'ROI' object has no attribute 'reference_images'

[neuromusic]

Steps to Reproduce

import numpy as np

NA = 'THIS REQUIRED ATTRIBUTE INTENTIONALLY LEFT BLANK.'

from pynwb import image, ophys
max_proj = image.ImageSeries(
    name = 'Maximum Projection Image',
    source = NA,
    data = np.random.rand(10,10),
    unit = NA,
    format = 'raw',
    timestamps = [0.0], 
)

roi = ophys.ROI(
    name = NA,
    source = NA,
    roi_description = NA,
    pix_mask = [],
    pix_mask_weight = [],
    img_mask = np.random.rand(10,10),
    reference_images = max_proj, 
)

print roi.reference_images

Environment

Please describe your environment according to the following bullet points.

• Python Executable: Conda
• Python Version: Python 2.7
• Operating System: CentOS
• Pynwb Version: 0.2.0

Checklist

• [x] Have you ensured the feature or change was not already reported ?
• [x] Have you included a brief and descriptive title?
• [x] Have you included a clear description of the problem you are trying to solve?
• [x] Have you included a minimal code snippet that reproduces the issue you are encountering?

[neuromusic]

looking more closely at the ROI object... https://github.com/NeurodataWithoutBorders/pynwb/blob/936c4383415d335ef2f901f040c02e843ca8c2a8/src/pynwb/ophys.py#L165

• docval requires reference_images
• but it doesn't get added as an attribute of the ROI instance
• and it isn't specified in __nwbfields__ which seems important (cc @nicain)

so the immediate fix here seems pretty clear, however...

• Note that I can write an NWB file with this malformed object without a problem. However, it breaks when I try to read it. Perhaps we need to add read tests to the integration tests? @nicain?
• reference_images is specified as a required attribute of an ROI in the nwb-schema yaml files... why does pynwb need to respecify the req in three places (docval, adding attributes in __init__, and __nwbfields__)? Should all of this be inspected from nwb-schema to prevent these kinds of bugs?

[neuromusic]

so #308 fixes this for creating the object, but I can't read it back out after writing to file.

---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
<ipython-input-5-b4cc30c9675b> in <module>()
      2 
      3 io = HDF5IO('{}.nwb'.format(lims_id),mode='r')
----> 4 nwb = io.read()
      5 io.close()

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/backends/io.pyc in read(self, **kwargs)
     30     def read(self, **kwargs):
     31         f_builder = self.read_builder()
---> 32         container = self.__manager.construct(f_builder)
     33         return container
     34 

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
     66         result = self.__containers.get(builder_id)
     67         if result is None:
---> 68             result = self.__type_map.construct(builder, self)
     69             self.prebuilt(result, builder)
     70         return result

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
   1012                              % str(container.__class__.__name__))  # noqa: F821
   1013         else:
-> 1014             return attr_map.construct(builder, build_manager)
   1015 
   1016     @docval({"name": "container", "type": Container, "doc": "the container to convert to a Builder"},

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
    615         cls = manager.get_cls(builder)
    616         # gather all subspecs
--> 617         subspecs = self.__get_subspec_values(builder, self.spec, manager)
    618         # get the constructor argument each specification corresponds to
    619         const_args = dict()

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in __get_subspec_values(self, builder, spec, manager)
    601                             ret[subspec] = val
    602                     else:
--> 603                         result = self.__get_subspec_values(sub_builder, subspec, manager)
    604                         ret.update(result)
    605         else:

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in __get_subspec_values(self, builder, spec, manager)
    592                     if self.__data_type_key in sub_builder.attributes or \
    593                        not (subspec.data_type_inc is None and subspec.data_type_def is None):
--> 594                         val = manager.construct(sub_builder)
    595                         if subspec.is_many():
    596                             if subspec in ret:

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
     66         result = self.__containers.get(builder_id)
     67         if result is None:
---> 68             result = self.__type_map.construct(builder, self)
     69             self.prebuilt(result, builder)
     70         return result

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
   1012                              % str(container.__class__.__name__))  # noqa: F821
   1013         else:
-> 1014             return attr_map.construct(builder, build_manager)
   1015 
   1016     @docval({"name": "container", "type": Container, "doc": "the container to convert to a Builder"},

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
    615         cls = manager.get_cls(builder)
    616         # gather all subspecs
--> 617         subspecs = self.__get_subspec_values(builder, self.spec, manager)
    618         # get the constructor argument each specification corresponds to
    619         const_args = dict()

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in __get_subspec_values(self, builder, spec, manager)
    592                     if self.__data_type_key in sub_builder.attributes or \
    593                        not (subspec.data_type_inc is None and subspec.data_type_def is None):
--> 594                         val = manager.construct(sub_builder)
    595                         if subspec.is_many():
    596                             if subspec in ret:

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
     66         result = self.__containers.get(builder_id)
     67         if result is None:
---> 68             result = self.__type_map.construct(builder, self)
     69             self.prebuilt(result, builder)
     70         return result

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
   1012                              % str(container.__class__.__name__))  # noqa: F821
   1013         else:
-> 1014             return attr_map.construct(builder, build_manager)
   1015 
   1016     @docval({"name": "container", "type": Container, "doc": "the container to convert to a Builder"},

/local1/Code/pynwb/src/pynwb/form/utils.pyc in func_call(*args, **kwargs)
    304                     msg = ', '.join(parse_err)
    305                     raise_from(TypeError(msg), None)
--> 306                 return func(self, **parsed['args'])
    307         else:
    308             def func_call(*args, **kwargs):

/local1/Code/pynwb/src/pynwb/form/build/map.pyc in construct(self, **kwargs)
    643             details = '%s: %s (%s)' % (ex, cls.__name__, builder.name)
    644             msg = 'Could not construct %s object\n    %s' % (cls.__name__, details)
--> 645             raise_from(Exception(msg), ex)
    646         return obj
    647 

/local1/miniconda2/envs/ophys_nwb/lib/python2.7/site-packages/six.pyc in raise_from(value, from_value)
    716 else:
    717     def raise_from(value, from_value):
--> 718         raise value
    719 
    720 

Exception: Could not construct ROI object
    missing argument 'reference_images': ROI (ROI_0067)

[ajtritt]

@neuromusic can you provide a gist of the code you used to write the file that causes this exception?