Skip to content
Snippets Groups Projects
Commit 447666f1 authored by fima's avatar fima :beers:
Browse files

slices_grid calls refactoring

parent 5505b582
No related branches found
No related tags found
1 merge request!139Refactoring v1.0 prep
Show whitespace changes
Inline Side-by-side
Showing
with 36 additions and 36 deletions
docs/notebooks/blob_detection.ipynb
+ 2
− 2
View file @ 447666f1
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
import qim3d import qim3d
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Blob detection notebook ### Blob detection notebook
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
This notebook shows how to do **blob detection** in a 3D volume using the `qim3d` library. This notebook shows how to do **blob detection** in a 3D volume using the `qim3d` library.
Blob detection is done by using the `qim3d.processing.blob_detection` method, which detects blobs by using the Difference of Gaussian (DoG) blob detection method, and returns two arrays: Blob detection is done by using the `qim3d.processing.blob_detection` method, which detects blobs by using the Difference of Gaussian (DoG) blob detection method, and returns two arrays:
- `blobs`: The blobs found in the volume stored as `(p, r, c, radius)` - `blobs`: The blobs found in the volume stored as `(p, r, c, radius)`
- `binary_volume`: A binary mask of the volume with the blobs marked as `True` - `binary_volume`: A binary mask of the volume with the blobs marked as `True`
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### **Example 1**: Blob detection in cement volume ### **Example 1**: Blob detection in cement volume
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
**Applying Gaussian filter to volume** **Applying Gaussian filter to volume**
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# Import 3D volume of cement # Import 3D volume of cement
cement = qim3d.examples.cement_128x128x128 cement = qim3d.examples.cement_128x128x128
# Visualize slices of the original cement volume # Visualize slices of the original cement volume
qim3d.viz.slices(cement, n_slices = 5, show = True) qim3d.viz.slices_grid(cement, n_slices = 5, show = True)
# Apply Gaussian filter to the cement volume # Apply Gaussian filter to the cement volume
cement_filtered = qim3d.processing.gaussian(cement, sigma = 2) cement_filtered = qim3d.processing.gaussian(cement, sigma = 2)
# Visualize slices of the filtered cement volume # Visualize slices of the filtered cement volume
qim3d.viz.slices(cement_filtered) qim3d.viz.slices_grid(cement_filtered)
``` ```
%% Output %% Output
<Figure size 1000x200 with 5 Axes> <Figure size 1000x200 with 5 Axes>
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
**Detecting blobs in volume** **Detecting blobs in volume**
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# Detect blobs, and get binary mask # Detect blobs, and get binary mask
blobs, mask = qim3d.processing.blob_detection( blobs, mask = qim3d.processing.blob_detection(
cement_filtered, cement_filtered,
min_sigma=1, min_sigma=1,
max_sigma=8, max_sigma=8,
threshold=0.001, threshold=0.001,
overlap=0.1, overlap=0.1,
background="bright" background="bright"
) )
# Number of blobs found # Number of blobs found
print(f'Number of blobs found in the volume: {len(blobs)} blobs') print(f'Number of blobs found in the volume: {len(blobs)} blobs')
``` ```
%% Output %% Output
Bright background selected, volume will be inverted. Bright background selected, volume will be inverted.
Number of blobs found in the volume: 1813 blobs Number of blobs found in the volume: 1813 blobs
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# Visualize blobs on slices of cement volume # Visualize blobs on slices of cement volume
qim3d.viz.detection.circles(blobs, cement, alpha = 0.8, show = True, color = 'red') qim3d.viz.detection.circles(blobs, cement, alpha = 0.8, show = True, color = 'red')
``` ```
%% Output %% Output
interactive(children=(IntSlider(value=64, description='Slice', max=127), Output()), layout=Layout(align_items=… interactive(children=(IntSlider(value=64, description='Slice', max=127), Output()), layout=Layout(align_items=…
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
**Binary mask of detected blobs** **Binary mask of detected blobs**
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
# Visualize binary mask # Visualize binary mask
qim3d.viz.slicer(mask) qim3d.viz.slicer(mask)
``` ```
%% Output %% Output
interactive(children=(IntSlider(value=64, description='Slice', max=127), Output()), layout=Layout(align_items=… interactive(children=(IntSlider(value=64, description='Slice', max=127), Output()), layout=Layout(align_items=…
......
docs/notebooks/local_thickness.ipynb
+ 2
− 2
View file @ 447666f1
%% Cell type:code id: tags: %% Cell type:code id: tags:
   
