feat: Convert arrays back to confs

Author: zmitchell

fmo_analysis/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '0.17.1'
+__version__ = '0.17.2'
 
 import ham2spec

fmo_analysis/exciton.py

@@ -62,6 +62,21 @@ def confs_to_arrays(confs: List[Dict]) -> Tuple[np.ndarray, np.ndarray, np.ndarr
     return hams, mus, rs
 
 
+def arrays_to_confs(hams: np.ndarray, mus: np.ndarray, rs: np.ndarray):
+    """Convert arrays to a list of confs"""
+    n_confs, n_pigs, _ = hams.shape
+    confs = list()
+    for i in range(n_confs):
+        ham = hams[i]
+        mus_single = mus[i]
+        rs_single = rs[i]
+        pigs = list()
+        for j in range(n_pigs):
+            pigs.append(Pigment(rs_single[j], mus_single[j]))
+        confs.append({"ham": ham, "pigs": pigs})
+    return confs
+
+
 def stick_spectrum(config, ham, pigs):
     """Computes the stick spectra and eigenvalues/eigenvectors for the system."""
     mus, rs = pigs_to_arrays(pigs)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fmo_analysis"
-version = "0.17.1"
+version = "0.17.2"
 description = ""
 authors = ["Zach Mitchell <zmitchell@fastmail.com>"]
 

tests/test_computation.py

@@ -1,6 +1,7 @@
 from fmo_analysis import exciton, util
 import numpy.testing as npt
 from pytest import raises
+from numpy.random import random
 
 
 def test_can_construct_config():
@@ -163,4 +164,14 @@ def test_computes_het_broadened_spectrum_from_hams(config, ham, pigments, abs, c
 
 def test_broadened_spec_isnt_readonly(config, stick_spec):
     b_spec = exciton.broadened_spectrum_from_stick(config, stick_spec)
-    b_spec["abs"] *= 0
+    b_spec["abs"] *= 0
+
+
+def test_array_to_conf_conversion():
+    dummy_hams = random(size=(100, 8, 8))
+    dummy_mus = random(size=(100, 8, 3))
+    dummy_rs = random(size=(100, 8, 3))
+    hams, mus, rs = exciton.confs_to_arrays(exciton.arrays_to_confs(dummy_hams, dummy_mus, dummy_rs))
+    npt.assert_array_almost_equal(dummy_hams, hams, decimal=4)
+    npt.assert_array_almost_equal(dummy_mus, mus, decimal=4)
+    npt.assert_array_almost_equal(dummy_rs, rs, decimal=4)