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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 .project
1 .project
2 .pydevproject
2 .pydevproject
3 build/
3 build/
4 *.pyc
4 *.pyc
5 *.so
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 # Signal Chain
1 # Signal Chain
2
2
3 ## Introduction
3 ## Introduction
4
4
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.
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 ## Installation
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 $ 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
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
13 $ sudo pip install numpy
14 $ cd schainpy-2.2.5
14 $ git clone http://jro-dev.igp.gob.pe/rhodecode/schain/
15 $ cd schain
15 $ sudo pip install ./
16 $ sudo pip install ./
16 ```
17 ```
17
18
18 **Its recommended to install schain in a virtual environment**
19 **Its recommended to install schain in a virtual environment**
19
20
20 ```
21 ```
21 $ sudo pip install virtualenv
22 $ sudo pip install virtualenv
22 $ virtualenv /path/to/virtual --system-site-packages
23 $ virtualenv /path/to/virtual --system-site-packages
23 $ source /path/to/virtual/bin/activate
24 $ source /path/to/virtual/bin/activate
24 (virtual) $ cd schainpy-2.2.5
25 (virtual) $ cd schain
25 (virtual) $ pip install ./
26 (virtual) $ pip install ./
26 ```
27 ```
27
28
28 ## First Script
29 ## First Script
29
30
30 Read Spectra data (.pdata) - remove dc - plot spectra & RTI
31 Read Spectra data (.pdata) - remove dc - plot spectra & RTI
31
32
32 Import SCh and creating a project
33 Import SCh and creating a project
33
34
34 ```python
35 ```python
35 #!/usr/bin/python
36 #!/usr/bin/python
36
37
37 from schainpy.controller import Project
38 from schainpy.controller import Project
38
39
39 controller = Project()
40 controller = Project()
40 controller.setup(id = '100',
41 controller.setup(id = '100',
41 name='test',
42 name='test',
42 description='Basic experiment')
43 description='Basic experiment')
43
44
44
45
45 ```
46 ```
46
47
47 Adding read unit and operations
48 Adding read unit and operations
48
49
49 ```python
50 ```python
50 read_unit = controller.addReadUnit(datatype='Spectra',
51 read_unit = controller.addReadUnit(datatype='Spectra',
51 path='/path/to/pdata/',
52 path='/path/to/pdata/',
52 startDate='2014/01/31',
53 startDate='2014/01/31',
53 endDate='2014/03/31',
54 endDate='2014/03/31',
54 startTime='00:00:00',
55 startTime='00:00:00',
55 endTime='23:59:59',
56 endTime='23:59:59',
56 online=0,
57 online=0,
57 walk=0)
58 walk=0)
58
59
59 proc_unit = controller.addProcUnit(datatype='Spectra',
60 proc_unit = controller.addProcUnit(datatype='Spectra',
60 inputId=read_unit.getId())
61 inputId=read_unit.getId())
61
62
62 op = proc_unit.addOperation(name='selectChannels')
63 op = proc_unit.addOperation(name='selectChannels')
63 op.addParameter(name='channelList', value='0,1', format='intlist')
64 op.addParameter(name='channelList', value='0,1', format='intlist')
64
65
65 op = proc_unit.addOperation(name='selectHeights')
66 op = proc_unit.addOperation(name='selectHeights')
66 op.addParameter(name='minHei', value='80', format='float')
67 op.addParameter(name='minHei', value='80', format='float')
67 op.addParameter(name='maxHei', value='200', format='float')
68 op.addParameter(name='maxHei', value='200', format='float')
68
69
69 op = proc_unit.addOperation(name='removeDC')
70 op = proc_unit.addOperation(name='removeDC')
70
71
71 ```
72 ```
72
73
73 Plotting data & start project
74 Plotting data & start project
74
75
75 ```python
76 ```python
76 op = proc_unit.addOperation(name='SpectraPlot', optype='other')
77 op = proc_unit.addOperation(name='SpectraPlot', optype='other')
77 op.addParameter(name='id', value='1', format='int')
78 op.addParameter(name='id', value='1', format='int')
78 op.addParameter(name='wintitle', value='Spectra', format='str')
79 op.addParameter(name='wintitle', value='Spectra', format='str')
79
80
80 op = procUnitConfObj1.addOperation(name='RTIPlot', optype='other')
81 op = procUnitConfObj1.addOperation(name='RTIPlot', optype='other')
81 op.addParameter(name='id', value='2', format='int')
82 op.addParameter(name='id', value='2', format='int')
82 op.addParameter(name='wintitle', value='RTI', format='str')
83 op.addParameter(name='wintitle', value='RTI', format='str')
83
84
84 controller.start()
85 controller.start()
85
86
86 ```
87 ```
87
88
88 Full script
89 Full script
89
90
90
91
91 ```python
92 ```python
92 #!/usr/bin/python
93 #!/usr/bin/python
93
94
94 from schainpy.controller import Project
95 from schainpy.controller import Project
95
96
96 controller = Project()
97 controller = Project()
97 controller.setup(id = '100',
98 controller.setup(id = '100',
98 name='test',
99 name='test',
99 description='Basic experiment')
