Add BIDS reading support and prepare input loading for pydra workflow

.all-contributorsrc

@@ -25,7 +25,7 @@
         "code",
         "ideas",
         "infra",
-        "review",
+        "review"
       ]
     },
     {
@@ -38,7 +38,7 @@
         "data",
         "ideas",
         "infra",
-        "projectManagement",
+        "projectManagement"
       ]
     },
     {
@@ -51,6 +51,20 @@
         "review",
         "test"
       ]
+    },
+    {
+      "login": "maestroque",
+      "name": "George Kikas",
+      "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4",
+      "profile": "https://github.com/maestroque",
+      "contributions": [
+        "code",
+        "ideas",
+        "infra",
+        "bug",
+        "test",
+        "review"
+      ]
     }
   ],
   "contributorsPerLine": 7,

README.md

@@ -40,6 +40,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="http://rossmarkello.com"><img src="https://avatars0.githubusercontent.com/u/14265705?v=4" width="100px;" alt=""/><br /><sub><b>Ross Markello</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=rmarkello" title="Code">💻</a> <a href="#ideas-rmarkello" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-rmarkello" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Armarkello" title="Reviewed Pull Requests">👀</a></td>
     <td align="center"><a href="https://github.com/smoia"><img src="https://avatars3.githubusercontent.com/u/35300580?v=4" width="100px;" alt=""/><br /><sub><b>Stefano Moia</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=smoia" title="Code">💻</a> <a href="#data-smoia" title="Data">🔣</a> <a href="#ideas-smoia" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-smoia" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#projectManagement-smoia" title="Project Management">📆</a></td>
     <td align="center"><a href="https://github.com/eurunuela"><img src="https://avatars0.githubusercontent.com/u/13706448?v=4" width="100px;" alt=""/><br /><sub><b>Eneko Uruñuela</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Aeurunuela" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Tests">⚠️</a></td>
+    <td align="center"><a href="https://github.com/maestroque"><img src="https://avatars.githubusercontent.com/u/74024609?v=4?s=100" width="100px;" alt="George Kikas"/><br /><sub><b>George Kikas</b></sub></a><br /><a href="https://github.com/physiopy/phys2denoise/commits?author=maestroque" title="Code">💻</a> <a href="#ideas-maestroque" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-maestroque" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/phys2denoise/issues?q=author%3Amaestroque" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2denoise/commits?author=maestroque" title="Tests">⚠️</a> <a href="https://github.com/physiopy/phys2denoise/pulls?q=is%3Apr+reviewed-by%3Amaestroque" title="Reviewed Pull Requests">👀</a></td>
   </tr>
 </table>
 

physutils/io.py

@@ -9,7 +9,6 @@
 import os.path as op
 
 import numpy as np
-from bids import BIDSLayout
 from loguru import logger
 
 from physutils import physio
@@ -28,7 +27,7 @@ def load_from_bids(
     suffix="physio",
 ):
     """
-    Load physiological data from BIDS-formatted directory
+    Load physiological data from BIDS-formatted directory.
 
     Parameters
     ----------
@@ -50,6 +49,12 @@ def load_from_bids(
     data : :class:`physutils.Physio`
         Loaded physiological data
     """
+    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]`"
+        )
 
     # check if file exists and is in BIDS format
     if not op.exists(bids_path):

physutils/tasks.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""Helper class for holding physiological data and associated metadata information."""
+
+import logging
+
+from .io import load_from_bids, load_physio
+from .physio import Physio
+from .utils import is_bids_directory
+
+# from loguru import logger
+
+try:
+    from pydra.mark import task
+except ImportError:
+    from .utils import task
+
+
+LGR = logging.getLogger(__name__)
+LGR.setLevel(logging.DEBUG)
+
+
+@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}")
+
+    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)
+
+    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

physutils/tests/data/non-bids-dir/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_physio.json

@@ -0,0 +1,12 @@
+{
+    "SamplingFrequency": 10000.0,
+    "StartTime": -3,
+    "Columns": [
+        "time",
+        "respiratory_chest",
+        "trigger",
+        "cardiac",
+        "respiratory_CO2",
+        "respiratory_O2"
+    ]
+}

physutils/tests/data/non-bids-dir/sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_recording-cardiac_physio.json

@@ -0,0 +1,12 @@
+{
+    "SamplingFrequency": 10000.0,
+    "StartTime": -3,
+    "Columns": [
+        "time",
+        "respiratory_chest",
+        "trigger",
+        "cardiac",
+        "respiratory_CO2",
+        "respiratory_O2"
+    ]
+}

physutils/tests/test_tasks.py

@@ -0,0 +1,107 @@
+"""Tests for physutils.tasks and their integration."""
+
+import os
+
+import physutils.tasks as tasks
+from physutils import physio
+from physutils.tests.utils import create_random_bids_structure
+
+
+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
+
+    task()
+
+    physio_obj = task.result().output.out
+    assert isinstance(physio_obj, physio.Physio)
+    assert physio_obj.fs == 1000
+    assert physio_obj.data.shape == (44611,)
+
+
+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",
+    )
+
+    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"
+
+    task()
+
+    physio_obj = task.result().output.out
+    assert isinstance(physio_obj, physio.Physio)
+
+
+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",
+    )
+
+    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"
+
+    task()
+
+    physio_obj = task.result().output.out
+    assert isinstance(physio_obj, physio.Physio)
+
+
+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",
+    )
+
+    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"
+
+    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
+        )

physutils/utils.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""Helper class for holding physiological data and associated metadata information."""
+
+import logging
+from functools import wraps
+
+from loguru import logger
+
+LGR = logging.getLogger(__name__)
+LGR.setLevel(logging.DEBUG)
+
+
+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
+    """
+
+    @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"
+        )
+
+    return wrapper
+
+
+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

setup.cfg

@@ -11,7 +11,7 @@ classifiers =
     License :: OSI Approved :: Apache Software License
     Programming Language :: Python :: 3
 license = Apache-2.0
-description = Set of utilities meant to be used with Physiopy's libraries
+description = Set of utilities meant to be used with Physiopy libraries
 long_description = file:README.md
 long_description_content_type = text/markdown; charset=UTF-8
 platforms = OS Independent
@@ -23,9 +23,7 @@ python_requires = >=3.6.1
 install_requires =
     matplotlib
     numpy >=1.9.3
-    scipy
     loguru
-    pybids
 tests_require =
     pytest >=3.6
 test_suite = pytest
@@ -34,6 +32,10 @@ packages = find:
 include_package_data = True
 
 [options.extras_require]
+pydra =
+    pydra
+bids =
+    pybids
 doc =
     sphinx >=2.0
     sphinx-argparse
@@ -49,6 +51,8 @@ test =
     scipy
     pytest >=5.3
     pytest-cov
+    %(pydra)s
+    %(bids)s
     %(style)s
 devtools =
     pre-commit