fix paths and module name

docs/background/README.md

@@ -35,7 +35,7 @@ plot_00_conceptual_intro.md
 
 ```{eval-rst}
 
-.. plot:: scripts/basis_table_figs.py plot_raised_cosine_linear
+.. plot:: scripts/basis_figs.py plot_raised_cosine_linear
    :show-source-link: False
    :height: 100px
 ```

docs/background/basis/README.md

@@ -17,47 +17,47 @@
      - **Evaluation/Convolution**
      - **Preferred Mode**
    * - **B-Spline**
-     - .. plot:: scripts/basis_table_figs.py plot_bspline
+     - .. plot:: scripts/basis_figs.py plot_bspline
           :show-source-link: False
           :height: 80px
      - :ref:`Grid cells <grid_cells_nemos>`
      - :class:`~nemos.basis.BSplineEval` :raw-html:`<br />`
        :class:`~nemos.basis.BSplineConv`
      - 🟢 Eval
    * - **Cyclic B-Spline**
-     - .. plot:: scripts/basis_table_figs.py plot_cyclic_bspline
+     - .. plot:: scripts/basis_figs.py plot_cyclic_bspline
           :show-source-link: False
           :height: 80px
      - :ref:`Place cells <basis_eval_place_cells>`
      - :class:`~nemos.basis.CyclicBSplineEval`  :raw-html:`<br />`
        :class:`~nemos.basis.CyclicBSplineConv`
      - 🟢 Eval
    * - **M-Spline**
-     - .. plot:: scripts/basis_table_figs.py plot_mspline
+     - .. plot:: scripts/basis_figs.py plot_mspline
           :show-source-link: False
           :height: 80px
      - :ref:`Place cells <basis_eval_place_cells>`
      - :class:`~nemos.basis.MSplineEval`  :raw-html:`<br />`
        :class:`~nemos.basis.MSplineConv`
      - 🟢 Eval
    * - **Linearly Spaced Raised Cosine**
-     - .. plot:: scripts/basis_table_figs.py plot_raised_cosine_linear
+     - .. plot:: scripts/basis_figs.py plot_raised_cosine_linear
           :show-source-link: False
           :height: 80px
      - 
      - :class:`~nemos.basis.RaisedCosineLinearEval`  :raw-html:`<br />`
        :class:`~nemos.basis.RaisedCosineLinearConv`
      - 🟢 Eval
    * - **Log Spaced Raised Cosine**
-     - .. plot:: scripts/basis_table_figs.py plot_raised_cosine_log
+     - .. plot:: scripts/basis_figs.py plot_raised_cosine_log
           :show-source-link: False
           :height: 80px
      - :ref:`Head Direction <head_direction_reducing_dimensionality>`
      - :class:`~nemos.basis.RaisedCosineLogEval`  :raw-html:`<br />`
        :class:`~nemos.basis.RaisedCosineLogConv`
      - 🔵 Conv
    * - **Orthogonalized Exponential Decays**
-     - .. plot:: scripts/basis_table_figs.py plot_orth_exp_basis
+     - .. plot:: scripts/basis_figs.py plot_orth_exp_basis
           :show-source-link: False
           :height: 80px
      - 
@@ -101,9 +101,12 @@ NeMoS provides a variety of basis functions (see the [table](table_basis) above)
 
 :::{grid-item-card}
 
-<figure>
-<img src="../../_static/thumbnails/background/plot_01_1D_basis_function.svg" style="height: 100px", alt="One-Dimensional Basis."/>
-</figure>
+```{eval-rst}
+
+.. plot:: scripts/basis_figs.py plot_1d_basis_thumbnail
+   :show-source-link: False
+   :height: 100px
+```
 
 ```{toctree}
 :maxdepth: 2
@@ -114,9 +117,12 @@ plot_01_1D_basis_function.md
 
 :::{grid-item-card}
 
-<figure>
-<img src="../../_static/thumbnails/background/plot_02_ND_basis_function.svg" style="height: 100px", alt="N-Dimensional Basis."/>
-</figure>
+```{eval-rst}
+
+.. plot:: scripts/basis_figs.py plot_nd_basis_thumbnail
+   :show-source-link: False
+   :height: 100px
+```
 
