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schain
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Update setup and README
Juan C. Espinoza -
r1000:7e21d40a79b3 v2.2.5
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1 import h5py
2 import numpy
3 import matplotlib.pyplot as plt
4 import glob
5 import os
6
7 #---------------------- Functions ---------------------
8
9 def findFiles(path):
10
11 dirList = []
12 fileList = []
13
14 for thisPath in os.listdir(path):
15 dirList.append(os.path.join(path,thisPath))
16 dirList.sort()
17
18 for thisDirectory in dirList:
19 files = glob.glob1(thisDirectory, "*.hdf5")
20 files.sort()
21 for thisFile in files:
22 fileList.append(os.path.join(thisDirectory,thisFile))
23
24 return fileList
25
26 def readFiles(fileList):
27
28 meteors_array = numpy.zeros((1,4))
29
30 for thisFile in fileList:
31
32 #Leer
33 f1 = h5py.File(thisFile,'r')
34 grp1 = f1['Data']
35 grp2 = grp1['data_output']
36 meteors1 = grp2['table0'][:]
37 meteors_array = numpy.vstack((meteors_array,meteors1))
38 #cerrar
39 f1.close()
40
41 meteors_array = numpy.delete(meteors_array, 0, axis=0)
42 meteors_list = [meteors_array[:,0],meteors_array[:,1],meteors_array[:,2],meteors_array[:,3]]
43 return meteors_list
44
45 def estimateMean(offset_list):
46
47 mean_off = []
48 axisY_off = []
49 axisX_off = []
50
51 for thisOffset in offset_list:
52 mean_aux = numpy.mean(thisOffset, axis = 0)
53 mean_off.append(mean_aux)
54 axisX_off.append(numpy.array([0,numpy.size(thisOffset)]))
55 axisY_off.append(numpy.array([mean_aux,mean_aux]))
56
57 return mean_off, axisY_off, axisX_off
58
59 def plotPhases(offset0, axisY0, axisX0, title):
60 f, axarr = plt.subplots(4, sharey=True)
61 color = ['b','g','r','c']
62 # plt.grid()
63 for i in range(len(offset0)):
64 thisMeteor = offset0[i]
65 thisY = axisY0[i]
66 thisX = axisX0[i]
67 thisColor = color[i]
68
69 opt = thisColor + 'o'
70 axarr[i].plot(thisMeteor,opt)
71 axarr[i].plot(thisX, thisY, thisColor)
72 axarr[i].set_ylabel('Offset ' + str(i))
73
74 plt.ylim((-180,180))
75 axarr[0].set_title(title + ' Offsets')
76 axarr[3].set_xlabel('Number of estimations')
77
78 return
79
80 def filterOffsets(offsets0, stdvLimit):
81 offsets1 = []
82
83 for thisOffset in offsets0:
84 pstd = numpy.std(thisOffset)*stdvLimit
85 pmean = numpy.mean(thisOffset)
86 outlier1 = thisOffset > pmean - pstd
87 outlier2 = thisOffset < pmean + pstd
88 not_outlier = numpy.logical_and(outlier1,outlier2)
89 thisOffset1 = thisOffset[not_outlier]
90 offsets1.append(thisOffset1)
91
92 return offsets1
93
94 #---------------------- Setup ---------------------------
95
96 path = '/home/jespinoza/Pictures/JASMET30/201608/phase'
97 stdvLimit = 0.5
98
99 #---------------------- Script ---------------------------
100
101 fileList = findFiles(path)
102 offsets0 = readFiles(fileList)
103 mean0, axisY0, axisX0 = estimateMean(offsets0)
104 plotPhases(offsets0, axisY0, axisX0, 'Original')
105
106 offsets1 = filterOffsets(offsets0, stdvLimit)
107 mean1, axisY1, axisX1 = estimateMean(offsets1)
108 plotPhases(offsets1, axisY1, axisX1, 'Filtered')
109
110 print "Original Offsets: %.2f, %.2f, %.2f, %.2f" % (mean0[0],mean0[1],mean0[2],mean0[3])
111 print "Filtered Offsets: %.2f, %.2f, %.2f, %.2f" % (mean1[0],mean1[1],mean1[2],mean1[3])
112
113 plt.show()
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1 1 .project
2 2 .pydevproject
3 3 build/
4 4 *.pyc
5 5 *.so
6 *.egg-info/ No newline at end of file
6 *.egg-info/
7
8 # eclipse
9 .project
10 .pydevproject
11
12 # vscode
13 .vscode No newline at end of file
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1 1 # Signal Chain
2 2
3 3 ## Introduction
4 4
5 5 Signal Chain (SCh) is a radar data processing library developed using [Python](www.python.org) at JRO. SCh provides modules to read, write, process and plot data.
