Handle negative phase0 in LCModel .COORD files

suspect/io/lcmodel.py

@@ -1,9 +1,11 @@
-import numpy
-import os
 import itertools
-import parsley
+import os
+import re
 import warnings
 
+import numpy
+import parsley
+
 basis_grammar = r"""
 namelist = '$' name:n pairs:p ws -> (n, dict(p))
 pairs = (pair:first (pair)*:rest -> [first] + rest) | -> []
@@ -166,6 +168,13 @@ def write_all_files(filename, data, wref_data=None, params=None, filbas="/home/s
 
 
 def read_coord(filename):
+
+    # This regex pattern finds any sequence that is an integer or a float.
+    # -?      matches an optional negative sign.
+    # \d+     matches one or more digits.
+    # \.?\d* matches an optional decimal point followed by zero or more digits.
+    number_pattern = r'-?\d+\.?\d*'
+
     with open(filename, 'rt') as fin:
         coord_lines = fin.readlines()
 
@@ -212,12 +221,13 @@ def read_coord(filename):
     # misc_output_info_line = metabolite_table_info_line + metabolite_table_line_count + 1
     misc_output_line_count = int(coord_lines[misc_output_info_line].split()[0])
     misc_output_lines = coord_lines[(misc_output_info_line + 1):(misc_output_info_line + misc_output_line_count + 1)]
+    [phase0, phase1] = map(float, re.findall(number_pattern, misc_output_lines[2]))
     misc_output = {
         "fwhm": float(misc_output_lines[0].split()[2]),
         "snr": float(misc_output_lines[0].split()[6]),
         "frequency_shift": float(misc_output_lines[1].split("=")[1].split()[0]),
-        "phase0": float(misc_output_lines[2].split()[1]),
-        "phase1": float(misc_output_lines[2].split()[3])
+        "phase0": phase0,
+        "phase1": phase1
     }
 
     # get the ppm axis

tests/test_data/lcmodel/liver.COORD

@@ -19,7 +19,7 @@
    5 lines in following misc. output table
   FWHM = 0.297 ppm    S/N =  24                                            
   Data shift =-0.019 ppm                                                   
-  Ph:  36 deg       0.3 deg/ppm                                            
+  Ph:-136 deg       0.3 deg/ppm                                            
   alphaB,S = 1.2E+02,   2.2E-02                                            
     6 spline knots.   Ns = 0(1)                                            
   821 points on ppm-axis = NY

tests/test_mrs/test_io.py

@@ -1,15 +1,15 @@
-import suspect
-import suspect.io.tarquin
-import pytest
-import unittest.mock
 import builtins
-from unittest.mock import patch
 import os
-
-from suspect.io._common import complex_array_from_iter
+import unittest.mock
+from math import isclose
+from unittest.mock import patch
 
 import numpy
 
+import suspect
+import suspect.io.tarquin
+from suspect.io._common import complex_array_from_iter
+
 
 def test_complex_from_iter():
     float_list = [1.0, 0.0, 0.0, 1.0]
@@ -76,10 +76,14 @@ def test_lcmodel_all_files():
 def test_lcmodel_read_coord():
     fitting_result = suspect.io.lcmodel.read_coord("tests/test_data/lcmodel/svs_97.COORD")
     assert len(fitting_result["metabolite_fits"]) == 41
+    assert isclose(fitting_result["misc_output"]["phase0"], 21.0)
+    assert isclose(fitting_result["misc_output"]["phase1"], 12.2)
 
 
 def test_lcmodel_read_liver_coord():
     fitting_result = suspect.io.lcmodel.read_coord("tests/test_data/lcmodel/liver.COORD")
+    assert isclose(fitting_result["misc_output"]["phase0"], -136.0)
+    assert isclose(fitting_result["misc_output"]["phase1"], 0.3)
 
 
 def test_lcmodel_read_basis():