New Layered Surface Segmentation

docs/cli.md

@@ -30,6 +30,8 @@ This offers quick interactions, making it ideal for tasks that require efficienc
 | `--data-explorer` | Starts the Data Explorer |
 | `--iso3d` | Starts the 3D Isosurfaces visualization |
 | `--local-thickness` | Starts the Local thickness tool |
+| `--anotation-tool` | Starts the annotation tool |
+| `--layers` | Starts the tool for segmenting layers |
 | `--host` | Desired host for the server. By default runs on `0.0.0.0`  |
 | `--platform` | Uses the Qim platform API for a unique path and port depending on the username |
 

docs/gui.md

@@ -36,3 +36,7 @@ For details see [here](cli.md#qim3d-gui).
 ::: qim3d.gui.annotation_tool
     options:
         members: False
+
+::: qim3d.gui.layers2d
+    options:
+        members: False
\ No newline at end of file

docs/processing.md

@@ -14,6 +14,8 @@ Here, we provide functionalities designed specifically for 3D image analysis and
             - maximum
             - minimum
             - tophat
+            - get_lines
+            - segment_layers
             - create_mesh
 
 ::: qim3d.processing.Pipeline

qim3d/cli.py

@@ -34,6 +34,9 @@ def main():
     gui_parser.add_argument(
         "--local-thickness", action="store_true", help="Run local thickness tool."
     )
+    gui_parser.add_argument(
+        "--layers", action="store_true", help="Run Layers."
+    )
     gui_parser.add_argument("--host", default="0.0.0.0", help="Desired host.")
     gui_parser.add_argument(
         "--platform", action="store_true", help="Use QIM platform address"
@@ -137,6 +140,8 @@ def main():
             interface_class = qim3d.gui.annotation_tool.Interface
         elif args.local_thickness:
             interface_class = qim3d.gui.local_thickness.Interface
+        elif args.layers:
+            interface_class = qim3d.gui.layers2d.Interface
         else:
             print(
                 "Please select a tool by choosing one of the following flags:\n\t--data-explorer\n\t--iso3d\n\t--annotation-tool\n\t--local-thickness"

qim3d/gui/__init__.py

@@ -4,6 +4,7 @@ from . import data_explorer
 from . import iso3d
 from . import local_thickness
 from . import annotation_tool
+from . import layers2d
 from .qim_theme import QimTheme
 
 

qim3d/gui/interface.py

@@ -48,6 +48,9 @@ class BaseInterface(ABC):
     def set_invisible(self):
         return gr.update(visible=False)
     
+    def change_visibility(self, is_visible):
+        return gr.update(visible = is_visible)
+
     def launch(self, img=None, force_light_mode: bool = True, **kwargs):
         """
         img: If None, user can upload image after the interface is launched.

qim3d/processing/__init__.py

@@ -4,4 +4,5 @@ from .detection import blob_detection
 from .filters import *
 from .operations import *
 from .cc import get_3d_cc
+from .layers2d import segment_layers, get_lines
 from .mesh import create_mesh

qim3d/processing/layers2d.py

+import numpy as np
+from slgbuilder import GraphObject 
+from slgbuilder import MaxflowBuilder
+
+def segment_layers(data:np.ndarray, inverted:bool = False, n_layers:int = 1, delta:float = 1, min_margin:int = 10, max_margin:int = None, wrap:bool = False):
+    """
+    Works on 2D and 3D data.
+    Light one function wrapper around slgbuilder https://github.com/Skielex/slgbuilder to do layer segmentation
+    Now uses only MaxflowBuilder for solving.
+
+    Args:
+        data: 2D or 3D array on which it will be computed
+        inverted: if True, it will invert the brightness of the image
+        n_layers: How many layers are we looking for (result in a layer and background)
+        delta: Smoothness parameter
+        min_margin: If we want more layers, we have to have a margin otherwise they are all going to be exactly the same
+        max_margin: Maximum margin between layers
+        wrap: If True, starting and ending point of the border between layers are at the same level
+
+    Returns:
+        segmentations: list of numpy arrays, even if n_layers == 1, each array is only 0s and 1s, 1s segmenting this specific layer
+
+    Raises:
+        TypeError: If Data is not np.array, if n_layers is not integer.
+        ValueError: If n_layers is less than 1, if delta is negative or zero
+
+    Example:
+        Example is only shown on 2D image, but segment_layers can also take 3D structures.
+        ```python
+        import qim3d
+
+        layers_image = qim3d.io.load('layers3d.tif')[:,:,0]
+        layers = qim3d.processing.segment_layers(layers_image, n_layers = 2)
+        layer_lines = qim3d.processing.get_lines(layers)
+
+        from matplotlib import pyplot as plt
+
+        plt.imshow(layers_image, cmap='gray')
+        plt.axis('off')
+        for layer_line in layer_lines:
+            plt.plot(layer_line, linewidth = 3)
+        ```
+        ![layer_segmentation](assets/screenshots/layers.png)
+        ![layer_segmentation](assets/screenshots/segmented_layers.png)
+
+    """
+    if isinstance(data, np.ndarray):
+        data = data.astype(np.int32)
+        if inverted:
+            data = ~data
+    else:
+        raise TypeError(F"Data has to be type np.ndarray. Your data is of type {type(data)}")
+    
+    helper = MaxflowBuilder()
+    if not isinstance(n_layers, int):
+        raise TypeError(F"Number of layers has to be positive integer. You passed {type(n_layers)}")
+    
+    if n_layers == 1:
+        layer = GraphObject(data)
+        helper.add_object(layer)
+    elif n_layers > 1:
+        layers = [GraphObject(data) for _ in range(n_layers)]
+        helper.add_objects(layers)
+        for i in range(len(layers)-1):
+            helper.add_layered_containment(layers[i], layers[i+1], min_margin=min_margin, max_margin=max_margin) 
+
+    else:
+        raise ValueError(F"Number of layers has to be positive integer. You passed {n_layers}")
+    
+    helper.add_layered_boundary_cost()
+
+    if delta > 1:
+        delta = int(delta)
+    elif delta <= 0:
+        raise ValueError(F'Delta has to be positive number. You passed {delta}')
+    helper.add_layered_smoothness(delta=delta, wrap = bool(wrap))
+    helper.solve()
+    if n_layers == 1:
+        segmentations =[helper.what_segments(layer)]
+    else:
+        segmentations = [helper.what_segments(l).astype(np.int32) for l in layers]
+
+    return segmentations
+
+def get_lines(segmentations:list|np.ndarray) -> list:
+    """
+    Expects list of arrays where each array is 2D segmentation with only 2 classes. This function gets the border between those two
+    so it could be plotted. Used with qim3d.processing.segment_layers
+
+    Args:
+        segmentations: list of arrays where each array is 2D segmentation with only 2 classes
+
+    Returns:
+        segmentation_lines: list of 1D numpy arrays
+    """
+    segmentation_lines = [np.argmin(s, axis=0) - 0.5 for s in segmentations]
+    return segmentation_lines
\ No newline at end of file

qim3d/processing/operations.py

@@ -200,7 +200,7 @@ def fade_mask(
 
 
 def overlay_rgb_images(
-    background: np.ndarray, foreground: np.ndarray, alpha: float = 0.5
+    background: np.ndarray, foreground: np.ndarray, alpha: float = 0.5, hide_black:bool = True,
 ) -> np.ndarray:
     """
     Overlay an RGB foreground onto an RGB background using alpha blending.
@@ -209,6 +209,7 @@ def overlay_rgb_images(
         background (numpy.ndarray): The background RGB image.
         foreground (numpy.ndarray): The foreground RGB image (usually masks).
         alpha (float, optional): The alpha value for blending. Defaults to 0.5.
+        hide_black (bool, optional): If True, black pixels will have alpha value 0, so the black won't be visible. Used for segmentation where we don't care about background. Defaults to True.
 
     Returns:
         composite (numpy.ndarray): The composite RGB image with overlaid foreground.
@@ -218,18 +219,36 @@ def overlay_rgb_images(
 
     Note:
         - The function performs alpha blending to overlay the foreground onto the background.
-        - It ensures that the background and foreground have the same shape before blending.
+        - It ensures that the background and foreground have the same first two dimensions (image size matches).
+        - It can handle greyscale images, values from 0 to 1, raw values which are negative or bigger than 255.
         - It calculates the maximum projection of the foreground and blends them onto the background.
-        - Brightness outside the foreground is adjusted to maintain consistency with the background.
     """
 
-    # Igonore alpha in case its there
-    background = background[..., :3]
-    foreground = foreground[..., :3]
+    def to_uint8(image:np.ndarray):
+        if np.min(image) < 0:
+            image = image - np.min(image)
+
+        maxim = np.max(image)
+        if maxim > 255:
+            image = (image / maxim)*255
+        elif maxim <= 1:
+            image = image*255
+
+        if image.ndim == 2:
+            image = np.repeat(image[..., None], 3, -1)
+        elif image.ndim == 3:
+            image = image[..., :3] # Ignoring alpha channel
+        else:
+            raise ValueError(F'Input image can not have higher dimension than 3. Yours have {image.ndim}')
+        
+        return image.astype(np.uint8)
+        
+    background = to_uint8(background)
+    foreground = to_uint8(foreground)
 
     # Ensure both images have the same shape
     if background.shape != foreground.shape:
-        raise ValueError("Input images must have the same shape")
+        raise ValueError(F"Input images must have the same first two dimensions. But background is of shape {background.shape} and foreground is of shape {foreground.shape}")
 
