Feat/improve iou speed (#3582)

This PR vectorizes the computation of element overlap to speed up
deduplication process of extracted elements.

## test

This PR adds unit test to the new vectorized IOU and subregion
computation functions.

In addition, running partition on large files with many elements like
this slide:

[002489.pdf](https://github.com/user-attachments/files/16823176/002489.pdf)

shows a reduction of runtime from around 15min on the main branch to
less than 4min with this branch.

Profiling results show that the new implementation greatly reduces the
time cost of computation and now most of the time is spend on getting
the coordinates from a list of bboxes.

![Screenshot 2024-08-30 at 9 29
27 PM](https://github.com/user-attachments/assets/6c186838-54c7-483b-ac3e-7342c23ff3a6)

Author: badGarnet

CHANGELOG.md

@@ -1,7 +1,9 @@
-## 0.15.10-dev1
+## 0.15.10-dev2
 
 ### Enhancements
+
 * **Modified analysis drawing tools to dump to files and draw from dumps** If the parameter `analysis` of the `partition_pdf` function is set to `True`, the layout for Object Detection, Pdfminer Extraction, OCR and final layouts will be dumped as json files. The drawers now accept dict (dump) objects instead of internal classes instances.
+* **Vectorize pdfminer elements deduplication computation**. Use `numpy` operations to compute IOU and sub-region membership instead of using simply loop. This improves the speed of deduplicating elements for pages with a lot of elements.
 
 ### Features
 

test_unstructured/partition/pdf_image/test_pdfminer_processing.py

@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 from PIL import Image
 from unstructured_inference.constants import Source as InferenceSource
@@ -6,6 +7,8 @@
 
 from unstructured.partition.pdf_image.pdfminer_processing import (
     aggregate_embedded_text_by_block,
+    bboxes1_is_almost_subregion_of_bboxes2,
+    boxes_self_iou,
     clean_pdfminer_duplicate_image_elements,
     clean_pdfminer_inner_elements,
 )
@@ -153,3 +156,56 @@ def test_aggregate_by_block():
 
     text = aggregate_embedded_text_by_block(target_region, embedded_regions)
     assert text == expected
+
+
+@pytest.mark.parametrize(
+    ("coords1", "coords2", "expected"),
+    [
+        (
+            [[0, 0, 10, 10], [10, 0, 20, 10], [10, 10, 20, 20]],
+            [[0, 0, 10, 10], [0, 0, 12, 12]],
+            [[True, True], [False, False], [False, False]],
+        ),
+        (
+            [[0, 0, 10, 10], [10, 0, 20, 10], [10, 10, 20, 20]],
+            [[0, 0, 10, 10], [10, 10, 22, 22], [0, 0, 5, 5]],
+            [[True, False, False], [False, False, False], [False, True, False]],
+        ),
+        (
+            [[0, 0, 10, 10], [10, 10, 10, 10]],
+            [[0, 0, 10, 10], [10, 10, 22, 22], [0, 0, 5, 5]],
+            [[True, False, False], [True, True, False]],
+        ),
+    ],
+)
+def test_bboxes1_is_almost_subregion_of_bboxes2(coords1, coords2, expected):
+    bboxes1 = [Rectangle(*row) for row in coords1]
+    bboxes2 = [Rectangle(*row) for row in coords2]
+    np.testing.assert_array_equal(
+        bboxes1_is_almost_subregion_of_bboxes2(bboxes1, bboxes2), expected
+    )
+
+
+@pytest.mark.parametrize(
+    ("coords", "threshold", "expected"),
+    [
+        (
+            [[0, 0, 10, 10], [2, 2, 12, 12], [10, 10, 20, 20]],
+            0.5,
+            [[True, True, False], [True, True, False], [False, False, True]],
+        ),
+        (
+            [[0, 0, 10, 10], [2, 2, 12, 12], [10, 10, 20, 20]],
+            0.9,
+            [[True, False, False], [False, True, False], [False, False, True]],
+        ),
+        (
+            [[0, 0, 10, 10], [10, 10, 10, 10]],
+            0.5,
+            [[True, False], [False, True]],
+        ),
+    ],
+)
+def test_boxes_self_iou(coords, threshold, expected):
+    bboxes = [Rectangle(*row) for row in coords]
+    np.testing.assert_array_equal(boxes_self_iou(bboxes, threshold), expected)

unstructured/__version__.py

@@ -1 +1 @@
-__version__ = "0.15.10-dev1"  # pragma: no cover
+__version__ = "0.15.10-dev2"  # pragma: no cover

unstructured/partition/pdf_image/pdfminer_processing.py

@@ -1,5 +1,6 @@
 from typing import TYPE_CHECKING, BinaryIO, List, Optional, Union, cast
 
