Merge branch 'dev'

Author: ratal

.idea/inspectionProfiles/Project_Default.xml

@@ -83,25 +83,30 @@ Command example in ipython:
 ```python
     import mdfreader
     # loads whole mdf file content in yop mdf object.
-    yop=mdfreader.mdf('NameOfFile')
+    yop=mdfreader.Mdf('NameOfFile')
     # you can print file content in ipython with a simple:
     yop
     # alternatively, for max speed and smaller memory footprint, read only few channels
-    yop=mdfreader.mdf('NameOfFile',channelList=['channel1', 'channel2'],convertAfterRead=False)
+    yop=mdfreader.Mdf('NameOfFile', channelList=['channel1', 'channel2'], convertAfterRead=False)
     # also possible to keep data compressed for small memory footprint, using Blosc module
-    yop=mdfreader.mdf('NameOfFile',compression=True)
+    yop=mdfreader.Mdf('NameOfFile', compression=True)
     # for interactive file exploration, possible to read the file but not its data to save memory
-    yop=mdfreader.mdf('NameOfFile',noDataLoading=True) # channel data will be loaded from file if needed
+    yop=mdfreader.Mdf('NameOfFile', noDataLoading=True) # channel data will be loaded from file if needed
+    # parsing xml metadata from mdf4.x for many channels can take more than just reading data.
+    # You can reduce to minimum metadata reading with below argument (no source information, attachment, etc.) 
+    yop=mdfreader.Mdf('NameOfFile', metadata=0)  # 0: full, 2: minimal
+    # only for mdf4.x, you can search for the mdf key of a channel name that can have been recorded by different sources
+    yop.get_channel_name4('channelName', 'source path or name')  # returns list of mdf keys
     # to yield one channel and keep its content in mdf object
-    yop.getChannel('channelName')
+    yop.get_channel('channelName')
     # to yield one channel numpy array
-    yop.getChannelData('channelName')
+    yop.get_channel_data('channelName')
     # to get file mdf version
     yop.MDFVersionNumber
     # to get file structure or attachments, you can create a mdfinfo instance
-    info=mdfreader.mdfinfo()
-    info.listChannels('NameOfFile') # returns only the list of channels
-    info.readinfo('NameOfFile') # complete file structure object
+    info=mdfreader.MdfInfo()
+    info.list_channels('NameOfFile') # returns only the list of channels
+    info.read_info('NameOfFile') # complete file structure object
     yop.info # same class is stored in mdfreader class
     # to list channels names after reading
     yop.keys()
@@ -113,22 +118,22 @@ Command example in ipython:
     # file manipulations
     yop.resample(0.1)
     # or
-    yop.resample(masterChannel='master3')
+    yop.resample(master_channel='master3')
     # keep only data between begin and end
     yop.cut(begin=10, end=15)
     # export to other file formats :
-    yop.exporToCSV(sampling=0.01)
-    yop.exportToNetCDF()
-    yop.exportToHDF5()
-    yop.exportToMatlab()
-    yop.exportToXlsx()
+    yop.export_to_csv(sampling=0.01)
+    yop.export_to_NetCDF()
+    yop.export_to_hdf5()
+    yop.export_to_matlab()
+    yop.export_to_xlsx()
     # converts data groups into pandas dataframes
-    yop.convertToPandas()
+    yop.convert_to_pandas()
     # drops all the channels except the one in argument
-    yop.keepChannels({'channel1','channel2','channel3'})
+    yop.keep_channels({'channel1','channel2','channel3'})
     # merge 2 files
-    yop2=mdfreader.mdf('NameOfFile_2')
-    yop=mergeMDF(yop2)
+    yop2=mdfreader.Mdf('NameOfFile_2')
+    yop.merge_mdf(yop2)
     # can write mdf file after modifications or creation from scratch
     # write4 and write3 also allow to convert file versions
     yop.write('NewNameOfFile')  # write in same version as original file after modifications

README.md

@@ -25,7 +25,8 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'numpydoc', 'rst2pdf.pdfbuilder']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'numpydoc', 'sphinx.ext.intersphinx',
+              'sphinx.ext.coverage']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -41,16 +42,16 @@
 
 # General information about the project.
 project = u'mdfreader'
-copyright = u'2015, Aymeric Rateau'
+copyright = u'2018, Aymeric Rateau'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2.7.5'
+version = '2.8'
