Probable fix of memory leak

README.md

@@ -36,20 +36,40 @@ in a sister repository in a later stage.
 If you have any question(s), please feel free to contact us: info@ascee.nl.
 
 
-## Installation
+# Building from source
 
-### Compilation
+## Dependencies
 
-#### Archlinux
+Optional dependencies, which can be turned ON/OFF using CMake:
+
+- Build tools, including [http://cmake.org](CMake).
+- FFTW (For really fast FFT's)
+- libUlDAQ, for the Measurement Computing DT9837A USB DAQ box
+    - GNU Autotools, for compiling libUlDAQ
+- RtAudio, for Audio DAQ backends
+- Cython, for wrapping the C-code to Python.
+- The following Python packages need also be available:
+  - `Scipy` (which includes Numpy). Install with `sudo apt install
+    python3-scipy`, or `pacman -S scipy`.
+  - `appdirs`, which can be grabbed from [https://pypi.org](Pypi)
+
+## Installation of dependencies
+
+
+
+
+## Compilation of LASP
+
+### Archlinux
 
 Compiling the code on Archlinux requires the following packages to be available:
 
 - openblas-lapack (AUR)
-- Python 3.7
+- Python>=3.7
 - Numpy (Python-numpy)
 - Cython
 
-#### Ubuntu / Linux Mint
+### Ubuntu / Linux Mint
 
 *Only tested with Linux Mint 18.04*, we require the following packages for
 compilation:
@@ -62,17 +82,3 @@ compilation:
 - libopenblas-base
 - libopenblas-dev
 
-#### Windows specific
-
-Tested using a Anacond / Miniconda Python environment. Please first run the following command:
-
-`conda install fftw`
-
-in case you want the *FFTW* fft backend. 
-
-### Dependencies
-
-#### Ubuntu / Linux Mint
-
-*Only tested with Linux Mint 18.04*. The following Dependencies are required
-for Ubuntu:

lasp/device/lasp_cppuldaq.cpp

@@ -40,91 +40,91 @@ class DT9837A : public Daq {
 
   us nFramesPerBlock;
 
-public:
+  public:
   DT9837A(const DeviceInfo &devinfo, const DaqConfiguration &config)
-      : Daq(devinfo, config) {
+    : Daq(devinfo, config) {
 
-    // Some sanity checks
+      // Some sanity checks
-    if (eninchannels.size() != 4) {
+      if (eninchannels.size() != 4) {
-      throw runtime_error("Invalid length of enabled inChannels vector");
+        throw runtime_error("Invalid length of enabled inChannels vector");
-    }
-
-    if (enoutchannels.size() != 1) {
-      throw runtime_error("Invalid length of enabled outChannels vector");
-    }
-
-    stopThread = false;
-
-    nFramesPerBlock = availableFramesPerBlock[framesPerBlockIndex];
-
-    if (nFramesPerBlock < 24 || nFramesPerBlock > 8192) {
-      throw runtime_error("Unsensible number of samples per block chosen");
-    }
-
-    if (samplerate() < 10000 || samplerate() > 51000) {
-      throw runtime_error("Invalid sample rate");
-    }
-
-    DaqDeviceDescriptor devdescriptors[MAX_DEV_COUNT_PER_API];
-    DaqDeviceDescriptor descriptor;
-    DaqDeviceInterface interfaceType = ANY_IFC;
-
-    UlError err;
-
-    us numdevs = MAX_DEV_COUNT_PER_API;
-    err = ulGetDaqDeviceInventory(interfaceType, devdescriptors, (unsigned*) &numdevs);
-    if (err != ERR_NO_ERROR) {
-      throw runtime_error("Device inventarization failed");
-    }
-
-    if ((us) api_specific_devindex >= numdevs) {
-      throw runtime_error("Device number {deviceno} too high {err}. This could "
-                          "happen when the device is currently not connected");
-    }
-
-    descriptor = devdescriptors[api_specific_devindex];
-
-    // get a handle to the DAQ device associated with the first descriptor
-    handle = ulCreateDaqDevice(descriptor);
-
-    if (handle == 0) {
-      throw runtime_error("Unable to create a handle to the specified DAQ "
-          "device. Is the device currently in use? Please make sure to set "
-          "the DAQ configuration in duplex mode if simultaneous input and "
-          "output is required.");
-    }
-
-    err = ulConnectDaqDevice(handle);
-    if (err != ERR_NO_ERROR) {
-      showErr(err);
-      ulReleaseDaqDevice(handle);
-      handle = 0;
-      throw runtime_error("Unable to connect to device: {err}");
-    }
-
-    for (us ch = 0; ch < 4; ch++) {
-
-      err = ulAISetConfigDbl(handle, AI_CFG_CHAN_SENSOR_SENSITIVITY, ch, 1.0);
-      showErr(err);
-      if (err != ERR_NO_ERROR) {
-        throw runtime_error("Fatal: could normalize channel sensitivity");
       }
 
