[Bug]: IndexSeries: Linked Images has no parent.

[zhiwen10]

What happened?

I'm adding image indexSeries to existing NWB files, like example here.

However, I'm getting an error message below:
OrphanContainerBuildError: stimuli (stimuli): Linked Images 'images_name' has no parent. Remove the link or ensure the linked container is added properly.

Mostly likely a bug in my own code, since I'm new to this. Any ideas?

Steps to Reproduce

# open the NWB file in r+ mode and add manip trigger to acquisition and stim1, stim2 to stimulus
from PIL import Image
import matplotlib.pyplot as plt

img0 = Image.open(r"E:\DANDI\image_series\natural_scene_0.tiff") 
img1 = Image.open(r"E:\DANDI\image_series\natural_scene_1.tiff") 
image0 = GrayscaleImage(name='natural_scene_0', data= np.array(img0));
image1 = GrayscaleImage(name='natural_scene_1', data= np.array(img1));
img_sequence = [image0,image1]

# plt.imshow(img1,cmap = 'gray')
images = Images(
    name="images_name", 
    images = img_sequence,
    description="images description",
    order_of_images = ImageReferences("order_of_images", img_sequence),
)

idx_series = IndexSeries(name="stimuli",data=[0, 1, 0, 1],indexed_images=images,unit="N/A",timestamps=[0.1, 0.2, 0.3, 0.4])

with NWBHDF5IO(filename, "r+") as io:
    read_nwbfile = io.read()
    read_nwbfile.add_stimulus(idx_series)

