diff options
| -rwxr-xr-x | Wrappers/Python/ccpi/framework/framework.py | 75 | ||||
| -rwxr-xr-x | Wrappers/Python/test/test_DataContainer.py | 30 |
2 files changed, 87 insertions, 18 deletions
diff --git a/Wrappers/Python/ccpi/framework/framework.py b/Wrappers/Python/ccpi/framework/framework.py index dbe7d0a..4a2a9e8 100755 --- a/Wrappers/Python/ccpi/framework/framework.py +++ b/Wrappers/Python/ccpi/framework/framework.py @@ -63,7 +63,8 @@ class ImageGeometry(object): center_x=0, center_y=0, center_z=0, - channels=1): + channels=1, + **kwargs): self.voxel_num_x = voxel_num_x self.voxel_num_y = voxel_num_y @@ -80,25 +81,41 @@ class ImageGeometry(object): if self.channels > 1: if self.voxel_num_z>1: self.length = 4 - self.shape = (self.channels, self.voxel_num_z, self.voxel_num_y, self.voxel_num_x) + shape = (self.channels, self.voxel_num_z, self.voxel_num_y, self.voxel_num_x) dim_labels = [ImageGeometry.CHANNEL, ImageGeometry.VERTICAL, ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] else: self.length = 3 - self.shape = (self.channels, self.voxel_num_y, self.voxel_num_x) + shape = (self.channels, self.voxel_num_y, self.voxel_num_x) dim_labels = [ImageGeometry.CHANNEL, ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] else: if self.voxel_num_z>1: self.length = 3 - self.shape = (self.voxel_num_z, self.voxel_num_y, self.voxel_num_x) + shape = (self.voxel_num_z, self.voxel_num_y, self.voxel_num_x) dim_labels = [ImageGeometry.VERTICAL, ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] else: self.length = 2 - self.shape = (self.voxel_num_y, self.voxel_num_x) + shape = (self.voxel_num_y, self.voxel_num_x) dim_labels = [ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] - self.dimension_labels = dim_labels + labels = kwargs.get('dimension_labels', None) + if labels is None: + self.shape = shape + self.dimension_labels = dim_labels + else: + order = [] + for i, el in enumerate(labels): + for j, ek in enumerate(dim_labels): + if el == ek: + order.append(j) + break + if order != [0,1,2]: + # resort + self.shape = tuple([shape[i] for i in order]) + self.dimension_labels = labels + + def get_min_x(self): return self.center_x - 0.5*self.voxel_num_x*self.voxel_size_x @@ -146,7 +163,10 @@ class ImageGeometry(object): return repres def allocate(self, value=0, dimension_labels=None, **kwargs): '''allocates an ImageData according to the size expressed in the instance''' - out = ImageData(geometry=self) + if dimension_labels is None: + out = ImageData(geometry=self, dimension_labels=self.dimension_labels) + else: + out = ImageData(geometry=self, dimension_labels=dimension_labels) if isinstance(value, Number): if value != 0: out += value @@ -164,9 +184,7 @@ class ImageGeometry(object): out.fill(numpy.random.randint(max_value,size=self.shape)) else: raise ValueError('Value {} unknown'.format(value)) - if dimension_labels is not None: - if dimension_labels != self.dimension_labels: - return out.subset(dimensions=dimension_labels) + return out # The following methods return 2 members of the class, therefore I # don't think we need to implement them. @@ -244,6 +262,8 @@ class AcquisitionGeometry(object): self.channels = channels self.angle_unit=kwargs.get(AcquisitionGeometry.ANGLE_UNIT, AcquisitionGeometry.DEGREE) + + # default labels if channels > 1: if pixel_num_v > 1: shape = (channels, num_of_angles , pixel_num_v, pixel_num_h) @@ -262,9 +282,27 @@ class AcquisitionGeometry(object): else: shape = (num_of_angles, pixel_num_h) dim_labels = [AcquisitionGeometry.ANGLE, AcquisitionGeometry.HORIZONTAL] - self.shape = shape + + labels = kwargs.get('dimension_labels', None) + if labels is None: + self.shape = shape + self.dimension_labels = dim_labels + else: + if len(labels) != len(dim_labels): + raise ValueError('Wrong number of labels. Expected {} got {}'.format(len(dim_labels), len(labels))) + order = [] + for i, el in enumerate(labels): + for j, ek in enumerate(dim_labels): + if el == ek: + order.append(j) + break + if order != [0,1,2]: + # resort + self.shape = tuple([shape[i] for i in order]) + self.dimension_labels = labels + + - self.dimension_labels = dim_labels def clone(self): '''returns a copy of the AcquisitionGeometry''' @@ -292,7 +330,10 @@ class AcquisitionGeometry(object): return repres def allocate(self, value=0, dimension_labels=None): '''allocates an AcquisitionData according to the size expressed in the instance''' - out = AcquisitionData(geometry=self) + if dimension_labels is None: + out = AcquisitionData(geometry=self, dimension_labels=self.dimension_labels) + else: + out = AcquisitionData(geometry=self, dimension_labels=dimension_labels) if isinstance(value, Number): if value != 0: out += value @@ -310,9 +351,7 @@ class AcquisitionGeometry(object): out.fill(numpy.random.randint(max_value,size=self.shape)) else: raise ValueError('Value {} unknown'.format(value)) - if dimension_labels is not None: - if dimension_labels != self.dimension_labels: - return out.subset(dimensions=dimension_labels) + return out class DataContainer(object): @@ -658,7 +697,7 @@ class DataContainer(object): # geometry=self.geometry) return out else: - raise ValueError(message(type(self),"Wrong size for data memory: ", out.shape,self.shape)) + raise ValueError(message(type(self),"Wrong size for data memory: out {} x2 {} expected {}".format( out.shape,x2.shape ,self.shape))) elif issubclass(type(out), DataContainer) and isinstance(x2, (int,float,complex)): if self.check_dimensions(out): kwargs['out']=out.as_array() @@ -806,7 +845,7 @@ class ImageData(DataContainer): self.geometry = kwargs.get('geometry', None) if array is None: if self.geometry is not None: - shape, dimension_labels = self.get_shape_labels(self.geometry) + shape, dimension_labels = self.get_shape_labels(self.geometry, dimension_labels) array = numpy.zeros( shape , dtype=numpy.float32) super(ImageData, self).__init__(array, deep_copy, diff --git a/Wrappers/Python/test/test_DataContainer.py b/Wrappers/Python/test/test_DataContainer.py index e92d4c6..4c53df8 100755 --- a/Wrappers/Python/test/test_DataContainer.py +++ b/Wrappers/Python/test/test_DataContainer.py @@ -487,6 +487,13 @@ class TestDataContainer(unittest.TestCase): self.assertNumpyArrayEqual(vol1.as_array(), numpy.ones(vol.shape) * 4) self.assertEqual(vol.number_of_dimensions, 3) + + ig2 = ImageGeometry (voxel_num_x=2,voxel_num_y=3,voxel_num_z=4, + dimension_labels=[ImageGeometry.HORIZONTAL_X, ImageGeometry.HORIZONTAL_Y, + ImageGeometry.VERTICAL]) + data = ig2.allocate() + self.assertNumpyArrayEqual(numpy.asarray(data.shape), numpy.asarray(ig2.shape)) + self.assertNumpyArrayEqual(numpy.asarray(data.shape), data.as_array().shape) def test_AcquisitionData(self): sgeometry = AcquisitionGeometry(dimension=2, angles=numpy.linspace(0, 180, num=10), @@ -494,6 +501,29 @@ class TestDataContainer(unittest.TestCase): pixel_num_h=5, channels=2) sino = AcquisitionData(geometry=sgeometry) self.assertEqual(sino.shape, (2, 10, 3, 5)) + + ag = AcquisitionGeometry (pixel_num_h=2,pixel_num_v=3,channels=4, dimension=2, angles=numpy.linspace(0, 180, num=10), + geom_type='parallel', ) + print (ag.shape) + print (ag.dimension_labels) + + data = ag.allocate() + self.assertNumpyArrayEqual(numpy.asarray(data.shape), numpy.asarray(ag.shape)) + self.assertNumpyArrayEqual(numpy.asarray(data.shape), data.as_array().shape) + + print (data.shape, ag.shape, data.as_array().shape) + + ag2 = AcquisitionGeometry (pixel_num_h=2,pixel_num_v=3,channels=4, dimension=2, angles=numpy.linspace(0, 180, num=10), + geom_type='parallel', + dimension_labels=[AcquisitionGeometry.VERTICAL , + AcquisitionGeometry.ANGLE, AcquisitionGeometry.HORIZONTAL, AcquisitionGeometry.CHANNEL]) + + data = ag2.allocate() + print (data.shape, ag2.shape, data.as_array().shape) + self.assertNumpyArrayEqual(numpy.asarray(data.shape), numpy.asarray(ag2.shape)) + self.assertNumpyArrayEqual(numpy.asarray(data.shape), data.as_array().shape) + + def test_ImageGeometry_allocate(self): vgeometry = ImageGeometry(voxel_num_x=4, voxel_num_y=3, channels=2) image = vgeometry.allocate() |