[chronojump] Added processMultiDatabase program
- From: Xavier de Blas <xaviblas src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [chronojump] Added processMultiDatabase program
- Date: Thu, 19 Dec 2019 22:43:58 +0000 (UTC)
commit f86c6812a55fc5e32aa99ac6ebaa1075e2642707
Author: Xavier de Blas <xaviblas gmail com>
Date: Thu Dec 19 23:42:30 2019 +0100
Added processMultiDatabase program
processMultiDatabases/callR.cs | 227 +++++++++++++++++++++++
processMultiDatabases/constants.cs | 43 +++++
processMultiDatabases/encoderGraphOptions.cs | 98 ++++++++++
processMultiDatabases/encoderParams.cs | 120 +++++++++++++
processMultiDatabases/encoderSQL.cs | 88 +++++++++
processMultiDatabases/encoderStruct.cs | 51 ++++++
processMultiDatabases/howto_compile.txt | 1 +
processMultiDatabases/processMultiDatabases.cs | 239 +++++++++++++++++++++++++
processMultiDatabases/util.cs | 130 ++++++++++++++
processMultiDatabases/utilEncoder.cs | 154 ++++++++++++++++
10 files changed, 1151 insertions(+)
---
diff --git a/processMultiDatabases/callR.cs b/processMultiDatabases/callR.cs
new file mode 100644
index 00000000..06571327
--- /dev/null
+++ b/processMultiDatabases/callR.cs
@@ -0,0 +1,227 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+using System.IO; //"File" things. TextWriter. Path
+using System.Diagnostics; //for detect OS and for Process
+
+public class CallR
+{
+ private string optionsFile;
+ private EncoderStruct es;
+
+ public EncoderGraphROptions.AnalysisModes analysisMode;
+
+ public CallR(EncoderStruct es)
+ {
+ this.es = es;
+ this.analysisMode = EncoderGraphROptions.AnalysisModes.INDIVIDUAL_CURRENT_SET;
+
+ writeOptionsFile();
+
+ callRStart();
+ }
+
+ private bool callRStart()
+ {
+ ProcessStartInfo pinfo = new ProcessStartInfo();
+ string pBin="Rscript";
+
+ /*
+ if (UtilAll.IsWindows()) {
+ //On win32 R understands backlash as an escape character and
+ //a file path uses Unix-like path separator '/'
+ optionsFile = optionsFile.Replace("\\","/");
+ }
+ */
+
+ //on Windows we need the \"str\" to call without problems in path with spaces
+ pinfo.Arguments = "\"" + getEncoderScriptCallGraph() + "\" " + optionsFile;
+
+ Console.WriteLine("Arguments:", pinfo.Arguments);
+ Console.WriteLine("--- 1 --- " + optionsFile.ToString() + " ---");
+ //Console.WriteLine("--- 2 --- " + scriptOptions + " ---");
+ Console.WriteLine("--- 3 --- " + pinfo.Arguments.ToString() + " ---");
+
+ string outputFileCheck = "";
+ string outputFileCheck2 = "";
+
+ //Wait until this to update encoder gui (if don't wait then treeview will be outdated)
+ //exportCSV is the only one that doesn't have graph. all the rest Analysis have graph and data
+ if(es.Ep.Analysis == "exportCSV")
+ outputFileCheck = es.OutputData1;
+ else {
+ //outputFileCheck = es.OutputGraph;
+ //
+ //OutputData1 because since Chronojump 1.3.6,
+ //encoder analyze has a treeview that can show the curves
+ //when a graph analysis is done, curves file has to be written
+ outputFileCheck = es.OutputData1;
+ //check also the otuput graph
+ outputFileCheck2 = es.OutputGraph;
+ }
+
+ Console.WriteLine("outputFileChecks");
+ Console.WriteLine(outputFileCheck);
+ Console.WriteLine(outputFileCheck2);
+
+ pinfo.FileName=pBin;
+
+ pinfo.CreateNoWindow = true;
+ pinfo.UseShellExecute = false;
+ pinfo.RedirectStandardInput = true;
