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Apr 8, 2025
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Version 0.0.21 #248

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9 changes: 9 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,14 @@
# Change Log

## Changes in version 0.0.21

### Fixes:

* [116](https://github.com/pymupdf/RAG/issues/116) - Handling Graphical Images & Superscripts

### Other Changes:


## Changes in version 0.0.20

### Fixes:
Expand Down
2 changes: 1 addition & 1 deletion pymupdf4llm/pymupdf4llm/__init__.py
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@@ -1,6 +1,6 @@
from .helpers.pymupdf_rag import IdentifyHeaders, to_markdown

__version__ = "0.0.20"
__version__ = "0.0.21"
version = __version__
version_tuple = tuple(map(int, version.split(".")))

Expand Down
18 changes: 9 additions & 9 deletions pymupdf4llm/pymupdf4llm/helpers/multi_column.py
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Expand Up @@ -64,7 +64,7 @@

import pymupdf

pymupdf.TOOLS.set_small_glyph_heights(True)
pymupdf.TOOLS.unset_quad_corrections(True)


def column_boxes(
Expand Down Expand Up @@ -237,7 +237,7 @@ def join_rects_phase2(bboxes):
if (
abs(r.x0 - r0.x0) <= 3
and abs(r.x1 - r0.x1) <= 3
and abs(r0.y1 - r.y0) <= 12
and abs(r0.y1 - r.y0) <= 10
):
r0 |= r
new_rects[-1] = r0
Expand Down Expand Up @@ -344,7 +344,7 @@ def join_rects_phase3(bboxes, path_rects, cache):
]

if textpage is None:
textpage = page.get_textpage(clip=clip, flags=pymupdf.TEXTFLAGS_TEXT)
textpage = page.get_textpage(clip=clip, flags=pymupdf.TEXT_ACCURATE_BBOXES)

bboxes = []

Expand Down Expand Up @@ -417,7 +417,6 @@ def join_rects_phase3(bboxes, path_rects, cache):
# immediately return of no text found
if bboxes == []:
return []

# --------------------------------------------------------------------
# Join bboxes to establish some column structure
# --------------------------------------------------------------------
Expand Down Expand Up @@ -467,7 +466,8 @@ def join_rects_phase3(bboxes, path_rects, cache):
return nblocks

# several phases of rectangle joining
nblocks = join_rects_phase1(nblocks)
# TODO: disabled for now as too aggressive:
# nblocks = join_rects_phase1(nblocks)
nblocks = join_rects_phase2(nblocks)
nblocks = join_rects_phase3(nblocks, path_rects, cache)

Expand All @@ -491,14 +491,14 @@ def join_rects_phase3(bboxes, path_rects, cache):
# check if footer margin is given
if len(sys.argv) > 2:
footer_margin = int(sys.argv[2])
else: # use default vaue
footer_margin = 50
else:
footer_margin = 0

# check if header margin is given
if len(sys.argv) > 3:
header_margin = int(sys.argv[3])
else: # use default vaue
header_margin = 50
else:
header_margin = 0

# open document
doc = pymupdf.open(filename)
Expand Down
103 changes: 57 additions & 46 deletions pymupdf4llm/pymupdf4llm/helpers/pymupdf_rag.py
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Expand Up @@ -157,6 +157,8 @@ def get_header_id(self, span: dict, page=None) -> str:
markdown header prefix string of 0 to n concatenated '#' characters.
"""
fontsize = round(span["size"]) # compute fontsize
if fontsize <= self.body_limit:
return ""
hdr_id = self.header_id.get(fontsize, "")
return hdr_id

Expand Down Expand Up @@ -278,7 +280,7 @@ def to_markdown(
ignore_code: (bool) suppress code-like formatting (mono-space fonts)
extract_words: (bool) include "words"-like output in page chunks
show_progress: (bool) print progress as each page is processed.
glyph_fallback: (bool) replace the Invalid Unicode by glyph number.
use_glyphs: (bool) replace the Invalid Unicode by glyph numbers.

