ground truth filters based on IOU (#18)

* The coords are `int` now.

* Added `get_gt_max_thresh` to generate ground truth boxes and extra ground truth boxes with thresholding IOUs

* Added `get_gt_max_iou` to generate ground truth boxes and extra ground truth boxes from largest IOUs

* update unittests and workflow

* run export and build

* update README.md

* Create python-publish.yml

.github/workflows/python-publish.yml

@@ -0,0 +1,44 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --upgrade build
+    - name: Get version
+      run: |
+        export PYBX_VERSION=$(cat settings.ini| grep "version =" | cut -d' ' -f3)
+        echo "setting PYBX_VERSION = $PYBX_VERSION"
+        echo "$(ls dist/*$PYBX_VERSION*)$"
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pytests.yml → .github/workflows/unittests.yml

@@ -18,10 +18,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v3
         with:
-          python-version: "3.7"
+          python-version: "3.8"
       - name: Install pip
         run: |
           python -m pip install --upgrade pip
@@ -40,6 +40,7 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Test with pytest
+      - name: Test with unittests
         run: |
-          pytest .
+          # pytest .
+          python -m unittest tests/test_*.py

.gitignore

@@ -133,3 +133,9 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# kdev
+*.kdev4
+*.kdev4/
+changes
+

.pre-commit-config.yaml

@@ -3,4 +3,4 @@ repos:
   rev: 2.3.7
   hooks:
   - id: nbdev_clean
-  - id: nbdev_export
+  - id: nbdev_export 

Pipfile

@@ -22,4 +22,4 @@ black = "*"
 pybx = {editable = true, path = "."}
 
 [requires]
-python_version = "3.7"
+python_version = "3.8"

README.md

@@ -1,16 +1,18 @@
+Use ground truth boxes for model training
+================
+
+<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
 [![PyPI
 version](https://badge.fury.io/py/pybx.svg)](https://badge.fury.io/py/pybx)
 [![Open In
-Collab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/thatgeeman/pybx/blob/master/nbs/pybx_walkthrough.ipynb)
+Collab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/thatgeeman/pybx/blob/master/examples/pybx_walkthrough_0.4.ipynb)
 
 A simple python package to generate anchor boxes for multi-box object
 detection models.
 
 Calculated anchor boxes are in `pascal_voc` format by default.
 
-<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
-
 ### Installation
 
 ``` shell
@@ -25,7 +27,7 @@ ratio, given the image size:
 ``` python
 from pybx import anchor, ops
 
-image_sz = (300, 300)
+image_sz = (256, 256)
 feature_sz = (10, 10)
 asp_ratio = 1/2.
 
@@ -48,8 +50,7 @@ descriptive:
 coords[-1], labels[-1]
 ```
 
-    ([274.3933982822018, 263.7867965644036, 295.6066017177982, 300.0],
-     'a_10x10_0.5_99')
+    ([234, 225, 252, 256], 'a_10x10_0.5_99')
 
 To calculate anchor boxes for **multiple** feature sizes and aspect
 ratios, we use `anchor.bxs` instead:
@@ -71,14 +72,13 @@ identify to which feature map size or aspect ratios they belong to.
 coords[101], labels[101]
 ```
 
-    (array([34.39339828,  0.        , 55.60660172, 36.21320344]), 'a_10x10_0.5_1')
+    (array([29,  0, 47, 30]), 'a_10x10_0.5_1')
 
 ``` python
 coords[-1], labels[-1]
 ```
 
-    (array([254.73349571, 267.99174785, 300.        , 294.50825215]),
-     'a_8x8_2.0_63')
+    (array([217, 228, 256, 251]), 'a_8x8_2.0_63')
 
 #### [`MultiBx`](https://thatgeeman.github.io/pybx/basics.html#multibx) methods
 
@@ -122,14 +122,13 @@ its own set of methods and properties.
 boxes[-1]
 ```
 
-    BaseBx(coords=[[254.73349570550448, 267.9917478527522, 300.0, 294.5082521472478]], label=['a_8x8_2.0_63'])
+    BaseBx(coords=[[217, 228, 256, 251]], label=['a_8x8_2.0_63'])
 
