Changeset 1219 for framspy

Timestamp:

04/17/23 01:50:13 (21 months ago)

Author:

Maciej Komosinski

Message:

Less misleading parameter and variable name (library vs. module)

File:

• framspy/dissimilarity/density-distribution.py (modified) (4 diffs)

framspy/dissimilarity/density-distribution.py

@@ -8 +8 @@
     libm = cdll.LoadLibrary(find_library('m'))
     EPSILON = 0.0001
-    def __init__(self, FramsLib=None, density = 10, steps = 3, reduce=True, frequency=False, metric = 'emd', fixedZaxis=False, verbose=False):
+    def __init__(self, frams_module=None, density = 10, steps = 3, reduce=True, frequency=False, metric = 'emd', fixedZaxis=False, verbose=False):
         """ __init__
         Args:
@@ -20 +20 @@
             verbose (bool, optional): Turning on logging, works only for calculateEMDforGeno. Defaults to False.            
         """
-        if FramsLib == None:
-            raise ValueError('Frams library not provided!')
-        self.frams_lib = FramsLib
+        if frams_module is None:
+            raise ValueError('Framsticks module not provided!')
+        self.frams = frams_module
 
         self.density = density
@@ -220 +220 @@
             np.array([np.array(,dtype=float)]: list of voxels representing model.
         """
-        model = self.frams_lib.Model.newFromString(geno)
+        model = self.frams.Model.newFromString(geno)
         align(model, self.fixedZaxis)
-        model_geometry = self.frams_lib.ModelGeometry.forModel(model)
+        model_geometry = self.frams.ModelGeometry.forModel(model)
 
         model_geometry.geom_density = self.density
@@ -296 +296 @@
 
     def calculateDissimforGeno(self, geno1, geno2):
-        """Calculates EMD for pair of genos.
+        """Calculates EMD for a pair of genotypes.
         Args:
             geno1 (string): representation of model1 in one of the formats handled by frams http://www.framsticks.com/a/al_genotype.html