Allow read-only HDF5 access

ismrmrd/constants.py

@@ -68,6 +68,7 @@
 IMTYPE_REAL      = 3
 IMTYPE_IMAG      = 4
 IMTYPE_COMPLEX   = 5
+IMTYPE_RGB       = 6
 
 # Image flags
 IMAGE_IS_NAVIGATION_DATA  =  1

ismrmrd/file.py

@@ -375,7 +375,21 @@ def has_acquisitions(self):
 class File(Folder):
 
     def __init__(self, filename, mode='a'):
-        self.__file = h5py.File(filename, mode,driver='stdio')
+        """Open an ISMRMRD File.
+
+        Parameters
+        ----------
+        filename : str
+            Path to the HDF5 file.
+        mode : str, optional
+            h5py file-open mode.  Defaults to ``'a'`` (read/write, create if
+            needed).  Pass ``'r'`` for read-only access without touching the
+            file's modification time.  Valid values are the same as for
+            :func:`h5py.File`: ``'r'``, ``'r+'``, ``'w'``, ``'w-'``/``'x'``,
+            and ``'a'``.  See
+            https://docs.h5py.org/en/stable/high/file.html for details.
+        """
+        self.__file = h5py.File(filename, mode, driver='stdio')
         super().__init__(self.__file)
 
     def __enter__(self):

ismrmrd/hdf5.py

@@ -144,12 +144,34 @@ def fileinfo(fname):
 
 
 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):
+        """Open an ISMRMRD Dataset backed by an HDF5 file.
+
+        Parameters
+        ----------
+        filename : str
+            Path to the HDF5 file.
+        dataset_name : str, optional
+            Name of the dataset group inside the file.
+        create_if_needed : bool, optional
+            When True (default) the file is opened in append mode ('a'),
+            creating it if it does not exist.  When False the file must
+            already exist and is opened in read/write mode ('r+').
+        mode : str, optional
+            Explicit h5py file-open mode.  When provided, overrides the
+            behaviour implied by *create_if_needed*.  Valid values are the
+            same as for :func:`h5py.File`: ``'r'``, ``'r+'``, ``'w'``,
+            ``'w-'``/``'x'``, and ``'a'``.  See
+            https://docs.h5py.org/en/stable/high/file.html for details.
+        """
         # 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+'
+
+        self._file = h5py.File(filename, mode)
 
         self._dataset_name = dataset_name
 

ismrmrd/waveform.py

@@ -69,6 +69,12 @@ def from_array(data, **kwargs):
 
         channels, nsamples = data.shape
 
+        uint16_max = np.iinfo(np.uint16).max
+        if nsamples > uint16_max:
+            raise ValueError(f"Array has {nsamples} samples, which is greater than the maximum of {uint16_max}")
+        if channels > uint16_max:
+            raise ValueError(f"Array has {channels} channels, which is greater than the maximum of {uint16_max}")
+
         array_data = {
             'version': 1,
             'channels': channels,

tests/test_hdf5.py

@@ -103,3 +103,19 @@ def test_read_and_write_waveforms_to_hdf5():
 
 def test_waveform_hdf5_size():
     assert ismrmrd.hdf5.waveform_header_dtype.itemsize == 40
+
+
+def test_dataset_read_only_mode():
+    filename = os.path.join(temp_dir, 'read_only.h5')
+
+    dataset = ismrmrd.Dataset(filename)
+    dataset.append_acquisition(create_random_acquisition())
+    dataset.close()
+
+    ro_dataset = ismrmrd.Dataset(filename, create_if_needed=False, mode='r')
+    assert ro_dataset.number_of_acquisitions() == 1
+    ro_dataset.close()
+
+    with pytest.raises(Exception):
+        ro_dataset2 = ismrmrd.Dataset(filename, create_if_needed=False, mode='r')
+        ro_dataset2.append_acquisition(create_random_acquisition())

tests/test_waveform.py

@@ -51,6 +51,20 @@ def test_initialization_with_illegal_header_value():
         ismrmrd.Waveform.from_array(common.create_random_waveform_data(), version='Bad version')
 
 
+def test_from_array_raises_on_too_many_samples():
+    uint16_max = np.iinfo(np.uint16).max
+    data = np.zeros((1, uint16_max + 1), dtype=np.uint32)
+    with pytest.raises(ValueError):
+        ismrmrd.Waveform.from_array(data)
+
+
+def test_from_array_raises_on_too_many_channels():
+    uint16_max = np.iinfo(np.uint16).max
+    data = np.zeros((uint16_max + 1, 1), dtype=np.uint32)
+    with pytest.raises(ValueError):
+        ismrmrd.Waveform.from_array(data)
+
+
 def test_serialize_and_deserialize():
     waveform = common.create_random_waveform()