+ pinfo.RedirectStandardError = true;
+
+ /*
+ * if redirect this there are problems because the buffers get saturated
+ * pinfo.RedirectStandardOutput = true;
+ * if is not redirected, then prints are shown by console (but not in logB
+ * best solution is make the prints as write("message", stderr())
+ * and then will be shown in logB by readError
+ */
+
+
+ //delete output file check(s)
+ Util.DeleteFile(outputFileCheck);
+ if(outputFileCheck2 != "")
+ Util.DeleteFile(outputFileCheck2);
+
+ //delete status-6 mark used on export csv
+ if(es.Ep.Analysis == "exportCSV")
+ Util.DeleteFile(getEncoderStatusTempBaseFileName() + "6.txt");
+
+ //delete SpecialData if exists
+ string specialData = getEncoderSpecialDataTempFileName();
+ if (File.Exists(specialData))
+ Util.DeleteFile(specialData);
+
+
+ Console.WriteLine("process a");
+// try {
+ Process p = new Process();
+ p.StartInfo = pinfo;
+
+ //do not redirect ouptut. Read above
+ //p.OutputDataReceived += new DataReceivedEventHandler(readingOutput);
+ p.ErrorDataReceived += new DataReceivedEventHandler(readingError);
+
+ p.Start();
+
+ //don't do this ReadToEnd because then this method never ends
+ //Console.WriteLine(p.StandardOutput.ReadToEnd());
+ //LogB.Warning(p.StandardError.ReadToEnd());
+
+ // Start asynchronous read of the output.
+ // Caution: This has to be called after Start
+ //p.BeginOutputReadLine();
+ p.BeginErrorReadLine();
+
+ Console.WriteLine("process b");
+
+
+ if(outputFileCheck2 == "")
+ while ( ! ( Util.FileReadable(outputFileCheck) )); //|| CancelRScript) );
+ else
+ while ( ! ( (Util.FileReadable(outputFileCheck) &&
Util.FileReadable(outputFileCheck2)) ));//|| CancelRScript ) );
+
+ /*
+ //copy export from temp file to the file that user has selected
+ if(es.Ep.Analysis == "exportCSV")// && ! CancelRScript)
+ copyExportedFile();
+ */
+
+ Console.WriteLine("process c");
+ p.StandardInput.WriteLine("Q");
+ //p.WaitForExit();
+
+ Console.WriteLine("process d");
+
+// } catch {
+// Console.WriteLine("catched at startProcess");
+// return false;
+// }
+
+ return true;
+ }
+
+ private void readingError (object sendingProcess, DataReceivedEventArgs errorFromR)
+ {
+ if (String.IsNullOrEmpty(errorFromR.Data))
+ return;
+
+ string str = errorFromR.Data;
+ if(str.Length > 6 && str.StartsWith("***") && str.EndsWith("***")) {
+ /*
+ * 0123456
+ * ***1***
+ * str.Substring(3,1) 1 is the length
+ */
+ str = str.Substring(3, str.Length -6);
+// if(Util.IsNumber(str,false))
+// CurvesReaded = Convert.ToInt32(str);
+
+ return;
+ }
+
+ Console.WriteLine(str);
+ }
+
+ private string getEncoderScriptCallGraph()
+ {
+ /*
+ return System.IO.Path.Combine(
+ Util.GetDataDir(), "encoder", Constants.EncoderScriptCallGraph);
+ */
+ return "/home/xavier/informatica/progs_meus/chronojump/chronojump/encoder/call_graph.R";
//hardcoded
+ }
+
+ private string getEncoderStatusTempBaseFileName() {
+ return Path.Combine(Path.GetTempPath(), Constants.EncoderStatusTempBase);
+ }
+
+ private string getEncoderSpecialDataTempFileName() {
+ return Path.Combine(Path.GetTempPath(), Constants.EncoderSpecialDataTemp);
+ }
+
+ private void writeOptionsFile()
+ {
+ optionsFile = Path.GetTempPath() + "Roptions.txt";
+
+ string scriptOptions = UtilEncoder.PrepareEncoderGraphOptions(
+ "hola", //title,
+ es,
+ false, //neuromuscularProfileDo,
+ false, //translate,
+ false, //Debug,
+ false, //CrossValidate,
+ false, //cutByTriggers,
+ "-1", //printTriggers(),
+ false, //SeparateSessionInDays,
+ analysisMode
+ ).ToString();
+
+ TextWriter writer = File.CreateText(optionsFile);
+ writer.Write(scriptOptions);
+ writer.Flush();
+ writer.Close();
+ ((IDisposable)writer).Dispose();
+ }
+}
+
diff --git a/processMultiDatabases/constants.cs b/processMultiDatabases/constants.cs
new file mode 100644
index 00000000..ee55568d
--- /dev/null
+++ b/processMultiDatabases/constants.cs
@@ -0,0 +1,43 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+
+public class Constants
+{
+ public static string EncoderDataTemp = "chronojump-last-encoder-data.txt";
+ public static string EncoderScriptCallGraph = "call_graph.R";
+ public static string EncoderStatusTempBase = "chronojump-encoder-status-";
+ public static string EncoderSpecialDataTemp = "chronojump-special-data.txt"; //variable;result (eg.
"1RM;82.78")
+ public static string EncoderCurvesTemp = "chronojump-last-encoder-curves.txt";
+ //public static string EncoderAnalyzeTableTemp = "chronojump-last-encoder-analyze-table.txt";
+ public static string EncoderGraphTemp = "chronojump-last-encoder-graph.png";
+
+ public static string FileNotFoundStr()
+ {
+ return "Error. File not found.";
+ }
+
+ public static string FileCopyProblemStr()
+ {
+ return "Error. Cannot copy file.";
+ }
+}
+
diff --git a/processMultiDatabases/encoderGraphOptions.cs b/processMultiDatabases/encoderGraphOptions.cs
new file mode 100644
index 00000000..758cdc4d
--- /dev/null
+++ b/processMultiDatabases/encoderGraphOptions.cs
@@ -0,0 +1,98 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+
+public class EncoderGraphROptions
+{
+ public string inputData;
+ public string outputGraph;
+ public string outputData1;
+ public string encoderRPath;
+ public string encoderTempPath;
+ public EncoderParams ep;
+ public string title;
+ public string operatingSystem;
+ public string englishWords;
+ public string translatedWords;
+ public bool debug;
+ public bool crossValidate;
+ private bool cutByTriggers;
+ private string triggerList;
+ public bool separateSessionInDays;
+ public AnalysisModes analysisMode; //the four analysisModes
+
+ public enum AnalysisModes { CAPTURE, INDIVIDUAL_CURRENT_SET, INDIVIDUAL_CURRENT_SESSION,
INDIVIDUAL_ALL_SESSIONS, GROUPAL_CURRENT_SESSION }
+
+ public EncoderGraphROptions(
+ string inputData, string outputGraph, string outputData1,
+ string encoderRPath, string encoderTempPath,
+ EncoderParams ep,
+ string title, string operatingSystem,
+ string englishWords, string translatedWords,
+ bool debug, bool crossValidate, bool cutByTriggers, string triggerList,
+ bool separateSessionInDays, AnalysisModes analysisMode)
+ {
+ this.inputData = inputData;
+ this.outputGraph = outputGraph;
+ this.outputData1 = outputData1;
+ this.encoderRPath = encoderRPath;
+ this.encoderTempPath = encoderTempPath;
+ this.ep = ep;
+ this.title = title;
+ this.operatingSystem = operatingSystem;
+ this.englishWords = englishWords;
+ this.translatedWords = translatedWords;
+ this.debug = debug;
+ this.crossValidate = crossValidate;
+ this.cutByTriggers = cutByTriggers;
+ this.triggerList = triggerList;
+ this.separateSessionInDays = separateSessionInDays;
