Changeset 1220

Timestamp:

04/17/23 02:30:51 (13 months ago)

Author:

Maciej Komosinski

Message:

Added support for two more phenetic dissimilarity estimation methods, which compare the distributions of samples in the two phenotypes (bodies)

File:

• framspy/FramsticksLib.py (modified) (3 diffs)

framspy/FramsticksLib.py

@@ -41 +41 @@
 
         def __init__(self, frams_path, frams_lib_name, sim_settings_files):
+                self.dissim_measure_density_distribution = None  # will be initialized only when necessary (for rare dissimilarity methods)
+
                 if frams_lib_name is None:
                         frams.init(frams_path)  # could add support for setting alternative directories using -D and -d
@@ -148 +150 @@
         def dissimilarity(self, genotype_list: List[str], method: int) -> np.ndarray:
                 """
-                        :param method: -1 = genetic Levenshtein distance; 0, 1, 2 = phenetic dissimilarity (SimilMeasureGreedy, SimilMeasureHungarian, SimilMeasureDistribution)
+                        :param method: -1 = genetic Levenshtein distance; 0, 1, 2 = phenetic dissimilarity (SimilMeasureGreedy, SimilMeasureHungarian, SimilMeasureDistribution); -2, -3 = phenetic density distribution (count, frequency).
+                        See also prepareDissimilarityCalculation().
                         :return: A square array with dissimilarities of each pair of genotypes.
                 """
@@ -174 +177 @@
                                 for j in range(n):  # maybe calculate only one triangle if you really need a 2x speedup
                                         square_matrix[i][j] = Levenshtein.distance(genotype_list[i], genotype_list[j])
+                elif method in (-2, -3):
+                        if self.dissim_measure_density_distribution is None:
+                                from dissimilarity.densityDistribution import DensityDistribution
+                                self.dissim_measure_density_distribution = DensityDistribution(frams)
+                        self.dissim_measure_density_distribution.frequency = (method == -3)
+                        square_matrix = self.dissim_measure_density_distribution.getDissimilarityMatrix(genotype_list)
                 else:
-                        raise Exception("Don't know what to do with dissimilarity method = %d" % method)
+                        raise ValueError("Don't know what to do with dissimilarity method = %d" % method)
 
                 for i in range(n):