eegdash 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

eegdash/SignalStore/tests/unit/store/test_unit_of_work.py

@@ -1,7 +0,0 @@
-
-
-class TestUnitOfWork:
-
-    def test_initialize(self, unit_of_work):
-        with unit_of_work as uow:
-            pass

eegdash/SignalStore/tests/unit/test_ci_cd.py

@@ -1,8 +0,0 @@
-import pytest
-
-def test_fast_ci_cd():
-    assert 5 == 5
-
-@pytest.mark.slow()
-def test_slow_ci_cd():
-    assert 10 == 10

eegdash/aws_ingest.py

@@ -1,29 +0,0 @@
-import sys 
-sys.path.append('..')
-import argparse
-from src.signalstore_data_utils import SignalstoreBIDS
-
-def add_bids_dataset(args):
-    signalstore_aws = SignalstoreBIDS(
-        dbconnectionstring='mongodb://23.21.113.214:27017/?directConnection=true&serverSelectionTimeoutMS=2000&appName=mongosh+2.2.1',
-        local_filesystem=False,
-        project_name='eegdash',
-    )
-    signalstore_aws.add_bids_dataset(dataset=args.dataset, data_dir=args.data, raw_format='eeglab')
-
-def main():
-    # Create the parser
-    parser = argparse.ArgumentParser(description="A simple command line argument parser")
-
-    # Add arguments
-    parser.add_argument('--data', type=str, default="/mnt/nemar/openneuro/ds004186", help="Path to data directory (Default: /mnt/nemar/openneuro/ds004186)")
-    parser.add_argument('--dataset', type=str, default="ds004186", help="Dataset name (Default: ds004186)")
-
-    # Parse the arguments
-    args = parser.parse_args()
-    print('Arguments:', args)
-
-    add_bids_dataset(args)
-
-if __name__ == "__main__":
-    main()

eegdash/main.py

@@ -1,17 +0,0 @@
-from eegdash.signalstore_data_utils import SignalstoreBIDS
-
-class EEGDash:
-    def __init__(self):
-        self.sstore = SignalstoreBIDS(
-            # dbconnectionstring='mongodb://127.0.0.1:27017/?directConnection=true&serverSelectionTimeoutMS=2000&appName=mongosh+2.3.1',
-            dbconnectionstring='mongodb+srv://eegdash-user:mdzoMjQcHWTVnKDq@cluster0.vz35p.mongodb.net/?retryWrites=true&w=majority&appName=Cluster0',
-            is_public=True,
-            local_filesystem=False,
-            project_name='eegdash'
-        )
-    
-    def find(self, *args):
-        return self.sstore.find(*args)
-    
-    def get(self, *args):
-        return self.sstore.get(*args)

