Changed some hard_coded values to parameters + general changes

Author: robertkleef

dedisperse/dedisperse.py

@@ -1,18 +1,21 @@
 '''
-    Dedisperses data
+Dedisperses data
 '''
 # pylint: disable-msg=C0103
 import numpy as np
 
-def dedisperse(samples, dm=None):
+def dedisperse(samples, highest_x=None, max_delay=None, dm=None):
     '''
     This method performs dedispersion on the filterbank data
+    The maximum_delay specifies between the currently considered pulsar signal and the next pulsar signal should be
+    The highest_x specifies the amount of intensities that are used for estimating the minimum pulsar intensity
     '''
 
     # Check if parameters contain a DM, if not, estimate one
     if dm is None:
-        print("Finding possible DM's")
-        dm = find_dm(samples)
+        # Estimates the minimum for an intensity to be considered a pulsar
+        pulsar_intensity = find_estimation_intensity(samples, highest_x)
+        dm = find_dm(samples, pulsar_intensity, max_delay)
 
     # Distribute the DM over the amount of samples
     delays_per_sample = np.round(np.linspace(dm, 0, samples.shape[1])).astype(int)
@@ -31,42 +34,30 @@ def dedisperse(samples, dm=None):
 
     return samples
 
-def find_dm(samples):
+def find_dm(samples, pulsar_intensity, max_delay):
     '''
     This method attempts to find a dispersion measure
     '''
-    
-    # Estimates the minimum for an intensity to be considered a pulsar
-    pulsar_intensity = find_estimation_intensity(samples)
-
-    # Determine what the maximum delay between the currently considered pulsar signal
-    # and the next pulsar signal should be
-    max_delay = round(samples.shape[0] / 50)
-    
-    print(max_delay)
-    
-    #max_delay = 100
-    
-    # Loop through the samples to find
+
+    # Loop through the samples to find a pulsar intensity to start calculating from
     for s, sample in enumerate(samples[:, 0]):
 
         # If the sample meets the minimum intensity, attempt to find a line continuing from this intensity
         if(sample > pulsar_intensity):
             start_sample_index = s
-            #print("\n\nAttempting to find line on freq,", 0, "sample", s)
+
             # Attempt to find a line, line_coordinates contains the first and last index of the pulsar
             line_coordinates = find_line(samples, start_sample_index, max_delay, pulsar_intensity)
 
             # If a line is found, calculate and return the dispersion measure
             if(line_coordinates is not None):
                 dm = line_coordinates[1] - line_coordinates[0]
-                print(dm)
                 return dm
-            
+
     return None
 
 
-def find_line(samples, start_sample_index, max_delay, average_intensity):
+def find_line(samples, start_sample_index, max_delay, pulsar_intensity):
     '''
     This method tries to find a line starting from the sample index given in the parameters
     it stops if there is no intensity within the max_delay higher than the average_intensity
@@ -76,7 +67,6 @@ def find_line(samples, start_sample_index, max_delay, average_intensity):
 
     failed_to_find_line = True
 
-
     # Loop through the frequencies
     for f, frequency in enumerate(samples[1]):
 
@@ -88,40 +78,34 @@ def find_line(samples, start_sample_index, max_delay, average_intensity):
                 failed_to_find_line = False
                 break
 
-            # If the intensity is higher than the average_intensity, continue finding a signal
-            if(intensity > average_intensity):
-                #print("Continuing to find line on freq,", f, "sample", previous_sample_index + i, intensity)
+            # If the intensity is higher than the pulsar_intensity, continue finding a signal
+            if(intensity > pulsar_intensity):
                 previous_sample_index = previous_sample_index + i
                 failed_to_find_line = False
                 break
 
         # If there is no line found, return None
         if failed_to_find_line: 
-            print(average_intensity)
             return None
 
     # If all frequencies are looped through, a line is found, so we return the start and end index of the line
     return start_sample_index, previous_sample_index
 
 
-def find_estimation_intensity(samples):
+def find_estimation_intensity(samples, highest_x):
     '''
-    This method finds the average intensity for top x intensities
+    This method finds the average intensity for the highest x intensities
     The average_intensity is considered a requirement for intensities to be considered a pulsar 
     '''
 
     # Sum of all intensities
     sum_intensities = 0
 
-    # Top x intensities used to estimate 
-    #top = round((samples.shape[0]) / 50)
-    top = 10
-
     # Looks for the top x highest intensities in the samples and adds them up together
     for sample in samples:
-        sum_intensities += np.sum(sorted(sample, reverse=True)[:top])
+        sum_intensities += np.sum(sorted(sample, reverse=True)[:highest_x])
 
     # Calculates the average_intensity
-    average_intensity = (sum_intensities) / (samples.shape[0] * top)
+    average_intensity = (sum_intensities) / (samples.shape[0] * highest_x)
 
     return average_intensity

examples/dedisperse_stream.py

@@ -18,20 +18,27 @@
 
 from clipping import clipping
 
-# Read filterbank data
+# Read filterbank data,
 
 # Standard file
-#special_pspm = fb.Filterbank(filename = "../data/my_special_pspm.fil")
+special_pspm = fb.Filterbank(filename = "../data/my_special_pspm.fil")
+highest_x=10
+max_delay=10
 
 # Files with low signal to noise ratio
-#special_pspm = fb.Filterbank(filename = "../data/new_pspm_2.fil")
-#special_pspm = fb.Filterbank(filename = "../data/my_uber_pspm.fil")
+# special_pspm = fb.Filterbank(filename = "../data/my_uber_pspm.fil")
+# highest_x=10
+# max_delay=10
 
 # File with 10000 samples
-#special_pspm = fb.Filterbank(filename = "../data/pspm_4_2.fil")
+# special_pspm = fb.Filterbank(filename = "../data/pspm_4_2.fil")
+# highest_x=10
+# max_delay=100
 
 # File with 10000 samples with low signal to noise ratio
-#special_pspm = fb.Filterbank(filename = "../data/pspm_4_1.fil")
+# special_pspm = fb.Filterbank(filename = "../data/pspm_4_1.fil")
+# highest_x=10
+# max_delay=100
 
 special_pspm.read_filterbank()
 
@@ -62,7 +69,7 @@
 plt.show()
 
 # Dedisperse the samples
-samples = dedisperse.dedisperse(samples)
+samples = dedisperse.dedisperse(samples, highest_x, max_delay)
 
 # Plot the dedispersed data
 plt.subplot(2,1,1)