set_toc does not correctly set y-positions

[chadlester]

Description of the bug

doc.set_toc does not always properly set y-positions. In my example pdf, they will be off by 90 pts.

How to reproduce the bug

buggy_toc_positions.pdf

doc = fitz.open("buggy_toc_positions.pdf")
toc = [[1, 'Engine Fire In Flight', 0, 304.6222839355469]]
doc.set_toc(toc)
read_toc = doc.get_toc(simple=False)
desired_y_position = toc[0][3]
actual_y_position = read_toc[0][3]["to"][1]
if (desired_y_position != actual_y_position):
    print ("BUG FOUND!", desired_y_position, actual_y_position)
else:
    print ("Success!")

Output:
BUG FOUND! 304.6222839355469 394.62229

PyMuPDF version

1.25.5

Operating system

MacOS

Python version

3.13

[JorjMcKie]

The problem is caused by the page's CropBox deviating from its MediaBox:

import pymupdf
doc=pymupdf.open("test.pdf")
page=doc[0]
print(doc.xref_object(page.xref))
<<
  /Type /Page
  /MediaBox [ 0 0 612 792 ]
  /Parent 2 0 R
  /Resources 4 0 R
  /CropBox [ 108 90 504 702 ]
  /Rotate 0
  /StructParents 37
  /Contents 3 0 R
>>
page.mediabox
Rect(0.0, 0.0, 612.0, 792.0)

page.cropbox
Rect(108.0, 90.0, 504.0, 702.0)

page.rect
Rect(0.0, 0.0, 396.0, 612.0)

The destination position is currently expected to be provided as coordinates relative to the MediaBox. This causes the deviation by 90 points.
For the time being, you can do this:

delta_y = page.cropbox.y0 - page.mediabox.y0  # cope with any difference here
final_position = desired_position - delta_y
toc = [[1, title, page.number + 1, final_position]]

Please remember that page numbers in TOC lists are 1-based.

[JorjMcKie]

The above recipe always works: in the majority of cases, the CropBox is no different from MediaBox, "final_position" and "desired_position" are the same.