Introduce QC report generation

[peristeri]

For the commands sct_propseg, sct_label_vertebrae and
sct_register_to_template, an extra parameter is added. The parameter takes a
output path and generates png images of the input and segmentaion output as well
as log of output values.

Partial implements #1247

[jcohenadad]

is it ready to be tested?

[peristeri]

@jcohenadad yes it is.

[jcohenadad]

warning after propseg, then error after sct_qc (the folder ~/qc_data is empty):

Done! To view results, type:
fslview t2.nii.gz t2_seg.nii.gz -l Red -b 0,1 -t 0.7 &

/Users/julien/code/sct/python/lib/python2.7/site-packages/scipy/ndimage/measurements.py:1301: RuntimeWarning: invalid value encountered in double_scalars
  for dir in range(input.ndim)]
WARNING:/Users/julien/code/sct/spinalcordtoolbox/reports/qc.py:Can not get GIT hash value
Sucessfully generate the QC results in ~/qc_data/qc_results.json
Use "sct_qc -folder ~/qc_data" to see the results on a browser
julien-macbook:~/data/temp/sct_015/t2 $ sct_qc -folder ~/qc_data

--
Spinal Cord Toolbox (qc-generator/af8edf141656c541c5d75d7bad47387ae46d690b)
Running /Users/julien/code/sct/scripts/sct_qc.py -folder /Users/julien/qc_data
Check folder existence...
Can not start the quality control viewer. This is not a proper QC folder

/Users/julien/code/sct/scripts/sct_qc.pyNone

[peristeri]

@jcohenadad can you list me the contents of the ~/qc_data folder?

[jcohenadad]

it is empty

[jcohenadad]

I do this and nothing happens (nothing in my browser):

sct_qc -folder ~/qc_data/

--
Spinal Cord Toolbox (qc-generator/dcb7cbff9c58599894aa0ba145c1d0fa8ef9c5dc)
Running /Users/julien/code/sct/scripts/sct_qc.py -folder /Users/julien/qc_data/
Check folder existence...
QC viewer started on http://127.0.0.1:8888
Press "Ctrl" + "C" to stop sct_qc

Update: if i copy/paste URL in browser, it works. But people cannot guess it. Possible to open browser automatically? If not, indicate to the user that he/she has to click on index.html

[jcohenadad]

can you please make the segmentation blink twice as fast?

[jcohenadad]

I've added another command for the same subject (label_vertebrae), but when generating the report i only get the view for propseg.

[jcohenadad]

• error with label_vertebrae: /Users/julien/code/sct/python/lib/python2.7/site-packages/scipy/ndimage/measurements.py:1301: RuntimeWarning: invalid value encountered in double_scalars
  for dir in range(input.ndim)]
• bug: update the json if the html server is running
• get rid of the warning
• use top/down instead of left/right to switch between rows
• I've added another command for the same subject (label_vertebrae), but when generating the report i only get the view for propseg.
• sct_register_to_template does not show up in the report either
• under qc_data, i would put subject then contrast, instead of the other way around (to keep consistency with data structure)
• QC for label_vertebrae and register_to_template: divide width by factor 4
• can you please make the segmentation blink twice as fast?
• Sucessfully generate --> Sucessfully generated
• put in next line: sct_qc -folder /Users/julien/qc_data, and in green ('info' in printv)
• change sct_qc message for "Please open a browser and copy/paste this link "next line" sct_qc -folder /Users/julien/qc_data ('info' in printv)
• add small space between picture and table
• highlight the selected table in the browser
• enable arrow up/down to go through rows

[jcohenadad]

i unchecked some boxes after testing it:

thw warning:

WARNING:/Users/julien/code/sct/spinalcordtoolbox/reports/qc.pyc:Can not get GIT hash value

and also, after running "sct_label_vertebrae -i t1.nii.gz -s t1_seg.nii.gz -c t1", it does not show up in the html report, nor in the json

[jcohenadad]

Fantastic contribution 👍