+import numpy as np
 from pdfminer.utils import open_filename
 
 from unstructured.documents.elements import ElementType
@@ -19,6 +20,9 @@
     from unstructured_inference.inference.layout import DocumentLayout
 
 
+EPSILON_AREA = 0.01
+
+
 def process_file_with_pdfminer(
     filename: str = "",
     dpi: int = 200,
@@ -96,6 +100,57 @@ def _create_text_region(x1, y1, x2, y2, coef, text, source, region_class):
     )
 
 
+def get_coords_from_bboxes(bboxes) -> np.ndarray:
+    """convert a list of boxes's coords into np array"""
+    # preallocate memory
+    coords = np.zeros((len(bboxes), 4))
+
+    for i, bbox in enumerate(bboxes):
+        coords[i, :] = [bbox.x1, bbox.y1, bbox.x2, bbox.y2]
+
+    return coords
+
+
+def areas_of_boxes_and_intersection_area(
+    coords1: np.ndarray, coords2: np.ndarray, threshold: float = 0.5
+):
+    """compute intersection area and own areas for two groups of bounding boxes"""
+    x11, y11, x12, y12 = np.split(coords1, 4, axis=1)
+    x21, y21, x22, y22 = np.split(coords2, 4, axis=1)
+
+    xa = np.maximum(x11, np.transpose(x21))
+    ya = np.maximum(y11, np.transpose(y21))
+    xb = np.minimum(x12, np.transpose(x22))
+    yb = np.minimum(y12, np.transpose(y22))
+
+    inter_area = np.maximum((xb - xa + 1), 0) * np.maximum((yb - ya + 1), 0)
+    boxa_area = (x12 - x11 + 1) * (y12 - y11 + 1)
+    boxb_area = (x22 - x21 + 1) * (y22 - y21 + 1)
+
+    return inter_area, boxa_area, boxb_area
+
+
+def bboxes1_is_almost_subregion_of_bboxes2(bboxes1, bboxes2, threshold: float = 0.5) -> np.ndarray:
+    """compute if each element from bboxes1 is almost a subregion of one or more elements in
+    bboxes2"""
+    coords1, coords2 = get_coords_from_bboxes(bboxes1), get_coords_from_bboxes(bboxes2)
+
+    inter_area, boxa_area, boxb_area = areas_of_boxes_and_intersection_area(coords1, coords2)
+
+    return (inter_area / np.maximum(boxa_area, EPSILON_AREA) > threshold) & (
+        boxa_area <= boxb_area.T
+    )
+
+
+def boxes_self_iou(bboxes, threshold: float = 0.5) -> np.ndarray:
+    """compute iou for a group of elements"""
+    coords = get_coords_from_bboxes(bboxes)
+
+    inter_area, boxa_area, boxb_area = areas_of_boxes_and_intersection_area(coords, coords)
+
+    return (inter_area / np.maximum(EPSILON_AREA, boxa_area + boxb_area.T - inter_area)) > threshold
+
+
 @requires_dependencies("unstructured_inference")
 def merge_inferred_with_extracted_layout(
     inferred_document_layout: "DocumentLayout",
@@ -168,45 +223,71 @@ def clean_pdfminer_inner_elements(document: "DocumentLayout") -> "DocumentLayout
     """
 
