, 0, 0]]), metric="canberra")
 ```
 
 ## Features
@@ -765,27 +765,30 @@ DistClassiPy is released under the [GNU General Public License v3.0](https://www
 ## Citation
 
 If you use DistClassiPy in your research or project, please consider citing the paper:
-> Chaini, S., Mahabal, A., Kembhavi, A., & Bianco, F. B. (2024). Light Curve Classification with DistClassiPy: a new distance-based classifier. arXiv. https://doi.org/10.48550/arXiv.2403.12120
+> Chaini, S., Mahabal, A., Kembhavi, A., & Bianco, F. B. (2024). Light Curve Classification with DistClassiPy: a new distance-based classifier. Astronomy and Computing. https://doi.org/10.1016/j.ascom.2024.100850.
 
 ### Bibtex
 
 
 ```bibtex
-@ARTICLE{chaini2024light,
-       author = {{Chaini}, Siddharth and {Mahabal}, Ashish and {Kembhavi}, Ajit and {Bianco}, Federica B.},
-       title = "{Light Curve Classification with DistClassiPy: a new distance-based classifier}",
-       journal = {arXiv e-prints},
-       keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics, Computer Science - Machine Learning},
-       year = 2024,
-       month = mar,
-       eid = {arXiv:2403.12120},
-       pages = {arXiv:2403.12120},
-       archivePrefix = {arXiv},
+@ARTICLE{2024A&C....4800850C,
+       author = {{Chaini}, S. and {Mahabal}, A. and {Kembhavi}, A. and {Bianco}, F.~B.},
+        title = "{Light curve classification with DistClassiPy: A new distance-based classifier}",
+      journal = {Astronomy and Computing},
+     keywords = {Variable stars (1761), Astronomy data analysis (1858), Open source software (1866), Astrostatistics (1882), Classification (1907), Light curve classification (1954), Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics, Computer Science - Machine Learning},
+         year = 2024,
+        month = jul,
+       volume = {48},
+          eid = {100850},
+        pages = {100850},
+          doi = {10.1016/j.ascom.2024.100850},
+archivePrefix = {arXiv},
        eprint = {2403.12120},
-       primaryClass = {astro-ph.IM},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240312120C},
-       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024A&C....4800850C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
 ```
   
 

{distclassipy-0.1.5 → distclassipy-0.2.0a0}/README.md

@@ -40,9 +40,9 @@ X, y = make_classification(
     random_state=0,
     shuffle=False,
 )
-clf = dcpy.DistanceMetricClassifier(metric="canberra")
+clf = dcpy.DistanceMetricClassifier()
 clf.fit(X, y)
-print(clf.predict([[0, 0, 0, 0]]))
+print(clf.predict([[0, 0, 0, 0]]), metric="canberra")
 ```
 
 ## Features
@@ -65,27 +65,30 @@ DistClassiPy is released under the [GNU General Public License v3.0](https://www
 ## Citation
 
 If you use DistClassiPy in your research or project, please consider citing the paper:
-> Chaini, S., Mahabal, A., Kembhavi, A., & Bianco, F. B. (2024). Light Curve Classification with DistClassiPy: a new distance-based classifier. arXiv. https://doi.org/10.48550/arXiv.2403.12120
+> Chaini, S., Mahabal, A., Kembhavi, A., & Bianco, F. B. (2024). Light Curve Classification with DistClassiPy: a new distance-based classifier. Astronomy and Computing. https://doi.org/10.1016/j.ascom.2024.100850.
 
 ### Bibtex
 
 
 ```bibtex
-@ARTICLE{chaini2024light,
-       author = {{Chaini}, Siddharth and {Mahabal}, Ashish and {Kembhavi}, Ajit and {Bianco}, Federica B.},
-       title = "{Light Curve Classification with DistClassiPy: a new distance-based classifier}",
-       journal = {arXiv e-prints},
-       keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics, Computer Science - Machine Learning},
-       year = 2024,
-       month = mar,
-       eid = {arXiv:2403.12120},
-       pages = {arXiv:2403.12120},
-       archivePrefix = {arXiv},
+@ARTICLE{2024A&C....4800850C,
+       author = {{Chaini}, S. and {Mahabal}, A. and {Kembhavi}, A. and {Bianco}, F.~B.},
+        title = "{Light curve classification with DistClassiPy: A new distance-based classifier}",
+      journal = {Astronomy and Computing},
+     keywords = {Variable stars (1761), Astronomy data analysis (1858), Open source software (1866), Astrostatistics (1882), Classification (1907), Light curve classification (1954), Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics, Computer Science - Machine Learning},
+         year = 2024,
+        month = jul,
+       volume = {48},
+          eid = {100850},
+        pages = {100850},
+          doi = {10.1016/j.ascom.2024.100850},
+archivePrefix = {arXiv},
        eprint = {2403.12120},
-       primaryClass = {astro-ph.IM},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240312120C},
-       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024A&C....4800850C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
 ```
   
