Update trigger detection tutorial #191

vinferrer · 2020-03-27T11:49:37Z

Closes #190

Proposed Changes

Update howto.rst file so the trigger detection tutorial is updated
explain new automatic detection
Explain manual override
modify tutorial_file trigger so one of the triggers is not detected by the threshold

smoia · 2020-03-27T11:55:58Z

@RayStick can you have a look at this PR and help @vinferrer with the tutorial update, please?

codecov · 2020-03-27T11:57:20Z

Codecov Report

Merging #191 into master will increase coverage by 0.03%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #191      +/-   ##
==========================================
+ Coverage   94.42%   94.46%   +0.03%     
==========================================
  Files           7        7              
  Lines         574      578       +4     
==========================================
+ Hits          542      546       +4     
  Misses         32       32

Impacted Files	Coverage Δ
phys2bids/phys2bids.py	`90.44% <100.00%> (ø)`
phys2bids/physio_obj.py	`91.83% <100.00%> (+0.34%)`	⬆️

eurunuela · 2020-03-27T12:12:59Z

Also, @vinferrer take #181 into account on your PR title! 😉

RayStick · 2020-03-27T21:22:00Z

I can review this soon.
@vinferrer I can try and adapt the tutorial file so that one of the triggers is not detected, if you like?

vinferrer · 2020-03-27T21:24:33Z

This is still a draft for the moment. So you don't have to review it yet. However if you wanna modifiy the tutorial_file please do so. I recommend you to run the new version with the atomatic threshold

vinferrer · 2020-03-27T21:26:14Z

This way you can lower down one of the triggers below that threshold.

vinferrer · 2020-03-27T21:26:26Z

Thanks in advance @RayStick

RayStick · 2020-03-27T21:28:46Z

@vinferrer

I ran the latest phys2bids on the tutorial_file.txt (to check it works for me) and it works great (it automatically finds the threshold, and therefore the right number of time points). A really good improvement, thanks. I will use the threshold it finds to modify one of the triggers below that, and then see how the manual correction workflow can be implemented after that.

Let me know if there is anything else that would help you with this draft PR, before it is time to review.

vinferrer · 2020-03-27T21:32:17Z

The manual correction is already implemented. I want to modify the tutorial file just to make a tutorial where the user can see a case that this manual threshold is needed. Using the manual correction is pretty easy, you just have to enter a new threshold through -thr

RayStick · 2020-03-27T21:34:31Z

Ah yes, I understand the idea. I just meant (1) I will make the new file with one trigger different and (2) check the manual correction then works (for me).

vinferrer · 2020-03-27T21:35:04Z

Oh sure, sorry for the missinterpretation

vinferrer · 2020-03-27T21:35:12Z

Please check it

RayStick · 2020-03-27T22:05:14Z

I made a PR to your branch with two minor additions/changes: 

(1) I have added a file called tutorial_file_v2.txt - the first trigger has been altered. Specifically, I changed lines 256-295 to 1.0475.
(2) Not related to changes you have made but relevant to the tutorial files - I have renamed the tutorial_file.json file because it is at risk of being overwritten when running phys2bids. This is because the default filename for the json file that phys2bids generates is filename.json.

When running
phys2bids -in ../tutorial_file_v2.txt -info 
You get: 

When running
phys2bids -in ../tutorial_file_v2.txt -chtrig 1 -ntp 158 -tr 1.2 
You get:

When running:
phys2bids -in ../tutorial_file_v2.txt -chtrig 1 -ntp 158 -tr 1.2 -thr 1.04 
You get:   

So all seems to be working as expected. :)

vinferrer · 2020-03-27T22:20:05Z

Do you get a warning in the log saying that the expected trigger amount is no the one founded?

vinferrer · 2020-03-27T22:20:53Z

I mean in the first case when the thr is done automaticly

RayStick · 2020-03-27T22:26:50Z

Ah, sorry, should have included the output.

