removed wildcard imports; enforced usage of new transform method

Author: klytje

src/sas/qtgui/Calculators/Shape2SAS/ViewerModel.py

@@ -10,7 +10,8 @@
 
 # Local Perspectives
 from sas.qtgui.Calculators.Shape2SAS.ViewerAllOptions import ViewerButtons, ViewerModelRadius
-from sas.sascalc.shape2sas.Shape2SAS import ModelPointDistribution, TheoreticalScattering
+from sas.sascalc.shape2sas.Models import ModelPointDistribution
+from sas.sascalc.shape2sas.TheoreticalScattering import TheoreticalScattering
 
 
 class ViewerModel(QWidget):

src/sas/sascalc/shape2sas/ExperimentalScattering.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from sas.sascalc.shape2sas.Typing import *
+from sas.sascalc.shape2sas.Typing import Vector2D
 
 
 @dataclass

src/sas/sascalc/shape2sas/HelperFunctions.py

@@ -1,8 +1,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from sas.sascalc.shape2sas.Typing import *
-
 
 ################################ Shape2SAS helper functions ###################################
 class Qsampling:

src/sas/sascalc/shape2sas/Models.py

@@ -3,8 +3,10 @@
 import numpy as np
 
 from sas.sascalc.shape2sas.HelperFunctions import Qsampling, euler_rotation_matrix
-from sas.sascalc.shape2sas.models import *
-from sas.sascalc.shape2sas.Typing import *
+from sas.sascalc.shape2sas.models import \
+    Cube, Cuboid, Cylinder, CylinderRing, Disc, DiscRing, Ellipsoid, \
+    EllipticalCylinder, HollowCube, HollowSphere, Sphere, SuperEllipsoid
+from sas.sascalc.shape2sas.Typing import Vectors, Vector3D, Vector4D
 
 
 @dataclass
@@ -68,20 +70,22 @@ def __init__(self, matrix: np.ndarray, center_mass: np.ndarray):
         self.cm = center_mass  # center of mass
 Translation = np.ndarray
 
-def transform(coords: np.ndarray[Vector3D], T: Translation, R: Rotation):
+def transform(coords: np.ndarray[Vector3D], translate: Translation = np.array([0, 0, 0]), rotate: Rotation = Rotation(np.eye(3), np.array([0, 0, 0]))):
     """Transform a set of coordinates by a rotation R and translation T"""
+    if isinstance(rotate, np.ndarray): 
+        rotate = Rotation(rotate, np.array([0, 0, 0]))
     assert coords.shape[0] == 3
-    assert T.shape == (3,)
-    assert R.M.shape == (3, 3)
-    assert R.cm.shape == (3,)
+    assert translate.shape == (3,)
+    assert rotate.M.shape == (3, 3)
+    assert rotate.cm.shape == (3,)
 
     # The transform is:
     #   v' = R*(v - R_cm) + R_cm + T
     #      = R*v - R*R_cm + R_cm + T
-    #      = R*v + (-R*R_cm + R_cm + T)
+    #      = R*v + T'
 
-    Tp = -np.dot(R.M, R.cm) + R.cm + T
-    return np.dot(R.M, coords) + Tp[:, np.newaxis]
+    Tp = -np.dot(rotate.M, rotate.cm) + rotate.cm + translate
+    return np.dot(rotate.M, coords) + Tp[:, np.newaxis]
 
 
 class GeneratePoints:
@@ -226,7 +230,7 @@ def onCheckOverlap(
 
         if any(r != 0 for r in rotation):
             ## effective coordinates, shifted by (x_com,y_com,z_com)
-            x_eff, y_eff, z_eff = Translation(x, y, z, -com[0], -com[1], -com[2]).onTranslatingPoints()
+            x_eff, y_eff, z_eff = transform(np.vstack([x, y, z]), translate=np.array([-com[0], -com[1], -com[2]]))
 
