fix workflow pypi-deploy.yml for installing libiconv

* convert to UTF-8 for any non-empty codepage: fix buffer string
  conversion

.github/workflows/pypi-deploy.yml

@@ -40,6 +40,12 @@ jobs:
         with:
           name: wheel-config
           path: python/
+      - name: Install libiconv for windows
+        if: matrix.os == 'windows-2019'
+        run: |
+          git clone https://github.com/Microsoft/vcpkg.git
+          .\vcpkg\bootstrap-vcpkg.bat
+          vcpkg install libiconv
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         working-directory: python/

README.md

@@ -31,6 +31,8 @@ On the [Record Evolution Platform](https://www.record-evolution.de/en/home-en/),
 
 ## File format
 
+[Warning: Take a look at [this issue](https://github.com/RecordEvolution/IMCtermite/issues/14) when reading this section regarding the file format.]
+
 A data file of the _IMC Bus Format_ type with the extension _.raw_ is a _mixed text/binary
 file_ featuring a set of markers (keys) that indicate the start of various blocks
 of data that provide meta information and the actual measurement data. Every single
@@ -153,7 +155,8 @@ python3 -m pip install IMCtermite
 which provides binary wheels for multiple architectures on _Windows_ and _Linux_
 and most _Python 3.x_ distributions. However, if your platform/architecture is
 not supported you can still compile the source distribution yourself, which
-requires _python3_setuptools_ and _gcc version >= 10.2.0_.
+requires _python3_setuptools_ and an up-to-date compiler supporting C++11
+standard (e.g. _gcc version >= 10.2.0_).
 
 ## Usage
 
@@ -189,23 +192,23 @@ options `imctermite sample-data.raw -b -c -s '|'`.
 
 ### Python
 
-Given the `imctermite` module is available, we can import it and declare an instance
+Given the `IMCtermite` module is available, we can import it and declare an instance
 of it by passing a _raw_ file to the constructor:
 
 ```Python
-import imc_termite
+import IMCtermite
 
-imcraw = imc_termite.imctermite(b"sample/sampleA.raw")
+imcraw = IMCtermite.imctermite(b"sample/sampleA.raw")
 ```
 
 An example of how to create an instance and obtain the list of channels is:
 
 ```Python
-import imc_termite
+import IMCtermite
 
 # declare and initialize instance of "imctermite" by passing a raw-file
 try :
-    imcraw = imc_termite.imctermite(b"samples/sampleA.raw")
+    imcraw = IMCtermite.imctermite(b"samples/sampleA.raw")
 except RuntimeError as e :
     print("failed to load/parse raw-file: " + str(e))
 
@@ -230,3 +233,6 @@ can be found in the `python/examples` folder.
 - https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idstepsrun
 - https://github.com/pypa/cibuildwheel/blob/main/examples/github-deploy.yml
 - https://cibuildwheel.readthedocs.io/en/stable/deliver-to-pypi/
+- https://www.gnu.org/software/libiconv/
+- https://vcpkg.io/en/packages.html
+- https://vcpkg.io/en/getting-started

lib/imc_channel.hpp

@@ -9,6 +9,8 @@
 #include <math.h>
 #include <chrono>
 #include <ctime>
+#include <time.h>
+#include <iconv.h>
 
 //---------------------------------------------------------------------------//
 
@@ -142,6 +144,78 @@ namespace imc
     return sumstr;
   }
 
+  // convert encoding of any descriptions, channel-names, units etc.
+  class iconverter
+  {
+      std::string in_enc_, out_enc_;
+      iconv_t cd_;
+      size_t out_buffer_size_;
+
+    public:
+
+      iconverter(std::string in_enc, std::string out_enc, size_t out_buffer_size = 1024) :
+        in_enc_(in_enc), out_enc_(out_enc), out_buffer_size_(out_buffer_size)
+      {
+        // allocate descriptor for character set conversion
+        // (https://man7.org/linux/man-pages/man3/iconv_open.3.html)
+        cd_ = iconv_open(out_enc.c_str(), in_enc.c_str());
+
+        if ( (iconv_t)-1 == cd_ )
+        {
+          if ( errno == EINVAL )
+          {
+            std::string errmsg = std::string("The encoding conversion from ") + in_enc
+              + std::string(" to ") + out_enc + std::string(" is not supported by the implementation.");
+            throw std::runtime_error(errmsg);
+          }
+        }
+      }
+
+      void convert(std::string &astring)
+      {
+        if ( astring.empty() ) return;
+
+        std::vector<char> in_buffer(astring.begin(),astring.end());
+        char *inbuf = &in_buffer[0];
+        size_t inbytes = in_buffer.size();
+
+        std::vector<char> out_buffer(out_buffer_size_);
+        char *outbuf = &out_buffer[0];
+        size_t outbytes = out_buffer.size();
+
+        // perform character set conversion
+        // ( - https://man7.org/linux/man-pages/man3/iconv.3.html
+        //   - https://www.ibm.com/docs/en/zos/2.2.0?topic=functions-iconv-code-conversion )
+        while ( inbytes > 0 )
+        {
+          size_t res = iconv(cd_,&inbuf,&inbytes,&outbuf,&outbytes);
+
+          if ( (size_t)-1 == res )
+          {
+            std::string errmsg;
+            if ( errno == EILSEQ )
+            {
+              errmsg = std::string("An invalid multibyte sequence is encountered in the input.");
+              throw std::runtime_error(errmsg);
+            }
+            else if ( errno == EINVAL )
+            {
+              errmsg = std::string("An incomplete multibyte sequence is encountered in the input")
+                     + std::string(" and the input byte sequence terminates after it.");
+            }
+            else if ( errno == E2BIG )
+            {
+              errmsg = std::string("The output buffer has no more room for the next converted character.");
+            }
+            throw std::runtime_error(errmsg);
+          }
+        }
+
+        std::string outstring(out_buffer.begin(),out_buffer.end()-outbytes);
+        astring = outstring;
+      }
+  };
+
   // channel
   struct channel
   {
@@ -301,9 +375,12 @@ namespace imc
         double secs_int;
         trigger_time_frac_secs_ = modf((double)secs,&secs_int);
         tms.tm_sec = (int)secs_int;
+        //tms.tm_isdst = -1;
 
         // generate std::chrono::system_clock::time_point type
-        std::time_t ts = std::mktime(&tms);
+        // ( - https://www.gnu.org/software/libc/manual/html_node/Broken_002ddown-Time.html
+        //   - https://man7.org/linux/man-pages/man3/tzset.3.html )
+        std::time_t ts = timegm(&tms); //std::mktime(&tms);
         trigger_time_ = std::chrono::system_clock::from_time_t(ts);
       }
 
@@ -313,21 +390,24 @@ namespace imc
       // calculate absolute trigger-time
       absolute_trigger_time_ = trigger_time_ + std::chrono::seconds(addtime_);
       //                                       + std::chrono::nanoseconds((long int)(trigger_time_frac_secs_*1.e9));
+
+      // convert any non-UTF-8 codepage to UTF-8
+      convert_encoding();
     }
 
     // convert buffer to actual datatype
     void convert_buffer()
     {
-      // TODO no clue how/if/when to handle buffer offset/mask/subsequent_bytes
-      // etc. and whatever that shit is!
       std::vector<imc::parameter> prms = blocks_->at(chnenv_.CSuuid_).get_parameters();
       if ( prms.size() < 4)
       {
         throw std::runtime_error("CS block is invalid and features to few parameters");
       }
+
+      // extract (channel dependent) part of buffer
       unsigned long int buffstrt = prms[3].begin();
-      std::vector<unsigned char> CSbuffer( buffer_->begin()+buffstrt+1,
+      std::vector<unsigned char> CSbuffer( buffer_->begin()+buffstrt+buffer_offset_+1,
-                                           buffer_->begin()+buffstrt+buffer_size_+1 );
+                                           buffer_->begin()+buffstrt+buffer_offset_+buffer_size_+1 );
 
       // determine number of values in buffer
       unsigned long int num_values = (unsigned long int)(CSbuffer.size()/(signbits_/8));
@@ -400,6 +480,33 @@ namespace imc
       }
     }
 
+    // convert any description, units etc. to UTF-8 (by default)
+    void convert_encoding()
+    {
+      if ( !codepage_.empty() )
+      {
+        // construct iconv-compatible name for respective codepage
+        std::string cpn = std::string("CP") + codepage_;
+
+        // set up converter
+        std::string utf = std::string("UTF-8");
+        iconverter conv(cpn,utf);
+
+        conv.convert(name_);
+        conv.convert(comment_);
+        conv.convert(origin_);
+        conv.convert(origin_comment_);
+        conv.convert(text_);
+        conv.convert(language_code_);
+        conv.convert(yname_);
+        conv.convert(yunit_);
+        conv.convert(xname_);
+        conv.convert(xunit_);
+        conv.convert(group_name_);
+        conv.convert(group_comment_);
+      }
+    }
+
     // get info string
     std::string get_info(int width = 20)
     {
@@ -413,8 +520,8 @@ namespace imc
         <<std::setw(width)<<std::left<<"comment:"<<comment_<<"\n"
         <<std::setw(width)<<std::left<<"origin:"<<origin_<<"\n"
         <<std::setw(width)<<std::left<<"description:"<<text_<<"\n"
-        <<std::setw(width)<<std::left<<"trigger-time-nt:"<<std::put_time(std::localtime(&tt),"%FT%T")<<"\n"
+        <<std::setw(width)<<std::left<<"trigger-time-nt:"<<std::put_time(std::gmtime(&tt),"%FT%T")<<"\n"
-        <<std::setw(width)<<std::left<<"trigger-time:"<<std::put_time(std::localtime(&att),"%FT%T")<<"\n"
+        <<std::setw(width)<<std::left<<"trigger-time:"<<std::put_time(std::gmtime(&att),"%FT%T")<<"\n"
         <<std::setw(width)<<std::left<<"language-code:"<<language_code_<<"\n"
         <<std::setw(width)<<std::left<<"codepage:"<<codepage_<<"\n"
         <<std::setw(width)<<std::left<<"yname:"<<yname_<<"\n"
@@ -451,16 +558,16 @@ namespace imc
              <<"\",\"comment\":\""<<comment_
              <<"\",\"origin\":\""<<origin_
              <<"\",\"description\":\""<<text_
-             <<"\",\"trigger-time-nt\":\""<<std::put_time(std::localtime(&tt),"%FT%T")
+             <<"\",\"trigger-time-nt\":\""<<std::put_time(std::gmtime(&tt),"%FT%T")
-             <<"\",\"trigger-time\":\""<<std::put_time(std::localtime(&att),"%FT%T")
+             <<"\",\"trigger-time\":\""<<std::put_time(std::gmtime(&att),"%FT%T")
              <<"\",\"language-code\":\""<<language_code_
              <<"\",\"codepage\":\""<<codepage_
-             <<"\",\"yname\":\""<<yname_
+             <<"\",\"yname\":\""<<prepjsonstr(yname_)
-             <<"\",\"yunit\":\""<<yunit_
+             <<"\",\"yunit\":\""<<prepjsonstr(yunit_)
              <<"\",\"significantbits\":\""<<signbits_
              <<"\",\"addtime\":\""<<addtime_
-             <<"\",\"xname\":\""<<xname_
+             <<"\",\"xname\":\""<<prepjsonstr(xname_)
-             <<"\",\"xunit\":\""<<xunit_
+             <<"\",\"xunit\":\""<<prepjsonstr(xunit_)
              <<"\",\"xstepwidth\":\""<<xstepwidth_
              <<"\",\"xoffset\":\""<<xoffset_
              <<"\",\"group\":{"<<"\"index\":\""<<group_index_
@@ -477,6 +584,25 @@ namespace imc
       return ss.str();
     }
 
+    // prepare string value for usage in JSON dump
+    std::string prepjsonstr(std::string value)
+    {
+      std::stringstream ss;
+      ss<<quoted(value);
+      return strip_quotes(ss.str());
+    }
+
+    // remove any leading or trailing double quotes
+    std::string strip_quotes(std::string astring)
+    {
+      // head
+      if ( astring.front() == '"' ) astring.erase(astring.begin()+0);
+      // tail
+      if ( astring.back() == '"' ) astring.erase(astring.end()-1);
+
+      return astring;
+    }
+
     // print channel
     void print(std::string filename, const char sep = ',', int width = 25, int yprec = 9)
