Added DecayParallelMegacomplex.

glotaran/builtin/megacomplexes/decay/__init__.py

@@ -1,4 +1,7 @@
 from glotaran.builtin.megacomplexes.decay.decay_megacomplex import DecayMegacomplex
+from glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex import (
+    DecayParallelMegacomplex,
+)
 from glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex import (
     DecaySequentialMegacomplex,
 )

glotaran/builtin/megacomplexes/decay/decay_parallel_megacomplex.py

@@ -0,0 +1,40 @@
+"""This package contains the decay megacomplex item."""
+from __future__ import annotations
+
+from typing import List
+
+import numpy as np
+
+from glotaran.builtin.megacomplexes.decay.decay_megacomplex_base import DecayMegacomplexBase
+from glotaran.builtin.megacomplexes.decay.irf import Irf
+from glotaran.builtin.megacomplexes.decay.k_matrix import KMatrix
+from glotaran.model import DatasetModel
+from glotaran.model import megacomplex
+from glotaran.parameter import Parameter
+
+
+@megacomplex(
+    dimension="time",
+    properties={
+        "compartments": List[str],
+        "rates": List[Parameter],
+    },
+    dataset_model_items={
+        "irf": {"type": Irf, "allow_none": True},
+    },
+    register_as="decay-parallel",
+)
+class DecayParallelMegacomplex(DecayMegacomplexBase):
+    def get_compartments(self, dataset_model: DatasetModel) -> list[str]:
+        return self.compartments
+
+    def get_initial_concentration(self, dataset_model: DatasetModel) -> np.ndarray:
+        return np.ones((len(self.compartments)), dtype=np.float64)
+
+    def get_k_matrix(self) -> KMatrix:
+        size = len(self.compartments)
+        k_matrix = KMatrix()
+        k_matrix.matrix = {
+            (self.compartments[i], self.compartments[i]): self.rates[i] for i in range(size)
+        }
+        return k_matrix

glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py

@@ -9,7 +9,6 @@
 from glotaran.model import Model
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Scheme
-from glotaran.testing.model_generators import SimpleModelGenerator
 
 
 def _create_gaussian_clp(labels, amplitudes, centers, widths, axis):
@@ -124,15 +123,56 @@ class OneComponentOneChannelGaussianIrf:
 
 
 class ThreeComponentParallel:
-    generator = SimpleModelGenerator(
-        rates=[300e-3, 500e-4, 700e-5],
-        irf={"center": 1.3, "width": 7.8},
-        k_matrix="parallel",
+    model = DecayModel.from_dict(
+        {
+            "megacomplex": {
+                "mc1": {
+                    "type": "decay-parallel",
+                    "compartments": ["s1", "s2", "s3"],
+                    "rates": [
+                        "kinetic.1",
+                        "kinetic.2",
+                        "kinetic.3",
+                    ],
+                },
+            },
+            "irf": {
+                "irf1": {
+                    "type": "multi-gaussian",
+                    "center": ["irf.center"],
+                    "width": ["irf.width"],
+                },
+            },
+            "dataset": {
+                "dataset1": {
+                    "irf": "irf1",
+                    "megacomplex": ["mc1"],
+                },
+            },
+        }
     )
-    model, initial_parameters = generator.model_and_parameters
 
-    generator.rates = [301e-3, 502e-4, 705e-5]
-    wanted_parameters = generator.parameters
+    initial_parameters = ParameterGroup.from_dict(
+        {
+            "kinetic": [
+                ["1", 501e-3],
+                ["2", 202e-4],
+                ["3", 105e-5],
+                {"non-negative": True},
+            ],
+            "irf": [["center", 1.3], ["width", 7.8]],
+        }
+    )
+    wanted_parameters = ParameterGroup.from_dict(
+        {
+            "kinetic": [
+                ["1", 501e-3],
+                ["2", 202e-4],
+                ["3", 105e-5],
+            ],
+            "irf": [["center", 1.3], ["width", 7.8]],
+        }
+    )
 
     time = np.arange(-10, 100, 1.5)
     pixel = np.arange(600, 750, 10)