[DOC] Imports and api for visualisation and transformers (#2404)

* transformation and vis api

* notebook

aeon/transformations/collection/__init__.py

@@ -8,8 +8,6 @@
     "ARCoefficientTransformer",
     "Centerer",
     "DownsampleTransformer",
-    "ElbowClassSum",
-    "ElbowClassPairwise",
     "DWTTransformer",
     "HOG1DTransformer",
     "MatrixProfile",
@@ -39,7 +37,3 @@
 from aeon.transformations.collection._slope import SlopeTransformer
 from aeon.transformations.collection._truncate import Truncator
 from aeon.transformations.collection.base import BaseCollectionTransformer
-from aeon.transformations.collection.channel_selection import (
-    ElbowClassPairwise,
-    ElbowClassSum,
-)

aeon/visualisation/__init__.py

@@ -18,17 +18,25 @@
     "plot_scatter_predictions",
     "plot_pairwise_scatter",
     "plot_score_vs_time_scatter",
+    "create_multi_comparison_matrix",
     # Estimator plotting
     "plot_series_with_profiles",
     "plot_cluster_algorithm",
     "plot_temporal_importance_curves",
+    "plot_network",
     "ShapeletVisualizer",
     "ShapeletTransformerVisualizer",
     "ShapeletClassifierVisualizer",
+    # Distance plotting
+    "plot_pairwise_distance_matrix",
 ]
 
+from aeon.visualisation.distances._pairwise_distance_matrix import (
+    plot_pairwise_distance_matrix,
+)
 from aeon.visualisation.estimator._clasp import plot_series_with_profiles
 from aeon.visualisation.estimator._clustering import plot_cluster_algorithm
+from aeon.visualisation.estimator._network_plot import plot_network
 from aeon.visualisation.estimator._shapelets import (
     ShapeletClassifierVisualizer,
     ShapeletTransformerVisualizer,
@@ -43,6 +51,7 @@
 )
 from aeon.visualisation.results._boxplot import plot_boxplot
 from aeon.visualisation.results._critical_difference import plot_critical_difference
+from aeon.visualisation.results._mcm import create_multi_comparison_matrix
 from aeon.visualisation.results._scatter import (
     plot_pairwise_scatter,
     plot_scatter_predictions,

aeon/visualisation/results/__init__.py

@@ -1,5 +1 @@
 """Plotting tools for estimator results."""
-
-__all__ = ["create_multi_comparison_matrix"]
-
-from aeon.visualisation.results._mcm import create_multi_comparison_matrix

docs/api_reference/transformations.rst

@@ -15,14 +15,6 @@ All transformers in `aeon` can be listed using the `aeon.registry
 Collection transformers
 -----------------------
 
-.. currentmodule:: aeon.transformations.collection.base
-
-.. autosummary::
-    :toctree: auto_generated/
-    :template: class.rst
-
-    BaseCollectionTransformer
-
 .. currentmodule:: aeon.transformations.collection
 
 .. autosummary::
@@ -31,6 +23,7 @@ Collection transformers
 
     AutocorrelationFunctionTransformer
     ARCoefficientTransformer
+    Centerer
     DownsampleTransformer
     DWTTransformer
     HOG1DTransformer
@@ -39,12 +32,11 @@ Collection transformers
     Normalizer
     Padder
     PeriodogramTransformer
-    Tabularizer
     Resizer
-    SimpleImputer
     SlopeTransformer
-    Standardizer
+    SimpleImputer
     Truncator
+    Tabularizer
 
 
 Channel selection
@@ -72,6 +64,7 @@ Compose
     :template: class.rst
 
     CollectionTransformerPipeline
+    CollectionId
 
 
 Convolution based
@@ -85,7 +78,6 @@ Convolution based
 
     Rocket
     MiniRocket
-    MiniRocketMultivariateVariable
     MultiRocket
     HydraTransformer
 
@@ -148,8 +140,6 @@ Shapelet based
     SAST
     RSAST
 
-
-
 Signature based
 ~~~~~~~~~~~~~~~
 
@@ -165,23 +155,13 @@ Signature based
 Series transforms
 -----------------
 
-.. currentmodule:: aeon.transformations.series.base
-
-.. autosummary::
-    :toctree: auto_generated/
-    :template: class.rst
-
-    BaseSeriesTransformer
-
-
 .. currentmodule:: aeon.transformations.series
 
 .. autosummary::
     :toctree: auto_generated/
     :template: class.rst
 
     AutoCorrelationSeriesTransformer
-    ClearSkyTransformer
     ClaSPTransformer
     DFTSeriesTransformer
     Dobin
@@ -193,9 +173,28 @@ Series transforms
     StatsModelsPACF
     BKFilter
     BoxCoxTransformer
-    YeoJohnsonTransformer
-    Dobin
     ScaledLogitSeriesTransformer
     SIVSeriesTransformer
     PCASeriesTransformer
     WarpingSeriesTransformer
+
+
+Base
+----
+
+.. currentmodule:: aeon.transformations.collection.base
+
+.. autosummary::
+    :toctree: auto_generated/
+    :template: class.rst
+
+    BaseCollectionTransformer
+
+
+.. currentmodule:: aeon.transformations.series.base
+
+.. autosummary::
+    :toctree: auto_generated/
+    :template: class.rst
+
+    BaseSeriesTransformer

docs/api_reference/visualisation.rst

@@ -3,9 +3,7 @@
 Visualisation
 =============
 
-.. automodule:: aeon.visualisation
-    :no-members:
-    :no-inherited-members:
+.. currentmodule:: aeon.visualisation
 
 .. autosummary::
     :toctree: auto_generated/
@@ -22,13 +20,20 @@ Visualisation
     plot_series
     plot_lags
     plot_correlations
-    plot_interval
-    plot_windows
+    plot_series_collection
+    plot_collection_by_class
+    plot_spectrogram
+    plot_series_windows
+    plot_series_with_change_points
     plot_critical_difference
+    plot_significance
     plot_boxplot
     plot_scatter_predictions
-    plot_scatter
-    plot_time_series_with_change_points
-    plot_time_series_with_profiles
+    plot_pairwise_scatter
+    plot_score_vs_time_scatter
+    create_multi_comparison_matrix
+    plot_series_with_profiles
     plot_cluster_algorithm
+    plot_temporal_importance_curves
     plot_network
+    plot_pairwise_distance_matrix

examples/visualisation/plotting_results.ipynb

@@ -431,7 +431,7 @@
     }
    ],
    "source": [
-    "from aeon.visualisation.results import create_multi_comparison_matrix\n",
+    "from aeon.visualisation import create_multi_comparison_matrix\n",
     "\n",
     "create_multi_comparison_matrix(df, fig_size=\"8,4\")"
    ]
@@ -464,7 +464,7 @@
     }
    ],
    "source": [
-    "from aeon.visualisation.results import create_multi_comparison_matrix\n",
+    "from aeon.visualisation import create_multi_comparison_matrix\n",
     "\n",
     "create_multi_comparison_matrix(\n",
     "    df, fig_size=\"8,4\", pvalue_test_params={\"alternative\": \"two-sided\"}\n",
@@ -499,7 +499,7 @@
     }
    ],
    "source": [
-    "from aeon.visualisation.results import create_multi_comparison_matrix\n",
+    "from aeon.visualisation import create_multi_comparison_matrix\n",
     "\n",
     "create_multi_comparison_matrix(\n",
     "    df,\n",
@@ -537,7 +537,7 @@
     }
    ],
    "source": [
-    "from aeon.visualisation.results import create_multi_comparison_matrix\n",
+    "from aeon.visualisation import create_multi_comparison_matrix\n",
     "\n",
     "create_multi_comparison_matrix(\n",
     "    df,\n",