Running
phys2bids -in ../tutorial_file_v2.txt -chtrig 1 -ntp 158 -tr 1.2 

Gives:

2020-03-27T17:24:42	phys2bids.phys2bids	INFO    	Currently running phys2bids version v1.3.0-beta+350.g7e783d4
2020-03-27T17:24:42	phys2bids.phys2bids	INFO    	Input file is ../tutorial_file_v2.txt
2020-03-27T17:24:42	phys2bids.utils	       INFO    	File extension is .txt
2020-03-27T17:24:42	phys2bids.utils	WARNING 	If both acq and txt files exist in the path, acq will be selected.
2020-03-27T17:24:42	phys2bids.phys2bids	INFO    	Reading the file ./../tutorial_file_v2.txt
2020-03-27T17:24:43	phys2bids.interfaces.txt	INFO    	phys2bids detected that your file is in Labchart format
2020-03-27T17:24:44	phys2bids.phys2bids	INFO    	Reading infos
2020-03-27T17:24:44	phys2bids.physio_obj	INFO    	
------------------------------------------------
File ../tutorial_file_v2.txt contains:
01. Trigger; sampled at 1000.0 Hz
02. CO2; sampled at 1000.0 Hz
03. O2; sampled at 1000.0 Hz
04. Pulse; sampled at 1000.0 Hz
------------------------------------------------

2020-03-27T17:24:44	phys2bids.physio_obj	INFO    	Counting trigger points
2020-03-27T17:24:44	phys2bids.physio_obj	INFO    	The number of timepoints according to the std_thr method is 157. The computed threshold is 1.1506977594943586
2020-03-27T17:24:44	phys2bids.physio_obj	INFO    	Checking number of timepoints
2020-03-27T17:24:44	phys2bids.physio_obj	WARNING 	Found 1 timepoints less than expected!
2020-03-27T17:24:44	phys2bids.physio_obj	WARNING 	Correcting time offset, assuming missing timepoints are at the beginning (try again with a more conservative thr)
2020-03-27T17:24:44	phys2bids.phys2bids	INFO    	Plot trigger
2020-03-27T17:24:45	phys2bids.phys2bids	INFO    	Preparing 1 output files.
2020-03-27T17:24:45	phys2bids.phys2bids	INFO    	Exporting files for freq 1000.0
2020-03-27T17:24:48	phys2bids.phys2bids	INFO    	
------------------------------------------------
Filename:            ../tutorial_file_v2.txt

Timepoints expected: 158
Timepoints found:    157
Sampling Frequency:  1000.0 Hz
Sampling started at: 0.2459999999998672 s
Tip: Time 0 is the time of first trigger
------------------------------------------------

smoia · 2020-03-27T23:05:17Z

Nice job people! Way to go!

vinferrer · 2020-03-28T07:45:28Z

I think we should have only one tutorial file so is more clear to the user. Therefore we can delete the previous one and leave @RayStick edited file. what do yo think?

tutorial update

Raystick/doc trig v2

vinferrer · 2020-04-02T07:26:19Z

Changes done

smoia

Ok, I think it flows very well, the changes make it clear, and if you can just add the two suggestion, I think we're ready to merge it in!

Good job guys!

docs/howto.rst

Co-Authored-By: Stefano Moia <s.moia@bcbl.eu>

vinferrer · 2020-04-02T13:17:09Z

I hope that's the last thing

smoia · 2020-04-02T14:16:29Z

@vinferrer I opened a PR to your branch with tiny things. As soon as you merge that in, we can merge this in!

RayStick · 2020-04-02T19:52:36Z

Because it says "some checks haven't been completed yet" - do I wait until that is completed before merging?

vinferrer · 2020-04-02T20:23:14Z

dont merge

vinferrer · 2020-04-02T20:23:55Z

i need to add smoia changes

Update skip trigger count message in both script and documentation

RayStick · 2020-04-02T21:02:36Z

Ah okay! As he had approved the PR, I thought you had already incorporated all his changes, sorry.

smoia · 2020-04-02T21:20:15Z

@vinferrer can you push an empty commit to restart the CI?

…oc_trig

vinferrer · 2020-04-03T07:01:08Z

pushing

vinferrer · 2020-04-03T07:07:13Z

I think we can merge now

RayStick · 2020-04-03T15:37:58Z

Great!

start modifying the howto.rst file

7a1851d

vinferrer added the Documentation This issue or PR is about the documentation label Mar 27, 2020

vinferrer requested review from smoia and RayStick March 27, 2020 11:49

vinferrer changed the title ~~start modifying the howto.rst file~~ Update trigger detection tutorial Mar 27, 2020

tutorial update

7e783d4

vinferrer added 5 commits March 28, 2020 16:12

Merge pull request #3 from RayStick/raystick/doc_trig_files

edbcdbc

tutorial update

new image

835880b

modify tutorial to add not automatic case

36fcb30

delete commas

5da33a5

add spaces

92bc844

vinferrer marked this pull request as ready for review March 30, 2020 10:42

Rachael Stickland and others added 6 commits April 1, 2020 10:16

Add new png output

0418426

Updated howto doc with middle trigger missing

981177e

Merge pull request #5 from RayStick/raystick/doc_trig_v2

dd4f588

Raystick/doc trig v2

change message if thr is inputed

a989080

change message if thr is inputed again

d12c87c

change message in docs

147f61c

smoia approved these changes Apr 2, 2020

View reviewed changes

docs/howto.rst Outdated Show resolved Hide resolved

docs/howto.rst Outdated Show resolved Hide resolved

docs/howto.rst Show resolved Hide resolved

docs/howto.rst Outdated Show resolved Hide resolved

vinferrer and others added 5 commits April 2, 2020 15:13

ntp and thr needed

e0c6e4e

Update docs/howto.rst

e2699e3

Co-Authored-By: Stefano Moia <s.moia@bcbl.eu>

same thing

f70f4e3

Merge branch 'doc_trig' of github.com:vinferrer/phys2bids into doc_trig

11095e0

Update docs/howto.rst

83b1903

Co-Authored-By: Stefano Moia <s.moia@bcbl.eu>

Update "skip trigger count" message in both script and documentation

d74ce84

RayStick approved these changes Apr 2, 2020

View reviewed changes

Merge pull request #6 from smoia/doc_trig

2d9a767

Update skip trigger count message in both script and documentation

Merge branch 'master' of https://github.com/physiopy/phys2bids into d…

f3e06ef

…oc_trig

vinferrer merged commit c37bb87 into physiopy:master Apr 3, 2020

vinferrer deleted the doc_trig branch April 3, 2020 11:55

smoia added the released This issue/pull request has been released. label Oct 14, 2020

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update trigger detection tutorial #191

Update trigger detection tutorial #191

vinferrer commented Mar 27, 2020

smoia commented Mar 27, 2020

codecov bot commented Mar 27, 2020 •

edited

Loading

eurunuela commented Mar 27, 2020

RayStick commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020 •

edited

Loading

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020

smoia commented Mar 27, 2020

vinferrer commented Mar 28, 2020

vinferrer commented Apr 2, 2020

smoia left a comment

vinferrer commented Apr 2, 2020

smoia commented Apr 2, 2020

RayStick commented Apr 2, 2020

vinferrer commented Apr 2, 2020

vinferrer commented Apr 2, 2020

RayStick commented Apr 2, 2020

smoia commented Apr 2, 2020

vinferrer commented Apr 3, 2020

vinferrer commented Apr 3, 2020

RayStick commented Apr 3, 2020

Update trigger detection tutorial #191

Update trigger detection tutorial #191

Conversation

vinferrer commented Mar 27, 2020

Proposed Changes

smoia commented Mar 27, 2020

codecov bot commented Mar 27, 2020 • edited Loading

Codecov Report

eurunuela commented Mar 27, 2020

RayStick commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020 • edited Loading

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020

vinferrer commented Mar 27, 2020

vinferrer commented Mar 27, 2020

RayStick commented Mar 27, 2020

smoia commented Mar 27, 2020

vinferrer commented Mar 28, 2020

vinferrer commented Apr 2, 2020

smoia left a comment

Choose a reason for hiding this comment

vinferrer commented Apr 2, 2020

smoia commented Apr 2, 2020

RayStick commented Apr 2, 2020

vinferrer commented Apr 2, 2020

vinferrer commented Apr 2, 2020

RayStick commented Apr 2, 2020

smoia commented Apr 2, 2020

vinferrer commented Apr 3, 2020

vinferrer commented Apr 3, 2020

RayStick commented Apr 3, 2020

codecov bot commented Mar 27, 2020 •

edited

Loading

RayStick commented Mar 27, 2020 •

edited

Loading