     # Perform alpha blending
     foreground_max_projection = np.amax(foreground, axis=2)
@@ -240,11 +259,18 @@ def overlay_rgb_images(
         foreground_max_projection = foreground_max_projection / np.max(
             foreground_max_projection
         )
+    # Check alpha validity
+    if alpha < 0:
+        raise ValueError(F'Alpha has to be positive number. You used {alpha}')
+    elif alpha > 1:
+        alpha = 1
+    
+    # If the pixel is black, its alpha value is set to 0, so it has no effect on the image
+    if hide_black:
+        alpha = np.full((background.shape[0], background.shape[1],1), alpha)
+        alpha[np.apply_along_axis(lambda x: (x == [0,0,0]).all(), axis = 2, arr = foreground)] = 0
 
     composite = background * (1 - alpha) + foreground * alpha
     composite = np.clip(composite, 0, 255).astype("uint8")
 
-    # Adjust brightness outside foreground
-    composite = composite + (background * (1 - alpha)) * (1 - foreground_max_projection)
-
     return composite.astype("uint8")
\ No newline at end of file

qim3d/utils/cli.py

+import argparse
+from qim3d.gui import data_explorer, iso3d, annotation_tool, local_thickness, layers2d
+
+def main():
+    parser = argparse.ArgumentParser(description='Qim3d command-line interface.')
+    subparsers = parser.add_subparsers(title='Subcommands', dest='subcommand')
+
+    # subcommands
+    gui_parser = subparsers.add_parser('gui', help = 'Graphical User Interfaces.')
+
+    gui_parser.add_argument('--data-explorer', action='store_true', help='Run data explorer.')
+    gui_parser.add_argument('--iso3d', action='store_true', help='Run iso3d.')
+    gui_parser.add_argument('--annotation-tool', action='store_true', help='Run annotation tool.')
+    gui_parser.add_argument('--local-thickness', action='store_true', help='Run local thickness tool.')
+    gui_parser.add_argument('--layers2d', action='store_true', help='Run layers2d.')
+    gui_parser.add_argument('--host', default='0.0.0.0', help='Desired host.')
+
+    args = parser.parse_args()
+
+    if args.subcommand == 'gui':
+        arghost = args.host
+        if args.data_explorer:
+            
+            data_explorer.run_interface(arghost)
+
+        elif args.iso3d:
+            iso3d.run_interface(arghost)
+        
+        elif args.annotation_tool:
+            annotation_tool.run_interface(arghost)
+        
+        elif args.local_thickness:
+            local_thickness.run_interface(arghost)
+
+        elif args.layers2d:
+            layers2d.run_interface(arghost)
+            
+if __name__ == '__main__':
+    main()
\ No newline at end of file

qim3d/viz/__init__.py

@@ -13,3 +13,4 @@ from .local_thickness_ import local_thickness
 from .structure_tensor import vectors
 from .metrics import plot_metrics, grid_overview, grid_pred, vol_masked
 from .preview import image_preview
+from . import layers2d

qim3d/viz/layers2d.py

+""" Provides a collection of visualisation functions for the Layers2d class."""
+import io
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+from PIL import Image
+
+
+def image_with_lines(image:np.ndarray, lines: list, line_thickness:float|int) -> Image:
+    """
+    Plots the image and plots the lines on top of it. Then extracts it as PIL.Image and in the same size as the input image was.
+    Paramters:
+    -----------
+    image: Image on which we put the lines
+    lines: list of 1D arrays to be plotted on top of the image
+    line_thickness: how thick is the line supposed to be
+
+    Returns:
+    ----------
+    image_with_lines: 
+    """
+    fig, ax = plt.subplots()
+    ax.imshow(image, cmap = 'gray')
+    ax.axis('off')
+
+    for line in lines:
+        ax.plot(line, linewidth = line_thickness)
+
+    buf = io.BytesIO()
+    plt.savefig(buf, format='png', bbox_inches='tight', pad_inches=0)
+    plt.close()
+
+    buf.seek(0)
+    return Image.open(buf).resize(size = image.squeeze().shape[::-1])
+

requirements.txt

@@ -10,7 +10,7 @@ Pillow>=10.0.1
 plotly>=5.14.1
 scipy>=1.11.2
 seaborn>=0.12.2
-pydicom>=2.4.4
+pydicom==2.4.4
 setuptools>=68.0.0
 tifffile>=2023.4.12
 torch>=2.0.1
@@ -29,3 +29,4 @@ zarr>=2.18.2
 ome_zarr>=0.9.0
 dask-image>=2024.5.3
 trimesh>=4.4.9
+slgbuilder>=0.2.1

setup.py

@@ -49,7 +49,7 @@ setup(
         "h5py>=3.9.0",
         "localthickness>=0.1.2",
         "matplotlib>=3.8.0",
-        "pydicom>=2.4.4",
+        "pydicom==2.4.4",
         "numpy>=1.26.0",
         "outputformat>=0.1.3",
         "Pillow>=10.0.1",