plot3d

README.md

@@ -77,13 +77,107 @@ If your OS doesn't have a backend GUI to render Matplotlib, you need to install
 
 
 
-plots
+## Plotting
 
-1. multiple 2D images
-just images, not mask or contour
 
-2. multiple 2D images and masks- layered plot
+### 3D plots
+1. Basic Usage:
+Plot a single image without any mask:
 
+```python
+    viz.plot3d('path/to/image.nii')
+```
+
+2. Plotting Multiple Images:
+If you have multiple images to plot:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    viz.plot3d(images)
+```
+
+3. Displaying Images with Masks:
+To visualize images along with their corresponding masks:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    viz.plot3d(images, masks=masks)
+```
+
+4. Using Custom Colors:
+To specify custom colors for the masks:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    colors = ['red', 'green']
+    viz.plot3d(images, masks=masks, colors=colors)
+```
+
+5. Displaying Titles:
+For adding titles to the plotted images:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    colors = ['red', 'green']
+    titles = ['Image 1', 'Image 2']
+    viz.plot3d(images, masks=masks, colors=colors, titles=titles)
+```
+
+6. Specifying Display Plane:
+You can visualize the images in different planes:
+
+```python
+    viz.plot3d('path/to/image.nii', plane="sagittal")
+```
+
+7. Saving the Plot:
+To save the plot to a specified location:
+
+```python
+    viz.plot3d('path/to/image.nii', save_path='path/to/save_directory/')
+```
+
+8. Specifying Rows and Columns:
+To organize multiple images into a specific number of rows and columns:
+
+Specify Rows:
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii', 'path/to/image3.nii']
+    viz.plot3d(images, rows=2)
+```
+
+This will generate a 2x2 grid, with the third image in the first cell of the second row.
+
+Specify Columns:
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii', 'path/to/image3.nii']
+    viz.plot3d(images, columns=2)
+```
+
+This will also generate a 2x2 grid similar to the previous example.
+
+Specifying Both Rows and Columns:
+For more control, you can specify both rows and columns:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii', 'path/to/image3.nii', 'path/to/image4.nii']
+    viz.plot3d(images, rows=2, columns=2)
+```
+This will arrange the images in a 2x2 grid with each cell having one image.
+
+9. Combining Multiple Options:
+You can also combine multiple options for a comprehensive view:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    titles = ["First Image with Mask", "Second Image with Mask"]
+    mask_colors = ["#FF0000", "#00FF00"]
+    viz.plot3d(images, masks=masks, mask_colors=mask_colors, titles=titles, save_path='path/to/save_directory/')
+```
 
 
 ## 2D plots
@@ -118,7 +212,7 @@ inpute:
     - an array of images
 
 ```python
-plot3d.images()
+viz.plot3d.images()
 ```
 
 2. 3D images and masks- layered plot with slider
@@ -128,7 +222,7 @@ inpute:
     - an array of masks
 
 ```python
-plot3d.images_masks()
+viz.plot3d.images_masks()
 ```
 
 

api/plot/README.md

@@ -0,0 +1,102 @@
+# Plotting
+
+## 3D plots
+1. Basic Usage:
+Plot a single image without any mask:
+
+```python
+    viz.plot3d('path/to/image.nii')
+```
+
+2. Plotting Multiple Images:
+If you have multiple images to plot:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    viz.plot3d(images)
+```
+
+3. Displaying Images with Masks:
+To visualize images along with their corresponding masks:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    viz.plot3d(images, masks=masks)
+```
+
+4. Using Custom Colors:
+To specify custom colors for the masks:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    colors = ['red', 'green']
+    viz.plot3d(images, masks=masks, colors=colors)
+```
+
+5. Displaying Titles:
+For adding titles to the plotted images:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    colors = ['red', 'green']
+    titles = ['Image 1', 'Image 2']
+    viz.plot3d(images, masks=masks, colors=colors, titles=titles)
+```
+
+6. Specifying Display Plane:
+You can visualize the images in different planes:
+
+```python
+    viz.plot3d('path/to/image.nii', plane="sagittal")
+```
+
+7. Saving the Plot:
+To save the plot to a specified location:
+
+```python
+    viz.plot3d('path/to/image.nii', save_path='path/to/save_directory/')
+```
+
+8. Specifying Rows and Columns:
+To organize multiple images into a specific number of rows and columns:
+
+Specify Rows:
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii', 'path/to/image3.nii']
+    viz.plot3d(images, rows=2)
+```
+
+This will generate a 2x2 grid, with the third image in the first cell of the second row.
+
+Specify Columns:
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii', 'path/to/image3.nii']
+    viz.plot3d(images, columns=2)
+```
+
+This will also generate a 2x2 grid similar to the previous example.
+
+Specifying Both Rows and Columns:
+For more control, you can specify both rows and columns:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii', 'path/to/image3.nii', 'path/to/image4.nii']
+    viz.plot3d(images, rows=2, columns=2)
+```
+This will arrange the images in a 2x2 grid with each cell having one image.
+
+9. Combining Multiple Options:
+You can also combine multiple options for a comprehensive view:
+
+```python
+    images = ['path/to/image1.nii', 'path/to/image2.nii']
+    masks = ['path/to/mask1.nii', 'path/to/mask2.nii']
+    titles = ["First Image with Mask", "Second Image with Mask"]
+    mask_colors = ["#FF0000", "#00FF00"]
+    viz.plot3d(images, masks=masks, mask_colors=mask_colors, titles=titles, save_path='path/to/save_directory/')
+```
+
+

api/plot/plot3d.py

@@ -0,0 +1,52 @@
+import medviz as viz
+
+viz.plot3d("/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1.nii")
+
+viz.plot3d(
+    images=[
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1.nii",
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/rt.dcm",
+    ],
+    masks=[
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1-label.nii",
+        None,
+    ],
+    rows=1,
+    columns=2,
+)
+
+viz.plot3d(
+    images=[
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1.nii",
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/rt.dcm",
+    ],
+    titles=["First ", "Second"],
+    rows=1,
+    columns=2,
+)
+
+viz.plot3d(
+    images=[
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/349090_CTE_AX_Res.nii",
+    ]
+)
+
+viz.plot3d(
+    images="/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1.nii",
+    masks="/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1-label.nii",
+    plane="coronal",
+)
+
+viz.plot3d(
+    images=[
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1.nii",
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/rt.dcm",
+    ],
+    masks=[
+        "/storage/sync/git/mohsen/medviz/test_local/dataset/plots/1-1-label.nii",
+        None,
+    ],
+    titles=["Image 1", "Image 2"],
+    rows=1,
+    columns=2,
+)