Support for ROIs with different size or resolution

src/silverlabnwb/header.py

@@ -9,6 +9,12 @@
 class LabViewVersions(Enum):
     pre2018 = "pre-2018 (original)"
     v231 = "2.3.1"
+    v300 = "3.0.0"
+
+    @property
+    def is_legacy(self):
+        """Return whether this version should trigger legacy behaviour."""
+        return self is self.pre2018
 
 
 class LabViewHeader(metaclass=abc.ABCMeta):
@@ -63,6 +69,8 @@ def from_file(cls, filename):
         else:
             if version == '2.3.1':
                 return LabViewHeader231(fields, parsed_fields)
+            elif version == '3.0.0':
+                return LabViewHeader300(fields, parsed_fields)
             else:
                 raise ValueError('Unsupported LabView version {}.'.format(version))
 
@@ -140,6 +148,11 @@ def get_raw_fields(self):
         """
         return self._raw_fields
 
+    @property
+    def allows_variable_rois(self):
+        """Check whether ROIs with variable shape or resolution are allowed."""
+        return False  # by default (in older versions), they are not
+
 
 class LabViewHeaderPre2018(LabViewHeader):
 
@@ -170,7 +183,7 @@ def _imaging_section(self):
         return self["GLOBAL PARAMETERS"]
 
 
-class LabViewHeader231(LabViewHeader):
+class LabViewHeaderPost2018(LabViewHeader):
 
     property_names = {
         "frame_size": "Frame Size",
@@ -182,18 +195,14 @@ class LabViewHeader231(LabViewHeader):
         "gain_green": "pmt 2",
     }
 
-    # In this version of LabView, the trial times are stored in their own
+    # In these versions of LabView, the trial times are stored in their own
     # (misleadingly titled) section of the header.
     trial_times_section = 'Intertrial FIFO Times'
 
     def __init__(self, fields, processed_fields):
         super().__init__(fields, processed_fields)
         self._parse_trial_times()
 
-    @property
-    def version(self):
-        return LabViewVersions.v231
-
     def _determine_imaging_mode(self):
         volume_imaging = self['IMAGING MODES']['Volume Imaging']
         functional_imaging = self['IMAGING MODES']['Functional Imaging']
@@ -216,8 +225,8 @@ def _determine_imaging_mode(self):
                              ' or "Functional Imaging" must be true.')
 
     def _imaging_section(self):
-        # In LabView version 2.3.1, imaging parameters are stored under the
-        # relevant imaging mode section.
+        # In LabView version 2.3.1 and newer, imaging parameters are stored
+        # under the relevant imaging mode section.
         imaging_section_name = ("VOLUME IMAGING"
                                 if self.imaging_mode is Modes.volume
                                 else "FUNCTIONAL IMAGING")
@@ -253,3 +262,20 @@ def determine_trial_times(self):
                 end = None  # determine final 'end' later from speed data
             trial_times.append((start, end))
         return trial_times
+
+
+class LabViewHeader231(LabViewHeaderPost2018):
+    @property
+    def version(self):
+        return LabViewVersions.v231
+
+
+class LabViewHeader300(LabViewHeaderPost2018):
+    @property
+    def version(self):
+        return LabViewVersions.v300
+
+    @property
+    def allows_variable_rois(self):
+        return (self._imaging_section()['Variable Length'] == 'TRUE'
+                or self._imaging_section()['Variable Resolution'] == 'TRUE')

src/silverlabnwb/metadata.py

@@ -3,7 +3,7 @@
 Handles loading the metadata YAML files.
 '''
 
-import collections
+import collections.abc
 import os
 
 import appdirs
@@ -71,7 +71,7 @@ def beautify_comment(comment_token):
 def read_comments(settings):
     comments = {}
     for k, v in settings.items():
-        if isinstance(v, collections.Mapping):
+        if isinstance(v, collections.abc.Mapping):
             comments[k] = read_comments(v)
         elif isinstance(v, list):
             comments[k] = [read_comments(entry) for entry in v]
@@ -121,7 +121,7 @@ def recursive_dict_update(base_settings, new_settings):
     recursive base_settings.update(new_settings).
     """
     for k, v in new_settings.items():
-        if isinstance(v, collections.Mapping):
+        if isinstance(v, collections.abc.Mapping):
             base_settings[k] = recursive_dict_update(base_settings.get(k, {}), v)
         else:
             base_settings[k] = new_settings[k]
@@ -138,7 +138,7 @@ def strip_strings(settings):
     for k, v in settings.items():
         if isinstance(v, str):
             result[k] = v.strip()
-        elif isinstance(v, collections.Mapping):
+        elif isinstance(v, collections.abc.Mapping):
             result[k] = strip_strings(v)
         else:
             result[k] = v

src/silverlabnwb/metadata.yaml

@@ -17,6 +17,8 @@ people:
   Harsha:
     name: Harsha Gurnani
     orcid: 0000-0001-6383-3104
+  Sameer:
+    name: Sameer Punde
 
 
 experiments:
@@ -114,4 +116,7 @@ sessions:
   Harsha:   # Should match a user id in the 'people' section
     description: One or two sentences describing the experiment and data in the file.
     experiment: template  # Should match an experiment defined above
+  Sameer:   # Should match a user id in the 'people' section
+    description: One or two sentences describing the experiment and data in the file.
+    experiment: template  # Should match an experiment defined above