100 description='Basic experiment')
100 read_unit = controller.addReadUnit(datatype='Spectra',
101 read_unit = controller.addReadUnit(datatype='Spectra',
101 path='/path/to/pdata/',
102 path='/path/to/pdata/',
102 startDate='2014/01/31',
103 startDate='2014/01/31',
103 endDate='2014/03/31',
104 endDate='2014/03/31',
104 startTime='00:00:00',
105 startTime='00:00:00',
105 endTime='23:59:59',
106 endTime='23:59:59',
106 online=0,
107 online=0,
107 walk=0)
108 walk=0)
108
109
109 proc_unit = controller.addProcUnit(datatype='Spectra',
110 proc_unit = controller.addProcUnit(datatype='Spectra',
110 inputId=read_unit.getId())
111 inputId=read_unit.getId())
111
112
112 op = proc_unit.addOperation(name='selectChannels')
113 op = proc_unit.addOperation(name='selectChannels')
113 op.addParameter(name='channelList', value='0,1', format='intlist')
114 op.addParameter(name='channelList', value='0,1', format='intlist')
114
115
115 op = proc_unit.addOperation(name='selectHeights')
116 op = proc_unit.addOperation(name='selectHeights')
116 op.addParameter(name='minHei', value='80', format='float')
117 op.addParameter(name='minHei', value='80', format='float')
117 op.addParameter(name='maxHei', value='200', format='float')
118 op.addParameter(name='maxHei', value='200', format='float')
118
119
119 op = proc_unit.addOperation(name='removeDC')
120 op = proc_unit.addOperation(name='removeDC')
120
121
121 op = proc_unit.addOperation(name='SpectraPlot', optype='other')
122 op = proc_unit.addOperation(name='SpectraPlot', optype='other')
122 op.addParameter(name='id', value='6', format='int')
123 op.addParameter(name='id', value='6', format='int')
123 op.addParameter(name='wintitle', value='Spectra', format='str')
124 op.addParameter(name='wintitle', value='Spectra', format='str')
124
125
125 op = procUnitConfObj1.addOperation(name='RTIPlot', optype='other')
126 op = procUnitConfObj1.addOperation(name='RTIPlot', optype='other')
126 op.addParameter(name='id', value='2', format='int')
127 op.addParameter(name='id', value='2', format='int')
127 op.addParameter(name='wintitle', value='RTI', format='str')
128 op.addParameter(name='wintitle', value='RTI', format='str')
128
129
129 controller.start()
130 controller.start()
130
131
131 ```
132 ``` No newline at end of file
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1 '''
1 '''
2 Created on Jul 16, 2014
2 Created on Jul 16, 2014
3
3
4 @author: Miguel Urco
4 @author: Miguel Urco
5 '''
5 '''
6
6 import numpy
7 from schainpy import __version__
8 from setuptools import setup, Extension
7 from setuptools import setup, Extension
8 from schainpy import __version__
9
9
10 setup(name="schainpy",
10 setup(name="schainpy",
11 version=__version__,
11 version=__version__,
12 description="Python tools to read, write and process Jicamarca data",
12 description="Python tools to read, write and process Jicamarca data",
13 author="Miguel Urco",
13 author="Miguel Urco",
14 author_email="miguel.urco@jro.igp.gob.pe",
14 author_email="miguel.urco@jro.igp.gob.pe",
15 url="http://jro.igp.gob.pe",
15 url="http://jro.igp.gob.pe",
16 packages = {'schainpy',
16 packages = {'schainpy',
17 'schainpy.model',
17 'schainpy.model',
18 'schainpy.model.data',
18 'schainpy.model.data',
19 'schainpy.model.graphics',
19 'schainpy.model.graphics',
20 'schainpy.model.io',
20 'schainpy.model.io',
21 'schainpy.model.proc',
21 'schainpy.model.proc',
22 'schainpy.model.serializer',
22 'schainpy.model.serializer',
23 'schainpy.model.utils',
23 'schainpy.model.utils',
24 'schainpy.gui',
24 'schainpy.gui',
25 'schainpy.gui.figures',
25 'schainpy.gui.figures',
26 'schainpy.gui.viewcontroller',
26 'schainpy.gui.viewcontroller',
27 'schainpy.gui.viewer',
27 'schainpy.gui.viewer',
28 'schainpy.gui.viewer.windows'},
28 'schainpy.gui.viewer.windows'},
29 ext_package='schainpy',
29 ext_package='schainpy',
30 py_modules=[''],
30 py_modules=[''],
31 package_data={'': ['schain.conf.template'],
31 package_data={'': ['schain.conf.template'],
32 'schainpy.gui.figures': ['*.png','*.jpg'],
32 'schainpy.gui.figures': ['*.png','*.jpg'],
33 },
33 },
34 include_package_data=False,
34 include_package_data=False,
35 scripts =['schainpy/gui/schainGUI',
35 scripts =['schainpy/gui/schainGUI',
36 'schainpy/scripts/schain'],
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 install_requires=[
38 install_requires=[
39 "scipy >= 0.14.0",
39 "scipy >= 0.14.0",
40 "h5py >= 2.2.1",
40 "h5py >= 2.2.1",
41 "matplotlib >= 1.4.2",
41 "matplotlib >= 1.4.2",
42 "pyfits >= 3.4",
42 "pyfits >= 3.4",
43 "numpy >= 1.11.2",
43 "numpy >= 1.11.2",
44 "paramiko >= 2.1.2",
44 "paramiko >= 2.1.2",
45 "paho-mqtt >= 1.2",
45 "paho-mqtt >= 1.2",
46 "zmq",
46 "zmq",
47 ],
47 ],
48 ) No newline at end of file
48 )
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