Rename to AGILE

.coveragerc

@@ -1,5 +1,5 @@
 [run]
-source = combine1d
+source = agile1d
 omit =
     */tests/*
     */_version.py

.github/workflows/build-docker.yml

@@ -35,7 +35,7 @@ jobs:
       id: push-image
       uses: OGGM/docker-build-and-push-action@v2
       with:
-        only_on_repo: OGGM/COMBINE
+        only_on_repo: OGGM/AGILE
         user: ${{ github.actor }}
         pass: ${{ github.token }}
         registry: ghcr.io

README.md

@@ -1,10 +1,10 @@
-# COMBINE
-COMBINE - COst Minimization Bed INvErsion model for ice caps and valley glaciers
+# AGILE
+AGILE - Open Global Glacier Data Assimilation Framework
 
 Work in progress!
 
-This project is an adaption/extension to [OGGM](https://github.com/OGGM/oggm) and utilizes its dynamical model together with backwards functionalities (Automatic/Algorithmic Differentiation) of [PyTorch](https://pytorch.org/) to enable a cost function based inversion of bedrock topography.
+This project is an adaption/extension to [OGGM](https://github.com/OGGM/oggm) and utilizes its dynamical model together with backwards functionalities (Automatic/Algorithmic Differentiation) of [PyTorch](https://pytorch.org/) to enable a cost function based assimilation.
 
-COMBINE2D is based on a dynamical 2D Shallow-Ice-Approximation model, using surface outlines, surface topography, surface mass-balance time series and optionally also existing ice thickness measurements for ice caps. For further information look at the [master thesis](https://diglib.uibk.ac.at/ulbtirolhs/content/titleinfo/3086935/full.pdf) of @phigre ([Repository stage of master thesis](https://github.com/OGGM/COMBINE/tree/04aa57353f72f272a264be5a4c683ffa7dc5bf0f)).
+agile2D (previously called combine2d) is based on a dynamical 2D Shallow-Ice-Approximation model, using surface outlines, surface topography, surface mass-balance time series and optionally also existing ice thickness measurements for ice caps. For further information look at the [master thesis](https://diglib.uibk.ac.at/ulbtirolhs/content/titleinfo/3086935/full.pdf) of @phigre ([Repository stage of master thesis](https://github.com/OGGM/agile/tree/04aa57353f72f272a264be5a4c683ffa7dc5bf0f)).
 
-COMBINE1D is based on a dynamical 1D or flowline model, using flowline surface heights and widths as well as surface mass-balance time series for valley glaciers. For further information look at the [master thesis](https://diglib.uibk.ac.at/ulbtirolhs/content/titleinfo/6139027/full.pdf) of @pat-schmitt ([Repository stage of master thesis](https://github.com/OGGM/COMBINE/tree/bf2f7372787adf3e4f31ba5fd56e8968b9fb3347)).
+agile1D (previously called combine1d) is based on a dynamical 1D or flowline model, using flowline surface heights and widths as well as surface mass-balance time series for valley glaciers. For further information look at the [master thesis](https://diglib.uibk.ac.at/ulbtirolhs/content/titleinfo/6139027/full.pdf) of @pat-schmitt ([Repository stage of master thesis](https://github.com/OGGM/agile/tree/bf2f7372787adf3e4f31ba5fd56e8968b9fb3347)).

combine1d/core/cost_function.py → agile1d/core/cost_function.py

@@ -5,9 +5,9 @@
 import time
 from functools import partial
 
-from combine1d.core.dynamics import run_model_and_get_temporal_model_data
-from combine1d.core.massbalance import ConstantMassBalanceTorch, MBModelTorchWrapper
-from combine1d.core.flowline import MixedBedFlowline, FluxBasedModel
+from agile1d.core.dynamics import run_model_and_get_temporal_model_data
+from agile1d.core.massbalance import ConstantMassBalanceTorch, MBModelTorchWrapper
+from agile1d.core.flowline import MixedBedFlowline, FluxBasedModel
 from oggm.core.flowline import MixedBedFlowline as OggmFlowline
 from oggm.core.massbalance import MonthlyTIModel, ConstantMassBalance
 from oggm import cfg
@@ -221,7 +221,7 @@ def cost_fct(unknown_parameters, data_logger):
         Unknown parameter values for the optimisation variable (ice part of
         the glacier). For simultaneously optimisation of two variables contains
         both unknown variables consecutively.
-    data_logger : :py:class:`combine.core.data_logging.DataLogger`
+    data_logger : :py:class:`agile.core.data_logging.DataLogger`
         Keep track of all variables during the calculation.
 