 

{distclassipy-0.1.5 → distclassipy-0.2.0a0}/distclassipy/__init__.py

@@ -25,4 +25,4 @@ along with this program.  If not, see <https://www.gnu.org/licenses/>.
 from .classifier import DistanceMetricClassifier  # noqa
 from .distances import Distance  # noqa
 
-__version__ = "0.1.5"
+__version__ = "0.2.0a0"

{distclassipy-0.1.5 → distclassipy-0.2.0a0}/distclassipy/classifier.py

@@ -28,7 +28,6 @@ import pandas as pd
 import scipy
 
 from sklearn.base import BaseEstimator, ClassifierMixin
-from sklearn.neighbors import KernelDensity
 from sklearn.utils.multiclass import unique_labels
 from sklearn.utils.validation import check_X_y, check_array, check_is_fitted
 
@@ -41,6 +40,52 @@ METRIC_SOURCES_ = {
 }
 
 
+def initialize_metric_function(metric):
+    """Set the metric function based on the provided metric.
+
+    If the metric is a string, the function will look for a corresponding
+    function in scipy.spatial.distance or distances.Distance. If the metric
+    is a function, it will be used directly.
+    """
+    if callable(metric):
+        metric_fn_ = metric
+        metric_arg_ = metric
+
+    elif isinstance(metric, str):
+        metric_str_lowercase = metric.lower()
+        metric_found = False
+        for package_str, source in METRIC_SOURCES_.items():
+
+            # Don't use scipy for jaccard as their implementation only works with
+            # booleans - use custom jaccard instead
+            if (
+                package_str == "scipy.spatial.distance"
+                and metric_str_lowercase == "jaccard"
+            ):
+                continue
+
+            if hasattr(source, metric_str_lowercase):
+                metric_fn_ = getattr(source, metric_str_lowercase)
+                metric_found = True
+
+                # Use the string as an argument if it belongs to scipy as it is
+                # optimized
+                metric_arg_ = (
+                    metric if package_str == "scipy.spatial.distance" else metric_fn_
+                )
+                break
+        if not metric_found:
+            raise ValueError(
+                f"{metric} metric not found. Please pass a string of the "
+                "name of a metric in scipy.spatial.distance or "
+                "distances.Distance, or pass a metric function directly. For a "
+                "list of available metrics, see: "
+                "https://sidchaini.github.io/DistClassiPy/distances.html or "
+                "https://docs.scipy.org/doc/scipy/reference/spatial.distance.html"
+            )
+    return metric_fn_, metric_arg_
+
+
 class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
     """A distance-based classifier that supports different distance metrics.
 
@@ -54,8 +99,6 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
 
     Parameters
     ----------
-    metric : str or callable, default="euclidean"
-        The distance metric to use for calculating the distance between features.
     scale : bool, default=True
         Whether to scale the distance between the test object and the centroid for a
         class in the feature space. If True, the data will be scaled based on the
@@ -70,36 +113,15 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
 
         .. versionadded:: 0.1.0
 
-    calculate_kde : bool, default=False
-        Whether to calculate a kernel density estimate based confidence parameter.
-    calculate_1d_dist : bool, default=False
-        Whether to calculate the 1-dimensional distance based confidence parameter.
 
