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Crop extraction from tiled TIFF image file directory without whole page loading using tifffile
from tifffile import TiffFile
import numpy as np
def get_crop(page, i0, j0, h, w):
"""Extract a crop from a TIFF image file directory (IFD).
Only the tiles englobing the crop area are loaded and not the whole page.
This is usefull for large Whole slide images that can't fit int RAM.
Parameters
----------
page : TiffPage
TIFF image file directory (IFD) from which the crop must be extracted.
i0, j0: int
Coordinates of the top left corner of the desired crop.
h: int
Desired crop height.
w: int
Desired crop width.
Returns
-------
out : ndarray of shape (imagedepth, h, w, sampleperpixel)
Extracted crop.
"""
if not page.is_tiled:
raise ValueError("Input page must be tiled.")
im_width = page.imagewidth
im_height = page.imagelength
if h < 1 or w < 1:
raise ValueError("h and w must be strictly positive.")
if i0 < 0 or j0 < 0 or i0 + h >= im_height or j0 + w >= im_width:
raise ValueError("Requested crop area is out of image bounds.")
tile_width, tile_height = page.tilewidth, page.tilelength
i1, j1 = i0 + h, j0 + w
tile_i0, tile_j0 = i0 // tile_height, j0 // tile_width
tile_i1, tile_j1 = np.ceil([i1 / tile_height, j1 / tile_width]).astype(int)
tile_per_line = int(np.ceil(im_width / tile_width))
out = np.empty((page.imagedepth,
(tile_i1 - tile_i0) * tile_height,
(tile_j1 - tile_j0) * tile_width,
page.samplesperpixel), dtype=page.dtype)
fh = page.parent.filehandle
jpegtables = page.tags.get('JPEGTables', None)
if jpegtables is not None:
jpegtables = jpegtables.value
for i in range(tile_i0, tile_i1):
for j in range(tile_j0, tile_j1):
index = int(i * tile_per_line + j)
offset = page.dataoffsets[index]
bytecount = page.databytecounts[index]
fh.seek(offset)
data = fh.read(bytecount)
tile, indices, shape = page.decode(data, index, jpegtables)
im_i = (i - tile_i0) * tile_height
im_j = (j - tile_j0) * tile_width
out[:, im_i: im_i + tile_height, im_j: im_j + tile_width, :] = tile
im_i0 = i0 - tile_i0 * tile_height
im_j0 = j0 - tile_j0 * tile_width
return out[:, im_i0: im_i0 + h, im_j0: im_j0 + w, :]
@HowcanoeWang
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HowcanoeWang commented Sep 14, 2020

Thanks for this function and works great for my big geotiff file.

However, for some smaller geotiff file, their is_tiled value is false, can we do the similar thing without loading full image to memeory?

@HowcanoeWang
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HowcanoeWang commented Sep 15, 2020

Thanks for this function and works great for my big geotiff file.

However, for some smaller geotiff file, their is_tiled value is false, can we do the similar thing without loading full image to memeory?

Here is my code to specify this function, for those images without tiled, it reads one row once.

def get_untiled_crop(page, i0, j0, h, w):
    if page.is_tiled:
        raise ValueError("Input page must not be tiled")
    
    im_width = page.imagewidth
    im_height = page.imagelength
    
    if h < 1 or w < 1:
        raise ValueError("h and w must be strictly positive.")

    i1, j1 = i0 + h, j0 + w
    if i0 < 0 or j0 < 0 or i1 >= im_height or j1 >= im_width:
        raise ValueError(f"Requested crop area is out of image bounds.{i0}_{i1}_{im_height}, {j0}_{j1}_{im_width}")
        
    out = np.empty((page.imagedepth, h, w, page.samplesperpixel), dtype=np.uint8)
    fh = page.parent.filehandle
    
    for index in range(i0, i1):
        offset = page.dataoffsets[index]
        bytecount = page.databytecounts[index]

        fh.seek(offset)
        data = fh.read(bytecount)

        tile, indices, shape = page.decode(data, index)
        
        out[:,index-i0,:,:] = tile[:,:,j0:j1,:]
    
    return out

2022.07.22 Updates:

I met with an untiled geotiff that read 2 rows per time (not I assumed one row per time), and I changed the code as follows:
UTokyo-FieldPhenomics-Lab/EasyIDP@f02cd19
The same function name: get_untiled_crop (Line 285)

@rfezzani
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rfezzani commented Sep 15, 2020

Thanks for this function and works great for my big geotiff file.

Thank you @HowcanoeWang for your feedback, I am glad that this piece of code was useful for you 😉.
I will investigate on your problem ASAP.

@rfezzani
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rfezzani commented Sep 15, 2020

@HowcanoeWang, I think you need to play with the RowsPerStrip, StripOffsets and StripByteCounts tags. See the Strips section in this documentation for example.

@HowcanoeWang
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HowcanoeWang commented Sep 15, 2020

@HowcanoeWang, I think you need to play with the RowsPerStrip, StripOffsets and StripByteCounts tags. See the Strips section in this documentation for example.

