clean up repo, include print methods in cython, update README python docu
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README.md
40
README.md
@ -230,8 +230,44 @@ grpids = jack.get_channelgroup_ids()
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chnids = jack.get_channel_ids()
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```
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For a full example and to see how the actual data is extracted see the example
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`python/usage.py`.
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As a use case, we have look at listing the ids of all channelgroups and printing
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their data to separate files:
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```Python
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import tdm_reaper
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import re
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# create 'tdm_reaper' instance object
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try :
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jack = tdm_reaper.tdmreaper(b'samples/SineData.tdm',b'samples/SineData.tdx')
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except RuntimeError as e :
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print("failed to load/decode TDM files: " + str(e))
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# list ids of channelgroups
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grpids = jack.get_channelgroup_ids()
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grpids = [x.decode() for x in grpids]
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print("list of channelgroups: ",grpids)
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for grp in grpids :
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# obtain meta data of channelgroups
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grpinfo = jack.get_channelgroup_info(grp.encode())
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print( json.dumps(grpinfo,sort_keys=False,indent=4) )
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# write this channelgroup to file
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try :
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grpname = re.sub('[^A-Za-z0-9]','',grpinfo['name'])
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grpfile = "channelgroup_" + str(grp) + "_" + str(grpname) + ".csv"
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jack.print_channelgroup(grp.encode(), # id of group to be printed
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grpfile.encode(), # filename
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True, # include metadata as fileheader
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ord(' ') # delimiter char
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)
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except RuntimeError as e :
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print("failed to print channelgroup: " + str(grp) + " : " + str(e))
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```
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For a full example including more details see `python/usage.py`.
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## References
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@ -1,10 +1,8 @@
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# distutils: language = c++
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from tdm_reaper cimport tdm_reaper
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import json as jsn
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import json as jn
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import numpy as np
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# import re
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# import os
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cdef class tdmreaper:
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@ -29,40 +27,18 @@ cdef class tdmreaper:
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def get_channel(self, string id):
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return self.cpp_tdm.get_channel_as_double(id)
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# get meta-data of channel(-group)
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# get meta-data of channel(-group) (as dictionary)
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def get_channelgroup_info(self, string id):
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return self.cpp_tdm.get_channelgroup_info(id)
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grpstr = self.cpp_tdm.get_channelgroup_info(id)
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return jn.loads(grpstr.decode())
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def get_channel_info(self, string id):
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return self.cpp_tdm.get_channel_info(id)
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chnstr = self.cpp_tdm.get_channel_info(id)
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return jn.loads(chnstr.decode())
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# def set_file(self, string rawfile):
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# if not os.path.isfile(rawfile) :
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# raise ValueError("'" + str(rawfile) + "' does not exist")
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# self.rawit.set_file(rawfile)
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#
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# def do_conversion(self):
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# self.rawit.setup_and_conversion()
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#
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# def validity(self):
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# return self.rawit.get_valid()
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#
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# def channel_name(self):
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# return self.rawit.get_name()
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#
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# def unit(self):
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# return self.rawit.get_unit()
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#
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# def dt(self):
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# return self.rawit.get_dt()
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#
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# def time_unit(self):
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# return self.rawit.get_temp_unit()
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#
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# def get_time(self):
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# return self.rawit.get_time()
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#
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# def get_channel(self):
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# return self.rawit.get_data()
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#
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# def write_table(self, const char* csvfile, char delimiter):
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# self.rawit.write_table(csvfile,delimiter)
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# print a channel(-group)
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def print_channelgroup(self, string id, const char* filename,
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bool include_meta, char delimiter):
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self.cpp_tdm.print_group(id,filename,include_meta,delimiter)
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def print_channel(self, string id, const char* filename,
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bool include_meta):
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self.cpp_tdm.print_channel(id,filename,include_meta)
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@ -1,142 +0,0 @@