``` python ``` python
import qim3d import qim3d
``` ```
   
%% Output %% Output
   
WARNING:root:Could not load CuPy: No module named 'cupy' WARNING:root:Could not load CuPy: No module named 'cupy'
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
### Local thickness notebook ### Local thickness notebook
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
This notebook shows an example of how to determine the **local thickness** of an object in either 2D and 3D using the `qim3d` library. The local thickness at a point within the object is defined as the radius of the largest circle (2D) or sphere (3D) that contains the point and is inside the object. This notebook shows an example of how to determine the **local thickness** of an object in either 2D and 3D using the `qim3d` library. The local thickness at a point within the object is defined as the radius of the largest circle (2D) or sphere (3D) that contains the point and is inside the object.
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
In the following, the local thickness is computed for three examples: In the following, the local thickness is computed for three examples:
   
* **Example 1**: 2D image of blobs * **Example 1**: 2D image of blobs
* **Example 2**: 3D volume of shell * **Example 2**: 3D volume of shell
* **Example 3**: 3D volume of cement * **Example 3**: 3D volume of cement
   
The local thickness algorithm is applied by using the `qim3d.processing.local_thickness` function, which expects a binary image/volume. If the input is not already binary, then it will be binarized automatically using Otsu's thresholding method. The `qim3d.processing.local_thickness` function returns a 2D or 3D Numpy array representing the local thickness of the input image/volume. The local thickness algorithm is applied by using the `qim3d.processing.local_thickness` function, which expects a binary image/volume. If the input is not already binary, then it will be binarized automatically using Otsu's thresholding method. The `qim3d.processing.local_thickness` function returns a 2D or 3D Numpy array representing the local thickness of the input image/volume.
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
#### **Example 1**: Local thickness of 2D image #### **Example 1**: Local thickness of 2D image
This example uses a 2D image of blobs (256 x 256), which can be acquired from `qim3d.examples.blobs_256x256`. This example uses a 2D image of blobs (256 x 256), which can be acquired from `qim3d.examples.blobs_256x256`.
   
%% Cell type:code id: tags: %% Cell type:code id: tags:
   
``` python ``` python
# Import 2D image of blobs # Import 2D image of blobs
blobs = qim3d.examples.blobs_256x256 blobs = qim3d.examples.blobs_256x256
   
# Compute the local thickness of the blobs # Compute the local thickness of the blobs
lt_blobs = qim3d.processing.local_thickness(blobs, visualize = True) lt_blobs = qim3d.processing.local_thickness(blobs, visualize = True)
``` ```
   
%% Output %% Output
   
Input image is not binary. It will be binarized using Otsu's method with threshold: 74 Input image is not binary. It will be binarized using Otsu's method with threshold: 74
WARNING:qim3d:Input image is not binary. It will be binarized using Otsu's method with threshold: 74 WARNING:qim3d:Input image is not binary. It will be binarized using Otsu's method with threshold: 74
   
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
#### **Example 2**: Local thickness of 3D volume #### **Example 2**: Local thickness of 3D volume
This example uses a 3D volume of a shell (225 x 128 x 128), which can be acquired from `qim3d.examples.shell_225x128x128`. This example uses a 3D volume of a shell (225 x 128 x 128), which can be acquired from `qim3d.examples.shell_225x128x128`.
   
