Merge pull request #19 from TACC/18-move-imaging-data-etl-to-datastore

Simplify imaging api
TACC · Jul 26, 2024 · aa6fa2b · aa6fa2b
2 parents c806c99 + d36eff4
commit aa6fa2b
Showing 1 changed file with 7 additions and 3 deletions.
diff --git a/src/data_loading.py b/src/data_loading.py
@@ -175,8 +175,11 @@ def load_display_terms(display_terms_location):
 def get_local_imaging_data(imaging_filepath, qc_filepath):
     ''' Load data from local imaging files. '''
     try:
-        imaging = pd.read_csv(imaging_filepath)
-        qc = pd.read_csv(qc_filepath)
+        imaging_full = pd.read_csv(imaging_filepath)
+        imaging = subset_imaging_data(imaging_full)
+
+        qc_full = pd.read_csv(qc_filepath)
+        qc = subset_qc_data(qc_full)
 
         imaging_data_json = {
             'imaging' : imaging.to_dict('records'),
@@ -306,12 +309,13 @@ def get_api_consort_data(tapis_token,
 
 ## Function to rebuild dataset from apis
 
+
 def subset_imaging_data(imaging_full):
     imaging_columns_used = ['site', 'subject_id', 'visit','acquisition_week','Surgery Week','bids', 'dicom', 
     'T1 Indicated','DWI Indicated', '1st Resting State Indicated','fMRI Individualized Pressure Indicated', 
     'fMRI Standard Pressure Indicated','2nd Resting State Indicated',
     'T1 Received', 'DWI Received', 'fMRI Individualized Pressure Received', 'fMRI Standard Pressure Received',
-    '1st Resting State Received', '2nd Resting State Received']
+    '1st Resting State Received', '2nd Resting State Received','Cuff1 Applied Pressure']
 
     imaging = imaging_full[imaging_columns_used].copy() # Select subset of columns
     imaging = imaging.replace('na', np.nan) # Clean up data