From 2293f0eaf0a919cff1e5a6ba1e4a257e42358c09 Mon Sep 17 00:00:00 2001
From: s204159 <s204159@student.dtu.dk>
Date: Fri, 12 Apr 2024 13:38:22 +0200
Subject: [PATCH] Cc documentation
---
.../assets/screenshots/plot_cc_no_overlay.png | Bin 0 -> 4564 bytes
docs/assets/screenshots/plot_cc_overlay.png | Bin 0 -> 6814 bytes
docs/releases.md | 8 +++++-
docs/stylesheets/extra.css | 4 +++
qim3d/processing/cc.py | 10 ++++++--
qim3d/viz/cc.py | 23 +++++++++++++++---
6 files changed, 38 insertions(+), 7 deletions(-)
create mode 100644 docs/assets/screenshots/plot_cc_no_overlay.png
create mode 100644 docs/assets/screenshots/plot_cc_overlay.png
diff --git a/docs/assets/screenshots/plot_cc_no_overlay.png b/docs/assets/screenshots/plot_cc_no_overlay.png
new file mode 100644
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diff --git a/docs/releases.md b/docs/releases.md
index 3265d5d2..b4e7ba33 100644
--- a/docs/releases.md
+++ b/docs/releases.md
@@ -9,16 +9,22 @@ As the library is still in its early development stages, **there may be breaking
And remember to keep your pip installation [up to date](/qim3d/#upgrade) so that you have the latest features!
+### v0.3.4 (coming soon!)
+- Documentation for `qim3d.viz.plot_cc`
+
+
### v0.3.3 (11/04/2024)
- Introduction of `qim3d.viz.slicer` (and also `qim3d.viz.orthogonal` ) 🎉
- Introduction of `qim3d.gui.annotation_tool` 🎉
- Introduction of `qim3d.processing.Blob` for blob detection 🎉
- Introduction of `qim3d.processing.local_thickness` 🎉
- Introduction of `qim3d.processing.structure_tensor` 🎉
-- Support for loading DICOM files with `qim3d.io.load`🎉
+- Support for loading DICOM files with `qim3d.io.load`
- Introduction of `qim3d.processing.get_3d_cc` for 3D connected components and `qim3d.viz.plot_cc` for associated visualization 🎉
- Introduction of `qim3d.viz.colormaps` for easy visualization of e.g. multi-label segmentation results 🎉
- Introduction of `qim3d.processing.operations.background_removal` 🎉
+- Documentation refactoring
+- Fixed bug preventing `Data Explorer` to show files
### v0.3.2 (23/02/2024)
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
index ba35334e..d5d3f1dc 100644
--- a/docs/stylesheets/extra.css
+++ b/docs/stylesheets/extra.css
@@ -96,4 +96,8 @@ code {
.md-typeset .admonition.example, .md-typeset details.example {
border-color: #ff9900;
+}
+
+.md-typeset .example>.admonition-title:after, .md-typeset .example>summary:after {
+ color: #ff9900;
}
\ No newline at end of file
diff --git a/qim3d/processing/cc.py b/qim3d/processing/cc.py
index 0cc7cee7..d6ec0e85 100644
--- a/qim3d/processing/cc.py
+++ b/qim3d/processing/cc.py
@@ -72,7 +72,7 @@ class CC:
def get_3d_cc(image: np.ndarray | torch.Tensor) -> CC:
- """ Get the connected components of a 3D volume.
+ """ Returns an object (CC) containing the connected components of the input volume. Use plot_cc to visualize the connected components.
Args:
image (np.ndarray | torch.Tensor): An array-like object to be labeled. Any non-zero values in `input` are
@@ -80,8 +80,14 @@ def get_3d_cc(image: np.ndarray | torch.Tensor) -> CC:
Returns:
CC: A ConnectedComponents object containing the connected components and the number of connected components.
+
+ Example:
+ ```python
+ import qim3d
+ vol = qim3d.examples.cement_128x128x128[50:150]<60
+ cc = qim3d.processing.get_3d_cc(vol)
+ ```
"""
connected_components, num_connected_components = label(image)
log.info(f"Total number of connected components found: {num_connected_components}")
-
return CC(connected_components, num_connected_components)
diff --git a/qim3d/viz/cc.py b/qim3d/viz/cc.py
index 0f3ac8fd..7efee492 100644
--- a/qim3d/viz/cc.py
+++ b/qim3d/viz/cc.py
@@ -1,8 +1,11 @@
-import numpy as np
import matplotlib.pyplot as plt
+import numpy as np
+
+from qim3d.io.logger import log
+from qim3d.processing.cc import CC
from qim3d.viz import slices
from qim3d.viz.colormaps import objects as qim3dCmap
-from qim3d.processing.cc import CC
+
def plot_cc(
connected_components,
@@ -14,11 +17,11 @@ def plot_cc(
**kwargs,
) -> list[plt.Figure]:
"""
- Plot the connected components of an image.
+ Plots the connected components from a `qim3d.processing.cc.CC` object. If an overlay image is provided, the connected component will be masked to the overlay image.
Parameters:
connected_components (CC): The connected components object.
- components (list | tuple, optional): The components to plot. If None the first max_cc_to_plot=32 components will be plotted. Defaults to None.
+ component_indexs (list | tuple, optional): The components to plot. If None the first max_cc_to_plot=32 components will be plotted. Defaults to None.
max_cc_to_plot (int, optional): The maximum number of connected components to plot. Defaults to 32.
overlay (optional): Overlay image. Defaults to None.
crop (bool, optional): Whether to crop the image to the cc. Defaults to False.
@@ -27,6 +30,18 @@ def plot_cc(
Returns:
figs (list[plt.Figure]): List of figures, if `show=False`.
+
+ Example:
+ ```python
+ import qim3d
+ vol = qim3d.examples.cement_128x128x128[50:150]
+ vol_bin = vol<80
+ cc = qim3d.processing.get_3d_cc(vol_bin)
+ qim3d.viz.plot_cc(cc, crop=True, show=True, overlay=None, n_slices=5, component_indexs=[4,6,7])
+ qim3d.viz.plot_cc(cc, crop=True, show=True, overlay=vol, n_slices=5, component_indexs=[4,6,7])
+ ```
+ 
+ 
"""
# if no components are given, plot the first max_cc_to_plot=32 components
if component_indexs is None:
--
GitLab