     Attributes
     ----------
-    metric : str or callable
-        The distance metric used for classification.
     scale : bool
         Indicates whether the data is scaled.
     central_stat : str
         The statistic used for calculating central tendency.
     dispersion_stat : str
         The statistic used for calculating dispersion.
-    calculate_kde : bool
-        Indicates whether a kernel density estimate is calculated.
-    calculate_1d_dist : bool
-        Indicates whether 1-dimensional distances are calculated.
-
-    See Also
-    --------
-    scipy.spatial.dist : Other distance metrics provided in SciPy
-    distclassipy.Distance : Distance metrics included with DistClassiPy
-
-    Notes
-    -----
-    If using distance metrics supported by SciPy, it is desirable to pass a string,
-    which allows SciPy to use an optimized C version of the code instead of the slower
-    Python version.
 
     References
     ----------
@@ -122,66 +144,14 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
 
     def __init__(
         self,
-        metric: str | Callable = "euclidean",
         scale: bool = True,
         central_stat: str = "median",
         dispersion_stat: str = "std",
-        calculate_kde: bool = True,
-        calculate_1d_dist: bool = True,
     ):
         """Initialize the classifier with specified parameters."""
-        self.metric = metric
         self.scale = scale
         self.central_stat = central_stat
         self.dispersion_stat = dispersion_stat
-        self.calculate_kde = calculate_kde
-        self.calculate_1d_dist = calculate_1d_dist
-
-    def initialize_metric_function(self):
-        """Set the metric function based on the provided metric.
-
-        If the metric is a string, the function will look for a corresponding
-        function in scipy.spatial.distance or distances.Distance. If the metric
-        is a function, it will be used directly.
-        """
-        if callable(self.metric):
-            self.metric_fn_ = self.metric
-            self.metric_arg_ = self.metric
-
-        elif isinstance(self.metric, str):
-            metric_str_lowercase = self.metric.lower()
-            metric_found = False
-            for package_str, source in METRIC_SOURCES_.items():
-
-                # Don't use scipy for jaccard as their implementation only works with
-                # booleans - use custom jaccard instead
-                if (
-                    package_str == "scipy.spatial.distance"
-                    and metric_str_lowercase == "jaccard"
-                ):
-                    continue
-
-                if hasattr(source, metric_str_lowercase):
-                    self.metric_fn_ = getattr(source, metric_str_lowercase)
-                    metric_found = True
-
-                    # Use the string as an argument if it belongs to scipy as it is
-                    # optimized
-                    self.metric_arg_ = (
-                        self.metric
-                        if package_str == "scipy.spatial.distance"
-                        else self.metric_fn_
-                    )
-                    break
-            if not metric_found:
-                raise ValueError(
-                    f"{self.metric} metric not found. Please pass a string of the "
-                    "name of a metric in scipy.spatial.distance or "
-                    "distances.Distance, or pass a metric function directly. For a "
-                    "list of available metrics, see: "
-                    "https://sidchaini.github.io/DistClassiPy/distances.html or "
-                    "https://docs.scipy.org/doc/scipy/reference/spatial.distance.html"
-                )
 
     def fit(self, X: np.array, y: np.array, feat_labels: list[str] = None):
         """Calculate the feature space centroid for all classes.
@@ -209,9 +179,9 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
         """
         X, y = check_X_y(X, y)
         self.classes_ = unique_labels(y)
-        self.n_features_in_ = X.shape[1]
-
-        self.initialize_metric_function()
+        self.n_features_in_ = X.shape[
+            1
+        ]  # Number of features seen during fit - required for sklearn compatibility.
 
         if feat_labels is None:
             feat_labels = [f"Feature_{x}" for x in range(X.shape[1])]
@@ -256,27 +226,15 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
             )
             self.df_iqr_ = df_iqr
 
-        if self.calculate_kde:
-            self.kde_dict_ = {}
-
-            for cl in self.classes_:
-                subX = X[y == cl]
-                # Implement the following in an if-else to save computational time.
-                # kde = KernelDensity(bandwidth='scott', metric=self.metric)
-                # kde.fit(subX)
-                kde = KernelDensity(
-                    bandwidth="scott",
-                    metric="pyfunc",
-                    metric_params={"func": self.metric_fn_},
-                )
-                kde.fit(subX)
-                self.kde_dict_[cl] = kde
-
         self.is_fitted_ = True
 
         return self
 
-    def predict(self, X: np.array):
+    def predict(
+        self,
+        X: np.array,
+        metric: str | Callable = "euclidean",
+    ):
         """Predict the class labels for the provided X.
 