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from tdm_ripper cimport tdm_ripper
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import numpy as np
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import re
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cdef class pytdmripper:
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# pointer to C++ instance (since there's no nullary constructor)
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cdef tdm_ripper *cripp
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def __cinit__(self, string tdmfile, string tdxfile = b""):
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self.cripp = new tdm_ripper(tdmfile,tdxfile)
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def __dealloc__(self):
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del self.cripp
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def show_channels(self):
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self.cripp.list_channels()
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def show_groups(self):
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self.cripp.list_groups()
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def num_channels(self):
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return self.cripp.num_channels()
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def no_channels(self, int groupid):
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assert (groupid >= 0 and groupid < self.cripp.num_groups()), "index of group must be in [0,n-1]"
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return self.cripp.no_channels(groupid)
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def num_groups(self):
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return self.cripp.num_groups()
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def no_channel_groups(self):
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return self.cripp.num_groups()
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def channel_name(self,int groupid,int channelid):
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return self.cripp.channel_name(groupid,channelid).decode('utf-8')
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def group_name(self,int groupid):
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return self.cripp.group_name(groupid).decode('utf-8')
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def channel_unit(self,int groupid,int channelid):
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return (self.cripp.channel_unit(groupid,channelid))
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def channel_exists(self,int groupid, string channelname):
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return self.cripp.channel_exists(groupid,channelname)
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def obtain_channel_id(self,int groupid, int channelid):
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return self.cripp.obtain_channel_id(groupid,channelid)
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def get_channel(self, int channelid):
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return np.asarray(self.cripp.get_channel(channelid))
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def channel(self,int groupid,int channelid):
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return self.cripp.channel(groupid,channelid)
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def channel_length(self,int groupid, int channelid):
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return self.cripp.channel_length(groupid,channelid)
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def time_stamp(self,int groupid, bool startstop):
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return self.cripp.time_stamp(groupid,startstop)
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def get_min(self,int groupid, int channelid):
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return self.cripp.get_min(groupid,channelid)
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def get_max(self,int groupid, int channelid):
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return self.cripp.get_max(groupid,channelid)
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def print_channel(self, int channelid, const char* filename):
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self.cripp.print_channel(channelid,filename)
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def meta_info(self, string attribute_name):
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return self.cripp.get_meta(attribute_name)
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def print_meta(self, const char* filename):
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self.cripp.print_meta(filename)
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def close(self):
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dummy = ""
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#=============================================================================#
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def extract_all(string tdmfile, string tdxfile, string outdirx = b"./", string prfxnam = b""):
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"""
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Python function extracting all available data from .tdm and .tdx to .csv dump
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Args:
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tdmfile: path and filename of .tdm file
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tdxfile: path and filename of associated .tdx file
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outdirx: directory where all .csv output is dumped
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prfxnam: optionally specify a name prefix for all .csv files
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Return:
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None
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"""
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# TODO preliminary: assume utf-8
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encoding = 'utf-8'
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# set up instance of Cython ripper
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td = pytdmripper(tdmfile,tdxfile)
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# if no name prefix is given, .tdm filename will be used
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prfx = ""
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if prfxnam.decode(encoding) == prfx :
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prfx = tdmfile.decode(encoding).rstrip('.tdm').split('/')[-1]
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else:
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prfx = prfxnam.decode(encoding)
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# obtain number of available groups and channels
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numgr = td.num_groups()
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numch = td.num_channels()
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# generate list of all files produced
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filelist = []
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# dump all meta information
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metafile = outdirx.decode(encoding)+prfx+'.csv'
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td.print_meta(metafile.encode(encoding))
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filelist.append(metafile.lstrip("./"))
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# dump all available groups and channels
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for g in range(0,numgr):
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numgrch = td.no_channels(g)
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for c in range(0,numgrch):
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# obtained overall channel id
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chid = td.obtain_channel_id(g,c)
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# get group's and channel's name
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gname = td.group_name(g)
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cname = td.channel_name(g,c)
