schain-jc Commit - r1054:10ce564971bb

merge from master

José Chávez -

r1054:10ce564971bb

parent child

Context file:

r1054:10ce564971bb

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schainpy/CHANGELOG.md created 644 +108 0

@@ -0,0 +1,108
	1	## CHANGELOG:
	2
	3	### 2.3
	4	* Added high order function `multiSchain` for multiprocessing scripts.
	5	* Added two new Processing Units `PublishData` and `ReceiverData` for receiving and sending dataOut through multiple ways (tcp, ipc, inproc).
	6	* Added a new graphics Processing Unit `PlotterReceiver`. It is decoupled from normal processing sequence with support for data generated by multiprocessing scripts.
	7	* Added support for sending realtime graphic to web server.
	8	* XML command `schain` is now `schain --xml`.
	9	* Added a CLI tool named `schain`.
	10	* Scripts templates can be now generated with `schain generate`.
	11	* Now it is possible to search Processing Units and Operations with `schain search [module]` to get the right name and its allowed parameters.
	12	* Added suggestions when parameters are poorly written.
	13	* `Controller.start()` now runs in a different process than the process calling it.
	14	* Added `schainpy.utils.log` for log standarization.
	15	* Running script on online mode no longer ignores date and hour. Issue #1109.
	16	* Added support for receving voltage data directly from JARS (tcp, ipc).
	17	* Updated README for compatibility with MAC OS GUI installation.
	18	* Setup now installs numpy.
	19
	20	### 2.2.6
	21	* Graphics generated by the GUI are now the same as generated by scripts. Issue #1074.
	22	* Added support for C extensions.
	23	* Function `hildebrand_sehkon` optimized with a C wrapper.
	24	* Numpy version updated.
	25	* Migration to GIT.
	26
	27	### 2.2.5:
	28	* splitProfiles and combineProfiles modules were added to VoltageProc and Signal Chain GUI.
	29	* nProfiles of USRP data (hdf5) is the number of profiles thera are in one second.
	30	* jroPlotter works directly with data objects instead of dictionaries
	31	* script "schain" was added to Signal Chain installer
	32
	33	### 2.2.4.1:
	34	* jroIO_usrp.py is update to read Sandra's data
	35	* decimation in Spectra and RTI plots is always enabled.
	36	* time* window option added to GUI
	37
	38	### 2.2.4:
	39	* jroproc_spectra_lags.py added to schainpy
	40	* Bug fixed in schainGUI: ProcUnit was created with the same id in some cases.
	41	* Bug fixed in jroHeaderIO: Header size validation.
	42
	43	### 2.2.3.1:
	44	* Filtering block by time has been added.
	45	* Bug fixed plotting RTI, CoherenceMap and others using xmin and xmax parameters. The first day worked
	46	properly but the next days did not.
	47
	48	### 2.2.3:
	49	* Bug fixed in GUI: Error getting(reading) Code value
	50	* Bug fixed in GUI: Flip option always needs channelList field
	51	* Bug fixed in jrodata: when one branch modified a value in "dataOut" (example: dataOut.code) this value
	52	was modified for every branch (because this was a reference). It was modified in data.copy()
	53	* Bug fixed in jroproc_voltage.profileSelector(): rangeList replaces to profileRangeList.
	54
	55	### 2.2.2:
	56	* VoltageProc: ProfileSelector, Reshape, Decoder with nTxs!=1 and getblock=True was tested
	57	* Rawdata and testRawdata.py added to Signal Chain project
	58
	59	### 2.2.1:
	60	* Bugs fixed in GUI
	61	* Views were improved in GUI
	62	* Support to MST* ISR experiments
	63	* Bug fixed getting noise using hyldebrant. (minimum number of points > 20%)
	64	* handleError added to jroplotter.py
	65
	66	### 2.2.0:
	67	* GUI: use of external plotter
	68	* Compatible with matplotlib 1.5.0
	69
	70	### 2.1.5:
	71	* serializer module added to Signal Chain
	72	* jroplotter.py added to Signal Chain
	73
	74	### 2.1.4.2:
	75	* A new Plotter Class was added
	76	* Project.start() does not accept filename as a parameter anymore
	77
	78	### 2.1.4.1:
	79	* Send notifications when an error different to ValueError is detected
	80
	81	### 2.1.4:
	82	* Sending error notifications to signal chain administrator
	83	* Login to email server added
	84
	85	### 2.1.3.3:
	86	* Colored Button Icons were added to GUI
	87
	88	### 2.1.3.2:
	89	* GUI: user interaction enhanced
	90	* controller_api.py: Safe access to ControllerThead
	91
	92	### 2.1.3.1:
	93	* GUI: every icon were resized
	94	* jroproc_voltage.py: Print a message when "Read from code" option is selected and the code is not defined inside data file
	95
	96	### 2.1.3:
	97	* jroplot_heispectra.py: SpectraHeisScope was not showing the right channels
	98	* jroproc_voltage.py: Bug fixed selecting profiles (self.nProfiles took a wrong value),
	99	Bug fixed selecting heights by block (selecting profiles instead heights)
	100	* jroproc_voltage.py: New feature added: decoding data by block using FFT.
	101	* jroIO_heispectra.py: Bug fixed in FitsReader. Using local Fits instance instead schainpy.mode.data.jrodata.Fits.
	102	* jroIO_heispectra.py: Channel index list does not exist.
	103
	104	### 2.1.2:
	105	* jroutils_ftp.py: Bug fixed, Any error sending file stopped the Server Thread
	106	Server thread opens and closes remote server each time file list is sent
	107	* jroplot_spectra.py: Noise path was not being created when noise data is saved.
	108	* jroIO_base.py: startTime can be greater than endTime. Example: SpreadF [18:00 * 07:00] No newline at end of file