+ this.analysisMode = analysisMode;
+
+ //ensure triggerList is not null or blank
+ if(triggerList == null || triggerList == "")
+ triggerList = "-1";
+ }
+
+ public override string ToString() {
+ return
+ "#inputdata\n" + inputData + "\n" +
+ "#outputgraph\n" + outputGraph + "\n" +
+ "#outputdata1\n" + outputData1 + "\n" +
+ "#encoderRPath\n" + encoderRPath + "\n" +
+ "#encoderTempPath\n" + encoderTempPath + "\n" +
+ ep.ToStringROptions() + "\n" +
+ "#title\n" + title + "\n" +
+ "#operatingsystem\n" + operatingSystem + "\n" +
+ "#englishWords\n" + englishWords + "\n" +
+ "#translatedWords\n" + translatedWords + "\n" +
+ "#debug\n" + Util.BoolToRBool(debug) + "\n" +
+ "#crossValidate\n" + Util.BoolToRBool(crossValidate) + "\n" +
+ "#cutByTriggers\n" + Util.BoolToRBool(cutByTriggers) + "\n" +
+ "#triggerList\n" + triggerList + "\n" +
+ "#separateSessionInDays\n" + Util.BoolToRBool(separateSessionInDays) + "\n" +
+ "#analysisMode\n" + analysisMode.ToString() + "\n";
+ }
+
+
+ ~EncoderGraphROptions() {}
+}
+
diff --git a/processMultiDatabases/encoderParams.cs b/processMultiDatabases/encoderParams.cs
new file mode 100644
index 00000000..d92790f3
--- /dev/null
+++ b/processMultiDatabases/encoderParams.cs
@@ -0,0 +1,120 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+
+public class EncoderParams
+{
+ //graph.R need both to know displacedMass depending on encoderConfiguration
+ //and plot both as entry data in the table of result data
+ private string massBody; //to pass always as "." to R.
+ private string massExtra; //to pass always as "." to R
+
+ private int minHeight;
+ private int exercisePercentBodyWeight; //was private bool isJump; (if it's 0 is like "jump")
+ private string eccon;
+ private string analysis;
+ private string analysisVariables;
+ private string analysisOptions; //p: propulsive
+ private bool captureCheckFullyExtended;
+ private int captureCheckFullyExtendedValue;
+
+ //encoderConfiguration conversions
+ //in signals and curves, need to do conversions (invert, inertiaMomentum, diameter)
+ //private EncoderConfiguration encoderConfiguration;
+ private string encoderConfiguration;
+
+ private string smoothCon; //to pass always as "." to R
+ private int curve;
+ private int width;
+ private int height;
+ private string decimalSeparator; //used in export data from R to csv
+ //private bool inverted; //used only in runEncoderCapturePython. In graph.R will be used
encoderConfigurationName
+
+ public EncoderParams()
+ {
+ }
+
+
+ //to graph.R
+ public EncoderParams(int minHeight, int exercisePercentBodyWeight, string massBody, string massExtra,
+ string eccon, string analysis, string analysisVariables, string analysisOptions,
+ bool captureCheckFullyExtended, int captureCheckFullyExtendedValue,
+ string encoderConfiguration, //EncoderConfiguration encoderConfiguration,
+ string smoothCon, int curve, int width, int height, string decimalSeparator)
+ {
+ this.minHeight = minHeight;
+ this.exercisePercentBodyWeight = exercisePercentBodyWeight;
+ this.massBody = massBody;
+ this.massExtra = massExtra;
+ this.eccon = eccon;
+ this.analysis = analysis;
+ this.analysisVariables = analysisVariables;
+ this.analysisOptions = analysisOptions;
+ this.captureCheckFullyExtended = captureCheckFullyExtended;
+ this.captureCheckFullyExtendedValue = captureCheckFullyExtendedValue;
