nltools 0.6.0.dev0__py3-none-any.whl

nltools/plotting/decomposition.py

@@ -0,0 +1,111 @@
+"""ICA/PCA component viewer — interactive decomposition explorer."""
+
+import matplotlib.pyplot as plt
+import numpy as np
+import sklearn
+from numpy.fft import fft, fftfreq
+from nilearn.plotting import plot_stat_map
+
+from nltools.utils import _attempt_to_import
+
+# Optional dependencies
+ipywidgets = _attempt_to_import(
+    "ipywidgets",
+    fromlist=["interact", "fixed", "widgets", "BoundedFloatText", "BoundedIntText"],
+)
+
+
+def component_viewer(output, tr=2.0):
+    """Interactively view the results of a `BrainData.decompose()` run.
+
+    Args:
+        output (dict): Output dictionary from `BrainData.decompose()` (keys
+            `'components'`, `'weights'`, `'decomposition_object'`).
+        tr (float): Repetition time of the data in seconds. Default 2.0.
+
+    Note:
+        Returns nothing; the interactive widgets render inline.
+    """
+
+    if ipywidgets is None:
+        raise ImportError(
+            "ipywidgets is required for interactive plotting. Please install this package manually or install nltools with optional arguments: pip install 'nltools[interactive_plots]'"
+        )
+
+    def component_inspector(component, threshold):
+        """Render one decomposition component, for use with ipywidgets interactive controls.
+
+        Make sure you have tr and output assigned to variables.
+
+        Returns:
+            None (renders matplotlib figures inline)
+
+        Examples:
+            ```python
+            from ipywidgets import BoundedFloatText, BoundedIntText, interact
+
+            tr = 2.4
+            output = data_filtered_smoothed.decompose(
+                method='ica', n_components=30, axis='images', whiten=True
+            )
+
+            interact(
+                component_inspector,
+                component=BoundedIntText(
+                    description='Component',
+                    value=0,
+                    min=0,
+                    max=len(output['components']) - 1,
+                ),
+                threshold=BoundedFloatText(
+                    description='Threshold', value=2.0, min=0, max=4, step=0.1
+                ),
+            )
+            ```
+        """
+        _, ax = plt.subplots(nrows=3, figsize=(12, 8))
+        thresholded = (
+            output["components"][component] - output["components"][component].mean()
+        ) * (1 / output["components"][component].std())
+        thresholded.data[np.abs(thresholded.data) <= threshold] = 0
+        plot_stat_map(
+            thresholded.to_nifti(),
+            cut_coords=range(-40, 70, 10),
+            display_mode="z",
+            black_bg=True,
+            colorbar=True,
+            annotate=False,
+            draw_cross=False,
+            axes=ax[0],
+        )
+        if isinstance(output["decomposition_object"], (sklearn.decomposition.PCA)):
+            var_exp = output["decomposition_object"].explained_variance_ratio_[
+                component
+            ]
+            ax[0].set_title(
+                f"Component: {component}/{len(output['components'])}, Variance Explained: {var_exp:2.2}",
+                fontsize=18,
+            )
+        else:
+            ax[0].set_title(
+                f"Component: {component}/{len(output['components'])}", fontsize=18
+            )
+
+        ax[1].plot(output["weights"][:, component], linewidth=2, color="red")
+        ax[1].set_ylabel("Intensity (AU)", fontsize=18)
+        ax[1].set_title(f"Timecourse (TR={tr})", fontsize=16)
+        y = fft(output["weights"][:, component])
+        f = fftfreq(len(y), d=tr)
+        ax[2].plot(f[f > 0], np.abs(y)[f > 0] ** 2)
+        ax[2].set_ylabel("Power", fontsize=18)
+        ax[2].set_xlabel("Frequency (Hz)", fontsize=16)
+
+    ipywidgets.interact(
+        component_inspector,
+        component=ipywidgets.BoundedIntText(
+            description="Component", value=0, min=0, max=len(output["components"]) - 1
+        ),
+        threshold=ipywidgets.BoundedFloatText(
+            description="Threshold", value=2.0, min=0, max=4, step=0.1
+        ),
+    )

nltools/plotting/prediction.py

@@ -0,0 +1,110 @@
+"""Model output visualization — ROC curves and the cross-validated decoding figures.
+
+Every function here takes arrays, not a result table: `BrainData.predict` returns a
+`Predict` record plus the row-aligned out-of-fold decision values that go with it,
+and these draw from those directly.
+"""
+
+import matplotlib.pyplot as plt
+import numpy as np
+import seaborn as sns
+
+
+def _plot_predicted_versus_actual(y_true, y_pred, *, r=None, ax=None):
+    """Scatter cross-validated predictions against the observed target.
+
+    Args:
+        y_true (array-like): Observed target, one value per observation.
+        y_pred (array-like): Out-of-fold prediction for the same observations.
+        r (float, optional): Cross-validated Pearson correlation to name in the
+            title; omitted from the title when `None`.
+        ax (matplotlib.axes.Axes, optional): Axis to draw on; a new figure is
+            created when omitted.
+
+    Returns:
+        matplotlib.axes.Axes: The axis holding the scatter and its fit line.
+    """
+    if ax is None:
+        _, ax = plt.subplots(1)
+    axis = sns.regplot(
+        x=np.asarray(y_true, dtype=float), y=np.asarray(y_pred, dtype=float), ax=ax
+    )
+    axis.set_xlabel("Observed", fontsize=16)
+    axis.set_ylabel("Predicted", fontsize=16)
+    title = "Predicted vs actual" if r is None else f"Predicted vs actual (r = {r:.2f})"
+    axis.set_title(title, fontsize=18)
+    return axis
+
+
+def _plot_decision_margin(margins, y_true, *, ax=None):
+    """Plot each observation's signed distance from the decision boundary by class.
+
+    Args:
+        margins (array-like): Out-of-fold `decision_function` values, one per
+            observation.
+        y_true (array-like): Class label for the same observations.
+        ax (matplotlib.axes.Axes, optional): Axis to draw on; a new figure is
+            created when omitted.
+
+    Returns:
+        matplotlib.axes.Axes: The axis holding the margin figure.
+    """
+    if ax is None:
+        _, ax = plt.subplots(1)
+    axis = sns.stripplot(
+        x=np.asarray(y_true).astype(str),
+        y=np.asarray(margins, dtype=float),
+        ax=ax,
+    )
+    axis.axhline(0, color="gray", linestyle="--", linewidth=1)
+    axis.set_xlabel("Class", fontsize=16)
+    axis.set_ylabel("Distance from Hyperplane", fontsize=16)
+    axis.set_title("Classification margin", fontsize=18)
+    return axis
+
+
+def _plot_class_probability(probabilities, y_true, *, ax=None):
+    """Plot the predicted positive-class probability of each observation by class.
+
+    Args:
+        probabilities (array-like): Out-of-fold `predict_proba` values for the
+            positive class, one per observation.
+        y_true (array-like): Class label for the same observations.
+        ax (matplotlib.axes.Axes, optional): Axis to draw on; a new figure is
+            created when omitted.
+
+    Returns:
+        matplotlib.axes.Axes: The axis holding the probability figure.
+    """
+    if ax is None:
+        _, ax = plt.subplots(1)
+    axis = sns.stripplot(
+        x=np.asarray(y_true).astype(str),
+        y=np.asarray(probabilities, dtype=float),
+        ax=ax,
+    )
+    axis.axhline(0.5, color="gray", linestyle="--", linewidth=1)
+    axis.set_xlabel("Class", fontsize=16)
+    axis.set_ylabel("Predicted Probability", fontsize=16)
+    axis.set_title("Classification probability", fontsize=18)
+    return axis
+
+
+def _plot_roc(fpr, tpr):
+    """Plot 1-Specificity by Sensitivity.
+
+    Args:
+        fpr (np.ndarray): False positive rate per criterion value, from `Roc.calculate`.
+        tpr (np.ndarray): True positive rate per criterion value, from `Roc.calculate`.
+
+    Returns:
+        matplotlib.figure.Figure: The ROC figure.
+
+    """
+
+    fig = plt.figure()
+    plt.plot(fpr, tpr, color="red", linewidth=3)
+    plt.xlabel("(1 - Specificity)", fontsize=16)
+    plt.ylabel("Sensitivity", fontsize=16)
+    plt.title("ROC Plot", fontsize=18)
+    return fig

nltools/resources/covariates_example.csv

@@ -0,0 +1,161 @@
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nltools/resources/onsets_example.csv

@@ -0,0 +1,40 @@
+onset,duration,trial_type
+10.1605967,10,CoachTaylor
+18.190957161,10,LylaGarrity
+26.221317192,10,JulieTaylor
+33.252048014,10,LylaGarrity
+40.282787781,10,LandryClarke
+51.311997544,10,BuddyGarrity
+57.343152722,10,TamiTaylor
+63.37425517,10,BuddyGarrity
+69.405359036,10,SmashWilliams
+76.436088332,10,SmashWilliams
+83.466820048,10,GrandmaSaracen
+91.497193631,10,BillyRiggins
+101.526809594,10,MattSaracen
+108.557544453,10,TamiTaylor
+114.588578367,10,TamiTaylor
+120.61974369,10,GrandmaSaracen
+126.650846005,10,BillyRiggins
+132.681946075,10,LylaGarrity
+142.71156909,10,LandryClarke
+156.739712911,10,BuddyGarrity
+162.770814649,10,JasonStreet
+173.800055801,10,TimRiggins
+180.830786482,10,CoachTaylor
+186.86185978,10,JasonStreet
+192.892958472,10,CoachTaylor
+202.922615368,10,JasonStreet
+208.95371632,10,GrandmaSaracen
+220.982600503,10,MattSaracen
+234.011058731,10,BillyRiggins
+240.042214664,10,JasonStreet
+249.072207216,10,TimRiggins
+256.102931267,10,BillyRiggins
+263.133663523,10,JulieTaylor
+272.163655973,10,JulieTaylor
+281.193644014,10,JasonStreet
+289.223956762,10,TyraCollette
+297.254368242,10,GrandmaSaracen
+304.285099479,10,MattSaracen
+313.315087766,10,BuddyGarrity

nltools/templates/__init__.py

@@ -0,0 +1,51 @@
+"""Global MNI brain-space configuration for nltools.
+
+This module manages the default MNI template used by `BrainData` and
+related classes when no explicit mask is provided. Set it once (e.g., at
+the top of a notebook) and all subsequent operations pick it up
+automatically.
+
+Examples:
+    Set the global brain space:
+
+    ```python
+    import nltools
+
+    nltools.set_brainspace(template="fmriprep", resolution=2)
+    ```
+
+    Inspect the current configuration:
+
+    ```python
+    cfg = nltools.get_brainspace()
+    print(cfg.mask)
+    ```
+
+    Scope a change to a block:
+
+    ```python
+    with nltools.with_brainspace(resolution=1):
+        brain = BrainData(...)
+    ```
+"""
+
+# Internal package: these imports are re-exports for the rest of nltools, not
+# an advertised surface, so there is no `__all__` to mark them as used. The
+# four brain-space functions are advertised at `nltools`, `BrainSpaceConfig` at
+# `nltools.data`, and `fetch_resource`/`list_resources` at `nltools.datasets`.
+from .config import (  # noqa: F401
+    BrainSpaceConfig,
+    get_brainspace,
+    reset_brainspace,
+    set_brainspace,
+    with_brainspace,
+)
+from .fetch import fetch_resource, list_resources  # noqa: F401
+from .matching import (  # noqa: F401
+    _TemplateMatch,
+    _detect_resolution,
+    _get_bg_image,
+    _is_standard_space,
+    _match_resolution,
+)
+from .paths import _resolve_paths, _resolve_template_name  # noqa: F401