Added abillity to extend acquisitions and waveforms when using File interace

ismrmrd/file.py

@@ -37,6 +37,16 @@ def __setitem__(self, key, value):
     def __repr__(self):
         return type(self).__name__ + " containing " + self.data.__repr__()
 
+    def append(self,item):
+        self.extend([item])
+
+    def extend(self,iterable):
+        new_data = [self.to_numpy(v) for v in iterable]
+        old_size = self.data.shape[0]
+        new_size = old_size + len(new_data)
+        self.data.resize(new_size,axis=0)
+        self.data[old_size:] = new_data
+
     @classmethod
     def from_numpy(cls, raw):
         raise NotImplemented()
@@ -248,7 +258,7 @@ def __set_acquisitions(self, acquisitions):
         buffer = numpy.array([Acquisitions.to_numpy(a) for a in acquisitions], dtype=acquisition_dtype)
 
         self.__del_acquisitions()
-        self._contents['data'] = buffer
+        self._contents.create_dataset('data',data=buffer,maxshape=(None,),chunks=True)
 
     def __del_acquisitions(self):
         if 'data' in self._contents:
@@ -271,7 +281,7 @@ def __set_waveforms(self, waveforms):
         buffer = numpy.array([converter.to_numpy(w) for w in waveforms], dtype=waveform_dtype)
 
         self.__del_waveforms()
-        self._contents['waveforms'] = buffer
+        self._contents.create_dataset('waveforms', data=buffer, maxshape=(None,),chunks=True)
 
     def __del_waveforms(self):
         if 'waveforms' in self._contents:

schema/ismrmrd.xsd

@@ -67,7 +67,7 @@
       <xs:element minOccurs="0" name="seriesDate" type="xs:date" />
       <xs:element minOccurs="0" name="seriesTime" type="xs:time" />
       <xs:element minOccurs="1" name="patientPosition" type="patientPositionType" />
-      <xs:element minOccurs="0" name="relativeTablePosition" type="threeDimensionalFloat" />
+      <xs:element minOccurs="0" name="relativeTablePosition" type="threeDimensionalFloatType" />
       <xs:element minOccurs="0" name="initialSeriesNumber" type="xs:long" />
       <xs:element minOccurs="0" name="protocolName" type="xs:string" />
       <xs:element minOccurs="0" name="sequenceName" type="xs:string" />
@@ -174,6 +174,14 @@
     </xs:all>
   </xs:complexType>
 
+   <xs:complexType name="threeDimensionalFloatType">
+    <xs:sequence>
+      <xs:element maxOccurs="1" minOccurs="1" name="x" type="xs:float" />
+      <xs:element maxOccurs="1" minOccurs="1" name="y" type="xs:float" />
+      <xs:element maxOccurs="1" minOccurs="1" name="z" type="xs:float" />
+    </xs:sequence>
+  </xs:complexType>
+
   <xs:complexType name="encodingLimitsType">
     <xs:all>
       <xs:element maxOccurs="1" minOccurs="0" name="kspace_encoding_step_0" type="limitType" />

setup.py

@@ -58,7 +58,7 @@ def to_uri(filename):
 
 setup(
     name='ismrmrd',
-    version='1.12.5',
+    version='1.13.0',
     author='ISMRMRD Developers',
     description='Python implementation of the ISMRMRD',
     license='Public Domain',

tests/test_common.py

@@ -121,7 +121,7 @@ def create_random_image(seed=42):
     header = create_random_image_properties()
 
     image = ismrmrd.Image.from_array(data, **header)
-    image.attribute_string = "<?xml version='1.0' encoding='UTF-8'?>\n<ismrmrdMeta><meta><name>rando</name><value>{}</value></meta></ismrmrdMeta>".format(random.randint(0, 1000))
+    image.meta = {"Random attribute": random.randint(0,1000)}
 
     return image
 

tests/test_file.py

@@ -52,7 +52,7 @@ def test_file_returns_none_when_no_acquisitions_present():
         dataset = file['dataset']
 
         assert dataset.has_acquisitions()
-        assert dataset.acquisitions is not None
+        assert not (dataset.acquisitions is None)
 
 
 @nose.tools.with_setup(create_temp_dir, delete_temp_dir)
@@ -85,7 +85,7 @@ def test_file_can_delete_acquisitions():
 
         dataset.acquisitions = random_acquisitions(10)
 
-        assert dataset.acquisitions is not None
+        assert not (dataset.acquisitions is None)
         del dataset.acquisitions
         assert dataset.acquisitions is None
 
@@ -138,6 +138,26 @@ def test_file_can_write_random_acquisition():
         dataset = file['dataset']
         assert acquisition == dataset.acquisitions[200]
 
+@nose.tools.with_setup(create_temp_dir, delete_temp_dir)
+def test_file_can_append_acquisitions():
+
+    filename = os.path.join(temp_dir, "acquisitions.h5")
+    acquisitions = list(random_acquisitions(10))
+    acquisitions2 = list(random_acquisitions(10))
+    acquisition3 = next(random_acquisitions(1))
+
+    combined = acquisitions + acquisitions2 + [acquisition3]
+
+    with ismrmrd.File(filename) as file:
+        dataset = file['dataset']
+        dataset.acquisitions = acquisitions
+        dataset.acquisitions.extend(acquisitions2)
+        dataset.acquisitions.append(acquisition3)
+
+    with ismrmrd.File(filename) as file:
+        dataset = file['dataset']
+        for a, b in zip(combined, dataset.acquisitions):
+            assert a == b
 
 @nose.tools.with_setup(create_temp_dir, delete_temp_dir)
 def test_file_can_write_random_acquisition_slice():
@@ -187,6 +207,27 @@ def test_file_can_read_and_write_waveforms():
         for a, b in zip(waveforms, dataset.waveforms):
             assert a == b
 
+@nose.tools.with_setup(create_temp_dir, delete_temp_dir)
+def test_file_can_append_waveforms():
+
+    filename = os.path.join(temp_dir, "waveforms.h5")
+    waveforms = list(random_waveforms(10))
+    waveforms2 = list(random_waveforms(10))
+    waveform3 = next(random_waveforms(1))
+
+    combined = waveforms + waveforms2 + [waveform3]
+
+    with ismrmrd.File(filename) as file:
+        dataset = file['dataset']
+        dataset.waveforms = waveforms
+        dataset.waveforms.extend(waveforms2)
+        dataset.waveforms.append(waveform3)
+
+    with ismrmrd.File(filename) as file:
+        dataset = file['dataset']
+        for a, b in zip(combined, dataset.waveforms):
+            assert a == b
+
 
 @nose.tools.with_setup(create_temp_dir, delete_temp_dir)
 def test_file_can_read_and_write_images():

tests/test_image.py

@@ -30,7 +30,6 @@ def test_new_instance():
     img = ismrmrd.Image(head, attribute_string=attr)
     eq_(img.attribute_string, attr)
 
-
 def test_read_only_fields():
     img = ismrmrd.Image()
     for field in ['data_type', 'matrix_size', 'channels', 'attribute_string_len']: