removed height with the github version of peakdetect because it break…

…s findpeaks at several places

findpeaks/findpeaks.py

@@ -72,9 +72,7 @@ class findpeaks():
         * https://erdogant.github.io/findpeaks/
 
     """
-
     def __init__(self,
-                 height=None,
                  method=None,
                  whitelist=['peak', 'valley'],
                  lookahead=200,
@@ -88,6 +86,7 @@ def __init__(self,
                  cu=None,  # DEPRECATED IN LATER VERSIONS: specify in params
                  params_caerus={},  # DEPRECATED IN LATER VERSIONS: use params instead
                  params={'window': 3, 'delta': 0},
+                 # height=None,
                  figsize=(15, 8),
                  verbose=3):
         """Initialize findpeaks parameters.
@@ -209,7 +208,7 @@ def __init__(self,
         self.denoise = denoise
         self.figsize = figsize
         self.verbose = verbose
-        self.height = height
+        # self.height = height
 
         # Store parameters for caerus
         defaults = {}
@@ -331,14 +330,14 @@ def peaks1d(self, X, x=None, method='peakdetect', height=0):
         result = {}
 
         # Interpolation
-        if self.interpolate is not None:
+        if self.interpolate is not None and self.interpolate>0:
             X = interpolate.interpolate_line1d(X, n=self.interpolate, method=2, showfig=False, verbose=self.verbose)
 
         # Compute peaks based on method
         if method == 'peakdetect':
             # Peakdetect method
-            max_peaks, min_peaks = peakdetect(X, lookahead=self.lookahead, delta=self.params['delta'],
-                                              height=self.height)
+            # max_peaks, min_peaks = peakdetect(X, lookahead=self.lookahead, delta=self.params['delta'], height=self.height)
+            max_peaks, min_peaks = peakdetect(X, lookahead=self.lookahead, delta=self.params['delta'])
             # Post processing for the peak-detect
             result['peakdetect'] = stats._post_processing(X, Xraw, min_peaks, max_peaks, self.interpolate,
                                                           self.lookahead)

findpeaks/tests/test_findpeaks.py

@@ -91,6 +91,7 @@ def test_fit(self):
         assert np.all(np.isin(results['persistence'].columns, ['x', 'y', 'birth_level', 'death_level', 'score']))
 
         # CHECK RESULTS METHOD TOPOLOGY
+        # Let op, soms gaat deze ook op 6 vanwege een stochastic components
         assert results['persistence'].shape[0] == 7
 
         # CHECK RESULTS METHOD with LIMIT functionality
@@ -100,7 +101,8 @@ def test_fit(self):
         assert len(results['Xdetect'][results['Xdetect'] != 0]) == len(results['Xranked'][results['Xranked'] != 0])
 
         # CHECK OUTPUT METHOD PEAKDETECT
-        fp = findpeaks(method="peakdetect", lookahead=1, verbose=3, height=0)
+        # fp = findpeaks(method="peakdetect", lookahead=1, verbose=3, height=0)
+        fp = findpeaks(method="peakdetect", lookahead=1, verbose=3)
         X = fp.import_example('1dpeaks')
         results = fp.fit(X)
         assert fp.type == 'peaks1d'

requirements.txt

@@ -1,4 +1,3 @@
-peakdetect==1.1
 scipy==1.11.4
 matplotlib
 numpy
@@ -9,4 +8,5 @@ caerus>=0.1.9
 opencv-python
 xarray
 joblib
+peakdetect==1.1
 # git+https://github.com/arvinnick/peakdetect.git

setup.py

@@ -23,6 +23,7 @@
                        'caerus>=0.1.9',
                        'xarray',
                        'joblib'],
+     # dependency_links=['https://github.com/arvinnick/peakdetect/tarball/master#egg=peakdetect-1.2'],
      python_requires='>=3',
      name='findpeaks',
      version=new_version,