How to reduce the palette of PNG image in Python/Pillow to the colors being really used?

After processing a previously optimized indexed color PNG image with transparency (see here for some background, since this question refers to the same image file), using the following code, the PLTE chunk seems to be expanded with more colors than those effectively being used.

Mu current code:

#!/usr/bin/env/python3
import os

from PIL import Image


source_file = os.path.expanduser("~/Desktop/prob.png")
dest_file = os.path.expanduser("~/Desktop/processed_img.png")

img = Image.open(source_file)

# Convert all colors in the palette to grayscale and save the new palette
pal = img.getpalette()
for i in range(len(pal) // 3):
    # Using ITU-R 601-2 luma transform
    g = (pal[3*i] * 299 + pal[3*i+1] * 587 + pal[3*i+2] * 114) // 1000
    pal[3*i: 3*i+3] = [g, g, g]

img.putpalette(pal)

try:
    img.save(dest_file, optimize=True, format="PNG")
except IOError:
    ImageFile.MAXBLOCK = img.size[0] * img.size[1]
    img.save(dest_file, optimize=True, format="PNG")

Using pngcheck I get a small 16 colors palette for the original file:

$ pngcheck -tc7pv ~/Desktop/prob.png
File: /Users/victor/Desktop/prob.png (12562 bytes)
  chunk IHDR at offset 0x0000c, length 13
    825 x 825 image, 8-bit palette, non-interlaced
  chunk PLTE at offset 0x00025, length 48: 16 palette entries
     0:  (  0,  0,  0) = (0x00,0x00,0x00)
     1:  (230,230,230) = (0xe6,0xe6,0xe6)
     2:  (215,215,215) = (0xd7,0xd7,0xd7)
     3:  (199,199,199) = (0xc7,0xc7,0xc7)
     4:  (175,175,175) = (0xaf,0xaf,0xaf)
     5:  (143,143,143) = (0x8f,0x8f,0x8f)
     6:  (111,111,111) = (0x6f,0x6f,0x6f)
     7:  ( 79, 79, 79) = (0x4f,0x4f,0x4f)
     8:  ( 22, 22, 22) = (0x16,0x16,0x16)
     9:  (  0,  0,  0) = (0x00,0x00,0x00)
    10:  ( 47, 47, 47) = (0x2f,0x2f,0x2f)
    11:  (254,254,254) = (0xfe,0xfe,0xfe)
    12:  (115, 89,  0) = (0x73,0x59,0x00)
    13:  (225,176,  0) = (0xe1,0xb0,0x00)
    14:  (255,211,  0) = (0xff,0xd3,0x00)
    15:  (254,204,  0) = (0xfe,0xcc,0x00)
  chunk tRNS at offset 0x00061, length 1: 1 transparency entry
    0:    0 = 0x00
  chunk IDAT at offset 0x0006e, length 12432
    zlib: deflated, 32K window, maximum compression
  chunk IEND at offset 0x0310a, length 0
No errors detected in /Users/victor/Desktop/prob.png (5 chunks, 98.2% compression).

Then, after processing the image using the code sample above, pngcheck displays a much bigger PLTE chunk, filled with lots of (probably unused) color values:

$ pngcheck -tc7pv ~/Desktop/processed_img.png
File: /Users/victor/Desktop/processed_img.png (14680 bytes)
  chunk IHDR at offset 0x0000c, length 13
    825 x 825 image, 8-bit palette, non-interlaced
  chunk PLTE at offset 0x00025, length 768: 256 palette entries
      0:  (  0,  0,  0) = (0x00,0x00,0x00)
      1:  (230,230,230) = (0xe6,0xe6,0xe6)
      2:  (215,215,215) = (0xd7,0xd7,0xd7)
      3:  (199,199,199) = (0xc7,0xc7,0xc7)
      4:  (175,175,175) = (0xaf,0xaf,0xaf)
      5:  (143,143,143) = (0x8f,0x8f,0x8f)
      6:  (111,111,111) = (0x6f,0x6f,0x6f)
      7:  ( 79, 79, 79) = (0x4f,0x4f,0x4f)
      8:  ( 22, 22, 22) = (0x16,0x16,0x16)
      9:  (  0,  0,  0) = (0x00,0x00,0x00)
     10:  ( 47, 47, 47) = (0x2f,0x2f,0x2f)
     11:  (254,254,254) = (0xfe,0xfe,0xfe)
     12:  ( 86, 86, 86) = (0x56,0x56,0x56)
     13:  (170,170,170) = (0xaa,0xaa,0xaa)
     14:  (200,200,200) = (0xc8,0xc8,0xc8)
     15:  (195,195,195) = (0xc3,0xc3,0xc3)
     16:  ( 16, 16, 16) = (0x10,0x10,0x10)
     17:  ( 17, 17, 17) = (0x11,0x11,0x11)
     18:  ( 18, 18, 18) = (0x12,0x12,0x12)
     19:  ( 19, 19, 19) = (0x13,0x13,0x13)
     20:  ( 20, 20, 20) = (0x14,0x14,0x14)

(...) --- and it goes on listing all values up to 255:

    254:  (254,254,254) = (0xfe,0xfe,0xfe)
    255:  (255,255,255) = (0xff,0xff,0xff)
  chunk tRNS at offset 0x00331, length 1: 1 transparency entry
    0:    0 = 0x00
  chunk IDAT at offset 0x0033e, length 13830
    zlib: deflated, 32K window, maximum compression
  chunk IEND at offset 0x03950, length 0
No errors detected in /Users/victor/Desktop/processed_img.png (5 chunks, 97.8% compression).

Is this behavior normal on Pillow? Is there any way to save a shorter PLTE chunk, similar to the original file (I am trying to optimize for smaller file sizes)?

If Pillow can't do it, is there any other simple way to do it? Preferably using pure Python, but it could also be with numpy or some additional pure Python package, like PyPNG or PurePNG, if that helps.

I ran your code on the bee png with Pillow 9.2.0 and the output png had the same number colors in its palette as the original. Additionally, Image.convert() has the args palette and colors that can be used to control the output colors. For example, to keep the same number of colors as the input image:

from PIL import Image

img = Image.open('bee.png')
num_pixels = img.size[0]*img.size[1]
num_colors = len(img.getcolors(num_pixels))
# Max palette size = 256
if num_colors > 256:
    num_colors = 256

img = img.convert(mode='P', palette=1, colors=num_colors)
img.save('bee2.png', optimize=True, format="PNG")

Alternatively, if you're interested in reducing/managing image size I'd recommend compressing the image using the quality arg in Image.save() or utilizing another tool such as ExifTool to eliminate unnecessary metadata (These will likely have a limited effect on the bee png).

For more info on image modes in Pillow see Mark Setchell's answer: What is the difference between images in 'P' and 'L' mode in PIL?

Answers discussing file size reduction with Pillow: How to reduce the image file size using PIL

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