Closes #128 & clean up for loading results in om.Extractor

oslocyclotronlab · May 19, 2020 · 32572d5 · 32572d5
1 parent 5b669d0
commit 32572d5
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Showing 6 changed files with 39 additions and 64 deletions.
diff --git a/ompy/abstract_normalizer.py b/ompy/abstract_normalizer.py
@@ -8,7 +8,7 @@
 
 
 class AbstractNormalizer():
-    """ Abstract class for Matrix and Vector.
+    """ Abstract class for Normalizers.
 
         Do not initialize itself.
 

diff --git a/ompy/ensemble.py b/ompy/ensemble.py
@@ -76,7 +76,7 @@ class Ensemble:
     def __init__(self, raw: Optional[Matrix] = None,
                  bg: Optional[Matrix] = None,
                  bg_ratio: float = 1,
-                 path: Optional[Union[str, Path]] = None):
+                 path: Optional[Union[str, Path]] = 'saved_run/ensemble'):
         """ Sets up attributes and loads a saved ensemble if provided.
 
         Args:
@@ -97,7 +97,8 @@ def __init__(self, raw: Optional[Matrix] = None,
         self.prompt_w_bg: Optional[Matrix] = raw
 
         self.unfolder: Optional[Callable[[Matrix], Matrix]] = None
-        self.first_generation_method: Optional[Callable[[Matrix], Matrix]] = None
+        self.first_generation_method: \
+            Optional[Callable[[Matrix], Matrix]] = None
         self.size = 0
         self.regenerate = False
         self.action_prompt_w_bg = Action('matrix')
@@ -117,9 +118,11 @@ def __init__(self, raw: Optional[Matrix] = None,
         self.seed: int = 987654
         self.nprocesses: int = cpu_count()-1 if cpu_count() > 1 else 1
 
-        self.path = (Path(path) if path is not None
-                     else Path('saved_run/normalizers'))
-        self.path.mkdir(exist_ok=True, parents=True)
+        if path is None:
+            self.path = None
+        else:
+            self.path = Path(path)
+            self.path.mkdir(exist_ok=True, parents=True)
 
         self.raw.state = "raw"
 
@@ -133,6 +136,7 @@ def load(self, path: Optional[Union[str, Path]] = None):
                 value is None, 'self.path' will be used.
         """
         path = Path(path) if path is not None else Path(self.path)
+        LOG.info(f"loading from {path}")
 
         self.raw = Matrix(path=path / 'raw.npy')
         self.firstgen = Matrix(path=path / 'firstgen.npy')
@@ -238,7 +242,7 @@ def step(self, step: int, rsequence: np.random.SeedSequence,
         Returns:
             raw, unfolded, firstgen
         """
-        LOG.info(f"Generating {step}")
+        LOG.info(f"Generating/loading {step}")
         rstate = np.random.default_rng(rsequence)
         if self.bg is not None:
             prompt_w_bg = self.generate_perturbed(step, method,
@@ -281,14 +285,10 @@ def generate_perturbed(self, step: int, method: str, state: str,
         allowed = ["raw", "prompt+bg", "bg"]
         if state not in allowed:
             raise NotImplementedError(f"Matrix must be a state in {allowed}")
-        LOG.debug(f"Generating {state} ensemble {step}")
+        LOG.debug(f"Working on {state} ensemble {step}")
         path = self.path / f"{state}_{step}.npy"
         mat = self.load_matrix(path)
         if mat is None:
-            # if np.any(self.mat.values < 0):
-            #     raise ValueError("input matrix has to have positive"
-            #                      "entries only. Consider using fill and or"
-            #                      "remove negatives")
             LOG.debug(f"(Re)generating {path} using {method} process")
             if method == 'gaussian':
                 values = self.generate_gaussian(state, rstate)