-      CouplingMode cm = inputACCouplingMode[ch] ? CM_AC : CM_DC;
+      if (enoutchannels.size() != 1) {
-      err = ulAISetConfig(handle, AI_CFG_CHAN_COUPLING_MODE, ch, cm);
+        throw runtime_error("Invalid length of enabled outChannels vector");
+      }
+
+      stopThread = false;
+
+      nFramesPerBlock = availableFramesPerBlock[framesPerBlockIndex];
+
+      if (nFramesPerBlock < 24 || nFramesPerBlock > 8192) {
+        throw runtime_error("Unsensible number of samples per block chosen");
+      }
+
+      if (samplerate() < 10000 || samplerate() > 51000) {
+        throw runtime_error("Invalid sample rate");
+      }
+
+      DaqDeviceDescriptor devdescriptors[MAX_DEV_COUNT_PER_API];
+      DaqDeviceDescriptor descriptor;
+      DaqDeviceInterface interfaceType = ANY_IFC;
+
+      UlError err;
+
+      us numdevs = MAX_DEV_COUNT_PER_API;
+      err = ulGetDaqDeviceInventory(interfaceType, devdescriptors, (unsigned*) &numdevs);
+      if (err != ERR_NO_ERROR) {
+        throw runtime_error("Device inventarization failed");
+      }
+
+      if ((us) api_specific_devindex >= numdevs) {
+        throw runtime_error("Device number {deviceno} too high {err}. This could "
+            "happen when the device is currently not connected");
+      }
+
+      descriptor = devdescriptors[api_specific_devindex];
+
+      // get a handle to the DAQ device associated with the first descriptor
+      handle = ulCreateDaqDevice(descriptor);
+
+      if (handle == 0) {
+        throw runtime_error("Unable to create a handle to the specified DAQ "
+            "device. Is the device currently in use? Please make sure to set "
+            "the DAQ configuration in duplex mode if simultaneous input and "
+            "output is required.");
+      }
+
+      err = ulConnectDaqDevice(handle);
       if (err != ERR_NO_ERROR) {
         showErr(err);
-        throw runtime_error("Fatal: could not set AC/DC coupling mode");
+        ulReleaseDaqDevice(handle);
+        handle = 0;
+        throw runtime_error("Unable to connect to device: {err}");
       }
 
-      IepeMode iepe = inputIEPEEnabled[ch] ? IEPE_ENABLED : IEPE_DISABLED;
+      for (us ch = 0; ch < 4; ch++) {
-      err = ulAISetConfig(handle, AI_CFG_CHAN_IEPE_MODE, ch, iepe);
+
-      if (err != ERR_NO_ERROR) {
+        err = ulAISetConfigDbl(handle, AI_CFG_CHAN_SENSOR_SENSITIVITY, ch, 1.0);
         showErr(err);
-        throw runtime_error("Fatal: could not set IEPE mode");
+        if (err != ERR_NO_ERROR) {
+          throw runtime_error("Fatal: could normalize channel sensitivity");
+        }
+
+        CouplingMode cm = inputACCouplingMode[ch] ? CM_AC : CM_DC;
+        err = ulAISetConfig(handle, AI_CFG_CHAN_COUPLING_MODE, ch, cm);
+        if (err != ERR_NO_ERROR) {
+          showErr(err);
+          throw runtime_error("Fatal: could not set AC/DC coupling mode");
+        }
+
+        IepeMode iepe = inputIEPEEnabled[ch] ? IEPE_ENABLED : IEPE_DISABLED;
+        err = ulAISetConfig(handle, AI_CFG_CHAN_IEPE_MODE, ch, iepe);
+        if (err != ERR_NO_ERROR) {
+          showErr(err);
+          throw runtime_error("Fatal: could not set IEPE mode");
+        }
       }
     }
-  }
 
   DT9837A(const DT9837A &) = delete;
 
