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FIX: Split aCompCor into aCompCor, cCompCor, wCompCor #2523

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merged 7 commits into from
Sep 2, 2021
Merged

FIX: Split aCompCor into aCompCor, cCompCor, wCompCor #2523

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daf8e63
ENH: Add RenameACompCor interface
effigies Aug 30, 2021
318f9f1
ENH: Insert aCompCor renamer into confounds workflow
effigies Aug 30, 2021
be6a5be
TEST: Add regression test with some truncated aCompCor components
effigies Aug 31, 2021
4d479a9
ENH: Add interface for filtering out metadata of dropped components
effigies Sep 1, 2021
9fe66ec
TEST: Check FilterDropped
effigies Sep 1, 2021
291315d
ENH: Filter dropped tCompCor and aCompCor components
effigies Sep 1, 2021
f1f2333
DOC: Add docstrings for new interfaces [skip tests]
effigies Sep 2, 2021
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82 changes: 82 additions & 0 deletions fmriprep/interfaces/confounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,88 @@ def _run_interface(self, runtime):
return runtime


class _FilterDroppedInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, desc='input CompCor metadata')


class _FilterDroppedOutputSpec(TraitedSpec):
out_file = File(desc='filtered CompCor metadata')


class FilterDropped(SimpleInterface):
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can you add a docstring here?

input_spec = _FilterDroppedInputSpec
output_spec = _FilterDroppedOutputSpec

def _run_interface(self, runtime):
self._results["out_file"] = fname_presuffix(
self.inputs.in_file,
suffix='_filtered',
use_ext=True,
newpath=runtime.cwd)

metadata = pd.read_csv(self.inputs.in_file, sep='\t')
metadata[metadata.retained].to_csv(self._results["out_file"], sep='\t', index=False)

return runtime


class _RenameACompCorInputSpec(BaseInterfaceInputSpec):
components_file = File(exists=True, desc='input aCompCor components')
metadata_file = File(exists=True, desc='input aCompCor metadata')


class _RenameACompCorOutputSpec(TraitedSpec):
components_file = File(desc='output aCompCor components')
metadata_file = File(desc='output aCompCor metadata')


class RenameACompCor(SimpleInterface):
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and here?

input_spec = _RenameACompCorInputSpec
output_spec = _RenameACompCorOutputSpec

def _run_interface(self, runtime):
self._results["components_file"] = fname_presuffix(
self.inputs.components_file,
suffix='_renamed',
use_ext=True,
newpath=runtime.cwd)
self._results["metadata_file"] = fname_presuffix(
self.inputs.metadata_file,
suffix='_renamed',
use_ext=True,
newpath=runtime.cwd)

components = pd.read_csv(self.inputs.components_file, sep='\t')
metadata = pd.read_csv(self.inputs.metadata_file, sep='\t')
all_comp_cor = metadata[metadata["retained"]]

c_comp_cor = all_comp_cor[all_comp_cor["mask"] == "CSF"]
w_comp_cor = all_comp_cor[all_comp_cor["mask"] == "WM"]
a_comp_cor = all_comp_cor[all_comp_cor["mask"] == "combined"]

c_orig = c_comp_cor["component"]
c_new = [f"c_comp_cor_{i:02d}" for i in range(len(c_orig))]

w_orig = w_comp_cor["component"]
w_new = [f"w_comp_cor_{i:02d}" for i in range(len(w_orig))]

a_orig = a_comp_cor["component"]
a_new = [f"a_comp_cor_{i:02d}" for i in range(len(a_orig))]

(components.rename(columns=dict(zip(c_orig, c_new)))
.rename(columns=dict(zip(w_orig, w_new)))
.rename(columns=dict(zip(a_orig, a_new)))
).to_csv(self._results["components_file"], sep='\t', index=False)

metadata.loc[c_comp_cor.index, "component"] = c_new
metadata.loc[w_comp_cor.index, "component"] = w_new
metadata.loc[a_comp_cor.index, "component"] = a_new

metadata.to_csv(self._results["metadata_file"], sep='\t', index=False)

return runtime


class GatherConfoundsInputSpec(BaseInterfaceInputSpec):
signals = File(exists=True, desc='input signals')
dvars = File(exists=True, desc='file containing DVARS')
Expand Down
7 changes: 7 additions & 0 deletions fmriprep/interfaces/tests/conftest.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
import pytest
from pathlib import Path


