ds003 - model 1

%load_ext autoreload
%autoreload 2

import json
from pathlib import Path
from itertools import chain

import numpy as np
import pandas as pd

Preamble

We will use Datalad to manage our data, which in turn depends on git-annex.

! datalad get ds000003-fmriprep/sub-*/func/*_desc-confounds_*.tsv \
              ds000003-fmriprep/sub-*/func/*_desc-confounds_*.json \
              ds000003-fmriprep/dataset_description.json 

[ERROR  ] No working git-annex installation of version >= 8.20200309. Visit http://handbook.datalad.org/r.html?install for instructions on how to install DataLad and git-annex. 

from nilearn.plotting import plot_design_matrix

import bids
from bids.modeling import BIDSStatsModelsGraph
from bids.layout import BIDSLayout


def api(obj):
    return {attr: getattr(obj, attr) for attr in dir(obj) if not attr[0] == '_'}

layout = BIDSLayout('./ds000003', derivatives='./ds000003-fmriprep')

---------------------------------------------------------------------------
NotADirectoryError                        Traceback (most recent call last)
Cell In[4], line 1
----> 1 layout = BIDSLayout('./ds000003', derivatives='./ds000003-fmriprep')

File ~/work/model-zoo/model-zoo/src/pybids/bids/layout/layout.py:182, in BIDSLayout.__init__(self, root, validate, absolute_paths, derivatives, config, sources, regex_search, database_path, reset_database, indexer, is_derivative, **indexer_kwargs)
    180 if derivatives is True:
    181     derivatives = root / 'derivatives'
--> 182 self.add_derivatives(
    183     derivatives, parent_database_path=database_path,
    184     validate=validate, absolute_paths=absolute_paths,
    185     derivatives=None, sources=self, config=None,
    186     regex_search=regex_search, reset_database=reset_database,
    187     **indexer_kwargs)

File ~/work/model-zoo/model-zoo/src/pybids/bids/layout/layout.py:534, in BIDSLayout.add_derivatives(self, path, parent_database_path, **kwargs)
    529 if name in self.derivatives:
    530     raise BIDSDerivativesValidationError(
    531         f"Pipeline name {name} ({path!s}) has already been added to this "
    532         "BIDSLayout. Every added pipeline must have a unique name!"
    533     )
--> 534 self.derivatives[name] = BIDSLayout(path, is_derivative=True, **kwargs)

File ~/work/model-zoo/model-zoo/src/pybids/bids/layout/layout.py:176, in BIDSLayout.__init__(self, root, validate, absolute_paths, derivatives, config, sources, regex_search, database_path, reset_database, indexer, is_derivative, **indexer_kwargs)
    172     if indexer is None:
    173         indexer = BIDSLayoutIndexer(
    174             validate=validate and not is_derivative, **indexer_kwargs
    175         )
--> 176     indexer(self)
    178 # Add derivatives if any are found
    179 if derivatives:

File ~/work/model-zoo/model-zoo/src/pybids/bids/layout/index.py:150, in BIDSLayoutIndexer.__call__(self, layout)
    148 self._index_dir(self._layout._root, self._config)
    149 if self.index_metadata:
--> 150     self._index_metadata()

File ~/work/model-zoo/model-zoo/src/pybids/bids/layout/index.py:403, in BIDSLayoutIndexer._index_metadata(self)
    401 for pl, js_file in payloads[::-1]:
    402     try:
--> 403         file_md.update(pl())
    404     except FileNotFoundError:
    405         if not virtual_datafile:

File ~/work/model-zoo/model-zoo/src/pybids/bids/layout/index.py:293, in BIDSLayoutIndexer._index_metadata.<locals>.load_json(path)
    291 @lru_cache(maxsize=None)
    292 def load_json(path):
--> 293     with open(path, 'r', encoding='utf-8') as handle:
    294         try:
    295             return json.load(handle)

NotADirectoryError: [Errno 20] Not a directory: '/home/runner/work/model-zoo/model-zoo/model-zoo/exhibits/ds003/ds000003-fmriprep/sub-01/func/sub-01_task-rhymejudgment_desc-confounds_timeseries.json'

json_file = 'model-001_smdl.json'
spec = json.loads(Path(json_file).read_text())
spec

layout

graph = BIDSStatsModelsGraph(layout, spec)

graph.load_collections(scan_length=320) # Set scan_length in case images not available

graph.run_graph(transformation_history=True, node_reports=True, missing_values='fill')

collections = layout.get_collections('run', task='rhymejudgment', scan_length=320)

root_node = graph.root_node
root_node.get_collections()[-1].entities

specs = root_node.outputs_
len(specs)

specs[0]

plot_design_matrix(specs[0].X, rescale=False)