From e2cc0aa6fa6639e13299f7d39260648f60e26f19 Mon Sep 17 00:00:00 2001
From: Alessia Saccardo <s212246@dtu.dk>
Date: Tue, 26 Nov 2024 14:11:10 +0100
Subject: [PATCH] add additional thresholding method and remove blink effect
---
qim3d/viz/__init__.py | 1 +
qim3d/viz/explore.py | 144 +++++++++++++++++++++++++++++++++++++++++-
2 files changed, 144 insertions(+), 1 deletion(-)
diff --git a/qim3d/viz/__init__.py b/qim3d/viz/__init__.py
index 84b2e835..0e5338c8 100644
--- a/qim3d/viz/__init__.py
+++ b/qim3d/viz/__init__.py
@@ -7,6 +7,7 @@ from .explore import (
slicer,
slices,
chunks,
+ threshold,
)
from .itk_vtk_viewer import itk_vtk, Installer, NotInstalledError
from .k3d import vol, mesh
diff --git a/qim3d/viz/explore.py b/qim3d/viz/explore.py
index d7392cbd..8c4452e1 100644
--- a/qim3d/viz/explore.py
+++ b/qim3d/viz/explore.py
@@ -15,7 +15,8 @@ import matplotlib
import numpy as np
import zarr
from qim3d.utils.logger import log
-
+from ipywidgets import interact, IntSlider, FloatSlider, Dropdown
+from skimage.filters import threshold_otsu, threshold_isodata, threshold_li, threshold_mean, threshold_minimum, threshold_triangle, threshold_yen
import qim3d
@@ -775,3 +776,144 @@ def chunks(zarr_path: str, **kwargs):
# Display the VBox
display(final_layout)
+
+def threshold(
+ volume: np.ndarray,
+ axis: int = 0,
+ cmap_volume: str = 'gray',
+ cmap_threshold: str = 'gray',
+ vmin: float = None,
+ vmax: float = None,
+):
+ """
+ Interactive thresholding of a 3D volume.
+ Args:
+ volume (np.ndarray): 3D volume to threshold.
+ cmap_image (str, optional): Colormap for the original image. Defaults to 'gray'.
+ cmap_threshold (str, optional): Colormap for the thresholded image. Defaults to 'gray'.
+ Example:
+ ```python
+ import qim3d
+ vol = qim3d.examples.bone_128x128x128
+ qim3d.viz.threshold(vol)
+ ```
+ """
+ threshold_methods = {
+ 'Otsu': threshold_otsu,
+ 'Isodata': threshold_isodata,
+ 'Li': threshold_li,
+ 'Mean': threshold_mean,
+ 'Minimum': threshold_minimum,
+ 'Triangle': threshold_triangle,
+ 'Yen': threshold_yen
+ }
+
+ # Create the interactive widget
+ def _slicer(position, threshold, method):
+ fig, axes = plt.subplots(1, 3, figsize=(9, 3))
+
+ slice_img = volume[position, :, :]
+ # If vmin is higher than the highest value in the image ValueError is raised
+ # We don't want to override the values because next slices might be okay
+ new_vmin = (
+ None
+ if (isinstance(vmin, (float, int)) and vmin > np.max(slice_img))
+ else vmin
+ )
+ new_vmax = (
+ None
+ if (isinstance(vmax, (float, int)) and vmax < np.min(slice_img))
+ else vmax
+ )
+
+ axes[0].imshow(slice_img, cmap=cmap_volume, vmin=new_vmin, vmax=new_vmax)
+ axes[0].set_title('Original')
+ axes[0].axis('off')
+
+ if method == 'Manual':
+ threshold_slider.disabled = False
+ else:
+ # Apply the appropriate thresholding function
+ threshold_func = threshold_methods.get(method)
+ if threshold_func:
+ threshold = threshold_func(slice_img)
+ if threshold_slider.value != threshold:
+ threshold_slider.unobserve_all()
+ threshold_slider.value = threshold
+ threshold_slider.disabled = True
+ else:
+ raise ValueError(f"Unsupported thresholding method: {method}")
+
+
+ mask = slice_img > threshold
+ axes[1].imshow(mask, cmap=cmap_threshold)
+ axes[1].set_title('Binary mask')
+ axes[1].axis('off')
+
+ masked_volume = qim3d.processing.operations.overlay_rgb_images(
+ background = slice_img,
+ foreground = mask,
+ )
+ # If vmin is higher than the highest value in the image ValueError is raised
+ # We don't want to override the values because next slices might be okay
+ new_vmin = (
+ None
+ if (isinstance(vmin, (float, int)) and vmin > np.max(masked_volume))
+ else vmin
+ )
+ new_vmax = (
+ None
+ if (isinstance(vmax, (float, int)) and vmax < np.min(masked_volume))
+ else vmax
+ )
+ axes[2].imshow(masked_volume, cmap=cmap_threshold, vmin=new_vmin, vmax=new_vmax)
+ axes[2].set_title('Overlay')
+ axes[2].axis('off')
+
+ return fig
+
+ method_dropdown = widgets.Dropdown(
+ options=['Manual', 'Otsu', 'Isodata', 'Li', 'Mean', 'Minimum', 'Triangle', 'Yen'],
+ value='Manual', # default value
+ description='Method',
+ )
+
+ position_slider = widgets.IntSlider(
+ value=volume.shape[0] // 2,
+ min=0,
+ max=volume.shape[0] - 1,
+ description='Slice',
+ continuous_update=False,
+ )
+
+ threshold_slider = widgets.IntSlider(
+ value=int((volume.min() + volume.max()) / 2),
+ min=volume.min(),
+ max=volume.max(),
+ description='Threshold',
+ continuous_update=False,
+ )
+
+ slicer_obj = widgets.interactive(
+ _slicer,
+ position=position_slider,
+ threshold=threshold_slider,
+ method = method_dropdown,
+ )
+
+ #slicer_obj.layout = widgets.Layout(align_items='flex-start')
+
+ # Group sliders vertically (left column)
+ controls_left = widgets.VBox([position_slider, threshold_slider])
+
+ # Place the method dropdown in a separate column (right)
+ controls_right = widgets.VBox([method_dropdown])
+
+ # Combine the controls horizontally (sliders on the left, dropdown on the right)
+ controls_layout = widgets.HBox([controls_left, controls_right], layout=widgets.Layout(justify_content='space-between'))
+
+ # Combine the controls with the interactive slicer object
+ slicer_obj = widgets.VBox([controls_layout, slicer_obj.children[-1]]) # Add sliders + dropdown above the plot
+
+ return slicer_obj
+
--
GitLab