junifer 0.0.6.dev175__py3-none-any.whl → 0.0.6.dev194__py3-none-any.whl

{junifer-0.0.6.dev175.dist-info → junifer-0.0.6.dev194.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=uPLuY27S7AY4kFzJX0ncCpzHnWJdztveMJpY3Di-wwQ,482
-junifer/_version.py,sha256=kxb4jDdB46TYAsROV8U-peWvw8kJsVsZHpoSPS_JLT0,428
+junifer/_version.py,sha256=3Rg3rnSlDZ28mFFdWqzgj1pw9KotN5k2vqz_IgbP7SM,428
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
 junifer/api/__init__.py,sha256=aAXW_KAEGQ8aAP5Eni2G1R4MWBF7UgjKOgM6akLuJco,252
@@ -70,40 +70,54 @@ junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py,sha256=8jxpNZelXwpJG
 junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=NfEKlpaMNImiPLGyETDDCMoWZ7_oHGsiVAbQNYsfi3o,3252
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=xJDI2QKtdjcNzpd1oVFM3guh1SFHM6jKstl7pFmzOuk,267
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-junifer/data/coordinates.py,sha256=1HH2Kz5nzZKN6-wJRmYotPH76fPaL1yYbCt8AhONogk,12496
-junifer/data/masks.py,sha256=omKOJLnUpmI1yVUkckWy9HhzbFZuYbYdOyr49xFvEwU,21640
-junifer/data/parcellations.py,sha256=mw1xa6yFWAaVktTkkpCt2ZgSUapZbPwloN2UoPdLzdg,65490
+junifer/data/__init__.pyi,sha256=qYszjUYcbFi_2zO23MnbA2HhTW-Ad2oh1pqPQYd6yt0,542
+junifer/data/_dispatch.py,sha256=_hmlIXuuuLJBbY5VH6lohJzhbMB7KEhFkVFwRDEdR_E,6189
+junifer/data/pipeline_data_registry_base.py,sha256=_3NheI2Wu5RuKI87WwR1bRzcNyZv_0UcL9q07jmPdh8,1922
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 junifer/data/template_spaces.py,sha256=9uZuFztBGNZk3mhUI2h0oQMajjx6Wv31Fx11pGlDI20,6510
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 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz,sha256=j6EY8EtRnUuRxeKgD65Q6B0GPEPIALKDJEIje1TfnAU,88270
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.nii.gz,sha256=crb_y7YO1vjjf2PwbRJUm8KamPK6fx1y0B_l-E3g8FY,12862
 junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz,sha256=jfMe_4H9XEnArYms5bSQbqS2V1_HbLHTfI5amQa_Pes,8700
-junifer/data/tests/test_coordinates.py,sha256=BNkz9qFbnwAI0oVlIm_XrT-z4Vsia_rMtMVaoFXT6mU,4328
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 junifer/data/tests/test_data_utils.py,sha256=_DaiC8K79gs9HFHxr-udNeE2YTM6JA0-1i-K2cqK9qA,1087
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 junifer/data/tests/test_template_spaces.py,sha256=PJulN7xHpAcSOTY-UzTG_WPywZEBSlAZGiNG4gzk1_8,3144
 junifer/datagrabber/__init__.py,sha256=EHIK-lbjuvkt0V8ypFvLSt85OAAXSkaxBmVlCbNNz8M,323
 junifer/datagrabber/__init__.pyi,sha256=zOQE4TaCKXBTHnNqgmECtsszWIOHYiQ1CUEeXXFU9F4,832
@@ -167,22 +181,22 @@ junifer/markers/__init__.py,sha256=wHAxljlZppxgXimSJw21mp9oUYYyaID4LYfeBolva30,3
 junifer/markers/__init__.pyi,sha256=9a72D9k6esTzLvmvULXHOeaQtIchjtN7VELpCeaddsM,957
 junifer/markers/base.py,sha256=__Z0owDdjTwb7alQneOeoaUqaeCVbHwFRnaRZERi37M,8364
 junifer/markers/brainprint.py,sha256=WqK78RVaFX1e0AcwpkNzCUEZWRSMgoMCX1-wNOXDhmk,15116
