Write a huge (500,000 X 100,000) as .svs or .tiff format

[deepakanandece]

I am new to pyvips. I am inable to find the syntax for writing these huge images in *.svs or *.tiff format. Please help.

[jcupitt]

Hello, you can't write SVS, it's a read-only format.

Do you want a command-line? Try:

vips black x.tif 500000 100000

It'll obviously take a while!

[jcupitt]

Oh, sorry, pyvips. Try:

import pyvips

huge_image = pyvips.Image.black(500000, 100000)
huge_image.write_to_file("x.tif")

[deepakanandece]

Thanks for the quick reply. I have a numpy array of size that big. I want to write it as to be read compatibly by openslide which leaves me with an option of only tiff images.

[jcupitt]

You can go numpy -> vips like this:

https://github.com/libvips/pyvips/blob/master/examples/pil-numpy-pyvips.py

You probably saw.

I would save as a tiled jpeg bigtiff, so:

huge_image.tiffsave("x.tif", tile=true, compression=jpeg, bigtiff=true)

[deepakanandece]

I got this error:
I used numpy to vips conversion and wrote it into pyimg. sourcenorm is an numpy array for a color image. Here s is a string containing path for saving the .tif extension file.

pyimg = numpy2vips(sourcenorm)
 pyimg.tiffsave(s, tile=True, compression='jpeg', bigtiff=True)
  File "/home/deepakanand/.local/lib/python2.7/site-packages/pyvips/vimage.py", line 799, in call_function
    return pyvips.Operation.call(name, self, *args, **kwargs)
  File "/home/deepakanand/.local/lib/python2.7/site-packages/pyvips/voperation.py", line 132, in call
    op = Operation.new_from_name(operation_name)
  File "/home/deepakanand/.local/lib/python2.7/site-packages/pyvips/voperation.py", line 60, in new_from_name
    raise Error('no such operation {0}'.format(operation_name))
pyvips.error.Error: no such operation tiffsave
  VipsOperation: class "tiffsave" not found

[jcupitt]

Looks like your libvips has been built without tiff support. Did you make it yourself? Check the output of libvips configure and make sure you have the libtiff headers.

[deepakanandece]

Thanks for such response.
Can you provide me a stepwise instruction for rebuilding it. I was not able to build it as one go. There were errors. However, later it started to work.
I am running Ubuntu 16.04, python 2.7.

[jcupitt]

There's a chapter in the docs:

https://libvips.github.io/libvips/install.html#building-libvips-from-a-source-tarball

it's like building any linux project.

but are you sure you need to build libvips? The version that's included with Ubuntu 16.04 should work.

[deepakanandece]

If libvips is already there then how to add support for Tiffsave.

[jcupitt]

Because you have installed your own libvips which does not have tiff support. Remove it and install the Ubuntu one instead.

[deepakanandece]

Cool! I will do it and get back to you. Thanks again. You are one of the most active guys in handling issues.

[deepakanandece]

I was able to write the image as .tif format but openslide fails to read it. Do I need to read the created files using vips only?

[deepakanandece]

Openslide recognizes the file if it has multiple layers. Thanks a lot.

[jcupitt]

Ah OK, good to know. That's with pyramid=True I guess?

[deepakanandece]

Yes by doing pyramid=True. However is there any way to only restrict the number of layers alongwith pyramid? It gives 10 layers by default.