| Name | mask2bbox JSON |
| Version |
0.0.18
JSON |
| download |
| home_page | |
| Summary | Gets the bounding boxes from a mask file. |
| upload_time | 2024-03-01 13:23:33 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | |
| keywords |
cell
mask
bounding box
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
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No Travis.
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| coveralls test coverage |
No coveralls.
|
# mask2bbox
[](https://pypi.org/project/mask2bbox/)
For a given mask, gets the coordinates of bounding box of each element of the mask. It will also allow for more operations in the future.
## Instalation
```bash
pip install mask2bbox
```
## CLI
```bash
python isolate-cells -h
```
## Usage
```python
import numpy as np
from mask2bbox import BBoxes
# Create a BBoxes object
all_boxes = BBoxes.from_mask("path/to/mask.png")
# Expand the bounding boxes
all_boxes = all_boxes.expand(n=10)
# Remove the bounding boxes that are located on the edge of the image
all_boxes = all_boxes.remove_from_edge()
# Get the sides of all the bounding boxes
sides = all_boxes.get("sides")
# Filter the bounding boxes by the sides
filtered_boxes = all_boxes.filter("sides", np.greater_equal, (35, 35))
# Get the IoU matrix of all the bounding boxes
iou = filtered_boxes.iou_matrix()
# Save the overlapping pairs to
filtered_boxes.save_overlapping_pairs("path/to/save/overlapping_pairs.csv")
# Save the IOU matrix to a csv file
filtered_boxes.save_iou_matrix("path/to/save/iou_matrix.csv")
# Plot the bounding boxes on the mask image
filtered_boxes.draw(to="image", method="matplotlib", show="False", save="path/to/save/image.png")
# Save your bounding boxes
filtered_boxes.save_csv("path/to/bounding_boxes.csv")
# Get resize factors to resize the bounding boxes to a given size
resize_factors = filtered_boxes.de(desired_ratio=0.7, size=(256, 256))
# Extract the bounding boxes as images
filtered_boxes.extract(resize_factors, size=(256, 256), output="path/to/save/images")
```
## Version Notes
### 0.0.15 - Update
- Update:
- Add new entry points to the package to allow for improved CLI usage. New CLI usage is:`python isolate-cells -h`.
- Add:
- Add `mask2bbox/scripts` folder.
### 0.0.14 - Update
- Update:
- Remove LICENSE
- Rename `BBoxes.save_iou()` to `BBoxes.save_overlapping_pairs()` in the CLI.
- Convert `BBoxes._helper_box_drawer()` to static method.
- Add:
- Add logger to the package.
- Add `BBoxes.sample()` to get a random sample of the bounding boxes.
- Add `BBoxes.save_iou_matrix()` to save the IoU matrix to a csv file.
- Add `-os` to the CLI to save a sample of the isolated nuclei instead of the whole set.
- Add `-log` to speciy the log level in the CLI (Options are: info and debug).
### 0.0.13 - Update
- Update:
- Change setup.py to pyproject.toml.
- Add:
- Added entry points to the package to allow for CLI usage.
- Added dynamic versioning to the package `version.py` also accessible from the CLI `python -m mask2bbox -v`.
### 0.0.12 - Update
- Update:
- `BBoxes.from_mask()` now accepts an image parameter as an additional input, this removes the need of having to load the image separately.
- `__getitem__` magic attribute indexes based on the cell/mask id (making it base 1 instead of base 0).
- Replaced `BBoxes.extract_single()` and `BBoxes.grab()` -> with `BBoxes.grab_pixels_from()`
- `BBoxes.grab_pixels_from()` gets the pixels from the image/mask that are inside the bounding boxes.
- `BBoxes.grab_pixels_from()` makes optional the processing steps implemented in `BBoxes.extract()`.
### 0.0.11 - Added functionality
- Added `BBoxes.grab()`
- Replaced `plot_to_mask()` and `BBoxes.plot_to_image()` -> with `BBoxes.draw()`
- `BBoxes.draw()` allows to plot the bounding boxes on the mask or the image.
- `BBoxes.draw()` allows to choose between `matplotlib` and `numpy` to generate the plot.