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# use regular expression replacement to sanitize group and channel names
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gname = re.sub('[!@#$%^&*()-+= ,]','',gname)
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cname = re.sub('[!@#$%^&*()-+= ,]','',cname)
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# generate filename
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fichan = prfx + '_' + str(g+1) + '_' + str(c+1) + '_' + gname + '_' + cname + '.csv'
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# print channel
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td.print_channel(chid,(outdirx.decode(encoding)+fichan).encode(encoding))
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# append filename to list
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filelist.append(fichan)
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# return list of all files
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return filelist
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@ -23,20 +23,6 @@ cdef extern from "tdm_reaper.hpp":
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# get meta-data
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string get_channelgroup_info(string id) except+
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string get_channel_info(string id) except+
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# void set_file(string)
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# # perform conversion (pass any C++ exceptions to Python)
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# void setup_and_conversion() except +
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# # get validity of data format
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# bool get_valid()
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# # get channel name and unit
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# string get_name()
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# string get_unit()
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# # get time step and time unit
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# double get_dt()
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# string get_temp_unit()
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# # get data array of time and measured quantity's channel
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# vector[double] get_time()
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# vector[double] get_data()
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# # dump all data to .csv
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# void write_table(const char*,char delimiter)
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# print a channel(-group)
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void print_group(string id, const char* filename, bool include_meta, char delimiter)
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void print_channel(string id, const char* filename, bool include_meta)
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@ -1,36 +0,0 @@
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# cython: language_level = 3
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# distutils: language = c++
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# use some C++ STL libraries
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from libcpp.string cimport string
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from libcpp.vector cimport vector
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from libcpp cimport bool
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cdef extern from "tdm_ripper.cpp":
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pass
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cdef extern from "tdm_ripper.hpp":
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cdef cppclass tdm_ripper:
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tdm_ripper(string,string) except +
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void list_channels()
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void list_groups()
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int num_channels()
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int no_channels(int)
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int num_groups()
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int no_channel_groups()
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string channel_name(int,int)
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string group_name(int)
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string channel_unit(int,int)
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int channel_exists(int,string)
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int obtain_channel_id(int,int)
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vector[double] get_channel(int)
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int channel_length(int,int)
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string time_stamp(int,bool)
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double get_min(int,int)
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double get_max(int,int)
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vector[double] channel(int,int)
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void print_channel(int,const char*)
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string get_meta(string attribute_name)
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void print_meta(const char*)
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# dummy method for compatibility
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void close()
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@ -610,36 +610,44 @@ std::vector<tdmdatatype> tdm_reaper::get_channel(std::string& id)
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void tdm_reaper::print_channel(std::string &id, const char* filename, bool include_meta)
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{
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// declare file stream
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std::ofstream fou;
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try {
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fou.open(filename);
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} catch ( const std::exception& e) {
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throw std::runtime_error( std::string("failed to open file to dump channel")
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+ e.what() );
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}
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// get channel object
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tdm_channel chn = this->tdmchannels_.at(id);
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if ( include_meta )
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// check for channel id
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if ( this->tdmchannels_.count(id) != 1 )
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{
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int width = 20;
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fou<<std::setw(width)<<std::left<<"# channel-id:"<<chn.id_<<"\n";
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fou<<std::setw(width)<<std::left<<"# name:"<<chn.name_<<"\n";
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fou<<std::setw(width)<<std::left<<"# description:"<<chn.description_<<"\n";
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fou<<std::setw(width)<<std::left<<"# unit_string:"<<chn.unit_string_<<"\n";
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fou<<std::setw(width)<<std::left<<"# datatype:"<<chn.datatype_<<"\n";
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fou<<std::setw(width)<<std::left<<"# minimum:"<<chn.minimum_<<"\n";
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fou<<std::setw(width)<<std::left<<"# maximum:"<<chn.maximum_<<"\n";
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fou<<std::setw(width)<<std::left<<"# group:"<<chn.group_<<"\n";
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throw std::invalid_argument(std::string("channel id does not exist: ") + id);
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}
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else
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{
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// declare file stream
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std::ofstream fou;
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try {
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fou.open(filename);
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} catch ( const std::exception& e) {
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throw std::runtime_error( std::string("failed to open file to dump channel")
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+ e.what() );
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}
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// obtain channel data
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std::vector<tdmdatatype> chndata = this->get_channel(id);
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for ( auto el: chndata ) fou<<el<<"\n";
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// get channel object
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tdm_channel chn = this->tdmchannels_.at(id);
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if ( include_meta )
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{
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int width = 20;
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fou<<std::setw(width)<<std::left<<"# channel-id:"<<chn.id_<<"\n";
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fou<<std::setw(width)<<std::left<<"# name:"<<chn.name_<<"\n";
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fou<<std::setw(width)<<std::left<<"# description:"<<chn.description_<<"\n";
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fou<<std::setw(width)<<std::left<<"# unit_string:"<<chn.unit_string_<<"\n";
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fou<<std::setw(width)<<std::left<<"# datatype:"<<chn.datatype_<<"\n";
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fou<<std::setw(width)<<std::left<<"# minimum:"<<chn.minimum_<<"\n";
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fou<<std::setw(width)<<std::left<<"# maximum:"<<chn.maximum_<<"\n";
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fou<<std::setw(width)<<std::left<<"# group:"<<chn.group_<<"\n";
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}
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// close file
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fou.close();
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// obtain channel data
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std::vector<tdmdatatype> chndata = this->get_channel(id);
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for ( auto el: chndata ) fou<<el<<"\n";
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// close file
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fou.close();
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}
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}
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void tdm_reaper::print_group(std::string &id, const char* filename, bool include_meta, char sep)
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@ -1,56 +0,0 @@
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import tdm_ripper
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import numpy as np
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import matplotlib.pyplot as plt
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tdmpatha = b"samples/SineData.tdm"
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tdxpatha = b"samples/SineData.tdx"
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tdmpathb = b"/Users/mariofink/Downloads/CONTI_HBS_samples/config_id_1/001_Test_DIAdem/Messung.tdm"
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tdxpathb = b"/Users/mariofink/Downloads/CONTI_HBS_samples/config_id_1/001_Test_DIAdem/Messung.tdx"
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tdmpathchz = tdmpathb
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tdxpathchz = tdxpathb
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# create instance of ripper class
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# RP = tdm_ripper.pytdmripper(tdmpath)
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RP = tdm_ripper.pytdmripper(tdmpathchz,tdxpathchz)
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# provide overview of available channels
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RP.show_channels()
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print(RP.num_channels())
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print(RP.num_groups())
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for i in range(0,RP.num_groups()):
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print(str(i+1).rjust(10)+str(RP.no_channels(i)).rjust(10))
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# print particular channel to file
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RP.print_channel(1,b"SineData_extract.dat")
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# show some meta information
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print(RP.meta_info(b"SMP_Name").decode('utf-8'))
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print(RP.meta_info(b"Location").decode('utf-8'))
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print('\n')
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RP.print_meta(b"meta_information.dat")
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# extract channel and return it to numpy array
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# channels = RP.get_channel(1)
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# Nlen = len(channels)
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# channels = np.append(channels,RP.get_channel(2))
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# channels = np.append(channels,RP.get_channel(3))
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# channels = np.append(channels,RP.get_channel(4))
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# channels = np.append(channels,RP.get_channel(5))
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# channels = np.append(channels,RP.get_channel(6))
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# channels = np.append(channels,RP.get_channel(7))
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# channels = np.append(channels,RP.get_channel(8))
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# print(channels.shape)
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# print("\n\n")
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# print(channels[0:40])
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#
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# x = np.linspace(0,Nlen,Nlen)
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# plt.plot(x,channels[0:Nlen])
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# plt.plot(x,channels[Nlen:2*Nlen])
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# plt.plot(x,channels[2*Nlen:3*Nlen])
|
||||
#
|
||||
# plt.grid()
|
||||
# plt.show()
|
||||
@ -1,62 +0,0 @@
|
||||
import tdm_ripper
|
||||
import numpy as np
|
||||
import argparse
|
||||
import re
|
||||
|
||||
parser = argparse.ArgumentParser(description='provide path of both .tdm and corresponding .tdx file')
|
||||
parser.add_argument('tdm_file',type=str,help='path of .tdm file')
|
||||
parser.add_argument('tdx_file',type=str,help='path of .tdx file')
|
||||
#parser.add_argument('--tdx_file',type=str,help='path of .tdx file',default='')
|
||||
parser.add_argument('--out_directory',type=str,help='choose directory where to write data',default='./')
|
||||
parser.add_argument('--prefix_name',type=str,help='provide dataset name used as filename prefix',default='')
|
||||
args = parser.parse_args()
|
||||
#print(args)
|
||||
|
||||
# process arguments
|
||||
tdmpath = args.tdm_file #"samples/SineData.tdm"
|
||||
tdxpath = args.tdx_file #"samples/SineData.tdx"
|
||||
outdirx = args.out_directory
|
||||
fprefix = args.prefix_name
|
||||
|
||||
# if no prefix is given, .tdm filename will be used
|
||||
if fprefix == '' :
|
||||
fprefix = tdmpath.rstrip('.tdm').split('/')[-1]
