guts-base 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

guts_base/__init__.py

@@ -4,7 +4,7 @@ from . import data
 from . import prob
 from . import plot
 
-__version__ = "1.0.6"
+__version__ = "1.0.8"
 
 from .sim import (
     GutsBase,

guts_base/data/openguts.py

@@ -251,6 +251,8 @@ def import_data_to_database(path, database, preprocessing: Optional[Callable] =
     
     experiment.to_database(database=database)
 
+    print("Import to database successful.")
+
 
 def create_database_and_import_data_main(datasets_path, database_path, preprocessing=None, preprocessing_out=None):
     print("\n")

guts_base/data/time_of_death.py

@@ -225,7 +225,7 @@ def make_openguts_observation_table(
     experiment_start = get_unique_value(df["time_start_experiment"])
     experiment_end = get_unique_value(df["time_end_experiment"])
 
-    time = pd.date_range(experiment_start, experiment_end, freq=observation_schedule)
+    times_nominal = pd.date_range(experiment_start, experiment_end, freq=observation_schedule)
     timecol_name = f"time [{observation_schedule.lower()}]"
 
 
@@ -234,13 +234,17 @@ def make_openguts_observation_table(
     # calculate survival time
     df[timecol_name] = df["time_death"] - df["time_start_experiment"]
 
-    time_remainder = df[timecol_name] % pd.Timedelta(1, observation_schedule)
-    if (time_remainder > pd.Timedelta(0)).any():
-        raise ValueError(
-            "Observations should be entered at the same time as the experiment start "+
-            "df['time_death] - df['time_experiment_start'] should be a multiple of "+
-            f"the time resolution of the observation schedule. Here: 1{observation_schedule}"
-        )
+    # this seems to have been necessary, because reindexing removed times smaller than
+    # the observation_schedule interval. This is now resolved by concatenating true
+    # times and nominal times
+    # TODO: remove this commented block when there appear no more errors
+    # time_remainder = df[timecol_name] % pd.Timedelta(1, observation_schedule)
+    # if (time_remainder > pd.Timedelta(0)).any():
+    #     raise ValueError(
+    #         "Observations should be entered at the same time as the experiment start "+
+    #         "df['time_death] - df['time_experiment_start'] should be a multiple of "+
+    #         f"the time resolution of the observation schedule. Here: 1{observation_schedule}"
+    #     )
 
     if observation == "censored":
         # sum IDs that were marked as censored at time t
@@ -258,8 +262,12 @@ def make_openguts_observation_table(
     # df to wide frame
     df_wide = long_to_wide(df_long.reset_index(), id_columns, timecol_name, observation)
     
+    # get a time vector that contains all nominal observation times and also actually
+    # occurred days 
+    observation_times = np.unique(np.concatenate([df_wide.index, times_nominal-experiment_start]))
+
     # reindex wide dataframe on time
-    df_wide = df_wide.reindex(index=time-experiment_start, method=None)
+    df_wide = df_wide.reindex(index=observation_times, method=None)
     df_wide.index = df_wide.index.set_names(timecol_name)
     df_wide = df_wide.fillna(0)
 
@@ -299,8 +307,10 @@ class TimeOfDeathIO:
         self.data = self.from_file()
 
 def main(file: str, sheet: str, out:str, intervention_columns: List[str], 
+         extra_observation_columns: List[str] = [],
          observation_schedule="d", rect_interpolate=False):
     intervention_columns = clean_column_names(list(intervention_columns))
+    extra_observation_columns = clean_column_names(list(extra_observation_columns))
     processed_file = f"{out}/openguts_{os.path.basename(file)}"
     
     print("\n")
@@ -454,6 +464,17 @@ def main(file: str, sheet: str, out:str, intervention_columns: List[str],
         observation_schedule=observation_schedule,
     )
 
+    _extra_observations = []
+    for eob in extra_observation_columns:
+        ob_wide = make_openguts_observation_table(
+            data,
+            observation=eob,
+            observation_schedule=observation_schedule
+        )
+        _extra_observations.append(ob_wide)
+        excel_writer(ob_wide, file=processed_file, sheet=eob)
+
+
     deaths = lethality - censored
 
     # excel export
@@ -537,6 +558,7 @@ def main(file: str, sheet: str, out:str, intervention_columns: List[str],
     else:
         warnings.warn("No metadata found in sheets 'meta' or 'Info'.")
 
+    return processed_file
 
 @click.command()
 @click.option("--file", "-f", help="Path to the xlsx file")
@@ -544,12 +566,14 @@ def main(file: str, sheet: str, out:str, intervention_columns: List[str],
 @click.option("--out", "-o", help="Output directory", default="processed_data")
 @click.option("--observation_schedule", help="Schedule of the observations: d - daily, h - hourly", default="d")
 @click.option("--intervention_columns", "-c", multiple=True, type=str, help="Names of the columns that carry the exposure information")
-def time_of_death_to_openguts(file, sheet, out, observation_schedule, intervention_columns):
-    main(
+@click.option("--extra_observation_columns", "-e", multiple=True, type=str, default=[], help="Names of the columns that carry additional observations beside time-of-death and censoring")
+def time_of_death_to_openguts(file, sheet, out, observation_schedule, intervention_columns, extra_observation_columns):
+    _ = main(
         file=file, 
         sheet=sheet, 
         out=out, 
         intervention_columns=intervention_columns,
+        extra_observation_columns=extra_observation_columns,
         observation_schedule=observation_schedule
     )
 

guts_base/sim/base.py

@@ -49,6 +49,10 @@ class GutsBase(SimulationBase):
     results_interpolation: Tuple[float,float,int] = (np.nan, np.nan, 100)
     _skip_data_processing: bool = False
     ecx_mode: Literal["mean", "draws"] = "mean"
+    exposure_scenarios = {
+        "acute_1day": {"start": 0.0, "end": 1.0},
+        "chronic": {"start": 0.0, "end": None},
+    }
 
     def initialize(self, input: Optional[Dict] = None):
         """Initiaization goes through a couple of steps:
@@ -99,6 +103,8 @@ class GutsBase(SimulationBase):
         self.unit_time: Literal["day", "hour", "minute", "second"] = "day"
         if hasattr(self.config.simulation, "unit_time"):
             self.unit_time = self.config.simulation.unit_time  # type: ignore
+        else:
+            self.config.simulation.unit_time = self.unit_time
 
         if hasattr(self.config.simulation, "skip_data_processing"):
             self._skip_data_processing = not (
@@ -254,8 +260,9 @@ class GutsBase(SimulationBase):
                 observations=self.observations
             )
 
-        if "exposure" in self.observations:
-            self.config.data_structure.exposure.observed=False
+        if "exposure" not in self.observations:
+            self.observations["exposure"] = self.observations[self.config.simulation.substance]
+        self.config.data_structure.exposure.observed=False
 
     def _convert_exposure_units(self):
         """
@@ -485,21 +492,26 @@ class GutsBase(SimulationBase):
         for coord in exposure_coordinates:
             concentrations = np.where(coord == exposure_coordinates, 1.0, 0.0)
 
-            exposure_dict = {
-                coord: ExposureDataDict(start=0, end=1, concentration=conc)
-                for coord, conc in zip(exposure_coordinates, concentrations)
-            }
-
-            scenario = design_exposure_scenario(
-                exposures=exposure_dict,
-                t_max=time_max,
-                dt=1/24,
-                exposure_dimension=exposure_dimension
-            )
+            for _name, _expo_scenario in self.exposure_scenarios.items():
+                exposure_dict = {
+                    coord: ExposureDataDict(
+                        start=_expo_scenario["start"], 
+                        end=_expo_scenario["end"], 
+                        concentration=conc
+                    )
+                    for coord, conc in zip(exposure_coordinates, concentrations)
+                }
+
+                scenario = design_exposure_scenario(
+                    exposures=exposure_dict,
+                    t_max=time_max,
+                    dt=1/24,
+                    exposure_dimension=exposure_dimension
+                )
 
-            scenarios.update({
-                f"1day_exposure_{coord}": scenario
-            })
+                scenarios.update({
+                    f"{_name}_{coord}": scenario
+                })
 
         return scenarios
 

guts_base/sim/report.py

@@ -23,12 +23,13 @@ class GutsReport(Report):
     table_parameter_stat_focus = "mean"
     units = xr.Dataset({
         "metric": ["unit"],
-        "k_d": ("metric", ["1/t"])
+        "k_d": ("metric", ["1/T"])
     })
 
 
     def additional_reports(self, sim: "SimulationBase"):
         super().additional_reports(sim=sim)
+        self.model_input(sim)
         self.model_fits(sim)
         self.LCx_estimates(sim)
 
@@ -246,6 +247,7 @@ def flatten_coords(dataset: xr.Dataset, keep_dims):
     producing a array with harmonized dimensions
     """
     ds = dataset.copy()
+    ds = ds.reset_coords(drop=True)
     for var_name, data_var in ds.data_vars.items():
         extra_coords = [k for k in list(data_var.coords.keys()) if k not in keep_dims]
         if len(extra_coords) == 0:

{guts_base-1.0.6.dist-info → guts_base-1.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: guts_base
-Version: 1.0.6
+Version: 1.0.8
 Summary: Basic GUTS model implementation in pymob
 Author-email: Florian Schunck <fluncki@protonmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{guts_base-1.0.6.dist-info → guts_base-1.0.8.dist-info}/RECORD

@@ -1,25 +1,25 @@
-guts_base/__init__.py,sha256=mqsDPsRl9TvFmIRICGE6wDPG-d1TEAzO0Sj1Rfurl5A,227
+guts_base/__init__.py,sha256=YhfEv2scUmsDc-3-9-MK3-xNQJ_tIRQndJaQHDDDl8U,227
 guts_base/mod.py,sha256=AzOCg1A8FP5EtVfp-66HT7G7h_wnHkenieaxTc9qCyk,5796
 guts_base/plot.py,sha256=Sr_d0sXHNajPLPelcGl72yCOEEqB7NGNWhViKYAiTng,6692
 guts_base/prob.py,sha256=ITwo5dAGMHr5xTldilHMbKU6AFsWo4_ZwbfaXh97Gew,5443
 guts_base/data/__init__.py,sha256=JBgft1DTledwvB5hRZnyGiKWv-RXo1OIpb5kJXloOmo,826
 guts_base/data/expydb.py,sha256=Kcc6CeZMl3oEelk5UBN9VEfwgNF3CzTh13ooVkufAjE,8218
 guts_base/data/generator.py,sha256=rGOZU3B0Ho8V6KtfjcAmely8lnlqNFV8cRyGboayTRc,2910
-guts_base/data/openguts.py,sha256=WvhYl_AOdvNgzrcVS2f_PYbXNH_wSAz2uIBSR6BMSh0,11078
+guts_base/data/openguts.py,sha256=7C2wknBQBVxOYVgBL9UzuC9PEoqI2xaVp2pOyZwaIqY,11123
 guts_base/data/preprocessing.py,sha256=qggYkx2x62ingU1BNhJFyL1eQdFQsDJR2lefVfVWW2U,1732
 guts_base/data/survival.py,sha256=U-Ehloo8vnD81VeIglXLEUHX9lt7SjtEs2YEB0D9FHE,5096
-guts_base/data/time_of_death.py,sha256=hwngUwfRP3u8WmD3dHyXrphuu5d8ZJTKyBovGRwAHNQ,21014
+guts_base/data/time_of_death.py,sha256=dHG5jhK--WkemTxJtHVgfdo-FWlFHslBQ0PcYape9fI,22296
 guts_base/data/utils.py,sha256=u3gGDJK15MfRUP4iIxsS-I1oqxD2qH_ugsT7o_Eac18,236
 guts_base/sim/__init__.py,sha256=sbHmT1p2saN0MJ-iYnCDOHjkHtTcKgm7X-dHX5o0tYA,435
-guts_base/sim/base.py,sha256=xd4VroOS7KM8Ap7hYGaD85hB3n_8IT8GuEvecYu3TnE,37549
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 guts_base/sim/constructors.py,sha256=Kz9FHIH3EHsSIKd9sQgHa3eveniFifFlk1Hf-QR69Pg,875
 guts_base/sim/ecx.py,sha256=PeX8UVF1HMMNHaIU-jL6dml4JGezhWwiGSqPFJbOFM4,20808
 guts_base/sim/mempy.py,sha256=IHd87UrmdXpC7y7q0IjYQJH075frjbp2a-dMVBeqZ0U,10164
-guts_base/sim/report.py,sha256=o19MBhKcwty2auPjYWoz4QY91jjJFkA80UTzUuZo1oE,12720
+guts_base/sim/report.py,sha256=NmrnU8Xr1LKKg5ObdjSXaQ8a-Dv8k8xC8oq_EKDbgMo,12786
 guts_base/sim/utils.py,sha256=Qj_FPH6kywVxOwgCerS7w5CyuYR9HKmvBWFpmxwDFgk,256
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-guts_base-1.0.6.dist-info/RECORD,,
+guts_base-1.0.8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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