Merge branch 'release'

465b · May 22, 2020 · 403f5b4 · 403f5b4
2 parents 21cede4 + 66e37c2
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diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,4 @@
 *.log
 *.egg-info
 *dist
+example_files/
diff --git a/configuration_files/micro_baltic_model_config.yml b/configuration_files/micro_baltic_model_config.yml
diff --git a/doc/releases/v0.3.0.md b/doc/releases/v0.3.0.md
@@ -0,0 +1,17 @@
+# v0.3.0 (May 2020)
+
+This is a major release introducing scipy's integration and optimization routines into the framework.
+
+## New forward modelling
+
+* Replaced the self written *time_integration* routine with *scipy.integrate.solve_ivp*.
+* Adjusted *forward_model* and plotting routines accordingly and introduced supporting functions.
+
+## New inverse modelling
+
+* Replaced the self written *gradient_descent* method with *scipy.optimize.minimize*.
+* Adjusted *inverse_model* and plotting routines accordingly and introduced supporting functions.
+
+## Visualization
+
+* Added *initial_guess* plotting function to visualize the model output before any optimization has been applied.
diff --git a/example_files/NPZD_oscillation_on_1990.csv b/example_files/NPZD_oscillation_on_1990.csv
diff --git a/configuration_files/exemplary_NPZD_model.yml → example_files/exemplary_NPZD_model.yml b/configuration_files/exemplary_NPZD_model.yml → example_files/exemplary_NPZD_model.yml
@@ -9,87 +9,91 @@
 # List of all present compartments in the model.
 compartment:
   N:              # name of the compartment
-    value: 1.0    # initial value of the compartment
+    value:  1     # initial value of the compartment
     optimise:     # if the above value shall not be optimized, this remains empty
-      lower: 0    # if not, lower and
+      lower: 1.0e-9    # if not, lower and
       upper: 2    # upper constraints must be defined 
   P:
-    value: 1.0
+    value: 1 #.20835024e+00
     optimise:
-      lower: 0
+      lower: 1.0e-9
       upper: 2
   Z:
-    value: 1.0
+    value: 1 #8.84333950e-01
     optimise:
-      lower: 0
+      lower: 1.0e-9
       upper: 2
   D:
-    value: 0
+    value: 1 # 8.57333742e-01
     optimise:
-      lower: 0
+      lower: 1.0e-9
       upper: 2
 
 # List of all interactions/flows between compartments
 interactions:
   # Note, that the functions are automatically multiplied by the current value
   # of the secondly named compartment 
 
-  N:P:                              # names of the interacting compartments
+  P:N:                              # names of the interacting compartments
   - fkt: nutrition_limited_growth   # name of the type of interaction 
-    sign: '-1'                      # direction of flow (from P to N in this case)
     parameters:                     # list of parameters required for interaction
     - 'N'                           # Parameters can also be other compartments
     - 0.27
     - 0.7
     optimise:                       # whether or not some of these parameters
                                     # shall be optimized
-  P:Z:
+  Z:P:
   - fkt: holling_type_III
-    sign: '-1'
     parameters:
     - 'P'
-    - 1.6
-    - 1.575 
+    - 0.02
+    - 0.575 
     optimise:
+      - parameter_no: 2
+        lower: 0.015
+        upper: 0.025
+      - parameter_no: 3
+        lower: 0.5
+        upper: 0.6
   D:P:
   - fkt: linear_mortality
-    sign: '+1'
     parameters:
+    - 'P'
     - 0.04
     optimise:
   D:Z:
   - fkt: linear_mortality
-    sign: '+1'
     parameters:
+    - 'Z'
     - 0.01
     optimise:
   N:D:
   - fkt: remineralisation
-    sign: '+1'
     parameters:
-    - 0.048
+    - 'D'
+    - 0.148
     optimise:
 
 
 # list of details for the forward and inverse modelling modules
 configuration:
   # time evolution / forward modelling
-  integration_scheme: euler_forward
-  time_evo_max: 300
-  dt_time_evo: 0.1
-  ode_coeff_model: interaction_model_generator
-  # convergence criteria for forward and inverse modelling
-  stability_rel_tolerance: 1.0e-3
-  tail_length_stability_check: 10
-  start_stability_check: 50
+  time_evo_max: 1000
+  dt_time_evo: 1
+
+  # optional keys:
+  # --------------
+
+  # integration_scheme: euler_forward
+
   # fitting - details for the inverse modelling
-  fit_model: direct_fit_model
-  fit_target: [1.,0.5,1.,0.1]
-  # sinks and sources 
-  ## models are expected to conserve their model currency/quantity.
-  ## if something enters or leave the model they should be labled here
-  sources: null
-  sinks: null
-  ## if not null then this may look for example like:
-  ## sources: 'N'
-  ## sinks: 'D'
+  fit_data_path: 'example_files/NPZD_oscillation_on_1990.csv'
+
+  ## sinks and sources 
+  # models are expected to conserve their model currency/quantity.
+  # if something enters or leave the model they should be labled here
+  # if not null then this may look for example like:
+  # sources: 'N'
+  # sinks: 'D'
+  # sources: null
+  # sinks: null
diff --git a/examples.py b/examples.py
@@ -4,7 +4,7 @@
 import gemf
 
 # provide the path of model/system configuration
-path = ('configuration_files/exemplary_NPZD_model.yml')
+path = ('example_files/exemplary_NPZD_model.yml')
 
 # load the model configuration
 model_config = gemf.model_class(path)
@@ -19,7 +19,6 @@
 
 
 # if the model shall be fitted as well call:
-output_dict = gemf.inverse_model(model_config,
-    sample_sets=1, gd_max_iter=100, grad_scale=1e-1)
+output_dict = gemf.inverse_model(model_config)
 # to plot the results:
 gemf.output_summary(output_dict)
diff --git a/gemf/__init__.py b/gemf/__init__.py
@@ -10,7 +10,6 @@
 
 from gemf.caller import forward_model as forward_model 
 from gemf.caller import inverse_model as inverse_model
-from gemf.caller import time_evolution as time_evolution
 
 from gemf.plot import output_summary as output_summary
 from gemf.plot import interaction_graph as interaction_graph