Updating the default config to be compatible with adult recordings. (lina-usc#173)

* Updating the default config to be compatible with adult recordings.

* Code linting.

* Fixing tests.

* Fixing spelling.

* Fixing simulation test.

Author: christian-oreilly

pylossless/assets/ll_default_config_adults.yaml

@@ -0,0 +1,144 @@
+######################### General properties #########################
+#ref_loc_file: derivatives/pylossless/code/misc/standard_1020_ll_ref19.elc
+#montage_info: [0.0, -16.0, 0.0, -0.02, 0.0, -1.58, 10.7, 11.5, 11.5]
+
+################## General info about the project ####################
+project:
+  readme: "# Description of the dataset"
+
+  # Montage use to make file BIDS compliant.
+  # Can be path to digitized montage OR a string of one of mne's built in
+  # standard montages as specified by mne.channels.get_builtin_montages().
+  # Can be left empty if the input dataset is already in BIDS format.
+  bids_montage: GSN-HydroCel-129
+
+  # montage used while running the lossless pipeline.
+  # if empty, the pipeline will use the electrodes.tsv sidecar file, if created
+  # during the BIDS conversion.
+  # If specified, needs to be a string of one of mne's built in standard montages.
+  analysis_montage: ""
+
+  set_montage_kwargs: {}
+
+  coordsys:
+    EEGCoordinateSystem: Other
+    EEGCoordinateUnits: metres
+
+  general_info:
+    authors: [Unspecified]
+    institution_Name: Unspecified
+    institution_address: Unspecified
+    dataset_doi: []
+    funding: Unspecified
+    how_to_acknowledge: tba
+    license: ""
+    name: Unspecified
+    references_and_links: []
+
+  t_info:
+    EEG_placement_scheme: EGI 129
+    cap_manufacturer: EGI
+    cap_manufacturers_model_name: Hydrocel 129 Channel
+    hardware_filters: n/a
+    manufacturer: Electrical Geodesics
+    manufacturers_model_name: NetAmps300
+    power_line_frequency: 60
+    software_filters: n/a
+    software_versions: NetStation V4.5
+
+######################## Task break detection ########################
+# See arguments definition from mne.preprocessing.annotate_breaks
+find_breaks:
+
+############################## epoching ##############################
+epoching:
+  overlap: 0
+
+  # See arguments definition from mne.Epochs
+  epochs_args:
+    baseline: null
+    tmax: 1
+    tmin: 0
+
+########################### EEG filtering ############################
+# See arguments definition from mne.io.Raw.filter & mne.io.Raw.notch_filter
+filtering:
+  filter_args:
+    h_freq: 100
+    l_freq: 1
+  notch_filter_args:
+    freqs: [60]
+
+############################## SLURM #################################
+# Options for running the pipeline on a cluster
+# through SLURM
+slurm_options:
+  account: def-emayada
+  job_name: pylossless
+  memory: 16g
+  mpi: false
+  num_tasks: 1
+  program_options: []
+  threads_per_task: []
+  time_limit: 2h
+
+########################## Nearest neighbor ##########################
+nearest_neighbors:
+  n_nbr_ch: 3
+  n_nbr_epoch: 3
+
+####################### Pipeline steps config ########################
+bridged_channels:
+  bridge_trim: 40
+  bridge_z: 6
+
+noisy_channels:
+  flag_crit: 0.2
+  outlier_method: quantile
+  outliers_kwargs:
+    k: 6
+    lower: 0.25
+    upper: 0.75
+
+uncorrelated_channels:
+  flag_crit: 0.2
+  outlier_method: quantile
+  outliers_kwargs:
+    k: 6
+    lower: 0.25
+    upper: 0.75
+
+noisy_epochs:
+  flag_crit: 0.2
+  outlier_method: quantile
+  outliers_kwargs:
+    k: 6
+    lower: 0.25
+    upper: 0.75
+
+uncorrelated_epochs:
+  flag_crit: 0.2
+  outlier_method: quantile
+  outliers_kwargs:
+    k: 6
+    lower: 0.25
+    upper: 0.75
+
+################################ ICA #################################
+ica:
+  noisy_ic_epochs:
+    flag_crit: 0.2
+    outlier_method: quantile
+    outliers_kwargs:
+      k: 6
+      lower: 0.25
+      upper: 0.75
+
+  # See arguments definition from mne.preprocessing.ICA
+  ica_args:
+    run1:
+      method: fastica
+    run2:
+      method: infomax
+      fit_params:
+        extended: True

pylossless/assets/ll_default_config.yaml renamed to pylossless/assets/ll_default_config_infants.yaml

@@ -1,16 +1,10 @@
 ######################### General properties #########################
-aref_trim: 30
-order: 1
-out_path: derivatives/EEG-IP-L
-ref_loc_file: derivatives/EEG-IP-L/code/misc/standard_1020_ll_ref19.elc
-save_f_res: 1
-sd_t_pad: 1
-in_path: []
-montage_info: [0.0, -16.0, 0.0, -0.02, 0.0, -1.58, 10.7, 11.5, 11.5]
+#ref_loc_file: derivatives/pylossless/code/misc/standard_1020_ll_ref19.elc
+#montage_info: [0.0, -16.0, 0.0, -0.02, 0.0, -1.58, 10.7, 11.5, 11.5]
 
 ################## General info about the project ####################
 project:
-  readme: "# Q1K ACAR Dataset"
+  readme: "# Description of the dataset"
 
   # Montage use to make file BIDS compliant.
   # Can be path to digitized montage OR a string of one of mne's built in
@@ -31,14 +25,14 @@ project:
     EEGCoordinateUnits: metres
 
   general_info:
-    authors: [Q1K Neuroimaging group]
-    institution_Name: McGill University
-    institution_address: 3775 Rue University, Montreal, QC
+    authors: [Unspecified]
+    institution_Name: Unspecified
+    institution_address: Unspecified
     dataset_doi: []
-    funding: Azrieli Foundationt
+    funding: Unspecified
     how_to_acknowledge: tba
     license: ""
-    name: Q1K Mismatched Negativity
+    name: Unspecified
     references_and_links: []
 
   t_info:

pylossless/config/config.py

@@ -15,7 +15,7 @@ class ConfigMixin(dict):
     """Base configuration file class for pipeline procedures."""
 
     DEFAULT_CONFIG_PATH = (
-        Path(__file__).parent.parent / "assets" / "ll_default_config.yaml"
+        Path(__file__).parent.parent / "assets"
     )
 
     def read(self, file_name):
@@ -51,11 +51,16 @@ def print(self):
 class Config(ConfigMixin):
     """Representation of configuration file for running the pipeline."""
 
-    DEFAULT_CONFIG_PATH = (
-        Path(__file__).parent.parent / "assets" / "ll_default_config.yaml"
-    )
+    def load_default(self, kind="adults"):
+        """Get the default pylossless config file.
 
-    def load_default(self):
-        """Get the default pylossless config file."""
-        self.read(Config.DEFAULT_CONFIG_PATH)
+        Parameters
+        ----------
+        kind : str | pathlib.Path
+            Can be either 'adults' or 'infants'. Default to 'adults'.
+        """
+        path = Config.DEFAULT_CONFIG_PATH / f"ll_default_config_{kind}.yaml"
+        if not path.exists():
+            raise ValueError(f"No default configuration for kind '{kind}'.")
+        self.read(path)
         return self

pylossless/conftest.py

@@ -18,7 +18,7 @@
 def pipeline_fixture():
     """Return a namedTuple containing MNE eyetracking raw data and events."""
     raw, config, bids_path = load_openneuro_bids()
-    raw.crop(tmin=0, tmax=60)  # take 60 seconds for speed
+    # raw.crop(tmin=0, tmax=60)  # Too short for ICA to converge in some tests.
     annots = Annotations(
         onset=[1, 15], duration=[1, 1], description=["test_annot", "test_annot"]
     )
@@ -28,6 +28,7 @@ def pipeline_fixture():
     config["find_breaks"]["min_break_duration"] = 9
     config["find_breaks"]["t_start_after_previous"] = 1
     config["find_breaks"]["t_stop_before_next"] = 0
+    config["ica"]["ica_args"]["run1"]["max_iter"] = 5000
     config.save("test_config.yaml")
     pipeline = ll.LosslessPipeline("test_config.yaml")
     not_in_1020 = ["EXG1", "EXG2", "EXG3", "EXG4", "EXG5", "EXG6", "EXG7", "EXG8"]

pylossless/datasets/datasets.py

@@ -33,7 +33,10 @@ def load_openneuro_bids(subject="pd6"):
     openneuro = ll.utils.import_optional_dependency("openneuro")
 
     config = ll.config.Config()
-    config.load_default()
+    # TODO: Tests were developed using this configuration. The adult version
+    # should probably be used instead, but this change will require fixing the
+    # tests accordingly.
+    config.load_default("infants")
     config["project"]["bids_montage"] = ""
     config["project"]["analysis_montage"] = "standard_1020"
     config["project"]["set_montage_kwargs"]["on_missing"] = "warn"

pylossless/tests/test_simulated.py

@@ -11,7 +11,7 @@
 
 # LOAD DEFAULT CONFIG
 config = ll.config.Config()
-config.load_default()
+config.load_default("infants")
 config["noisy_channels"]["outliers_kwargs"]["lower"] = 0.25
 config["noisy_channels"]["outliers_kwargs"]["upper"] = 0.75
 # short file, raise threshold so epochs w/ blinks dont cause flag

pylossless/tests/test_utils.py

@@ -5,14 +5,18 @@ def test_import_optional_dependency():
     from pylossless.utils import check
 
     # Test the case where the package is not installed.
-    with pytest.raises(ImportError, match="Missing optional dependency 'astropy'."):
-        # choosing a package that will probably never be added to the requirements!
-        check.import_optional_dependency("astropy")
+    package = "sdgssfersfsdesdfsefsdfsdt"
+    with pytest.raises(ImportError, match=f"Missing optional dependency '{package}'."):
+        # Choosing a package that will probably never be added to the requirements!
+        # We also choose a name of a package that is likely not to exist at all
+        # to avoid the corresponding package is installed in the development
+        # environment of developers.
+        check.import_optional_dependency(package)
 
     # Test the case where the package is installed.
     mne = check.import_optional_dependency("mne", raise_error=False)
     assert mne is not None
 
     # Test the where case package is not installed but we don't want to raise an error.
-    astropy = check.import_optional_dependency("astropy", raise_error=False)
-    assert astropy is None
+    ret_val = check.import_optional_dependency(package, raise_error=False)
+    assert ret_val is None