.gitignore +10 0

             # eclipse
             .project
             .pydevproject
+            <<<<<<< HEAD
             # vscode
             schaingui/node_modules/
             schainpy/scripts/
+            =======
+            .svn/
+            *.png
+            *.pyc
+            schainpy/scripts
+            .vscode
+            schaingui/node_modules
+            trash
+            >>>>>>> master

README.md +23 -7

@@ -6,24 +6,40 Signal Chain (SCh) is a radar data processing library developed using [Python](w
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	### Linux based system
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	$ 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	$ sudo pip install numpy
14	$ cd schainpy-2.2.5	15	$ git clone http://jro-dev.igp.gob.pe/rhodecode/schain/
		16	$ cd schain
15	$ sudo pip install ./	17	$ sudo pip install ./
16	```
17
18	Its recommended to install schain in a virtual environment
19		18
20	```	19	```
		20	It is recommended to install schain in a virtual environment
		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 schain~~py-2.2.5~~	25	(virtual) $ cd schain
25	(virtual) $ pip install ./	26	(virtual) $ pip install ./
		27
		28	```
		29
		30	### MAC Os
26	```	31	```
		32	$ brew install cartr/qt4/pyqt
		33	$ git clone http://jro-dev.igp.gob.pe/rhodecode/schain/
		34	$ cd schain
		35	$ pip install ./
		36	```
		37
		38	if ```pip install ./``` does not work, install a proper python enviroment, and repeat the steps.
		39	```
		40	$ brew install python
		41	```
		42
27		43
28	## First Script	44	## First Script
29		45

schainpy/__init__.py +1 0

             @author $Author$
             @version $Id$
             '''
             __version__ = "2.3"

schainpy/controller.py +1 -1

                         sts = self.procUnitObj.call(opType = opConfObj.type,
                                                     opName = opConfObj.name,
                                                     opId = opConfObj.id,
+                                                    **kwargs)
                         #             total_time = time.time() - ini
                         #

schainpy/controller_api.py +1 -1

                                 continue
                             if thisOpObj.name in plotterList:
-                                thisOpObj.type = "plotter"
+                                thisOpObj.type = "other"
                 def setPlotterQueue(self, plotter_queue):

schainpy/model/data/jrodata.py 0 -2

                     return fmax
                 def getFmax(self):
                     PRF = 1./(self.ippSeconds * self.nCohInt)
                     fmax = PRF
                     return fmax
                 def getVmax(self):

schainpy/model/graphics/jroplot_spectra.py +2 -2

                     self.isConfig = False
                     self.__nsubplots = 1
-                    self.WIDTH = 250
+                    self.WIDTH = 1000
-                    self.HEIGHT = 250
+                    self.HEIGHT = 1000
                     self.WIDTHPROF = 120
                     self.HEIGHTPROF = 0
                     self.counter_imagwr = 0