     Returns
@@ -881,7 +881,7 @@ def detach_flowline(final_fl_in):
         bed_h=final_fl_in.bed_h.detach().to('cpu').numpy().astype(np.float64),
         section=final_fl_in.section.detach().to('cpu').numpy().astype(np.float64),
         bed_shape=final_fl_in.bed_shape.detach().to('cpu').numpy().astype(np.float64),
-        # here we need 'logical_or' as COMBINE separates rectangular and
+        # here we need 'logical_or' as agile separates rectangular and
         # trapezoidal whereas OGGM do not separate
         is_trapezoid=np.logical_or(
             final_fl_in.is_trapezoid.detach().to('cpu').numpy().astype(bool),

combine1d/core/data_logging.py → agile1d/core/data_logging.py

@@ -5,9 +5,9 @@
 import numpy as np
 import xarray as xr
 import time
-from combine1d.core.arithmetics import RMSE, mean_BIAS, max_dif
-from combine1d.core.exception import MaxCalculationTimeReached
-from combine1d.core.flowline import FluxBasedModel, SemiImplicitModel
+from agile1d.core.arithmetics import RMSE, mean_BIAS, max_dif
+from agile1d.core.exception import MaxCalculationTimeReached
+from agile1d.core.flowline import FluxBasedModel, SemiImplicitModel
 import os
 import warnings
 import copy
@@ -117,7 +117,7 @@ def __init__(self, gdir, fls_init, inversion_input, climate_filename,
             self.is_rectangular = self.flowline_init.is_rectangular
             self.is_parabolic = ~self.flowline_init.is_trapezoid
         else:
-            raise TypeError('COMBINE 1D only works with MixedBedFlowline!')
+            raise TypeError('agile 1D only works with MixedBedFlowline!')
 
         self.climate_filename = climate_filename
         self.climate_filesuffix = climate_filesuffix
@@ -338,11 +338,11 @@ def create_and_save_dataset(self):
         #     b = pickle.load(handle)
 
 
-def initialise_DataLogger(gdir, inversion_input_filesuffix='_combine',
+def initialise_DataLogger(gdir, inversion_input_filesuffix='_agile',
                           init_model_filesuffix=None,
                           init_model_fls='_trapezoidal',
                           climate_filename='climate_historical',
-                          climate_filesuffix='', output_filesuffix='_combine',
+                          climate_filesuffix='', output_filesuffix='_agile',
                           output_filepath=None):
     '''
     extract information out of gdir and save in datalogger. TODO
@@ -362,7 +362,7 @@ def initialise_DataLogger(gdir, inversion_input_filesuffix='_combine',
         fls_init = copy.deepcopy(init_model_fls)
 
     if len(fls_init) > 1:
-        raise NotImplementedError('COMBINE only works with single flowlines!')
+        raise NotImplementedError('agile only works with single flowlines!')
 
     # include check if inversion_input file exist
     if not os.path.isfile(gdir.get_filepath('inversion_input',

combine1d/core/flowline.py → agile1d/core/flowline.py

@@ -23,7 +23,7 @@
 from oggm.core.flowline import FlowlineModel as FlowlineModelOGGM
 
 # help function for gradient calculation
-from combine1d.core.special_gradient_functions import para_width_from_thick,\
+from agile1d.core.special_gradient_functions import para_width_from_thick,\
     para_thick_from_section, SolveBandedPyTorch
 
 # Constants
@@ -833,7 +833,7 @@ def run_until_and_store(self, y1,
 
 
 class RectangularBedDiffusiveFlowlineModel(FlowlineModelTorch):
-    """A rectangular bed diffusive model, not used in the Thesis of COMBINE1D.
+    """A rectangular bed diffusive model, not used in the Thesis of agile1D.
     The actual model, only valid for RectangularBedFlowline"""
 
     def __init__(self, flowlines, mb_model=None, y0=0., glen_a=None, fs=0.,
@@ -861,7 +861,7 @@ def __init__(self, flowlines, mb_model=None, y0=0., glen_a=None, fs=0.,
             raise ValueError('Model does not work with tributaries.')
 
         # TODO: check if RectangularBedFlowline
-        # if type(self.fls[0]) == combine.core.flowline_adapted.RectangularBedFlowline:
+        # if type(self.fls[0]) == agile.core.flowline_adapted.RectangularBedFlowline:
         #    raise TypeError('Only can use RectangularBedFlowline')
 
         self.dt_warning = False,
@@ -1105,7 +1105,7 @@ def step(self, dt):
         if (dt_use != dt) and (dt_use / self.max_dt < 0.0001):
             raise MemoryError('Stopping dynamics run to avoid memory overflow')
 
