diff --git a/docs/assets/screenshots/CLI-k3d.png b/docs/assets/screenshots/CLI-k3d.png
index 41e8fc499041c463e3c0763aecff2c844a3f7f7c..88967ae209d2ca3b6f89629cdd18060c09620dff 100644
Binary files a/docs/assets/screenshots/CLI-k3d.png and b/docs/assets/screenshots/CLI-k3d.png differ
diff --git a/docs/assets/screenshots/local_thickness_2d.png b/docs/assets/screenshots/local_thickness_2d.png
index de3b9bc38c230efca50a6fd2d6743ffa583837af..3c8a64cd59b8e16b34f6314f7a51d4adab4a7fcd 100644
Binary files a/docs/assets/screenshots/local_thickness_2d.png and b/docs/assets/screenshots/local_thickness_2d.png differ
diff --git a/docs/assets/screenshots/synthetic_blob_slices.png b/docs/assets/screenshots/synthetic_blob_slices.png
index 549ae27ebf837cc108ecea7454849de480c4a44b..bbfeb3a59046a70c4083d36640ba0e04e9dead47 100644
Binary files a/docs/assets/screenshots/synthetic_blob_slices.png and b/docs/assets/screenshots/synthetic_blob_slices.png differ
diff --git a/docs/cli.md b/docs/cli.md
index 6295a98c2d38e575a45a8efc863d854c88375b43..a8d1d42e681b5b990b8d89060324c022115511ef 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -142,12 +142,20 @@ You can launch volumetric visualizations directly from the command line. By defa
```
``` title="Output"
- Loading data from blobs_256x256x256.tif
- Done, volume shape: (256, 256, 256)
+ Loading data from cement_128x128x128.tif
+ Loading: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.02MB/2.02MB [00:00<00:00, 936MB/s]
+ Volume using 2.0 MB of memory
+
+ System memory:
+ • Total.: 31.0 GB
+ • Used..: 18.8 GB (60.8%)
+ • Free..: 12.1 GB (39.2%)
+ Done, volume shape: (128, 128, 128)
Generating k3d plot...
Done, plot available at <k3d.html>
Opening in default browser...
+
```
And a new tab will be opened in the default browser with the interactive k3d plot:
@@ -155,17 +163,26 @@ You can launch volumetric visualizations directly from the command line. By defa
Or an specific path for destination can be used. We can also choose to not open the browser:
-!!! Example "Example using k3d, saving html to custom path"
- ``` title="Command"
- qim3d viz --source blobs_256x256x256.tif --destination my_plot.html --no-browser
+!!! Example
+ ```
+ qim3d viz cement_128x128x128.tif --destination my_plot.html --no-browser
+
```
``` title="Output"
- Loading data from blobs_256x256x256.tif
- Done, volume shape: (256, 256, 256)
+ Loading data from cement_128x128x128.tif
+ Loading: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.02MB/2.02MB [00:00<00:00, 909MB/s]
+ Volume using 2.0 MB of memory
+
+ System memory:
+ • Total.: 31.0 GB
+ • Used..: 18.9 GB (61.1%)
+ • Free..: 12.0 GB (38.9%)
+ Done, volume shape: (128, 128, 128)
Generating k3d plot...
Done, plot available at <my_plot.html>
+
```
This writes to disk the `my_plot.html` file.
diff --git a/qim3d/generate/blob_.py b/qim3d/generate/blob_.py
index 58a030f47fed687b32de06f94796be98005b080c..ed7f6f6c25b4d8be64853bcba674d5d8b761c046 100644
--- a/qim3d/generate/blob_.py
+++ b/qim3d/generate/blob_.py
@@ -39,7 +39,7 @@ def blob(
import qim3d
# Generate synthetic blob
- synthetic_blob = qim3d.generate.blob(noise_scale = 0.05)
+ synthetic_blob = qim3d.generate.blob(noise_scale = 0.015)
# Visualize slices
qim3d.viz.slices(synthetic_blob, vmin = 0, vmax = 255, n_slices = 15)
diff --git a/qim3d/io/loading.py b/qim3d/io/loading.py
index f00dc33b020420edab64d2124ce3ad1059924b17..ce3f8f1360fce70315ba11e35165f1a1dbba116a 100644
--- a/qim3d/io/loading.py
+++ b/qim3d/io/loading.py
@@ -51,10 +51,6 @@ class DataLoader:
load_txrm(path): Load a TXRM/TXM/XRM file from the specified path
load_vol(path): Load a VOL file from the specified path. Path should point to the .vgi metadata file
load(path): Load a file or directory based on the given path
-
- Example:
- loader = qim3d.io.DataLoader(virtual_stack=True)
- data = loader.load_tiff("image.tif")
"""
def __init__(self, **kwargs):
@@ -675,10 +671,6 @@ class DataLoader:
ValueError: If the format is not supported
ValueError: If the file or directory does not exist.
