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Add license, update setup and changelog
Juan C. Espinoza -
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1 This software, unless otherwise noted, is licensed under the BSD 3-clause.
2
3 Copyright (c) 2012-2020 Jicamarca Radio Observatory
4
5 Redistribution and use in source and binary forms, with or without
6 modification, are permitted provided that the following conditions are met:
7
8 * Redistributions of source code must retain the above copyright notice, this
9 list of conditions and the following disclaimer.
10
11 * Redistributions in binary form must reproduce the above copyright notice,
12 this list of conditions and the following disclaimer in the documentation
13 and/or other materials provided with the distribution.
14
15 * Neither the name of the copyright holder nor the names of its
16 contributors may be used to endorse or promote products derived from
17 this software without specific prior written permission.
18
19 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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@@ -100,15 +100,3 ENV/
100 100 # eclipse
101 101 .project
102 102 .pydevproject
103 # vscode
104
105 .vscode
106
107 schaingui/node_modules/
108 schainpy/scripts/
109 .svn/
110 *.png
111 *.pyc
112 .vscode
113 trash
114 *.log
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@@ -1,15 +1,19
1 # CHANGELOG:
1 # CHANGELOG
2
3 ## 3.0.0
2 4
3 ## 3.0
4 5 * Python 3.x & 2.X compatible
5 6 * New architecture with multiprocessing support
6 7 * Add @MPDecorator for multiprocessing Operations (Plots, Writers and Publishers)
7 8 * Added new type of operation `external` for non-locking operations
8 9 * New plotting architecture with buffering/throttle capabilities to speed up plots
9 10 * Clean controller to optimize scripts (format & optype are no longer required)
11 * Replace ParamReader and ParamWriter with new flexible HDFReader and HDFWriter
10 12 * New GUI with dinamic load of Units and operations (use Kivy framework)
13 * Clean code
11 14
12 15 ## 2.3
16
13 17 * Added support for Madrigal formats (reading/writing).
14 18 * Added support for reading BLTR parameters (*.sswma).
15 19 * Added support for reading Julia format (*.dat).
@@ -17,11 +21,11
17 21 * Added two new Processing Units `PublishData` and `ReceiverData` for receiving and sending dataOut through multiple ways (tcp, ipc, inproc).
18 22 * Added a new graphics Processing Unit `PlotterReceiver`. It is decoupled from normal processing sequence with support for data generated by multiprocessing scripts.
19 23 * Added support for sending realtime graphic to web server.
20 * GUI command `schain` is now `schainGUI`.
21 * Added a CLI tool named `schain`.
22 * Scripts templates can be now generated with `schain generate`.
23 * Now it is possible to search Processing Units and Operations with `schain search [module]` to get the right name and its allowed parameters.
24 * `schain xml` to run xml scripts.
24 * GUI command `schain` is now `schainGUI`.
25 * Added a CLI tool named `schain`.
26 * Scripts templates can be now generated with `schain generate`.
27 * Now it is possible to search Processing Units and Operations with `schain search [module]` to get the right name and its allowed parameters.
28 * `schain xml` to run xml scripts.
25 29 * Added suggestions when parameters are poorly written.
26 30 * `Controller.start()` now runs in a different process than the process calling it.
27 31 * Added `schainpy.utils.log` for log standarization.
@@ -31,6 +35,7
31 35 * Setup now installs numpy.
32 36
33 37 ## 2.2.6
38
34 39 * Graphics generated by the GUI are now the same as generated by scripts. Issue #1074.
35 40 * Added support for C extensions.
36 41 * Function `hildebrand_sehkon` optimized with a C wrapper.
@@ -38,27 +43,32
38 43 * Migration to GIT.
39 44
40 45 ## 2.2.5:
46
41 47 * splitProfiles and combineProfiles modules were added to VoltageProc and Signal Chain GUI.
42 48 * nProfiles of USRP data (hdf5) is the number of profiles thera are in one second.
43 49 * jroPlotter works directly with data objects instead of dictionaries
44 50 * script "schain" was added to Signal Chain installer
45 51
46 52 ## 2.2.4.1:
53
47 54 * jroIO_usrp.py is update to read Sandra's data
48 55 * decimation in Spectra and RTI plots is always enabled.