-junifer/markers/ets_rss.py,sha256=4b1rUIMt4RISNSMQqATJadYheyT-YOnadWZDwGsFELk,4273
-junifer/markers/parcel_aggregation.py,sha256=WKS_GILu80JF6IMK0BsHLvq7NefqlHt6u37b2lOx7_Q,8349
+junifer/markers/ets_rss.py,sha256=xbAO0T3k12XMuzf88OMEDaFh0yytIs-2OVkLABMLN6A,4256
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 junifer/markers/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/markers/sphere_aggregation.py,sha256=E_f6bEf_EzuK1WDreO1Hstsp2hXTwaVBysbVX9gnX2Y,7910
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 junifer/markers/utils.py,sha256=b6Bt_isqsOD2OF7oHvEpHyilauxYZzyz8YcbGWq6J4A,3833
 junifer/markers/complexity/__init__.py,sha256=6ZoTQy7hU_vnH65VlJbi61VfPAdg-RpuV84aXhzr8j0,552
 junifer/markers/complexity/__init__.pyi,sha256=I2IbSuKnUEf03Yunv884ASBxKjQ9_fenACccjaxTkyc,495
 junifer/markers/complexity/complexity_base.py,sha256=_JIqrglcPG8lEzCdM27o0KLOyLcncebk_YVBq_-pPak,4165
-junifer/markers/complexity/hurst_exponent.py,sha256=gx8ZRzfJq6UIwnfPFXhZrHdMuhWO-arqM12iZx7ZzBo,4697
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 junifer/markers/complexity/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 junifer/markers/complexity/tests/test_complexity_base.py,sha256=0E0AjjBqenIb6ZzK-EMie24J4vVjWUjAPfkvvognu9Y,453
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 junifer/markers/complexity/tests/test_multiscale_entropy_auc.py,sha256=UDScZLPYc1S1kpL04_Rcj2U_dgRhq2VzNOEDv5O8WGE,2382
@@ -196,51 +210,51 @@ junifer/markers/falff/__init__.pyi,sha256=X-q2zBjUX0imQ37yN2Cg5gKfDvq8sh_9y2hRH4
 junifer/markers/falff/_afni_falff.py,sha256=QNi_4MU4_sfnfXedrYHT-kn17KCDE6a7ELfSGmRZPmA,4521
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 junifer/markers/falff/falff_base.py,sha256=1VjEZMd7BpXDc2subm0VzZNxFp6uxMb9QjBmMC6tDVg,4903
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-junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py,sha256=nAvTT4ZLqW-uDAQ_r5hT__TbxFTqTkjm4BJ-1YD7a7s,4745
-junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py,sha256=atV7iNjnFbIKbzBkzFYtgF0cbetESvv3a5R-SLzrt6Y,5412
+junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py,sha256=4vRiph2nHK6iBQcbhAo6LACp_QLOvA8ADyXSUQvXvfQ,4736
+junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py,sha256=BZYiUv_E3VYCr500zKGeb3q7WpN816UxR0_gRvawkvA,5405
 junifer/markers/functional_connectivity/functional_connectivity_base.py,sha256=dUv-pfgAhkHuz_zSKClEYeOkcIdhjdJ1fiNvvWhATDg,5639
-junifer/markers/functional_connectivity/functional_connectivity_parcels.py,sha256=pefRn1EhYegN1KCs1VvMOe4vj4KO-5kSzXJxoUzHSvw,4213
-junifer/markers/functional_connectivity/functional_connectivity_spheres.py,sha256=-N-OO3vl1Djl1nSTJAey_Re3BH2tpyr4UpXfR38ogWw,4946
+junifer/markers/functional_connectivity/functional_connectivity_parcels.py,sha256=lSgzwfQzfLB73CAZNqNpuGuQ-ENcGhG2c_yiVsJY0Pw,4204
+junifer/markers/functional_connectivity/functional_connectivity_spheres.py,sha256=qM82D9h1FmFH8sCfJuA7WEqnzCH-4Lizpk7mQYuf7xA,4939
 junifer/markers/functional_connectivity/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py,sha256=CP8ZZoTciMoI9c-VVsLF9mJivyzPB6C4mZE0tlL52pI,3231
 junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py,sha256=y0O-eBjOzUp77g6o_II7D5KB2rKtDz_a_hez-MPDU3M,2482
 junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py,sha256=NYWe8kdSVVXlluLm074koDE6xw_t0bhPn47kRYMg1vA,2522
 junifer/markers/functional_connectivity/tests/test_functional_connectivity_base.py,sha256=RmPTrG0uLKb5RgdHXUnH6lon60FxN1JCtr-dsTBaX28,522
-junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py,sha256=GiRtQ-cbbmM4_oekGjIDtFaNkmYON_eSf3F4jzS0XCo,3876
-junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py,sha256=Bu2vicoxET-eHYqmfiPtYmFOhBCjBsXO7vv9UzLdYJQ,4143
+junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py,sha256=EVJTTtCws93g3AYVzA0XDIYY_BUMun4v40dsS_YXUBs,3891
+junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py,sha256=OU2FWAH0Gb4gEOF0m1PAoo5xLKVPetNkwV-ssQTZ1Yw,4157
 junifer/markers/reho/__init__.py,sha256=WZf4A0XaRThjl8SlFOhvTLUfhTHp5koLxZgowsgTSAE,211
 junifer/markers/reho/__init__.pyi,sha256=_aFb-Ry_EP2OMU6xRL4GlfuDpSl_egHllL-fz7vXjcE,118
 junifer/markers/reho/_afni_reho.py,sha256=iaZFPJbyB9-QQAZ5-kKxwN0APB5MH85pOAChq-JFLNI,6469
 junifer/markers/reho/_junifer_reho.py,sha256=7-jD28YQQWb3dfT6SxyYfGugFSq8wi7_2hUA-ryiGAo,9307
 junifer/markers/reho/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/markers/reho/reho_base.py,sha256=Tdnl5SJ66p461UJ-UilEGKrMdEPwGMemN_QIQgmc8o8,4065
-junifer/markers/reho/reho_parcels.py,sha256=GTYy1cMe0RdAgkvgZnnIGlQ-u3EfkxhRmBloPNUrFuk,6421
-junifer/markers/reho/reho_spheres.py,sha256=dTTTksT1iqtPnc0lMtbVU-FmeLAO8Ml6N3fBLGyIaac,7015
+junifer/markers/reho/reho_parcels.py,sha256=tfGasSaAI-ioxVBTD2L_4gJQthoAq5Fp9e5iRS3mXhI,6404
+junifer/markers/reho/reho_spheres.py,sha256=5IcqWfGO4dgBFaWB4s1QIJnt2M3li0VUz5oeQimG_BA,7008
 junifer/markers/reho/tests/test_reho_parcels.py,sha256=bRtDi91qRcRYaRqqQjuSU6NuNz-KwLVCoTYo-e5VmsI,4075
 junifer/markers/reho/tests/test_reho_spheres.py,sha256=VyyQ3hhD6ArFc1BmigmAdePACB1EMQlo1mDr2QKvT2I,3989
 junifer/markers/temporal_snr/__init__.py,sha256=86hNMyaSfWlWOXZ6m9reSDtMIgUaByOXjcxCvo7LmDw,235
 junifer/markers/temporal_snr/__init__.pyi,sha256=20FhG9ZkAHQfmJ0r5p6fRMxhK8xrFQeFr0cgTrqu3ik,162
 junifer/markers/temporal_snr/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/markers/temporal_snr/temporal_snr_base.py,sha256=xWBTrwsrI44DCV5okRaliLJHrlvDs5LkD0xLEIGZcMc,3874
-junifer/markers/temporal_snr/temporal_snr_parcels.py,sha256=f85zsqYVox7B4WNGXe8XigBGaVxWannz8EmTc4S7GpQ,3279
-junifer/markers/temporal_snr/temporal_snr_spheres.py,sha256=sU0VzxQdr5a1XESUPwPsGF5NAT7EzSLnmPT9nxCKcLA,3987
+junifer/markers/temporal_snr/temporal_snr_parcels.py,sha256=O8kBU-Jzlf12m-DaBLxZtHEVVqBW0jiGlbMgdFk8ots,3262
+junifer/markers/temporal_snr/temporal_snr_spheres.py,sha256=DPh4CziLyMNbdfzqobR2RHx2aKSy6UfZMRS5aGfNuF8,3980
 junifer/markers/temporal_snr/tests/test_temporal_snr_base.py,sha256=KRln5ibLTJJQ_f3pnioATfwyhK5htGc2o2J7CPcoyfs,426
 junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py,sha256=JnsLIF0qT4L3JfSIBeHxFsugQ89P9by0CmNwNJiFnZY,2042
 junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py,sha256=cxYnKreFRauIs3NYaaB1EKeFEHZxPplxOuywWNcUnLg,2175
 junifer/markers/tests/test_brainprint.py,sha256=fjwGQZk0Or0VUaMxcOr8i_onXRInfspcm3wD_qjqxDs,1588
-junifer/markers/tests/test_ets_rss.py,sha256=KCPVx0e1Xcku8ktPjKUXG7OQA6a_dgc7kuzTIVSRff0,2603
+junifer/markers/tests/test_ets_rss.py,sha256=kKjdpn6QlJuE4D-JvFcwp9MlxLYzeS_X_O-egM2d0H0,2618
 junifer/markers/tests/test_marker_utils.py,sha256=SR3ADWI3uGv4ozYqVu-rMZnJVqP6JnjLBgo6qUm16Wk,1478
 junifer/markers/tests/test_markers_base.py,sha256=XYe1Z_88h2g1WX6Em4aM8VMyBuCpy5sNHbbpC0I89m4,2979
-junifer/markers/tests/test_parcel_aggregation.py,sha256=FkB0O0HjTk1CnLOn-dzNs_9_byUOISRc4jV92shN2Kc,27655
-junifer/markers/tests/test_sphere_aggregation.py,sha256=TGn5S7zKK0SJ4nHIxRZQSCpqRBmz7c8Sb8C79dLoHjE,10611
+junifer/markers/tests/test_parcel_aggregation.py,sha256=04OqtY_Z-KW4W1jU5K6GeWnLpBYheM1shcH1Jgw_L3k,27798
+junifer/markers/tests/test_sphere_aggregation.py,sha256=HPaLD6xKdewTt0iANz3nYOD7ZI-g7BqMTiRdV-4sM8M,10669
 junifer/onthefly/__init__.py,sha256=TA6tPuw54ynDlumb9Ii-2p59hw2rGoCMe1-vQ89JzZ8,238
 junifer/onthefly/_brainprint.py,sha256=-q5j5xOkuZD_f-pjWi-b8VRqM9ZXDk1TnccuQDfLwz4,3860
 junifer/onthefly/read_transform.py,sha256=kZ-N_fKe9glaBTjhj_HXrdTtWXGI-fMoBpsawcOgsTw,4340
@@ -248,7 +262,7 @@ junifer/onthefly/tests/test_read_transform.py,sha256=D2C3IpXQHdsJSF07v8rEwGntLGX
 junifer/pipeline/__init__.py,sha256=rxKQGRwc6_sts1KhVIcVVpuXeiFABf11mQQ2h5jgA3U,194
 junifer/pipeline/__init__.pyi,sha256=hhcvNcABhtLaUQiZdTjo5sMWC3rtDkwVshL0sxD5JAE,399
 junifer/pipeline/marker_collection.py,sha256=1xcJqeOZ_IerB7PAMN1itWBv8UR6lUW9xXRoIu4qLXU,5557
-junifer/pipeline/pipeline_component_registry.py,sha256=fyGIEv30w01IhLBvKDmnxWtAi-Z9pRq-T1hpamDceyY,9481
+junifer/pipeline/pipeline_component_registry.py,sha256=TVtAFf0QjeES7TFovc6_nUlkczNeQnDpq85aqNr5Gjg,9484
 junifer/pipeline/pipeline_step_mixin.py,sha256=wakimkG8GC0PWkFHMHIfgzM2yak41xLrzbVRH0oe8D4,7613
 junifer/pipeline/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/pipeline/singleton.py,sha256=c5U8Xn10MQqaXjlLzxLbw3AmSYW6aTw_iSL0rDkbuMU,1011
@@ -266,7 +280,7 @@ junifer/preprocess/base.py,sha256=v6azVA3RwDe3HriYlcaISOX1A6gYgFUKNzQeIDLx92Q,66
 junifer/preprocess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/preprocess/confounds/__init__.py,sha256=L3CquKcndFb2b8yVo-XLi-zsNCe8MMKUN41UOVdooWc,270
 junifer/preprocess/confounds/__init__.pyi,sha256=iC70cqcWNMX4JM42RcUgKb9YX8ciK8oVERdWWjo-13c,102
-junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=WW4ybrUJJiTHcigRhNxuz1gyAqrSjufL4CinDvjqkAM,20307
+junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=XVF3CUXk-UX3Jb36bjZLdfE_hfzHize21PFbNXQBBKU,20369
 junifer/preprocess/confounds/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=xN9tPkktuRHQtmY1UOP0H_sXT7LXPY282kMgYkoQTFE,19973
 junifer/preprocess/smoothing/__init__.py,sha256=7aTwvAG522kA76QQwqxwY5zV_6asyPaaH2uSMTaKQls,216
@@ -321,10 +335,10 @@ junifer/utils/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev175.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev175.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev175.dist-info/METADATA,sha256=CsgsHCA_JZ2DN2_3uysC3HhYOZVpzOouUOgF1l7OJxs,8448
-junifer-0.0.6.dev175.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-junifer-0.0.6.dev175.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev175.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev175.dist-info/RECORD,,
+junifer-0.0.6.dev194.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev194.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev194.dist-info/METADATA,sha256=6DbhevG928yw2l9pvkrhTN-fDl_Y9GEcgc2GDrNUi7U,8448
+junifer-0.0.6.dev194.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+junifer-0.0.6.dev194.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev194.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev194.dist-info/RECORD,,

{junifer-0.0.6.dev175.dist-info → junifer-0.0.6.dev194.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (75.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

junifer/data/coordinates.py

@@ -1,408 +0,0 @@
-"""Functions for coordinates manipulation."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import typing
-from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple, Union
-
-import numpy as np
-import pandas as pd
-from numpy.typing import ArrayLike
-
-from ..pipeline import WorkDirManager
-from ..utils import logger, raise_error, run_ext_cmd
-
-
-__all__ = [
-    "register_coordinates",
-    "list_coordinates",
-    "get_coordinates",
-    "load_coordinates",
-]
-
-
-# Path to the VOIs
-_vois_path = Path(__file__).parent / "VOIs"
-
-# Path to the metadata of the VOIs
-_vois_meta_path = _vois_path / "meta"
-
-# A dictionary containing all supported coordinates and their respective file
-# or data.
-
-# Each entry is a dictionary that must contain at least the following keys:
-# * 'space': the coordinates' space (e.g., 'MNI')
-
-# The built-in coordinates are files that are shipped with the package in the
-# data/VOIs directory. The user can also register their own coordinates, which
-# will be stored as numpy arrays in the dictionary.
-_available_coordinates: Dict[
-    str, Dict[str, Union[Path, ArrayLike, List[str]]]
-] = {
-    "CogAC": {
-        "path": _vois_meta_path / "CogAC_VOIs.txt",
-        "space": "MNI",
-    },
-    "CogAR": {
-        "path": _vois_meta_path / "CogAR_VOIs.txt",
-        "space": "MNI",
-    },
-    "DMNBuckner": {
-        "path": _vois_meta_path / "DMNBuckner_VOIs.txt",
-        "space": "MNI",
-    },
-    "eMDN": {
-        "path": _vois_meta_path / "eMDN_VOIs.txt",
-        "space": "MNI",
-    },
-    "Empathy": {
-        "path": _vois_meta_path / "Empathy_VOIs.txt",
-        "space": "MNI",
-    },
-    "eSAD": {
-        "path": _vois_meta_path / "eSAD_VOIs.txt",
-        "space": "MNI",
-    },
-    "extDMN": {
-        "path": _vois_meta_path / "extDMN_VOIs.txt",
-        "space": "MNI",
-    },
-    "Motor": {
-        "path": _vois_meta_path / "Motor_VOIs.txt",
-        "space": "MNI",
-    },
-    "MultiTask": {
-        "path": _vois_meta_path / "MultiTask_VOIs.txt",
-        "space": "MNI",
-    },
-    "PhysioStress": {
-        "path": _vois_meta_path / "PhysioStress_VOIs.txt",
-        "space": "MNI",
-    },
-    "Rew": {
-        "path": _vois_meta_path / "Rew_VOIs.txt",
-        "space": "MNI",
-    },
-    "Somatosensory": {
-        "path": _vois_meta_path / "Somatosensory_VOIs.txt",
-        "space": "MNI",
-    },
-    "ToM": {
-        "path": _vois_meta_path / "ToM_VOIs.txt",
-        "space": "MNI",
-    },
-    "VigAtt": {
-        "path": _vois_meta_path / "VigAtt_VOIs.txt",
-        "space": "MNI",
-    },
-    "WM": {
-        "path": _vois_meta_path / "WM_VOIs.txt",
-        "space": "MNI",
-    },
-    "Power": {
-        "path": _vois_meta_path / "Power2011_MNI_VOIs.txt",
-        "space": "MNI",
-    },
-    "Power2011": {
-        "path": _vois_meta_path / "Power2011_MNI_VOIs.txt",
-        "space": "MNI",
-    },
-    "Dosenbach": {
-        "path": _vois_meta_path / "Dosenbach2010_MNI_VOIs.txt",
-        "space": "MNI",
-    },
-    "Power2013": {
-        "path": _vois_meta_path / "Power2013_MNI_VOIs.tsv",
-        "space": "MNI",
-    },
-    "AutobiographicalMemory": {
-        "path": _vois_meta_path / "AutobiographicalMemory_VOIs.txt",
-        "space": "MNI",
-    },
-}
-
-
-def register_coordinates(
-    name: str,
-    coordinates: ArrayLike,
-    voi_names: List[str],
-    space: str,
-    overwrite: Optional[bool] = False,
-) -> None:
-    """Register a custom user coordinates.
-
-    Parameters
-    ----------
-    name : str
-        The name of the coordinates.
-    coordinates : numpy.ndarray
-        The coordinates. This should be a 2-dimensional array with three
-        columns. Each row corresponds to a volume-of-interest (VOI) and each
-        column corresponds to a spatial dimension (i.e. x, y, and
-        z-coordinates).
-    voi_names : list of str
-        The names of the VOIs.
-    space : str
-        The space of the coordinates, for e.g., "MNI".
-    overwrite : bool, optional
-        If True, overwrite an existing list of coordinates with the same name.
-        Does not apply to built-in coordinates (default False).
-
-    Raises
-    ------
-    ValueError
-        If the coordinates name is already registered and overwrite is set to
-        False or if the coordinates name is a built-in coordinates or if the
-        ``coordinates`` is not a 2D array or if coordinate value does not have
-        3 components or if the ``voi_names`` shape does not match the
-        ``coordinates`` shape.
-    TypeError
-        If ``coordinates`` is not a ``numpy.ndarray``.
-
-    """
-    if name in _available_coordinates:
-        if isinstance(_available_coordinates[name].get("path"), Path):
-            raise_error(
-                f"Coordinates {name} already registered as built-in "
-                "coordinates."
-            )
-        if overwrite is True:
-            logger.info(f"Overwriting coordinates {name}")
-        else:
-            raise_error(
-                f"Coordinates {name} already registered. "
-                "Set `overwrite=True` to update its value."
-            )
-
-    if not isinstance(coordinates, np.ndarray):
-        raise_error(
-            f"Coordinates must be a `numpy.ndarray`, not {type(coordinates)}.",
-            klass=TypeError,
-        )
-    if coordinates.ndim != 2:
-        raise_error(
-            f"Coordinates must be a 2D array, not {coordinates.ndim}D."
-        )
-    if coordinates.shape[1] != 3:
-        raise_error(
-            f"Each coordinate must have 3 values, not {coordinates.shape[1]} "
-        )
-    if len(voi_names) != coordinates.shape[0]:
-        raise_error(
-            f"Length of `voi_names` ({len(voi_names)}) does not match the "
-            f"number of `coordinates` ({coordinates.shape[0]})."
-        )
-    _available_coordinates[name] = {
-        "coords": coordinates,
-        "voi_names": voi_names,
-        "space": space,
-    }
-
-
-def list_coordinates() -> List[str]:
-    """List all the available coordinates (VOIs).
-
-    Returns
-    -------
-    list of str
-        A list with all available coordinates names.
-
-    """
-    return sorted(_available_coordinates.keys())
-
-
-def get_coordinates(
-    coords: str,
-    target_data: Dict[str, Any],
-    extra_input: Optional[Dict[str, Any]] = None,
-) -> Tuple[ArrayLike, List[str]]:
-    """Get coordinates, tailored for the target image.
-
-    Parameters
-    ----------
-    coords : str
-        The name of the coordinates.
-    target_data : dict
-        The corresponding item of the data object to which the coordinates
-        will be applied.
-    extra_input : dict, optional
-        The other fields in the data object. Useful for accessing other data
-        kinds that needs to be used in the computation of coordinates
-        (default None).
-
-    Returns
-    -------
-    numpy.ndarray
-        The coordinates.
-    list of str
-        The names of the VOIs.
-
-    Raises
-    ------
-    RuntimeError
-        If warp / transformation file extension is not ".mat" or ".h5".
-    ValueError
-        If ``extra_input`` is None when ``target_data``'s space is native.
-
-    """
-    # Load the coordinates
-    seeds, labels, _ = load_coordinates(name=coords)
-
-    # Transform coordinate if target data is native
-    if target_data["space"] == "native":
-        # Check for extra inputs
-        if extra_input is None:
-            raise_error(
-                "No extra input provided, requires `Warp` and `T1w` "
-                "data types in particular for transformation to "
-                f"{target_data['space']} space for further computation."
-            )
-
-        # Create component-scoped tempdir
-        tempdir = WorkDirManager().get_tempdir(prefix="coordinates")
-
-        # Create element-scoped tempdir so that transformed coordinates is
-        # available later as numpy stores file path reference for
-        # loading on computation
-        element_tempdir = WorkDirManager().get_element_tempdir(
-            prefix="coordinates"
-        )
-
-        # Check for warp file type to use correct tool
-        warp_file_ext = extra_input["Warp"]["path"].suffix
-        if warp_file_ext == ".mat":
-            # Save existing coordinates to a component-scoped tempfile
-            pretransform_coordinates_path = (
-                tempdir / "pretransform_coordinates.txt"
-            )
-            np.savetxt(pretransform_coordinates_path, seeds)
-
-            # Create an element-scoped tempfile for transformed coordinates
-            # output
-            transformed_coords_path = (
-                element_tempdir / "coordinates_transformed.txt"
-            )
-
-            logger.debug("Using FSL for coordinates transformation")
-            # Set img2imgcoord command
-            img2imgcoord_cmd = [
-                "cat",
-                f"{pretransform_coordinates_path.resolve()}",
-                "| img2imgcoord -mm",
-                f"-src {target_data['path'].resolve()}",
-                f"-dest {target_data['reference_path'].resolve()}",
-                f"-warp {extra_input['Warp']['path'].resolve()}",
-                f"> {transformed_coords_path.resolve()};",
-                f"sed -i 1d {transformed_coords_path.resolve()}",
-            ]
-            # Call img2imgcoord
-            run_ext_cmd(name="img2imgcoord", cmd=img2imgcoord_cmd)
-
-            # Load coordinates
-            seeds = np.loadtxt(transformed_coords_path)
-
-        elif warp_file_ext == ".h5":
-            # Save existing coordinates to a component-scoped tempfile
-            pretransform_coordinates_path = (
-                tempdir / "pretransform_coordinates.csv"
-            )
-            np.savetxt(
-                pretransform_coordinates_path,
-                seeds,
-                delimiter=",",
-                # Add header while saving to make ANTs work
-                header="x,y,z",
-            )
-
-            # Create an element-scoped tempfile for transformed coordinates
-            # output
-            transformed_coords_path = (
-                element_tempdir / "coordinates_transformed.csv"
-            )
-
-            logger.debug("Using ANTs for coordinates transformation")
-            # Set antsApplyTransformsToPoints command
-            apply_transforms_to_points_cmd = [
-                "antsApplyTransformsToPoints",
-                "-d 3",
-                "-p 1",
-                "-f 0",
-                f"-i {pretransform_coordinates_path.resolve()}",
-                f"-o {transformed_coords_path.resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()};",
-            ]
-            # Call antsApplyTransformsToPoints
-            run_ext_cmd(
-                name="antsApplyTransformsToPoints",
-                cmd=apply_transforms_to_points_cmd,
-            )
-
-            # Load coordinates
-            seeds = np.loadtxt(
-                # Skip header when reading
-                transformed_coords_path,
-                delimiter=",",
-                skiprows=1,
-            )
-
-        else:
-            raise_error(
-                msg=(
-                    "Unknown warp / transformation file extension: "
-                    f"{warp_file_ext}"
-                ),
-                klass=RuntimeError,
-            )
-
-        # Delete tempdir
-        WorkDirManager().delete_tempdir(tempdir)
-
-    return seeds, labels
-
-
-def load_coordinates(name: str) -> Tuple[ArrayLike, List[str], str]:
-    """Load coordinates.
-
-    Parameters
-    ----------
-    name : str
-        The name of the coordinates.
-
-    Returns
-    -------
-    numpy.ndarray
-        The coordinates.
-    list of str
-        The names of the VOIs.
-    str
-        The space of the coordinates.
-
-    Raises
-    ------
-    ValueError
-        If ``name`` is invalid.
-
-    """
-    # Check for valid coordinates name
-    if name not in _available_coordinates:
-        raise_error(
-            f"Coordinates {name} not found. "
-            f"Valid options are: {list_coordinates()}"
-        )
-    # Load coordinates
-    t_coord = _available_coordinates[name]
-    if isinstance(t_coord.get("path"), Path):
-        # Load via pandas
-        df_coords = pd.read_csv(t_coord["path"], sep="\t", header=None)
-        coords = df_coords.iloc[:, [0, 1, 2]].to_numpy()
-        names = list(df_coords.iloc[:, [3]].values[:, 0])
-    else:
-        coords = t_coord["coords"]
-        coords = typing.cast(ArrayLike, coords)
-        names = t_coord["voi_names"]
-        names = typing.cast(List[str], names)
-
-    return coords, names, t_coord["space"]