MemoryError: If file size exceeds available memory and force_load is not set to True. In check_size function.
-
- Example:
- loader = qim3d.io.DataLoader()
- data = loader.load("image.tif")
"""
# Stringify path in case it is not already a string
diff --git a/qim3d/io/saving.py b/qim3d/io/saving.py
index a89206a2c1526a1bc3b88515f76908a81cf67cc2..4ba7ef00dfe12fe7bbec2e44e6731529b87db75c 100644
--- a/qim3d/io/saving.py
+++ b/qim3d/io/saving.py
@@ -6,18 +6,20 @@ Example:
```python
import qim3d
- vol = qim3d.examples.fly_150x256x256
+ # Generate synthetic blob
+ synthetic_blob = qim3d.generate.blob(noise_scale = 0.015)
- qim3d.io.save("fly.tif", vol)
+ qim3d.io.save("fly.tif", synthetic_blob)
```
Volumes can also be saved with one file per slice:
```python
import qim3d
- vol = qim3d.examples.fly_150x256x256
+ # Generate synthetic blob
+ synthetic_blob = qim3d.generate.blob(noise_scale = 0.015)
- qim3d.io.save("slices", vol, basename="fly-slices", sliced_dim=0)
+ qim3d.io.save("slices", synthetic_blob, basename="fly-slices", sliced_dim=0)
```
"""
@@ -53,11 +55,6 @@ class DataSaver:
Methods:
save_tiff(path,data): Save data to a TIFF file to the given path.
load(path,data): Save data to the given path.
-
- Example:
- image = qim3d.examples.blobs_256x256
- saver = qim3d.io.DataSaver(compression=True)
- saver.save_tiff("image.tif",image)
"""
def __init__(self, **kwargs):
@@ -319,12 +316,6 @@ class DataSaver:
ValueError: If the provided path does not exist and self.basename is not provided
ValueError: If a file extension is not provided.
ValueError: if a file with the specified path already exists and replace=False.
-
- Example:
- image = qim3d.examples.blobs_256x256
- saver = qim3d.io.DataSaver(compression=True)
- saver.save("image.tif",image)
-
"""
path = stringify_path(path)
@@ -438,8 +429,20 @@ def save(
```python
import qim3d
- vol = qim3d.examples.blobs_256x256x256
- qim3d.io.save("blobs.tif", vol)
+ # Generate synthetic blob
+ synthetic_blob = qim3d.generate.blob(noise_scale = 0.015)
+
+ qim3d.io.save("blob.tif", synthetic_blob, replace=True)
+ ```
+
+ Volumes can also be saved with one file per slice:
+ ```python
+ import qim3d
+
+ # Generate synthetic blob
+ synthetic_blob = qim3d.generate.blob(noise_scale = 0.015)
+
+ qim3d.io.save("slices", synthetic_blob, basename="blob-slices", sliced_dim=0)
```
"""
diff --git a/qim3d/models/unet.py b/qim3d/models/unet.py
index 3d25a78af9f2ecc5305807228c39d790e06c6960..6c57f55e44eb13403a39d36b8a85c5d400cc00ea 100644
--- a/qim3d/models/unet.py
+++ b/qim3d/models/unet.py
@@ -22,11 +22,6 @@ class UNet(nn.Module):
Raises:
ValueError: If `size` is not one of 'small', 'medium', or 'large'.
-
- Example:
- ```python
- model = UNet(size='large')
- ```
"""
def __init__(
@@ -104,13 +99,21 @@ class Hyperparameters:
Example:
```
- hyperparams = Hyperparameters(model=my_model, n_epochs=20, learning_rate=0.001)
+ import qim3d
- params_dict = hyperparams() # Get the hyperparameters
+ # This examples shows how to define a UNet model and its hyperparameters.
+ # Defining the model
+ my_model = qim3d.models.UNet(size='medium')
+
+ # Choosing the hyperparameters
+ hyperparams = qim3d.models.Hyperparameters(model=my_model, n_epochs=20, learning_rate=0.001)
+
+ params_dict = hyperparams() # Get the hyperparameters
optimizer = params_dict['optimizer']
criterion = params_dict['criterion']
n_epochs = params_dict['n_epochs']
+
```
"""
diff --git a/qim3d/processing/local_thickness_.py b/qim3d/processing/local_thickness_.py
index 96968519c0f9723db9828ea9798b2f00e9834d30..f106cbcbb6de1f14e47d256fd654106a9e5ff5ac 100644
--- a/qim3d/processing/local_thickness_.py
+++ b/qim3d/processing/local_thickness_.py
@@ -48,8 +48,14 @@ def local_thickness(
```python
import qim3d
- blobs = qim3d.examples.blobs_256x256 # 2D image
- lt_blobs = qim3d.processing.local_thickness(blobs, visualize=True)
+ # Generate synthetic collection of blobs
+ num_objects = 15
+ synthetic_collection, labels = qim3d.generate.collection(num_objects = num_objects)
+
+ # Extract one slice to show that localthickness works on 2D slices too
+ slice = synthetic_collection[:,:,50]
+ lt_blobs = qim3d.processing.local_thickness(slice, visualize=True)
+
```
diff --git a/qim3d/processing/mesh.py b/qim3d/processing/mesh.py
index e0ea24336bb37e98b1b1050d79db58b6033e8f69..88ff3de80351e3a345983b55c6e920b713967d3d 100644
--- a/qim3d/processing/mesh.py
+++ b/qim3d/processing/mesh.py
@@ -2,6 +2,7 @@ import numpy as np
from skimage import measure, filters
import trimesh
from typing import Tuple, Any
+from qim3d.utils.logger import log
def create_mesh(
@@ -35,7 +36,7 @@ def create_mesh(
threshold=0.5,
dtype='uint8'
)
- mesh = qim3d.processing.create_mesh(vol step_size=3)
+ mesh = qim3d.processing.create_mesh(vol, step_size=3)
qim3d.viz.mesh(mesh.vertices, mesh.faces)
```
@@ -46,7 +47,7 @@ def create_mesh(
# Compute the threshold level if not provided
if level is None:
level = filters.threshold_otsu(volume)
- print(f"Computed level using Otsu's method: {level}")
+ log.info(f"Computed level using Otsu's method: {level}")
# Apply padding to the volume
if padding is not None:
@@ -58,15 +59,13 @@ def create_mesh(
mode="constant",
constant_values=padding_value,
)
- print(f"Padded volume with {padding} to shape: {volume.shape}")
+ log.info(f"Padded volume with {padding} to shape: {volume.shape}")
# Call skimage.measure.marching_cubes with user-provided kwargs
verts, faces, normals, values = measure.marching_cubes(
volume, level=level, step_size=step_size, **kwargs
)
- print(len(verts))
-
# Create the Trimesh object
mesh = trimesh.Trimesh(vertices=verts, faces=faces)
diff --git a/qim3d/processing/operations.py b/qim3d/processing/operations.py
index 946605e89486b1e808900e2f917ac49accb273a2..982c6960378ea49b987a655a9840937621171f63 100644
--- a/qim3d/processing/operations.py
+++ b/qim3d/processing/operations.py
@@ -73,7 +73,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
import qim3d
vol = qim3d.examples.cement_128x128x128
- binary = qim3d.processing.filters.gaussian(vol, 2)<60
+ binary = qim3d.processing.filters.gaussian(vol, sigma = 2)<60
qim3d.viz.slices(binary, axis=1)
```
@@ -83,7 +83,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
labeled_volume, num_labels = qim3d.processing.operations.watershed(binary)
cmap = qim3d.viz.colormaps.objects(num_labels)
- qim3d.viz.slices(labeled_volume, axis = 1, cmap=cmap)
+ qim3d.viz.slices(labeled_volume, axis = 1, cmap = cmap)
```
diff --git a/qim3d/viz/colormaps.py b/qim3d/viz/colormaps.py
index e99b0fd81c5e6371cdd43464c029049a98df99aa..ac9fb66c3721120e1738efb3cd5eb45d57ac827e 100644
--- a/qim3d/viz/colormaps.py
+++ b/qim3d/viz/colormaps.py
@@ -78,7 +78,7 @@ def objects(
import qim3d
vol = qim3d.examples.cement_128x128x128
- binary = qim3d.processing.filters.gaussian(vol, 2) < 60
+ binary = qim3d.processing.filters.gaussian(vol, sigma = 2) < 60
labeled_volume, num_labels = qim3d.processing.operations.watershed(binary)
cmap = qim3d.viz.colormaps.objects(num_labels, style = 'bright')
diff --git a/qim3d/viz/explore.py b/qim3d/viz/explore.py
index 8dfa322eb72b1da84cd750d976137f7287aa5db3..54a4b03449dbb3e0c95d5238ae5fff9e0947d5ff 100644
--- a/qim3d/viz/explore.py
+++ b/qim3d/viz/explore.py
@@ -411,7 +411,7 @@ def interactive_fade_mask(vol: np.ndarray, axis: int = 0,cmap:str = 'viridis', v
return fig
shape_dropdown = widgets.Dropdown(
- options=["spherical", "cylindrical"],
+ options=["spherical", "cylindrical"],
value="spherical", # default value
description="Geometry",
)