-        # get massbalance with COMBINE MassBalanceModel
+        # get massbalance with agile MassBalanceModel
         m_dot = self.get_mb(S,
                             year=self.yr,
                             fl_id=0)  # 0 because only one flowline

combine1d/core/inversion.py → agile1d/core/inversion.py

@@ -5,19 +5,19 @@
 import time
 
 # External libs
-from combine1d.core.dynamics import run_model_and_get_model_values
-from combine1d.core.flowline import MixedBedFlowline
+from agile1d.core.dynamics import run_model_and_get_model_values
+from agile1d.core.flowline import MixedBedFlowline
 from scipy.optimize import minimize, Bounds
 import numpy as np
 
 # Locals
 from oggm import utils, cfg, workflow, tasks, entity_task
 from oggm.cfg import G
-from combine1d.core.cost_function import create_cost_fct, initialise_mb_models, \
+from agile1d.core.cost_function import create_cost_fct, initialise_mb_models, \
     initialise_flowline, do_height_shift_spinup
-from combine1d.core.data_logging import initialise_DataLogger
-from combine1d.core.exception import MaxCalculationTimeReached
-from combine1d.core.first_guess import get_first_guess
+from agile1d.core.data_logging import initialise_DataLogger
+from agile1d.core.exception import MaxCalculationTimeReached
+from agile1d.core.first_guess import get_first_guess
 
 # Module logger
 log = logging.getLogger(__name__)
@@ -200,8 +200,8 @@ def add_setting():
     _key = "experiment_description"
     _doc = "Explanation of the current experiment. If a dataset is saved this" \
            "is the filename of the resulting nc datafile. " \
-           "Default: 'COMBINE_inversion_results'"
-    _default = 'COMBINE_inversion_results'
+           "Default: 'agile_inversion_results'"
+    _default = 'agile_inversion_results'
     add_setting()
 
     _key = "spinup_options"
@@ -228,7 +228,7 @@ def add_setting():
            "control variable (with constant dx also can be considered as " \
            " initial volume distribution), it is similar to 'surface_h' option " \
            "but also takes grid cells of different sizes into account. It " \
-           "should be combined with a regularisation term which smoothes the " \
+           "should be agiled with a regularisation term which smoothes the " \
            "initial ice flux. With 'extra_grid_points' you can define how " \
            "many grid points you want to allow an advance/retreat of the " \
            "glacier at the inital state." \
@@ -291,8 +291,8 @@ def add_setting():
 
 
 @entity_task(log, writes=['inversion_input'])
-def prepare_for_combine_inversion(gdir, inversion_settings=None,
-                                  filesuffix='_combine'):
+def prepare_for_agile_inversion(gdir, inversion_settings=None,
+                                  filesuffix='_agile'):
     """TODO
     """
     if inversion_settings is None:
@@ -458,10 +458,10 @@ def save_past_evolution_to_disk(gdir, data_logger):
 
 
 @entity_task(log, writes=['model_flowlines'])
-def combine_inversion(gdir, inversion_input_filesuffix='_combine',
+def agile_inversion(gdir, inversion_input_filesuffix='_agile',
                       init_model_filesuffix=None, init_model_fls='_trapezoidal',
                       climate_filename='climate_historical',
-                      climate_filesuffix='', output_filesuffix='_combine_output',
+                      climate_filesuffix='', output_filesuffix='_agile_output',
                       output_filepath=None, save_dataset=True,
                       give_data_logger_back=False, save_past_evolution=True):
     """TODO
@@ -527,7 +527,7 @@ def combine_inversion(gdir, inversion_input_filesuffix='_combine',
 
     gdir.write_pickle(data_logger.flowlines[-1], 'model_flowlines',
                       filesuffix=output_filesuffix)
-    log.debug('Combine Inversion finished')
+    log.debug('agile Inversion finished')
 
     if give_data_logger_back:
         return data_logger

combine1d/core/massbalance.py → agile1d/core/massbalance.py

@@ -6,11 +6,11 @@
 from oggm.utils import SuperclassMeta, ncDataset
 from oggm.utils._funcs import date_to_floatyear, floatyear_to_date
 
-# packages for COMBINE
+# packages for agile
 import torch
 
 # help functions
-from combine1d.core.torch_interp1d import Interp1d
+from agile1d.core.torch_interp1d import Interp1d
 
 # other stuff
 from functools import partial

combine1d/core/utils.py → agile1d/core/utils.py

@@ -14,7 +14,7 @@
 from oggm.utils import GlacierDirectory, mkdir
 from oggm.utils._funcs import multipolygon_to_polygon
 from oggm.exceptions import InvalidParamsError
-from combine2d.core.data_logging import write_pickle, load_pickle
+from agile2d.core.data_logging import write_pickle, load_pickle
 # TODO: move pickle methods
 
 
@@ -24,7 +24,7 @@ class InversionGlacierDirectory(GlacierDirectory):
 
     def __init__(self, rgi_entity, base_dir=None, reset=False, from_tar=False, delete_tar=False):
         """
-        Initializes the glacier directory for COMBINE
+        Initializes the glacier directory for agile
 
