zea 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

zea/visualize.py

@@ -6,8 +6,11 @@ from typing import List, Optional, Tuple, Union
 import matplotlib.pyplot as plt
 import numpy as np
 from keras.ops.image import crop_images
+from matplotlib.patches import PathPatch, Rectangle
+from matplotlib.path import Path as pltPath
 from mpl_toolkits.axes_grid1 import ImageGrid
 from scipy.ndimage import zoom
+from skimage import measure
 
 from zea.display import frustum_convert_rtp2xyz
 
@@ -37,13 +40,13 @@ def plot_image_grid(
     interpolation: Optional[str] = "auto",
     titles: Optional[List[str]] = None,
     suptitle: Optional[str] = None,
-    aspect: Optional[str] = None,
+    aspect: Optional[Union[str, int, float, List[Union[str, int, float]]]] = None,
     figsize: Optional[Tuple[float, float]] = None,
     fig: Optional[plt.Figure] = None,
     fig_contents: Optional[List] = None,
     remove_axis: Optional[bool] = True,
-    background_color: Optional[str] = "black",
-    text_color: Optional[str] = "white",
+    background_color: Optional[str] = None,
+    text_color: Optional[str] = None,
     **kwargs,
 ) -> Tuple[plt.Figure, List]:
     """Plot a batch of images in a grid.
@@ -65,16 +68,33 @@ def plot_image_grid(
         fig (figure, optional): Matplotlib figure object. Defaults to None. Can
             be used to plot on an existing figure.
         fig_contents (list, optional): List of matplotlib image objects. Defaults to None.
-        remove_axis (bool, optional): Whether to remove axis. Defaults to True. If
-            False, the axis will be removed and the spines will be hidden, which allows
-            for the labels to still be visible if plotted after the fact.
-        background_color (str, optional): Background color. Defaults to None.
+        remove_axis (bool, optional): Whether to remove axis. Defaults to True. If False, axes r
+            emain but spines are colored to background and ticks/labels are hidden,
+            allowing later label drawing to remain visible.
+        background_color (str, optional): Background color. Defaults to None. (Matplotlib default)
+        text_color (str, optional): Text color. Defaults to None. (Matplotlib default)
         **kwargs: arguments for plt.Figure.
 
     Returns:
         fig (figure): Matplotlib figure object
         fig_contents (list): List of matplotlib image objects.
 
+    Example:
+        .. doctest::
+
+            >>> from zea.visualize import plot_image_grid
+            >>> import numpy as np
+
+            >>> images = [np.random.rand(128, 128) for _ in range(6)]
+
+            >>> fig, fig_contents = plot_image_grid(
+            ...     images,
+            ...     ncols=3,
+            ...     cmap="gray",
+            ...     vmin=0,
+            ...     vmax=1,
+            ... )
+
     """
     if ncols is None:
         factors = [i for i in range(1, len(images) + 1) if len(images) % i == 0]
@@ -86,15 +106,21 @@ def plot_image_grid(
     if figsize is None:
         figsize = (ncols * 2, nrows * 2 / aspect_ratio)
 
+    # get default colors for matplotlib
+    if background_color is None:
+        background_color = plt.rcParams["axes.facecolor"]
+    if text_color is None:
+        text_color = plt.rcParams["text.color"]
+
     # either supply both fig and fig_contents or neither
     assert (fig is None) == (fig_contents is None), "Supply both fig and fig_contents or neither"
 
     if fig is None:
         fig = plt.figure(figsize=figsize, **kwargs)
         axes = ImageGrid(fig, 111, nrows_ncols=(nrows, ncols), axes_pad=0.1)
-        if background_color:
+        if background_color is not None:
             fig.patch.set_facecolor(background_color)
-        fig.set_tight_layout({"pad": 0.1})
+        fig.set_layout_engine("tight", pad=0.1)
     else:
         axes = fig.axes[: len(images)]
 
@@ -104,7 +130,7 @@ def plot_image_grid(
         if cmap is None:
             cmap = [None] * len(images)
         assert len(cmap) == len(images), (
-            f"cmap must be a string or list of strings of length {len(images)}"
+            f"cmap must be a string or list of strings of length {len(images)}, but got {cmap}"
         )
 
     if isinstance(vmin, (int, float)):
@@ -113,7 +139,7 @@ def plot_image_grid(
         if vmin is None:
             vmin = [None] * len(images)
         assert len(vmin) == len(images), (
-            f"vmin must be a float or list of floats of length {len(images)}"
+            f"vmin must be a float or list of floats of length {len(images)}, but got {vmin}"
         )
 
     if isinstance(vmax, (int, float)):
@@ -122,7 +148,17 @@ def plot_image_grid(
         if vmax is None:
             vmax = [None] * len(images)
         assert len(vmax) == len(images), (
-            f"vmax must be a float or list of floats of length {len(images)}"
+            f"vmax must be a float or list of floats of length {len(images)}, but got {vmax}"
+        )
+
+    if isinstance(aspect, (int, float, str)):
+        aspect = [aspect] * len(images)
+    else:
+        if aspect is None:
+            aspect = [None] * len(images)
+        assert len(aspect) == len(images), (
+            "aspect must be a float, int, str, or list of these "
+            f"of length {len(images)}, but got {aspect}"
         )
 
     if fig_contents is None:
@@ -135,7 +171,7 @@ def plot_image_grid(
                 cmap=cmap[i],
                 vmin=vmin[i],
                 vmax=vmax[i],
-                aspect=aspect,
+                aspect=aspect[i],
                 interpolation=interpolation,
             )
             fig_contents[i] = im
@@ -164,7 +200,7 @@ def plot_image_grid(
     if suptitle:
         fig.suptitle(suptitle, color=text_color)
 
-    fig.set_tight_layout(False)
+    fig.set_layout_engine("none")
     # use bbox_inches="tight" for proper tight layout when saving
     return fig, fig_contents
 
@@ -382,10 +418,10 @@ def plot_frustum_vertices(
     rho_plane=None,
     fig=None,
     ax=None,
-    color_frustum="blue",
-    phi_color="yellow",
-    theta_color="green",
-    rho_color="red",
+    frustum_style=None,
+    phi_style=None,
+    theta_style=None,
+    rho_style=None,
 ):
     """
     Plots the vertices of a frustum in spherical coordinates and highlights specified planes.
@@ -406,6 +442,18 @@ def plot_frustum_vertices(
             Defaults to None. Can be used to reuse the figure in a loop.
         ax (matplotlib.axes.Axes3DSubplot, optional): Axes object to plot on.
             Defaults to None. Can be used to reuse the axes in a loop.
+        frustum_style (dict, optional): Style dictionary for frustum edges. Can include
+            'color', 'linestyle', 'linewidth', 'alpha', etc.
+            Defaults to {'color': 'blue', 'linestyle': '-', 'linewidth': 2}.
+        phi_style (dict, optional): Style dictionary for phi plane(s). Can include
+            'color', 'linestyle', 'linewidth', 'alpha', etc.
+            Defaults to {'color': 'yellow', 'linestyle': '-'}.
+        theta_style (dict, optional): Style dictionary for theta plane(s). Can include
+            'color', 'linestyle', 'linewidth', 'alpha', etc.
+            Defaults to {'color': 'green', 'linestyle': '--'}.
+        rho_style (dict, optional): Style dictionary for rho plane(s). Can include
+            'color', 'linestyle', 'linewidth', 'alpha', etc.
+            Defaults to {'color': 'red', 'linestyle': '--'}.
 
     Returns:
         tuple: A tuple containing the figure and axes objects (fig, ax).
@@ -414,19 +462,22 @@ def plot_frustum_vertices(
         ValueError: If no plane is specified (phi_plane, theta_plane, or rho_plane).
 
     Example:
-        >>> from zea.visualize import plot_frustum_vertices
-        >>> rho_range = [0.1, 10]  # in mm
-        >>> theta_range = [-0.6, 0.6]  # in rad
-        >>> phi_range = [-0.6, 0.6]  # in rad
-        >>> fig, ax = plot_frustum_vertices(
-        ...     rho_range,
-        ...     theta_range=theta_range,
-        ...     phi_range=phi_range,
-        ...     phi_plane=0,
-        ...     phi_color="red",
-        ...     theta_plane=0.2,
-        ...     color_frustum="blue",
-        ... )
+        .. doctest::
+
+            >>> from zea.visualize import plot_frustum_vertices
+            >>> rho_range = [0.1, 10]  # in mm
+            >>> theta_range = [-0.6, 0.6]  # in rad
+            >>> phi_range = [-0.6, 0.6]  # in rad
+            >>> fig, ax = plot_frustum_vertices(
+            ...     rho_range,
+            ...     theta_range=theta_range,
+            ...     phi_range=phi_range,
+            ...     phi_plane=0,
+            ...     phi_style={"color": "red", "linestyle": "--", "linewidth": 2},
+            ...     theta_plane=0.2,
+            ...     theta_style={"color": "green", "linestyle": ":", "alpha": 0.7},
+            ...     frustum_style={"color": "blue", "linewidth": 1.5},
+            ... )
     """
     # Convert single values to lists
     phi_plane = [phi_plane] if isinstance(phi_plane, (int, float)) else phi_plane
@@ -437,6 +488,19 @@ def plot_frustum_vertices(
     if all(p is None for p in [phi_plane, theta_plane, rho_plane]):
         raise ValueError("At least one plane must be specified")
 
+    # Build style dictionaries with defaults
+    if frustum_style is None:
+        frustum_style = {"color": "blue", "linestyle": "-", "linewidth": 2}
+
+    if phi_style is None:
+        phi_style = {"color": "yellow", "linestyle": "-"}
+
+    if theta_style is None:
+        theta_style = {"color": "green", "linestyle": "--"}
+
+    if rho_style is None:
+        rho_style = {"color": "red", "linestyle": "--"}
+
     # Define edges of the frustum
     edges = []
 
@@ -479,14 +543,14 @@ def plot_frustum_vertices(
     if ax is None:
         ax = fig.add_subplot(111, projection="3d")
 
-    def _plot_edges(edges, color, alpha=1.0, linestyle="-", **kwargs):
+    def _plot_edges(edges, **kwargs):
         for edge in edges:
             rho_pts, theta_pts, phi_pts = generate_edge_points(edge[0], edge[1], num_points)
             x, y, z = frustum_convert_rtp2xyz(rho_pts, theta_pts, phi_pts)
-            ax.plot(x, y, -z, color=color, alpha=alpha, linestyle=linestyle, **kwargs)
+            ax.plot(x, y, -z, **kwargs)
 
     # Plot frustum edges
-    _plot_edges(edges, color=color_frustum, alpha=1, lw=2)
+    _plot_edges(edges, **frustum_style)
 
     def get_plane_edges(plane_value, plane_type):
         """Generate edges for a specific plane type (phi, theta, or rho)"""
@@ -550,16 +614,16 @@ def plot_frustum_vertices(
 
     # Plot plane edges
     plane_configs = [
-        (phi_plane, "phi", phi_color, "-"),
-        (theta_plane, "theta", theta_color, "--"),
-        (rho_plane, "rho", rho_color, "--"),
+        (phi_plane, "phi", phi_style),
+        (theta_plane, "theta", theta_style),
+        (rho_plane, "rho", rho_style),
     ]
 
-    for planes, plane_type, color, line in plane_configs:
+    for planes, plane_type, style_dict in plane_configs:
         if planes is not None:
             for plane_value in planes:
                 plane_edges = get_plane_edges(plane_value, plane_type)
-                _plot_edges(plane_edges, color=color, linestyle=line)
+                _plot_edges(plane_edges, **style_dict)
 
