XA30 compatibility

bidsphysio.acq2bids/bidsphysio/acq2bids/info.py

@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ ="21.06.24"
+__version__ ="21.07.01"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"
@@ -24,8 +24,8 @@
 PYTHON_REQUIRES = ">=3.6"
 
 REQUIRES = [
-    'bidsphysio.base>=21.5.27',
-    'bidsphysio.session>=21.06.24',
+    'bidsphysio.base>=21.07.01',
+    'bidsphysio.session>=21.07.01',
     'bioread[mat]>=2.0.0',
 ]
 

bidsphysio.base/bidsphysio/base/info.py

@@ -1,4 +1,4 @@
-__version__ ="21.06.24"
+__version__ ="21.07.01"
 __author__ = "Pablo Velasco, Chrysa Papadaniil"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

bidsphysio.dcm2bids/bidsphysio/dcm2bids/info.py

@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ = "21.06.24"
+__version__ = "21.07.01"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"
@@ -24,8 +24,8 @@
 PYTHON_REQUIRES = ">=3.6"
 
 REQUIRES = [
-    'bidsphysio.base >= 1.4.0',
-    'bidsphysio.session >= 1.4.0',
+    'bidsphysio.base >= 21.07.01',
+    'bidsphysio.session >= 21.07.01',
     'numpy >= 1.17.1',
     'pydicom >= 1.4.1',
 ]

bidsphysio.edf2bids/bidsphysio/edf2bids/info.py

@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ ="21.06.24"
+__version__ ="21.07.01"
 __author__ = "Chrysa Papadaniil"
 __author_email__ = "chrysa@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"
@@ -24,9 +24,9 @@
 PYTHON_REQUIRES = ">=3.6"
 
 REQUIRES = [
-    'bidsphysio.base>=21.5.18',
-    'bidsphysio.session>=21.5.18',
-    'bidsphysio.events>=21.5.27',
+    'bidsphysio.base>=21.07.01',
+    'bidsphysio.session>=21.07.01',
+    'bidsphysio.events>=21.07.01',
     'pyedfread',
     'h5py>=2.9.0',
     'Cython>=0.29.13',

bidsphysio.events/bidsphysio/events/info.py

@@ -1,4 +1,4 @@
-__version__ ="21.06.24"
+__version__ ="21.07.01"
 __author__ = "Chrysa Papadaniil, Pablo Velasco"
 __author_email__ = "chrysa@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

bidsphysio.physio2bids/bidsphysio/physio2bids/info.py

@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ ="21.06.24"
+__version__ ="21.07.01"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"
@@ -24,7 +24,7 @@
 PYTHON_REQUIRES = ">=3.6"
 
 REQUIRES = [
-    'bidsphysio >= 4.3.3',
+    'bidsphysio >= 21.07.01',
 ]
 
 TESTS_REQUIRES = [

bidsphysio.pmu2bids/bidsphysio/pmu2bids/info.py

@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ ="21.06.24"
+__version__ ="21.07.01"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"
@@ -24,7 +24,7 @@
 PYTHON_REQUIRES = ">=3.6"
 
 REQUIRES = [
-    'bidsphysio.base >= 1.3.1',
+    'bidsphysio.base >= 21.07.01',
 ]
 
 TESTS_REQUIRES = [

bidsphysio.pmu2bids/bidsphysio/pmu2bids/pmu2bidsphysio.py

@@ -182,7 +182,7 @@ def readpmu(physio_file, softwareVersion=None, verbose=False):
     """
 
     # Check for known software versions:
-    knownVersions = ['VB15A', 'VE11C', 'VBX']
+    knownVersions = ['XA30', 'VB15A', 'VE11C', 'VBX']
 
     if not (
             softwareVersion in knownVersions or
@@ -199,7 +199,9 @@ def readpmu(physio_file, softwareVersion=None, verbose=False):
         # try to read all new versions, if successful, return the results.
         # If unsuccessful, it will print a warning and try the next versionToTest
         try:
-            if sv == 'VE11C':
+            if sv == 'XA30':
+                return readXA30Cpmu(physio_file)
+            elif sv == 'VE11C':
                 return readVE11Cpmu(physio_file)
             elif sv == 'VB15A':
                 return readVB15Apmu(physio_file)
@@ -306,6 +308,104 @@ def readVE11Cpmu(physio_file, forceRead=False):
 
     return physio_type, MDHTime, sampling_rate, physio_signal
 
+def readXA30Cpmu(physio_file, forceRead=False):
+    """
+    Function to read the physiological signal from a XA30 Siemens PMU physio file
+
+    Parameters
+    ----------
+    physio_file : str
+        path to a file with a Siemens PMU recording
+    forceRead : bool
+        flag indicating to read the file whether the format seems correct or not
+
+    Returns
+    -------
+    physio_type : str
+        type of physiological recording
+    MDHTime : list
+        list of two integers indicating the time in ms since last midnight.
+        MDHTime[0] gives the start of the recording
+        MDHTime[1] gives the end   of the recording
+    sampling_rate : int
+        number of samples per second
+    physio_signal : list of int
+        signal proper. NaN indicate points for which there was no recording
+        (the scanner found a trigger in the signal)
+    """
+
+    # Read the file, splitting by lines and removing the "newline" (and any blank space)
+    #   at the end of the line:
+    lines = [line.rstrip() for line in open(physio_file)]
+
+    # According to Siemens (IDEA documentation), the sampling rate is 2.5ms for all signals:
+    sampling_rate = int(400)    # 1000/2.5
+
+    # For that first line, different information regions are bound by "5002 and "6002".
+    #   Find them:
+    s = re.split('5002(.*?)6002', lines[0])
+    if len(s) == 1:
+        # we failed to find even one "5002 ... 6002" group.
+        raise PMUFormatError(
+                  'File %r does not seem to be a valid XA30 PMU file',
+                  physio_file,
+                  '5002(.*?)6002',
+                  s[0]
+              )
+
+    # The first group contains the triggering method, gate open and close times, etc for
+    #   compatibility with previous versions. Ignore it.
+    # The second group tells us the type of signal ('RESP', 'PULS', etc.)
+    try:
+        physio_type = re.search('LOGVERSION_([A-Z]*)', s[1]).group(1)
+        log_version = re.findall(r'\d+', s[1])[0]
+    except AttributeError:
+        print('Could not find type of recording for ' + physio_file)
+        if not forceRead:
+            raise PMUFormatError(
+                      'File %r does not seem to be a valid XA30 PMU file',
+                      physio_file,
+                      'LOGVERSION_([A-Z]*)',
+                      s[1]
+                  )
+        else:
+            print('Setting recording type to "Unknown"')
+            physio_type = "Unknown"
+            # (continue reading the file)
+
+    if len(s) <= 5:
+        raise PMUFormatError(
+            'There is a very high chance %r is a VE11C file...',
+            physio_file
+        )
+
+    raw_signal = ''
+
+    if log_version == '1':
+        # The third and following groups give us the physio signal itself.
+        for ii in range(2, len(s), 2):
+            raw_signal = raw_signal + s[ii][1:]
+
+        raw_signal = raw_signal.split(' ')
+        physio_signal = parserawPMUsignal(raw_signal)
+
+    elif log_version == '3' and physio_type == 'RESP':
+        # we have five signals interleaved, we only need the first
+        for ii in range(10, len(s), 2):
+            raw_signal = raw_signal + s[ii][1:]
+
+        raw_signal = raw_signal.split(' ')
+        physio_signal = parserawPMUsignal(raw_signal)
+
+        n_channels = 5
+        physio_signal = physio_signal[::n_channels]
+
+    # The rest of the lines have statistics about the signals, plus start and finish times.
+    # Get timing:
+    MPCUTime, MDHTime = getPMUtiming(lines[1:])
+
+    return physio_type, MDHTime, sampling_rate, physio_signal
+
 
 def readVB15Apmu(physio_file, forceRead=False):
     """
@@ -552,9 +652,14 @@ def parserawPMUsignal(signal):
 
     # Values "5000" and "6000" indicate "trigger on" and "trigger off", respectively, so they
     #   are not a real physio_signal value. So replace them with NaN:
-    for idx, v in enumerate(signal):
-        if v == 5000 or v == 6000:
-            signal[idx] = float('NaN')
+    #for idx, v in enumerate(signal):
+    #    if v == 5000 or v == 6000:
+    #        signal[idx] = float('NaN')
+
+    # Values "5000" and "6000" indicate "trigger on" and "trigger off", respectively, so they
+    #   are not a real physio_signal value. Here we exclude them.
+    signal = [x for x in signal if str(x) != '5000']
+    signal = [x for x in signal if str(x) != '6000']
 
     return signal
 
@@ -563,7 +668,7 @@ def testSamplingRate(
         sampling_rate=0,
         Nsamples=0,
         logTimes=[0,0],
-        tolerance=0.1
+        tolerance=0.2
         ):
     """
     Function to test if the sampling rate is correct.
@@ -601,7 +706,7 @@ def testSamplingRate(
 def main():
 
     # Parse command line arguments
-    parser = argparse.ArgumentParser(description='Convert Siemens physiology files to BIDS-compliant physiology recording')
+    parser = argparse.ArgumentParser(description='Convert Siemens physiology files to BIDS-compliant physiology recording.')
     parser.add_argument('-i', '--infiles', nargs='+', required=True, help='.puls or .resp physio file(s)')
     parser.add_argument('-b', '--bidsprefix', required=True, help='Prefix of the BIDS file. It should match the _bold.nii.gz')
     parser.add_argument('-v', '--verbose', action="store_true", default=False, help='verbose screen output')

bidsphysio.pmu2bids/tests/data/pmu_XA30_cardiac.json

@@ -0,0 +1,7 @@
+{
+    "Columns": [
+        "cardiac"
+    ],
+    "SamplingFrequency": 400,
+    "StartTime": 63115152.0
+}