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NeurodataWithoutBorders / matnwb

A Matlab interface for reading and writing NWB files
BSD 2-Clause "Simplified" License
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[Bug]: Broken comments in MultiChannelVolumeSeries.m #548

Closed RR-N closed 9 months ago

RR-N commented 9 months ago

What happened?

Trying to load any .nwb file containing a MultiChannelVolumeSeries results in an error pointing to the line 16 in MultiChannelVolumeSeries.m:

    format; %  (char) Format of image. If this is 'external', then the attribute 'external_file'
                             contains the path information to the image files. If this is 'raw', then the raw
                             (single-channel) binary data is stored in the 'data' dataset. If this attribute
                             is not present, then the default format='raw' case is assumed.     

    starting_frame; %  (int32) Each external image may contain one or more consecutive frames of the full
                             ImageSeries. This attribute serves as an index to indicate which frames each file
                             contains, to faciliate random access. The 'starting_frame' attribute, hence,
                             contains a list of frame numbers within the full ImageSeries of the first frame
                             of each file listed in the parent 'external_file' dataset. Zero-based indexing is
                             used (hence, the first element will always be zero). For example, if the
                             'external_file' dataset has three paths to files and the first file has 5 frames,
                             the second file has 10 frames, and the third file has 20 frames, then this
                             attribute will have values [0, 5, 15]. If there is a single external file that
                             holds all of the frames of the ImageSeries (and so there is a single element in
                             the 'external_file' dataset), then this attribute should have value [0].

Wrapping all new lines in comments fixes the issue:

    format; %  (char) Format of image. If this is 'external', then the attribute 'external_file'
                             % contains the path information to the image files. If this is 'raw', then the raw
                             % (single-channel) binary data is stored in the 'data' dataset. If this attribute
                             % is not present, then the default format='raw' case is assumed.     

    starting_frame; %  (int32) Each external image may contain one or more consecutive frames of the full
                             % ImageSeries. This attribute serves as an index to indicate which frames each file
                             % contains, to faciliate random access. The 'starting_frame' attribute, hence,
                             % contains a list of frame numbers within the full ImageSeries of the first frame
                             % of each file listed in the parent 'external_file' dataset. Zero-based indexing is
                             % used (hence, the first element will always be zero). For example, if the
                             % 'external_file' dataset has three paths to files and the first file has 5 frames,
                             % the second file has 10 frames, and the third file has 20 frames, then this
                             % attribute will have values [0, 5, 15]. If there is a single external file that
                             % holds all of the frames of the ImageSeries (and so there is a single element in
                             % the 'external_file' dataset), then this attribute should have value [0].
>> nwb = nwbRead('E:\scape-data\neuropal20220729_worm1run2.nwb', 'ignorecache')

nwb = 

  NwbFile with properties:

                                             nwb_version: '2.6.0'
                                        file_create_date: [1×1 types.untyped.DataStub]
                                              identifier: '20220729/worm-1/run-2'
                                                           ...

Steps to Reproduce

1. Install NeurodataWithoutBorders/matnwb from MATLAB Add-On Explorer.
2. Open any NWB file containing a MultiChannelVolumeSeries:
   `nwb = nwbRead('E:\scape-data\neuropal20220729_worm1run2.nwb', 'ignorecache')`

Error Message

>> nwb = nwbRead('E:\scape-data\neuropal20220729_worm1run2.nwb', 'ignorecache')
Error using types.ndx_multichannel_volume.MultiChannelVolumeSeries
File: MultiChannelVolumeSeries.m Line: 16 Column: 43
Invalid expression. Check for missing multiplication operator, missing or unbalanced delimiters, or other syntax error. To construct matrices, use brackets instead of parentheses.

Error in io.parseGroup (line 85)
    parsed = eval([Type.typename '(kwargs{:})']);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in nwbRead (line 79)
    nwb = io.parseGroup(filename, h5info(filename), Blacklist);

Operating System

Windows

Matlab Version

-----------------------------------------------------------------------------------------------------
MATLAB Version: 9.13.0.2193358 (R2022b) Update 5
MATLAB License Number: 40702059
Operating System: Microsoft Windows 10 Pro Version 10.0 (Build 19045)
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
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Code of Conduct

RR-N commented 9 months ago

Looks like this is a dynamically generated file pulled from an nwb extension. Closing issue as it doesn't relate to this repo.

rly commented 9 months ago

@RR-N did you use MatNWB to generate MultiChannelVolumeSeries.m? If so, I think this is still an issue that should be solved -- that is, the dynamical extension generation should create long comments correctly.

lawrence-mbf commented 9 months ago

fyi, there are no issues with MultiChannelVolumeSeries generation at the tip of master (for both ndx-multichannel-volume and MatNWB) so it might have been an issue in a previous version.

RR-N commented 9 months ago

Yes, I reached out to Daniel (author of the extension) and they pushed a fix yesterday.

And yes, that .m file was generated with matnwb, so handling long comments (or, more specifically, newlines in comments) is definitely something that ought to be looked at.

On Tue, Oct 3, 2023, 09:46 Lawrence @.***> wrote:

fyi, there are no issues with MultiChannelVolumeSeries generation at the tip of master (for both ndx-multichannel-volume https://urldefense.com/v3/__https://github.com/focolab/ndx-multichannel-volume__;!!IBzWLUs!SSrSUbJF7TcBbf8TDdd0C5GmVBkcUMTE9M1n-3QEPZ6MxZzdtVdNtf-7tCIS7o2F4T3xgfyNHAumxmFkRyd3D40xrvMn$ and MatNWB) so it might have been an issue in a previous version.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/NeurodataWithoutBorders/matnwb/issues/548*issuecomment-1745013247__;Iw!!IBzWLUs!SSrSUbJF7TcBbf8TDdd0C5GmVBkcUMTE9M1n-3QEPZ6MxZzdtVdNtf-7tCIS7o2F4T3xgfyNHAumxmFkRyd3D5S5YS0_$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AF4UHMZNKVBXAXDKDOC3M2LX5QJJZAVCNFSM6AAAAAA5OYJNJ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBVGAYTGMRUG4__;!!IBzWLUs!SSrSUbJF7TcBbf8TDdd0C5GmVBkcUMTE9M1n-3QEPZ6MxZzdtVdNtf-7tCIS7o2F4T3xgfyNHAumxmFkRyd3D0ENb2sQ$ . You are receiving this because you were mentioned.Message ID: @.***>

lawrence-mbf commented 9 months ago

@RR-N Noted and will look into that.