Crop to physical space #6
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Before review, can you explain the failing tests? |
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Those failed tests are from the second-to-last commit I think. There I made a mistake in the zyx/xyz order convention, which I fixed later. The PR has all tests passing. |
src/picai_prep/preprocessing.py
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| """ | ||
| # input conversion and verification | ||
| if physical_size is not None: | ||
| # convert physical size to voxel size (only supported for SimpleITK) | ||
| assert isinstance(image, sitk.Image), "Crop/padding by physical size is only supported for SimpleITK images." |
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assert should not be used in production code. use if/raise instead.
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I agree, made a new commit to tackle this. Also, added a new function crop where a maximum size can be specified. I need this functionality and think others may benefit from it as well, do you think this is the right place to store this function? (as it is not used inside the picai_prep module itself, but does pertain to preprocessing).
- Shared verification of crop/pad plan - Raise error instead of assert - Separate crop function that won't pad (i.e., size is a max size)
src/picai_prep/preprocessing.py
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| @@ -305,15 +317,33 @@ def resample_spacing(self, spacing: Optional[Iterable[float]] = None): | |||
| if self.lbl is not None: | |||
| self.lbl = resample_img(self.lbl, out_spacing=spacing, is_label=True) | |||
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| def centre_crop_or_pad(self): | |||
| """Centre crop adn/or pad scans and label""" | |||
src/picai_prep/preprocessing.py
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| # perform centre crop and/or pad | ||
| self.centre_crop_or_pad() | ||
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| if self.settings.max_matrix_size is not None or self.settings.max_physical_size is not None: |
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while I know in the post_init neither matrix or max_matrix can be both set, I still think its safer to change this to elif
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Thanks for checking out the changes! I agree fully, implementing the |
src/picai_prep/preprocessing.py
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| if reference_scan_preprocessed is not None: | ||
| image.CopyInformation(reference_scan_preprocessed) | ||
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| if interpolator is None: | ||
| # determine interpolation method based on image dtype | ||
| if "integer" in image.GetPixelIDTypeAsString(): |
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add
pixel_id_type = image.GetPixelIDTypeAsString()
Allow crop/pad of scans based on physical size