Merge pull request #496 from PEtab-dev/prepare_new_release

Release 0.1.14

Author: dweindl

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 ## 0.1 series
 
+### 0.1.14
+
+* Fix sampling of priors in `parameterScale` (#492)
+* Clarify documentation of `parameterScale` priors
+* Improvements in `petab.simulate` (#479):
+  * Fix default noise distributions
+  * Add option for non-negative synthetic data
+
 ### 0.1.13
 
 * Fix for pandas 1.2.0 -- use `get_handle` instead of `get_filepath_or_buffer`

doc/documentation_data_format.rst

@@ -537,6 +537,9 @@ Detailed field description
 
   Prior parameters used for sampling of initial points for optimization,
   separated by a semicolon. Defaults to ``lowerBound;upperBound``.
+  The parameters are expected to be in linear scale except for the
+  ``parameterScale`` priors, where the prior parameters are expected to be
+  in parameter scale.
 
   So far, only numeric values will be supported, no parameter names.
   Parameters for the different prior types are:

petab/parameters.py

@@ -343,7 +343,8 @@ def get_priors_from_df(parameter_df: pd.DataFrame,
         # if no prior is specified, we assume a non-informative (uniform) one
         if prior_type == 'nan':
             prior_type = PARAMETER_SCALE_UNIFORM
-            prior_pars = (row[LOWER_BOUND], row[UPPER_BOUND])
+            prior_pars = (scale(row[LOWER_BOUND], par_scale),
+                          scale(row[UPPER_BOUND], par_scale))
 
         prior_list.append((prior_type, prior_pars, par_scale, par_bounds))
 

petab/simulate.py

@@ -1,3 +1,5 @@
+"""PEtab simulator base class and related functions."""
+
 import abc
 import numpy as np
 import pathlib
@@ -10,8 +12,8 @@
 
 
 class Simulator(abc.ABC):
-    """
-    Base class that specific simulators should inherit.
+    """Base class that specific simulators should inherit.
+
     Specific simulators should minimally implement the
     `simulate_without_noise` method.
     Example (AMICI): https://bit.ly/33SUSG4
@@ -32,10 +34,14 @@ class Simulator(abc.ABC):
             directory and its contents may be modified and deleted, and
             should be considered ephemeral.
     """
-    def __init__(self,
-                 petab_problem: petab.Problem,
-                 working_dir: Optional[Union[pathlib.Path, str]] = None):
-        """
+
+    def __init__(
+        self,
+        petab_problem: petab.Problem,
+        working_dir: Optional[Union[pathlib.Path, str]] = None,
+    ):
+        """Initialize the simulator.
+
         Initialize the simulator with sufficient information to perform a
         simulation. If no working directory is specified, a temporary one is
         created.
@@ -64,14 +70,16 @@ def __init__(self,
         self.rng = np.random.default_rng()
 
     def remove_working_dir(self, force: bool = False, **kwargs) -> None:
-        """
-        Remove the simulator working directory and all files within (see the
-        `__init__` method arguments).
+        """Remove the simulator working directory, and all files within.
+
+        See the `__init__` method arguments.
 
         Arguments:
             force:
                 If True, the working directory is removed regardless of
                 whether it is a temporary directory.
+            **kwargs:
+                Additional keyword arguments are passed to `shutil.rmtree`.
         """
         if force or self.temporary_working_dir:
             shutil.rmtree(self.working_dir, **kwargs)
@@ -85,17 +93,18 @@ def remove_working_dir(self, force: bool = False, **kwargs) -> None:
 
     @abc.abstractmethod
     def simulate_without_noise(self) -> pd.DataFrame:
-        """
-        Simulate a PEtab problem. This is an abstract method that should be
-        implemented in a simulation package. Links to examples of this are in
-        the class docstring.
+        """Simulate the PEtab problem.
+
+        This is an abstract method that should be implemented with a simulation
+        package. Examples of this are referenced in the class docstring.
 
         Returns:
             Simulated data, as a PEtab measurements table, which should be
             equivalent to replacing all values in the `petab.C.MEASUREMENT`
             column of the measurements table (of the PEtab problem supplied to
             the `__init__` method), with simulated values.
         """
+        raise NotImplementedError
 
     def simulate(
             self,
@@ -109,6 +118,9 @@ def simulate(
             noise: If True, noise is added to simulated data.
             noise_scaling_factor:
                 A multiplier of the scale of the noise distribution.
+            **kwargs:
+                Additional keyword arguments are passed to
+                `simulate_without_noise`.
 
         Returns:
             Simulated data, as a PEtab measurements table.
@@ -122,6 +134,7 @@ def add_noise(
             self,
             simulation_df: pd.DataFrame,
             noise_scaling_factor: float = 1,
+            **kwargs
     ) -> pd.DataFrame:
         """Add noise to simulated data.
 
@@ -130,6 +143,8 @@ def add_noise(
                 A PEtab measurements table that contains simulated data.
             noise_scaling_factor:
                 A multiplier of the scale of the noise distribution.
+            **kwargs:
+                Additional keyword arguments are passed to `sample_noise`.
 
         Returns:
             Simulated data with noise, as a PEtab measurements table.
@@ -143,6 +158,7 @@ def add_noise(
                 self.noise_formulas,
                 self.rng,
                 noise_scaling_factor,
+                **kwargs,
             )
             for _, row in simulation_df_with_noise.iterrows()
         ]
@@ -156,6 +172,7 @@ def sample_noise(
         noise_formulas: Optional[Dict[str, sp.Expr]] = None,
         rng: Optional[np.random.Generator] = None,
         noise_scaling_factor: float = 1,
+        zero_bounded: bool = False,
 ) -> float:
     """Generate a sample from a PEtab noise distribution.
 
@@ -176,6 +193,10 @@ def sample_noise(
             A NumPy random generator.
         noise_scaling_factor:
             A multiplier of the scale of the noise distribution.
+        zero_bounded:
+            Return zero if the sign of the return value and `simulated_value`
+            differ. Can be used to ensure non-negative and non-positive values,
+            if the sign of `simulated_value` should not change.
 
     Returns:
         The sample from the PEtab noise distribution.
@@ -200,9 +221,20 @@ def sample_noise(
         .loc[measurement_row[petab.C.OBSERVABLE_ID]]
         .get(petab.C.NOISE_DISTRIBUTION, petab.C.NORMAL)
     )
+    # an empty noise distribution column in an observables table can result in
+    # `noise_distribution == float('nan')`
+    if pd.isna(noise_distribution):
+        noise_distribution = petab.C.NORMAL
 
     # below is e.g.: `np.random.normal(loc=simulation, scale=noise_value)`
-    return getattr(rng, noise_distribution)(
+    simulated_value_with_noise = getattr(rng, noise_distribution)(
         loc=simulated_value,
         scale=noise_value * noise_scaling_factor
     )
+
+    if (
+            zero_bounded and
+            np.sign(simulated_value) != np.sign(simulated_value_with_noise)
+    ):
+        return 0.0
+    return simulated_value_with_noise

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = '0.1.13'
+__version__ = '0.1.14'

tests/test_simulate.py

@@ -65,15 +65,67 @@ def test_remove_working_dir(petab_problem):
     assert not pathlib.Path(simulator.working_dir).is_dir()
 