@pytest.fixture(scope="module")
def data_dir():
return Path(__file__).parent / "data"
Empty file added fmriprep/interfaces/tests/data/__init__.py
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51 changes: 51 additions & 0 deletions fmriprep/interfaces/tests/data/acompcor_renamed.tsv
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51 changes: 51 additions & 0 deletions fmriprep/interfaces/tests/data/acompcor_truncated.tsv
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61 changes: 61 additions & 0 deletions fmriprep/interfaces/tests/data/component_metadata_filtered.tsv
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@@ -0,0 +1,61 @@
component mask singular_value variance_explained cumulative_variance_explained retained
a_comp_cor_00 CSF 303.3879065215 0.0822378515 0.0822378515 True
a_comp_cor_01 CSF 265.3127089823 0.0628914102 0.1451292617 True
a_comp_cor_02 CSF 246.9403411402 0.0544827867 0.1996120484 True
a_comp_cor_03 CSF 230.7904478523 0.0475894718 0.2472015202 True
a_comp_cor_04 CSF 204.1002458456 0.0372187926 0.2844203128 True
a_comp_cor_05 CSF 191.4965421158 0.0327640136 0.3171843264 True
a_comp_cor_06 CSF 164.3946836008 0.0241463095 0.3413306359 True
a_comp_cor_07 CSF 163.0617292465 0.023756328 0.3650869639 True
a_comp_cor_08 CSF 155.6055929068 0.0216334423 0.3867204062 True
a_comp_cor_09 CSF 142.6779990644 0.0181881801 0.4049085863 True
a_comp_cor_10 CSF 132.7833535167 0.0157529716 0.4206615579 True
a_comp_cor_11 CSF 125.5448815801 0.0140822888 0.4347438468 True
a_comp_cor_12 CSF 114.4560888929 0.0117045044 0.4464483511 True
a_comp_cor_13 CSF 109.7800169819 0.0107676719 0.457216023 True
a_comp_cor_14 CSF 98.9016427614 0.0087394124 0.4659554354 True
a_comp_cor_15 CSF 95.592760075 0.0081644179 0.4741198534 True
a_comp_cor_16 CSF 93.2993710837 0.0077773682 0.4818972215 True
a_comp_cor_17 CSF 89.7572859278 0.0071980465 0.489095268 True
a_comp_cor_18 CSF 85.4637024159 0.0065258732 0.4956211413 True
a_comp_cor_19 CSF 83.3739078155 0.0062106283 0.5018317696 True
a_comp_cor_20 WM 195.3633011611 0.0249509989 0.0249509989 True
a_comp_cor_21 WM 152.0507341632 0.0151139858 0.0400649847 True
a_comp_cor_22 WM 143.1829225994 0.0134024567 0.0534674414 True
a_comp_cor_23 WM 119.7135045391 0.0093688925 0.0628363339 True
a_comp_cor_24 WM 110.7818275484 0.0080230411 0.070859375 True
a_comp_cor_25 WM 100.5105167828 0.0066042724 0.0774636474 True
a_comp_cor_26 WM 94.344414343 0.0058188124 0.0832824598 True
a_comp_cor_27 WM 92.150833289 0.0055513742 0.0888338339 True
a_comp_cor_28 WM 90.5254087866 0.0053572629 0.0941910968 True
a_comp_cor_29 WM 88.523526571 0.0051229413 0.0993140381 True
a_comp_cor_30 WM 86.0931701872 0.0048455086 0.1041595467 True
a_comp_cor_31 WM 84.7990437222 0.004700931 0.1088604777 True
a_comp_cor_32 WM 83.3114198348 0.0045374415 0.1133979192 True
a_comp_cor_33 WM 81.0694160734 0.0042965123 0.1176944314 True
a_comp_cor_34 WM 80.4668446429 0.0042328795 0.121927311 True
a_comp_cor_35 WM 79.4022991891 0.0041216217 0.1260489326 True
a_comp_cor_36 WM 78.1613446177 0.0039937972 0.1300427299 True
a_comp_cor_37 WM 77.3254517928 0.003908831 0.1339515609 True
a_comp_cor_38 WM 77.0534117377 0.003881376 0.1378329369 True
a_comp_cor_39 WM 76.2953999669 0.0038053856 0.1416383225 True
a_comp_cor_169 combined 198.9777037853 0.0252962205 0.0252962205 True
a_comp_cor_170 combined 154.343866075 0.0152203822 0.0405166027 True
a_comp_cor_171 combined 144.8823205662 0.0134115075 0.0539281102 True
a_comp_cor_172 combined 120.8445698188 0.0093304178 0.063258528 True
a_comp_cor_173 combined 112.8109339075 0.0081310981 0.071389626 True
a_comp_cor_174 combined 103.1053103638 0.0067921752 0.0781818012 True
a_comp_cor_175 combined 101.536218232 0.0065870169 0.0847688181 True
a_comp_cor_176 combined 94.2588177592 0.0056766326 0.0904454507 True
a_comp_cor_177 combined 92.4469798367 0.0054604982 0.0959059488 True
a_comp_cor_178 combined 91.5242270524 0.005352035 0.1012579839 True
a_comp_cor_179 combined 89.1481999125 0.0050777576 0.1063357415 True
a_comp_cor_180 combined 86.0081616799 0.0047263528 0.1110620943 True
a_comp_cor_181 combined 84.3147231404 0.0045420681 0.1156041625 True
a_comp_cor_182 combined 83.821614868 0.0044890956 0.1200932581 True
a_comp_cor_183 combined 81.5457945837 0.0042486401 0.1243418982 True
a_comp_cor_184 combined 80.7942317719 0.0041706863 0.1285125845 True
a_comp_cor_185 combined 78.7768936096 0.0039650121 0.1324775965 True
a_comp_cor_186 combined 77.8233137548 0.0038696015 0.1363471981 True
a_comp_cor_187 combined 77.7936337977 0.0038666506 0.1402138486 True
a_comp_cor_188 combined 77.0694477923 0.0037949958 0.1440088445 True
121 changes: 121 additions & 0 deletions fmriprep/interfaces/tests/data/component_metadata_renamed.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,121 @@
component mask singular_value variance_explained cumulative_variance_explained retained
c_comp_cor_00 CSF 303.3879065215 0.0822378515 0.0822378515 True
c_comp_cor_01 CSF 265.3127089823 0.0628914102 0.1451292617 True
c_comp_cor_02 CSF 246.9403411402 0.0544827867 0.1996120484 True
c_comp_cor_03 CSF 230.7904478523 0.0475894718 0.2472015202 True
c_comp_cor_04 CSF 204.1002458456 0.0372187926 0.2844203128 True
c_comp_cor_05 CSF 191.4965421158 0.0327640136 0.3171843264 True
c_comp_cor_06 CSF 164.3946836008 0.0241463095 0.3413306359 True
c_comp_cor_07 CSF 163.0617292465 0.023756328 0.3650869639 True
c_comp_cor_08 CSF 155.6055929068 0.0216334423 0.3867204062 True
c_comp_cor_09 CSF 142.6779990644 0.0181881801 0.4049085863 True
c_comp_cor_10 CSF 132.7833535167 0.0157529716 0.4206615579 True
c_comp_cor_11 CSF 125.5448815801 0.0140822888 0.4347438468 True
c_comp_cor_12 CSF 114.4560888929 0.0117045044 0.4464483511 True
c_comp_cor_13 CSF 109.7800169819 0.0107676719 0.457216023 True
c_comp_cor_14 CSF 98.9016427614 0.0087394124 0.4659554354 True
c_comp_cor_15 CSF 95.592760075 0.0081644179 0.4741198534 True
c_comp_cor_16 CSF 93.2993710837 0.0077773682 0.4818972215 True
c_comp_cor_17 CSF 89.7572859278 0.0071980465 0.489095268 True
c_comp_cor_18 CSF 85.4637024159 0.0065258732 0.4956211413 True
c_comp_cor_19 CSF 83.3739078155 0.0062106283 0.5018317696 True
dropped0 CSF 81.1499858901 0.0058837217 0.5077154913 False
dropped1 CSF 79.5953753795 0.0056604492 0.5133759405 False
dropped2 CSF 77.2577614056 0.0053328512 0.5187087917 False
dropped3 CSF 75.5079204435 0.0050940153 0.523802807 False
dropped4 CSF 73.5288160796 0.0048304809 0.5286332879 False
dropped5 CSF 71.9710349644 0.004627972 0.5332612599 False
dropped6 CSF 71.5010523346 0.0045677265 0.5378289864 False
dropped7 CSF 70.2484154012 0.0044090832 0.5422380695 False
dropped8 CSF 68.485370616 0.0041905483 0.5464286178 False
dropped9 CSF 68.1403689881 0.004148434 0.5505770518 False
dropped10 CSF 66.7913214051 0.0039857981 0.5545628499 False
dropped11 CSF 65.7544720308 0.0038630098 0.5584258597 False
dropped12 CSF 64.9251957319 0.003766186 0.5621920457 False
dropped13 CSF 63.8149558968 0.0036384815 0.5658305272 False
dropped14 CSF 62.3065499093 0.0034685075 0.5692990347 False
dropped15 CSF 60.5440181278 0.0032750483 0.5725740829 False
dropped16 CSF 60.148632541 0.0032324122 0.5758064952 False
dropped17 CSF 58.8915186625 0.0030987086 0.5789052037 False
dropped18 CSF 57.6950186454 0.0029740746 0.5818792784 False
dropped19 CSF 57.2791049695 0.00293135 0.5848106283 False
w_comp_cor_00 WM 195.3633011611 0.0249509989 0.0249509989 True
w_comp_cor_01 WM 152.0507341632 0.0151139858 0.0400649847 True
w_comp_cor_02 WM 143.1829225994 0.0134024567 0.0534674414 True
w_comp_cor_03 WM 119.7135045391 0.0093688925 0.0628363339 True
w_comp_cor_04 WM 110.7818275484 0.0080230411 0.070859375 True
w_comp_cor_05 WM 100.5105167828 0.0066042724 0.0774636474 True
w_comp_cor_06 WM 94.344414343 0.0058188124 0.0832824598 True
w_comp_cor_07 WM 92.150833289 0.0055513742 0.0888338339 True
w_comp_cor_08 WM 90.5254087866 0.0053572629 0.0941910968 True
w_comp_cor_09 WM 88.523526571 0.0051229413 0.0993140381 True
w_comp_cor_10 WM 86.0931701872 0.0048455086 0.1041595467 True
w_comp_cor_11 WM 84.7990437222 0.004700931 0.1088604777 True
w_comp_cor_12 WM 83.3114198348 0.0045374415 0.1133979192 True
w_comp_cor_13 WM 81.0694160734 0.0042965123 0.1176944314 True
w_comp_cor_14 WM 80.4668446429 0.0042328795 0.121927311 True
w_comp_cor_15 WM 79.4022991891 0.0041216217 0.1260489326 True
w_comp_cor_16 WM 78.1613446177 0.0039937972 0.1300427299 True
w_comp_cor_17 WM 77.3254517928 0.003908831 0.1339515609 True
w_comp_cor_18 WM 77.0534117377 0.003881376 0.1378329369 True
w_comp_cor_19 WM 76.2953999669 0.0038053856 0.1416383225 True
dropped543 WM 57.974868005 0.0021972603 0.503144646 False
dropped544 WM 57.8953856222 0.0021912396 0.5053358856 False
dropped545 WM 57.8412263429 0.0021871419 0.5075230275 False
dropped546 WM 57.712694931 0.0021774324 0.5097004598 False
dropped547 WM 57.6881631871 0.0021755817 0.5118760415 False
dropped548 WM 57.5332376458 0.002163912 0.5140399535 False
dropped549 WM 57.4248728403 0.0021557681 0.5161957217 False
dropped550 WM 57.2839446853 0.0021452001 0.5183409217 False
dropped551 WM 57.2749923068 0.0021445296 0.5204854513 False
dropped552 WM 57.2083731386 0.0021395437 0.522624995 False
dropped553 WM 57.1224483551 0.0021331215 0.5247581165 False
dropped554 WM 57.0580867294 0.0021283173 0.5268864338 False
dropped555 WM 56.8779500159 0.0021149 0.5290013338 False
