From 7cf61d413a2d61a29ff18b9a8f68c73ce2bf90b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yasser=20Alem=C3=A1n=20G=C3=B3mez?= Date: Wed, 14 Aug 2024 18:02:19 +0200 Subject: [PATCH] Major organization changes --- .travis.yml | 2 +- MANIFEST.in | 4 ++++ chimera/__init__.py | 2 +- chimera/chimera.py | 12 +++++------- {config => chimera/config}/parcTypes_orig.json | 0 {config => chimera/config}/pipe_config.json | 0 .../config}/supraregions/Amygdala.tsv | 0 .../config}/supraregions/AuxiliaryLUTTable.tsv | 0 .../config}/supraregions/Brainstem.tsv | 0 .../config}/supraregions/Cerebellum.tsv | 0 .../config}/supraregions/Hippocampus.tsv | 0 .../config}/supraregions/Hypothalamus.tsv | 0 .../config}/supraregions/Subcortical.tsv | 0 .../config}/supraregions/Thalamus.tsv | 0 .../config}/supraregions/WhiteMatter.csv | 0 .../config}/supraregions_dictionary.json | 14 +++++++++++++- .../data}/annot_atlases/annot_atlases.txt | 0 ...4k_atlas-Lausanne2018_scale-1_dseg.label.annot | Bin 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...fer2018_seg-kong17n_scale-600_dseg.label.annot | Bin ...fer2018_seg-kong17n_scale-700_dseg.label.annot | Bin ...fer2018_seg-kong17n_scale-800_dseg.label.annot | Bin ...fer2018_seg-kong17n_scale-900_dseg.label.annot | Bin ...en-164k_atlas-Yeo2011_seg-17n_dseg.label.annot | Bin ...den-164k_atlas-Yeo2011_seg-7n_dseg.label.annot | Bin ...-R_den-164k_atlas-brainnetome_dseg.label.annot | Bin .../data}/gcs_atlases/gcs_atlases.txt | 0 ...-L_den-164k_atlas-Broadmann1909_dseg.label.gcs | Bin ...i-L_den-164k_atlas-Campbell1905_dseg.label.gcs | Bin ...den-164k_atlas-DKT2012_scale-40_dseg.label.gcs | Bin ...i-L_den-164k_atlas-Flechsig1920_dseg.label.gcs | Bin ...L_den-164k_atlas-HCPMM1_seg-5p3_dseg.label.gcs | Bin ...L_den-164k_atlas-HCPMM1_seg-6p0_dseg.label.gcs | Bin ...L_den-164k_atlas-HCPMM1_seg-7p1_dseg.label.gcs | Bin ...emi-L_den-164k_atlas-Kleist1934_dseg.label.gcs | Bin ...hemi-L_den-164k_atlas-Smith1907_dseg.label.gcs | Bin ...L_den-164k_atlas-Yeo2011_seg-7n_dseg.label.gcs | Bin ...L_den-164k_atlas-vonEconomo1925_dseg.label.gcs | Bin ...-R_den-164k_atlas-Broadmann1909_dseg.label.gcs | Bin ...i-R_den-164k_atlas-Campbell1905_dseg.label.gcs | Bin ...den-164k_atlas-DKT2012_scale-40_dseg.label.gcs | Bin ...i-R_den-164k_atlas-Flechsig1920_dseg.label.gcs | Bin ...R_den-164k_atlas-HCPMM1_seg-5p3_dseg.label.gcs | Bin ...R_den-164k_atlas-HCPMM1_seg-6p0_dseg.label.gcs | Bin ...R_den-164k_atlas-HCPMM1_seg-7p1_dseg.label.gcs | Bin ...emi-R_den-164k_atlas-Kleist1934_dseg.label.gcs | Bin ...hemi-R_den-164k_atlas-Smith1907_dseg.label.gcs | Bin ...R_den-164k_atlas-Yeo2011_seg-7n_dseg.label.gcs | Bin ...R_den-164k_atlas-vonEconomo1925_dseg.label.gcs | Bin ...m_res-01_atlas-FSLCerebellumFnirt_probseg.tsv# | 0 .../tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz | Bin ...NLin2009cAsym_res-01_atlas-SUIT_probseg.nii.gz | Bin ...152NLin2009cAsym_res-01_atlas-SUIT_probseg.tsv | 0 setup.py | 2 +- 121 files changed, 25 insertions(+), 11 deletions(-) rename {config => chimera/config}/parcTypes_orig.json (100%) rename {config => chimera/config}/pipe_config.json (100%) rename {config => chimera/config}/supraregions/Amygdala.tsv (100%) rename {config => chimera/config}/supraregions/AuxiliaryLUTTable.tsv (100%) rename {config => chimera/config}/supraregions/Brainstem.tsv (100%) rename {config => chimera/config}/supraregions/Cerebellum.tsv (100%) rename {config => chimera/config}/supraregions/Hippocampus.tsv (100%) rename {config => chimera/config}/supraregions/Hypothalamus.tsv (100%) rename {config => chimera/config}/supraregions/Subcortical.tsv (100%) rename {config => chimera/config}/supraregions/Thalamus.tsv (100%) rename {config => chimera/config}/supraregions/WhiteMatter.csv (100%) rename {config => chimera/config}/supraregions_dictionary.json (97%) rename {data => chimera/data}/annot_atlases/annot_atlases.txt (100%) rename {data => chimera/data}/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-1_dseg.label.annot (100%) rename 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(100%) rename {data => chimera/data}/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-vonEconomo1925_dseg.label.gcs (100%) rename {data => chimera/data}/vol_atlases/.~lock.tpl-MNI152NLin2009cAsym_res-01_atlas-FSLCerebellumFnirt_probseg.tsv# (100%) rename {data => chimera/data}/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz (100%) rename {data => chimera/data}/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.nii.gz (100%) rename {data => chimera/data}/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.tsv (100%) diff --git a/.travis.yml b/.travis.yml index 30fca5c..9e52770 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,7 +19,7 @@ script: tox deploy: provider: pypi distributions: sdist bdist_wheel - user: to specific regions of interest to the research question. Although widely applied, combining parcellations obtained with different approaches remains a challenging task. Here, we propose Chimera to flexibly integrate + user: yasseraleman password: secure: PLEASE_REPLACE_ME on: diff --git a/MANIFEST.in b/MANIFEST.in index 965b2dd..99cce5d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -9,3 +9,7 @@ recursive-exclude * __pycache__ recursive-exclude * *.py[co] recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif + +packages = ['.','data','config','docs'], + +package_data={'data':['*'],'config':['*'],'docs':['*'],}, diff --git a/chimera/__init__.py b/chimera/__init__.py index 8d1c047..0ea9f25 100644 --- a/chimera/__init__.py +++ b/chimera/__init__.py @@ -2,4 +2,4 @@ __author__ = """Yasser Aleman Gomez""" __email__ = 'yasseraleman@gmail.com' -__version__ = 'parcelations derived from different atlases and methodologies to produce a customized individual parcellation of the brain.' +__version__ = '0.1.0' diff --git a/chimera/chimera.py b/chimera/chimera.py index 260accc..233c849 100644 --- a/chimera/chimera.py +++ b/chimera/chimera.py @@ -80,8 +80,7 @@ def __init__(self, parc_code, """ - cwd = os.path.dirname(os.path.abspath(__file__)) - chim_dir = os.path.dirname(cwd) + chim_dir = os.path.dirname(os.path.abspath(__file__)) # Rise an error if the parcellation code is not provided if parc_code is None: @@ -1152,8 +1151,8 @@ def _build_parcellation1(self, t1:str, bids_dir:str, nmid_subc = len(mid_parc.index) - if "WhiteMatter" in supra_names: - self.supra_dict[supra][supra][atlas_code]["none"]["index"] + # if "WhiteMatter" in supra_names: + #self.supra_dict[supra][supra][atlas_code]["none"]["index"] @@ -1383,7 +1382,7 @@ def _pipeline_info(pipe_json:str=None): """ cwd = os.path.dirname(os.path.abspath(__file__)) - cwd = os.path.dirname(cwd) + # Get the absolute of this file if pipe_json is None: @@ -1419,8 +1418,7 @@ def _load_parcellations_info(parc_json:str=None, supra_folder:str=None): Dictionary containing the supraregions information """ - cwd = os.path.dirname(os.path.abspath(__file__)) - chim_dir = os.path.dirname(cwd) + chim_dir = os.path.dirname(os.path.abspath(__file__)) # Get the absolute of this file if parc_json is None: diff --git a/config/parcTypes_orig.json b/chimera/config/parcTypes_orig.json similarity index 100% rename from config/parcTypes_orig.json rename to chimera/config/parcTypes_orig.json diff --git a/config/pipe_config.json b/chimera/config/pipe_config.json similarity index 100% rename from config/pipe_config.json rename to chimera/config/pipe_config.json diff --git a/config/supraregions/Amygdala.tsv b/chimera/config/supraregions/Amygdala.tsv similarity index 100% rename from config/supraregions/Amygdala.tsv rename to chimera/config/supraregions/Amygdala.tsv diff --git a/config/supraregions/AuxiliaryLUTTable.tsv b/chimera/config/supraregions/AuxiliaryLUTTable.tsv similarity index 100% rename from config/supraregions/AuxiliaryLUTTable.tsv rename to chimera/config/supraregions/AuxiliaryLUTTable.tsv diff --git a/config/supraregions/Brainstem.tsv b/chimera/config/supraregions/Brainstem.tsv similarity index 100% rename from config/supraregions/Brainstem.tsv rename to chimera/config/supraregions/Brainstem.tsv diff --git a/config/supraregions/Cerebellum.tsv b/chimera/config/supraregions/Cerebellum.tsv similarity index 100% rename from config/supraregions/Cerebellum.tsv rename to chimera/config/supraregions/Cerebellum.tsv diff --git a/config/supraregions/Hippocampus.tsv b/chimera/config/supraregions/Hippocampus.tsv similarity index 100% rename from config/supraregions/Hippocampus.tsv rename to chimera/config/supraregions/Hippocampus.tsv diff --git a/config/supraregions/Hypothalamus.tsv b/chimera/config/supraregions/Hypothalamus.tsv similarity index 100% rename from config/supraregions/Hypothalamus.tsv rename to chimera/config/supraregions/Hypothalamus.tsv diff --git a/config/supraregions/Subcortical.tsv b/chimera/config/supraregions/Subcortical.tsv similarity index 100% rename from config/supraregions/Subcortical.tsv rename to chimera/config/supraregions/Subcortical.tsv diff --git a/config/supraregions/Thalamus.tsv b/chimera/config/supraregions/Thalamus.tsv similarity index 100% rename from config/supraregions/Thalamus.tsv rename to chimera/config/supraregions/Thalamus.tsv diff --git a/config/supraregions/WhiteMatter.csv b/chimera/config/supraregions/WhiteMatter.csv similarity index 100% rename from config/supraregions/WhiteMatter.csv rename to chimera/config/supraregions/WhiteMatter.csv diff --git a/config/supraregions_dictionary.json b/chimera/config/supraregions_dictionary.json similarity index 97% rename from config/supraregions_dictionary.json rename to chimera/config/supraregions_dictionary.json index 23ae792..9d64b5b 100644 --- a/config/supraregions_dictionary.json +++ b/chimera/config/supraregions_dictionary.json @@ -423,6 +423,17 @@ "OutVolLocation":"freesurfer"} }, "WhiteMatter": { + "F": {"atlas":"Aseg", + "name":"Aseg", + "description":"# 10. White matter parcellation (F): Aseg subcortical parcellation.", + "citation":"(Fischl et al, 2002)", + "source": "freesurfer", + "reference":"conform", + "parcels":"custom", + "mask":"custom", + "type":"custom", + "deriv_volfold":"freesurfer"}, + "J": {"atlas":"Hua2008", "name":"JHU", "description":"# 10. Tract probability maps in stereotaxic spaces (J): White matter segmentation.", @@ -433,5 +444,6 @@ "mask":"custom", "type":"maxprob", "OutVolLocation":"freesurfer"} + } -} \ No newline at end of file +} diff --git a/data/annot_atlases/annot_atlases.txt b/chimera/data/annot_atlases/annot_atlases.txt similarity index 100% rename from data/annot_atlases/annot_atlases.txt rename to chimera/data/annot_atlases/annot_atlases.txt diff --git a/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-1_dseg.label.annot b/chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-1_dseg.label.annot similarity index 100% rename from data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-1_dseg.label.annot rename to chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-1_dseg.label.annot diff --git a/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-2_dseg.label.annot b/chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-2_dseg.label.annot similarity index 100% rename from data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-2_dseg.label.annot rename to chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-2_dseg.label.annot diff --git a/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-3_dseg.label.annot b/chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-3_dseg.label.annot similarity index 100% rename from data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-3_dseg.label.annot rename to chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-3_dseg.label.annot diff --git a/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-4_dseg.label.annot b/chimera/data/annot_atlases/tpl-fsaverage_hemi-L_den-164k_atlas-Lausanne2018_scale-4_dseg.label.annot 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--git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Flechsig1920_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Flechsig1920_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Flechsig1920_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Flechsig1920_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-5p3_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-5p3_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-5p3_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-5p3_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-6p0_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-6p0_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-6p0_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-6p0_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-7p1_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-7p1_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-7p1_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-HCPMM1_seg-7p1_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Kleist1934_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Kleist1934_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Kleist1934_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Kleist1934_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Smith1907_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Smith1907_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Smith1907_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Smith1907_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Yeo2011_seg-7n_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Yeo2011_seg-7n_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Yeo2011_seg-7n_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-Yeo2011_seg-7n_dseg.label.gcs diff --git a/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-vonEconomo1925_dseg.label.gcs b/chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-vonEconomo1925_dseg.label.gcs similarity index 100% rename from data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-vonEconomo1925_dseg.label.gcs rename to chimera/data/gcs_atlases/tpl-fsaverage_hemi-R_den-164k_atlas-vonEconomo1925_dseg.label.gcs diff --git a/data/vol_atlases/.~lock.tpl-MNI152NLin2009cAsym_res-01_atlas-FSLCerebellumFnirt_probseg.tsv# b/chimera/data/vol_atlases/.~lock.tpl-MNI152NLin2009cAsym_res-01_atlas-FSLCerebellumFnirt_probseg.tsv# similarity index 100% rename from data/vol_atlases/.~lock.tpl-MNI152NLin2009cAsym_res-01_atlas-FSLCerebellumFnirt_probseg.tsv# rename to chimera/data/vol_atlases/.~lock.tpl-MNI152NLin2009cAsym_res-01_atlas-FSLCerebellumFnirt_probseg.tsv# diff --git a/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz b/chimera/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz similarity index 100% rename from data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz rename to chimera/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz diff --git a/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.nii.gz b/chimera/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.nii.gz similarity index 100% rename from data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.nii.gz rename to chimera/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.nii.gz diff --git a/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.tsv b/chimera/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.tsv similarity index 100% rename from data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.tsv rename to chimera/data/vol_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-SUIT_probseg.tsv diff --git a/setup.py b/setup.py index bd6d9fc..67d125d 100644 --- a/setup.py +++ b/setup.py @@ -44,6 +44,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/yasseraleman/chimera', - version='parcelations derived from different atlases and methodologies to produce a customized individual parcellation of the brain.', + version='0.1.0', zip_safe=False, )