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Merge pull request #7 from maestroque/add-pydra
Add BIDS reading support and prepare input loading for pydra workflow
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
|
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| """Helper class for holding physiological data and associated metadata information.""" | ||
|
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| import logging | ||
|
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| from .io import load_from_bids, load_physio | ||
| from .physio import Physio | ||
| from .utils import is_bids_directory | ||
|
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| # from loguru import logger | ||
|
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| try: | ||
| from pydra.mark import task | ||
| except ImportError: | ||
| from .utils import task | ||
|
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|
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| LGR = logging.getLogger(__name__) | ||
| LGR.setLevel(logging.DEBUG) | ||
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|
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| @task | ||
| def generate_physio( | ||
| input_file: str, mode="auto", fs=None, bids_parameters=dict(), col_physio_type=None | ||
| ) -> Physio: | ||
| """ | ||
| Load a physio object from either a BIDS directory or an exported physio object. | ||
| Parameters | ||
| ---------- | ||
| input_file : str | ||
| Path to input file | ||
| mode : 'auto', 'physio', or 'bids', optional | ||
| Mode to operate with | ||
| fs : None, optional | ||
| Set or force set sapmling frequency (Hz). | ||
| bids_parameters : dictionary, optional | ||
| Dictionary containing BIDS parameters | ||
| col_physio_type : int or None, optional | ||
| Object to pick up in a BIDS array of physio objects. | ||
| """ | ||
| LGR.info(f"Loading physio object from {input_file}") | ||
|
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| if mode == "auto": | ||
| if input_file.endswith((".phys", ".physio", ".1D", ".txt", ".tsv", ".csv")): | ||
| mode = "physio" | ||
| elif is_bids_directory(input_file): | ||
| mode = "bids" | ||
| else: | ||
| raise ValueError( | ||
| "Could not determine input mode automatically. Please specify it manually." | ||
| ) | ||
| if mode == "physio": | ||
| physio_obj = load_physio(input_file, fs=fs, allow_pickle=True) | ||
|
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| elif mode == "bids": | ||
| if bids_parameters is {}: | ||
| raise ValueError("BIDS parameters must be provided when loading from BIDS") | ||
| else: | ||
| physio_array = load_from_bids(input_file, **bids_parameters) | ||
| physio_obj = ( | ||
| physio_array[col_physio_type] if col_physio_type else physio_array | ||
| ) | ||
| else: | ||
| raise ValueError(f"Invalid generate_physio mode: {mode}") | ||
|
|
||
| return physio_obj |
12 changes: 12 additions & 0 deletions
12
...ils/tests/data/non-bids-dir/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_physio.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| { | ||
| "SamplingFrequency": 10000.0, | ||
| "StartTime": -3, | ||
| "Columns": [ | ||
| "time", | ||
| "respiratory_chest", | ||
| "trigger", | ||
| "cardiac", | ||
| "respiratory_CO2", | ||
| "respiratory_O2" | ||
| ] | ||
| } |
12 changes: 12 additions & 0 deletions
12
...-bids-dir/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_recording-cardiac_physio.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| { | ||
| "SamplingFrequency": 10000.0, | ||
| "StartTime": -3, | ||
| "Columns": [ | ||
| "time", | ||
| "respiratory_chest", | ||
| "trigger", | ||
| "cardiac", | ||
| "respiratory_CO2", | ||
| "respiratory_O2" | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| """Tests for physutils.tasks and their integration.""" | ||
|
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| import os | ||
|
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| import physutils.tasks as tasks | ||
| from physutils import physio | ||
| from physutils.tests.utils import create_random_bids_structure | ||
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| def test_generate_physio_phys_file(): | ||
| """Test generate_physio task.""" | ||
| physio_file = os.path.abspath("physutils/tests/data/ECG.phys") | ||
| task = tasks.generate_physio(input_file=physio_file, mode="physio") | ||
| assert task.inputs.input_file == physio_file | ||
| assert task.inputs.mode == "physio" | ||
| assert task.inputs.fs is None | ||
|
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| task() | ||
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| physio_obj = task.result().output.out | ||
| assert isinstance(physio_obj, physio.Physio) | ||
| assert physio_obj.fs == 1000 | ||
| assert physio_obj.data.shape == (44611,) | ||
|
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| def test_generate_physio_bids_file(): | ||
| """Test generate_physio task.""" | ||
| create_random_bids_structure("physutils/tests/data", recording_id="cardiac") | ||
| bids_parameters = { | ||
| "subject": "01", | ||