diff --git a/ompy/ensembleNormalizer.py b/ompy/ensembleNormalizer.py
@@ -67,7 +67,7 @@ def __init__(self, *, extractor: Extractor,
                  normalizer_nld: Optional[NormalizerNLD] = None,
                  normalizer_gsf: Optional[NormalizerGSF] = None,
                  normalizer_simultan: Optional[NormalizerSimultan] = None,
-                 path: Optional[Union[str, Path]] = None,
+                 path: Optional[Union[str, Path]] = 'saved_run/normalizers',
                  regenerate: bool = False):
         """
         Args:
@@ -89,9 +89,11 @@ def __init__(self, *, extractor: Extractor,
 
         self.res: Optional[List[ResultsNormalized]] = None
 
-        self.path = (Path(path) if path is not None
-                     else Path('saved_run/normalizers'))
-        self.path.mkdir(exist_ok=True, parents=True)
+        if path is None:
+            self.path = None
+        else:
+            self.path = Path(path)
+            self.path.mkdir(exist_ok=True, parents=True)
 
     def normalize(self) -> None:
         """ Normalize ensemble """
@@ -623,7 +625,6 @@ def save_results_txt(self, path: Optional[Union[str, Path]] = None,
         path = Path(path) if path is not None else Path(self.path)
         path.mkdir(exist_ok=True, parents=True)
         for i, res in enumerate(self.res):
-
             super().save_results_txt(path, nld=res.nld, gsf=res.gsf,
                                      samples=res.samples, suffix=i)
 

diff --git a/ompy/extractor.py b/ompy/extractor.py
@@ -67,7 +67,8 @@ class Extractor:
     """
     def __init__(self, ensemble: Optional[Ensemble] = None,
                  trapezoid: Optional[Action] = None,
-                 path: Optional[Union[str, Path]] = None):
+                 path: Optional[Union[str, Path]] =
+                 'saved_run/extractor'):
         """
         ensemble (Ensemble, optional): see above
         trapezoid (Action[Matrix], optional): see above
@@ -81,12 +82,10 @@ def __init__(self, ensemble: Optional[Ensemble] = None,
         self.gsf: List[Vector] = []
         self.trapezoid = trapezoid
 
-        if path is not None:
-            self.path = Path(path)
-            self.path.mkdir(exist_ok=True, parents=True)
-            self.load(self.path)
+        if path is None:
+            self.path = None
         else:
-            self.path = Path('saved_run/extraction_ensemble')
+            self.path = Path(path)
             self.path.mkdir(exist_ok=True, parents=True)
 
         self.x0 = None
@@ -132,7 +131,7 @@ def extract_from(self, ensemble: Optional[Ensemble] = None,
             raise ValueError("A 'trapezoid' cut must be given'")
         if regenerate is None:
             regenerate = self.regenerate
-        self.path = Path(self.path)  # TODO: Fix
+        self.path = Path(self.path)
 
         nlds = []
         gsfs = []
@@ -141,6 +140,7 @@ def extract_from(self, ensemble: Optional[Ensemble] = None,
             nld_path = self.path / f'nld_{i}.npy'
             gsf_path = self.path / f'gsf_{i}.npy'
             if nld_path.exists() and gsf_path.exists() and not regenerate:
+                LOG.debug(f"loading from {nld_path} and {gsf_path}")
                 nlds.append(Vector(path=nld_path))
                 gsfs.append(Vector(path=gsf_path))
             else:
@@ -489,37 +489,6 @@ def fFWHM(E, p):
         fwhm_pars = np.array([73.2087, 0.50824, 9.62481e-05])
         return fFWHM(matrix.Ex, fwhm_pars)
 
-    def load(self, path: Optional[Union[str, Path]] = None) -> None:
-        """ Load already extracted nld and gsf from file
-
-        Args:
-            path: The path to the directory containing the
-                files.
-        """
-        if path is not None:
-            path = Path(path)
-        else:
-            path = Path(self.path)  # TODO: Fix pathing
-        LOG.debug("Loading from %s", path)
-
-        if not path.exists():
-            raise IOError(f"The path {path} does not exist.")
-        if self.nld or self.gsf:
-            warnings.warn("Loading nld and gsf into non-empty instance")
-
-        for fname in path.glob("nld_[0-9]*.npy"):
-            self.nld.append(Vector(path=fname))
-
-        for fname in path.glob("gsf_[0-9]*.npy"):
-            self.gsf.append(Vector(path=fname))
-
-        assert len(self.nld) == len(self.gsf), "Corrupt files"
-
-        if not self.nld:
-            warnings.warn("Found no files")
-
-        self.size = len(self.nld)
-
     def plot(self, ax: Optional[Any] = None, scale: str = 'log',
              plot_mean: bool = False,
              color='k', **kwargs) -> None:

diff --git a/ompy/normalizer_gsf.py b/ompy/normalizer_gsf.py
@@ -49,7 +49,7 @@ def __init__(self, *, normalizer_nld: Optional[NormalizerNLD] = None,
                  nld_model: Optional[Callable[..., Any]] = None,
                  alpha: Optional[float] = None,
                  gsf: Optional[Vector] = None,
-                 path: Optional[Union[str, Path]] = None,
+                 path: Optional[Union[str, Path]] = 'saved_run/normalizers',
                  regenerate: bool = False,
                  norm_pars: Optional[NormalizationParameters] = None,
                  ) -> None:
@@ -71,7 +71,8 @@ def __init__(self, *, normalizer_nld: Optional[NormalizerNLD] = None,
 
         Args:
             normalizer_nld (Optional[NormalizerNLD], optional): NormalizerNLD
-                to retrieve parameters. If `nld` and/or `nld_model` are not set, they are taken from `normalizer_nld.res` in `normalize`.
+                to retrieve parameters. If `nld` and/or `nld_model` are not
+                set, they are taken from `normalizer_nld.res` in `normalize`.
             nld (Optional[Vector], optional): NLD. If not set it is taken from
                 `normalizer_nld.res` in `normalize`.
             nld_model (Optional[Callable[..., Any]], optional): Model for nld
@@ -115,9 +116,11 @@ def __init__(self, *, normalizer_nld: Optional[NormalizerNLD] = None,
         self._saved_spincutPars = None
         self._saved_SpinSum_args = None
 
-        self.path = (Path(path) if path is not None
-                     else Path('saved_run/normalizers'))
-        self.path.mkdir(exist_ok=True, parents=True)
+        if path is None:
+            self.path = None
+        else:
+            self.path = Path(path)
+            self.path.mkdir(exist_ok=True, parents=True)
 
     def normalize(self, *, gsf: Optional[Vector] = None,
                   normalizer_nld: Optional[NormalizerNLD] = None,

diff --git a/ompy/normalizer_simultan.py b/ompy/normalizer_simultan.py
@@ -55,7 +55,7 @@ def __init__(self, *,
                  nld: Optional[Vector] = None,
                  normalizer_nld: Optional[NormalizerNLD] = None,
                  normalizer_gsf: Optional[NormalizerGSF] = None,
-                 path: Optional[Union[str, Path]] = None,
+                 path: Optional[Union[str, Path]] = 'saved_run/normalizers',
                  regenerate: bool = False):
         """
         TODO:
@@ -91,9 +91,11 @@ def __init__(self, *,
         self.multinest_path: Optional[Path] = Path('multinest')
         self.multinest_kwargs: dict = {"seed": 65498, "resume": False}
 
-        self.path = (Path(path) if path is not None
-                     else Path('saved_run/normalizers'))
-        self.path.mkdir(exist_ok=True, parents=True)
+        if path is None:
+            self.path = None
+        else:
+            self.path = Path(path)
+            self.path.mkdir(exist_ok=True, parents=True)
 
     def normalize(self, *, num: int = 0,
                   gsf: Optional[Vector] = None,