libvips
Reading in image a second time breaks on qptiff file
Reading in an image from a qptiff file breaks when I run the same code twice.
If I run the below once it works. If I run it again (I'm using a jupyter notebook) it throws an error. If I run it a third time it throws a different error.
I'm not able to post the image publicly but I've emailed it to @jcupitt.
import pyvips
import matplotlib.pyplot as plt
fpath = 'myfile.qptiff'
page_idx = 17
location = (0, 0)
size = (375, 483) # this is the entire image
# read patch via crop
vips_image = pyvips.Image.new_from_file(vips_filename=fpath, page=page_idx)
patch_crop = vips_image.crop(location[0], location[1], size[0], size[1])
patch_crop = patch_crop.numpy()
plt.imshow(patch_crop)
Error message after second call
---------------------------------------------------------------------------
Error Traceback (most recent call last)
Cell In[4], line 11
9 vips_image = pyvips.Image.new_from_file(vips_filename=fpath, page=page_idx)
10 patch_crop = vips_image.crop(location[0], location[1], size[0], size[1])
---> 11 patch_crop = patch_crop.numpy()# [:, :, 0:3]
12 plt.imshow(patch_crop)
File ~/anaconda3/envs/cpath/lib/python3.8/site-packages/pyvips/vimage.py:1273, in Image.numpy(self, dtype)
1252 def numpy(self, dtype=None):
1253 """Convenience function to allow numpy conversion to be at the end
1254 of a method chain.
1255
(...)
1271 strings to numpy dtype strings.
1272 """
-> 1273 return self.__array__(dtype=dtype)
File ~/anaconda3/envs/cpath/lib/python3.8/site-packages/pyvips/vimage.py:1234, in Image.__array__(self, dtype)
1208 """Conversion to a NumPy array.
1209
1210 Args:
(...)
1229 See Also `Image.new_from_array` for the inverse operation. #TODO
1230 """
1231 import numpy as np
1233 arr = (
-> 1234 np.frombuffer(self.write_to_memory(),
1235 dtype=FORMAT_TO_TYPESTR[self.format])
1236 .reshape(self.height, self.width, self.bands)
1237 )
1239 if self.bands == 1:
1240 # flatten single-band images
1241 arr = arr.squeeze(axis=-1)
File ~/anaconda3/envs/cpath/lib/python3.8/site-packages/pyvips/vimage.py:944, in Image.write_to_memory(self)
942 pointer = vips_lib.vips_image_write_to_memory(self.pointer, psize)
943 if pointer == ffi.NULL:
--> 944 raise Error('unable to write to memory')
945 pointer = ffi.gc(pointer, glib_lib.g_free)
947 return ffi.buffer(pointer, psize[0])
Error: unable to write to memory
tiff2vips: out of order read -- at line 483, but line 0 requested
Error message after third call
---------------------------------------------------------------------------
Error Traceback (most recent call last)
Cell In[5], line 11
9 vips_image = pyvips.Image.new_from_file(vips_filename=fpath, page=page_idx)
10 patch_crop = vips_image.crop(location[0], location[1], size[0], size[1])
---> 11 patch_crop = patch_crop.numpy()
12 plt.imshow(patch_crop)
File ~/anaconda3/envs/cpath/lib/python3.8/site-packages/pyvips/vimage.py:1273, in Image.numpy(self, dtype)
1252 def numpy(self, dtype=None):
1253 """Convenience function to allow numpy conversion to be at the end
1254 of a method chain.
1255
(...)
1271 strings to numpy dtype strings.
1272 """
-> 1273 return self.__array__(dtype=dtype)
File ~/anaconda3/envs/cpath/lib/python3.8/site-packages/pyvips/vimage.py:1234, in Image.__array__(self, dtype)
1208 """Conversion to a NumPy array.
1209
1210 Args:
(...)