|
||||
# TODO better use os.path !!
|
||||
|
||||
#print(fprefix)
|
||||
|
||||
# create instance of ripper class
|
||||
RP = tdm_ripper.pytdmripper(tdmpath.encode('utf-8'),tdxpath.encode('utf-8'))
|
||||
|
||||
# provide overview over available groups and channels
|
||||
#RP.show_groups()
|
||||
#RP.show_channels()
|
||||
|
||||
# obtain number of available groups and channels
|
||||
numgr = RP.num_groups()
|
||||
numch = RP.num_channels()
|
||||
|
||||
# dump all meta information
|
||||
RP.print_meta((outdirx+fprefix+'.csv').encode('utf-8'))
|
||||
|
||||
# dump all available groups and channels
|
||||
for g in range(0,numgr):
|
||||
numgrch = RP.no_channels(g)
|
||||
for c in range(0,numgrch):
|
||||
#print(str(g).rjust(10)+str(c).rjust(10))
|
||||
# print(str(RP.channel_length(g,c)))
|
||||
# print(RP.channel_name(g,c))
|
||||
#print(RP.channel(g,c))
|
||||
# obtained overall channel id
|
||||
chid = RP.obtain_channel_id(g,c)
|
||||
# get group's and channel's name
|
||||
gname = RP.group_name(g)
|
||||
cname = RP.channel_name(g,c)
|
||||
#print(gname.rjust(30)+cname.rjust(30))
|
||||
# use regular expression replacement to sanitize group and channel names
|
||||
gname = re.sub('[!@#$%^&*()-+= ,]','',gname)
|
||||
cname = re.sub('[!@#$%^&*()-+= ,]','',cname)
|
||||
# generate filename
|
||||
fichan = fprefix + '_' + str(g+1) + '_' + str(c+1) + '_' + gname + '_' + cname + '.csv'
|
||||
# print channel
|
||||
RP.print_channel(chid,(outdirx+fichan).encode('utf-8'))
|
||||
@ -2,11 +2,12 @@
|
||||
import tdm_reaper
|
||||
import numpy as np
|
||||
import json
|
||||
import re
|
||||
|
||||
# create 'tdm_reaper' instance object
|
||||
try :
|
||||
jack = tdm_reaper.tdmreaper(b'samples/SineData.tdm',b'samples/SineData.tdx')
|
||||
except RuntimeError as e:
|
||||
except RuntimeError as e :
|
||||
print("failed to load/decode TDM files: " + str(e))
|
||||
|
||||
# list ids of channelgroups
|
||||
@ -14,27 +15,42 @@ grpids = jack.get_channelgroup_ids()
|
||||
grpids = [x.decode() for x in grpids]
|
||||
print("list of channelgroups: ",grpids)
|
||||
|
||||
# obtain meta data of channelgroups
|
||||
for grp in grpids[0:2] :
|
||||
grpinfostr = jack.get_channelgroup_info(grp.encode())
|
||||
grpinfostr = grpinfostr.decode()
|
||||
grpinfo = json.loads(grpinfostr)
|
||||
|
||||
# obtain meta data of channelgroups
|
||||
grpinfo = jack.get_channelgroup_info(grp.encode())
|
||||
print( json.dumps(grpinfo,sort_keys=False,indent=4) )
|
||||
|
||||
# write channelgroup to file
|
||||
try :
|
||||
grpname = re.sub('[^A-Za-z0-9]','',grpinfo['name'])
|
||||
grpfile = "channelgroup_" + str(grp) + "_" + str(grpname) + ".csv"
|
||||
jack.print_channelgroup(grp.encode(),grpfile.encode(),True,ord(' '))
|
||||
except RuntimeError as e :
|
||||
print("failed to print channelgroup: " + str(grp) + " : " + str(e))
|
||||
|
||||
# list ids of channels
|
||||
chnids = jack.get_channel_ids()
|
||||
chnids = [x.decode() for x in chnids]
|
||||
print("list of channels: ",chnids)
|
||||
|
||||
# get (meta-)data of channels
|
||||
for chn in chnids[0:3] :
|
||||
for chn in chnids[0:2] :
|
||||
|
||||
# obtain meta-data
|
||||
chninfostr = jack.get_channel_info(chn.encode())
|
||||
chninfostr = chninfostr.decode()
|
||||
chninfo = json.loads(chninfostr)
|
||||
chninfo = jack.get_channel_info(chn.encode())
|
||||
print( json.dumps(chninfo,sort_keys=False,indent=4) )
|
||||
|
||||
# channel data
|
||||
chndata = jack.get_channel(chn.encode())
|
||||
try :
|
||||
chndata = jack.get_channel(chn.encode())
|
||||
except RuntimeError as e :
|
||||
print("failed to extract channel: " + str(chn) + " : " + str(e))
|
||||
|
||||
print(str(chndata[0:6]) + " ...")
|
||||
|
||||
# write channel to file
|
||||
chnfile = "channel_" + str(chn) + ".csv"
|
||||
try :
|
||||
jack.print_channel(chn.encode(),chnfile.encode(),True)
|
||||
except RuntimeError as e :
|
||||
print("failed to print channel: " + str(chn) + " : " + str(e))
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user