v0.8.1: bugfix for using subtomogram averages in the list of shapes f…

…or a segment

CHANGELOG.md

@@ -1,5 +1,9 @@
 #Changes by release
 
+## [0.8.1] - 2023-09-26
+
+* bugfix for using `SubtomogramAverage` class in `SFFShapePrimitiveList` class
+
 ## [0.8.0] - 2023-09-25
 
 * added `SFFSubtomogramAverage` class

sfftkrw/conf.py

@@ -1,2 +1,2 @@
-SFFTKRW_VERSION = 'v0.8.0'
+SFFTKRW_VERSION = 'v0.8.1'
 SFFTKRW_ENTRY_POINT = 'sff'

sfftkrw/schema/adapter_v0_8_0_dev1.py

@@ -1709,6 +1709,7 @@ class SFFShapePrimitiveList(SFFListType):
         (_sff.cuboid, SFFCuboid),
         (_sff.cylinder, SFFCylinder),
         (_sff.ellipsoid, SFFEllipsoid),
+        (_sff.three_d_volume_type, SFFSubtomogramAverage),
     ]
 
     def _shape_count(self, shape_type):
@@ -1734,9 +1735,9 @@ def num_cones(self):
         """The number of cones in this container"""
         return self._shape_count(_sff.cone)
 
-    #     @property
-    #     def num_subtomogram_averages(self):
-    #         return self._shape_count(sff.subtomogramAverage)
+    @property
+    def num_subtomogram_averages(self):
+        return self._shape_count(_sff.three_d_volume_type)
 
     def as_json(self, args=None):
         slist = list()
@@ -1757,6 +1758,8 @@ def from_json(cls, data, args=None):
                     obj.append(SFFCylinder.from_json(shape, args=args))
                 elif shape[u'shape'] == u'ellipsoid':
                     obj.append(SFFEllipsoid.from_json(shape, args=args))
+                elif shape[u'shape'] == u'subtomogram_average':
+                    obj.append(SFFSubtomogramAverage.from_json(shape, args=args))
                 else:
                     raise SFFTypeError(u"cannot convert shape '{}'".format(data[u'shape']))
             else:
@@ -1785,6 +1788,8 @@ def from_hff(cls, parent_group, name=u'shape_primitive_list', args=None):
                     obj.append(SFFCylinder.from_hff(subgroup, args=args))
                 elif _decode(subgroup[u'shape'][()], 'utf-8') == u'ellipsoid':
                     obj.append(SFFEllipsoid.from_hff(subgroup, args=args))
+                elif _decode(subgroup['shape'][()], 'utf-8') == 'subtomogram_average':
+                    obj.append(SFFSubtomogramAverage.from_hff(subgroup, args=args))
                 else:
                     raise SFFTypeError(u"cannot convert shape '{}'".format(subgroup[u'shape'][()]))
             else:

sfftkrw/unittests/test_adapter_v0_7_0_dev0.py

@@ -2882,7 +2882,7 @@ def test_create_from_gds_type(self):
         s = adapter.SFFSegment.from_gds_type(_s)
         self.assertRegex(
             _str(s),
-            r"""SFFSegment\(id=None, parentID=\d+, biologicalAnnotation=None, colour=None, """ \
+            r"""SFFSegment\(id=None, parentID=\d+, biologicalAnnotation=None, colour=None, """ 
             r"""threeDVolume=None, meshList=SFFMeshList\(\[\]\), shapePrimitiveList=SFFShapePrimitiveList\(\[\]\)\)"""
         )
         # change ID
@@ -2892,7 +2892,7 @@ def test_create_from_gds_type(self):
         self.assertEqual(s.id, _id)
         self.assertRegex(
             _str(s),
-            r"""SFFSegment\(id={}, parentID=\d+, biologicalAnnotation=None, colour=None, """ \
+            r"""SFFSegment\(id={}, parentID=\d+, biologicalAnnotation=None, colour=None, """ 
             r"""threeDVolume=None, meshList=SFFMeshList\(\[\]\), shapePrimitiveList=SFFShapePrimitiveList\(\[\]\)\)""".format(
                 _id)
         )
@@ -2904,7 +2904,7 @@ def test_create_from_gds_type(self):
         self.assertEqual(s.parent_id, _parent_id)
         self.assertRegex(
             _str(s),
-            r"""SFFSegment\(id={}, parentID={}, biologicalAnnotation=None, colour=None, """ \
+            r"""SFFSegment\(id={}, parentID={}, biologicalAnnotation=None, colour=None, """ 
             r"""threeDVolume=None, meshList=SFFMeshList\(\[\]\), shapePrimitiveList=SFFShapePrimitiveList\(\[\]\)\)""".format(
                 None,
                 _parent_id

sfftkrw/unittests/test_adapter_v0_8_0_dev1.py

@@ -3393,7 +3393,14 @@ def get_sff_shapes(counts=_random_integers(count=4, start=2, stop=10)):
                 z=_random_float(10),
             )
         ]
-        return cones, cuboids, cylinders, ellipsoids
+        subtomogram_averages = [
+            adapter.SFFSubtomogramAverage(
+                lattice_id=_random_integer(),
+                value=_random_float(10),
+                transform_id=_random_integer(),
+            )
+        ]
+        return cones, cuboids, cylinders, ellipsoids, subtomogram_averages
 
     @staticmethod
     def get_gds_shapes(counts=_random_integers(count=4, start=2, stop=10)):
@@ -3420,46 +3427,57 @@ def get_gds_shapes(counts=_random_integers(count=4, start=2, stop=10)):
                 z=_random_float(10),
             )
         ]
-        return cones, cuboids, cylinders, ellipsoids
+        subtomogram_averages = [
+            emdb_sff.three_d_volume_type(
+                lattice_id=_random_integer(),
+                value=_random_float(10),
+                transform_id=_random_integer(),
+            )
+        ]
+        return cones, cuboids, cylinders, ellipsoids, subtomogram_averages
 
     def test_default(self):
         """Test default settings"""
         S = adapter.SFFShapePrimitiveList()
-        cones, cuboids, cylinders, ellipsoids = TestSFFShapePrimitiveList.get_sff_shapes()
+        cones, cuboids, cylinders, ellipsoids, subtomogram_averages = TestSFFShapePrimitiveList.get_sff_shapes()
         [S.append(c) for c in cones]
         [S.append(c) for c in cuboids]
         [S.append(c) for c in cylinders]
         [S.append(c) for c in ellipsoids]
+        [S.append(c) for c in subtomogram_averages]
         self.assertRegex(
             _str(S),
             r"""SFFShapePrimitiveList\(\[.*\]\)"""
         )
-        total_shapes = len(cones) + len(cuboids) + len(cylinders) + len(ellipsoids)
+        total_shapes = len(cones) + len(cuboids) + len(cylinders) + len(ellipsoids) + len(subtomogram_averages)
         self.assertEqual(len(S), total_shapes)
         self.assertEqual(list(S.get_ids()), list(_xrange(total_shapes)))
         s_id = random.choice(list(_xrange(total_shapes)))
         s = S.get_by_id(s_id)
-        self.assertIsInstance(s, (adapter.SFFCone, adapter.SFFCuboid, adapter.SFFCylinder, adapter.SFFEllipsoid))
+        self.assertIsInstance(s, (
+        adapter.SFFCone, adapter.SFFCuboid, adapter.SFFCylinder, adapter.SFFEllipsoid, adapter.SFFSubtomogramAverage))
 
     def test_create_from_gds_type(self):
         """Test that we can create from gds_type"""
         _S = emdb_sff.shape_primitive_listType()
-        cones, cuboids, cylinders, ellipsoids = TestSFFShapePrimitiveList.get_gds_shapes()
+        cones, cuboids, cylinders, ellipsoids, subtomogram_averages = TestSFFShapePrimitiveList.get_gds_shapes()
         [_S.add_shape_primitive(c) for c in cones]
         [_S.add_shape_primitive(c) for c in cuboids]
         [_S.add_shape_primitive(c) for c in cylinders]
         [_S.add_shape_primitive(c) for c in ellipsoids]
+        [_S.add_shape_primitive(c) for c in subtomogram_averages]
         S = adapter.SFFShapePrimitiveList.from_gds_type(_S)
         self.assertRegex(
             _str(S),
             r"""SFFShapePrimitiveList\(\[.*\]\)"""
         )
-        total_shapes = len(cones) + len(cuboids) + len(cylinders) + len(ellipsoids)
+        total_shapes = len(cones) + len(cuboids) + len(cylinders) + len(ellipsoids) + len(subtomogram_averages)
         self.assertEqual(len(S), total_shapes)
         self.assertEqual(list(S.get_ids()), list())
         s_id = random.choice(list(_xrange(total_shapes)))
         s = S[s_id]
-        self.assertIsInstance(s, (adapter.SFFCone, adapter.SFFCuboid, adapter.SFFCylinder, adapter.SFFEllipsoid))
+        self.assertIsInstance(s, (
+        adapter.SFFCone, adapter.SFFCuboid, adapter.SFFCylinder, adapter.SFFEllipsoid, adapter.SFFSubtomogramAverage))
 
     def test_json(self):
         """Interconvert to JSON"""
@@ -3532,6 +3550,15 @@ def test_hff(self):
                 transform_id=transform_id,
             )
         ) for _ in _xrange(no_ellipsoids)]
+        no_subtomogram_averages = _random_integer(start=2, stop=10)
+        transform_id = _random_integer()
+        [S.append(
+            adapter.SFFSubtomogramAverage(
+                lattice_id=_random_integer(),
+                value=_random_float(10),
+                transform_id=transform_id,
+            )
+        ) for _ in _xrange(no_subtomogram_averages)]
         with h5py.File(self.test_hdf5_fn, u'w') as h:
             group = h.create_group(u'container')
             group = S.as_hff(group)
@@ -3549,6 +3576,9 @@ def test_hff(self):
                     self.assertEqual(s.x, group[u'shape_primitive_list/{}/x'.format(i)][()])
                     self.assertEqual(s.y, group[u'shape_primitive_list/{}/y'.format(i)][()])
                     self.assertEqual(s.z, group[u'shape_primitive_list/{}/z'.format(i)][()])
+                elif isinstance(s, (adapter.SFFSubtomogramAverage,)):
+                    self.assertEqual(s.lattice_id, group[f'shape_primitive_list/{i}/lattice_id'][()])    
+                    self.assertEqual(s.value, group[f'shape_primitive_list/{i}/value'][()])    
                 self.assertEqual(s.transform_id, group[u'shape_primitive_list/{}/transform_id'.format(i)][()])
         with h5py.File(self.test_hdf5_fn, u'r') as h:
             S2 = adapter.SFFShapePrimitiveList.from_hff(h[u'container'])

sfftkrw/unittests/test_base.py

@@ -13,13 +13,13 @@
 import numpy
 from random_words import RandomWords, LoremIpsum
 
-rw = RandomWords()
-li = LoremIpsum()
-
 from . import _random_integer, Py23FixTestCase, _random_float, _random_floats
 from .. import EMDB_SFF_VERSION
 from ..core import _xrange, _str
-from ..schema import base  # , emdb_sff
+from ..schema import base
+
+rw = RandomWords()
+li = LoremIpsum()
 
 # dynamically import the latest schema generateDS API
 emdb_sff_name = 'sfftkrw.schema.v{schema_version}'.format(
@@ -65,7 +65,7 @@ class _SomeEntity(base.SFFType):
             """Empty entity"""
 
         with self.assertRaisesRegex(ValueError, r'.*gds_type.*'):
-            _s = _SomeEntity()
+            _SomeEntity()
 
     def test_create_from_gds_type(self):
         """Test creating an `SFFType` subclass object from a `gds_type' object"""
@@ -90,7 +90,7 @@ def test_create_from_gds_type_raises_error(self):
         as the one provided"""
         _r = emdb_sff.biological_annotationType()
         with self.assertRaisesRegex(base.SFFTypeError, r".*is not object of type.*"):
-            r = adapter.SFFRGBA.from_gds_type(_r)
+            adapter.SFFRGBA.from_gds_type(_r)
 
     def test_ref_attr(self):
         """Test the `gds_tag_name` attribute"""
@@ -413,7 +413,7 @@ class _Cone(_Shape):
             ref = "cone"
 
         with self.assertRaisesRegex(AttributeError, r".*superclass does not have an 'update_counter' classmethod"):
-            _cone = _Cone()
+            _Cone()
 
     def test_errors(self):
         """Test that we get the right exceptions"""
@@ -646,7 +646,6 @@ def test_copy(self):
         self.assertNotEqual(id(C), id(D))
         # shapes
         Sh = adapter.SFFShapePrimitiveList()
-        _no_shapes = 3
         Sh.append(adapter.SFFCone())
         Sh.append(adapter.SFFCuboid())
         Sh.append(adapter.SFFCylinder())

sfftkrw/unittests/test_core.py

@@ -9,14 +9,14 @@
 
 from random_words import RandomWords, LoremIpsum
 
-rw = RandomWords()
-li = LoremIpsum()
-
 from . import TEST_DATA_PATH, _random_integer, Py23FixTestCase
 from ..core import print_tools
 from ..core import utils
 from ..core.parser import parse_args, tool_list
 
+rw = RandomWords()
+li = LoremIpsum()
+
 __author__ = "Paul K. Korir, PhD"
 __email__ = "pkorir@ebi.ac.uk, paul.korir@gmail.com"
 __date__ = "2017-05-15"
@@ -63,7 +63,7 @@ def test_print_date_default(self):
         data = self.temp_file.readlines()[0]
         _words = data.split(' ')
         self.assertIn(_words[0], self._weekdays)  # the first part is a date
-        self.assertEqual(_words[-1][-1], '\n')  #  the last letter is a newline
+        self.assertEqual(_words[-1][-1], '\n')  # the last letter is a newline
 
     def test_print_date_non_basestring(self):
         """Test exception when print_string is not a basestring subclass"""