Merge pull request #324 from MIT-LCP/header-syntax

Allow hyphens in segment names, and fix basic parsing issues

Author: tompollard

wfdb/io/_header.py

@@ -100,27 +100,44 @@
 
 # Regexp objects for reading headers
 # Record line
-_rx_record = re.compile(''.join(
-    ["(?P<record_name>[-\w]+)/?(?P<n_seg>\d*)[ \t]+",
-     "(?P<n_sig>\d+)[ \t]*(?P<fs>\d*\.?\d*)/*(?P<counter_freq>-?\d*\.?\d*)",
-     "\(?(?P<base_counter>-?\d*\.?\d*)\)?[ \t]*(?P<sig_len>\d*)[ \t]*",
-     "(?P<base_time>\d{,2}:?\d{,2}:?\d{,2}\.?\d{,6})[ \t]*",
-     "(?P<base_date>\d{,2}/?\d{,2}/?\d{,4})"])
-)
+_rx_record = re.compile(
+    r'''
+    [ \t]* (?P<record_name>[-\w]+)
+           /?(?P<n_seg>\d*)
+    [ \t]+ (?P<n_sig>\d+)
+    [ \t]* (?P<fs>\d*\.?\d*)
+           /*(?P<counter_freq>-?\d*\.?\d*)
+           \(?(?P<base_counter>-?\d*\.?\d*)\)?
+    [ \t]* (?P<sig_len>\d*)
+    [ \t]* (?P<base_time>\d{,2}:?\d{,2}:?\d{,2}\.?\d{,6})
+    [ \t]* (?P<base_date>\d{,2}/?\d{,2}/?\d{,4})
+    ''', re.VERBOSE)
 
 # Signal line
-_rx_signal = re.compile(''.join(
-    ["(?P<file_name>~?[-\w]*\.?[\w]*)[ \t]+(?P<fmt>\d+)x?"
-     "(?P<samps_per_frame>\d*):?(?P<skew>\d*)\+?(?P<byte_offset>\d*)[ \t]*",
-     "(?P<adc_gain>-?\d*\.?\d*e?[\+-]?\d*)\(?(?P<baseline>-?\d*)\)?",
-     "/?(?P<units>[\w\^\-\?%\/]*)[ \t]*(?P<adc_res>\d*)[ \t]*",
-     "(?P<adc_zero>-?\d*)[ \t]*(?P<init_value>-?\d*)[ \t]*(?P<checksum>-?\d*)",
-     "[ \t]*(?P<block_size>\d*)[ \t]*(?P<sig_name>[\S]?[^\t\n\r\f\v]*)"])
-)
+_rx_signal = re.compile(
+    r'''
+    [ \t]* (?P<file_name>~?[-\w]*\.?[\w]*)
+    [ \t]+ (?P<fmt>\d+)
+           x?(?P<samps_per_frame>\d*)
+           :?(?P<skew>\d*)
+           \+?(?P<byte_offset>\d*)
+    [ \t]* (?P<adc_gain>-?\d*\.?\d*e?[\+-]?\d*)
+           \(?(?P<baseline>-?\d*)\)?
+           /?(?P<units>[\w\^\-\?%\/]*)
+    [ \t]* (?P<adc_res>\d*)
+    [ \t]* (?P<adc_zero>-?\d*)
+    [ \t]* (?P<init_value>-?\d*)
+    [ \t]* (?P<checksum>-?\d*)
+    [ \t]* (?P<block_size>\d*)
+    [ \t]* (?P<sig_name>[\S]?[^\t\n\r\f\v]*)
+    ''', re.VERBOSE)
 
 # Segment line
-_rx_segment = re.compile('(?P<seg_name>\w*~?)[ \t]+(?P<seg_len>\d+)')
-
+_rx_segment = re.compile(
+    r'''
+    [ \t]* (?P<seg_name>[-\w]*~?)
+    [ \t]+ (?P<seg_len>\d+)
+    ''', re.VERBOSE)
 
 class BaseHeaderMixin(object):
     """
@@ -879,11 +896,14 @@ def _parse_record_line(record_line):
     record_fields = {}
 
     # Read string fields from record line
+    match = _rx_record.match(record_line)
+    if match is None:
+        raise HeaderSyntaxError('invalid syntax in record line')
     (record_fields['record_name'], record_fields['n_seg'],
      record_fields['n_sig'], record_fields['fs'],
      record_fields['counter_freq'], record_fields['base_counter'],
      record_fields['sig_len'], record_fields['base_time'],
-     record_fields['base_date']) = re.findall(_rx_record, record_line)[0]
+     record_fields['base_date']) = match.groups()
 
     for field in RECORD_SPECS.index:
         # Replace empty strings with their read defaults (which are
@@ -942,14 +962,17 @@ def _parse_signal_lines(signal_lines):
 
     # Read string fields from signal line
     for ch in range(n_sig):
+        match = _rx_signal.match(signal_lines[ch])
+        if match is None:
+            raise HeaderSyntaxError('invalid syntax in signal line')
         (signal_fields['file_name'][ch], signal_fields['fmt'][ch],
          signal_fields['samps_per_frame'][ch], signal_fields['skew'][ch],
          signal_fields['byte_offset'][ch], signal_fields['adc_gain'][ch],
          signal_fields['baseline'][ch], signal_fields['units'][ch],
          signal_fields['adc_res'][ch], signal_fields['adc_zero'][ch],
          signal_fields['init_value'][ch], signal_fields['checksum'][ch],
          signal_fields['block_size'][ch],
-         signal_fields['sig_name'][ch]) = _rx_signal.findall(signal_lines[ch])[0]
+         signal_fields['sig_name'][ch]) = match.groups()
 
         for field in SIGNAL_SPECS.index:
             # Replace empty strings with their read defaults (which are mostly None)
@@ -998,7 +1021,11 @@ def _read_segment_lines(segment_lines):
 
     # Read string fields from signal line
     for i in range(len(segment_lines)):
-        (segment_fields['seg_name'][i], segment_fields['seg_len'][i]) = _rx_segment.findall(segment_lines[i])[0]
+        match = _rx_segment.match(segment_lines[i])
+        if match is None:
+            raise HeaderSyntaxError('invalid syntax in segment line')
+        (segment_fields['seg_name'][i],
+         segment_fields['seg_len'][i]) = match.groups()
 
         # Typecast strings for numerical field
         if field == 'seg_len':
@@ -1007,6 +1034,10 @@ def _read_segment_lines(segment_lines):
     return segment_fields
 
 
+class HeaderSyntaxError(ValueError):
+    """Invalid syntax found in a WFDB header file."""
+
+
 def lines_to_file(file_name, write_dir, lines):
     """
     Write each line in a list of strings to a text file.