eegdash/signalstore_data_utils.py

@@ -1,280 +0,0 @@
-from pathlib import Path
-from dotenv import load_dotenv
-import re
-import numpy as np
-import xarray as xr
-import os
-from eegdash.SignalStore.signalstore.store import UnitOfWorkProvider
-# from mongomock import MongoClient
-from pymongo.mongo_client import MongoClient
-from pymongo.server_api import ServerApi
-from fsspec.implementations.local import LocalFileSystem
-from fsspec.implementations.dirfs import DirFileSystem
-import pandas as pd
-import json
-import s3fs
-from eegdash.data_utils import BIDSDataset
-
-
-class SignalstoreBIDS():
-    AWS_BUCKET = 'eegdash'
-    def __init__(self, 
-                 project_name=AWS_BUCKET,
-                 dbconnectionstring="mongodb://127.0.0.1:27017/?directConnection=true&serverSelectionTimeoutMS=2000&appName=mongosh+2.3.1",
-                 is_public=False,
-                 local_filesystem=True,
-                 ):
-        self.is_public = is_public
-        if is_public:
-            dbconnectionstring='mongodb+srv://eegdash-user:mdzoMjQcHWTVnKDq@cluster0.vz35p.mongodb.net/?retryWrites=true&w=majority&appName=Cluster0',
-        else:
-            load_dotenv()
-            dbconnectionstring = os.getenv('DB_CONNECTION_STRING')
-
-        # Create a new client and connect to the server
-        client = MongoClient(dbconnectionstring, server_api=ServerApi('1'))
-        # Send a ping to confirm a successful connection
-        try:
-            client.admin.command('ping')
-            print("Pinged your deployment. You successfully connected to MongoDB!")
-        except Exception as e:
-            print(e)
-
-        memory_store = {}
-        filesystem = self.set_up_filesystem(is_local=local_filesystem)
-        self.uow_provider = UnitOfWorkProvider(
-            mongo_client=client,
-            filesystem=filesystem,
-            memory_store=memory_store,
-            default_filetype='zarr'
-        )
-
-        self.project_name=project_name
-        self.uow = self.uow_provider(self.project_name)
-        # self.load_domain_models()
-
-    def set_up_filesystem(self, is_local=True):
-        if is_local:
-            cache_path='/mnt/nemar/dtyoung/eeg-ssl-data'                  # path where signalstore netCDF files are stored
-            # Create a directory for the dataset
-            store_path = Path(cache_path)
-            if not os.path.exists(store_path):
-                os.makedirs(store_path)
-
-            filesystem = LocalFileSystem()
-            tmp_dir_fs = DirFileSystem(
-                store_path,
-                filesystem=filesystem
-            )
-            return tmp_dir_fs
-        else:
-            if self.is_public:
-                s3 = s3fs.S3FileSystem(anon=True, client_kwargs={'region_name': 'us-east-2'})
-            else:
-                s3 = s3fs.S3FileSystem(client_kwargs={'region_name': 'us-east-2'})
-            return s3
-
-    def load_domain_models(self):
-        cwd = Path.cwd()
-        domain_models_path = cwd / f"DomainModels/{self.project_name}/data_models.json"
-        metamodel_path = cwd / f"DomainModels/{self.project_name}/metamodels.json"
-        property_path = cwd / f"DomainModels/{self.project_name}/property_models.json"
-        with open(metamodel_path) as f:
-            metamodels = json.load(f)
-
-        with open(property_path) as f:
-            property_models = json.load(f)
-            
-        # load domain models json file
-        with open(domain_models_path) as f:
-            domain_models = json.load(f)
-            
-        with self.uow as uow:
-            for property_model in property_models:
-                uow.domain_models.add(property_model)
-                model = uow.domain_models.get(property_model['schema_name'])
-                print('property model: ', model['schema_name'])
-            for metamodel in metamodels:
-                uow.domain_models.add(metamodel)
-                model = uow.domain_models.get(metamodel['schema_name'])
-                print('meta model: ', model['schema_name'])
-            for domain_model in domain_models:
-                uow.domain_models.add(domain_model)
-                model = uow.domain_models.get(domain_model['schema_name'])
-                print('domain model: ', model['schema_name'])
-                uow.commit()
-
-    def extract_attribute(self, pattern, filename):
-        match = re.search(pattern, filename)
-        return match.group(1) if match else None
-
-    def load_eeg_attrs_from_bids_file(self, bids_dataset: BIDSDataset, bids_file):
-        '''
-        bids_file must be a file of the bids_dataset
-        '''
-        if bids_file not in bids_dataset.files:
-            raise ValueError(f'{bids_file} not in {bids_dataset.dataset}')
-        f = os.path.basename(bids_file)
-        attrs = {
-            'schema_ref': 'eeg_signal',
-            'data_name': f'{bids_dataset.dataset}_{f}',
-            'dataset': bids_dataset.dataset,
-            'subject': bids_dataset.subject(bids_file),
-            'task': bids_dataset.task(bids_file),
-            'session': bids_dataset.session(bids_file),
-            'run': bids_dataset.run(bids_file),
-            'sampling_frequency': bids_dataset.sfreq(bids_file), 
-            'modality': 'EEG',
-        }
-
-        return attrs
-
-    def load_eeg_data_from_bids_file(self, bids_dataset: BIDSDataset, bids_file, eeg_attrs=None):
-        '''
-        bids_file must be a file of the bids_dataset
-        '''
-        if bids_file not in bids_dataset.files:
-            raise ValueError(f'{bids_file} not in {bids_dataset.dataset}')
-
-        attrs = self.load_eeg_attrs_from_bids_file(bids_dataset, bids_file) if eeg_attrs is None else eeg_attrs
-
-        eeg_data = bids_dataset.load_and_preprocess_raw(bids_file)
-        print('data shape:', eeg_data.shape)
-    
-        fs = attrs['sampling_frequency']
-        max_time = eeg_data.shape[1] / fs
-        time_steps = np.linspace(0, max_time, eeg_data.shape[1]).squeeze() # in seconds
-        # print('time steps', len(time_steps))
-
-        # replace eeg.set with channels.tsv
-        # todo this is still a hacky way
-        channels_tsv = bids_dataset.get_bids_metadata_files(bids_file, 'channels.tsv')
-        channels_tsv = Path(channels_tsv[0]) 
-        if channels_tsv.exists():
-            channels = pd.read_csv(channels_tsv, sep='\t') 
-            # get channel names from channel_coords
-            channel_names = channels['name'].values
-
-        eeg_xarray = xr.DataArray(
-            data=eeg_data,
-            dims=['channel','time'],
-            coords={
-                'time': time_steps,
-                'channel': channel_names
-            },
-            attrs=attrs
-        )
-        return eeg_xarray
-
-    def exist(self, schema_ref='eeg_signal', data_name=''):
-        with self.uow as uow:
-            query = {
-                "schema_ref": schema_ref,
-                "data_name": data_name
-            }
-            sessions = uow.data.find(query)
-            if len(sessions) > 0:
-                return True
-            else:
-                return False
-
-    def add_bids_dataset(self, dataset, data_dir, raw_format='eeglab', overwrite=False, record_only=False):
-        if self.is_public:
-            raise ValueError('This operation is not allowed for public users')
-
-        bids_dataset = BIDSDataset(
-            data_dir=data_dir,
-            dataset=dataset,
-            raw_format=raw_format,
-        )
-        for bids_file in bids_dataset.get_files():
-            print('bids raw file', bids_file)
-
-            signalstore_data_id = f"{dataset}_{os.path.basename(bids_file)}"
-            if overwrite:
-                self.remove(signalstore_data_id)
-
-            if self.exist(data_name=signalstore_data_id):
-                print('data already exist. skipped')
-                continue
-            else:
-                eeg_attrs = self.load_eeg_attrs_from_bids_file(bids_dataset, bids_file)
-                with self.uow as uow:
-                    # Assume raw data already exists, recreating record only
-                    eeg_attrs['has_file'] = True
-                    print('adding record', eeg_attrs['data_name'])
-                    uow.data.add(eeg_attrs)
-                    uow.commit()
-                if  not record_only:
-                    eeg_xarray = self.load_eeg_data_from_bids_file(bids_dataset, bids_file, eeg_attrs)
-                    with self.uow as uow:
-                        print('adding data', eeg_xarray.attrs['data_name'])
-                        uow.data.add(eeg_xarray)
-                        uow.commit()
-
-    def remove(self, schema_ref='eeg_signal', data_name=''):
-        if self.is_public:
-            raise ValueError('This operation is not allowed for public users')
-
-        with self.uow as uow:
-            sessions = uow.data.find({'schema_ref': schema_ref, 'data_name': data_name})
-            if len(session) > 0:
-                for session in range(len(sessions)):
-                    uow.data.remove(session['schema_ref'], session['data_name'])
-                    uow.commit()
-
-    def remove_all(self):
-        if self.is_public:
-            raise ValueError('This operation is not allowed for public users')
-
-        with self.uow as uow:
-            sessions = uow.data.find({})
-            print(len(sessions))
-            for session in range(len(sessions)):
-                uow.data.remove(session['schema_ref'], session['data_name'])
-                uow.commit()
-
-            uow.purge()
-            
-            print('Verifying deletion job. Dataset length: ', len(uow.data.find({})))
-
-    def find(self, query:dict, validate=False, get_data=False):
-        '''
-        query: {
-            'dataset': 'dsxxxx',
-
-        }'''
-        with self.uow as uow:
-            sessions = uow.data.find(query, validate=validate, get_data=get_data)
-            if sessions:
-                print(f'Found {len(sessions)} records')
-                return sessions
-            else:
-                return []
-
-    def get(self, query:dict, validate=False):
-        '''
-        query: {
-            'dataset': 'dsxxxx',
-
-        }'''
-        with self.uow as uow:
-            sessions = uow.data.find(query, validate=validate, get_data=True)
-            if sessions:
-                print(f'Found {len(sessions)} records')
-                return sessions
-            else:
-                return []
-
-if __name__ == "__main__":
-    # sstore_hbn = SignalstoreHBN()
-    # sstore_hbn.add_data()
-    # sstore_ds004584 = SignalstoreHBN(
-    #     data_path='/mnt/nemar/openneuro/ds004584',
-    #     dataset_name='eegdash',
-    #     local_filesystem=False,
-    #     dbconnectionstring='mongodb://23.21.113.214:27017/?directConnection=true&serverSelectionTimeoutMS=2000&appName=mongosh+2.2.1'
-    # )
-    # sstore_ds004584.load_domain_models()
-    # sstore_ds004584.add_data()
-    pass

eegdash-0.0.1.dist-info/RECORD

@@ -1,72 +0,0 @@
-eegdash/__init__.py,sha256=hgxE8COvPu3EV2Tq3GqtMk68fsd7bYvOs_0GO6rrzfk,32
-eegdash/aws_ingest.py,sha256=imXA9rvFm49-pSmMaq6RT37k9USfTLAhOgu4WrDdlBc,1045
-eegdash/data_utils.py,sha256=0nF6JaQrkBaxS2zVPjkeUMcWVbh1eigG-nZYPYfBJ38,8927
-eegdash/main.py,sha256=ANyrsVCvDiKNiQAmlQt9FcyOeCoD4Oe6Gq25LM2o38o,675
-eegdash/signalstore_data_utils.py,sha256=YffTIAm5KBBFpl99aEAWTaDPZpBt2ghrBqlTTrrNh8I,10760
-eegdash/SignalStore/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-eegdash/SignalStore/signalstore/__init__.py,sha256=vejaZm3K4LxIgyXxhrT1C4ZNY6BgmmRhYdHOF84kdkk,124
-eegdash/SignalStore/signalstore/adapters/read_adapters/abstract_read_adapter.py,sha256=ktrVx_oJ08FmuvxTatkJ0rUmb5l66gLhWzi9zBMt4Kg,317
-eegdash/SignalStore/signalstore/adapters/read_adapters/domain_modeling/schema_read_adapter.py,sha256=HRBaVTLoRajjDRmFCBuAW6KX1tSLgRW6amCyrV9--Ko,497
-eegdash/SignalStore/signalstore/adapters/read_adapters/domain_modeling/vocabulary_read_adapter.py,sha256=LRa2s6mssWZsw9Dk4PKNy8QYJu7Z-jjkUfLIDxBqpCs,691
-eegdash/SignalStore/signalstore/adapters/read_adapters/handmade_records/excel_study_organizer_read_adapter.py,sha256=-dYuGZ297ZpozwX2wE9bmOyEUT_w-6jBiI5JE32OpdA,4351
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/axona/axona_read_adapter.py,sha256=IMY9x66SgE-SzsWJ6ca2A_CcrMIrsgQ--bl80vb0rUU,33850
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/ReadIntanSpikeFile.py,sha256=knuR9RjHWcwcPKYxDt6sclUSjJG8cmeyPQumghC8ubs,5061
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/intan_read_adapter.py,sha256=T9KTVdtlNgDg4ffX8SRDb00GJxRWcqWoy77iRdMAQzo,1044
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/load_intan_rhd_format.py,sha256=zK2vsrKvjLc0z562zBeQF5IaRGN-a6zz1rn2aAi7ltk,10166
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/data_to_result.py,sha256=O8rgWMzBKSBdj-qt9wzr3kCgFYHdAo7If96iXZfXhX4,2649
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/get_bytes_per_data_block.py,sha256=bivIog0luN9iyY2dLEW7l6KxBd9oHzvLy0Nhl4mrUd4,1607
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/notch_filter.py,sha256=sSRDQtmaGrZUF8_7nyMnAESbbPRFi_nLsyxX3Sn0jVU,1417
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/qstring.py,sha256=IC_-R-fSQX7XVKHZPteS3sGtC-cISy0CeuBhHZDjv6o,995
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/read_header.py,sha256=4-zZvYeiD8CEz2XCKixMlucw7CF1zt_ba8BChMEPSa8,6591
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhd_format/intanutil/read_one_data_block.py,sha256=3EWCnyWN4dop-8D4VqllSy92s9CYyv4CUzUWbPz1ODk,3604
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/load_intan_rhs_format.py,sha256=uTffoEfY4PbDGmoAgJtjk5-cLIybAp0A99KFSFM662A,10868
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/data_to_result.py,sha256=m1tMeDtkl3vrhzDtTyBupEq31apPgHZHqPAio10rgH8,2475
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/get_bytes_per_data_block.py,sha256=lrz360FqFDctvTQClt8TDZ3BE4r6P_o2RB-fs5c2kKM,1374
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/notch_filter.py,sha256=sSRDQtmaGrZUF8_7nyMnAESbbPRFi_nLsyxX3Sn0jVU,1417
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/qstring.py,sha256=zHCsxlWZvOK9c9tWltMHSnL8a-aAJAOuLrwtmGiGT6g,991
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/read_header.py,sha256=2CDcC8j07R-5I3UkLIqT6-JKHAFByaQj-tHxuMXi3WY,7523
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/intan/load_intan_rhs_format/intanutil/read_one_data_block.py,sha256=OmTCVwUsQh1t-QZE3oDv7rpWzahtGtdTmlcI_rFlkrk,2499
-eegdash/SignalStore/signalstore/adapters/read_adapters/recording_acquisitions/neurodata_without_borders/neurodata_without_borders_read_adapter.py,sha256=lzOMKfwKIiIaiJb5zNzhtlcWLHvOQ6yaPtu2j8Bfoq4,475
-eegdash/SignalStore/signalstore/operations/__init__.py,sha256=AMPuZfqN16WexHAS9qxAH5HGKXR5B0jlMFz6M0Deyxk,222
-eegdash/SignalStore/signalstore/operations/handler_executor.py,sha256=lwyDFmIck_fWpEr729bmeMVR0DkTg0wBU_RD31K9jmc,695
-eegdash/SignalStore/signalstore/operations/handler_factory.py,sha256=UEXZfVgEALmveN5x0YW1a2icIcNlxYBfuZU4HzR4WAk,1867
-eegdash/SignalStore/signalstore/operations/handlers/base_handler.py,sha256=ORgr3TOZsXvGBXpk0O-Aj_CWErW9pGVfsXQZf3f-A34,1538
-eegdash/SignalStore/signalstore/operations/handlers/domain/property_model_handlers.py,sha256=JvCMoBTV_ahe--xZ2vsGMf0FnK4g009Q_RWrJU4yLVI,2836
-eegdash/SignalStore/signalstore/operations/handlers/domain/schema_handlers.py,sha256=Muolz87jNkOH4KmQ_ykFYLaHTSogeW4wtyzmjyE7Iis,100
-eegdash/SignalStore/signalstore/operations/helpers/abstract_helper.py,sha256=OPrnroapxGJXKl2aFOhsy1YMdi79hvb8hLD-kYGMJYk,503
-eegdash/SignalStore/signalstore/operations/helpers/neuroscikit_extractor.py,sha256=NN8os2H5JDopV_al4R8zAaXcRwNTYh0S4ht8krS1pOc,1533
-eegdash/SignalStore/signalstore/operations/helpers/neuroscikit_rawio.py,sha256=-3EAuIA9N8s6tLchgd5Da7izO555cU1RYwFgDvwK4O8,7056
-eegdash/SignalStore/signalstore/operations/helpers/spikeinterface_helper.py,sha256=TVY6QTyexgpJX2tAn-fjEFxedoKgQRSCiTpQUteltGs,3671
-eegdash/SignalStore/signalstore/operations/helpers/wrappers/neo_wrappers.py,sha256=BYlyVxoHXDfaqswT7BEjyRwKmEdq1CAPiL3ZwjfDul0,912
-eegdash/SignalStore/signalstore/operations/helpers/wrappers/nwb_wrappers.py,sha256=cx08mIK_JOOyGJdG3fUMwfFsbexHl_uptBy0mGtbYxA,640
-eegdash/SignalStore/signalstore/store/__init__.py,sha256=F40V_BqwUi8VsyLwMl_M8lvn_P9agBWhwSs_sQtQI1I,324
-eegdash/SignalStore/signalstore/store/data_access_objects.py,sha256=gR6-2oVIvPLR2pHikKCSgGOaLARnb4SpuMIIFopl00M,52892
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