     {

lib/imc_key.hpp

@@ -84,6 +84,7 @@ namespace imc
     // noncritical keys
     key(false,"NO","origin of data",1),
     key(false,"NT","timestamp of trigger",1),
+    key(false,"NT","timestamp of trigger",2),
     key(false,"ND","(color) display properties",1),
     key(false,"NU","user defined key",1),
     key(false,"Np","property of channel",1),

lib/imc_raw.hpp

@@ -236,13 +236,27 @@ namespace imc
             // provide UUID for channel
             chnenv.uuid_ = chnenv.CNuuid_;
 
+            // for multichannel data there may be multiple channels referring to
+            // the same (final) CS block (in contrast to what the IMC software
+            // documentation seems to suggest) resulting in all channels missing
+            // a CS block except for the very last
+            if ( chnenv.CSuuid_.empty() ) {
+              for ( imc::block blkCS: rawblocks_ ) {
+                if ( blkCS.get_key().name_ == "CS"
+                  && blkCS.get_begin() > (unsigned long int)stol(chnenv.uuid_) ) {
+                  chnenv.CSuuid_ = blkCS.get_uuid();
+                }
+              }
+            }
+
             // create channel object and add it to the map of channels
             channels_.insert( std::pair<std::string,imc::channel>
               (chnenv.CNuuid_,imc::channel(chnenv,&mapblocks_,&buffer_))
             );
 
             // reset channel uuid
-            chnenv.CNuuid_.clear();
+            chnenv.reset();
+            //chnenv.CNuuid_.clear();
           }
         }
 
@@ -254,7 +268,6 @@ namespace imc
       }
     }
 
-
   public:
 
     // provide buffer size

makefile

@@ -3,15 +3,18 @@
 SHELL := /bin/bash
 
 # name of executable and CLI tool
-EXE = IMCtermite
+EXE = imctermite
 
 # directory names
 SRC = src/
 LIB = lib/
 PYT = python/
 
-# list headers
+# list headers and include directories
 HPP = $(wildcard $(LIB)/*.hpp)
+IPP = $(shell find $(LIB) -type f -name '*.hpp')
+KIB = $(shell find $(LIB) -type d)
+MIB = $(foreach dir,$(KIB),-I $(dir))
 
 # choose compiler and its options
 CC = g++ -std=c++17
@@ -31,17 +34,17 @@ INST := /usr/local/bin
 #-----------------------------------------------------------------------------#
 # C++ and CLI tool
 
-# build exectuable
+# build executable
 $(EXE): check-tags $(GVSN) main.o
 	$(CC) $(OPT) main.o -o $@
 
 # build main.cpp and include git version/commit tag
-main.o: src/main.cpp $(HPP)
+main.o: src/main.cpp $(IPP)
 	@cp $< $<.cpp
 	@sed -i 's/TAGSTRING/$(GTAG)/g' $<.cpp
 	@sed -i 's/HASHSTRING/$(GHSH)/g' $<.cpp
 	@sed -i 's/TIMESTAMPSTRING/$(TMS)/g' $<.cpp
-	$(CC) -c $(OPT) -I $(LIB) $<.cpp -o $@
+	$(CC) -c $(OPT) $(MIB) $<.cpp -o $@
 	@rm $<.cpp
 
 install: $(EXE)

python/IMCtermite.pyx

@@ -20,8 +20,8 @@ cdef class imctermite:
     self.cppimc.set_file(rawfile)
 
   # get JSON list of channels
-  def get_channels(self, bool data):
+  def get_channels(self, bool include_data):
-    chnlst = self.cppimc.get_channels(True,data)
+    chnlst = self.cppimc.get_channels(True,include_data)
     chnlstjn = [jn.loads(chn.decode(errors="ignore")) for chn in chnlst]
     return chnlstjn
 

python/MANIFEST.in

@@ -2,3 +2,4 @@ include lib/*.hpp
 include *.cpp
 include *.pyx
 include *.pxd
+include VERSION

python/VERSION

@@ -1 +1 @@
-2.0.0
+2.0.9

python/examples/multichannel.py

@@ -0,0 +1,43 @@
+
+import IMCtermite
+import pandas
+import datetime
+
+def add_trigger_time(trigger_time, add_time) :
+    trgts = datetime.datetime.strptime(trigger_time,'%Y-%m-%dT%H:%M:%S')
+    dt = datetime.timedelta(seconds=add_time)
+    return (trgts + dt).strftime('%Y-%m-%dT%H:%M:%S:%f')
+
+if __name__ == "__main__" :
+
+    # read file and extract data
+    imctm = IMCtermite.imctermite(b"Measurement.raw")
+    chns = imctm.get_channels(True)
+    
+    # prepare abscissa
+    xcol = "time ["+chns[0]['xunit']+"]"
+    #xcol = "timestamp"
+    xsts = [add_trigger_time(chns[0]['trigger-time'],tm) for tm in chns[0]['xdata']]
+
+    # sort channels
+    chnnms = sorted([chn['name'] for chn in chns], reverse=False)
+    chnsdict = {}
+    for chn in chns :
+        chnsdict[chn['name']] = chn
+
+    # construct dataframe
+    df = pandas.DataFrame()
+    df[xcol] = pandas.Series(chns[0]['xdata'])
+    #df[xcol] = pandas.Series(xsts)
+    #for idx,chn in enumerate(chns) :
+    for chnnm in chnnms :
+        chn = chnsdict[chnnm]
+        #xcol = (chn['xname'] if chn['xname'] != '' else "x_"+str(idx))+" ["+chn['xunit']+"]"
+        #df[xcol] = pandas.Series(chn['xdata'])
+        ycol = chn['yname']+" ["+chn['yunit']+"]"
+        df[ycol] = pandas.Series(chn['ydata'])
+
+    # show entire dataframe and write file
+    print(df)
+    df.to_csv("Measurement.csv",header=True,sep='\t',index=False)
+