schainpy/model/graphics/jroplotter.py 0 0

NO CONTENT: modified file

schainpy/model/io/jroIO_base.py 0 -33

@@ -1340,39 +1340,6 class JRODataReader(JRODataIO):
1340	return	1340	return
1341		1341
1342	self.fileIndex = -1	1342	self.fileIndex = -1
1343	self.pathList = pathList
1344	self.filenameList = filenameList
1345	file_name = os.path.basename(filenameList[-1])
1346	basename, ext = os.path.splitext(file_name)
1347	last_set = int(basename[-3:])
1348
1349	self.online = online
1350	self.realtime = realtime
1351	self.delay = delay
1352	ext = ext.lower()
1353	self.ext = ext
1354	self.getByBlock = getblock
1355	self.nTxs = nTxs
1356	self.startTime = startTime
1357	self.endTime = endTime
1358
1359	#Added-----------------
1360	self.selBlocksize = blocksize
1361	self.selBlocktime = blocktime
1362
1363	# Verbose-----------
1364	self.verbose = verbose
1365	self.warnings = warnings
1366
1367	if not(self.setNextFile()):
1368	if (startDate!=None) and (endDate!=None):
1369	print "[Reading] No files in range: %s - %s" %(datetime.datetime.combine(startDate,startTime).ctime(), datetime.datetime.combine(endDate,endTime).ctime())
1370	elif startDate != None:
1371	print "[Reading] No files in range: %s" %(datetime.datetime.combine(startDate,startTime).ctime())
1372	else:
1373	print "[Reading] No files"
1374
1375	self.fileIndex = -1
1376	self.pathList = []	1343	self.pathList = []
1377	self.filenameList = []	1344	self.filenameList = []
1378	return	1345	return

schainpy/model/io/jroIO_digitalRF.py +38 -16

                     self.__nCode = None
                     self.__nBaud = None
                     self.__code = None
+                    self.dtype = None
                 def close(self):
                     print 'Average of writing to digital rf format is ', self.oldAverage * 1000
                     nProfiles = 1.0/ippSeconds  # Number of profiles in one second
+                    try:
                         self.dataOut.radarControllerHeaderObj = RadarControllerHeader(self.__radarControllerHeader)
+                    except:
+                        self.dataOut.radarControllerHeaderObj = RadarControllerHeader(
+                                                                                    txA=0,
+                                                                                    txB=0,
+                                                                                    nWindows=1,
+                                                                                    nHeights=self.__nSamples,
+                                                                                    firstHeight=self.__firstHeigth,
+                                                                                    deltaHeight=self.__deltaHeigth,
+                                                                                    codeType=self.__codeType,
+                                                                                    nCode=self.__nCode, nBaud=self.__nBaud,
+                                                                                    code = self.__code)
+                    try:
                         self.dataOut.systemHeaderObj = SystemHeader(self.__systemHeader)
+                    except:
+                        self.dataOut.systemHeaderObj = SystemHeader(nSamples=self.__nSamples,
+                                                                    nProfiles=nProfiles,
+                                                                    nChannels=len(self.__channelList),
+                                                                    adcResolution=14)
                     self.dataOut.type = "Voltage"
                     self.dataOut.data = None
                     self.dataOut.errorCount = 0
-                    self.dataOut.nCohInt = self.fixed_metadata_dict['nCohInt']
+                    try:
+                        self.dataOut.nCohInt = self.fixed_metadata_dict.get('nCohInt', 1)
                         self.dataOut.flagDecodeData = self.fixed_metadata_dict['flagDecodeData'] # asumo que la data esta decodificada
                         self.dataOut.flagShiftFFT = self.fixed_metadata_dict['flagShiftFFT']
                         self.dataOut.useLocalTime = self.fixed_metadata_dict['useLocalTime']
+                    except:
+                        pass
                     self.dataOut.ippSeconds = ippSeconds
                     top_properties = self.digitalReadObj.get_properties(channelNameList[channelList[0]])
                     self.__num_subchannels = top_properties['num_subchannels']
                     self.__sample_rate = 1.0 * top_properties['sample_rate_numerator'] / top_properties['sample_rate_denominator']
                     # self.__samples_per_file = top_properties['samples_per_file'][0]
                     self.__deltaHeigth = 1e6*0.15/self.__sample_rate ## why 0.15?
                     this_metadata_file = self.digitalReadObj.get_digital_metadata(channelNameList[channelList[0]])
                     metadata_bounds = this_metadata_file.get_bounds()
                     self.fixed_metadata_dict = this_metadata_file.read(metadata_bounds[0])[metadata_bounds[0]] ## GET FIRST HEADER
+                    try:
                         self.__processingHeader = self.fixed_metadata_dict['processingHeader']
                         self.__radarControllerHeader = self.fixed_metadata_dict['radarControllerHeader']
                         self.__systemHeader = self.fixed_metadata_dict['systemHeader']
                         self.dtype = cPickle.loads(self.fixed_metadata_dict['dtype'])
+                    except:
+                        pass
-                    self.__frequency = None
-                    try:
-                        self.__frequency = self.fixed_metadata_dict['frequency']
-                    except:
                     self.__frequency = None
-                    try:
+                    self.__frequency = self.fixed_metadata_dict.get('frequency', 1)
-                        self.__timezone = self.fixed_metadata_dict['timezone'] * 60
-                    except:
+                    self.__timezone = self.fixed_metadata_dict.get('timezone', 300)
-                        self.__timezone = 0
                     try:
                     nBaud = 1
                     code = numpy.ones((nCode, nBaud), dtype=numpy.int)
+                    try:
                         if codeType:
                             nCode = self.__radarControllerHeader['nCode']
                             nBaud = self.__radarControllerHeader['nBaud']
                             code = self.__radarControllerHeader['code']
+                    except:
+                        pass
                     if not ippKm:
                         try:
                         except:
                             ippKm = None
                     ####################################################
+                    self.__ippKm = ippKm
                     startUTCSecond = None
                     endUTCSecond = None
                     self.profileIndex = 0
                     self.i= 0
                     self.__delay = delay
-                    self.__ippKm = ippKm
                     self.__codeType = codeType
                     self.__nCode = nCode
                     self.__nBaud = nBaud
                     Operation.__init__(self, **kwargs)
                     self.metadata_dict = {}
                     self.dataOut = None
+                    self.dtype = None
                 def setHeader(self):

schainpy/model/proc/jroproc_spectra.py 0 -1

                     return self.__initime, avgdata_spc, avgdata_cspc, avgdata_dc
                 def run(self, dataOut, n=None, timeInterval=None, overlapping=False):
                     if n==1:
                         return

schainpy/model/utils/jroutils_ftp.py +4 -4

                     None
                 Written by:
                     "Miguel Urco":mailto:miguel.urco@jro.igp.gob.pe Jun. 03, 2015
                 """
                 server = None
                     return fullfilenameList
                 def run(self, **kwargs):
                     if not self.isConfig:
                         self.init = time.time()
                         self.setup(**kwargs)
                         self.isConfig = True
+                    if not self.clientObj.is_alive():
+                        print "[Remote Server]: Restarting connection "
+                        self.setup(**kwargs)
                     if time.time() - self.init >= self.period:
                         fullfilenameList = self.findFiles()
                         if self.clientObj.updateFileList(fullfilenameList):
                             print "[Remote Server]: Sending the next files ", str(fullfilenameList)
                         self.init = time.time()
                 def close(self):

schainpy/scripts/schain.xml +1 -1

	@@ -1,1 +1,1
	1	<Project description="Testing USRP data reader" id="191" name="test01"><ReadUnit datatype="Voltage" id="1911" inputId="0" name="VoltageReader"><Operation id="19111" name="run" priority="1" type="self"><Parameter format="str" id="191111" name="datatype" value="Voltage" /><Parameter format="str" id="191112" name="path" value="/home/nanosat/data/John" /><Parameter format="date" id="191113" name="startDate" value="2000/07/03" /><Parameter format="date" id="191114" name="endDate" value="2017/07/03" /><Parameter format="time" id="191115" name="startTime" value="00:00:00" /><Parameter format="time" id="191116" name="endTime" value="23:59:59" /><Parameter format="int" id="191118" name="blockTime" value="100" /><Parameter format="int" id="191119" name="walk" value="0" /><Parameter format="int" id="191120" name="online" value="0" /></Operation></ReadUnit><ProcUnit datatype="VoltageProc" id="1912" inputId="1911" name="VoltageProc"><Operation id="19121" name="run" priority="1" type="self" /><Operation id="19122" name="Decoder" priority="2" type="external"><Parameter format="intlist" id="191221" name="code" value="1,-1,-1,1,-1" /><Parameter format="int" id="191222" name="nCode" value="5" /><Parameter format="int" id="191223" name="nBaud" value="1" /></Operation></ProcUnit></Project> No newline at end of file		1	<Project description="Claire" id="002" name="script02"><ReadUnit datatype="VoltageReader" id="21" inputId="0" name="VoltageReader"><Operation id="211" name="run" priority="1" type="self"><Parameter format="str" id="2111" name="datatype" value="VoltageReader" /><Parameter format="str" id="2112" name="path" value="/media/nanosat/0BDE10E00BDE10E0/CLAIRE" /><Parameter format="date" id="2113" name="startDate" value="2017/07/26" /><Parameter format="date" id="2114" name="endDate" value="2017/07/26" /><Parameter format="time" id="2115" name="startTime" value="15:00:00" /><Parameter format="time" id="2116" name="endTime" value="16:00:00" /><Parameter format="int" id="2118" name="delay" value="30" /><Parameter format="int" id="2119" name="walk" value="1" /><Parameter format="int" id="2120" name="online" value="0" /></Operation><Operation id="212" name="printNumberOfBlock" priority="2" type="self" /></ReadUnit><ProcUnit datatype="VoltageProc" id="22" inputId="21" name="VoltageProc"><Operation id="221" name="run" priority="1" type="self" /></ProcUnit><ProcUnit datatype="SpectraProc" id="23" inputId="22" name="SpectraProc"><Operation