ENH: Adds support for EXT signal for CMRR physio data

Addresses #5 Versions 4.3.3 (full pkg) and 1.4.3 (sub-pkgs)
cbinyu · Nov 30, 2020 · 4ff8ad4 · 4ff8ad4
1 parent 5565f3f
commit 4ff8ad4
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Showing 9 changed files with 24 additions and 23 deletions.
diff --git a/bidsphysio.acq2bids/bidsphysio/acq2bids/info.py b/bidsphysio.acq2bids/bidsphysio/acq2bids/info.py
@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

diff --git a/bidsphysio.base/bidsphysio/base/info.py b/bidsphysio.base/bidsphysio/base/info.py
@@ -1,4 +1,4 @@
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 __author__ = "Pablo Velasco, Chrysa Papadaniil"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

diff --git a/bidsphysio.dcm2bids/bidsphysio/dcm2bids/dcm2bidsphysio.py b/bidsphysio.dcm2bids/bidsphysio/dcm2bids/dcm2bidsphysio.py
@@ -209,32 +209,33 @@ def parse_log(physio_log, verbose=False):
         # Divide the line at whitespace
         parts = line.split()
 
-        # Data lines have the form "<tag> = <value>" or "<time> <name> <signal>"
-        if len(parts) == 3:
+        # Data lines have the form "<tag> = <value>" or "<time> <name/channel> <value>"
+        # Data lines with trigger have a forth column with "PULS_TRIGGER", which we can ignore
+        if len(parts) >= 3:
 
-            p1, p2, p3 = parts
+            p1, p2, p3 = parts[:3]
 
-            if 'UUID' in p1:
+            if 'PULS' in p2 or 'RESP' in p2 or 'EXT' in p2:
+                # The times are in multiples of 2.5 ms
+                t_list.append(2.5 * int(p1))
+                # in principle, these will also be int, but let's make them
+                #  float to support more general signals:
+                s_list.append(float(p3))
+
+            elif 'UUID' in p1:
                 uuid = p3
 
-            if 'ScanDate' in p1:
+            elif 'ScanDate' in p1:
                 scan_date = p3
 
-            if 'LogDataType' in p1:
+            elif 'LogDataType' in p1:
                 waveform_name = p3
 
-            if 'SampleTime' in p1:
+            elif 'SampleTime' in p1:
                 # 'SampleTime' is in units of 2.5 ms
                 # 'dt' is in ms:
                 dt = 2.5 * float(p3)
 
-            if 'PULS' in p2 or 'RESP' in p2:
-                # The times are in multiples of 2.5 ms
-                t_list.append(2.5 * int(p1))
-                # in principle, these will also be int, but let's make them
-                #  float to support more general signals:
-                s_list.append(float(p3))
-
         # Detect the scanner trigger by going through the ACQUISITION_INFO
         # and detecting when a new volume has been started:
         if waveform_name == 'ACQUISITION_INFO':

diff --git a/bidsphysio.dcm2bids/bidsphysio/dcm2bids/info.py b/bidsphysio.dcm2bids/bidsphysio/dcm2bids/info.py
@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

diff --git a/bidsphysio.dcm2bids/tests/test_dcm2bidsphysio.py b/bidsphysio.dcm2bids/tests/test_dcm2bidsphysio.py
@@ -257,4 +257,4 @@ def test_timing(
     expected_TR = int(re.findall(r'alTR\[0\]\s+=\s+(\d+)', header)[0])/1000000
 
     TRs = get_physio_TRs(outbids)
-    assert  all(TRs) == expected_TR
+    assert all(TRs) == expected_TR
diff --git a/bidsphysio.physio2bids/bidsphysio/physio2bids/info.py b/bidsphysio.physio2bids/bidsphysio/physio2bids/info.py
@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 __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 >= 4.3.2',
+    'bidsphysio >= 4.3.3',
 ]
 
 TESTS_REQUIRES = [

diff --git a/bidsphysio.pmu2bids/bidsphysio/pmu2bids/info.py b/bidsphysio.pmu2bids/bidsphysio/pmu2bids/info.py
@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

diff --git a/bidsphysio.session/bidsphysio/session/info.py b/bidsphysio.session/bidsphysio/session/info.py
@@ -2,7 +2,7 @@
 need to also bump up the version of the dependencies
 """
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 __author__ = "Pablo Velasco, Chrysa Papadaniil"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"

diff --git a/bidsphysio/info.py b/bidsphysio/info.py
@@ -1,7 +1,7 @@
 import os.path as op
 from os import scandir
 
-__version__ = "4.3.2"
+__version__ = "4.3.3"
 __author__ = "Pablo Velasco"
 __author_email__ = "pablo.velasco@nyu.edu"
 __url__ = "https://github.com/cbinyu/bidsphysio"