%% Cell type:code id: tags: %% Cell type:code id: tags:
   
``` python ``` python
# Import 3D volume of shell # Import 3D volume of shell
shell = qim3d.examples.shell_225x128x128 shell = qim3d.examples.shell_225x128x128
   
# Compute the local thickness of shell # Compute the local thickness of shell
lt_shell = qim3d.processing.local_thickness(shell, visualize = True, axis = 0) lt_shell = qim3d.processing.local_thickness(shell, visualize = True, axis = 0)
``` ```
   
%% Output %% Output
   
Input image is not binary. It will be binarized using Otsu's method with threshold: 65 Input image is not binary. It will be binarized using Otsu's method with threshold: 65
WARNING:qim3d:Input image is not binary. It will be binarized using Otsu's method with threshold: 65 WARNING:qim3d:Input image is not binary. It will be binarized using Otsu's method with threshold: 65
   
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
#### **Example 3**: Local thickness of (binary) 3D volume #### **Example 3**: Local thickness of (binary) 3D volume
This example uses a 3D volume of cement (128 x 128 x 128), which can be acquired from `qim3d.examples.cement_128x128x128`. This example uses a 3D volume of cement (128 x 128 x 128), which can be acquired from `qim3d.examples.cement_128x128x128`.
   
For the previous two examples, the original image/volume was passed directly to the `qim3d.processing.local_thickness` function, which automatically binarized the input prior to computing the local thickness. For the previous two examples, the original image/volume was passed directly to the `qim3d.processing.local_thickness` function, which automatically binarized the input prior to computing the local thickness.
   
For this example, the original volume will instead first be manually binarized with the `qim3d.processing.Blob.get_mask` method (see details in the documentation for `qim3d.processing.Blob`). Then the binarized volume (i.e. mask) will be passed to the `qim3d.processing.local_thickness` function, which can then directly compute the local thickness. For this example, the original volume will instead first be manually binarized with the `qim3d.processing.Blob.get_mask` method (see details in the documentation for `qim3d.processing.Blob`). Then the binarized volume (i.e. mask) will be passed to the `qim3d.processing.local_thickness` function, which can then directly compute the local thickness.
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
**Importing, filtering and visualizing volume** **Importing, filtering and visualizing volume**
   
%% Cell type:code id: tags: %% Cell type:code id: tags:
   
``` python ``` python
# Import 3D volume of cement # Import 3D volume of cement
cement = qim3d.examples.cement_128x128x128 cement = qim3d.examples.cement_128x128x128
   
# Visualize slices of the original cement volume # Visualize slices of the original cement volume
qim3d.viz.slices(cement, n_slices = 5, show = True) qim3d.viz.slices_grid(cement, n_slices = 5, show = True)
   
# Apply Gaussian filter to the cement volume # Apply Gaussian filter to the cement volume
cement_filtered = qim3d.processing.gaussian(cement, sigma = 2) cement_filtered = qim3d.processing.gaussian(cement, sigma = 2)
   
# Visualize slices of the filtered cement volume # Visualize slices of the filtered cement volume
qim3d.viz.slices(cement_filtered) qim3d.viz.slices_grid(cement_filtered)
``` ```
   
%% Output %% Output
   
   
<Figure size 1000x200 with 5 Axes> <Figure size 1000x200 with 5 Axes>
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
**Detecting blobs in volume, creating binary mask** **Detecting blobs in volume, creating binary mask**
   
%% Cell type:code id: tags: %% Cell type:code id: tags:
   
``` python ``` python
# Initialize Blob detector # Initialize Blob detector
blob_detector = qim3d.processing.Blob( blob_detector = qim3d.processing.Blob(
min_sigma=1, min_sigma=1,
max_sigma=8, max_sigma=8,
threshold=0.001, threshold=0.001,
overlap=0.1, overlap=0.1,
background="bright" background="bright"
) )
   
# Detect blobs # Detect blobs
cement_blobs = blob_detector.detect(cement_filtered) cement_blobs = blob_detector.detect(cement_filtered)
   
# Get binary mask and visualize # Get binary mask and visualize
cement_mask = blob_detector.get_mask() cement_mask = blob_detector.get_mask()
qim3d.viz.slicer(cement_mask) qim3d.viz.slicer(cement_mask)
``` ```
   
