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Read/write nrrd from/to memory #108

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arnegroskurth opened this issue Mar 10, 2020 · 4 comments
Closed

Read/write nrrd from/to memory #108

arnegroskurth opened this issue Mar 10, 2020 · 4 comments

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@arnegroskurth
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The library seems to be missing an interface to simply parse a nrrd-record from another source then an actual file on disk.

Would e.g. an interface based on a provided instance of _IOBase make sense for you?
@addisonElliott
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Hello,

The nrrd.read_header and nrrd.read_data functions accept file handles that I think should work for any IOBase class. Have you tested that yet to see if it fails?

The read_header function accepts any string iterable and just calls next() on it to get another line. The read_data calls close, seek, readline, read, all of which are present in IOBase.

If these functions are not able to accept any generic IOBase class, then I agree they should be generalized to do so if possible.

The nrrd.read() function calls the other two functions after opening the file locally. I'd be okay with adapting nrrd.read() to accept a file handle/stream instead of a filename. One thing to keep in mind is that the filename is used to determine the detached header or data filename, so this functionality will be broken.

@arnegroskurth
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Reading actually works by passing in an instance of io.BytesIO.

But what about writing an nrrd record to memoy?

bernardopericacho added a commit to bernardopericacho/pynrrd that referenced this issue Jun 11, 2022
@bernardopericacho
Allow writing a NRRD record to memory. Ref mhe#108
86c9fbd
addisonElliott pushed a commit that referenced this issue Jun 17, 2022
@bernardopericacho
Allow writing a NRRD record to memory. Ref #108 (#117)
a8667a5 
## Changes

- `write` now supports as a parameter either a filename or a `io.BytesIO` object.
- refactor write method into:
   - `_write_default_header_entries` to write the default header entries generated by this package
   - `_handle_header_fields` to determine the headers based on the specified headers, data and index order
   - `_write_header` that used the logic from `_write_default_header_entries` and `_handle_header_fields` to write the headers
   - `write` used the methods above to encapsulate and reuse better the code
   - added new tests to check the functionality. Coverage still 100% after these changes
@moshecSeetrue
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Hi,
Does anyone know when a new version with this commit should be out?

@addisonElliott
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I can’t give a timeline, but we’re waiting to add some other improvements to the library and then a v1.0.0 release is happening (with breaking changes).

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@addisonElliott @arnegroskurth @moshecSeetrue