Merge pull request #27 from mtorabi59/main

change behavior of load_TS

pydfc/data_loader.py

@@ -6,6 +6,7 @@
 """
 
 import os
+from copy import deepcopy
 
 import h5py
 import numpy as np
@@ -16,10 +17,10 @@
 ################################# DATA_LOADER functions ######################################
 
 
-def find_subj_list(data_root, sessions):
+def find_subj_list(data_root):
     """
     find the list of subjects in data_root
-    the files must follow the format: subjectID_sessionID
+    the files must follow the format: sub-subjectID
     only these files should be in the data_root
     """
     if data_root[-1] != "/":
@@ -31,32 +32,13 @@ def find_subj_list(data_root, sessions):
     FOLDERS.sort()
     SUBJECTS = list()
     for s in FOLDERS:
-        num = s[: s.find("_")]
-        SUBJECTS.append(num)
-    # the subjects might be repeated because of different sessions
-    SUBJECTS = list(set(SUBJECTS))
+        if "sub-" in s:
+            SUBJECTS.append(s)
     SUBJECTS.sort()
 
-    print(str(len(SUBJECTS)) + " subjects were found. ")
-
-    failed_subjs = []
-    kept_subjs = []
-    for subj in SUBJECTS:
-        kept_subjs.append(subj)
-        for session in sessions:
-            if not os.path.exists(f"{data_root}{subj}_{session}"):
-                failed_subjs.append(subj)
-                kept_subjs.remove(subj)
-                break
-
-    print(
-        str(len(failed_subjs))
-        + " subjects had missing sessions. "
-        + str(len(kept_subjs))
-        + " subjects were kept. "
-    )
+    print(f"{len(SUBJECTS)} subjects were found. ")
 
-    return kept_subjs
+    return SUBJECTS
 
 
 def load_from_array(subj_id2load=None, **params):
@@ -83,7 +65,7 @@ def load_from_array(subj_id2load=None, **params):
 
     SESSIONs = params["SESSIONs"]  # list of sessions
     if subj_id2load is None:
-        SUBJECTS = find_subj_list(params["data_root"], sessions=SESSIONs)
+        SUBJECTS = find_subj_list(params["data_root"])
     else:
         SUBJECTS = [subj_id2load]
 
@@ -337,12 +319,22 @@ def multi_nifti2timeseries(
     return BOLD_multi
 
 
-def load_TS(data_root, file_name, SESSIONs, subj_id2load=None):
+def load_TS(
+    data_root,
+    file_name,
+    SESSIONs,
+    subj_id2load=None,
+    task=None,
+    run=None,
+):
     """
     load a TIME_SERIES object from a .npy file
     if SESSIONs is a list, it will load all the sessions,
         if it is a string, it will load that session
     if subj_id2load is None, it will load all the subjects
+    file_name: name of the file to load
+        format example: {subj_id}_{task}_{run}_time-series.npy
+        (keep the {} for the variables)
     """
     # check if SESSIONs is a list or a string
     flag = False
@@ -351,17 +343,28 @@ def load_TS(data_root, file_name, SESSIONs, subj_id2load=None):
         flag = True
 
     if subj_id2load is None:
-        SUBJECTS = find_subj_list(data_root, sessions=SESSIONs)
+        SUBJECTS = find_subj_list(data_root)
     else:
+        assert "sub-" in subj_id2load, "subj_id2load must start with 'sub-'"
         SUBJECTS = [subj_id2load]
 
     TS = {}
     for session in SESSIONs:
         TS[session] = None
         for subj in SUBJECTS:
-            subj_fldr = f"{subj}_{session}"
+            subj_fldr = subj
+            # make the file_name
+            TS_file = deepcopy(file_name)
+            if "{subj_id}" in file_name:
+                TS_file = TS_file.replace("{subj_id}", subj)
+            if "{task}" in file_name:
+                assert task is not None, "task must be provided"
+                TS_file = TS_file.replace("{task}", task)
+            if "{run}" in file_name:
+                assert run is not None, "run must be provided"
+                TS_file = TS_file.replace("{run}", run)
             time_series = np.load(
-                f"{data_root}/{subj_fldr}/{file_name}", allow_pickle="True"
+                f"{data_root}/{subj_fldr}/{TS_file}", allow_pickle="True"
             ).item()
             if TS[session] is None:
                 TS[session] = time_series