Added native python process manager to circumvent issue #6 for now.

Author: thomasms

examples/realspectrum.py

@@ -21,14 +21,10 @@
 snippedCounts = hist_raw.Y
 
 # process manager
-pm = pkd.core.SimpleProcessManager()
-
-# smooth
-sg = pkd.core.SavitzkyGolaySmoother(31)
-pm.append(sg)
-
-# peak finding
-pm.append(pkd.core.MovingAveragePeakFinder(400))
+pm = pkd.core.PySimpleProcessManager(processes=[
+    pkd.core.SavitzkyGolaySmoother(31),
+    pkd.core.MovingAveragePeakFinder(400)
+])
 
 # process
 processed_counts = pm.run(snippedCounts)

peakingduck/core/__init__.py

@@ -2,4 +2,5 @@
 from PEAKINGDUCK.core import *
 
 # python additional
-from peakingduck.core.smoothing import *
+from peakingduck.core.smoothing import *
+from peakingduck.core.process import *

peakingduck/core/process.py

@@ -0,0 +1,34 @@
+# raw C++ bindings library
+from PEAKINGDUCK.core import IProcessManager
+
+"""
+    Add other processes and/or process managers here.
+"""
+
+class PySimpleProcessManager(IProcessManager):
+    """
+        Instead of using the C++ SimpleProcessManager
+        we make a python native version to avoid 
+        ref counting issues
+
+        Easy to extend also.
+    """
+    def __init__(self, processes=None):
+        self.processes = []
+        if processes:
+            self.processes = processes
+    
+    def append(self, process):
+        self.processes.append(process)
+    
+    def __len__(self):
+        return len(self.processes)
+
+    def __item__(self, i):
+        return self.processes[i]
+
+    def run(self, data):
+        newdata = data
+        for p in self.processes:
+            newdata = p.go(newdata)
+        return newdata