         The prediction is based on the distance of each data point in the input sample
@@ -287,18 +245,33 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
         ----------
         X : array-like of shape (n_samples, n_features)
             The input samples.
+        metric : str or callable, default="euclidean"
+            The distance metric to use for calculating the distance between features.
 
         Returns
         -------
         y : ndarray of shape (n_samples,)
             The predicted classes.
+
+        See Also
+        --------
+        scipy.spatial.dist : Other distance metrics provided in SciPy
+        distclassipy.Distance : Distance metrics included with DistClassiPy
+
+        Notes
+        -----
+        If using distance metrics supported by SciPy, it is desirable to pass a string,
+        which allows SciPy to use an optimized C version of the code instead of the
+        slower Python version.
         """
         check_is_fitted(self, "is_fitted_")
         X = check_array(X)
 
+        metric_fn_, metric_arg_ = initialize_metric_function(metric)
+
         if not self.scale:
             dist_arr = scipy.spatial.distance.cdist(
-                XA=X, XB=self.df_centroid_.to_numpy(), metric=self.metric_arg_
+                XA=X, XB=self.df_centroid_.to_numpy(), metric=metric_arg_
             )
 
         else:
@@ -315,16 +288,18 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
                 w = wtdf.loc[cl].to_numpy()  # 1/std dev
                 XB = XB * w  # w is for this class only
                 XA = X * w  # w is for this class only
-                cl_dist = scipy.spatial.distance.cdist(
-                    XA=XA, XB=XB, metric=self.metric_arg_
-                )
+                cl_dist = scipy.spatial.distance.cdist(XA=XA, XB=XB, metric=metric_arg_)
                 dist_arr_list.append(cl_dist)
             dist_arr = np.column_stack(dist_arr_list)
 
         y_pred = self.classes_[dist_arr.argmin(axis=1)]
         return y_pred
 
-    def predict_and_analyse(self, X: np.array):
+    def predict_and_analyse(
+        self,
+        X: np.array,
+        metric: str | Callable = "euclidean",
+    ):
         """Predict the class labels for the provided X and perform analysis.
 
         The prediction is based on the distance of each data point in the input sample
@@ -338,18 +313,35 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
         ----------
         X : array-like of shape (n_samples, n_features)
             The input samples.
+        metric : str or callable, default="euclidean"
+            The distance metric to use for calculating the distance between features.
+
 
         Returns
         -------
         y : ndarray of shape (n_samples,)
             The predicted classes.
+
+        See Also
+        --------
+        scipy.spatial.dist : Other distance metrics provided in SciPy
+        distclassipy.Distance : Distance metrics included with DistClassiPy
+
+        Notes
+        -----
+        If using distance metrics supported by SciPy, it is desirable to pass a string,
+        which allows SciPy to use an optimized C version of the code instead
+        of the slower Python version.
+
         """
         check_is_fitted(self, "is_fitted_")
         X = check_array(X)
 
+        metric_fn_, metric_arg_ = initialize_metric_function(metric)
+
         if not self.scale:
             dist_arr = scipy.spatial.distance.cdist(
-                XA=X, XB=self.df_centroid_.to_numpy(), metric=self.metric_arg_
+                XA=X, XB=self.df_centroid_.to_numpy(), metric=metric_arg_
             )
 
         else:
@@ -366,9 +358,7 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
                 w = wtdf.loc[cl].to_numpy()  # 1/std dev
                 XB = XB * w  # w is for this class only
                 XA = X * w  # w is for this class only
-                cl_dist = scipy.spatial.distance.cdist(
-                    XA=XA, XB=XB, metric=self.metric_arg_
-                )
+                cl_dist = scipy.spatial.distance.cdist(XA=XA, XB=XB, metric=metric_arg_)
                 dist_arr_list.append(cl_dist)
             dist_arr = np.column_stack(dist_arr_list)
 
@@ -381,68 +371,15 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
 
         y_pred = self.classes_[dist_arr.argmin(axis=1)]
 
