Flexible subject reading

src/silverlabnwb/header.py

@@ -131,6 +131,14 @@ def determine_trial_times(self):
         """
         raise NotImplementedError
 
+    def get_subject_info(self):
+        """Extract information about the subject if there is any in the header.
+
+        Return an empty string if no information is found. This is always the case in legacy LabView versions,
+        and sometimes the case in newer LabView versions.
+        """
+        return ""
+
     def get_raw_fields(self):
         """Get the fields of the header as directly read from the file.
 
@@ -253,3 +261,10 @@ def determine_trial_times(self):
                 end = None  # determine final 'end' later from speed data
             trial_times.append((start, end))
         return trial_times
+
+    def get_subject_info(self):
+        return "\n".join(
+            f'{field}: {value}'
+            for field, value in self['BIOLOGY INFORMATION'].items()
+            if value
+        )

src/silverlabnwb/nwb_file.py

@@ -74,6 +74,7 @@ def __init__(self, nwb_path, mode='r', verbose=True):
         self.custom_silverlab_dict = dict()
         self.labview_version = None
         self.imaging_info = None
+        self.subject = None
         self.trial_times = None
         self.compress = None
 
@@ -220,6 +221,10 @@ def add_core_metadata(self):
         # even though it is still stored under /general/stimulus
         if 'stimulus' in self.experiment:
             self.add_general_info('stimulus_notes', self.experiment['stimulus'])
+        # If both metadata and header have a non-empty subject entry, the header gets priority.
+        # If neither have an entry, pynwb defaults to not writing a subject field in the file.
+        if self.subject:
+            self.add_subject(self.subject)
         if 'subject' in self.experiment:
             self.add_subject(self.experiment['subject'])
         # Update the file on disk:

tests/data/real life Experiment Header v231 pointing.ini

@@ -175,6 +175,11 @@ Integral Scale Z = 20.000
 Scan Interval = 2.000
 Ref Plot Refresh Rate = 0.000
 
+[BIOLOGY INFORMATION]
+Animal Code or Name = ""
+Animal DoB = ""
+Animal Age = ""
+
 [Intertrial FIFO Times]
 0.000000	16.428930
 1.000000	32.850058

tests/data/synthetic experiment Header v231 no last time.ini

@@ -17,6 +17,11 @@ Functional Mode = "Patch"
 [VOLUME IMAGING]
 Functional Mode = "Point"
 
+[BIOLOGY INFORMATION]
+Animal Code or Name = ""
+Animal DoB = ""
+Animal Age = ""
+
 [Intertrial FIFO Times]
 0.000000	0.000000
 1.000000	12.345678

tests/data/synthetic experiment Header v231.ini

@@ -17,6 +17,12 @@ Functional Mode = "Patch"
 [VOLUME IMAGING]
 Functional Mode = "Point"
 
+[BIOLOGY INFORMATION]
+Animal Code or Name = "Test1"
+Animal DoB = ""
+Region of brain imaged = "crus"
+
+
 [Intertrial FIFO Times]
 0.000000	0.000000
 1.000000	12.345678

tests/test_header.py

@@ -59,6 +59,15 @@ def test_pre2018_trial_times_raises_error(self, header):
         with pytest.raises(NotImplementedError):
             header.determine_trial_times()
 
+    @pytest.mark.parametrize("header, expected_subject",
+                             [(synthetic_header_path_v231, "Animal Code or Name: Test1\nRegion of brain imaged: crus"),
+                              (synthetic_header_path_v231_no_last_time, ""),
+                              (synthetic_header_path_pre2018, ""),
+                              (real_life_header_path_v231_pointing, "")],
+                             indirect=["header"])
+    def test_subject_info(self, header, expected_subject):
+        assert header.get_subject_info() == expected_subject
+
     def test_unrecognised_line_causes_warning(self):
         with pytest.warns(UserWarning) as list_of_warnings:
             LabViewHeader.from_file(os.path.join("tests", "data", self.header_with_unrecognised_line_path))