id="231" name="run" priority="1" type="self"><Parameter format="int" id="2311" name="nFFTPoints" value="128" /><Parameter format="int" id="2312" name="nProfiles" value="128" /><Parameter format="pairslist" id="2313" name="pairsList" value="(0,1),(0,2),(1,2)" /></Operation><Operation id="232" name="setRadarFrequency" priority="2" type="self"><Parameter format="float" id="2321" name="frequency" value="445000000.0" /></Operation><Operation id="233" name="IncohInt" priority="3" type="other"><Parameter format="float" id="2331" name="timeInterval" value="128" /></Operation><Operation id="234" name="removeDC" priority="4" type="self"><Parameter format="int" id="2341" name="mode" value="2" /></Operation><Operation id="235" name="SpectraPlot" priority="5" type="external"><Parameter format="int" id="2351" name="id" value="235" /><Parameter format="str" id="2352" name="wintitle" value="SpectraPlot" /><Parameter format="str" id="2353" name="xaxis" value="frequency" /><Parameter format="float" id="2354" name="zmin" value="15.0" /><Parameter format="float" id="2355" name="zmax" value="50.0" /><Parameter format="int" id="2356" name="exp_code" value="21" /><Parameter format="int" id="2357" name="ftp_wei" value="0" /><Parameter format="int" id="2358" name="plot_pos" value="0" /></Operation></ProcUnit></Project> No newline at end of file

setup.py +18 -15

             @author: Miguel Urco
             """
-            from schainpy import __version__
             from setuptools import setup, Extension
+            from setuptools.command.build_ext import build_ext as _build_ext
+            from schainpy import __version__
+            class build_ext(_build_ext):
+                def finalize_options(self):
+                    _build_ext.finalize_options(self)
+                    # Prevent numpy from thinking it is still in its setup process:
+                    __builtins__.__NUMPY_SETUP__ = False
+                    import numpy
+                    self.include_dirs.append(numpy.get_include())
             setup(name="schainpy",
                     version=__version__,
                                   'schainpy.gui.figures': ['*.png','*.jpg'],
                                   },
                     include_package_data=False,
-                  entry_points={
+                    scripts =['schainpy/gui/schainGUI',
-                    'console_scripts': [
+                              'schainpy/scripts/schain'],
-                        'schain = schaincli.cli:main',
+                    ext_modules=[
-                    ],
+                      Extension("cSchain", ["schainpy/model/proc/extensions.c"]
-                  },
+                    )],
-                  scripts=['schainpy/gui/schainGUI'],
+                    cmdclass={'build_ext':build_ext},
-                  ext_modules=[Extension("cSchain", ["schainpy/model/proc/extensions.c"], include_dirs=[numpy.get_include()])],
+                    setup_requires=["numpy >= 1.11.2"],
                     install_requires=[
                                       "scipy >= 0.14.0",
                                       "h5py >= 2.2.1",
                                       "matplotlib >= 1.4.2",
                                       "pyfits >= 3.4",
-                                  "numpy >= 1.11.2",
-                                  "paramiko >= 2.1.2",
                                       "paho-mqtt >= 1.2",
                                       "zmq",
-                                  "fuzzywuzzy",
-                                  "click",
-                                  "colorama",
-                                  "python-Levenshtein"
                                       ],
                   )

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