%% Output %% Output
   
interactive(children=(IntSlider(value=64, description='Slice', max=127), Output()), layout=Layout(align_items=… interactive(children=(IntSlider(value=64, description='Slice', max=127), Output()), layout=Layout(align_items=…
   
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
   
**Computing local thickness** **Computing local thickness**
   
%% Cell type:code id: tags: %% Cell type:code id: tags:
   
``` python ``` python
# Compute the local thickness of cement (input: binary mask) # Compute the local thickness of cement (input: binary mask)
lt_cement = qim3d.processing.local_thickness(cement_mask, visualize = True, axis = 0) lt_cement = qim3d.processing.local_thickness(cement_mask, visualize = True, axis = 0)
``` ```
   
%% Output %% Output
   
......
docs/releases.md
+ 2
− 2
View file @ 447666f1
...@@ -114,7 +114,7 @@ This version focus on the increased usability of the `qim3d` library ...@@ -114,7 +114,7 @@ This version focus on the increased usability of the `qim3d` library
- Online documentation available at [https://platform.qim.dk/qim3d](https://platform.qim.dk/qim3d) - Online documentation available at [https://platform.qim.dk/qim3d](https://platform.qim.dk/qim3d)
- Virtual stacks also available for `txm` files - Virtual stacks also available for `txm` files
- Updated GUI launch pipeline - Updated GUI launch pipeline
- New functionalities for `qim3d.viz.slices` - New functionalities for `qim3d.viz.slices_grid`
- Introduction of `qim3d.processing.filters` 🎉 - Introduction of `qim3d.processing.filters` 🎉
- Introduction of `qim3d.viz.vol` 🎉 - Introduction of `qim3d.viz.vol` 🎉
...@@ -140,7 +140,7 @@ Includes new develoments toward the usability of the library, as well as its int ...@@ -140,7 +140,7 @@ Includes new develoments toward the usability of the library, as well as its int
- For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality. - For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
- Improved data loader - Improved data loader
- Now the extensions `tif`, `h5` and `txm` are supported. - Now the extensions `tif`, `h5` and `txm` are supported.
- Added `qim3d.viz.slices` for easy slice visualization. - Added `qim3d.viz.slices_grid` for easy slice visualization.
- U-net model creation - U-net model creation
- Model availabe from `qim3d.models.UNet` - Model availabe from `qim3d.models.UNet`
- Data augmentation class at `qim3d.utils.Augmentation` - Data augmentation class at `qim3d.utils.Augmentation`
......
qim3d/filters.py
+ 2
− 2
View file @ 447666f1
...@@ -119,7 +119,7 @@ class Pipeline: ...@@ -119,7 +119,7 @@ class Pipeline:
vol = qim3d.examples.fly_150x256x256 vol = qim3d.examples.fly_150x256x256
# Show original # Show original
qim3d.viz.slices(vol, axis=0, show=True) qim3d.viz.slices_grid(vol, axis=0, show=True)
# Create filter pipeline # Create filter pipeline
pipeline = Pipeline( pipeline = Pipeline(
...@@ -134,7 +134,7 @@ class Pipeline: ...@@ -134,7 +134,7 @@ class Pipeline:
vol_filtered = pipeline(vol) vol_filtered = pipeline(vol)
# Show filtered # Show filtered
qim3d.viz.slices(vol_filtered, axis=0) qim3d.viz.slices_grid(vol_filtered, axis=0)
``` ```
![original volume](assets/screenshots/filter_original.png) ![original volume](assets/screenshots/filter_original.png)
![filtered volume](assets/screenshots/filter_processed.png) ![filtered volume](assets/screenshots/filter_processed.png)