         TODO
         """
@@ -33,7 +33,7 @@ def __init__(self, rgi_entity, base_dir=None, reset=False, from_tar=False, delet
 
         # add aditional BASENAMES used by the Inversion
         cfg.add_to_basenames('inversion_settings', 'inversion_settings.pkl', 'Contains the needed information for the '
-                                                                             'COMBINE inversion. TODO: doc needed '
+                                                                             'agile inversion. TODO: doc needed '
                                                                              'information')
 
 

combine1d/sandbox/calculate_statistics.py → agile1d/sandbox/calculate_statistics.py

@@ -68,7 +68,7 @@ def calculate_result_statistics(gdir, data_logger, print_statistic=False):
             ds.unknown_parameters[-1][control_indices[control_var]].values
     controls_true = {}
     fls_true = gdir.read_pickle('model_flowlines',
-                                filesuffix='_combine_true_init')[0]
+                                filesuffix='_agile_true_init')[0]
     for control_var in controls_mdl:
         if control_var in ['bed_h', 'area_bed_h']:
             controls_true[control_var] = \
@@ -149,7 +149,7 @@ def get_volume(fl):
     with xr.open_dataset(fp) as ds_diag:
         past_evol_mdl = ds_diag.load()
     fp = gdir.get_filepath('model_diagnostics',
-                           filesuffix='_combine_true_total_run')
+                           filesuffix='_agile_true_total_run')
     with xr.open_dataset(fp) as ds_diag:
         past_evol_true = ds_diag.load()
 
@@ -164,7 +164,7 @@ def get_volume(fl):
     # how well do we match today's glacier state ------------------------------
     fls_end_mdl = data_logger.flowlines[-1]
     fls_end_true = gdir.read_pickle('model_flowlines',
-                                    filesuffix='_combine_true_end')[0]
+                                    filesuffix='_agile_true_end')[0]
 
     today_state_stats = {}
     for var in ['thick', 'area_m2', 'volume_m3']:
@@ -195,7 +195,7 @@ def get_volume(fl):
     with xr.open_dataset(fp) as ds_diag:
         future_evol_mdl = ds_diag.load()
     fp = gdir.get_filepath('model_diagnostics',
-                           filesuffix='_combine_true_future')
+                           filesuffix='_agile_true_future')
     with xr.open_dataset(fp) as ds_diag:
         future_evol_true = ds_diag.load()
 
@@ -291,7 +291,7 @@ def calculate_default_oggm_statistics(gdir):
 
         # how well do we match the observations -------------------------------
         obs_given = gdir.read_pickle('inversion_input',
-                                     filesuffix='_combine_measurements')
+                                     filesuffix='_agile_measurements')
         obs_stats = {}
         for obs_key in obs_given.keys():
             obs_stats[obs_key] = {}
@@ -373,9 +373,9 @@ def calculate_default_oggm_statistics(gdir):
         controls_mdl = {}
         controls_true = {}
         fls_mdl = gdir.read_pickle('model_flowlines',
-                                   filesuffix='_combine_first_guess')[0]
+                                   filesuffix='_agile_first_guess')[0]
         fls_true = gdir.read_pickle('model_flowlines',
-                                    filesuffix='_combine_true_init')[0]
+                                    filesuffix='_agile_true_init')[0]
 
         for control_var in all_control_vars:
             if control_var in ['bed_h', 'area_bed_h']:
@@ -434,7 +434,7 @@ def get_volume(fl):
         # how well do we match the past glacier evolution ---------------------
         past_evol_mdl = diag_past
         fp = gdir.get_filepath('model_diagnostics',
-                               filesuffix='_combine_true_total_run')
+                               filesuffix='_agile_true_total_run')
         with xr.open_dataset(fp) as ds_diag:
             past_evol_true = ds_diag.load()
 
@@ -449,7 +449,7 @@ def get_volume(fl):
         # how well do we match today's glacier state --------------------------
         fls_end_mdl = fl_diag_past.sel(time=fl_diag_past.time[-1])
         fls_end_true = gdir.read_pickle('model_flowlines',
-                                        filesuffix='_combine_true_end')[0]
+                                        filesuffix='_agile_true_end')[0]
 
         today_state_stats = {}
         for var in ['thick', 'area_m2', 'volume_m3']:
@@ -479,7 +479,7 @@ def get_volume(fl):
         # how well do we match the future glacier evolution -------------------
         future_evol_mdl = diag_future
         fp = gdir.get_filepath('model_diagnostics',
-                               filesuffix='_combine_true_future')
+                               filesuffix='_agile_true_future')
         with xr.open_dataset(fp) as ds_diag:
             future_evol_true = ds_diag.load()