Merge pull request #6 from individual-brain-charting/fetch_raw_preproc

Fetching raw and preprocessed data is now possible. Also adds databases for all ibc datasets on ebrains with consistent columns/info

README.md

@@ -16,21 +16,21 @@ pip install git+https://github.com/individual-brain-charting/api.git#egg=ibc_api
 ```python
 import ibc_api.utils as ibc
 
-# Returns a link that takes you to EBRAINS login page and stores an access token locally
-ibc.authenticate()
-
 # Fetch info on all available files
 # Load as a pandas dataframe and save as ibc_data/available_{data_type}.csv 
 db = ibc.get_info(data_type="volume_maps")
 
 # Keep statistic maps for sub-08, for task-Discount
-filtered_db = ibc.filter_data(db, subject_list=["sub-08"], task_list=["Discount"])
+filtered_db = ibc.filter_data(db, subject_list=["08"], task_list=["Discount"])
+
+# Authenticate with EBRAINS before downloading
+# Returns a link that takes you to EBRAINS login page and stores an access token locally
+ibc.authenticate()
 
 # Download all statistic maps for sub-08, task-Discount 
-# Saved under ibc_data/resulting_smooth_maps/sub-08/task-Discount
 # Also creates ibc_data/downloaded_volume_maps.csv 
-# which contains downloaded file paths and time of download
-downloaded_db = ibc.download_data(filtered_db, organise_by='task')
+# which contains local file paths and time of download
+downloaded_db = ibc.download_data(filtered_db)
 ```
 # Note
 Since this api is under active development, make sure to update it regularly

examples/example.py

@@ -1,17 +1,17 @@
 import ibc_api.utils as ibc
 
-# Returns a link that takes you to EBRAINS login page and stores an access token locally
-ibc.authenticate()
-
 # Fetch info on all available files
-# Load as a pandas dataframe and save as ibc_data/available_{data_type}.csv 
+# Load as a pandas dataframe and save as ibc_data/available_{data_type}.csv
 db = ibc.get_info(data_type="volume_maps")
 
 # Keep statistic maps for sub-08, for task-Discount
-filtered_db = ibc.filter_data(db, subject_list=["sub-08"], task_list=["Discount"])
+filtered_db = ibc.filter_data(db, subject_list=["08"], task_list=["Discount"])
+
+# Authenticate with EBRAINS before downloading
+# Returns a link that takes you to EBRAINS login page and stores an access token locally
+ibc.authenticate()
 
-# Download all statistic maps for sub-08, task-Discount 
-# Saved under ibc_data/resulting_smooth_maps/sub-08/task-Discount
-# Also creates ibc_data/downloaded_volume_maps.csv 
-# which contains downloaded file paths and time of download
-downloaded_db = ibc.download_data(filtered_db, organise_by='task')
+# Download all statistic maps for sub-08, task-Discount
+# Also creates ibc_data/downloaded_volume_maps.csv
+# which contains local file paths and time of download
+downloaded_db = ibc.download_data(filtered_db)