     for page in document.pages:
-        tables = [e for e in page.elements if e.type == ElementType.TABLE]
+        table_boxes = [e.bbox for e in page.elements if e.type == ElementType.TABLE]
+        element_boxes = []
+        element_to_subregion_map = {}
+        subregion_indice = 0
         for i, element in enumerate(page.elements):
             if element.source != Source.PDFMINER:
                 continue
-            subregion_threshold = env_config.EMBEDDED_TEXT_AGGREGATION_SUBREGION_THRESHOLD
-            element_inside_table = [
-                element.bbox.is_almost_subregion_of(t.bbox, subregion_threshold) for t in tables
-            ]
-            if sum(element_inside_table) == 1:
-                page.elements[i] = None
-        page.elements = [e for e in page.elements if e]
+            element_boxes.append(element.bbox)
+            element_to_subregion_map[i] = subregion_indice
+            subregion_indice += 1
+
+        is_element_subregion_of_tables = (
+            bboxes1_is_almost_subregion_of_bboxes2(
+                element_boxes,
+                table_boxes,
+                env_config.EMBEDDED_TEXT_AGGREGATION_SUBREGION_THRESHOLD,
+            ).sum(axis=1)
+            == 1
+        )
+
+        page.elements = [
+            e
+            for i, e in enumerate(page.elements)
+            if (
+                (i not in element_to_subregion_map)
+                or not is_element_subregion_of_tables[element_to_subregion_map[i]]
+            )
+        ]
 
     return document
 
 
 def clean_pdfminer_duplicate_image_elements(document: "DocumentLayout") -> "DocumentLayout":
     """Removes duplicate image elements extracted by PDFMiner from a document layout."""
 
-    from unstructured_inference.inference.elements import (
-        region_bounding_boxes_are_almost_the_same,
-    )
-
     for page in document.pages:
-        image_elements = []
+        image_bboxes = []
+        texts = []
+        bbox_to_iou_mapping = {}
+        current_idx = 0
         for i, element in enumerate(page.elements):
             if element.source != Source.PDFMINER or element.type != ElementType.IMAGE:
                 continue
+            image_bboxes.append(element.bbox)
+            texts.append(element.text)
+            bbox_to_iou_mapping[i] = current_idx
+            current_idx += 1
+
+        iou = boxes_self_iou(image_bboxes, env_config.EMBEDDED_IMAGE_SAME_REGION_THRESHOLD)
 
-            # check if this element is a duplicate
+        filtered_elements = []
+        for i, element in enumerate(page.elements[:-1]):
+            if element.source != Source.PDFMINER or element.type != ElementType.IMAGE:
+                filtered_elements.append(element)
+                continue
+            text = element.text
+            this_idx = bbox_to_iou_mapping[i]
             if any(
-                e.text == element.text
-                and region_bounding_boxes_are_almost_the_same(
-                    e.bbox, element.bbox, env_config.EMBEDDED_IMAGE_SAME_REGION_THRESHOLD
-                )
-                for e in image_elements
+                text == texts[potential_match + this_idx + 1]
+                for potential_match in np.where(iou[this_idx, this_idx + 1 :])[0]
             ):
-                page.elements[i] = None
-            image_elements.append(element)
-        page.elements = [e for e in page.elements if e]
+                continue
+            else:
+                filtered_elements.append(element)
+        page.elements[:-1] = filtered_elements
 
     return document
 
@@ -218,11 +299,11 @@ def aggregate_embedded_text_by_block(
     """Extracts the text aggregated from the elements of the given layout that lie within the given
     block."""
 
-    subregion_threshold = env_config.EMBEDDED_TEXT_AGGREGATION_SUBREGION_THRESHOLD
-    filtered_blocks = [
-        obj
-        for obj in pdf_objects
-        if obj.bbox.is_almost_subregion_of(text_region.bbox, subregion_threshold)
-    ]
-    text = " ".join([x.text for x in filtered_blocks if x.text])
+    mask = bboxes1_is_almost_subregion_of_bboxes2(
+        [obj.bbox for obj in pdf_objects],
+        [text_region.bbox],
+        env_config.EMBEDDED_TEXT_AGGREGATION_SUBREGION_THRESHOLD,
+    ).sum(axis=1)
+
+    text = " ".join([obj.text for i, obj in enumerate(pdf_objects) if (mask[i] and obj.text)])
     return text