1229 See Also `Image.new_from_array` for the inverse operation. #TODO
1230 """
1231 import numpy as np
1233 arr = (
-> 1234 np.frombuffer(self.write_to_memory(),
1235 dtype=FORMAT_TO_TYPESTR[self.format])
1236 .reshape(self.height, self.width, self.bands)
1237 )
1239 if self.bands == 1:
1240 # flatten single-band images
1241 arr = arr.squeeze(axis=-1)
File ~/anaconda3/envs/cpath/lib/python3.8/site-packages/pyvips/vimage.py:944, in Image.write_to_memory(self)
942 pointer = vips_lib.vips_image_write_to_memory(self.pointer, psize)
943 if pointer == ffi.NULL:
--> 944 raise Error('unable to write to memory')
945 pointer = ffi.gc(pointer, glib_lib.g_free)
947 return ffi.buffer(pointer, psize[0])
Error: unable to write to memory
System details
import platform; print(platform.platform())
import sys; print('python', sys.version)
import pyvips; print('pyvips', pyvips.__version__)
import openslide; print('openslide', openslide.__version__)
macOS-10.16-x86_64-i386-64bit
python 3.8.18 (default, Sep 11 2023, 08:17:33)
[Clang 14.0.6 ]
pyvips 2.2.1
openslide 1.3.0
I installed pyvips using conda install.
Hi again @idc9,
You'll get that error if you make an out of order read from a sequential image. Perhaps you passed access="sequential" by mistake?
It's usually best to post small, complete, runnable programs rather than code fragments, or I won't be able to test them unless I spend some time writing a code harness.
I tried:
#!/usr/bin/env python3
import sys
import pyvips
level = int(sys.argv[2])
image = pyvips.Image.new_from_file(sys.argv[1], page=level)
for _ in range(100):
patch = image.crop(0, 0, image.width, image.height).numpy()
Then ran it with:
$ vips copy ~/pics/nina.jpg x.tif[pyramid,compression=jpeg,tile]
$ ./crop2.py x.tif 6
$
Add it seems to work.
I had a look at your test file, it's a Perkin-Elmer QPI, so it won't work with a standard TIFF loader. You'll need a specialized load library for this file format.
Perhaps you could save as OME-TIFF? That should load OK.
Thanks again for the very fast response!
Access
It's usually best to post small, complete, runnable programs rather than code fragments
That is a complete runnable program (edited to add the imports!), not a part of a larger script. I had not previously called 'access=sequential'`.
In fact the exact same behavior occurs when I try any of the access options (None, sequential, random). Note I restart the notebook before calling the different options.
vips_image = pyvips.Image.new_from_file(vips_filename=fpath, page=page_idx)
vips_image = pyvips.Image.new_from_file(vips_filename=fpath, page=page_idx, access='random')
vips_image = pyvips.Image.new_from_file(vips_filename=fpath, page=page_idx, access='sequential')
qptifff
pyvips seems to work otherwise with this image format. So far the only issue I've encoutnered is this double loading issue. This seems like a bug in pyvips to me since it works on the first load, but not the second load.
Perhaps you could save as OME-TIFF?
That would be a problem for our application; we would like to use pyvips on the original image.
pyvips seems to work otherwise with this image format
It's a plane-separated pyramid, unfortunately, so it won't work. It's to do with the way the reduced resolution levels are coded -- OME-TIFF (which libvips does support) puts the reduced res levels into subifds, but this QPI has them all one after the other, with the metadata about the file structure coded into the XML in the imagedescription.
Have a look at the tiffinfo output (and get a large mug of tea ready first).
Does the fact that reading in the image twice throws an error not suggest there is an issue with pyvips?
That's just a minor symptom -- the cause is this TIFF file being way outside the supported range for any general purpose TIFF reader.
Options off the top of my head:
- You could probably read it with a low-level TIFF library, like
tifffile, but getting a nice RGB image will take some work. Maybe a week's effort? It depends how much of the QPI format you want to support. - I expect PE will sell you an SDK (I've not checked).
- The gold standard solution would be to add support for the format to openslide. That would be (guess?) several weeks of effort and you'd need a good C programmer.
- ... and of course, another option is to switch to a format that's not locked to a vendor, or a scanner manufacturer who don't attack their customers by forcing them to use a non-interoperable format. Most of the people I know are moving to wg26 DICOM now, perhaps PE support something like that? I've not looked.