    # write the modified NWB file
    io.write(read_nwbfile)

### Traceback

```python
---------------------------------------------------------------------------
OrphanContainerBuildError                 Traceback (most recent call last)
Cell In[53], line 9
      7 read_nwbfile.add_stimulus(idx_series)
      8 # write the modified NWB file
----> 9 io.write(read_nwbfile)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\backends\hdf5\h5tools.py:377, in HDF5IO.write(self, **kwargs)
    372     raise UnsupportedOperation(("Cannot write to file %s in mode '%s'. "
    373                                 "Please use mode 'r+', 'w', 'w-', 'x', or 'a'")
    374                                % (self.source, self.__mode))
    376 cache_spec = popargs('cache_spec', kwargs)
--> 377 super().write(**kwargs)
    378 if cache_spec:
    379     self.__cache_spec()

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\backends\io.py:98, in HDMFIO.write(self, **kwargs)
     95     herd.to_zip(path=self.herd_path)
     97 """Write a container to the IO source."""
---> 98 f_builder = self.__manager.build(container, source=self.__source, root=True)
     99 self.write_builder(f_builder, **kwargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py:180, in BuildManager.build(self, **kwargs)
    175 elif not self.__is_active_builder(result) and container.modified:
    176     # if builder was built on file read and is then modified (append mode), it needs to be rebuilt
    177     self.logger.debug("Rebuilding modified %s '%s' (source: %s, extended spec: %s)"
    178                       % (container.__class__.__name__, container.name,
    179                          repr(source), spec_ext is not None))
--> 180     result = self.__type_map.build(container, self, builder=result, source=source, spec_ext=spec_ext,
    181                                    export=export)
    182     self.logger.debug("Done rebuilding %s '%s'" % (container.__class__.__name__, container.name))
    183 else:

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py:770, in TypeMap.build(self, **kwargs)
    768 if manager is None:
    769     manager = BuildManager(self)
--> 770 builder = obj_mapper.build(container, manager, builder=builder, source=source, spec_ext=spec_ext, export=export)
    772 # add additional attributes (namespace, data_type, object_id) to builder
    773 namespace, data_type = self.get_container_ns_dt(container)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:717, in ObjectMapper.build(self, **kwargs)
    715         builder = GroupBuilder(name, parent=parent, source=source)
    716     self.__add_datasets(builder, self.__spec.datasets, container, manager, source, export)
--> 717     self.__add_groups(builder, self.__spec.groups, container, manager, source, export)
    718     self.__add_links(builder, self.__spec.links, container, manager, source, export)
    719 else:

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:1037, in ObjectMapper.__add_groups(self, builder, groups, container, build_manager, source, export)
   1035 self.__add_datasets(sub_builder, spec.datasets, container, build_manager, source, export)
   1036 self.__add_links(sub_builder, spec.links, container, build_manager, source, export)
-> 1037 self.__add_groups(sub_builder, spec.groups, container, build_manager, source, export)
   1038 empty = sub_builder.is_empty()
   1039 if not empty or (empty and spec.required):

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:1037, in ObjectMapper.__add_groups(self, builder, groups, container, build_manager, source, export)
   1035 self.__add_datasets(sub_builder, spec.datasets, container, build_manager, source, export)
   1036 self.__add_links(sub_builder, spec.links, container, build_manager, source, export)
-> 1037 self.__add_groups(sub_builder, spec.groups, container, build_manager, source, export)
   1038 empty = sub_builder.is_empty()
   1039 if not empty or (empty and spec.required):

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:1050, in ObjectMapper.__add_groups(self, builder, groups, container, build_manager, source, export)
   1048 self.__check_quantity(attr_value, spec, container)
   1049 if attr_value is not None:
-> 1050     self.__add_containers(builder, spec, attr_value, build_manager, source, container, export)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:1108, in ObjectMapper.__add_containers(self, builder, spec, value, build_manager, source, parent_container, export)
   1106 elif isinstance(value, list):
   1107     for container in value:
-> 1108         self.__add_containers(builder, spec, container, build_manager, source, parent_container, export)
   1109 else:  # pragma: no cover
   1110     msg = ("Received %s, expected AbstractContainer or a list of AbstractContainers."
   1111            % value.__class__.__name__)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:1070, in ObjectMapper.__add_containers(self, builder, spec, value, build_manager, source, parent_container, export)
   1068 self.logger.debug("    Building newly instantiated %s '%s'" % (value.__class__.__name__, value.name))
   1069 if isinstance(spec, BaseStorageSpec):
-> 1070     new_builder = build_manager.build(value, source=source, spec_ext=spec, export=export)
   1071 else:
   1072     new_builder = build_manager.build(value, source=source, export=export)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py:171, in BuildManager.build(self, **kwargs)
    167             raise ValueError("Cannot change container_source once set: '%s' %s.%s"
    168                              % (container.name, container.__class__.__module__,
    169                                 container.__class__.__name__))
    170 # NOTE: if exporting, then existing cached builder will be ignored and overridden with new build result
--> 171 result = self.__type_map.build(container, self, source=source, spec_ext=spec_ext, export=export)
    172 self.prebuilt(container, result)
    173 self.__active_prebuilt(result)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\manager.py:770, in TypeMap.build(self, **kwargs)
    768 if manager is None:
    769     manager = BuildManager(self)
--> 770 builder = obj_mapper.build(container, manager, builder=builder, source=source, spec_ext=spec_ext, export=export)
    772 # add additional attributes (namespace, data_type, object_id) to builder
    773 namespace, data_type = self.get_container_ns_dt(container)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\utils.py:668, in docval.<locals>.dec.<locals>.func_call(*args, **kwargs)
    666 def func_call(*args, **kwargs):
    667     pargs = _check_args(args, kwargs)
--> 668     return func(args[0], **pargs)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:718, in ObjectMapper.build(self, **kwargs)
    716     self.__add_datasets(builder, self.__spec.datasets, container, manager, source, export)
    717     self.__add_groups(builder, self.__spec.groups, container, manager, source, export)
--> 718     self.__add_links(builder, self.__spec.links, container, manager, source, export)
    719 else:
    720     if builder is None:

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:973, in ObjectMapper.__add_links(self, builder, links, container, build_manager, source, export)
    971     self.logger.debug("        Skipping link - no attribute value")
    972     continue
--> 973 self.__add_containers(builder, spec, attr_value, build_manager, source, container, export)

File E:\anaconda3\envs\pynwb\lib\site-packages\hdmf\build\objectmapper.py:1063, in ObjectMapper.__add_containers(self, builder, spec, value, build_manager, source, parent_container, export)
   1058 if value.parent is None:
   1059     if (value.container_source == parent_container.container_source or
   1060             build_manager.get_builder(value) is None):
   1061         # value was removed (or parent not set) and there is a link to it in same file
   1062         # or value was read from an external link
-> 1063         raise OrphanContainerBuildError(builder, value)
   1065 if value.modified or export:
   1066     # writing a newly instantiated container (modified is False only after read) or as if it is newly
   1067     # instantianted (export=True)
   1068     self.logger.debug("    Building newly instantiated %s '%s'" % (value.__class__.__name__, value.name))

OrphanContainerBuildError: stimuli (stimuli): Linked Images 'images_name' has no parent. Remove the link or ensure the linked container is added properly.

Operating System

Windows

Python Executable

Conda

Python Version

3.8

Package Versions

No response

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?

[oruebel]

At first glance, I think the images needs to be added to the NWB file as well. Can you try adding read_nwbfile.add_acquisition(images) to see if that fixes the issue? I.e., I think the code should look as follows:

with NWBHDF5IO(filename, "r+") as io:
    read_nwbfile = io.read()
    read_nwbfile.add_acquisition(images)
    read_nwbfile.add_stimulus(idx_series)

    # write the modified NWB file
    io.write(read_nwbfile)

[zhiwen10]

That worked!
For structural clarity, i did read_nwbfile.add_stimulus_template(images) instead, which also worked well.
Many thanks!

[oruebel]

Glad that worked! I'm closing this issue for now.