 
+def test_zero_bounded(petab_problem):
+    """Test `zero_bounded` argument of `sample_noise`."""
+    positive = np.spacing(1)
+    negative = -positive
+
+    simulator = TestSimulator(petab_problem)
+    # Set the random seed to ensure predictable tests.
+    simulator.rng = np.random.default_rng(seed=0)
+
+    # Set approximately half of the measurements to negative values, and the
+    # rest to positive values.
+    n_measurements = len(petab_problem.measurement_df)
+    neg_indices = range(round(n_measurements / 2))
+    pos_indices = range(len(neg_indices), n_measurements)
+    measurements = [
+        negative if index in neg_indices else
+        (positive if index in pos_indices else np.nan)
+        for index in range(n_measurements)
+    ]
+    synthetic_data_df = simulator.simulate().assign(**{
+        petab.C.MEASUREMENT: measurements
+    })
+    # All measurements are non-zero
+    assert (synthetic_data_df['measurement'] != 0).all()
+    # No measurements are NaN
+    assert not (np.isnan(synthetic_data_df['measurement'])).any()
+
+    synthetic_data_df_with_noise = simulator.add_noise(
+        synthetic_data_df,
+    )
+    # Both negative and positive values are returned by default.
+    assert all([
+        (synthetic_data_df_with_noise['measurement'] <= 0).any(),
+        (synthetic_data_df_with_noise['measurement'] >= 0).any(),
+    ])
+
+    synthetic_data_df_with_noise = simulator.add_noise(
+        synthetic_data_df,
+        zero_bounded=True,
+    )
+    # Values with noise that are different in sign to values without noise are
+    # zeroed.
+    assert all([
+        (synthetic_data_df_with_noise['measurement'][neg_indices] <= 0).all(),
+        (synthetic_data_df_with_noise['measurement'][pos_indices] >= 0).all(),
+        (synthetic_data_df_with_noise['measurement'][neg_indices] == 0).any(),
+        (synthetic_data_df_with_noise['measurement'][pos_indices] == 0).any(),
+        (synthetic_data_df_with_noise['measurement'][neg_indices] < 0).any(),
+        (synthetic_data_df_with_noise['measurement'][pos_indices] > 0).any(),
+    ])
+
+
 def test_add_noise(petab_problem):
     """Test the noise generating method."""
 
     tested_noise_distributions = {'normal', 'laplace'}
     assert set(petab.C.NOISE_MODELS) == tested_noise_distributions, (
         'The noise generation methods have only been tested for '
-        f'{tested_noise_distributions}. Please edit this test '
-        'to include this distribution in its tested distributions. The '
-        'appropriate SciPy distribution will need to be added to '
+        f'{tested_noise_distributions}. Please edit this test to include this '
+        'distribution in its tested distributions. The appropriate SciPy '
+        'distribution will need to be added to '
         '`petab_numpy2scipy_distribution` in `_test_add_noise`.'
     )
 
@@ -94,6 +146,8 @@ def _test_add_noise(petab_problem) -> None:
     }
 
     simulator = TestSimulator(petab_problem)
+    # Set the random seed to ensure predictable tests.
+    simulator.rng = np.random.default_rng(seed=0)
     synthetic_data_df = simulator.simulate()
 
     # Generate samples of noisy data
@@ -144,26 +198,30 @@ def row2cdf(row, index) -> Callable:
             getattr(
                 scipy.stats,
                 petab_numpy2scipy_distribution[
-                    expected_noise_distributions[index]]
-            ).cdf, loc=row[MEASUREMENT], scale=expected_noise_values[index])
+                    expected_noise_distributions[index]
+                ]
+            ).cdf,
+            loc=row[MEASUREMENT],
+            scale=expected_noise_values[index]
+        )
 
     # Test whether the distribution of the samples is equal to the expected
     # distribution, for each measurement.
     results = []
     for index, row in synthetic_data_df.iterrows():
-        r = scipy.stats.ks_1samp(
+        results.append(scipy.stats.ks_1samp(
             samples[:, index],
             row2cdf(row, index)
-        )
-        results.append(r)
+        ))
     observed_fraction_above_threshold = (
-        sum(r.pvalue > ks_1samp_pvalue_threshold for r in results) /
-        len(results)
+        sum(r.pvalue > ks_1samp_pvalue_threshold for r in results)
+        / len(results)
     )
     # Sufficient distributions of measurement samples are sufficiently similar
     # to the expected distribution
     assert (
-        observed_fraction_above_threshold > minimum_fraction_above_threshold)
+        observed_fraction_above_threshold > minimum_fraction_above_threshold
+    )
 
     simulator.remove_working_dir()
     assert not pathlib.Path(simulator.working_dir).is_dir()