add read_cxyz and write_cxyz

[normanrz]

Description:

• Added View.{read,write}_cxyz to normalize any non-default axis orderings

Todos:

Make sure to delete unnecessary points or to check all before merging:

• Updated Changelog
• Updated Documentation
• Added / Updated Tests

[gemini-code-assist]

Code Review

This pull request introduces read_cxyz and write_cxyz methods to the View and MagView classes, enabling data access in a standardized (c, x, y, z) order regardless of the underlying storage layout. Additionally, fastremap is now an optional dependency, and NDBoundingBox has been updated to handle missing spatial axes. The review feedback suggests refactoring to reduce code duplication in the new methods and argument parsing logic, and recommends using polymorphism instead of explicit type checks for better extensibility.

[gemini-code-assist]

This write_cxyz method is almost an exact copy of View.write_cxyz. This code duplication can make future maintenance more difficult, as changes would need to be applied in two places.

Since MagView inherits from View, you could refactor this to call super().write_cxyz. The main challenge is passing the allow_resize parameter, as View.write_cxyz doesn't know about it.

A potential solution is to make View.write_cxyz more extensible by having it accept arbitrary keyword arguments (**kwargs) and pass them to self.write. Because self.write will resolve to MagView.write when called on a MagView instance, the allow_resize argument would be correctly handled.

This would allow you to simplify MagView.write_cxyz to something like this:

def write_cxyz(self, ..., allow_resize: bool = False, ...) -> None:
    super().write_cxyz(
        ...,
        allow_resize=allow_resize,
    )

This approach would remove the code duplication and improve maintainability.

[gemini-code-assist]

Using type(self) is View is generally considered an anti-pattern as it breaks the principles of polymorphism and can make the code brittle. If a new subclass of View is introduced in the future, this check would need to be updated.

A better approach would be to define a class attribute in View that can be overridden by subclasses. For example:

In View:

class View:
    _default_offset_param_name = "relative_offset"
    # ...

In MagView:

class MagView(View):
    _default_offset_param_name = "absolute_offset"
    # ...

Then you can replace the if/else block with:

offset_param = self._default_offset_param_name

This makes the code more robust and easier to extend.

[gemini-code-assist]

The argument parsing logic at the beginning of this method (lines 836-893) is identical to the logic in the read() method. This duplication can lead to maintenance issues, where a bug fix or change in one place might be missed in the other.

To improve this, you could extract the common argument parsing logic into a private helper method, for example _resolve_read_bbox(...). Both read() and read_cxyz() could then call this helper to get the mag1_bbox, keeping the code DRY.

Example:

def _resolve_read_bbox(self, size, relative_offset, absolute_offset, relative_bounding_box, absolute_bounding_box) -> NormalizedBoundingBox:
    # ... duplicated argument parsing logic ...
    mag1_bbox = self._get_mag1_bbox(...)
    # ... assertions on mag1_bbox ...
    return mag1_bbox

def read(self, ...):
    mag1_bbox = self._resolve_read_bbox(...)
    return self._read_without_checks(mag1_bbox.in_mag(self._mag))

def read_cxyz(self, ...):
    mag1_bbox = self._resolve_read_bbox(...)
    data = self._read_without_checks(mag1_bbox.in_mag(self._mag))
    # ... reordering logic ...
    return data

This would make the code more maintainable.

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
11510	9724	84%	80%	🟢

New Files

No new covered files...

Modified Files

File	Coverage	Status
webknossos/webknossos/cli/export_as_tiff.py	50%	🟢
webknossos/webknossos/client/_download_dataset.py	94%	🟢
webknossos/webknossos/dataset/_utils/pims_czi_reader.py	83%	🟢
webknossos/webknossos/dataset/layer/_downsampling_utils.py	74%	🟢
webknossos/webknossos/dataset/layer/_upsampling_utils.py	93%	🟢
webknossos/webknossos/dataset/layer/view/mag_view.py	90%	🟢
webknossos/webknossos/dataset/layer/view/view.py	84%	🟢
webknossos/webknossos/geometry/nd_bounding_box.py	89%	🟢
TOTAL	82%	🟢

updated for commit: 3dba419 by action🐍