- Modified `BBoxes.extract_single()`
- `BBoxes.extract_single()` adds pre-processing steps such as `BBoxes.extract()`
### 0.0.10 - Added functionality
- Added `extract_single()`: This method allows to extract a single bounding box form the image/mask.
- Added check to `BBoxes.from_mask()`: Now the method checks if the mask contains any element or not and raises an error if it doesn't.
### 0.0.9 - Fix bug in `BBoxes.extract()`
- Fix bug in `BBoxes.extract()` that caused the images to be saved with the wrong name amd created a new folder.
### 0.0.8 - Change methods, change constructor, added functionality.
- **Constructor:** BBox object is now constructed with the syntax `BBoxes.from_mask(mask)` instead of `BBoxes(mask)`.
- **Operations:** BBox object operations are no longer performed in place, the affected methods are:
- `BBoxes.remove_from_edge()`
- `BBoxes.expand()`
- `BBoxes.filter()`
- **Removed methods:**
- `is_area_smaller_than()`
- `is_area_larger_than()`
- `are_dims_smaller_than()`
- `are_dims_larger_than()`
- `filter_identities()`
These methods used in-place operations and are no longer needed, they were substituted with.
- **Renamed:**
- `BBoxes.get_bbox_areas()` -> `BBoxes.get_areas()`
- `BBoxes.get_bbox_dims()` -> `BBoxes.get_sizes()`
- `BBoxes.get_bbox_centers()` -> `BBoxes.get_centers()`
- `BBoxes.get_bbox_ratios()` -> `BBoxes.get_ratios()`
- **New methods:**
- `BBoxes.filter():` This method allows to filter the bounding boxes by any of the attributes in the object specifying the comparison operator and threshold value. It returns a new BBoxes object with the filtered values.
- `BBoxes.get():` This method allows to get the values of the attributes in the object. It works as a simplification to `BBoxes.get_areas()`, `BBoxes.get_centers()`, `BBoxes.get_sizes()` and `BBoxes.get_ratios()`.
- `BBoxes.extract():` This new method isolates the bounding boxes as images and saves them to the desired location.
- `BBoxes.calculate_resizing_factor():` This method calculates the resizing factor needed to resize the bounding boxes to a given size.
- `BBoxes._pad_crop():` Helper method to pad or crop the bounding boxes to a desired output size.
- `BBoxes.plot_to_image():` This method plots the bounding boxes to the corresponding image and saves it to the desired location.
### 0.0.7 - Improved functionality
Improvements in IoU calculation
### 0.0.6 - Added functionality
### 0.0.5 - Added functionality
- IoU related operations:
- `boxes.get_iou_matrix()` - Gets the IoU of all the bounding boxes.
- `boxes.are_overlaping()` - Returns identities where the IoU is greater than 0
- `boxes.overlaping_pais()` - Returns the pairs of bounding boxes that are overlaping.
- `boxes.save_iou()` - Saves the IoU matrix to a csv file.
- Plots
- `boxes.plot_to_mask()` Plots the bounding boxes on the mask image.
Example of `boxes.plot_to_mask()`
### 0.0.4 - Added functionality
Now is possible to extract:
- Bounding boxes dimensions `BBoxes.get_bbox_dims()`
- Bounding boxes area `BBoxes.get_bbox_areas()`
- Bounding boxes center `BBoxes.get_bbox_centers()`
- Bounding boxes ratios `BBoxes.get_bbox_ratios()`
### 0.0.3 - Added functionality
Added the remove_edge_boxes method to remove the bounding boxes that are located on the edge of the image.
### 0.0.2 - Added the expand method to expand the bounding boxes by a given number of pixels.
Added the expand method to expand the bounding boxes by a given number of pixels.
Fixed a bug in the setup.py file that made it hard to import the package.
### 0.0.1 - Initial release of the package.
Initial release of the package. It allows to get the bounding boxes of a mask and save them to a csv file.
