diff --git a/docs/assets/screenshots/generate_volume.png b/docs/assets/screenshots/generate_volume.png
new file mode 100644
index 0000000000000000000000000000000000000000..02ee3b73643630316aec6f00c8d6e00866a06ec7
Binary files /dev/null and b/docs/assets/screenshots/generate_volume.png differ
diff --git a/docs/index.md b/docs/index.md
index 5a3ca251190a1d906061f4bd23871d19e599185e..ea6111ebbe6f4a893f5aaaf65c99f42418f43386 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -131,8 +131,21 @@ You can find us at Gitlab:
[https://lab.compute.dtu.dk/QIM/tools/qim3d](https://lab.compute.dtu.dk/QIM/tools/qim3d
)
-This project is licensed under the MIT License.
+This project is licensed under the [MIT License](https://lab.compute.dtu.dk/QIM/tools/qim3d/-/blob/main/LICENSE).
+### Contributors
+
+Below is a list of contributors to the project, arranged in chronological order of their first commit to the repository:
+
+| Author | Commits | First commit |
+|:--------------------------|----------:|-------------:|
+| Felipe Delestro | 170 | 2023-05-12 |
+| Stefan Engelmann Jensen | 29 | 2023-06-29 |
+| Oskar Kristoffersen | 15 | 2023-07-05 |
+| Christian Kento Rasmussen | 19 | 2024-02-01 |
+| Alessia Saccardo | 7 | 2024-02-19 |
+| David Grundfest | 4 | 2024-04-12 |
+| Anna Bøgevang Ekner | 3 | 2024-04-18 |
## Support
diff --git a/docs/processing.md b/docs/processing.md
index 558f857e94aa01cbc128a3d3245b668ca82c1998..cd68efaba653a77ae1f938ca088e17e8b0f81ae7 100644
--- a/docs/processing.md
+++ b/docs/processing.md
@@ -16,6 +16,11 @@ Here, we provide functionalities designed specifically for 3D image analysis and
- minimum
- tophat
+::: qim3d.processing.Pipeline
+ options:
+ members:
+ - append
+
::: qim3d.processing.operations
options:
members:
@@ -23,7 +28,3 @@ Here, we provide functionalities designed specifically for 3D image analysis and
- watershed
- edge_fade
- fade_mask
-::: qim3d.processing
- options:
- members:
- - Pipeline
\ No newline at end of file
diff --git a/docs/utils.md b/docs/utils.md
index f86074f1b190446ad487521be309c3aa17515761..6425ef1ad29341cdeda23ac62c413ea604e47e1d 100644
--- a/docs/utils.md
+++ b/docs/utils.md
@@ -5,6 +5,7 @@ A set of tools to ease managment of the system, with the common needs for large
::: qim3d.utils.img
options:
members:
+ - generate_volume
- overlay_rgb_images
::: qim3d.utils.system
diff --git a/mkdocs.yml b/mkdocs.yml
index df02fdf5b76c459bb6035d146a84d808f00a8c5f..02e9b73b47a1dfdff8e6d6ed7831683ae8ec7a30 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -62,6 +62,7 @@ markdown_extensions:
- admonition
- attr_list
- md_in_html
+ - tables
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.details
@@ -84,5 +85,5 @@ plugins:
show_root_full_path: true
show_object_full_path: true
show_symbol_type_heading: true
- show_symbol_type_toc: true
+ show_symbol_type_toc: false
separate_signature: true
\ No newline at end of file
diff --git a/qim3d/io/loading.py b/qim3d/io/loading.py
index 42eef66c7e73dcda4619c83690a74c09c30eb528..e45eb1216013b0a0b55d19778795e86833a2b3c7 100644
--- a/qim3d/io/loading.py
+++ b/qim3d/io/loading.py
@@ -749,6 +749,16 @@ def load(
"""
Load data from the specified file or directory.
+ Supported formats:
+
+ - `Tiff` (including file stacks)
+ - `HDF5`
+ - `TXRM`/`TXM`/`XRM`
+ - `NIfTI`
+ - `PIL` (including file stacks)
+ - `VOL`/`VGI`
+ - `DICOM`
+
Args:
path (str or os.PathLike): The path to the file or directory.
virtual_stack (bool, optional): Specifies whether to use virtual
@@ -833,14 +843,17 @@ class ImgExamples:
shell_225x128x128 (numpy.ndarray): A 3D volume of a shell.
