Generate HDF5 from TRKs #985
Conversation
|
Hello @frheault, Thank you for updating ! Comment last updated at 2024-05-22 20:24:47 UTC |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #985 +/- ##
==========================================
+ Coverage 68.01% 68.05% +0.04%
==========================================
Files 419 420 +1
Lines 21567 21667 +100
Branches 3241 3257 +16
==========================================
+ Hits 14668 14745 +77
- Misses 5608 5632 +24
+ Partials 1291 1290 -1
|
This week, hein ;) |
| help='Save empty connections. Then, the list of possible ' | ||
| p.add_argument('--save_empty', nargs='?', metavar='labels_list', | ||
| dest='labels_list', const=True, | ||
| help='Save empty connections. The list of possible ' |
There was a problem hiding this comment.
I would add in the description that the labels_list is now facultative.
There was a problem hiding this comment.
Why not change the dest to labels_file instead. It sounds like args.labels_list should be a list.
There was a problem hiding this comment.
We could change that later in all the scripts and functions.
| |-- LABEL1_LABEL2.trk | ||
| |-- [...] | ||
| |-- LABEL90_LABEL90.trk | ||
|
|
There was a problem hiding this comment.
Didn't read the code yet. But from a user point of view reading this doc, here's a question: what happens if one is missing? Ex, if there is not file LABEL1_LABEL2.trk. Do you infer from other files all existing labels? Do you raise a warning? Will it work nonetheless?
There was a problem hiding this comment.
There is no problem with missing labels, this is why all the other scripts need a labels_list (to know what is and what is not missing).
I added: "The value of first labels should be smaller or equal to the second labels.
Connectivity scripts in scilpy only consider the upper triangular part of the
connectivity matrix."
| p.add_argument('in_bundles', nargs='+', | ||
| help='Path of the input connections or bundles.') | ||
| p.add_argument('out_hdf5', | ||
| help='Output HDF5 filename (.h5).') |
There was a problem hiding this comment.
I had a question concerning this. In dwi_ml, I save my hdf5 files as .hdf5, not .h5. Any difference? Do we always accept them? Should we change the doc in all hdf5 scripts?
There was a problem hiding this comment.
There is no difference, when I looked at stuff done in Vanderbilt and Dipy, they used .h5 so I used the same
https://figshare.com/articles/dataset/DIPY_Synb0_weights/20277522/2
| This script is useful to convert a set of connections or bundles to a single | ||
| HDF5 file. The HDF5 file will contain a group for each input file, with the | ||
| streamlines stored in the specified space and origin. | ||
|
|
There was a problem hiding this comment.
Maybe, something like: Most of our scripts using hdf5 files deal with any space and origin, so just choose your favorite option?
There was a problem hiding this comment.
All of my scripts for connectivity assume vox/corner (to avoid as much computation on 100k connections).
So I added: (keep the default if you are going to use the connectivity scripts in scilpy).
Quick description
New script to generate a HDF5 in the same style as for connectomics from a list of TRKs.
(Tests for the script will come this week)
...
Type of change
Check the relevant options.
Provide data, screenshots, command line to test (if relevant)
...
Checklist