No checkerboard visible in output image

[lalet]

• mrivis version: 0.2.8
• Python version: 3.4
• Operating System: CentOS7

Description

from mrivis import checkerboard
plot = checkerboard('T2w_acpc.nii.gz','T2w_acpc_centos7.nii.gz',patch_size=10)
plot.savefig("T2w_tilt.png")

These two files are output from two operating systems.   
They are completely off w.r.t alignment and we tried to visualize the differences using checkerboard. 
But no checkerboard is visible in the output image.  
Thanks for fixing the other issue, but it would be greatly appreciated if you have any hint on this one. Please find attached the output image.

@glatard

[raamana]

that's weird - did you try producing collages for them separately, and be sure that they are indeed off?

[raamana]

e.g.

from mrivis import collage
plot1 = collage('T2w_acpc.nii.gz')
plot2 = collage('T2w_acpc_centos7.nii.gz')

[lalet]

Let me try that

[lalet]

To give you and idea, this is how it looks using fsleyes while I flicker through both files.

[raamana]

I see - did you try different checker sizes, like 3 and 5 voxels etc..

Is it possible for you to share the files with me, so I can try it myself? Its perfectly fine if you can't.

[lalet]

Sure ! Can I have your mail id ?

[raamana]

It is praamana@research.baycrest.org

[raamana]

they might be too big for email - so upload to some google drive or dropbox and send a link

[lalet]

Thank you. I have sent a mail.

[raamana]

Hi Lalet,

I can see the differences with smaller patch sizes..

try this

import os
from os.path import join as pjoin, abspath, realpath, basename, dirname, exists as pexists
from mrivis import checkerboard, color_mix, voxelwise_diff

test_dir = dirname(realpath(__file__))
base_dir = realpath(pjoin(test_dir, '..', '..', 'example_datasets'))
out_dir = realpath(pjoin(base_dir, 'centos_ver_diff'))
os.makedirs(out_dir, exist_ok=True)

c7 = pjoin(base_dir, 'T2w_acpc_centos7.nii.gz')
not_c7 = pjoin(base_dir, 'T2w_acpc.nii.gz')

im_sets = ((c7, not_c7, 'CentOS different versions'),
           )

num_rows = 1
num_cols = 3
img_lim = None 
rescaling='each'

patch_set = (1, 2, 3, 5, 8, 10, 25, 40)
for im_set in im_sets:
    for ps in patch_set:
        comb_id = 'checkerboard patch size {}'.format(ps)
        out_path = pjoin(out_dir, comb_id.replace(' ', '_'))
        checkerboard(im_set[0], im_set[1],
                     patch_size=ps,
                     rescale_method=rescaling,
                     num_rows=num_rows,
                     num_cols=num_cols,
                     annot=comb_id,
                     output_path=out_path)

Perhaps the rescale method is making a difference.. need to check.

[raamana]

change the base_dir to where the images are.

[raamana]

and voxelwise_diff or color_mix is probably better suited for this purpose:

num_rows = 2
num_cols = 5
img_lim = None # [0, 4000]
rescaling='each'

for im_set in im_sets:
    comb_id = 'voxelwise_diff'
    out_path = pjoin(out_dir, comb_id.replace(' ', '_'))
    voxelwise_diff(im_set[0], im_set[1],
                   rescale_method=rescaling,
                   overlay_image=True,
                   overlay_alpha=0.7,
                   background_threshold=25,
                   num_rows=num_rows,
                   num_cols=num_cols,
                   annot=comb_id,
                   output_path=out_path)

[raamana]

color mix - you see the red along the borders?

voxel wise diff

[lalet]

Yes yes ! This is awesome. Thank you @raamana

[raamana]

Hi @glatard, can you take a look at this thread, and let me know your comments? I just want to make sure I fix the bug in my checkerboard implementation if it exists.