Allow read-only h5 access, define IMTYPE_RGB, explicit error on too-large Waveforms#87
Allow read-only h5 access, define IMTYPE_RGB, explicit error on too-large Waveforms#87kspaceKelvin wants to merge 6 commits into
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kspaceKelvin
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Jan 21, 2026
kspaceKelvin
commented
- Issue Opening and closing MRD file via File interface updates file modified time #78 is resolved by allowing file mode to be specified when opening an HDF5 file
- An enum for IMTYPE_RGB is added as described in https://ismrmrd.readthedocs.io/en/latest/mrd_image_data.html#data-types
- An explicit TypeError is raised if attempting to create a Waveform that exceeds the maximum size
As described in tefra/xsdata#1128
| IMTYPE_REAL = 3 | ||
| IMTYPE_IMAG = 4 | ||
| IMTYPE_COMPLEX = 5 | ||
| IMTYPE_RGB = 6 |
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I don't see where this is defined in the C++ implementation?
What does RGB mean for each of the possible ISMRMRD image types? i.e. How is RGB decoded from a 32-bit complex float? How many bits for each RGB channel if the image is 32-bit vs 16-bit?
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I see this in the docs now (https://ismrmrd.readthedocs.io/en/latest/mrd_image_data.html#image-types).
But I still don't understand. How long has this been documented without actually being implemented in ISMRMRD or ismrmrd-python?
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| class Dataset(object): | ||
| def __init__(self, filename, dataset_name="dataset", create_if_needed=True): | ||
| def __init__(self, filename, dataset_name="dataset", create_if_needed=True, mode=None): |
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We should document the valid arguments for mode: https://docs.h5py.org/en/stable/high/file.html#opening-creating-files
| channels, nsamples = data.shape | ||
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| if nsamples > np.iinfo(np.uint16).max: | ||
| raise TypeError(f"Array has {nsamples} samples, which is greater than the maximum of {np.iinfo(np.uint16).max}") |
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This is a ValueError not a TypeError.
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I'm happy to make the suggested changes and merge this 👍 |
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Pull request overview
This PR updates the Python ISMRMRD helpers to (1) support more explicit control over how HDF5 files are opened, (2) expose the missing IMTYPE_RGB image type constant, and (3) fail fast when constructing Waveforms that exceed header representable sizes.
Changes:
- Add an optional
modeparameter toismrmrd.hdf5.Datasetto control theh5py.File(...)open mode. - Define
IMTYPE_RGB = 6inismrmrd.constants. - Add an explicit error in
Waveform.from_arraywhennumber_of_samplesexceeds theuint16maximum.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
ismrmrd/waveform.py |
Adds a size guard when building Waveforms from numpy arrays. |
ismrmrd/hdf5.py |
Extends Dataset to accept an explicit HDF5 open mode. |
ismrmrd/constants.py |
Adds the missing IMTYPE_RGB constant. |
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| channels, nsamples = data.shape | ||
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| if nsamples > np.iinfo(np.uint16).max: | ||
| raise TypeError(f"Array has {nsamples} samples, which is greater than the maximum of {np.iinfo(np.uint16).max}") | ||
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| if nsamples > np.iinfo(np.uint16).max: | ||
| raise TypeError(f"Array has {nsamples} samples, which is greater than the maximum of {np.iinfo(np.uint16).max}") | ||
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| def __init__(self, filename, dataset_name="dataset", create_if_needed=True, mode=None): | ||
| # Open the file | ||
| if create_if_needed: | ||
| self._file = h5py.File(filename, 'a') | ||
| else: | ||
| self._file = h5py.File(filename, 'r+') | ||
| if mode is None: | ||
| if create_if_needed: | ||
| mode = 'a' | ||
| else: | ||
| mode = 'r+' | ||
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| self._file = h5py.File(filename, mode) |
| def __init__(self, filename, dataset_name="dataset", create_if_needed=True, mode=None): | ||
| # Open the file | ||
| if create_if_needed: | ||
| self._file = h5py.File(filename, 'a') | ||
| else: | ||
| self._file = h5py.File(filename, 'r+') | ||
| if mode is None: | ||
| if create_if_needed: | ||
| mode = 'a' | ||
| else: | ||
| mode = 'r+' | ||
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| self._file = h5py.File(filename, mode) |