             #rotate backwards with minus rotation angles
             alpha, beta, gam = rotation
@@ -235,12 +239,12 @@ def onCheckOverlap(
             beta = np.radians(beta)
             gam = np.radians(gam)
 
-            x_eff, y_eff, z_eff = Rotation(x_eff, y_eff, z_eff, -alpha, -beta, -gam, rotp_x, rotp_y, rotp_z).onRotatingPoints()
+            rotation = Rotation(euler_rotation_matrix(-alpha, -beta, -gam), np.array([rotp_x, rotp_y, rotp_z]))
+            x_eff, y_eff, z_eff = transform(np.vstack([x_eff, y_eff, z_eff]), rotate=rotation)
 
         else:
             ## effective coordinates, shifted by (x_com,y_com,z_com)
-            x_eff, y_eff, z_eff = Translation(x, y, z, -com[0], -com[1], -com[2]).onTranslatingPoints()
-
+            x_eff, y_eff, z_eff = transform(np.vstack([x, y, z]), translate=np.array([-com[0], -com[1], -com[2]]))
 
         idx = subunitClass(dimensions).checkOverlap(x_eff, y_eff, z_eff)
         x_add, y_add, z_add, p_add = x[idx], y[idx], z[idx], p[idx]

src/sas/sascalc/shape2sas/Shape2SAS.py

@@ -5,11 +5,13 @@
 
 import numpy as np
 
-from sas.sascalc.shape2sas.ExperimentalScattering import *
+from sas.sascalc.shape2sas.ExperimentalScattering import SimulateScattering, getSimulatedScattering
 from sas.sascalc.shape2sas.HelperFunctions import generate_pdb, plot_2D, plot_results
-from sas.sascalc.shape2sas.Models import *
+from sas.sascalc.shape2sas.Models import Qsampling, ModelProfile, SimulationParameters, getPointDistribution
 from sas.sascalc.shape2sas.StructureFactor import StructureFactor
-from sas.sascalc.shape2sas.TheoreticalScattering import *
+from sas.sascalc.shape2sas.TheoreticalScattering import \
+    TheoreticalScatteringCalculation, ModelSystem, ITheoretical, WeightedPairDistribution, \
+    getTheoreticalScattering, getTheoreticalHistogram
 
 ################################ Shape2SAS batch version ################################
 if __name__ == "__main__":

src/sas/sascalc/shape2sas/StructureFactor.py

@@ -1,8 +1,7 @@
 
 import numpy as np
 
-from sas.sascalc.shape2sas.structure_factors import *
-from sas.sascalc.shape2sas.Typing import *
+from sas.sascalc.shape2sas.structure_factors import HardSphereStructure, Aggregation, NoStructure
 
 
 class StructureFactor:

src/sas/sascalc/shape2sas/TheoreticalScattering.py

@@ -5,7 +5,7 @@
 from sas.sascalc.shape2sas.HelperFunctions import sinc
 from sas.sascalc.shape2sas.Models import ModelSystem, SimulationParameters
 from sas.sascalc.shape2sas.StructureFactor import StructureFactor
-from sas.sascalc.shape2sas.Typing import *
+from sas.sascalc.shape2sas.Typing import Vector2D, Vector3D
 
 
 @dataclass

src/sas/sascalc/shape2sas/Typing.py

@@ -1,4 +1,3 @@
-
 import numpy as np
 
 Vectors = list[list[float]]

src/sas/sascalc/shape2sas/models/Cube.py

@@ -1,4 +1,5 @@
-from sas.sascalc.shape2sas.Typing import *
+import numpy as np
+from sas.sascalc.shape2sas.Typing import Vector3D
 
 
 class Cube:

src/sas/sascalc/shape2sas/models/Cuboid.py

@@ -1,4 +1,5 @@
-from sas.sascalc.shape2sas.Typing import *
+import numpy as np
+from sas.sascalc.shape2sas.Typing import Vector3D
 
 
 class Cuboid: