funcnodes-span 0.3.0__tar.gz → 0.3.1__tar.gz

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: funcnodes-span
-Version: 0.3.0
+Version: 0.3.1
 Summary: Spectral Peak ANalysis (SPAN) for funcnodes
 License: MIT
 Author: Kourosh Rezaei

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/funcnodes_span/__init__.py

@@ -7,7 +7,7 @@ from .baseline import BASELINE_NODE_SHELF as BASELINE
 from funcnodes_lmfit import NODE_SHELF as LMFIT_NODE_SHELF
 from .curves import CURVES_NODE_SHELF
 
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 
 NODE_SHELF = fn.Shelf(
     name="Spectral Analysis",

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/funcnodes_span/_curves.py

@@ -47,7 +47,7 @@ def knee_point_detection(x, y) -> Tuple[int, float, float]:
 
 
 def estimate_noise(
-    x, y, is_baseline_region: Optional[np.ndarray] = None, std_factor=3
+    x, y, is_baseline_region: Optional[np.ndarray] = None, std_factor: float = 3
 ) -> float:
     """
     Estimate the noise level in a signal.

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/funcnodes_span/curves.py

@@ -16,6 +16,6 @@ estimate_noise_node = fn.NodeDecorator(
 CURVES_NODE_SHELF = fn.Shelf(
     nodes=[knee_point_detection_node, estimate_noise_node],
     subshelves=[],
-    name="Smoothing",
-    description="Smoothing of the spectra",
+    name="Curves",
+    description="Analysis of curves and spectra",
 )

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/funcnodes_span/fitting.py

@@ -5,6 +5,12 @@ from lmfit.model import ModelResult
 from lmfit.models import GaussianModel
 from .peaks import PeakProperties
 from funcnodes_lmfit.model import AUTOMODELMAP
+import funcnodes as fn
+
+AutoModelEnum = fn.DataEnum("AutoModelEnum", AUTOMODELMAP)
+# class AutoModelEnum(fn.DataEnum):
+#     GaussianModel = AUTOMODELMAP["GaussianModel"]
+#     LorentzianModel = AUTOMODELMAP["LorentzianModel"]
 
 
 def group_signals(
@@ -106,11 +112,11 @@ def fit_local_peak(
         Model: The fitted model for the peak.
     """
 
-    if isinstance(model_class, str):
-        model_class = AUTOMODELMAP[model_class]
+    x = np.asarray(x)
+    y = np.asarray(y)
 
-    if isinstance(incomplete_peak_model_class, str):
-        incomplete_peak_model_class = AUTOMODELMAP[incomplete_peak_model_class]
+    model_class = AutoModelEnum.v(model_class)
+    incomplete_peak_model_class = AutoModelEnum.v(incomplete_peak_model_class)
 
     pf = f"p{peak.id}_"
     model = model_class(prefix=pf)  # Initialize the model
@@ -129,11 +135,8 @@ def fit_local_peak(
     if peak.yfull is None:
         peak.yfull = y
 
-    if isinstance(model_class, str):
-        model_class = AUTOMODELMAP[model_class]
-
-    if isinstance(incomplete_peak_model_class, str):
-        incomplete_peak_model_class = AUTOMODELMAP[incomplete_peak_model_class]
+    model_class = AutoModelEnum.v(model_class)
+    incomplete_peak_model_class = AutoModelEnum.v(incomplete_peak_model_class)
 
     if np.abs(yf[-1] - yf[0]) > incomplete_threshold * (local_max - local_min):
         # Handle incomplete peak by extending the range and filling gaps
@@ -226,11 +229,11 @@ def fit_peak_group(
         Model: The fitted model for the group of peaks.
     """
 
-    if isinstance(model_class, str):
-        model_class = AUTOMODELMAP[model_class]
+    x = np.asarray(x)
+    y = np.asarray(y)
 
-    if isinstance(incomplete_peak_model_class, str):
-        incomplete_peak_model_class = AUTOMODELMAP[incomplete_peak_model_class]
+    model_class = AutoModelEnum.v(model_class)
+    incomplete_peak_model_class = AutoModelEnum.v(incomplete_peak_model_class)
 
     groupmodel = None
     most_left = min([p.i_index for p in peaks])  # Find the leftmost index in the group
@@ -278,12 +281,12 @@ def fit_peaks(
     peaks: List[PeakProperties],
     x: np.ndarray,
     y: np.ndarray,
-    model_class: Type[Model] = GaussianModel,
+    model_class: AutoModelEnum = AutoModelEnum.GaussianModel,
     filter_negatives: bool = True,
     baseline_factor: float = 0.001,
     incomplete_threshold: float = 0.8,
     incomplete_x_extend: float = 2.0,
-    incomplete_peak_model_class: Type[Model] = GaussianModel,
+    incomplete_peak_model_class: AutoModelEnum = AutoModelEnum.GaussianModel,
     iter_cb=None,
 ) -> Tuple[List[PeakProperties], Model, ModelResult]:
     """
@@ -337,11 +340,10 @@ def fit_peaks(
     Returns:
         Model: The fitted model for the global signal.
     """
-    if isinstance(model_class, str):
-        model_class = AUTOMODELMAP[model_class]
-
-    if isinstance(incomplete_peak_model_class, str):
-        incomplete_peak_model_class = AUTOMODELMAP[incomplete_peak_model_class]
+    model_class = AutoModelEnum.v(model_class)
+    incomplete_peak_model_class = AutoModelEnum.v(incomplete_peak_model_class)
+    x = np.asarray(x)
+    y = np.asarray(y)
 
     if len(peaks) == 0:
         raise ValueError("No peaks provided for fitting.")
@@ -381,3 +383,25 @@ def fit_peaks(
         peak.model = get_submodel_by_prefix(global_model, f"p{peak.id}_")
 
     return peaks, global_model, global_fit
+
+
+def peaks_from_fitted(fitted_peaks: List[PeakProperties]) -> List[PeakProperties]:
+    peaks = []
+    from .peak_analysis import peak_finder  # noaq Avoid circular import
+
+    for p in fitted_peaks:
+        model = p.model
+        mparams = model.make_params()
+        y = model.eval(x=p.xfull, params=mparams)
+        pf: List[PeakProperties] = peak_finder.o_func(y=y, x=p.xfull)[0]
+        if len(pf) != 1:
+            raise ValueError("Expected one peak")
+        pf = pf[0]
+        pf._id = f"fitted_{p.id}"
+        pf.model = model
+        p.add_serializable_property("model", str(model))
+        for k, v in mparams.items():
+            p.add_serializable_property(k.replace(model.prefix, ""), v.value)
+        peaks.append(pf)
+
+    return peaks

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/funcnodes_span/peak_analysis.py

@@ -12,7 +12,13 @@ import plotly.graph_objs as go
 from .normalization import density_normalization
 from .peaks import PeakProperties
 
-from .fitting import fit_peaks, AUTOMODELMAP, fit_local_peak
+from .fitting import fit_peaks, AUTOMODELMAP, fit_local_peak, peaks_from_fitted
+
+# make enum from AUTOMODELMAP
+AutoModelEnum = fn.DataEnum(
+    "AutoModelEnum",
+    AUTOMODELMAP,
+)
 
 
 @NodeDecorator(
@@ -547,18 +553,47 @@ fit_peak_node = fn.NodeDecorator(
     id="span.peaks.fit_peak",
     name="Fit Peak",
     outputs=[{"name": "fitted_peak"}, {"name": "model"}, {"name": "fit_result"}],
-    # separate_process=True,
+    separate_process=True,
 )(fit_local_peak)
 
+
 fit_peaks_node = fn.NodeDecorator(
     id="span.peaks.fit_peaks",
     name="Fit Peaks",
     outputs=[{"name": "fitted_peaks"}, {"name": "model"}, {"name": "fit_results"}],
-    default_io_options={
-        "modelname": {"value_options": {"options": list(AUTOMODELMAP.keys())}},
-    },
-    separate_process=True,
+    # separate_process=True,
 )(fit_peaks)
+# @fn.controlled_wrapper(fit_peaks, wrapper_attribute="__fnwrapped__")
+# def fit_peaks_node(
+#     peaks: List[PeakProperties],
+#     x: np.ndarray,
+#     y: np.ndarray,
+#     model_class: AutoModelEnum = AutoModelEnum.v("GaussianModel"),
+#     filter_negatives: bool = True,
+#     baseline_factor: float = 0.001,
+#     incomplete_threshold: float = 0.8,
+#     incomplete_x_extend: float = 2.0,
+#     incomplete_peak_model_class: AutoModelEnum = AutoModelEnum.v("GaussianModel"),
+# ) -> Tuple[List[PeakProperties], Model, ModelResult]:
+#     return fit_peaks(
+#         peaks,
+#         x,
+#         y,
+#         model_class=AutoModelEnum.v(model_class),
+#         filter_negatives=filter_negatives,
+#         baseline_factor=baseline_factor,
+#         incomplete_threshold=incomplete_threshold,
+#         incomplete_x_extend=incomplete_x_extend,
+#         incomplete_peak_model_class=AutoModelEnum.v(incomplete_peak_model_class),
+#     )
+
+
+peaks_from_fitted_node = fn.NodeDecorator(
+    id="span.peaks.peaks_from_fitted",
+    name="Peaks from fitted",
+    description="converts the fit data in peaks to regular peaks",
+    outputs=[{"name": "peaks"}],
+)(peaks_from_fitted)
 
 PEAKS_NODE_SHELF = Shelf(
     nodes=[
@@ -568,6 +603,7 @@ PEAKS_NODE_SHELF = Shelf(
         plot_peaks,
         fit_peaks_node,
         fit_peak_node,
+        peaks_from_fitted_node,
         plot_fitted_peaks,
         plot_peak,
     ],

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/funcnodes_span/smoothing.py

@@ -93,12 +93,14 @@ def _smooth(
 
     if mode not in _SMOOTHING_MAPPER.keys():
         raise ValueError(f"Unsupported smoothing mode: {mode}")
-
+    y = np.asarray(y)
     if x is not None:
+        x = np.asarray(x)
         med_xdiff = np.nanmedian(np.diff(x))
         window = window / med_xdiff
     window = int(window)
-
+    if window == 0:
+        return y.copy()
     return _SMOOTHING_MAPPER[mode](y, window)
 
 

{funcnodes_span-0.3.0 → funcnodes_span-0.3.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "funcnodes-span"
-version = "0.3.0"
+version = "0.3.1"
 description = "Spectral Peak ANalysis (SPAN) for funcnodes"
 authors = ["Kourosh Rezaei <kouroshrezaei90@gmail.com>"]
 readme = "README.md"
@@ -28,7 +28,7 @@ funcnodes-lmfit = "*"
 [tool.poetry.group.dev.dependencies]
 pytest = "*"
 pre-commit = "*"
-funcnodes-module = "*"
+funcnodes-module = "^0.1.19"
 pooch = "*"