49 56 * time* window option added to GUI
50 57
51 58 ## 2.2.4:
59
52 60 * jroproc_spectra_lags.py added to schainpy
53 61 * Bug fixed in schainGUI: ProcUnit was created with the same id in some cases.
54 62 * Bug fixed in jroHeaderIO: Header size validation.
55 63
56 64 ## 2.2.3.1:
65
57 66 * Filtering block by time has been added.
58 67 * Bug fixed plotting RTI, CoherenceMap and others using xmin and xmax parameters. The first day worked
59 68 properly but the next days did not.
60 69
61 70 ## 2.2.3:
71
62 72 * Bug fixed in GUI: Error getting(reading) Code value
63 73 * Bug fixed in GUI: Flip option always needs channelList field
64 74 * Bug fixed in jrodata: when one branch modified a value in "dataOut" (example: dataOut.code) this value
@@ -66,10 +76,12 was modified for every branch (because this was a reference). It was modified in
66 76 * Bug fixed in jroproc_voltage.profileSelector(): rangeList replaces to profileRangeList.
67 77
68 78 ## 2.2.2:
79
69 80 * VoltageProc: ProfileSelector, Reshape, Decoder with nTxs!=1 and getblock=True was tested
70 81 * Rawdata and testRawdata.py added to Signal Chain project
71 82
72 83 ## 2.2.1:
84
73 85 * Bugs fixed in GUI
74 86 * Views were improved in GUI
75 87 * Support to MST* ISR experiments
@@ -77,36 +89,45 was modified for every branch (because this was a reference). It was modified in
77 89 * handleError added to jroplotter.py
78 90
79 91 ## 2.2.0:
92
80 93 * GUI: use of external plotter
81 94 * Compatible with matplotlib 1.5.0
82 95
83 96 ## 2.1.5:
97
84 98 * serializer module added to Signal Chain
85 99 * jroplotter.py added to Signal Chain
86 100
87 101 ## 2.1.4.2:
102
88 103 * A new Plotter Class was added
89 104 * Project.start() does not accept filename as a parameter anymore
90 105
91 106 ## 2.1.4.1:
107
92 108 * Send notifications when an error different to ValueError is detected
93 109
94 110 ## 2.1.4:
111
95 112 * Sending error notifications to signal chain administrator
96 113 * Login to email server added
97 114
98 115 ## 2.1.3.3:
116
99 117 * Colored Button Icons were added to GUI
100 118
101 119 ## 2.1.3.2:
120
102 121 * GUI: user interaction enhanced
103 122 * controller_api.py: Safe access to ControllerThead
104 123
105 124 ## 2.1.3.1:
125
106 126 * GUI: every icon were resized
107 127 * jroproc_voltage.py: Print a message when "Read from code" option is selected and the code is not defined inside data file
108 128
109 129 ## 2.1.3:
130
110 131 * jroplot_heispectra.py: SpectraHeisScope was not showing the right channels
111 132 * jroproc_voltage.py: Bug fixed selecting profiles (self.nProfiles took a wrong value),
112 133 Bug fixed selecting heights by block (selecting profiles instead heights)
@@ -115,6 +136,7 was modified for every branch (because this was a reference). It was modified in
115 136 * jroIO_heispectra.py: Channel index list does not exist.
116 137
117 138 ## 2.1.2:
139
118 140 * jroutils_ftp.py: Bug fixed, Any error sending file stopped the Server Thread
119 141 Server thread opens and closes remote server each time file list is sent
120 142 * jroplot_spectra.py: Noise path was not being created when noise data is saved.
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@@ -1,48 +1,50
1 1 # Signal Chain
2 2
3 ## Introduction
3 Signal Chain is a radar data processing library wich includes modules to read,
4 and write different files formats, besides modules to process and visualize the
5 data.
4 6
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.
7 ## Dependencies
6 8
7 ## Installation
8
9 Install system dependencies, clone the latest version from [here](http://jro-dev.igp.gob.pe/rhodecode/schain/) and install it as a normal python package, we strongly recommend to use Anaconda or a virtual environment for the installation.
10
11 ### Dependencies
12 9 - GCC (gcc or gfortran)
13 10 - Python.h (python-dev or python-devel)
14 11 - Python-TK (python-tk)
15 12 - HDF5 libraries (libhdf5-dev)
16 13
17 ### Linux based system (e.g. ubuntu)
18 ```
19 $ git clone http://jro-dev.igp.gob.pe/rhodecode/schain/
20 $ cd schain
21 $ git checkout `schain-branch` (optional)
22 $ sudo pip install ./
23 ```
14 ## Installation
24 15
25 ### MAC Os
26 ```
27 $ brew install python
28 $ git clone http://jro-dev.igp.gob.pe/rhodecode/schain/
29 $ cd schain
30 $ git checkout `schain-branch` (optional)
31 $ sudo pip install ./
16 To get started the easiest way to install it is through [PyPI](https://pypi.org/project/schainpy/) with pip:
17
18 ```bash
19 pip install schainpy
32 20 ```
33 21
34 ### Docker
22 ### From source
35 23
36 Download Dockerfile from the repository, and create a docker image
24 First, ensure that you have the above-listed dependencies installed, then clone
25 the repository and install as normal python package:
37 26
27 ```bash
28 git clone https://github.com/JRO-Peru/schain.git
29 cd schain
30 git checkout `branch-name` (optional)
31 sudo pip install ./
38 32 ```
39 $ docker build -t schain .
40 ```
41 33
42 You can run a container using an xml file or a schain script also you need to mount a volume for the data input and for the output files/plots
34 ### Using Docker
35
36 Download Dockerfile from the repository, and create a docker image:
37
38 ```bash
39 docker build -t schain .
43 40 ```
44 $ docker run -it --rm --volume /path/to/host/data:/data schain xml /data/test.xml
45 $ docker run -it --rm --volume /path/to/host/data:/data --entrypoint /urs/local/bin/python schain /data/test.py
41
42 You can run a container using an xml file or a schain script also you need to
43 mount a volume for the data input and for the output files/plots:
44
45 ```bash
46 docker run -it --rm --volume /path/to/host/data:/data schain xml /data/test.xml
47 docker run -it --rm --volume /path/to/host/data:/data --entrypoint /urs/local/bin/python schain /data/test.py
46 48 ```
47 49
48 50 ## CLI (command line interface)
@@ -52,12 +54,10 Signal Chain provides the following commands:
52 54 - schainGUI: Open the GUI
53 55 - schain: Signal chain command line
54 56
57 ## Example
55 58
56 ## First Script
57
58 Here you can find an script to read Spectra data (.pdata), remove dc and plot spectra & RTI
59
60 First import SCh and creating a project
59 Here you can find an script to read Spectra data (.pdata), remove dc and plot
60 self-spectra & RTI:
61 61
62 62 ```python
63 63 #!/usr/bin/python
@@ -65,16 +65,7 First import SCh and creating a project
65 65 from schainpy.controller import Project
66 66
67 67 prj = Project()
68 prj.setup(
69 id = '100',
70 name='test',
71 description='Basic experiment'
72 )
73 ```
74 68
75 Add read unit and operations
76
77 ```python
78 69 read_unit = prj.addReadUnit(
79 70 datatype='Spectra',
80 71 path='/path/to/pdata/',
@@ -86,57 +77,10 read_unit = prj.addReadUnit(
86 77 walk=0
87 78 )
88 79
89 proc_unit = prj.addProcUnit(datatype='Spectra', inputId=read_unit.getId())
90
91 op = proc_unit.addOperation(name='selectChannels')
92 op.addParameter(name='channelList', value='0,1')
93
94 op = proc_unit.addOperation(name='selectHeights')
95 op.addParameter(name='minHei', value='80')
96 op.addParameter(name='maxHei', value='200')
97
98 op = proc_unit.addOperation(name='removeDC')
99
100 ```
101
102 Plot data & start project
103
104 ```python
105 op = proc_unit.addOperation(name='SpectraPlot')
106 op.addParameter(name='id', value='1')
107 op.addParameter(name='wintitle', value='Spectra')
108
109 op = procUnitConfObj1.addOperation(name='RTIPlot')
110 op.addParameter(name='id', value='2')
111 op.addParameter(name='wintitle', value='RTI')
112
113 prj.start()
114
115 ```
116
117 Full script
118
119
120 ```python
121 #!/usr/bin/python
122
123 from schainpy.prj import Project
124
125 prj = Project()
126 prj.setup(id = '100',
127 name='test',
128 description='Basic experiment')
129 read_unit = prj.addReadUnit(datatype='Spectra',
130 path='/path/to/pdata/',
131 startDate='2014/01/31',
132 endDate='2014/03/31',
133 startTime='00:00:00',
134 endTime='23:59:59',
135 online=0,
136 walk=0)
137
138 proc_unit = prj.addProcUnit(datatype='Spectra',
139 inputId=read_unit.getId())
80 proc_unit = prj.addProcUnit(
81 datatype='Spectra',
82 inputId=read_unit.getId()
83 )
140 84
141 85 op = proc_unit.addOperation(name='selectChannels')
142 86 op.addParameter(name='channelList', value='0,1')
@@ -155,4 +99,4 op.addParameter(name='wintitle', value='RTI', format='str')
155 99
156 100 prj.start()
157 101
158 ``` No newline at end of file
102 ```
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@@ -1,7 +1,5
1 '''
2 Created on Jul 3, 2018
1 """Signal chain python package"""
3 2
4 @author $Author$
5 @version $Id$
6 '''
7 __version__ = '3.0'
3 from .controller import Project
4
5 __version__ = '3.0.0'
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@@ -1,6 +1,11
1 '''
2 Main routines to create a Signal Chain project
3 '''
1 # Copyright (c) 2012-2020 Jicamarca Radio Observatory
2 # All rights reserved.