 # The full version, including alpha/beta/rc tags.
-release = '2.7.5'
+release = '2.8'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -247,3 +248,6 @@
    # rst2pdf - name of the generated pdf
    # Sample rst2pdf doc - title of the pdf
    # Your Name - author name in the pdf
+
+napoleon_numpy_docstring = True
+numpydoc_show_class_members = False

dataRead.c

@@ -11,10 +11,10 @@ Contents:
 .. toctree::
    :maxdepth: 3
 
-   mdf/index
-   
    mdfreader/index
 
+   mdf/index
+
    mdf3reader/index
 
    mdfinfo3/index

dataRead.pyx

@@ -17,8 +17,8 @@
 from veusz.plugins.datasetplugin import Dataset1D as ImportDataset1D
 from veusz.plugins.field import FieldFloat as ImportFieldFloat
 try:
-    from mdfreader import mdf
-    from mdfreader import mdfinfo
+    from mdfreader import Mdf
+    from mdfreader import MdfInfo
 except ImportError:
     try:
         from veusz.plugins.mdfreader import mdf
@@ -29,11 +29,11 @@
         import os.path
         sys.path.append(os.getcwdu())
         print(os.path.join(os.getcwdu(), 'plugins'))
-        from mdfreader import mdf
-        from mdfreader import mdfinfo
+        from mdfreader import Mdf
+        from mdfreader import MdfInfo
 
 
-class ImportPlugin(mdfinfo):
+class ImportPlugin(MdfInfo):
 
     """Define a plugin to read data in a particular format.
 
@@ -58,7 +58,7 @@ def getPreview(self, params):
         Returns (text, okaytoimport)
         """
 
-        info = mdfinfo(fileName=params.filename)
+        info = MdfInfo()
 
         if info.mdfversion < 400:
             f = ''
@@ -85,7 +85,7 @@ def getPreview(self, params):
                     f += 'Project Name: ' + Comment['project'] + '\n'
                 if 'subject' in Comment:
                     f += 'Subject: ' + Comment['subject'] + '\n' + 'Channel List:\n'
-        for channelName in info.listChannels():
+        for channelName in info.list_channels():
             f += '   ' + channelName + '\n'
         return f, True
 
@@ -97,7 +97,7 @@ def doImport(self, params):
         return []
 
 
-class MdfImportPlugin(ImportPlugin, mdf):
+class MdfImportPlugin(ImportPlugin, Mdf):
 
     """Plugin to import mdf (Mostly ETAS INCA or CANape files)"""
 
@@ -115,8 +115,8 @@ def doImport(self, params):
         Return a list of ImportDataset1D, ImportDataset2D objects
         """
 
-        data = mdf(params.filename)
-        data.resample(samplingTime=params.field_results['mult'])
+        data = Mdf(params.filename)
+        data.resample(sampling_time=params.field_results['mult'])
         List = []
         for channelName in list(data.keys()):
             if len(data[channelName]['data']) > 0 and not data[channelName]['data'].dtype.kind in ['S', 'U']:

docs/conf.py

@@ -12,4 +12,4 @@
 # along with this program.  If not, see http://www.gnu.org/licenses.
 #
 # ----------------------------------------------------------------------
-__version__ = "2.7.8"
+__version__ = "3.0"

docs/index.rst

@@ -35,8 +35,8 @@ def __init__(self, parent=None):
         QMainWindow.__init__(self, parent)
         self.setupUi(self)
         self.fileNames = []  # files to convert
-        self.mdfClass = mdf()  # instance of mdf
-        self.mdfinfoClass = mdfinfo()  # instance of mdfinfo
+        self.mdfClass = Mdf()  # instance of mdf
+        self.mdfinfoClass = MdfInfo()  # instance of mdfinfo
         self.convertSelection = 'Matlab'  # by default Matlab conversion is selected
         self.MergeFiles = False  # by default
         self.labFileName = []  # .lab file name
@@ -66,7 +66,7 @@ def on_browse_clicked(self):
             self.mdfinfoClass.__init__()
             self.cleanChannelList()
             self.cleanSelectedChannelList()
-            ChannelList = convertChannelList(self.mdfinfoClass.listChannels(str(self.fileNames[0])))
+            ChannelList = convertChannelList(self.mdfinfoClass.list_channels(str(self.fileNames[0])))
             self.SelectedChannelList.addItems(ChannelList)
             self.FileList.setItemSelected(self.FileList.item(0), True)
 
@@ -145,20 +145,20 @@ def on_Convert_clicked(self):
                     buffer.update(res[0])  # assigns next class to buffer
                     buffer.masterChannelList = res[1]
                     fileNameList.append(res[2])
-                    self.mdfClass.mergeMdf(buffer)  # merge buffer to merged class mdfClass
+                    self.mdfClass.merge_mdf(buffer)  # merge buffer to merged class mdfClass
                 # Export
                 if self.convertSelection == 'Matlab':
-                    self.mdfClass.exportToMatlab()
+                    self.mdfClass.export_to_matlab()
                 elif self.convertSelection == 'csv':
-                    self.mdfClass.exportToCSV()
+                    self.mdfClass.export_to_csv()
                 elif self.convertSelection == 'netcdf':
-                    self.mdfClass.exportToNetCDF()
+                    self.mdfClass.export_to_NetCDF()
                 elif self.convertSelection == 'hdf5':
-                    self.mdfClass.exportToHDF5()
+                    self.mdfClass.export_to_hdf5()
                 elif self.convertSelection == 'excel':
-                    self.mdfClass.exportToExcel()
+                    self.mdfClass.export_to_excel()
                 elif self.convertSelection == 'excel2010':
-                    self.mdfClass.exportToXlsx()
+                    self.mdfClass.export_to_xlsx()
                 elif self.convertSelection == 'mdf3':
                     self.mdfClass.write(fileName + '_new')
                 self.cleanChannelList()
@@ -176,7 +176,7 @@ def on_FileList_itemClicked(self, item):
         self.mdfinfoClass.__init__()
         # self.mdfinfoClass.readinfo(item)
         self.cleanChannelList()
-        ChannelList = convertChannelList(self.mdfinfoClass.listChannels(str(item.text())))
+        ChannelList = convertChannelList(self.mdfinfoClass.list_channels(str(item.text())))
         self.channelList.addItems(ChannelList)
         self.mdfinfoClass.__init__()  # clean object to free memory
 
@@ -301,26 +301,26 @@ def on_MergeFiles_toggled(self, checked):
 
 def processMDF(fileName, channelist, resampleFlag, resampleValue, convertFlag, convertSelection):
     # Will process file according to defined options
-    yop = mdf()
+    yop = Mdf()
     yop.multiProc = False  # already multiprocessed
     yop.convertAfterRead = True
     yop.read(fileName)  # reads complete file
-    yop.keepChannels(channelist)  # removes unnecessary channels
+    yop.keep_channels(channelist)  # removes unnecessary channels
     if resampleFlag:
         yop.resample(resampleValue)
     if convertFlag:
         if convertSelection == 'Matlab':
-            yop.exportToMatlab()
+            yop.export_to_matlab()
         elif convertSelection == 'csv':
-            yop.exportToCSV()
+            yop.export_to_csv()
         elif convertSelection == 'netcdf':
-            yop.exportToNetCDF()
+            yop.export_to_NetCDF()
         elif convertSelection == 'hdf5':
-            yop.exportToHDF5()
+            yop.export_to_hdf5()
         elif convertSelection == 'excel':
-            yop.exportToExcel()
+            yop.export_to_excel()
         elif convertSelection == 'excel2010':
-            yop.exportToXlsx()
+            yop.export_to_xlsx()
         elif convertSelection == 'mdf3':
             yop.write(fileName + '_new')
     yopPicklable = {}  # picklable dict and not object