6 6
7 7 ## Installation
8 8
9 Install system dependencies, download the latest stable release from [svn](http://jro-dev.igp.gob.pe/svn/jro_soft/schain/Releases/) e.g. schainpy-2.2.5.tar.gz. and install it as a normal python package.
9 Install system dependencies, clone the latest version from [git](http://jro-dev.igp.gob.pe/rhodecode/schain/) and install it as a normal python package.
10 10
11 11 ```
12 12 $ sudo apt-get install python-pip python-dev gfortran libpng-dev freetype* libblas-dev liblapack-dev libatlas-base-dev python-qt4 python-tk libssl-dev libhdf5-dev
13 $ tar xvzf schainpy-2.2.5.tar.gz
14 $ cd schainpy-2.2.5
13 $ sudo pip install numpy
14 $ git clone http://jro-dev.igp.gob.pe/rhodecode/schain/
15 $ cd schain
15 16 $ sudo pip install ./
16 17 ```
17 18
18 19 **Its recommended to install schain in a virtual environment**
19 20
20 21 ```
21 22 $ sudo pip install virtualenv
22 23 $ virtualenv /path/to/virtual --system-site-packages
23 24 $ source /path/to/virtual/bin/activate
24 (virtual) $ cd schainpy-2.2.5
25 (virtual) $ cd schain
25 26 (virtual) $ pip install ./
26 27 ```
27 28
28 29 ## First Script
29 30
30 31 Read Spectra data (.pdata) - remove dc - plot spectra & RTI
31 32
32 33 Import SCh and creating a project
33 34
34 35 ```python
35 36 #!/usr/bin/python
36 37
37 38 from schainpy.controller import Project
38 39
39 40 controller = Project()
40 41 controller.setup(id = '100',
41 42 name='test',
42 43 description='Basic experiment')
43 44
44 45
45 46 ```
46 47
47 48 Adding read unit and operations
48 49
49 50 ```python
50 51 read_unit = controller.addReadUnit(datatype='Spectra',
51 52 path='/path/to/pdata/',
52 53 startDate='2014/01/31',
53 54 endDate='2014/03/31',
54 55 startTime='00:00:00',
55 56 endTime='23:59:59',
56 57 online=0,
57 58 walk=0)
58 59
59 60 proc_unit = controller.addProcUnit(datatype='Spectra',
60 61 inputId=read_unit.getId())
61 62
62 63 op = proc_unit.addOperation(name='selectChannels')
63 64 op.addParameter(name='channelList', value='0,1', format='intlist')
64 65
65 66 op = proc_unit.addOperation(name='selectHeights')
66 67 op.addParameter(name='minHei', value='80', format='float')
67 68 op.addParameter(name='maxHei', value='200', format='float')
68 69
69 70 op = proc_unit.addOperation(name='removeDC')
70 71
71 72 ```
72 73
73 74 Plotting data & start project
74 75
75 76 ```python
76 77 op = proc_unit.addOperation(name='SpectraPlot', optype='other')
77 78 op.addParameter(name='id', value='1', format='int')
78 79 op.addParameter(name='wintitle', value='Spectra', format='str')
79 80
80 81 op = procUnitConfObj1.addOperation(name='RTIPlot', optype='other')
81 82 op.addParameter(name='id', value='2', format='int')
82 83 op.addParameter(name='wintitle', value='RTI', format='str')
83 84
84 85 controller.start()
85 86
86 87 ```
87 88
88 89 Full script
89 90
90 91
91 92 ```python
92 93 #!/usr/bin/python
93 94
94 95 from schainpy.controller import Project
95 96
96 97 controller = Project()
97 98 controller.setup(id = '100',
98 99 name='test',
99 100 description='Basic experiment')
100 101 read_unit = controller.addReadUnit(datatype='Spectra',
101 102 path='/path/to/pdata/',
102 103 startDate='2014/01/31',
103 104 endDate='2014/03/31',
104 105 startTime='00:00:00',
105 106 endTime='23:59:59',
106 107 online=0,
107 108 walk=0)
108 109
109 110 proc_unit = controller.addProcUnit(datatype='Spectra',
110 111 inputId=read_unit.getId())
111 112
112 113 op = proc_unit.addOperation(name='selectChannels')
113 114 op.addParameter(name='channelList', value='0,1', format='intlist')
114 115
115 116 op = proc_unit.addOperation(name='selectHeights')
116 117 op.addParameter(name='minHei', value='80', format='float')
117 118 op.addParameter(name='maxHei', value='200', format='float')
118 119
119 120 op = proc_unit.addOperation(name='removeDC')
120 121
121 122 op = proc_unit.addOperation(name='SpectraPlot', optype='other')
122 123 op.addParameter(name='id', value='6', format='int')
123 124 op.addParameter(name='wintitle', value='Spectra', format='str')
124 125
125 126 op = procUnitConfObj1.addOperation(name='RTIPlot', optype='other')
126 127 op.addParameter(name='id', value='2', format='int')
127 128 op.addParameter(name='wintitle', value='RTI', format='str')
128 129
129 130 controller.start()
130 131
131 ```
132 ``` No newline at end of file
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1 1 '''
2 2 Created on Jul 16, 2014
3 3
4 4 @author: Miguel Urco
5 5 '''
6
7 from schainpy import __version__
6 import numpy
8 7 from setuptools import setup, Extension
8 from schainpy import __version__
9 9
10 10 setup(name="schainpy",
11 11 version=__version__,
12 12 description="Python tools to read, write and process Jicamarca data",
13 13 author="Miguel Urco",
14 14 author_email="miguel.urco@jro.igp.gob.pe",
15 15 url="http://jro.igp.gob.pe",
16 16 packages = {'schainpy',
17 17 'schainpy.model',
18 18 'schainpy.model.data',
19 19 'schainpy.model.graphics',
20 20 'schainpy.model.io',
21 21 'schainpy.model.proc',
22 22 'schainpy.model.serializer',
23 23 'schainpy.model.utils',
24 24 'schainpy.gui',
25 25 'schainpy.gui.figures',
26 26 'schainpy.gui.viewcontroller',
27 27 'schainpy.gui.viewer',
28 28 'schainpy.gui.viewer.windows'},
29 29 ext_package='schainpy',
30 30 py_modules=[''],
31 31 package_data={'': ['schain.conf.template'],
32 32 'schainpy.gui.figures': ['*.png','*.jpg'],
33 33 },
34 34 include_package_data=False,
35 35 scripts =['schainpy/gui/schainGUI',
36 36 'schainpy/scripts/schain'],
37 ext_modules=[Extension("cSchain", ["schainpy/model/proc/extensions.c"])],
37 ext_modules=[Extension("cSchain", ["schainpy/model/proc/extensions.c"], include_dirs=[numpy.get_include()])],
38 38 install_requires=[
39 39 "scipy >= 0.14.0",
40 40 "h5py >= 2.2.1",
41 41 "matplotlib >= 1.4.2",
42 42 "pyfits >= 3.4",
43 43 "numpy >= 1.11.2",
44 44 "paramiko >= 2.1.2",
45 45 "paho-mqtt >= 1.2",
46 46 "zmq",
47 47 ],
48 48 ) No newline at end of file
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