| "session": "01", | ||
| "task": "rest", | ||
| "run": "01", | ||
| "recording": "cardiac", | ||
| } | ||
| bids_dir = os.path.abspath("physutils/tests/data/bids-dir") | ||
| task = tasks.generate_physio( | ||
| input_file=bids_dir, | ||
| mode="bids", | ||
| bids_parameters=bids_parameters, | ||
| col_physio_type="cardiac", | ||
| ) | ||
|
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| assert task.inputs.input_file == bids_dir | ||
| assert task.inputs.mode == "bids" | ||
| assert task.inputs.fs is None | ||
| assert task.inputs.bids_parameters == bids_parameters | ||
| assert task.inputs.col_physio_type == "cardiac" | ||
|
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| task() | ||
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| physio_obj = task.result().output.out | ||
| assert isinstance(physio_obj, physio.Physio) | ||
|
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| def test_generate_physio_auto(): | ||
| create_random_bids_structure("physutils/tests/data", recording_id="cardiac") | ||
| bids_parameters = { | ||
| "subject": "01", | ||
| "session": "01", | ||
| "task": "rest", | ||
| "run": "01", | ||
| "recording": "cardiac", | ||
| } | ||
| bids_dir = os.path.abspath("physutils/tests/data/bids-dir") | ||
| task = tasks.generate_physio( | ||
| input_file=bids_dir, | ||
| mode="auto", | ||
| bids_parameters=bids_parameters, | ||
| col_physio_type="cardiac", | ||
| ) | ||
|
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| assert task.inputs.input_file == bids_dir | ||
| assert task.inputs.mode == "auto" | ||
| assert task.inputs.fs is None | ||
| assert task.inputs.bids_parameters == bids_parameters | ||
| assert task.inputs.col_physio_type == "cardiac" | ||
|
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| task() | ||
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| physio_obj = task.result().output.out | ||
| assert isinstance(physio_obj, physio.Physio) | ||
|
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| def test_generate_physio_auto_error(caplog): | ||
| bids_dir = os.path.abspath("physutils/tests/data/non-bids-dir") | ||
| task = tasks.generate_physio( | ||
| input_file=bids_dir, | ||
| mode="auto", | ||
| col_physio_type="cardiac", | ||
| ) | ||
|
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| assert task.inputs.input_file == bids_dir | ||
| assert task.inputs.mode == "auto" | ||
| assert task.inputs.fs is None | ||
| assert task.inputs.col_physio_type == "cardiac" | ||
|
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| try: | ||
| task() | ||
| except Exception: | ||
| assert caplog.text.count("ERROR") == 1 | ||
| assert ( | ||
| caplog.text.count( | ||
| "dataset_description.json' is missing from project root. Every valid BIDS dataset must have this file." | ||
| ) | ||
| == 1 | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
|
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| """Helper class for holding physiological data and associated metadata information.""" | ||
|
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| import logging | ||
| from functools import wraps | ||
|
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| from loguru import logger | ||
|
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| LGR = logging.getLogger(__name__) | ||
| LGR.setLevel(logging.DEBUG) | ||
|
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|
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| def task(func): | ||
| """ | ||
| Fake task decorator to import when pydra is not installed/used. | ||
| Parameters | ||
| ---------- | ||
| func: function | ||
| Function to run the wrapper around | ||
| Returns | ||
| ------- | ||
| function | ||
| """ | ||
|
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| @wraps(func) | ||
| def wrapper(*args, **kwargs): | ||
| return func(*args, **kwargs) | ||
| LGR.debug( | ||
| "Pydra is not installed, thus generate_physio is not available as a pydra task. Using the function directly" | ||
| ) | ||
|
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| return wrapper | ||
|
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| def is_bids_directory(path_to_dir): | ||
| """ | ||
| Check if a directory is a BIDS compliant directory. | ||
| Parameters | ||
| ---------- | ||
| path_to_dir : os.path or str | ||
| Path to (supposed) BIDS directory | ||
| Returns | ||
| ------- | ||
| bool | ||
| True if the given path is a BIDS directory, False is not. | ||
| """ | ||
| try: | ||
| from bids import BIDSLayout | ||
| except ImportError: | ||
| raise ImportError( | ||
| "To use BIDS-based feature, pybids must be installed. Install manually or with `pip install physutils[bids]`" | ||
| ) | ||
| try: | ||
| # Attempt to create a BIDSLayout object | ||
| _ = BIDSLayout(path_to_dir) | ||
| return True | ||
| except Exception as e: | ||
| # Catch other exceptions that might indicate the directory isn't BIDS compliant | ||
| logger.error( | ||
| f"An error occurred while trying to load {path_to_dir} as a BIDS Layout object: {e}" | ||
| ) | ||
| return False |
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