funcnodes-span 0.3.1__tar.gz → 0.3.3__tar.gz

{funcnodes_span-0.3.1 → funcnodes_span-0.3.3}/PKG-INFO

@@ -1,7 +1,7 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: funcnodes-span
-Version: 0.3.1
-Summary: Spectral Peak ANalysis (SPAN) for funcnodes
+Version: 0.3.3
+Summary: SPectral ANalysis (SPAN) for funcnodes
 License: MIT
 Author: Kourosh Rezaei
 Author-email: kouroshrezaei90@gmail.com
@@ -25,5 +25,5 @@ Project-URL: source, https://github.com/Linkdlab/funcnodes_span
 Project-URL: tracker, https://github.com/Linkdlab/funcnodes_span/issues
 Description-Content-Type: text/markdown
 
-Spectral Peak ANalysis (SPAN) for funcnodes
+SPectral ANalysis (SPAN) for funcnodes
 

funcnodes_span-0.3.3/README.md

@@ -0,0 +1 @@
+SPectral ANalysis (SPAN) for funcnodes

{funcnodes_span-0.3.1 → funcnodes_span-0.3.3}/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__ = "0.3.1"
+__version__ = "0.3.3"
 
 NODE_SHELF = fn.Shelf(
     name="Spectral Analysis",

{funcnodes_span-0.3.1 → funcnodes_span-0.3.3}/funcnodes_span/fitting.py

@@ -44,6 +44,7 @@ def group_signals(
     # Assign each peak to its respective group based on start and end indices
     for pi, p in enumerate(peaks):
         ingroup = (baseline_cut >= p.i_index) & (baseline_cut <= p.f_index)
+
         if ingroup.sum() == 0:
             ingroup[(baseline_cut >= p.i_index).argmax()] = True
 
@@ -63,6 +64,9 @@ def group_signals(
         else:
             current_peak_group.update(pg)
 
+    if len(current_peak_group) > 0:
+        connected_peaks.append(list(current_peak_group))
+
     # Return a list of grouped PeakProperties
     return [[peaks[pi] for pi in cp] for cp in connected_peaks if len(cp) > 0]
 
@@ -111,7 +115,6 @@ def fit_local_peak(
     Returns:
         Model: The fitted model for the peak.
     """
-
     x = np.asarray(x)
     y = np.asarray(y)
 
@@ -135,13 +138,11 @@ def fit_local_peak(
     if peak.yfull is None:
         peak.yfull = y
 
-    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
         m_complete = incomplete_peak_model_class()
         guess = m_complete.guess(data=yf, x=xf)
+        guess["center"].set(min=min(xf), max=max(xf))
         fr_complete = m_complete.fit(data=yf, x=xf, params=guess, iter_cb=iter_cb)
 
         fwhm = 2 * np.sqrt(2 * np.log(2)) * fr_complete.params["sigma"].value
@@ -350,10 +351,14 @@ def fit_peaks(
 
     # Group peaks based on the baseline factor
     connected_peaks = group_signals(x, y, peaks, baseline_factor=baseline_factor)
+    if len(connected_peaks) == 0:
+        raise ValueError("No peaks after grouping.")
 
     global_model = None
     # Fit each peak group
     for pg in connected_peaks:
+        if len(pg) == 0:
+            continue
         m = fit_peak_group(
             x,
             y,
@@ -371,6 +376,9 @@ def fit_peaks(
             # Combine models for all peak groups
             global_model += m
 
+    if global_model is None:
+        raise ValueError("No model created")
+
     # Fit the global model to the full data
     global_fit = global_model.fit(data=y, x=x, iter_cb=iter_cb)
 

{funcnodes_span-0.3.1 → funcnodes_span-0.3.3}/funcnodes_span/peak_analysis.py

@@ -2,7 +2,7 @@ from funcnodes import NodeDecorator, Shelf
 import funcnodes as fn
 import numpy as np
 from exposedfunctionality import controlled_wrapper
-from typing import Optional, List, Tuple, Union
+from typing import Optional, List, Tuple
 from scipy.signal import find_peaks
 from scipy.stats import norm
 from scipy import signal, interpolate
@@ -223,32 +223,32 @@ def interpolation_1d(
 def force_peak_finder(
     x: np.array,
     y: np.array,
-    basic_peaks: Union[List[PeakProperties], PeakProperties],
+    basic_peak: PeakProperties,
 ) -> List[PeakProperties]:
-    # """
-    # Identify and return the two peaks around the main peak in the given peaks dictionary.
-
-    # Parameters:
-    # - peaks (dict): A dictionary containing peak information.
-    #                 It should have the keys 'peaks' and 'data'.
-    #                 'peaks' should contain a list of dictionaries with keys 'Initial index', 'Index',
-    #                  and 'Ending index'.
-    #                 'data' should contain arrays 'x' and 'y'.
-
-    # Returns:
-    # - dict: A dictionary containing information about the two identified peaks.
-    # """
-    if isinstance(basic_peaks, (list, np.ndarray, tuple)):
-        if len(basic_peaks) != 1:
-            raise ValueError(
-                "This method accepts one and only one main peak as an input."
-            )
-        basic_peaks = basic_peaks[0]
+    """
+    Breaks down a given main peak into two individual peaks.
+
+    The function works by calculating the first and second derivatives of the signal and
+    finding the local maxima and minima of the derivatives. It then determines which peak
+    is on the left and right side of the main peak by comparing the distance between the
+    main peak and the closest peak on either side.
+
+    Parameters:
+    - x (np.array): The x-values of the signal.
+    - y (np.array): The y-values of the signal.
+    - basic_peak (PeakProperties): The main peak.
+
+    Returns:
+    - List[PeakProperties]: A list of two PeakProperties objects, one for each of the
+      individual peaks.
+    """
+    if not isinstance(basic_peak, PeakProperties):
+        raise TypeError("The basic peak must be a single PeakProperties object.")
 
-    peaks = copy.deepcopy(basic_peaks)
-    main_peak_i_index = peaks.i_index
-    main_peak_r_index = peaks.index
-    main_peak_f_index = peaks.f_index
+    peak = copy.deepcopy(basic_peak)
+    main_peak_i_index = peak.i_index
+    main_peak_r_index = peak.index
+    main_peak_f_index = peak.f_index
     y_array = y
     x_array = x
     # Calculate first and second derivatives
@@ -266,9 +266,9 @@ def force_peak_finder(
     max_pp = signal.argrelmax(y_array_pp)[0]
     # min_pp = signal.argrelmin(y_array_pp)[0]
 
-    # main_peak_i_index = peaks.i_index
-    # main_peak_r_index = peaks.index
-    # main_peak_f_index = peaks.f_index
+    # main_peak_i_index = peak.i_index
+    # main_peak_r_index = peak.index
+    # main_peak_f_index = peak.f_index
 
     # Determine which peak is on the left and right side of the main peak
     if (
@@ -306,10 +306,11 @@ def force_peak_finder(
     peak_lst = []
     peak_lst.append([peak1["I.Index"], peak1["R.Index"], peak1["F.Index"]])
     peak_lst.append([peak2["I.Index"], peak2["R.Index"], peak2["F.Index"]])
+
     peak_properties_list = []
     for peak_nr, peak in enumerate(peak_lst):
         peak_properties = PeakProperties(
-            id=basic_peaks.id + f"_{peak_nr + 1}",
+            id=basic_peak.id + f"_{peak_nr + 1}",
             i_index=peak[0],
             index=peak[1],
             f_index=peak[2],
@@ -328,7 +329,16 @@ def force_peak_finder(
     default_render_options={"data": {"src": "figure"}},
     outputs=[{"name": "figure"}],
 )
-def plot_peaks(x: np.array, y: np.array, peaks: List[PeakProperties]) -> go.Figure:
+def plot_peaks(
+    x: np.array,
+    y: np.array,
+    peaks: List[PeakProperties],
+    fill_rectangles: bool = True,
+    xaxis_title: str = "x",
+    yaxis_title: str = "y",
+    title: str = "",
+    show_legend: bool = True,
+) -> go.Figure:
     fig = go.Figure()
 
     # Set up line plot
@@ -354,14 +364,16 @@ def plot_peaks(x: np.array, y: np.array, peaks: List[PeakProperties]) -> go.Figu
                     peak.x_at_i_index,
                 ],
                 y=[plot_y_min, plot_y_min, peak_height, peak_height],
-                fill="toself",
-                fillcolor=peaks_colors[index % len(peaks_colors)],
-                opacity=0.3,
-                line=dict(width=0),
+                fill="toself" if fill_rectangles else None,
+                fillcolor=peaks_colors[index % len(peaks_colors)]
+                if fill_rectangles
+                else None,
+                opacity=0.3 if fill_rectangles else 1,
+                line=dict(width=0 if fill_rectangles else 2),
                 mode="lines",
                 name=f"Peak {peak.id}",
                 legendgroup=f"Peak {peak.id}",  # Group by Peak id
-                showlegend=True,
+                showlegend=show_legend,
             )
         )
         # Add an X marker at the exact peak position
@@ -389,14 +401,18 @@ def plot_peaks(x: np.array, y: np.array, peaks: List[PeakProperties]) -> go.Figu
                         dash="dash", color=peaks_colors[index % len(peaks_colors)]
                     ),
                     legendgroup=f"Peak {peak.id}",
+                    showlegend=show_legend,
                 ),
             )
 
     # Customize layout (axes labels and title can be added here if needed)
     fig.update_layout(
-        xaxis_title="x",
-        yaxis_title="y",
-        template="plotly_white",
+        xaxis_title=xaxis_title,
+        yaxis_title=yaxis_title,
+        title=title,
+        plot_bgcolor="white",
+        paper_bgcolor="white",
+        showlegend=show_legend,
     )
 
     return fig

{funcnodes_span-0.3.1 → funcnodes_span-0.3.3}/pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "funcnodes-span"
-version = "0.3.1"
-description = "Spectral Peak ANalysis (SPAN) for funcnodes"
+version = "0.3.3"
+description = "SPectral ANalysis (SPAN) for funcnodes"
 authors = ["Kourosh Rezaei <kouroshrezaei90@gmail.com>"]
 readme = "README.md"
 license = "MIT"

funcnodes_span-0.3.1/README.md

@@ -1 +0,0 @@
-Spectral Peak ANalysis (SPAN) for funcnodes