Get Open Ephys info from xml file

dataman/lib/dirstats.py

@@ -13,12 +13,31 @@ EXT_SOUND = ['.wav', '.mp3', '.snd', '.wma']
 EXT_IMAGE = ['.png', '.bmp', '.jpg', '.jpeg', '.pgm']
 EXT_DOC = ['.md', '.toml', '.xml', '.tsv', '.csv', '.txt', '.doc', '.rst']
 
+DEFAULT_COLS = ['fname', 'size', 'num_files', 'num_vid', 'num_img', 'num_snd', 'num_doc', 'data_fmt']
+COLUMNS = {'fname': ['F']}
+
+class Column:
+    def __init__(self, name, width=3, fmt=':', align='^', *args, **kwargs):
+        self.name = name
+        self.w = width
+        self.align = align
+        self.fmt = '{'+fmt+align+str(width)+'}'
+
+    def header(self):
+        if self.name in COLUMNS:
+            return self.fmt.format(COLUMNS[self.name])
+        else:
+            return self.fmt.format('Unknown')
+
+    def row(self, data):
+        return self.fmt.format(data)
+
 table_hdr = "{:^28}{sep}{:^6}{sep}{:>3}{sep}{:>3}{sep}{:>3}{sep}{:>3}{sep}{:>3}{sep}{:^10}{sep}".format(
 "Folder name", "size", "#fil", "#vid", "#img", "#snd", '#doc', "format", sep=" ")
 
 _row = "{0:<28}{1}{2:>4}{3:>4}{4:>4}{5:>4}{6:>10}"
 
-def contains_dataset(root, dirs=None, files=None):
+def contains_data(root, dirs=None, files=None):
     """Check if directory or list of files contains a dataset of known format (OE, Kwik, etc.)"""
     if None in [dirs, files]:
         _, dirs, files = dir_content(root)
@@ -41,12 +60,17 @@ def dir_details(path):
     num_img= len([f for f in files if fext(f) in EXT_IMAGE])
     num_snd = len([f for f in files if fext(f) in EXT_SOUND])
     num_doc = len([f for f in files if fext(f) in EXT_DOC])
-    data_fmt = contains_dataset(path)
+    data_fmt = contains_data(path)
 
     return dict(fname=name, size=size, num_files=num_files, num_vid=num_vid,
             num_img=num_img, num_snd=num_snd, num_doc=num_doc,
             data_fmt=data_fmt)
 
+def data_stats(path):
+    fmt = contains_data(path)
+    assert(fmt)
+
+
 def gather(path):
     """Gather details on the path and its subdirectories.
 
@@ -82,9 +106,7 @@ def fit_str(string, max_len=10, weight=0.7):
     tail = int((max_len-len(indicator))*weight)
     return string[:head]+indicator+string[-tail:]
 
-def mk_row(row, colorized=True, cols=['fname', 'size', 'num_files',
-                                         'num_vid', 'num_img', 'num_snd', 'num_doc',
-                                         'data_fmt'], sepr='|'):
+def mk_row(row, colorized=True, cols=DEFAULT_COLS, sepr='|'):
     row_str = ''
     for c in cols:
         if c == 'fname':

dataman/lib/open_ephys.py

@@ -3,9 +3,10 @@
 
 from __future__ import print_function
 import os
-import xml.etree.ElementTree as etree
+import xml.etree.ElementTree as ET
 from .tools import fext, dir_content
 
+
 def detect(root=None, dirs=None, files=None):
     """Checks for existence of an open ephys formatted data set in the root directory.
 
@@ -19,24 +20,72 @@ def detect(root=None, dirs=None, files=None):
     """
     # TODO: Make all three optional and work with either
     if dirs is None or files is None:
-       _, dirs, files = dir_content(root)
+        _, dirs, files = dir_content(root)
 
     for f in files:
         if fext(f) in ['.continuous']:
-            fv = format_version(root, dirs, files)
+            settings_xml = _find_settings_xml(root)
+            if settings_xml is None:
+                fv = None
+            else:
+                fv = format_version(settings_xml)
+                # print(_fpga_node(settings_xml))
             return "OE_v{}".format(fv if fv else '???')
     else:
         return False
 
-def format_version(root, dirs=None, files=None):
+def _fpga_node(path):
+    chain = _config(path)['SIGNALCHAIN']
+    nodes = [p['attrib']['NodeId'] for p in chain if p['type']=='PROCESSOR' and 'FPGA' in p['attrib']['name']]
+    if len(nodes) == 1:
+        return nodes[0]
+    else:
+        raise BaseException('Node ID not found in xml file {}'.format(path))
+
+
+def format_version(path):
+        settings = _config(path)
+        return settings['INFO']['VERSION']
+
+
+def _find_settings_xml(base, dirs=None, files=None):
     if dirs is None or files is None:
-        _, dirs, files = dir_content(root)
+        _, dirs, files = dir_content(base)
     if "settings.xml" in files:
-        root = etree.parse(os.path.join(root, 'settings.xml'))
-        version = root.findall("INFO/VERSION")
-        if not len(version):
-            return None
-        else:
-            return version[0].text
+        return os.path.join(base, 'settings.xml')
     else:
         return None
+
+
+def _config(path):
+    """Reads Open Ephys XML settings file and returns dictionary with relevant information.
+        - Info field
+            Dict(GUI version, date, OS, machine),
+        - Signal chain
+            List(Processor or Switch dict(name, nodeID). Signal chain is returned in ORDER OF OCCURRENCE
+            in the xml file, this represents the order in the signal chain. The nodeID does NOT reflect this order, but
+            but the order of assembling the chain.
+        - Audio
+            Int bufferSize
+
+    Args:
+        path: Path to settings.xml file
+
+    Returns:
+        Dict{INFO, SIGNALCHAIN, AUDIO}
+    """
+    root = ET.parse(path).getroot()
+    info = dict(
+        VERSION = root.find('INFO/VERSION').text,
+        DATE = root.find('INFO/DATE').text,
+        OS = root.find('INFO/OS').text,
+        MACHINE = root.find('INFO/VERSION').text
+    )
+
+    sc = root.find('SIGNALCHAIN')
+    chain = [dict(type=e.tag, attrib=e.attrib) for e in sc.getchildren()]
+
+    audio = root.find('AUDIO').attrib
+    return dict(INFO=info,
+                SIGNALCHAIN=chain,
+                AUDIO=audio)

docs/TODO.md

+[ ] dm ls should return number of datasets on subfolders
+