3 #
4 # Distributed under the terms of the BSD 3-clause license.
5 """API to create signal chain projects
6
7 The API is provide through class: Project
8 """
4 9
5 10 import re
6 11 import sys
@@ -312,13 +317,16 class ReadUnitConf(ProcUnitConf):
312 317
313 318
314 319 class Project(Process):
320 """API to create signal chain projects"""
315 321
316 322 ELEMENTNAME = 'Project'
317 323
318 324 def __init__(self):
319 325
320 Process.__init__(self)
321 self.id = None
326 Process.__init__(self, name='')
327 self.id = '1'
328 if name:
329 self.name = '{} ({})'.format(Process.__name__, name)
322 330 self.filename = None
323 331 self.description = None
324 332 self.email = None
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@@ -1,15 +1,21
1 '''
2 Created on Jul 16, 2014
1 # Copyright (c) 2012-2020 Jicamarca Radio Observatory
2 # All rights reserved.
3 #
4 # Distributed under the terms of the BSD 3-clause license.
5 """schainpy is an open source library to read, write and process radar data
3 6
4 @author: Miguel Urco
5 @author: Juan C. Espinoza
6 '''
7 Signal Chain is a radar data processing library wich includes modules to read,
8 and write different files formats, besides modules to process and visualize the
9 data.
10 """
7 11
8 12 import os
9 13 from setuptools import setup, Extension
10 14 from setuptools.command.build_ext import build_ext as _build_ext
11 15 from schainpy import __version__
12 16
17 DOCLINES = __doc__.split("\n")
18
13 19 class build_ext(_build_ext):
14 20 def finalize_options(self):
15 21 _build_ext.finalize_options(self)
@@ -21,10 +27,27 class build_ext(_build_ext):
21 27 setup(
22 28 name = "schainpy",
23 29 version = __version__,
24 description = "Python tools to read, write and process Jicamarca data",
25 author = "Miguel Urco, Juan C. Espinoza",
26 author_email = "juan.espinoza@jro.igp.gob.pe",
27 url = "http://jro-dev.igp.gob.pe/rhodecode/schain",
30 description = DOCLINES[0],
31 long_description = "\n".join(DOCLINES[2:]),
32 url = "https://github.com/JRO-Peru/schain",
33 author = "Jicamarca Radio Observatory",
34 author_email = "jro-developers@igp.gob.pe",
35 license="BSD-3-Clause",
36 classifiers=[
37 "Development Status :: 4 - Beta",
38 "Environment :: Console",
39 "Intended Audience :: Science/Research",
40 "License :: OSI Approved :: BSD License",
41 "Operating System :: MacOS :: MacOS X",
42 "Operating System :: POSIX :: Linux",
43 "Programming Language :: Python :: 2",
44 "Programming Language :: Python :: 2.7",
45 "Programming Language :: Python :: 3",
46 "Programming Language :: Python :: 3.5",
47 "Programming Language :: Python :: 3.6",
48 "Programming Language :: Python :: 3.7",
49 "Topic :: Scientific/Engineering",
50 ],
28 51 packages = {
29 52 'schainpy',
30 53 'schainpy.model',
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