"""
if write_images is False and embed_images is False and force_text is False:
Expand Down Expand Up @@ -427,8 +429,8 @@ def write_text(
if clip is None:
clip = parms.clip
out_string = ""
# This is a list of tuples (linerect, spanlist)

# This is a list of tuples (linerect, spanlist)
nlines = get_raw_lines(parms.textpage, clip=clip, tolerance=3)
nlines = [
l for l in nlines if not intersects_rects(l[0], parms.tab_rects.values())
Expand All @@ -450,21 +452,18 @@ def write_text(
# Pick up tables ABOVE this text block
# ------------------------------------------------------------
if tables:
tab_candidates = sorted(
[
(i, tab_rect)
for i, tab_rect in parms.tab_rects.items()
if tab_rect.y1 <= lrect.y0
and i not in parms.deleted_tables
and (
0
or lrect.x0 <= tab_rect.x0 < lrect.x1
or lrect.x0 < tab_rect.x1 <= lrect.x1
or tab_rect.x0 <= lrect.x0 < lrect.x1 <= tab_rect.x1
)
],
key=lambda j: (j[1].y1, j[1].x0),
)
tab_candidates = [
(i, tab_rect)
for i, tab_rect in parms.tab_rects.items()
if tab_rect.y1 <= lrect.y0
and i not in parms.written_tables
and (
0
or lrect.x0 <= tab_rect.x0 < lrect.x1
or lrect.x0 < tab_rect.x1 <= lrect.x1
or tab_rect.x0 <= lrect.x0 < lrect.x1 <= tab_rect.x1
)
]
for i, _ in tab_candidates:
out_string += "\n" + parms.tabs[i].to_markdown(clean=False) + "\n"
if EXTRACT_WORDS:
Expand All @@ -481,14 +480,14 @@ def write_text(
key=lambda c: (c.y1, c.x0),
)
parms.line_rects.extend(cells)
parms.deleted_tables.append(i)
parms.written_tables.append(i)

# ------------------------------------------------------------
# Pick up images / graphics ABOVE this text block
# ------------------------------------------------------------
if images:
for i in range(len(parms.img_rects)):
if i in parms.deleted_images:
if i in parms.written_images:
continue
r = parms.img_rects[i]
if r.y1 <= lrect.y0 and (
Expand All @@ -502,7 +501,7 @@ def write_text(
out_string += GRAPHICS_TEXT % pathname

# recursive invocation
if force_text:
if force_text is True:
img_txt = write_text(
parms,
r,
Expand All @@ -513,7 +512,7 @@ def write_text(

if not is_white(img_txt):
out_string += img_txt
parms.deleted_images.append(i)
parms.written_images.append(i)

parms.line_rects.append(lrect)

Expand Down Expand Up @@ -668,7 +667,7 @@ def output_tables(parms, text_rect):
[j for j in parms.tab_rects.items() if j[1].y1 <= text_rect.y0],
key=lambda j: (j[1].y1, j[1].x0),
):
if i in parms.deleted_tables:
if i in parms.written_tables:
continue
this_md += parms.tabs[i].to_markdown(clean=False)
if EXTRACT_WORDS:
Expand All @@ -685,14 +684,11 @@ def output_tables(parms, text_rect):
key=lambda c: (c.y1, c.x0),
)
parms.line_rects.extend(cells)
del parms.tab_rects[i] # do not touch this table twice
parms.written_tables.append(i) # do not touch this table twice

else: # output all remaining tables
for i, trect in sorted(
parms.tab_rects.items(),
key=lambda j: (j[1].y1, j[1].x0),
):
if i in parms.deleted_tables:
for i, trect in parms.tab_rects.items():
if i in parms.written_tables:
continue
this_md += parms.tabs[i].to_markdown(clean=False)
if EXTRACT_WORDS:
Expand All @@ -709,10 +705,10 @@ def output_tables(parms, text_rect):
key=lambda c: (c.y1, c.x0),
)
parms.line_rects.extend(cells)
del parms.tab_rects[i] # do not touch this table twice
parms.written_tables.append(i) # do not touch this table twice
return this_md

def output_images(parms, text_rect):
def output_images(parms, text_rect, force_text):
"""Output images and graphics above text rectangle."""
if not parms.img_rects:
return ""
Expand All @@ -723,10 +719,10 @@ def output_images(parms, text_rect):
continue
if img_rect.x0 >= text_rect.x1 or img_rect.x1 <= text_rect.x0:
continue
if i in parms.deleted_images:
if i in parms.written_images:
continue
pathname = save_image(parms, img_rect, i)
parms.deleted_images.append(i) # do not touch this image twice
parms.written_images.append(i) # do not touch this image twice
if pathname:
this_md += GRAPHICS_TEXT % pathname
if force_text:
Expand All @@ -741,10 +737,10 @@ def output_images(parms, text_rect):
this_md += img_txt
else: # output all remaining images
for i, img_rect in enumerate(parms.img_rects):
if i in parms.deleted_images:
if i in parms.written_images:
continue
pathname = save_image(parms, img_rect, i)
parms.deleted_images.append(i) # do not touch this image twice
parms.written_images.append(i) # do not touch this image twice
if pathname:
this_md += GRAPHICS_TEXT % pathname
if force_text:
Expand Down Expand Up @@ -867,6 +863,9 @@ def get_page_output(
# extract external links on page
parms.links = [l for l in page.get_links() if l["kind"] == pymupdf.LINK_URI]