Raw data
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"description": "# mask2bbox\n[](https://pypi.org/project/mask2bbox/)\n\nFor a given mask, gets the coordinates of bounding box of each element of the mask. It will also allow for more operations in the future.\n\n## Instalation\n\n```bash\npip install mask2bbox\n```\n\n## CLI\n\n```bash\npython isolate-cells -h\n```\n\n## Usage\n\n```python\nimport numpy as np\nfrom mask2bbox import BBoxes\n\n# Create a BBoxes object\nall_boxes = BBoxes.from_mask(\"path/to/mask.png\")\n\n# Expand the bounding boxes\nall_boxes = all_boxes.expand(n=10)\n\n# Remove the bounding boxes that are located on the edge of the image\nall_boxes = all_boxes.remove_from_edge()\n\n# Get the sides of all the bounding boxes\nsides = all_boxes.get(\"sides\")\n\n# Filter the bounding boxes by the sides\nfiltered_boxes = all_boxes.filter(\"sides\", np.greater_equal, (35, 35))\n\n# Get the IoU matrix of all the bounding boxes\niou = filtered_boxes.iou_matrix()\n\n# Save the overlapping pairs to\nfiltered_boxes.save_overlapping_pairs(\"path/to/save/overlapping_pairs.csv\")\n\n# Save the IOU matrix to a csv file\nfiltered_boxes.save_iou_matrix(\"path/to/save/iou_matrix.csv\") \n\n# Plot the bounding boxes on the mask image\nfiltered_boxes.draw(to=\"image\", method=\"matplotlib\", show=\"False\", save=\"path/to/save/image.png\")\n\n# Save your bounding boxes\nfiltered_boxes.save_csv(\"path/to/bounding_boxes.csv\")\n\n# Get resize factors to resize the bounding boxes to a given size\nresize_factors = filtered_boxes.de(desired_ratio=0.7, size=(256, 256))\n\n# Extract the bounding boxes as images\nfiltered_boxes.extract(resize_factors, size=(256, 256), output=\"path/to/save/images\")\n```\n\n## Version Notes\n\n### 0.0.15 - Update\n- Update:\n - Add new entry points to the package to allow for improved CLI usage. New CLI usage is:`python isolate-cells -h`.\n- Add:\n - Add `mask2bbox/scripts` folder.\n\n### 0.0.14 - Update\n- Update:\n - Remove LICENSE\n - Rename `BBoxes.save_iou()` to `BBoxes.save_overlapping_pairs()` in the CLI.\n - Convert `BBoxes._helper_box_drawer()` to static method.\n- Add:\n - Add logger to the package.\n - Add `BBoxes.sample()` to get a random sample of the bounding boxes.\n - Add `BBoxes.save_iou_matrix()` to save the IoU matrix to a csv file.\n - Add `-os` to the CLI to save a sample of the isolated nuclei instead of the whole set.\n - Add `-log` to speciy the log level in the CLI (Options are: info and debug).\n\n### 0.0.13 - Update\n- Update:\n - Change setup.py to pyproject.toml.\n- Add:\n - Added entry points to the package to allow for CLI usage.\n - Added dynamic versioning to the package `version.py` also accessible from the CLI `python -m mask2bbox -v`.\n\n### 0.0.12 - Update\n- Update:\n - `BBoxes.from_mask()` now accepts an image parameter as an additional input, this removes the need of having to load the image separately.\n - `__getitem__` magic attribute indexes based on the cell/mask id (making it base 1 instead of base 0).\n- Replaced `BBoxes.extract_single()` and `BBoxes.grab()` -> with `BBoxes.grab_pixels_from()`\n - `BBoxes.grab_pixels_from()` gets the pixels from the image/mask that are inside the bounding boxes.\n - `BBoxes.grab_pixels_from()` makes optional the processing steps implemented in `BBoxes.extract()`.\n\n### 0.0.11 - Added functionality\n- Added `BBoxes.grab()`\n- Replaced `plot_to_mask()` and `BBoxes.plot_to_image()` -> with `BBoxes.draw()` \n - `BBoxes.draw()` allows to plot the bounding boxes on the mask or the image.\n - `BBoxes.draw()` allows to choose between `matplotlib` and `numpy` to generate the plot.\n- Modified `BBoxes.extract_single()`\n - `BBoxes.extract_single()` adds pre-processing steps such as `BBoxes.extract()`\n\n### 0.0.10 - Added functionality\n- Added `extract_single()`: This method allows to extract a single bounding box form the image/mask.\n- Added check to `BBoxes.from_mask()`: Now the method checks if the mask contains any element or not and raises an error if it doesn't.\n\n### 0.0.9 - Fix bug in `BBoxes.extract()`\n- Fix bug in `BBoxes.extract()` that caused the images to be saved with the wrong name amd created a new folder.\n\n### 0.0.8 - Change methods, change constructor, added functionality. \n- **Constructor:** BBox object is now constructed with the syntax `BBoxes.from_mask(mask)` instead of `BBoxes(mask)`.\n- **Operations:** BBox object operations are no longer performed in place, the affected methods are:\n - `BBoxes.remove_from_edge()`\n - `BBoxes.expand()`\n - `BBoxes.filter()`\n\n- **Removed methods:**\n - `is_area_smaller_than()`\n - `is_area_larger_than()`\n - `are_dims_smaller_than()`\n - `are_dims_larger_than()`\n - `filter_identities()` \n\nThese methods used in-place operations and are no longer needed, they were substituted with. \n- **Renamed:**\n - `BBoxes.get_bbox_areas()` -> `BBoxes.get_areas()`\n - `BBoxes.get_bbox_dims()` -> `BBoxes.get_sizes()`\n - `BBoxes.get_bbox_centers()` -> `BBoxes.get_centers()`\n - `BBoxes.get_bbox_ratios()` -> `BBoxes.get_ratios()`\n \n- **New methods:**\n - `BBoxes.filter():` This method allows to filter the bounding boxes by any of the attributes in the object specifying the comparison operator and threshold value. It returns a new BBoxes object with the filtered values.\n - `BBoxes.get():` This method allows to get the values of the attributes in the object. It works as a simplification to `BBoxes.get_areas()`, `BBoxes.get_centers()`, `BBoxes.get_sizes()` and `BBoxes.get_ratios()`.\n - `BBoxes.extract():` This new method isolates the bounding boxes as images and saves them to the desired location.\n - `BBoxes.calculate_resizing_factor():` This method calculates the resizing factor needed to resize the bounding boxes to a given size.\n - `BBoxes._pad_crop():` Helper method to pad or crop the bounding boxes to a desired output size.\n - `BBoxes.plot_to_image():` This method plots the bounding boxes to the corresponding image and saves it to the desired location.\n\n\n### 0.0.7 - Improved functionality\nImprovements in IoU calculation\n\n### 0.0.6 - Added functionality\n\n### 0.0.5 - Added functionality\n\n- IoU related operations:\n - `boxes.get_iou_matrix()` - Gets the IoU of all the bounding boxes.\n - `boxes.are_overlaping()` - Returns identities where the IoU is greater than 0\n - `boxes.overlaping_pais()` - Returns the pairs of bounding boxes that are overlaping.\n - `boxes.save_iou()` - Saves the IoU matrix to a csv file.\n\n- Plots\n - `boxes.plot_to_mask()` Plots the bounding boxes on the mask image.\n\nExample of `boxes.plot_to_mask()`\n\n\n### 0.0.4 - Added functionality\nNow is possible to extract:\n- Bounding boxes dimensions `BBoxes.get_bbox_dims()`\n- Bounding boxes area `BBoxes.get_bbox_areas()`\n- Bounding boxes center `BBoxes.get_bbox_centers()`\n- Bounding boxes ratios `BBoxes.get_bbox_ratios()`\n\n### 0.0.3 - Added functionality \nAdded the remove_edge_boxes method to remove the bounding boxes that are located on the edge of the image.\n\n### 0.0.2 - Added the expand method to expand the bounding boxes by a given number of pixels.\nAdded the expand method to expand the bounding boxes by a given number of pixels. \nFixed a bug in the setup.py file that made it hard to import the package.\n\n### 0.0.1 - Initial release of the package.\nInitial release of the package. 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