......
qim3d/generate/blob_.py
+ 3
− 3
View file @ 447666f1
...@@ -52,7 +52,7 @@ def blob( ...@@ -52,7 +52,7 @@ def blob(
```python ```python
# Visualize slices # Visualize slices
qim3d.viz.slices(synthetic_blob, vmin = 0, vmax = 255, n_slices = 15) qim3d.viz.slices_grid(synthetic_blob, vmin = 0, vmax = 255, n_slices = 15)
``` ```
![synthetic_blob](assets/screenshots/synthetic_blob_slices.png) ![synthetic_blob](assets/screenshots/synthetic_blob_slices.png)
...@@ -76,7 +76,7 @@ def blob( ...@@ -76,7 +76,7 @@ def blob(
```python ```python
# Visualize slices # Visualize slices
qim3d.viz.slices(vol, n_slices=15, axis=1) qim3d.viz.slices_grid(vol, n_slices=15, axis=1)
``` ```
![synthetic_blob_cylinder_slice](assets/screenshots/synthetic_blob_cylinder_slice.png) ![synthetic_blob_cylinder_slice](assets/screenshots/synthetic_blob_cylinder_slice.png)
...@@ -100,7 +100,7 @@ def blob( ...@@ -100,7 +100,7 @@ def blob(
```python ```python
# Visualize # Visualize
qim3d.viz.slices(vol, n_slices=15) qim3d.viz.slices_grid(vol, n_slices=15)
``` ```
![synthetic_blob_tube_slice](assets/screenshots/synthetic_blob_tube_slice.png) ![synthetic_blob_tube_slice](assets/screenshots/synthetic_blob_tube_slice.png)
""" """
......
qim3d/generate/collection_.py
+ 2
− 2
View file @ 447666f1
...@@ -255,7 +255,7 @@ def collection( ...@@ -255,7 +255,7 @@ def collection(
```python ```python
# Visualize slices # Visualize slices
qim3d.viz.slices(vol, n_slices=15) qim3d.viz.slices_grid(vol, n_slices=15)
``` ```
![synthetic_collection_cylinder](assets/screenshots/synthetic_collection_cylinder_slices.png) ![synthetic_collection_cylinder](assets/screenshots/synthetic_collection_cylinder_slices.png)
...@@ -285,7 +285,7 @@ def collection( ...@@ -285,7 +285,7 @@ def collection(
```python ```python
# Visualize slices # Visualize slices
qim3d.viz.slices(vol, n_slices=15, axis=1) qim3d.viz.slices_grid(vol, n_slices=15, axis=1)
``` ```
![synthetic_collection_tube](assets/screenshots/synthetic_collection_tube_slices.png) ![synthetic_collection_tube](assets/screenshots/synthetic_collection_tube_slices.png)
""" """
......
qim3d/processing/operations.py
+ 2
− 2
View file @ 447666f1
...@@ -29,7 +29,7 @@ def remove_background( ...@@ -29,7 +29,7 @@ def remove_background(
import qim3d import qim3d
vol = qim3d.examples.cement_128x128x128 vol = qim3d.examples.cement_128x128x128
qim3d.viz.slices(vol, vmin=0, vmax=255) qim3d.viz.slices_grid(vol, vmin=0, vmax=255)
``` ```
![operations-remove_background_before](assets/screenshots/operations-remove_background_before.png) ![operations-remove_background_before](assets/screenshots/operations-remove_background_before.png)
...@@ -37,7 +37,7 @@ def remove_background( ...@@ -37,7 +37,7 @@ def remove_background(
vol_filtered = qim3d.processing.operations.remove_background(vol, vol_filtered = qim3d.processing.operations.remove_background(vol,
min_object_radius=3, min_object_radius=3,
background="bright") background="bright")
qim3d.viz.slices(vol_filtered, vmin=0, vmax=255) qim3d.viz.slices_grid(vol_filtered, vmin=0, vmax=255)
``` ```
![operations-remove_background_after](assets/screenshots/operations-remove_background_after.png) ![operations-remove_background_after](assets/screenshots/operations-remove_background_after.png)
""" """
......
qim3d/segmentation/standard.py
+ 2
− 2
View file @ 447666f1
...@@ -26,7 +26,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i ...@@ -26,7 +26,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
vol = qim3d.examples.cement_128x128x128 vol = qim3d.examples.cement_128x128x128
binary = qim3d.processing.filters.gaussian(vol, sigma = 2)<60 binary = qim3d.processing.filters.gaussian(vol, sigma = 2)<60
qim3d.viz.slices(binary, axis=1) qim3d.viz.slices_grid(binary, axis=1)
``` ```
![operations-watershed_before](assets/screenshots/operations-watershed_before.png) ![operations-watershed_before](assets/screenshots/operations-watershed_before.png)
...@@ -34,7 +34,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i ...@@ -34,7 +34,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
labeled_volume, num_labels = qim3d.processing.operations.watershed(binary) labeled_volume, num_labels = qim3d.processing.operations.watershed(binary)
cmap = qim3d.viz.colormaps.objects(num_labels) cmap = qim3d.viz.colormaps.objects(num_labels)
qim3d.viz.slices(labeled_volume, axis = 1, cmap = cmap) qim3d.viz.slices_grid(labeled_volume, axis = 1, cmap = cmap)
``` ```
![operations-watershed_after](assets/screenshots/operations-watershed_after.png) ![operations-watershed_after](assets/screenshots/operations-watershed_after.png)
......
qim3d/tests/viz/test_img.py
+ 12
− 12
View file @ 447666f1
...@@ -52,14 +52,14 @@ def test_grid_pred(): ...@@ -52,14 +52,14 @@ def test_grid_pred():
# unit tests for slices function # unit tests for slices function
def test_slices_numpy_array_input(): def test_slices_numpy_array_input():
example_volume = np.ones((10, 10, 10)) example_volume = np.ones((10, 10, 10))
fig = qim3d.viz.slices(example_volume, n_slices=1) fig = qim3d.viz.slices_grid(example_volume, n_slices=1)
assert isinstance(fig, plt.Figure) assert isinstance(fig, plt.Figure)
def test_slices_wrong_input_format(): def test_slices_wrong_input_format():
input = "not_a_volume" input = "not_a_volume"
with pytest.raises(ValueError, match="Data type not supported"): with pytest.raises(ValueError, match="Data type not supported"):
qim3d.viz.slices(input) qim3d.viz.slices_grid(input)
def test_slices_not_volume(): def test_slices_not_volume():
...@@ -68,7 +68,7 @@ def test_slices_not_volume(): ...@@ -68,7 +68,7 @@ def test_slices_not_volume():
ValueError, ValueError,
match="The provided object is not a volume as it has less than 3 dimensions.", match="The provided object is not a volume as it has less than 3 dimensions.",
): ):
qim3d.viz.slices(example_volume) qim3d.viz.slices_grid(example_volume)
def test_slices_wrong_position_format1(): def test_slices_wrong_position_format1():
...@@ -77,7 +77,7 @@ def test_slices_wrong_position_format1(): ...@@ -77,7 +77,7 @@ def test_slices_wrong_position_format1():
ValueError, ValueError,
match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".', match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
): ):
qim3d.viz.slices(example_volume, position="invalid_slice") qim3d.viz.slices_grid(example_volume, position="invalid_slice")
def test_slices_wrong_position_format2(): def test_slices_wrong_position_format2():
...@@ -86,7 +86,7 @@ def test_slices_wrong_position_format2(): ...@@ -86,7 +86,7 @@ def test_slices_wrong_position_format2():
ValueError, ValueError,
match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".', match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
): ):