 ``` python
 boxes[-1].coords, boxes[-1].label
 ```
 
-    ((#1) [[254.73349570550448, 267.9917478527522, 300.0, 294.5082521472478]],
-     (#1) ['a_8x8_2.0_63'])
+    ([[217, 228, 256, 251]], (#1) ['a_8x8_2.0_63'])
 
 [`MultiBx`](https://thatgeeman.github.io/pybx/basics.html#multibx)
 objects can also be “added” which stacks them vertically to create a new
@@ -154,7 +153,7 @@ len(boxes_anchor)
 boxes_true
 ```
 
-    MultiBx(coords=[[150, 70, 270, 220], [10, 180, 115, 260]], label=['clock', 'frame'])
+    MultiBx(coords=[[130, 63, 225, 180], [13, 158, 90, 213]], label=['clock', 'frame'])
 
 ``` python
 boxes = boxes_true + boxes_anchor + boxes_true
@@ -165,3 +164,79 @@ len(boxes)
 ```
 
     496
+
+``` python
+from pybx.anchor import get_gt_thresh_iou, get_gt_max_iou
+from pybx.vis import VisBx
+```
+
+``` python
+image_sz
+```
+
+    (256, 256)
+
+``` python
+boxes_true
+```
+
+    MultiBx(coords=[[130, 63, 225, 180], [13, 158, 90, 213]], label=['clock', 'frame'])
+
+Calculate candidate anchor boxes for many aspect ratios and scales.
+
+``` python
+feature_szs = [(10, 10), (3, 3), (2, 2)]
+asp_ratios = [0.3, 1/2., 2.]
+
+anchors, labels = anchor.bxs(image_sz, feature_szs, asp_ratios)
+```
+
+Wrap using pybx methods. This step is not necessary but convenient.
+
+``` python
+boxes_anchor = get_bx(anchors, labels) 
+len(boxes_anchor)
+```
+
+    341
+
+The following function returns two positive ground truth anchors with
+largest IOU for each class in the label bounding boxes passed.
+
+``` python
+gt_anchors, gt_ious, gt_masks = get_gt_max_iou( 
+    true_annots=boxes_true, 
+    anchor_boxes=boxes_anchor,  # if plain numpy, pass anchor_boxes and anchor_labels 
+    update_labels=False,  # whether to replace ground truth labels with true labels
+    positive_boxes=1,  # can request extra boxes 
+)
+```
+
+``` python
+gt_anchors
+```
+
+    {'clock': BaseBx(coords=[[156, 0, 227, 180]], label=['a_2x2_0.3_1']),
+     'frame': BaseBx(coords=[[12, 152, 72, 256]], label=['a_3x3_0.5_6'])}
+
+``` python
+all_gt_anchors = gt_anchors['clock'] + gt_anchors['frame']
+all_gt_anchors
+```
+
+    /mnt/data/projects/pybx/pybx/basics.py:464: BxViolation: Change of object type imminent if trying to add <class 'pybx.basics.BaseBx'>+<class 'pybx.basics.BaseBx'>. Use <class 'pybx.basics.BaseBx'>+<class 'pybx.basics.BaseBx'> instead or basics.stack_bxs().
+      f"Change of object type imminent if trying to add "
+
+    MultiBx(coords=[[156, 0, 227, 180], [12, 152, 72, 256]], label=['a_2x2_0.3_1', 'a_3x3_0.5_6'])
+
+``` python
+v = VisBx(pth='../data/', img_fn='image.jpg', image_sz=image_sz)
+v.show(all_gt_anchors, color={'a_2x2_0.3_1':'red', 'a_3x3_0.5_6': 'red'})
+```
+
+    <AxesSubplot:>
+
+![](index_files/figure-commonmark/cell-26-output-2.png)
+
+More exploratory stuff in the [walkthrough
+notebook](../examples/pybx_walkthrough_0.4.ipynb)!