     # Set axes properties
     ax.set_xlim([x_min, x_max])
@@ -640,3 +704,77 @@ def pad_or_crop_extent(image, extent, target_extent):
         constant_values=0,
     )
     return image_padded
+
+
+def plot_rectangle_from_mask(ax, mask, **kwargs):
+    """Plots a rectangle box to axis from mask array.
+
+    Is a simplified version of plot_shape_from_mask for rectangles.
+    Useful for displaying bounding boxes on top of images.
+
+    Args:
+        ax (plt.ax): matplotlib axis
+        mask (ndarray): numpy array with rectangle non-zero
+            box defining the region of interest.
+    Kwargs:
+        edgecolor (str): color of the shape's edge
+        facecolor (str): color of the shape's face
+        linewidth (int): width of the shape's edge
+
+    Returns:
+        matplotlib.patches.Rectangle: the added rectangle patch, or None if mask is empty.
+    """
+    ys, xs = np.where(mask)
+    if ys.size == 0 or xs.size == 0:
+        return None
+    y1, y2 = ys.min(), ys.max()
+    x1, x2 = xs.min(), xs.max()
+    rect = Rectangle((x1, y1), x2 - x1 + 1, y2 - y1 + 1, **kwargs)
+    return ax.add_patch(rect)
+
+
+def plot_shape_from_mask(ax, mask, **kwargs):
+    """Plots a shape to axis from mask array.
+
+    Is useful for displaying irregular shapes such as segmentations
+    on top of images.
+
+    Args:
+        ax (plt.ax): matplotlib axis
+        mask (ndarray): numpy array with non-zero
+            shape defining the region of interest.
+    Kwargs:
+        edgecolor (str): color of the shape's edge
+        facecolor (str): color of the shape's face
+        linewidth (int): width of the shape's edge
+
+    Returns:
+        list[matplotlib.patches.PathPatch]: list of matplotlib patch objects
+            added to the axis.
+
+    Example:
+
+        .. code-block:: python
+
+            import matplotlib.pyplot as plt
+            import numpy as np
+
+            from zea.visualize import plot_shape_from_mask
+
+            y, x = np.ogrid[-50:50, -50:50]
+            mask = x**2 + y**2 <= 30**2
+            fig, ax = plt.subplots()
+            ax.imshow(np.random.rand(100, 100), cmap="gray")
+            plot_shape_from_mask(ax, mask, edgecolor="red", alpha=0.5)
+    """
+    # Pad mask to ensure edge contours are found
+    padded_mask = np.pad(mask, pad_width=1, mode="constant", constant_values=0)
+    contours = measure.find_contours(padded_mask, 0.5)
+    patches = []
+    for contour in contours:
+        # Remove padding offset
+        contour -= 1
+        path = pltPath(contour[:, ::-1])
+        patch = PathPatch(path, **kwargs)
+        patches.append(ax.add_patch(patch))
+    return patches

{zea-0.0.5.dist-info → zea-0.0.7.dist-info}/METADATA

@@ -1,7 +1,8 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: zea
-Version: 0.0.5
+Version: 0.0.7
 Summary: A Toolbox for Cognitive Ultrasound Imaging. Provides a set of tools for processing of ultrasound data, all built in your favorite machine learning framework.
+License-File: LICENSE
 Keywords: ultrasound,machine learning,beamforming
 Author: Tristan Stevens
 Author-email: t.s.w.stevens@tue.nl
@@ -21,6 +22,7 @@ Provides-Extra: display
 Provides-Extra: display-headless
 Provides-Extra: docs
 Provides-Extra: jax
+Provides-Extra: models
 Provides-Extra: tests
 Requires-Dist: IPython ; extra == "dev"
 Requires-Dist: IPython ; extra == "docs"
@@ -40,7 +42,7 @@ Requires-Dist: ipywidgets ; extra == "dev"
 Requires-Dist: ipywidgets ; extra == "tests"
 Requires-Dist: jax ; extra == "backends"
 Requires-Dist: jax[cuda12-pip] (>=0.4.26) ; extra == "jax"
-Requires-Dist: keras (>=3.11)
+Requires-Dist: keras (>=3.12)
 Requires-Dist: matplotlib (>=3.8)
 Requires-Dist: mock ; extra == "dev"
 Requires-Dist: mock ; extra == "docs"
@@ -49,6 +51,8 @@ Requires-Dist: myst-parser ; extra == "docs"
 Requires-Dist: nbsphinx ; extra == "dev"
 Requires-Dist: nbsphinx ; extra == "docs"
 Requires-Dist: numpy (>=1.24)
+Requires-Dist: onnxruntime (>=1.15) ; extra == "dev"
+Requires-Dist: onnxruntime (>=1.15) ; extra == "models"
 Requires-Dist: opencv-python (>=4) ; extra == "display"
 Requires-Dist: opencv-python-headless (>=4) ; extra == "dev"
 Requires-Dist: opencv-python-headless (>=4) ; extra == "display-headless"
@@ -78,6 +82,8 @@ Requires-Dist: sphinx-autodoc-typehints ; extra == "dev"
 Requires-Dist: sphinx-autodoc-typehints ; extra == "docs"
 Requires-Dist: sphinx-copybutton ; extra == "dev"
 Requires-Dist: sphinx-copybutton ; extra == "docs"
+Requires-Dist: sphinx-reredirects ; extra == "dev"
+Requires-Dist: sphinx-reredirects ; extra == "docs"
 Requires-Dist: sphinx_design ; extra == "dev"
 Requires-Dist: sphinx_design ; extra == "docs"
 Requires-Dist: sphinxcontrib-bibtex ; extra == "dev"

zea-0.0.7.dist-info/RECORD

@@ -0,0 +1,114 @@
+zea/__init__.py,sha256=ZJZo6amq5ABwN_fMAtlBG5lsR57TnrgI7nj-R0q8mZs,4119
+zea/__main__.py,sha256=4OCFujuZ5ooIDMF7xxE4Esin9dfFlgX9PdOi9uB64y8,1569
+zea/agent/__init__.py,sha256=0wnGArcPvSo_lDHN9-jE8d7IBP-bk3fuceoRu2VEVEw,976
+zea/agent/gumbel.py,sha256=WbvSrM8meXtZmDLkyXDGUyRzjB4dWZmNO_qzloRxB_s,3770
+zea/agent/masks.py,sha256=_vUhlzzw_g8_RN-k0mMqa_h4hfGHViJdkA24o6AYqYk,6666
+zea/agent/selection.py,sha256=ut8I_TcfcoDRQnBBsxiVjNqjFp_PLNNHxgoE1FTP4rw,27072
+zea/backend/__init__.py,sha256=XiBtxpXMYgcSBXjJ-uEWh7a92XqWs-4uDUh6NeKeUE4,6922
+zea/backend/autograd.py,sha256=buWy19ctDFsAoktZaLm5qyLN9nQRicI91-V3ND-t3f4,6868
+zea/backend/jax/__init__.py,sha256=AvO6tUDTMiyrRuY_M2KKwUpzzzqWIRlSh3NhI_lcw9w,1056
+zea/backend/tensorflow/__init__.py,sha256=FQAMCrUgvHm4LCVfnP9sXGACQSMFx3nIarPve_MgxYM,422
+zea/backend/tensorflow/dataloader.py,sha256=s0-2NF0pEofGw3W9AOtoN4s-Hj13gacjfDd7tQ9eXDY,14429
+zea/backend/tensorflow/layers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+zea/backend/tensorflow/layers/apodization.py,sha256=Pi5GpkoMSwPq8_FL1fqkuGINmOD-sIHkHXEtF62VNSc,826
+zea/backend/tensorflow/layers/utils.py,sha256=kiEH-6_Rq5dq0D7dkziUkhhqdOyf5O9POYZ-uXLHkNA,3446
+zea/backend/tensorflow/losses.py,sha256=q_U1FbSNFU0T_FY9ojdSqGn-TOiSieB3U5YBuFSoVIU,2081
+zea/backend/tensorflow/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+zea/backend/tensorflow/models/lista.py,sha256=S_UQcO8n3PVkVwSFYa_MOgJEnaF6iFQfEj4nvKvbpww,3088
+zea/backend/tensorflow/scripts/convert-echonet-dynamic.py,sha256=qREJcTvJXMH0EJGvpcs-BqoroS-EE-F54UKnuXlpBSU,3878
+zea/backend/tensorflow/scripts/convert-taesd.py,sha256=-i9XGi0ZPEKV88JQQxR0742qsrk3x7bNoW3myaht4S4,2396
+zea/backend/tensorflow/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+zea/backend/tensorflow/utils/callbacks.py,sha256=4biWDzQiqgnmE8YWF9mlxLZGxrVMMs-cpgBZI7iD2oI,57
+zea/backend/tensorflow/utils/utils.py,sha256=4uOLfbxko2xUsyVjw7bClTdLkif7-NYscIo7ljqON6U,1050
+zea/backend/tf2jax.py,sha256=qld6VecFEVOpUI4wUqA8wj9xvpsIjH2o72TcQqOyxbY,384
+zea/backend/torch/__init__.py,sha256=YMNTzqRqhPu7pjGPczupT3jo4SwjYpI8Ch97GI0OPDg,1119
+zea/backend/torch/losses.py,sha256=7ITD_p630eyJzjgAT79XUNiff7XmW-naMGOUgKFnAAQ,2114
+zea/beamform/__init__.py,sha256=rlRy-Og_KsbnU4Qm0NR8SP5ymePCwSr2aMW9jjOaeHI,1018
+zea/beamform/beamformer.py,sha256=XKG8HDj0Arje3rVRBwd20cdD8s87BJNn3KGNJ4u0cP8,20653
+zea/beamform/delays.py,sha256=ItD6_WavcWmXns4QJqo_oq674F5Q0s0mVVacfo_775U,5590
+zea/beamform/lens_correction.py,sha256=eqsVaooyi_EFWd8F3LxdQX2bLxxF_L8eGVkROKl3rOA,7828
+zea/beamform/pfield.py,sha256=2rJMV8EuGoDZk1ZVSjdkn7I_p3gQJWxlCGtM50qc1sA,14910
+zea/beamform/phantoms.py,sha256=zow6j4mPXOJjSl31dLQbuDW8rH_qEV2dsfcy-TqkhkI,1108
+zea/beamform/pixelgrid.py,sha256=XONJqgWC9XUkEL7iaphy0YBr6xLAyXz-yaTdPQju1r0,5432
+zea/config.py,sha256=q0ADj83bpFt7kXq32tJFQT3Kpcvrf-O_RCzTxxk1yHw,19811
+zea/data/__init__.py,sha256=DI0Z96aHdcAsNSQ4N4YQIiLBqid9qGkx-ZbZitPnow4,2040
+zea/data/__main__.py,sha256=xEXj3m3gJ6MoV1f9WbDl3QVPMbDXedTj1J9WeT83NrI,909
+zea/data/augmentations.py,sha256=R09_dVkhOFGHiiVFaTjP9pYcHCMtwri9Nz8wsM5mRPY,12686
+zea/data/convert/__init__.py,sha256=xuPIB-Dd8voTTRoQr-Mb5KTbPpWzk46alCgKQ_EZqzY,244
+zea/data/convert/camus.py,sha256=6eNDBlZYitrv8lIpulPxSpSCm_quepEo-W0Y3RVbk0w,9590
+zea/data/convert/echonet.py,sha256=VB5z1bl2m2v1aEreSmzFUn6JTrNTs8MQNEGwOceLs3g,13776
+zea/data/convert/echonetlvh/README.md,sha256=7YSeM-CBsN2x4gF8vTflFE0UwmW8-597-HfOk17l8FA,729
+zea/data/convert/echonetlvh/convert_raw_to_usbmd.py,sha256=lZq6OMXeZWJf7WSIYSVIfAkSQ5wolx1xYYQq4qm5bkQ,18051
+zea/data/convert/echonetlvh/precompute_crop.py,sha256=A-dSbGngEvL5QfAid3d9OoZRnxXMVt-QF7ivyBMDK-k,8302
+zea/data/convert/images.py,sha256=8a2oHqAA_fLhFuNnqBsNCjKTdX5pADX-ntZ6BHUoZdQ,5229
+zea/data/convert/matlab.py,sha256=cVFsQT-4sy5RVin1bRB9CGrlSqCnLZA5bLgAs9u5BhU,42258
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