dropped556 WM 56.6491198238 0.002097917 0.5310992508 False
dropped557 WM 56.5919145056 0.0020936821 0.5331929329 False
dropped558 WM 56.5520028524 0.00209073 0.5352836629 False
dropped559 WM 56.4734227579 0.0020849238 0.5373685867 False
dropped560 WM 56.3868665406 0.0020785376 0.5394471243 False
dropped561 WM 56.3074826046 0.0020726892 0.5415198135 False
dropped562 WM 56.1904069084 0.002064079 0.5435838926 False
a_comp_cor_00 combined 198.9777037853 0.0252962205 0.0252962205 True
a_comp_cor_01 combined 154.343866075 0.0152203822 0.0405166027 True
a_comp_cor_02 combined 144.8823205662 0.0134115075 0.0539281102 True
a_comp_cor_03 combined 120.8445698188 0.0093304178 0.063258528 True
a_comp_cor_04 combined 112.8109339075 0.0081310981 0.071389626 True
a_comp_cor_05 combined 103.1053103638 0.0067921752 0.0781818012 True
a_comp_cor_06 combined 101.536218232 0.0065870169 0.0847688181 True
a_comp_cor_07 combined 94.2588177592 0.0056766326 0.0904454507 True
a_comp_cor_08 combined 92.4469798367 0.0054604982 0.0959059488 True
a_comp_cor_09 combined 91.5242270524 0.005352035 0.1012579839 True
a_comp_cor_10 combined 89.1481999125 0.0050777576 0.1063357415 True
a_comp_cor_11 combined 86.0081616799 0.0047263528 0.1110620943 True
a_comp_cor_12 combined 84.3147231404 0.0045420681 0.1156041625 True
a_comp_cor_13 combined 83.821614868 0.0044890956 0.1200932581 True
a_comp_cor_14 combined 81.5457945837 0.0042486401 0.1243418982 True
a_comp_cor_15 combined 80.7942317719 0.0041706863 0.1285125845 True
a_comp_cor_16 combined 78.7768936096 0.0039650121 0.1324775965 True
a_comp_cor_17 combined 77.8233137548 0.0038696015 0.1363471981 True
a_comp_cor_18 combined 77.7936337977 0.0038666506 0.1402138486 True
a_comp_cor_19 combined 77.0694477923 0.0037949958 0.1440088445 True
dropped957 combined 58.498983616 0.0021864696 0.5028418222 False
dropped958 combined 58.4583451584 0.0021834329 0.5050252551 False
dropped959 combined 58.4084551025 0.0021797076 0.5072049627 False
dropped960 combined 58.358803729 0.0021760034 0.5093809661 False
dropped961 combined 58.0957193109 0.0021564286 0.5115373947 False
dropped962 combined 57.9803871837 0.0021478751 0.5136852698 False
dropped963 combined 57.9333367991 0.0021443906 0.5158296604 False
dropped964 combined 57.8646604218 0.0021393095 0.51796897 False
dropped965 combined 57.8129529833 0.0021354879 0.5201044579 False
dropped966 combined 57.6361694545 0.0021224479 0.5222269057 False
dropped967 combined 57.5798626323 0.0021183029 0.5243452086 False
dropped968 combined 57.529751472 0.0021146174 0.526459826 False
dropped969 combined 57.4223094632 0.0021067263 0.5285665523 False
dropped970 combined 57.386187055 0.0021040766 0.5306706289 False
dropped971 combined 57.1828951485 0.0020891955 0.5327598245 False
dropped972 combined 57.1115317726 0.0020839842 0.5348438087 False
dropped973 combined 56.9748270267 0.0020740195 0.5369178282 False
dropped974 combined 56.9346930627 0.0020710986 0.5389889268 False
dropped975 combined 56.9038934374 0.0020688584 0.5410577853 False
dropped976 combined 56.7830846208 0.0020600833 0.5431178685 False
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