From c0b349973445383cfc4bb630aff17b8a56d6c1e0 Mon Sep 17 00:00:00 2001
From: Jeff Stout <stoutjd@nih.gov>
Date: Thu, 25 Jul 2024 14:45:31 -0400
Subject: [PATCH] WIP - Added brainsight target file to bstags

Need to integrate this into bids pipeline
---
 nih2mne/bstags.py            | 57 ++++++++++++++++++++++++++++++++++++
 nih2mne/tests/test_bstags.py | 13 +++++++-
 2 files changed, 69 insertions(+), 1 deletion(-)

diff --git a/nih2mne/bstags.py b/nih2mne/bstags.py
index dfbd68d..e2cd845 100755
--- a/nih2mne/bstags.py
+++ b/nih2mne/bstags.py
@@ -63,6 +63,63 @@ def txt_to_tag_pd(txtname):
     return tags
 
 
+def tags_from_bsight_targetfile(fname, tag_template=['NAS','LPA','RPA']):
+    '''
+    If brainsight files are exported from the target menu, the headers are 
+    inconsistent the electrodes.txt style export file.  This strips out the 
+    non-matching column widths.
+
+    Parameters
+    ----------
+    fname : TYPE
+        DESCRIPTION.
+    tag_template : TYPE, optional
+        DESCRIPTION. The default is ['NAS','LPA','RPA'].
+
+    Raises
+    ------
+    ValueError
+        If start or stopping conditions in the target file can not be found 
+        this will result in an error.
+
+    Returns
+    -------
+    tags : dict
+        {"NAS": float, "LPA": float, "RPA": float}
+
+    '''
+    import pandas as pd
+    with open(fname) as f:
+        tmp = f.readlines()
+    
+    #Identify start and end of target section
+    idx=0; start_idx=0; end_idx=0
+    for i in tmp:
+        if i[0:8]=='# Sample':
+            start_idx=idx
+        if i[0:9]=='# Planned':
+            end_idx=idx
+        idx+=1
+    
+    if (start_idx==0) or (end_idx==0):
+        raise ValueError('Cannot find the start and end of localizer section')
+    
+    #Format text and create list
+    tmp_ = tmp[start_idx:end_idx]        
+    output = []
+    for i in tmp_:
+        output.append(i.strip('\n').split('\t'))
+    output[0]=['Sample Name']+output[0][1:]
+    
+    #Create dataframe and extract tags
+    dframe = pd.DataFrame(output[1:], columns=output[0])
+    tags ={}
+    for tag in tag_template:
+        tmp = dframe[dframe['Sample Name']==tag][['Loc. X','Loc. Y','Loc. Z']].values[0]
+        tags[tag] = [float(i) for i in tmp]
+    return tags
+
+
 def write_tagfile(tags, out_fname=None):
     ''''''
     
diff --git a/nih2mne/tests/test_bstags.py b/nih2mne/tests/test_bstags.py
index dfc128c..4491e40 100755
--- a/nih2mne/tests/test_bstags.py
+++ b/nih2mne/tests/test_bstags.py
@@ -6,10 +6,13 @@
 @author: jstout
 """
 
-from ..bstags import txt_to_tag, txt_to_tag_pd
+from ..bstags import txt_to_tag, txt_to_tag_pd, tags_from_bsight_targetfile
 from ..bstags import write_tagfile
 import pytest 
 import os
+import logging
+# logger = logging.get_logger()
+# err_logger = logging.get_logger()
 # =============================================================================
 # Tests
 # =============================================================================
@@ -63,7 +66,15 @@ def test_alt_exported():
     assert tags['Nasion']=="'Nasion' -6.0344 -114.7126 -2.6041"
     assert tags['Right Ear']=="'Right Ear' -67.2147 -18.6125 -36.5009"
     assert tags['Left Ear']=="'Left Ear' 64.1748 -28.3103 -32.4693"
+
+def test_tags_from_bsight_targetfile():
+    fname = os.path.join(test_dir, 'bsight_target_file.txt')
+    tmp = tags_from_bsight_targetfile(fname, tag_template=['NAS','LPA','RPA'])
     
+    testvals = {'NAS': [9.1961, 125.8807, 5.5038],
+                 'LPA': [-62.6752, 52.695, -39.5915],
+                 'RPA': [71.4232, 39.4116, -31.5812]}
+    assert tmp == testvals