-        if self.calculate_kde:
-            # NEW: Rescale in terms of median likelihoods - calculate here
-            scale_factors = np.exp(
-                [
-                    self.kde_dict_[cl].score_samples(
-                        self.df_centroid_.loc[cl].to_numpy().reshape(1, -1)
-                    )[0]
-                    for cl in self.classes_
-                ]
-            )
-
-            likelihood_arr = []
-            for k in self.kde_dict_.keys():
-                log_pdf = self.kde_dict_[k].score_samples(X)
-                likelihood_val = np.exp(log_pdf)
-                likelihood_arr.append(likelihood_val)
-            self.likelihood_arr_ = np.array(likelihood_arr).T
-
-            # NEW: Rescale in terms of median likelihoods - rescale here
-            self.likelihood_arr_ = self.likelihood_arr_ / scale_factors
-
-        if self.calculate_1d_dist:
-            conf_cl = []
-            Xdf_temp = pd.DataFrame(data=X, columns=self.df_centroid_.columns)
-            for cl in self.classes_:
-                sum_1d_dists = np.zeros(shape=(len(Xdf_temp)))
-                for feat in Xdf_temp.columns:
-                    dists = scipy.spatial.distance.cdist(
-                        XA=np.zeros(shape=(1, 1)),
-                        XB=(self.df_centroid_.loc[cl] - Xdf_temp)[feat]
-                        .to_numpy()
-                        .reshape(-1, 1),
-                        metric=self.metric_arg_,
-                    ).ravel()
-                    if self.scale and self.dispersion_stat == "std":
-                        sum_1d_dists = sum_1d_dists + dists / self.df_std_.loc[cl, feat]
-                    elif self.scale and self.dispersion_stat == "std":
-                        sum_1d_dists = sum_1d_dists + dists / self.df_iqr_.loc[cl, feat]
-                    else:
-                        sum_1d_dists = sum_1d_dists + dists
-                confs = 1 / np.clip(sum_1d_dists, a_min=np.finfo(float).eps, a_max=None)
-                conf_cl.append(confs)
-            conf_cl = np.array(conf_cl)
-            self.conf_cl_ = conf_cl
-
         self.analyis_ = True
 
         return y_pred
 
-    def calculate_confidence(self, method: str = "distance_inverse"):
+    def calculate_confidence(self):
         """Calculate the confidence for each prediction.
 
-        The confidence is calculated based on either the distance of each data point to
-        the centroids of the training data, optionally the kernel density estimate or
-        1-dimensional distance.
-
-        Parameters
-        ----------
-        method : {"distance_inverse", "1d_distance_inverse","kde_likelihood"},
-                 default="distance_inverse"
-            The method to use for calculating confidence. Default is
-            'distance_inverse'.
+        The confidence is calculated as the inverse of the distance of each data point
+        to the centroids of the training data.
         """
         check_is_fitted(self, "is_fitted_")
         if not hasattr(self, "analyis_"):
@@ -452,34 +389,11 @@ class DistanceMetricClassifier(BaseEstimator, ClassifierMixin):
             )
 
         # Calculate confidence for each prediction
-        if method == "distance_inverse":
-            self.confidence_df_ = 1 / np.clip(
-                self.centroid_dist_df_, a_min=np.finfo(float).eps, a_max=None
-            )
-            self.confidence_df_.columns = [
-                x.replace("_dist", "_conf") for x in self.confidence_df_.columns
-            ]
-
-        elif method == "1d_distance_inverse":
-            if not self.calculate_1d_dist:
-                raise ValueError(
-                    "method='1d_distance_inverse' is only valid if calculate_1d_dist "
-                    "is set to True"
-                )
-            self.confidence_df_ = pd.DataFrame(
-                data=self.conf_cl_.T, columns=[f"{x}_conf" for x in self.classes_]
-            )
-
-        elif method == "kde_likelihood":
-            if not self.calculate_kde:
-                raise ValueError(
-                    "method='kde_likelihood' is only valid if calculate_kde is set "
-                    "to True"
-                )
-
-            self.confidence_df_ = pd.DataFrame(
-                data=self.likelihood_arr_,
-                columns=[f"{x}_conf" for x in self.kde_dict_.keys()],
-            )
+        self.confidence_df_ = 1 / np.clip(
+            self.centroid_dist_df_, a_min=np.finfo(float).eps, a_max=None
+        )
+        self.confidence_df_.columns = [
+            x.replace("_dist", "_conf") for x in self.confidence_df_.columns
+        ]
 
         return self.confidence_df_.to_numpy()