Creating of example folder structure

.gitignore

@@ -10,3 +10,12 @@ __pycache__/
 # Data files
 *.dat
 *.fits
+*.fits.gz
+
+# Files downloades from Tammo-Jan gitlab
+filterbank.py
+sigproc.py
+psr_constants.py
+
+# Data directory on Kapteyn
+data

examples/B1133+16_filterbank/B1133+16param.yml

@@ -0,0 +1,17 @@
+# Information about the data file  
+
+FileName:       '2018-01-19-21:16:50_B1133+16.fil'
+
+# Folding parameters
+Folding:
+  nbins:          500           # Number of bins for folding 
+  nbinsdedisp:    500           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: false
+
+GrasMaaier: {}

examples/B1133+16_filterbank/getData.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+wget https://charon.camras.nl/public/pulsars/2018-01-19-21%3A16%3A50_B1133+16.txt
+
+wget https://charon.camras.nl/public/pulsars/2018-01-19-21%3A16%3A50_B1133+16.fil
+
+

examples/B1133+16_filterbank/run.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e 2018-01-19-21%3A16%3A50_B1133+16.txt ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py B1133+16param.yml
+else 
+    python ../../main.py B1133+16param.yml
+fi

examples/README.md

@@ -0,0 +1,15 @@
+# Examples
+
+In this folder there are several examples that use the code on different datasets. If you want to run an example go to the folder of the example and run the examle by doing:
+
+`./run.sh`
+
+This will run the example, show the output and store the output in the output folder. 
+
+## Type of examples
+
+Currently there are four types of examples:
+1. The pulsars with normal fits data.
+2. The pulsars with raw data.
+3. The pulsars with filterbank files (not working).
+4. The pulsars with a chifit (not working).

examples/buurpulsar/buurpulsarParam.yml

@@ -0,0 +1,17 @@
+# Information about the data file  
+
+FileName:       'B2016+28_10-04-2018.fits.gz'
+
+# Folding parameters
+Folding:
+  nbins:          500           # Number of bins for folding 
+  nbinsdedisp:    500           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: false
+
+GrasMaaier: {}

examples/buurpulsar/getData.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+wget www.astro.rug.nl/~camras/data/CAMRAS/obs-10-04-2018/B2016+28_10-04-2018.fits.gz
+
+

examples/buurpulsar/run.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e B2016+28_10-04-2018.fits.gz ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py buurpulsarParam.yml
+else 
+    python ../../main.py buurpulsarParam.yml
+fi
+

examples/buurpulsar_raw/buurpulsarRawParam.yml

@@ -0,0 +1,23 @@
+# Information about the data file  
+
+FileName:       'B2016-28_10-04-2018.dat'
+RawData:        true
+FileFormat:     'raw'
+ObsMetaData:
+  ObsDate:      '2017-12-30T12:30:00(UTC)'
+  PulsarName:   'B2016+28'
+  MixFreq:      405
+
+# Folding parameters
+Folding:
+  nbins:          200           # Number of bins for folding 
+  nbinsdedisp:    200           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: false
+
+GrasMaaier: {}

examples/buurpulsar_raw/getData.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://www.astro.rug.nl/~camras/data/obs-10-04-2018/B2016-28_10-04-2018.dat

examples/buurpulsar_raw/run.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e B2016+28_406MHz_2017-12-30.raw ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py buurpulsarRawParam.yml
+else 
+    python ../../main.py buurpulsarRawParam.yml
+fi
+

examples/huispulsar/getData.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+wget www.astro.rug.nl/~camras/data/obs-10-04-2018/B0329+54_10-04-2018.fits.gz
+
+

examples/huispulsar/huispulsarParam.yml

@@ -0,0 +1,17 @@
+# Information about the data file  
+
+FileName:       'B0329+54_10-04-2018.fits.gz'
+
+# Folding parameters
+Folding:
+  nbins:          500           # Number of bins for folding 
+  nbinsdedisp:    500           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: false
+
+GrasMaaier: {}

examples/huispulsar/run.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e B0329+54_10-04-2018.fits.gz ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py huispulsarParam.yml
+else
+    python ../../main.py huispulsarParam.yml
+fi
+

examples/huispulsar_chifit/chifitparam.yml

@@ -0,0 +1,22 @@
+# Information about the data file  
+
+FileName:       'B0329+54_10-04-2018.fits.gz'
+
+# Folding parameters
+Folding:
+  nbins:          500           # Number of bins for folding 
+  nbinsdedisp:    500           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: 
+  Ntries:      1000
+  nbins_time:  1000
+  nbins_freq:  1000
+  trywidth:    1e-3
+  FitFunc:     'Lorentzian'
+
+GrasMaaier: {}

examples/huispulsar_chifit/getData.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+wget www.astro.rug.nl/~camras/data/obs-10-04-2018/B0329+54_10-04-2018.fits.gz
+
+

examples/huispulsar_chifit/run.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e B0329+54_10-04-2018.fits.gz ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py huispulsarParam.yml
+else 
+    python ../../main.py huispulsarParam.yml
+fi

examples/huispulsar_filterbank/getData.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+wget https://charon.camras.nl/public/pulsars/2017-09-20-07%3A05%3A00_B0329+54.txt
+
+wget https://charon.camras.nl/public/pulsars/2017-09-20-07%3A05%3A00_B0329+54.fil	
+

examples/huispulsar_filterbank/huispulsarFilterbankParam.yml

@@ -0,0 +1,17 @@
+# Information about the data file  
+
+FileName:       '2017-09-20-07:05:00_B0329+54.fil'
+
+# Folding parameters
+Folding:
+  nbins:          500           # Number of bins for folding 
+  nbinsdedisp:    500           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: false
+
+GrasMaaier: {}

examples/huispulsar_filterbank/run.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e 2017-09-20-07:05:00_B0329+54.fil ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py huispulsarFilterbankParam.yml
+else 
+    python ../../main.py huispulsarFilterbankParam.yml
+fi
+

examples/huispulsar_raw/getData.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+wget -O B0329+54.2016.11.18.1038.5min.dat http://www.astro.rug.nl/~camras/data/obs-18-11-2016/B0329%2054.2016.11.18.1038.5min.dat
+

examples/huispulsar_raw/huispulsarParam.yml

@@ -0,0 +1,23 @@
+# Information about the data file  
+
+FileName:       'B0329+54.2016.11.18.1038.5min.dat'
+RawData:        true
+FileFormat:     'raw'
+ObsMetaData:
+  ObsDate:      '2016-11-18T10:38:00.00(UTC)'
+  PulsarName:   'B0329+54'
+  MixFreq:      405
+
+# Folding parameters
+Folding:
+  nbins:          500           # Number of bins for folding 
+  nbinsdedisp:    500           # Number of bins for dedispersed profile
+
+# Output parameters
+Output:
+  OutputDir:      './output'
+  SavePlots:      true
+
+ChiFit: false
+
+GrasMaaier: {}

examples/huispulsar_raw/run.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Download the observation data if it is not present
+if [ ! -e B0329+54.2016.11.18.1038.5min.dat ]
+then 
+	echo "Dowloading the observation data"
+	./getData.sh
+fi
+
+# Run PSF
+echo "Run PSF"
+if command -v python3 &>/dev/null; then
+    python3 ../../main.py huispulsarParam.yml
+else
+    python ../../main.py huispulsarParam.yml
+fi
+

filterBank.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+
+from collections import defaultdict
+
+# https://stackoverflow.com/questions/28385822/reading-data-separated-by-colon-per-line-in-python
+def filterBankReadMetaData(filename):
+    result = defaultdict(list)
+    with open(filename) as inf:
+        print(inf)
+        for line in inf:
+            name, score = line.split(": ", 1)
+            name = name.rstrip()
+            score = score.rstrip('\n')
+            result[name].append(score)
+    return result
+
+
+
+
+
+

observation.py

@@ -5,6 +5,9 @@
 from astropy import units as u
 from barcen import barcen_times, barcen_freqs
 from loadData import loader
+from pathlib import Path
+from filterBank import filterBankReadMetaData
+from blimpy import Waterfall
 
 def calc_central_freqs(mix_freq, throwhighestfreqaway=True):
     timevoltage = 1/(70e6) # (s), the time of each voltage measurement
@@ -43,20 +46,31 @@ def __init__(self, cfg=None, fitsfile=None):
             self.psr_name = header['SRC_NAME']
             self.obs_start_isot = header['DATE-OBS']
             self.mix_freq = header['FREQMIX']
+        elif fileformat.endswith('fil'):
+            self.using_fits = False 
+            obs = Waterfall(filename)
+            header = obs.header
+            self.psr_name = header[b'source_name']
+            self.obs_start_isot = header[b'tstart']
+            # Tammo-Jan doesn't store the mix frequency
+            self.mix_freq = header[b'fch1']-21.668359375
+            self.data = obs.data
+            #raise NotImplementedError('Filterbank supported yet!')
         else:
             self.using_fits = False
             self.psr_name = cfg.ObsMetaData.PulsarName
             self.obs_start_isot = cfg.ObsMetaData.ObsDate
             self.mix_freq = cfg.ObsMetaData.MixFreq
-            if fileformat.endswith('fil'):
-                raise NotImplementedError('Filterbank supported yet!')
-            elif fileformat.endswith('raw'):
+            if fileformat.endswith('raw'):
                 assert cfg.RawData, 'Need to supply the metadata!'
                 self.data = loader(cfg.FileName).astype(np.uint32)
             else:
                 raise ValueError('Unrecognized format')
 
-        self.obs_start = Time(self.obs_start_isot)
+        if fileformat.endswith('fil'):
+            self.obs_start = Time(self.obs_start_isot,format='jd')
+        else:
+            self.obs_start = Time(self.obs_start_isot)
         dt = 64*512/(70e6)
         self.obs_dur = len(self.data) * dt
         self.obs_end = self.obs_start +  self.obs_dur * u.s