 ```{toctree}
 :maxdepth: 2

docs/background/basis/plot_01_1D_basis_function.md

@@ -81,30 +81,6 @@ plt.plot(x, y, lw=2)
 plt.title("B-Spline Basis")
 ```
 
-```{code-cell} ipython3
-:tags: [hide-input]
-
-# save image for thumbnail
-from pathlib import Path
-import os
-
-root = os.environ.get("READTHEDOCS_OUTPUT")
-if root:
-   path = Path(root) / "html/_static/thumbnails/background"
-# if local store in ../_build/html/...
-else:
-   path = Path("../../_build/html/_static/thumbnails/background")
- 
-# make sure the folder exists if run from build
-if root or Path("../../_build/html/_static").exists():
-   path.mkdir(parents=True, exist_ok=True)
-
-if path.exists():
-  fig.savefig(path / "plot_01_1D_basis_function.svg")
-
-
-print(path.resolve(), path.exists())
-```
 
 ## Computing Features
 All bases in the `nemos.basis` module perform a transformation of one or more time series into a set of features. This operation is always carried out by the method  [`compute_features`](nemos.basis._basis.Basis.compute_features). 

docs/background/basis/plot_02_ND_basis_function.md

@@ -292,28 +292,6 @@ axs[2, 1].set_xlabel('y-coord')
 plt.tight_layout()
 ```
 
-```{code-cell} ipython3
-:tags: [hide-input]
-
-# save image for thumbnail
-from pathlib import Path
-import os
-
-root = os.environ.get("READTHEDOCS_OUTPUT")
-if root:
-   path = Path(root) / "html/_static/thumbnails/background"
-# if local store in ../_build/html/...
-else:
-   path = Path("../../_build/html/_static/thumbnails/background")
- 
-# make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
-   path.mkdir(parents=True, exist_ok=True)
-
-if path.exists():
-  fig.savefig(path / "plot_02_ND_basis_function.svg")
-```
-
 :::{note}
 Basis objects of different types can be combined through multiplication or addition.
 This feature is particularly useful when one of the axes represents a periodic variable and another is non-periodic.

docs/background/plot_03_1D_convolution.md

@@ -179,7 +179,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/background")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/how_to_guide/plot_02_glm_demo.md

@@ -450,7 +450,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/how_to_guide")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/how_to_guide/plot_03_population_glm.md

@@ -231,7 +231,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/how_to_guide")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/how_to_guide/plot_04_batch_glm.md

@@ -208,7 +208,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/how_to_guide")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/how_to_guide/plot_05_sklearn_pipeline_cv_demo.md

@@ -435,7 +435,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/how_to_guide")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/how_to_guide/plot_06_glm_pytree.md

@@ -261,7 +261,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/how_to_guide")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/scripts/basis_figs.py

@@ -0,0 +1,108 @@
+import matplotlib.pyplot as plt
+import numpy as np
+
+import nemos as nmo
+from nemos._inspect_utils.inspect_utils import trim_kwargs
+
+plt.rcParams.update(
+    {
+        "figure.dpi": 300,
+    }
+)
+
+KWARGS = dict(
+    n_basis_funcs=10,
+    decay_rates=np.arange(1, 10 + 1),
+    enforce_decay_to_zero=True,
+    order=4,
+    width=2,
+)
+
+
+def plot_basis(cls):
+    cls_params = cls._get_param_names()
+    new_kwargs = trim_kwargs(cls, KWARGS.copy(), {cls.__name__: cls_params})
+    bas = cls(**new_kwargs)
+    fig, ax = plt.subplots(1, 1, figsize=(5, 2.5))
+    ax.plot(*bas.evaluate_on_grid(300), lw=4)
+    for side in ["left", "right", "top", "bottom"]:
+        ax.spines[side].set_visible(False)
+    ax.set_xticks([])
+    ax.set_yticks([])
+    plt.subplots_adjust(left=0.02, right=0.98, top=0.98, bottom=0.02)
+
+
+def plot_raised_cosine_linear():
+    plot_basis(nmo.basis.RaisedCosineLinearEval)
+
+
+def plot_raised_cosine_log():
+    plot_basis(nmo.basis.RaisedCosineLogEval)
+
+
+def plot_mspline():
+    plot_basis(nmo.basis.MSplineEval)
+
+
+def plot_bspline():
+    plot_basis(nmo.basis.BSplineEval)
+
+
+def plot_cyclic_bspline():
+    plot_basis(nmo.basis.CyclicBSplineEval)
+
+
+def plot_orth_exp_basis():
+    plot_basis(nmo.basis.OrthExponentialEval)
+
+
+def plot_nd_basis_thumbnail():
+    a_basis = nmo.basis.MSplineEval(n_basis_funcs=15, order=3)
+    b_basis = nmo.basis.RaisedCosineLogEval(n_basis_funcs=14)
+    prod_basis = a_basis * b_basis
+
+    x_coord = np.linspace(0, 1, 1000)
+    y_coord = np.linspace(0, 1, 1000)
+
+    X, Y, Z = prod_basis.evaluate_on_grid(200, 200)
+
+    # basis element pairs
+    element_pairs = [[0, 0], [5, 1], [10, 5]]
+
+    # plot the 1D basis element and their product
+    fig, axs = plt.subplots(3,3,figsize=(8, 6))
+    cc = 0
+    for i, j in element_pairs:
+        # plot the element form a_basis
+        axs[cc, 0].plot(x_coord, a_basis.compute_features(x_coord), "grey", alpha=.3)
+        axs[cc, 0].plot(x_coord, a_basis.compute_features(x_coord)[:, i], "b")
+        axs[cc, 0].set_title(f"$a_{{{i}}}(x)$",color='b')
+
+        # plot the element form b_basis
+        axs[cc, 1].plot(y_coord, b_basis.compute_features(y_coord), "grey", alpha=.3)
+        axs[cc, 1].plot(y_coord, b_basis.compute_features(y_coord)[:, j], "b")
+        axs[cc, 1].set_title(f"$b_{{{j}}}(y)$",color='b')
+
+        # select & plot the corresponding product basis element
+        k = i * b_basis.n_basis_funcs + j
+        axs[cc, 2].contourf(X, Y, Z[:, :, k], cmap='Blues')
+        axs[cc, 2].set_title(fr"$A_{{{k}}}(x,y) = a_{{{i}}}(x) \cdot b_{{{j}}}(y)$", color='b')
+        axs[cc, 2].set_xlabel('x-coord')
+        axs[cc, 2].set_ylabel('y-coord')
+        axs[cc, 2].set_aspect("equal")
+
+        cc += 1
+    axs[2, 0].set_xlabel('x-coord')
+    axs[2, 1].set_xlabel('y-coord')
+
+    plt.tight_layout()
+
+def plot_1d_basis_thumbnail():
+    order = 4
+    n_basis = 10
+    bspline = nmo.basis.BSplineEval(n_basis_funcs=n_basis, order=order)
+    x, y = bspline.evaluate_on_grid(100)
+
+    plt.figure(figsize=(5, 3))
+    plt.plot(x, y, lw=2)
+    plt.title("B-Spline Basis")

docs/tutorials/plot_01_current_injection.md

@@ -635,7 +635,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/tutorials")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():

docs/tutorials/plot_02_head_direction.md

@@ -717,7 +717,7 @@ else:
    path = Path("../_build/html/_static/thumbnails/tutorials")
  
 # make sure the folder exists if run from build
-if root or Path("../_build/html/_static").exists():
+if root or Path("../assets/stylesheets").exists():
    path.mkdir(parents=True, exist_ok=True)
 
 if path.exists():