# extract annotation rectangles on page
parms.annot_rects = [a.rect for a in page.annots()]

# make a TextPage for all later extractions
parms.textpage = page.get_textpage(flags=textflags, clip=parms.clip)

Expand Down Expand Up @@ -904,10 +903,20 @@ def get_page_output(
parms.img_rects = [i["bbox"] for i in parms.images]

# Locate all tables on page
parms.written_tables = [] # stores already written tables
if table_strategy is None:
parms.tabs = []
else:
parms.tabs = page.find_tables(clip=parms.clip, strategy=table_strategy)
del_this = []
for i, t in enumerate(parms.tabs):
if t.row_count < 2 or t.col_count < 2:
# ignore tables with too few rows or columns
del_this.append(i)
for i in sorted(del_this, reverse=True):
del parms.tabs.tables[i]
parms.tabs.tables.sort(key=lambda t: (t.bbox[0], t.bbox[1]))

# Make a list of table boundary boxes.
# Must include the header bbox (which may exist outside tab.bbox)
tab_rects = {}
Expand All @@ -930,11 +939,13 @@ def get_page_output(
paths = [
p
for p in page.get_drawings()
if not intersects_rects(p["rect"], parms.tab_rects0)
and p["rect"] in parms.clip
and 3 < p["rect"].width < parms.clip.width
and 3 < p["rect"].height < parms.clip.height
and not (p["type"] == "f" and p["fill"] == parms.bg_color)
if p["rect"] in parms.clip
and p["rect"].width < parms.clip.width
and p["rect"].height < parms.clip.height
and (p["rect"].width > 3 or p["rect"].height > 3)
and not (p["fill"] == parms.bg_color and p["fill"] != None)
and not intersects_rects(p["rect"], parms.tab_rects0)
and not intersects_rects(p["rect"], parms.annot_rects)
]
else:
paths = []
Expand All @@ -948,19 +959,19 @@ def get_page_output(
vg_clusters0 = [] # worthwhile vector graphics go here

# walk through all vector graphics outside any table
for bbox in refine_boxes(page.cluster_drawings(drawings=paths)):
clusters = page.cluster_drawings(drawings=paths)
for bbox in clusters:
if is_significant(bbox, paths):
vg_clusters0.append(bbox)

# remove paths that are not in some relevant graphic
parms.actual_paths = [p for p in paths if is_in_rects(p["rect"], vg_clusters0)]

# also add image rectangles to the list
# also add image rectangles to the list and vice versa
vg_clusters0.extend(parms.img_rects)
parms.img_rects.extend(vg_clusters0)
parms.img_rects = sorted(set(parms.img_rects), key=lambda r: (r.y1, r.x0))
parms.deleted_images = []
parms.deleted_tables = []
parms.written_images = []
# these may no longer be pairwise disjoint:
# remove area overlaps by joining into larger rects
parms.vg_clusters0 = refine_boxes(vg_clusters0)
Expand Down Expand Up @@ -989,7 +1000,7 @@ def get_page_output(
for text_rect in text_rects:
# output tables above this rectangle
parms.md_string += output_tables(parms, text_rect)
parms.md_string += output_images(parms, text_rect)
parms.md_string += output_images(parms, text_rect, force_text)

# output text inside this rectangle
parms.md_string += write_text(
Expand All @@ -1004,7 +1015,7 @@ def get_page_output(

# write any remaining tables and images
parms.md_string += output_tables(parms, None)
parms.md_string += output_images(parms, None)
parms.md_string += output_images(parms, None, force_text)

parms.md_string += "\n-----\n\n"
while parms.md_string.startswith("\n"):
Expand Down Expand Up @@ -1153,7 +1164,7 @@ def extract_images_on_page_simple_drop(page, parms, image_size_limit):
import time

try:
filename = "slide12.pdf"
filename = "sample_document.pdf"
except IndexError:
print(f"Usage:\npython {os.path.basename(__file__)} input.pdf")
sys.exit()
Expand Down
2 changes: 1 addition & 1 deletion pymupdf4llm/setup.py
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Expand Up @@ -17,7 +17,7 @@

setuptools.setup(
name="pymupdf4llm",
version="0.0.20",
version="0.0.21",
author="Artifex",
author_email="support@artifex.com",
description="PyMuPDF Utilities for LLM/RAG",
Expand Down