qim3d.viz.slices(example_volume, position=1.5) qim3d.viz.slices_grid(example_volume, position=1.5)
def test_slices_wrong_position_format3(): def test_slices_wrong_position_format3():
...@@ -95,7 +95,7 @@ def test_slices_wrong_position_format3(): ...@@ -95,7 +95,7 @@ def test_slices_wrong_position_format3():
ValueError, ValueError,
match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".', match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
): ):
qim3d.viz.slices(example_volume, position=[1, 2, 3.5]) qim3d.viz.slices_grid(example_volume, position=[1, 2, 3.5])
def test_slices_invalid_axis_value(): def test_slices_invalid_axis_value():
...@@ -104,14 +104,14 @@ def test_slices_invalid_axis_value(): ...@@ -104,14 +104,14 @@ def test_slices_invalid_axis_value():
ValueError, ValueError,
match="Invalid value for 'axis'. It should be an integer between 0 and 2", match="Invalid value for 'axis'. It should be an integer between 0 and 2",
): ):
qim3d.viz.slices(example_volume, axis=3) qim3d.viz.slices_grid(example_volume, axis=3)
def test_slices_interpolation_option(): def test_slices_interpolation_option():
example_volume = np.ones((10, 10, 10)) example_volume = np.ones((10, 10, 10))
img_width = 3 img_width = 3
interpolation_method = "bilinear" interpolation_method = "bilinear"
fig = qim3d.viz.slices( fig = qim3d.viz.slices_grid(
example_volume, example_volume,
n_slices=1, n_slices=1,
img_width=img_width, img_width=img_width,
...@@ -130,7 +130,7 @@ def test_slices_multiple_slices(): ...@@ -130,7 +130,7 @@ def test_slices_multiple_slices():
example_volume = np.ones((10, 10, 10)) example_volume = np.ones((10, 10, 10))
img_width = 3 img_width = 3
n_slices = 3 n_slices = 3
fig = qim3d.viz.slices(example_volume, n_slices=n_slices, img_width=img_width) fig = qim3d.viz.slices_grid(example_volume, n_slices=n_slices, img_width=img_width)
# Add assertions for the expected number of subplots in the figure # Add assertions for the expected number of subplots in the figure
assert len(fig.get_axes()) == n_slices assert len(fig.get_axes()) == n_slices
...@@ -141,13 +141,13 @@ def test_slices_axis_argument(): ...@@ -141,13 +141,13 @@ def test_slices_axis_argument():
img_width = 3 img_width = 3
# Call the function with different values of the axis # Call the function with different values of the axis
fig_axis_0 = qim3d.viz.slices( fig_axis_0 = qim3d.viz.slices_grid(
example_volume, n_slices=1, img_width=img_width, axis=0 example_volume, n_slices=1, img_width=img_width, axis=0
) )
fig_axis_1 = qim3d.viz.slices( fig_axis_1 = qim3d.viz.slices_grid(
example_volume, n_slices=1, img_width=img_width, axis=1 example_volume, n_slices=1, img_width=img_width, axis=1
) )
fig_axis_2 = qim3d.viz.slices( fig_axis_2 = qim3d.viz.slices_grid(
example_volume, n_slices=1, img_width=img_width, axis=2 example_volume, n_slices=1, img_width=img_width, axis=2
) )
......
qim3d/viz/cc.py
+ 3
− 3
View file @ 447666f1
...@@ -30,7 +30,7 @@ def plot_cc( ...@@ -30,7 +30,7 @@ def plot_cc(
cmap (str, optional): Specifies the color map for the image. Defaults to "viridis". cmap (str, optional): Specifies the color map for the image. Defaults to "viridis".
vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None. vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None
**kwargs: Additional keyword arguments to pass to `qim3d.viz.slices`. **kwargs: Additional keyword arguments to pass to `qim3d.viz.slices_grid`.
Returns: Returns:
figs (list[plt.Figure]): List of figures, if `show=False`. figs (list[plt.Figure]): List of figures, if `show=False`.
...@@ -75,14 +75,14 @@ def plot_cc( ...@@ -75,14 +75,14 @@ def plot_cc(
else: else:
cc = connected_components.get_cc(component, crop=False) cc = connected_components.get_cc(component, crop=False)
overlay_crop = np.where(cc == 0, 0, overlay) overlay_crop = np.where(cc == 0, 0, overlay)
fig = qim3d.viz.slices(overlay_crop, show=show, cmap = cmap, vmin = vmin, vmax = vmax, **kwargs) fig = qim3d.viz.slices_grid(overlay_crop, show=show, cmap = cmap, vmin = vmin, vmax = vmax, **kwargs)
else: else:
# assigns discrete color map to each connected component if not given # assigns discrete color map to each connected component if not given
if "cmap" not in kwargs: if "cmap" not in kwargs:
kwargs["cmap"] = qim3d.viz.colormaps.objects(len(component_indexs)) kwargs["cmap"] = qim3d.viz.colormaps.objects(len(component_indexs))
# Plot the connected component without overlay # Plot the connected component without overlay
fig = qim3d.viz.slices( fig = qim3d.viz.slices_grid(
connected_components.get_cc(component, crop=crop), show=show, **kwargs connected_components.get_cc(component, crop=crop), show=show, **kwargs
) )
......
qim3d/viz/colormaps.py
+ 1
− 1
View file @ 447666f1
...@@ -89,7 +89,7 @@ def objects( ...@@ -89,7 +89,7 @@ def objects(
Tip: Tip:
It can be easily used when calling visualization functions as It can be easily used when calling visualization functions as
```python ```python
qim3d.viz.slices(segmented_volume, cmap = 'objects') qim3d.viz.slices_grid(segmented_volume, cmap = 'objects')
``` ```
which automatically detects number of unique classes which automatically detects number of unique classes
and creates the colormap object with defualt arguments. and creates the colormap object with defualt arguments.
......
qim3d/viz/data_exploration.py
+ 2
− 2
View file @ 447666f1
...@@ -77,7 +77,7 @@ def slices_grid( ...@@ -77,7 +77,7 @@ def slices_grid(
import qim3d import qim3d
vol = qim3d.examples.shell_225x128x128 vol = qim3d.examples.shell_225x128x128
qim3d.viz.slices_grid(vol, num_slices=15) qim3d.viz.slices_grid_grid(vol, num_slices=15)
``` ```
![Grid of slices](assets/screenshots/viz-slices.png) ![Grid of slices](assets/screenshots/viz-slices.png)
""" """
...@@ -690,7 +690,7 @@ def chunks(zarr_path: str, **kwargs): ...@@ -690,7 +690,7 @@ def chunks(zarr_path: str, **kwargs):
viz_widget = widgets.Output() viz_widget = widgets.Output()
with viz_widget: with viz_widget:
viz_widget.clear_output(wait=True) viz_widget.clear_output(wait=True)
fig = qim3d.viz.slices_grid(chunk, **kwargs) fig = qim3d.viz.slices_grid_grid(chunk, **kwargs)
display(fig) display(fig)
elif visualization_method == "volume": elif visualization_method == "volume":
viz_widget = widgets.Output() viz_widget = widgets.Output()
......
qim3d/viz/detection.py
+ 1
− 1
View file @ 447666f1
...@@ -29,7 +29,7 @@ def circles(blobs, vol, alpha=0.5, color="#ff9900", **kwargs): ...@@ -29,7 +29,7 @@ def circles(blobs, vol, alpha=0.5, color="#ff9900", **kwargs):
def _slicer(z_slice): def _slicer(z_slice):
clear_output(wait=True) clear_output(wait=True)
fig = qim3d.viz.slices( fig = qim3d.viz.slices_grid(
vol, vol,
n_slices=1, n_slices=1,
position=z_slice, position=z_slice,
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment