Merge pull request #54 from vinferrer/txt

Adding txt support for labchart

phys2bids/interfaces/txt.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+phys2bids interface for txt files.
+"""
+
+import numpy as np
+from phys2bids.physio_obj import BlueprintInput
+
+def populate_phys_input(filename, chtrig):
+    """
+    Populate object phys_input
+    for now this works only with labchart files
+        Input (Properties)
+    ------------------
+    filename: str 
+        path to the txt labchart file
+    chtrig : int
+        index of trigger channel
+
+    Output
+    ------------------
+    BlueprintInput object for more see BlueprintInput docs  
+    """
+
+    header = []
+    channel_list = []
+    with open(filename,'r') as f:
+        header_l = 0
+        for line in f:
+            line=line.rstrip('\n').split('\t')
+            try: 
+                float(line[0])
+            except ValueError:
+                header.append(line)
+                continue 
+            line = [float(i) for i in line]
+            channel_list.append(line)
+    # get frequency 
+    interval = header[0][1].split(" ")
+    if interval[-1] not in ['hr', 'min', 's','ms','µs']:
+        raise AttributeError(f'Interval unit "{interval[-1]}" is not in a valid LabChart time unit, '
+                             'this probably means your file is not in labchart format')
+
+    if interval[-1] != 's':
+        print('Interval is not in seconds. Converting its value.')
+        if interval[-1] == 'hr':
+            interval[0] = float(interval)[0]*3600
+            interval[-1] = 's'
+        elif interval[-1] == 'min':
+            interval[0] = float(interval[0])*60
+            interval[-1] = 's'
+        elif interval[-1] == 'ms':
+            interval[0] = float(interval[0])/1000
+            interval[-1] = 's'
+        elif interval[-1] == 'µs':
+            interval[0] = float(interval[0])/1000000
+            interval[-1] = 's'
+    else:
+        interval[0] = float(interval[0])
+    # get units
+    range_list = header[5][1:]
+    units = []
+    for item in range_list:
+        units.append(item.split(' ')[1])
+    # get names
+    orig_names=header[4][1:]
+    names = ['time','trigger']
+    orig_names.pop(chtrig)
+    names=names+orig_names
+    # get channels 
+    timeseries = np.matrix(channel_list).T.tolist()
+    freq = [1/interval[0]]*len(timeseries)
+    timeseries=[np.array(darray) for darray in timeseries]
+    ordered_timeseries=[timeseries[0],timeseries[chtrig]]
+    timeseries.pop(chtrig)
+    timeseries.pop(0)
+    ordered_timeseries=ordered_timeseries+timeseries
+    return BlueprintInput(ordered_timeseries, freq, names, units)

phys2bids/phys2bids.py

@@ -38,9 +38,6 @@
 from phys2bids.cli.run import _get_parser
 from phys2bids.physio_obj import BlueprintOutput
 
-# #!# This is hardcoded until we find a better solution
-HEADERLENGTH = 9
-
 
 def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, outfile):
     """
@@ -205,7 +202,7 @@ def _main(argv=None):
     if ftype == 'acq':
         from phys2bids.interfaces.acq import populate_phys_input
     elif ftype == 'txt':
-        raise NotImplementedError('txt not yet supported')
+        from phys2bids.interfaces.txt import populate_phys_input
     else:
         # #!# We should add a logger here.
         raise NotImplementedError('Currently unsupported file type.')

phys2bids/physio_obj.py

@@ -137,7 +137,7 @@ def __init__(self, timeseries, freq, ch_name, units):
         self.ch_amount = len(self.timeseries)
         self.freq = has_size(is_valid(freq, list,
                                       list_type=(int, float)),
-                             self.ch_amount, 0)
+                             self.ch_amount, 0.0)
         self.ch_name = has_size(ch_name, self.ch_amount, 'unknown')
         self.units = has_size(units, self.ch_amount, '[]')