Thank you for your guide, apologize I am a green hand of geotiff, digging the documentation to optimize my previous code may take a long time for me. But I have tested my previous code def get_untiled_crop, it does get the same result on the untiled geotiff, may you help me test how it works on your images? And quite glad if you could optimize it by the tags you mentioned before.

@rfezzani
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rfezzani commented Sep 15, 2020

I am really not a TIFF expert 😄. I just published this gist to help people that may face the same problem as me.
You may be can find more help for your specific problem on image.sc forum. BTW, I will try to investigate, but without any guaranty of success 😉

@Yuvi-416
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Yuvi-416 commented Dec 3, 2020

Hi there,
I try to run your code but I am getting an error as:
I am passing this command:
image = get_crop(page=page, i0=0, j0=1024, h=512, w=512)

raise ValueError("Input page must be tiled.")
ValueError: Input page must be tiled.

1

I can see in the above picture that is_tiled is false.
Does it create an error?
Thank you

@HowcanoeWang
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HowcanoeWang commented Dec 3, 2020

Hi there,
I try to run your code but I am getting an error as:
I am passing this command:
image = get_crop(page=page, i0=0, j0=1024, h=512, w=512)

raise ValueError("Input page must be tiled.")
ValueError: Input page must be tiled.

1

I can see in the above picture that is_tiled is false.
Does it create an error?
Thank you

please check whether my previous get_untiled_crop function helps or not

@Yuvi-416
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Yuvi-416 commented Dec 4, 2020

Hi there,
sorry for the late reply
I run your code but still, I am getting an error as below.
ERROR:
Traceback (most recent call last):
File "/home/yuvi/PycharmProjects/task-1/VIdeo_frame_extraction/NDPI-ext/Temp-2-Tifffile.py", line 147, in
Img = get_untiled_crop(page=page.parent.pages[0], i0=0, j0=0, h=1024, w=1024)
File "/home/yuvi/PycharmProjects/task-1/VIdeo_frame_extraction/NDPI-ext/Temp-2-Tifffile.py", line 128, in get_untiled_crop
fh.seek(offset)
File "/home/yuvi/anaconda3/envs/task-1/lib/python3.7/site-packages/tifffile/tifffile.py", line 8305, in seek
self._fh.seek(offset, whence)
AttributeError: 'NoneType' object has no attribute 'seek'

Process finished with exit code 1

Does the page file which I am trying to pass is correct or not?
Img = get_untiled_crop(page=page.parent.pages[0], i0=0, j0=0, h=1024, w=1024)

@HowcanoeWang
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HowcanoeWang commented Dec 5, 2020

Hi there,
sorry for the late reply
I run your code but still, I am getting an error as below.
ERROR:
Traceback (most recent call last):
File "/home/yuvi/PycharmProjects/task-1/VIdeo_frame_extraction/NDPI-ext/Temp-2-Tifffile.py", line 147, in
Img = get_untiled_crop(page=page.parent.pages[0], i0=0, j0=0, h=1024, w=1024)
File "/home/yuvi/PycharmProjects/task-1/VIdeo_frame_extraction/NDPI-ext/Temp-2-Tifffile.py", line 128, in get_untiled_crop
fh.seek(offset)
File "/home/yuvi/anaconda3/envs/task-1/lib/python3.7/site-packages/tifffile/tifffile.py", line 8305, in seek
self._fh.seek(offset, whence)
AttributeError: 'NoneType' object has no attribute 'seek'

Process finished with exit code 1

Does the page file which I am trying to pass is correct or not?
Img = get_untiled_crop(page=page.parent.pages[0], i0=0, j0=0, h=1024, w=1024)

why you use page.parent.pages[0] instead of simple page.pages[0]

@rfezzani
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rfezzani commented Dec 5, 2020

why you use page.parent.pages[0] instead of simple page.pages[0]

👍 Good point @HowcanoeWang!

@Yuvi-416
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Yuvi-416 commented Dec 5, 2020

Hi,
Bcoz of this one,
Screenshot from 2020-12-05 18-12-32

Do you know how can I resample this kind of image?
I have an .NDPI image whose image size is around 186496 × 36608. I want to downsample this image as in the range of ((186496, 36608), (93248, 18304), (46624, 9152), (23312, 4576), (11656, 2288), (5828, 1144), (2914, 572), (1457, 286), (728, 143)). Is it possible?

@HowcanoeWang
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HowcanoeWang commented Dec 6, 2020

Hi,
Bcoz of this one,
Screenshot from 2020-12-05 18-12-32

Do you know how can I resample this kind of image?
I have an .NDPI image whose image size is around 186496 × 36608. I want to downsample this image as in the range of ((186496, 36608), (93248, 18304), (46624, 9152), (23312, 4576), (11656, 2288), (5828, 1144), (2914, 572), (1457, 286), (728, 143)). Is it possible?

This is a task like clipping raster geotiff by polygon, maybe other python library (install by conda is recommended) like GDAL, osgeo, fiona have a neat function to do this job, rather than using this basic package.

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