Merge branch 'dev0'

docs/conf.py

@@ -22,7 +22,7 @@ copyright = '2020, Nikolay Ivanov'
 author = 'Nikolay Ivanov'
 
 # The full version, including alpha/beta/rc tags
-release = '0.3.5-r1'
+release = '0.3.6'
 
 
 # -- General configuration ---------------------------------------------------

pyrost/data_container.py

@@ -58,14 +58,14 @@ class DataContainer:
     attr_set, init_set = {}, {}
 
     def __init__(self, **kwargs):
-        self.__dict__['attr_dict'] = {}
+        self.__dict__['attr_dict'] = {key: None for key in self.attr_set | self.init_set}
         for attr in self.attr_set:
             if kwargs.get(attr) is None:
                 raise ValueError('Attribute {:s} has not been provided'.format(attr))
             else:
-                self.attr_dict[attr] = kwargs.get(attr)
+                self.__setattr__(attr, kwargs.get(attr))
         for attr in self.init_set:
-            self.attr_dict[attr] = kwargs.get(attr)
+            self.__setattr__(attr, kwargs.get(attr))
 
     def __iter__(self):
         return self.attr_dict.__iter__()

pyrost/data_processing.py

@@ -166,7 +166,10 @@ class STData(DataContainer):
 
     def __setattr__(self, attr, value):
         if attr in self.attr_set | self.init_set:
-            value = np.array(value, dtype=self.protocol.get_dtype(attr))
+            if isinstance(value, np.ndarray):
+                value = np.array(value, dtype=self.protocol.get_dtype(attr))
+            elif not value is None:
+                value = self.protocol.get_dtype(attr)(value)
             super(STData, self).__setattr__(attr, value)
         else:
             super(STData, self).__setattr__(attr, value)
@@ -491,11 +494,12 @@ class STData(DataContainer):
             if not val is None:
                 if attr in ['data', 'error_frame', 'mask', 'phase',
                             'pixel_abberations', 'pixel_map', 'whitefield']:
-                    val = val[..., self.roi[0]:self.roi[1], self.roi[2]:self.roi[3]]
+                    val = np.ascontiguousarray(val[..., self.roi[0]:self.roi[1],
+                                                        self.roi[2]:self.roi[3]])
                 if attr in ['basis_vectors', 'data', 'mask', 'pixel_translations',
                             'translations']:
-                    val = val[self.good_frames]
-            return np.ascontiguousarray(val)
+                    val = np.ascontiguousarray(val[self.good_frames])
+            return val
         else:
             return value
 

pyrost/simulation/st_sim.py

@@ -359,9 +359,6 @@ class STConverter:
         t_arr = np.zeros((st_params.n_frames, 3), dtype=self.protocol.get_dtype('translations'))
         t_arr[:, 0] = -smp_pos
         data_dict['translations'] = self.crd_rat * t_arr
-
-        for attr in data_dict:
-            data_dict[attr] = np.asarray(data_dict[attr], dtype=self.protocol.get_dtype(attr))
         return data_dict
 
     def export_data(self, data, sim_obj):

setup.py

@@ -39,7 +39,7 @@ with open('README.md', 'r') as readme:
     long_description = readme.read()
 
 setup(name='pyrost',
-      version='0.3.5-r1',
+      version='0.3.6',
       author='Nikolay Ivanov',
       author_email="nikolay.ivanov@desy.de",
       long_description=long_description,

tests/test_pyrost.py

@@ -115,8 +115,8 @@ def test_full(converter, ptych, sim_obj):
     data = converter.export_data(ptych, sim_obj)
     assert data.data.dtype == converter.protocol.known_types['float']
     st_obj = data.get_st()
-    st_res = st_obj.iter_update(sw_fs=10, ls_pm=2.5, ls_ri=15,
-                                verbose=True, n_iter=10)
+    st_res = st_obj.iter_update_gd(sw_fs=10, ls_pm=2.5, ls_ri=15,
+                                   verbose=True, n_iter=10)
     data = data.update_phase(st_res)
     fit = data.fit_phase(axis=1)
     assert (st_obj.pixel_map != st_res.pixel_map).any()