Merge origin/composite_operator_datacontainer into demos

Conflicts:
	Wrappers/Python/ccpi/framework/framework.py

3 files changed, 48 insertions, 18 deletions

diff --git a/Wrappers/Python/ccpi/framework/framework.py b/Wrappers/Python/ccpi/framework/framework.py
index fd0e0d8..acb59ae 100755
--- a/Wrappers/Python/ccpi/framework/framework.py
+++ b/Wrappers/Python/ccpi/framework/framework.py
@@ -245,12 +245,15 @@ class AcquisitionGeometry(object):
             source_to_center_dist (if parallel: NaN)
             center_to_detector_dist (if parallel: NaN)
         standard or nonstandard (vec) geometry
-        angles
+        angles is expected numpy array, dtype - float32
         angles_format radians or degrees
         """
         self.geom_type = geom_type   # 'parallel' or 'cone'
         self.dimension = dimension # 2D or 3D
-        self.angles = angles
+        if isinstance(angles, numpy.ndarray):
+            self.angles = angles
+        else:
+            raise ValueError('numpy array is expected')
         num_of_angles = len (angles)
         
         self.dist_source_center = dist_source_center
@@ -812,8 +815,7 @@ class DataContainer(object):
     
     def dot(self, other, *args, **kwargs):
         '''return the inner product of 2 DataContainers viewed as vectors'''
-        method = kwargs.get('method', 'reduce')
-
+        method = kwargs.get('method', 'numpy')
         if method not in ['numpy','reduce']:
             raise ValueError('dot: specified method not valid. Expecting numpy or reduce got {} '.format(
                     method))
diff --git a/Wrappers/Python/ccpi/io/NEXUSDataReader.py b/Wrappers/Python/ccpi/io/NEXUSDataReader.py
index cf67e27..e6d4d3b 100644
--- a/Wrappers/Python/ccpi/io/NEXUSDataReader.py
+++ b/Wrappers/Python/ccpi/io/NEXUSDataReader.py
@@ -35,9 +35,7 @@ class NEXUSDataReader(object):
         self.nexus_file = kwargs.get('nexus_file', None)
         
         if self.nexus_file is not None:
-            self.set_up(nexus_file = self.nexus_file,
-                        roi = self.roi,
-                        binning = self.binning)
+            self.set_up(nexus_file = self.nexus_file)
             
     def set_up(self, 
                nexus_file = None):
@@ -94,10 +92,20 @@ class NEXUSDataReader(object):
                                      dimension_labels = dimension_labels)
                     
                 else:   # AcquisitionData
+                    if ds_data.attrs.__contains__('dist_source_center'):
+                        dist_source_center = ds_data.attrs['dist_source_center']
+                    else:
+                        dist_source_center = None
+                    
+                    if ds_data.attrs.__contains__('dist_center_detector'):
+                        dist_center_detector = ds_data.attrs['dist_center_detector']
+                    else:
+                        dist_center_detector = None
+                    
                     self._geometry = AcquisitionGeometry(geom_type = ds_data.attrs['geom_type'],
                                                          dimension = ds_data.attrs['dimension'],
-                                                         dist_source_center = ds_data.attrs['dist_source_center'],
-                                                         dist_center_detector = ds_data.attrs['dist_center_detector'],
+                                                         dist_source_center = dist_source_center,
+                                                         dist_center_detector = dist_center_detector,
                                                          pixel_num_h = ds_data.attrs['pixel_num_h'],
                                                          pixel_size_h = ds_data.attrs['pixel_size_h'],
                                                          pixel_num_v = ds_data.attrs['pixel_num_v'],
@@ -140,4 +148,11 @@ image_data = reader.load_data()
 print(image_data)
 ig = reader.get_geometry()
 print(ig)
+
+reader = NEXUSDataReader()
+reader.set_up(nexus_file = '/home/evelina/test_nexus_ag.nxs')
+ad = reader.load_data()
+print(ad)
+ad = reader.get_geometry()
+print(ad)
 '''
diff --git a/Wrappers/Python/ccpi/io/NEXUSDataWriter.py b/Wrappers/Python/ccpi/io/NEXUSDataWriter.py
index f780f79..6f5c0b2 100644
--- a/Wrappers/Python/ccpi/io/NEXUSDataWriter.py
+++ b/Wrappers/Python/ccpi/io/NEXUSDataWriter.py
@@ -87,8 +87,10 @@ class NEXUSDataWriter(object):
             if (isinstance(self.data_container, AcquisitionData)):      
                 ds_data.attrs['geom_type'] = self.data_container.geometry.geom_type
                 ds_data.attrs['dimension'] = self.data_container.geometry.dimension
-                ds_data.attrs['dist_source_center'] = self.data_container.geometry.dist_source_center
-                ds_data.attrs['dist_center_detector'] = self.data_container.geometry.dist_center_detector
+                if self.data_container.geometry.dist_source_center is not None:
+                    ds_data.attrs['dist_source_center'] = self.data_container.geometry.dist_source_center
+                if self.data_container.geometry.dist_center_detector is not None:
+                    ds_data.attrs['dist_center_detector'] = self.data_container.geometry.dist_center_detector
                 ds_data.attrs['pixel_num_h'] = self.data_container.geometry.pixel_num_h
                 ds_data.attrs['pixel_size_h'] = self.data_container.geometry.pixel_size_h
                 ds_data.attrs['pixel_num_v'] = self.data_container.geometry.pixel_num_v
@@ -138,14 +140,25 @@ writer.write_file()
 
 ig = ImageGeometry(voxel_num_x = 100,
                    voxel_num_y = 100)
-
 im = ImageData(array = numpy.zeros((100, 100), dtype = 'float'),
                geometry = ig)
-
 im_writer = NEXUSDataWriter()
 
-writer.set_up(file_name = '/home/evelina/test_nexus_im.nxs',
-              data_container = im)
-
-writer.write_file()
-'''
+im_writer.set_up(file_name = '/home/evelina/test_nexus_im.nxs',
+                 data_container = im)
+im_writer.write_file()
+
+ag = AcquisitionGeometry(geom_type = 'parallel', 
+                         dimension = '2D', 
+                         angles = numpy.array([0, 1]), 
+                         pixel_num_h = 200, 
+                         pixel_size_h = 1, 
+                         pixel_num_v = 100, 
+                         pixel_size_v = 1)
+
+ad = ag.allocate()
+ag_writer = NEXUSDataWriter()
+ag_writer.set_up(file_name = '/home/evelina/test_nexus_ag.nxs',
+                 data_container = ad)
+ag_writer.write_file()
+'''
\ No newline at end of file