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Refactoring the API #66

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Refactoring the API #66

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arokem
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@arokem arokem commented May 26, 2018

Follow up on #65

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arokem commented May 26, 2018

Maybe needless to say: still WIP at this point.

@arokem arokem force-pushed the refactor_api branch 2 times, most recently from f3359f7 to 89d5ed6 Compare July 14, 2018 04:52
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arokem commented Jul 14, 2018

Still need to incorporate cleaning after merge of #77

@arokem arokem mentioned this pull request Jul 14, 2018
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arokem added 18 commits July 14, 2018 06:28
@arokem
Remove rebase artifacts.
6255b63 
Why does VS Code keep adding this in, I don't know.
@arokem
Reorganize things a tiny bit in the second loop through.
34abdfb 
The one where we reorient the streamlines.
@arokem
Add utility functions to convert between bundle dicts and tgrams.
19b28e3
@arokem
Make combination of tractograms flexible to data_per_streamline.
5cefee4
@arokem
BF: need only the row index from this (2D!) array.
39cbe3d
@arokem
Continuing to work on testing the API.
4c7d956 
Need to figure out the space of these streamlines...
@arokem
Testing for api (and some other fixes).
fb5217f
@arokem
HCP bucket currently unavailable, so switched this to temp location.
904fba9 
Kept the old one, in case they bring it back up in the same place.
@arokem
Fix a flake error.
796eee5
@arokem
BF: typo.
a90ed11
@arokem
Enable visualizing trk files without bundle designations.
342d379
@arokem
Speed up clean-up procedure, by reducing tests and using one array.
55a4ee8
@arokem
Special-case SLF, and generalize inclusion/exclusion criteria.
a80d206
@arokem
Adds some visualization functions; still need to finish them
270d970
@arokem
Actually use the bundles_list input.
44a26d1
@arokem
Start working on splitting streamlines. Still very much WIP.
c083e15
@arokem
Store the bundle_dict as an attribute of the object.
d40ff7f 
Also, fix up the uid assignment in SLF's allocation.
@arokem
BF: Return the cleaned bundles.
7bf1740
arokem added 20 commits July 19, 2018 12:05
@arokem
Move the ROI patching function to a new utility module
b08770a
@arokem
Co-visualize ROIs and streamlines.
e929ff3
@arokem
Add a b0 property.
4962b22
@arokem
Beginnings of volume visualization function.
6301683
@arokem
Changes in notebooks.
44de4f0
@arokem
Visualize b0 together with the ROIs and the streamlines.
50bce96
@arokem
First pass at full interactive visualization.
b5a9be7
@arokem
Split streamlines that cross under some height.
6627bf3
@arokem
PEP8: whitespace
b36567c
@arokem
Fix flakey code.
200feb1
@arokem
PEP8
312cbda
@arokem
Fix up tests for new API.
ede7695
@arokem
PEP8
e7fd22b
@arokem
Allow selecting a particular n_seeds for few streamlines.
4c7348d
@arokem
I think that I am closer to splitting streamlines correctly.
5a32eac
@arokem
Adding a prealignment before syn registration.
038a592
@arokem
Starting to work on a recobundles based segmentation method.
3c3f0a6
@arokem
More on the prealignment.
6df853a
@arokem
Assign this property.
3c414b9
@arokem
Notebook.
62757e5
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arokem commented Jul 3, 2019

This one was obsoleted through subsequent work

@arokem arokem closed this Jul 3, 2019
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