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Add 'all' option to --stat in compute_coherence() function #28

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Merged
ilariagabusi merged 10 commits into from
Mar 26, 2026
+187 −108
Merged

Add 'all' option to --stat in compute_coherence() function #28

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2397a77
coherence: added tsf support
Mar 16, 2026
14d35fb
Update documentation for trim parameter in compute_coherence()
giuliabiolo Mar 17, 2026
cab23aa
Performance mods
daducci Mar 18, 2026
6b54a03
Performance mods
daducci Mar 18, 2026
3112c07
Fix bug in filter() when dealing with TSF files
daducci Mar 19, 2026
96ac1c4
filter(): moved imports inside function for efficiency
daducci Mar 20, 2026
c93a960
assign(): fix import bug
daducci Mar 20, 2026
5ae1a23
Create empty header if no one is passed
daducci Mar 25, 2026
1fca09b
Fixed coherence
daducci Mar 26, 2026
9980802
Fix bug in computation of polar angles
daducci Mar 26, 2026
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9 changes: 1 addition & 8 deletions dicelib/connectivity.pyx
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Original file line number Diff line number Diff line change
@@ -1,19 +1,12 @@
# cython: language_level=3, c_string_type=str, c_string_encoding=ascii, boundscheck=False, wraparound=False, profile=False
# cython: language_level=3, c_string_type=str, c_string_encoding=ascii, boundscheck=False, wraparound=False, profile=False, nonecheck=False, cdivision=True, initializedcheck=False, binding=False
from concurrent.futures import ThreadPoolExecutor

from libc.math cimport round as cround, sqrt
from libcpp cimport bool

import nibabel as nib

import numpy as np

import os

from scipy.linalg import inv

from time import time

from dicelib.streamline import create_replicas
from dicelib.ui import ProgressBar, set_verbose, setup_logger
from dicelib.utils import check_params, File, Num, format_time
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6 changes: 3 additions & 3 deletions dicelib/scripts/dice_tractogram.py
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Expand Up @@ -443,8 +443,8 @@ def coherence():
[['tractogram'], {'help': desc['tractogram_filename']}],
[['sph_func'], {'help': desc['sph_func_filename']}],
[['out_weights'], {'help': desc['out_weights_filename']}],
[['--stat'], {'choices': ['min','mean','max'], 'default': 'min', 'help': desc['stat']}],
[['--normalize', '-n'], {'action': 'store_true', 'help': desc['normalize']}],
[['--stat'], {'choices': ['min','mean','max', 'all'], 'default': 'min', 'help': desc['stat']}],
[['--normalize', '-n'], {'type': str, 'default': None, 'help': desc['lobes_filename']}],
[['--trim', '-t'], {'type': float, 'default': 0.05, 'help': desc['trim']}],
[['--shift', '-s'], {'type': float, 'default': 0.5, 'help': desc['shift']}]
]
Expand All @@ -455,7 +455,7 @@ def coherence():
sph_func_filename=options.sph_func,
out_weights_filename=options.out_weights,
stat=options.stat,
normalize=options.normalize,
lobes_filename=options.normalize,
trim=options.trim,
shift=options.shift,
force=options.force,
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