Merge branch 'docs_update' into 'main'

Docs update

See merge request !97

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
 

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

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

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

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)
         ```
+        ![Grid of slices](assets/screenshots/viz-slices.png)
+
 
 
     """

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)
+        ```
+        ![generate_volume](assets/screenshots/generate_volume.png)
+
+        ```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:

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)
         ```
         ![Grid of slices](assets/screenshots/viz-slices.png)
     """

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: