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Compute metrics from segmentation #115

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Description

The objective of this PR is to add a new set of functions to be able to compute metrics from totalspineseg segmentation.

Metrics

  • Canal:
    • AP distance
    • CSA, excentricity, solidity…
  • Discs:
    • Disc height
    • Volume
    • Pfirmann score
  • Foramen:
    • Surface

@NathanMolinier
add image script
972fbc7
@NathanMolinier
init measure seg script
0cf3171
@NathanMolinier
extract foramen area
e531580
@NathanMolinier
update comments
f6d08f4
@NathanMolinier
add png
49fbcfc
@NathanMolinier
add mapping totalspineseg
82b865b
@NathanMolinier
add resolution measure_disc
24a44cd
@NathanMolinier
add missing functions + debug
a305c66
@NathanMolinier
init measure script
145981f
@NathanMolinier
add csv
6ab9c1c
@NathanMolinier
update canal metrics
9298b59
@NathanMolinier
add area
9b227bb
@NathanMolinier
convert diameters to mm
eb9c70e
@NathanMolinier
fetch disc SI signal
9df1765
@NathanMolinier
fetch csf signal
81fcc14
@NathanMolinier
use arry instead of Image class
66fe2e0
@NathanMolinier
update arguments and reorganize
003b9a2
@NathanMolinier
add function to measure vertebrae
64784b9
@NathanMolinier
fix function use
e67d3a4
@NathanMolinier
add function to save 3d isometric views
5304a1f
@NathanMolinier
add function to crop around binary volumes
5fba539
@NathanMolinier
add missing import
627b3b0
@NathanMolinier
remove cropping
8a8281e
@NathanMolinier
output volumes for vizualization
7b8300b
@NathanMolinier
save csv and images
b2cd345
@NathanMolinier
save vertebrae and foramen image
ee0af64
@NathanMolinier
rotate vertebrae to help visualization
a057f2d
@NathanMolinier
remove rotation
e1beda9
@NathanMolinier
fix variable name
0fc755d
@NathanMolinier
fix loop and mapping
2dc681d
@NathanMolinier
fix coords problem
1988cad
@NathanMolinier
take maximum intensity in the canal
72fd837
@NathanMolinier
extract 90th percentile for csf
f315ab2
@NathanMolinier
move discs back to beginning
c4099b7
@NathanMolinier
use gaussian mixture models to extract intensity peaks
3e2612f
@NathanMolinier
center disc thickness extraction far from edges
2006677
@NathanMolinier
remove print and warning
cb7ea31
@NathanMolinier
use percentile 95
14e5a75
@NathanMolinier
use most represented values
d46798f
@NathanMolinier
handle IndexError and check metrics[struc] size
96160b0
@NathanMolinier
add index error
faafcdc
@NathanMolinier
update csf signal extraction
e5e5be1
@NathanMolinier
find intensity peak in the inner and outer layer of the disc
85ac685
@NathanMolinier
try to account for signal loss
458c0d5
@NathanMolinier
try to estimate ap signal variations
84e4425
@NathanMolinier
add n4_bias_field_correction
369b1b6
@NathanMolinier
normalize with csf intensity
60444b3
@NathanMolinier
extract intensity from 2d slice and smooth
08c9b19
@NathanMolinier
generate report using demographics
cbd20eb
@NathanMolinier
incorporate disc grading
f37b359
@NathanMolinier
remove normalisations
fba5933
@NathanMolinier
update figure size
94110cf
@NathanMolinier
rename assymetry
caeabd5
@NathanMolinier
Update images and add canal images
573ac2d
@NathanMolinier
use metrics_dict to select displayed metrics
cf6e52c
@NathanMolinier
fix image aspect ratio
81d0936
@NathanMolinier
Merge remote-tracking branch 'refs/remotes/origin/nm/calculate_metric…
1edbe06 
…s' into nm/calculate_metrics
@NathanMolinier
fix image aspect ratio
71cc18a
@NathanMolinier
fix text size
2686a0f
@NathanMolinier
fix figure size
0e8d808
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@NathanMolinier