Tip:
- Call `qim3d.examples.<name>` to access the image examples easily as this class is instantiated when importing `qim3d`
+ Simply call `qim3d.examples.<name>` to access the image examples.
Example:
```python
import qim3d
- data = qim3d.examples.blobs_256x256
+ vol = qim3d.examples.shell_225x128x128
+ qim3d.viz.slices(vol, n_slices=15)
```
+ 
+
"""
diff --git a/qim3d/utils/img.py b/qim3d/utils/img.py
index 13f181faef80baa52dae596969d3d8a8c90e4651..6b91af384311662885897dcd6c5938fd18c67a84 100644
--- a/qim3d/utils/img.py
+++ b/qim3d/utils/img.py
@@ -82,9 +82,18 @@ def generate_volume(
ValueError: If `dtype` is not a valid numpy number type.
Example:
+ ```python
import qim3d
- vol = qim3d.utils.generate_volume()
- qim3d.viz.slices(vol, vmin=0, vmax=255)
+ vol = qim3d.utils.generate_volume(noise_scale=0.05, threshold=0.4)
+ qim3d.viz.slices(vol, vmin=0, vmax=255, n_slices=15)
+ ```
+ 
+
+ ```python
+ qim3d.viz.vol(vol)
+ ```
+ <iframe src="https://platform.qim.dk/k3d/synthetic_volume.html" width="100%" height="500" frameborder="0"></iframe>
+
"""
if not isinstance(final_shape, tuple) or len(final_shape) != 3:
diff --git a/qim3d/viz/img.py b/qim3d/viz/img.py
index 24980b5c6ab872652ce8ad04d89a84e3c9449314..f2293565675af6b6fc7cf76b4577d6fbedd2fa22 100644
--- a/qim3d/viz/img.py
+++ b/qim3d/viz/img.py
@@ -266,8 +266,8 @@ def slices(
```python
import qim3d
- img = qim3d.examples.shell_225x128x128
- qim3d.viz.slices(img, n_slices=15)
+ vol = qim3d.examples.shell_225x128x128
+ qim3d.viz.slices(vol, n_slices=15)
```
"""
diff --git a/qim3d/viz/k3d.py b/qim3d/viz/k3d.py
index 9271c56717b6f1ca95f674d16001c07ac3569dab..e612568b95e5a70b40ec99ccc2b914ff6ae71288 100644
--- a/qim3d/viz/k3d.py
+++ b/qim3d/viz/k3d.py
@@ -25,6 +25,7 @@ def vol(
cmap=None,
samples="auto",
max_voxels=412**3,
+ data_type="scaled_float16",
**kwargs,
):
"""
@@ -72,6 +73,7 @@ def vol(
```
"""
+
pixel_count = img.shape[0] * img.shape[1] * img.shape[2]
# target is 60fps on m1 macbook pro, using test volume: https://data.qim.dk/pages/foam.html
if samples == "auto":
@@ -88,10 +90,10 @@ def vol(
if aspectmode.lower() not in ["data", "cube"]:
raise ValueError("aspectmode should be either 'data' or 'cube'")
-
# check if image should be downsampled for visualization
original_shape = img.shape
img = downscale_img(img, max_voxels=max_voxels)
+
new_shape = img.shape
if original_shape != new_shape:
@@ -99,6 +101,17 @@ def vol(
f"Downsampled image for visualization. From {original_shape} to {new_shape}"
)
+ # Scale the image to float16 if needed
+ if save:
+ # When saving, we need float64
+ img = img.astype(np.float64)
+ else:
+
+ if data_type == "scaled_float16":
+ img = scale_to_float16(img)
+ else:
+ img = img.astype(data_type)
+
# Set color ranges
color_range = [np.min(img), np.max(img)]
if vmin:
@@ -106,8 +119,9 @@ def vol(
if vmax:
color_range[1] = vmax
+ # Create the volume plot
plt_volume = k3d.volume(
- scale_to_float16(img),
+ img,
bounds=(
[0, img.shape[2], 0, img.shape[1], 0, img.shape[0]]
if aspectmode.lower() == "data"
@@ -119,7 +133,6 @@ def vol(
)
plot = k3d.plot(grid_visible=grid_visible, **kwargs)
plot += plt_volume
-
if save:
# Save html to disk
with open(str(save), "w", encoding="utf-8") as fp: