cleanups

src/ibl_to_nwb/_scripts/convert_brainwide_map_processed_only_local_testing.py

@@ -24,7 +24,6 @@
 from ibl_to_nwb.testing._consistency_checks import check_written_nwbfile_for_consistency
 
 base_path = Path.home() / "ibl_scratch"  # local directory
-# session = "d32876dd-8303-4720-8e7e-20678dc2fd71"
 session = "caa5dddc-9290-4e27-9f5e-575ba3598614"  # a BWM session with dual probe
 
 nwbfile_path = base_path / "nwbfiles" / session / f"{session}.nwb"

src/ibl_to_nwb/_scripts/convert_brainwide_map_raw_only_local_testing.py

@@ -4,29 +4,18 @@
 from ibl_to_nwb.converters import BrainwideMapConverter, IblSpikeGlxConverter
 from ibl_to_nwb.datainterfaces import RawVideoInterface
 
-# eid = "d32876dd-8303-4720-8e7e-20678dc2fd71"
-eid = "caa5dddc-9290-4e27-9f5e-575ba3598614"  # a BWM session with dual probe
+# select eid
+# -> run download_data_local first with this eid to set up the local folder structure and one cache
+eid = "caa5dddc-9290-4e27-9f5e-575ba3598614"
 
-# %%
-# one_cache_folder = '/home/georg/ibl_scratch/ibl_conversion/caa5dddc-9290-4e27-9f5e-575ba3598614/cache'
-# data_folder = Path(
-#     "/media/georg/openlab/Downloads/ONE/openalyx.internationalbrainlab.org/steinmetzlab/Subjects/NR_0031/2023-07-14/001"
-# )
-# spikeglx_source_folder_path = data_folder / "raw_ephys_data"
-
-# Specify the revision of the pose estimation data
-# Setting to 'None' will use whatever the latest released revision is
-# revision = None
-
-# base_path = Path("E:/IBL")
-base_path = Path.home() / "ibl_scratch"  # local directory
+# folders
+base_path = Path.home() / "ibl_scratch"
 base_path.mkdir(exist_ok=True)
 nwbfiles_folder_path = base_path / "nwbfiles"
 nwbfiles_folder_path.mkdir(exist_ok=True)
 
 # Initialize IBL (ONE) client to download processed data for this session
-# one_cache_folder_path = base_path / "cache"
-one_cache_folder_path = "/home/georg/ibl_scratch/ibl_conversion/caa5dddc-9290-4e27-9f5e-575ba3598614/cache"
+one_cache_folder_path =  base_path / 'ibl_conversion' / eid / 'cache'
 one = ONE(
     base_url="https://openalyx.internationalbrainlab.org",
     password="international",
@@ -37,14 +26,12 @@
 data_interfaces = []
 
 # %% ephys
-# session_folder = one.eid2path(eid)
-# spikeglx_source_folder_path = session_folder / 'raw_ephys_data'
-
+session_folder = one.eid2path(eid)
+spikeglx_source_folder_path = session_folder / 'raw_ephys_data'
 
 # Specify the path to the SpikeGLX files on the server but use ONE API for timestamps
-# spikeglx_subconverter = IblSpikeGlxConverter(folder_path=spikeglx_source_folder_path, one=one, eid=eid)
-# data_interfaces.append(spikeglx_subconverter)
-
+spikeglx_subconverter = IblSpikeGlxConverter(folder_path=spikeglx_source_folder_path, one=one, eid=eid)
+data_interfaces.append(spikeglx_subconverter)
 
 # %% video
 # Raw video takes some special handling

src/ibl_to_nwb/_scripts/download_data.py

@@ -0,0 +1,44 @@
+# %%
+from pathlib import Path
+from one.api import ONE
+
+# %%
+eid = "caa5dddc-9290-4e27-9f5e-575ba3598614"  # a BWM eid with dual probe
+
+base_path = Path.home() / "ibl_scratch"  # local directory
+
+# Download behavior and spike sorted data for this eid
+session_path = base_path / "ibl_conversion" / eid
+cache_folder = base_path / "ibl_conversion" / eid / "cache"
+session_one = ONE(
+    base_url="https://openalyx.internationalbrainlab.org",
+    password="international",
+    silent=False,
+    cache_dir=cache_folder,
+)
+
+# %% latest revision
+revisions = session_one.list_revisions(eid)
+revision = revisions[-1]
+
+# %% list all datasets
+datasets = session_one.list_datasets(eid)
+
+# %% list all collections
+collections = session_one.list_collections(eid)
+
+# %%
+for dataset in datasets:
+    session_one.load_dataset(eid, dataset, download_only=True)
+
+# %% downloads all raw ephys data!
+collections = session_one.list_collections(eid, collection="raw_ephys_data/*")
+for collection in collections:
+    datasets = session_one.list_datasets(eid, collection=collection)
+    for dataset in datasets:
+        session_one.load_dataset(eid, dataset, download_only=True)
+
+# %% just the video data
+datasets = session_one.list_datasets(eid, collection="raw_video_data")
+for dataset in datasets:
+    session_one.load_dataset(eid, dataset, download_only=True)