@@ -163,12 +163,12 @@ public:
     if (hasinput) {
       assert(!inbuffer);
       inbuffer =
-          new double[neninchannels() * nFramesPerBlock * 2]; // Watch the 2!
+        new double[neninchannels() * nFramesPerBlock * 2]; // Watch the 2!
     }
     if (hasoutput) {
       assert(!outbuffer);
       outbuffer =
-          new double[nenoutchannels() * nFramesPerBlock * 2]; // Watch the 2!
+        new double[nenoutchannels() * nFramesPerBlock * 2]; // Watch the 2!
     }
     this->inqueue = inqueue;
     this->outqueue = outqueue;
@@ -203,6 +203,40 @@ public:
   friend void threadfcn(DT9837A *);
 };
 
+/**
+ * @brief Create an empty buffer and fill it with zeros.
+ *
+ * @param size The number of elements in the array
+ *
+ * @return Pointer to the array
+ */
+static double* createZeroBuffer(size_t size) {
+
+  double* buf = static_cast<double *>(
+      malloc(sizeof(double) * size));
+
+  for (us sample = 0; sample < size; sample++) {
+    buf[sample] = 0;
+  }
+  return buf;
+}
+/**
+ * @brief Copy samples from one linear array to the next.
+ *
+ * @param[in] from Buffer to copy from
+ * @param[out] to Buffer to copy to
+ * @param startFrom The position to start in the from-buffer
+ * @param startTo The position to start in the to-buffer
+ * @param N The number of samples to copy.
+ */
+static inline void copySamples(double* from,double* to,
+    const us startFrom,const us startTo,const us N) {
+
+  for (us sample = 0; sample < N; sample++) {
+    to[startTo + sample] = from[startFrom + sample];
+  }
+}
+
 void threadfcn(DT9837A *td) {
 
   std::cerr << "Starting DAQ Thread fcn" << endl;
@@ -271,9 +305,9 @@ void threadfcn(DT9837A *td) {
 
     cerr << "Starting output DAC" << endl;
     err = ulAOutScan(handle, 0, 0, BIP10VOLTS,
-                     /* BIP60VOLTS, */
+        /* BIP60VOLTS, */
-                     2 * td->nFramesPerBlock, // Watch the 2 here!
+        2 * td->nFramesPerBlock, // Watch the 2 here!
-                     &samplerate, scanoptions, outscanflags, outbuffer);
+        &samplerate, scanoptions, outscanflags, outbuffer);
 
     if (err != ERR_NO_ERROR) {
       showErr(err);
@@ -315,8 +349,8 @@ void threadfcn(DT9837A *td) {
 
     cerr << "Starting input ADC" << endl;
     err = ulDaqInScan(handle, indesc, neninchannels,
-                      2 * td->nFramesPerBlock, // Watch the 2 here!
+        2 * td->nFramesPerBlock, // Watch the 2 here!
-                      &samplerate, scanoptions, inscanflags, inbuffer);
+        &samplerate, scanoptions, inscanflags, inbuffer);
     if (err != ERR_NO_ERROR) {
       showErr(err);
       goto exit;
@@ -348,9 +382,9 @@ void threadfcn(DT9837A *td) {
 
       if (outxstat.currentScanCount > outTotalCount + 2 * nFramesPerBlock) {
         cerr << "***** WARNING: Missing output sample blocks, DAQ Scan count="
-             << outxstat.currentScanCount
+          << outxstat.currentScanCount
-             << " while loop count = " << outTotalCount
+          << " while loop count = " << outTotalCount
-             << ", probably due to too small buffer size. *****" << endl;
+          << ", probably due to too small buffer size. *****" << endl;
       }
       outTotalCount = outxstat.currentScanCount;
 
@@ -362,22 +396,16 @@ void threadfcn(DT9837A *td) {
         if (!botoutenqueued) {
           /* cerr << "Copying output buffer to bottom" << endl; */
           double *bufcpy;
+          assert(nenoutchannels > 0);
           if (!outqueue->empty()) {
             bufcpy = (double *)outqueue->dequeue();
           } else {
             cerr << "******* WARNING: OUTPUTQUEUE UNDERFLOW, FILLING SIGNAL "
-                    "QUEUE WITH ZEROS ***********"
+              "QUEUE WITH ZEROS ***********"
-                 << endl;
+              << endl;
-            bufcpy = static_cast<double *>(
+            bufcpy = createZeroBuffer(nFramesPerBlock*nenoutchannels);
-                malloc(sizeof(double) * nFramesPerBlock * nenoutchannels));
-            for (us sample = 0; sample < nFramesPerBlock; sample++) {
-              bufcpy[sample] = 0;
-            }
-          }
-          assert(nenoutchannels > 0);
-          for (us sample = 0; sample < nFramesPerBlock; sample++) {
-            outbuffer[buffer_mid_idx_out + sample] = bufcpy[sample];
           }
+          copySamples(bufcpy, outbuffer, 0, buffer_mid_idx_out, nFramesPerBlock);
           free(bufcpy);
           botoutenqueued = true;
         }
@@ -386,22 +414,16 @@ void threadfcn(DT9837A *td) {
         if (!topoutenqueued) {
           /* cerr << "Copying output buffer to top" << endl; */
           double *bufcpy;
+          assert(nenoutchannels > 0);
           if (!outqueue->empty()) {
             bufcpy = (double *)outqueue->dequeue();
           } else {
             cerr << "******* WARNING: OUTPUTQUEUE UNDERFLOW, FILLING SIGNAL "
-                    "QUEUE WITH ZEROS ***********"
+              "QUEUE WITH ZEROS ***********"
-                 << endl;
+              << endl;
-            bufcpy = static_cast<double *>(
+            bufcpy = createZeroBuffer(nFramesPerBlock*nenoutchannels);
-                malloc(sizeof(double) * nFramesPerBlock * nenoutchannels));
-            for (us sample = 0; sample < nFramesPerBlock; sample++) {
-              bufcpy[sample] = 0;
-            }
-          }
-          assert(nenoutchannels > 0);
-          for (us sample = 0; sample < nFramesPerBlock; sample++) {
-            outbuffer[sample] = bufcpy[sample];
           }
+          copySamples(bufcpy, outbuffer, 0, 0, nFramesPerBlock);
           free(bufcpy);
           topoutenqueued = true;
         }
@@ -417,10 +439,10 @@ void threadfcn(DT9837A *td) {
       assert(inscanstat == SS_RUNNING);
       if (inxstat.currentScanCount > inTotalCount + 2 * nFramesPerBlock) {
         cerr << "***** ERROR: Missing input sample blocks, count="
-             << inxstat.currentScanCount
+          << inxstat.currentScanCount
-             << ", probably due to too small buffer size. Exiting thread. "
+          << ", probably due to too small buffer size. Exiting thread. "
-                "*****"
+          "*****"
-             << endl;
+          << endl;
         break;
       }
       inTotalCount = inxstat.currentScanCount;
@@ -434,11 +456,11 @@ void threadfcn(DT9837A *td) {
           us monitoroffset = monitorOutput ? 1 : 0;
           assert(neninchannels > 0);
           for (us channel = 0; channel < (neninchannels - monitoroffset);
-               channel++) {
+              channel++) {
             for (us sample = 0; sample < nFramesPerBlock; sample++) {
               bufcpy[(monitoroffset + channel) * nFramesPerBlock + sample] =
-                  inbuffer[buffer_mid_idx_in + sample * neninchannels +
+                inbuffer[buffer_mid_idx_in + sample * neninchannels +
-                           channel];
+                channel];
             }
           }
           if (monitorOutput) {
@@ -447,7 +469,7 @@ void threadfcn(DT9837A *td) {
             us channel = neninchannels - 1;
             for (us sample = 0; sample < nFramesPerBlock; sample++) {
               bufcpy[sample] = inbuffer[buffer_mid_idx_in +
-                                        sample * neninchannels + channel];
+                sample * neninchannels + channel];
             }
           }
           inqueue->enqueue((void *)bufcpy);
@@ -461,10 +483,10 @@ void threadfcn(DT9837A *td) {
           us monitoroffset = monitorOutput ? 1 : 0;
           assert(neninchannels > 0);
           for (us channel = 0; channel < (neninchannels - monitoroffset);
-               channel++) {
+              channel++) {
             for (us sample = 0; sample < nFramesPerBlock; sample++) {
               bufcpy[(monitoroffset + channel) * nFramesPerBlock + sample] =
-                  inbuffer[sample * neninchannels + channel];
+                inbuffer[sample * neninchannels + channel];
             }
           }
           if (monitorOutput) {
@@ -510,7 +532,7 @@ exit:
 }
 
 Daq *createUlDaqDevice(const DeviceInfo &devinfo,
-                       const DaqConfiguration &config) {
+    const DaqConfiguration &config) {
 
   DT9837A *daq = NULL;