Reading directory of files into volume

[David Haberthür]

Dear all.

I have a directory of (PNG) files which come from tomography.

These files are slices of a stack which I would like to read into a volume with `imageio`.

I've had no luck with using `mimread` as specified here: http://imageio.readthedocs.io/en/stable/examples.html#read-medical-data-dicom

Could someone give me a pointer on how to read the stack of images as volume?

Currently I'm doing it like so

````python

import glob

import matplotlib.pyplot as plt

# Get a list of all the relevant files

recfolder = '/data/sample/reconstructions'
reconstructions = glob.glob(os.path.join(recfolder, '*rec*.png'))

# This shows me one image, as expected

rec=imageio.imread(reconstructions[123])

plt.imshow(rec)

````

This is all fine and well, but now I'd like to read more images into a volume (for further processing)

It does work with a crude loop as below, but then I have a list of images, which is not what I would like.

````python

# This loads some images into a list, but not a volume

iteration = 100
vol = [None] * len(reconstructions[::iteration])
for c, rec in enumerate(reconstructions[::iteration]):
    vol[c] = imageio.imread(rec)

````

I would expect this to read a subset of the images as volume, but get an error that imageion "could not find a format to read the specified file in mode 'v'"

````python

vol = imageio.volread(recfolder)

````

Also I would have expected that I can just put multiple filenames into `mimread` like below, but then I get an error about a non-understandable URI...

````python

vol = imageio.mimread(reconstructions[100:111])

````

I would greatly appreciate any pointers on how to read a bunch of images into a volume.

David Haberthür

[Almar Klein]

Hi David,

First some explanations as to where some of the things that you tried do not work:

> I would expect this to read a subset of the images as volume [...]  imageio.volread(recfolder)

This does actually work with the DICOM plugin, but most other plugins require a file, not a folder.

> Also I would have expected that I can just put multiple filenames into `mimread` [...]  imageio.mimread(reconstructions[100:111])

That's not how imageio works; it would not be very "Pythonic".

You were almost there when you had the list of images. One final step: np.stack(vol, 0)

You can write that bit more compactly using a list comprehension: np.stack([imageio.imread(rec) for rec in reconstructions[::iteration]], 0)

Regards,
  Almar

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[David Haberthür]

On Tuesday, July 31, 2018 at 11:12:51 AM UTC+2, Almar Klein wrote:

You were almost there when you had the list of images. One final step: np.stack(vol, 0)

You can write that bit more compactly using a list comprehension: np.stack([imageio.imread(rec) for rec in reconstructions[::iteration]], 0)

Thanks a lot for the help!