+ this.encoderConfiguration = encoderConfiguration;
+ this.smoothCon = smoothCon;
+ this.curve = curve;
+ this.width = width;
+ this.height = height;
+ this.decimalSeparator = decimalSeparator;
+ }
+
+ public string ToStringROptions ()
+ {
+ string capFullyExtendedStr = "-1";
+ if(captureCheckFullyExtended)
+ capFullyExtendedStr = captureCheckFullyExtendedValue.ToString();
+
+ return
+ "#minHeight\n" + minHeight + "\n" +
+ "#exercisePercentBodyWeight\n" + exercisePercentBodyWeight + "\n" +
+ "#massBody\n" + massBody + "\n" +
+ "#massExtra\n" + massExtra + "\n" +
+ "#eccon\n" + eccon + "\n" +
+ "#analysis\n" + analysis + "\n" +
+ "#analysisVariables\n" + analysisVariables + "\n" +
+ "#analysisOptions\n" + analysisOptions + "\n" +
+ "#captureCheckFullyExtended\n" + capFullyExtendedStr + "\n" +
+ //encoderConfiguration.ToStringOutput(EncoderConfiguration.Outputs.ROPTIONS) + "\n" +
+ "#name\nLINEAR\n" +
+ "#str_d\n-1\n" +
+ "#str_D\n-1\n" +
+ "#anglePush\n-1\n" +
+ "#angleWeight\n-1\n" +
+ "#inertiaTotal\n-1\n" +
+ "#gearedDown\n1\n" +
+ "#smoothCon\n" + smoothCon + "\n" +
+ "#curve\n" + curve + "\n" +
+ "#width\n" + width + "\n" +
+ "#height\n" + height + "\n" +
+ "#decimalSeparator\n" + decimalSeparator
+ ;
+ }
+
+ public string Analysis {
+ get { return analysis; }
+ }
+
+
+ ~EncoderParams() {}
+}
+
diff --git a/processMultiDatabases/encoderSQL.cs b/processMultiDatabases/encoderSQL.cs
new file mode 100644
index 00000000..cefa4d9d
--- /dev/null
+++ b/processMultiDatabases/encoderSQL.cs
@@ -0,0 +1,88 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+
+//different form chronojump/encoder EncoderSQL
+public class EncoderSQL
+{
+ public string uniqueID;
+ public int personID;
+ public int sessionID;
+ public int exerciseID;
+ public string eccon;
+ public string laterality;
+ public string extraWeight;
+ public string signalOrCurve;
+ public string filename;
+ public string url; //URL of data of signals and curves. Stored in DB as relative. Used in
software as absolute. See SqliteEncoder
+ public int time;
+ public int minHeight;
+ public string description;
+ public string status; //active or inactive curves
+ public string videoURL; //URL of video of signals. Stored in DB as relative. Used in software as
absolute. See SqliteEncoder
+
+ public string encoderConfiguration;
+ public string future1;
+ public string future2;
+ public string future3;
+
+ public EncoderSQL ()
+ {
+ }
+
+ public EncoderSQL (string uniqueID, int personID, int sessionID, int exerciseID,
+ string eccon, string laterality, string extraWeight, string signalOrCurve,
+ string filename, string url, int time, int minHeight,
+ string description, string status, string videoURL,
+ //EncoderConfiguration encoderConfiguration,
+ string encoderConfiguration,
+ string future1, string future2, string future3//,
+ //string exerciseName
+ )
+ {
+ this.uniqueID = uniqueID;
+ this.personID = personID;
+ this.sessionID = sessionID;
+ this.exerciseID = exerciseID;
+ this.eccon = eccon;
+ this.laterality = laterality;
+ this.extraWeight = extraWeight;
+ this.signalOrCurve = signalOrCurve;
+ this.filename = filename;
+ this.url = url;
+ this.time = time;
+ this.minHeight = minHeight;
+ this.description = description;
+ this.status = status;
+ this.videoURL = videoURL;
+ this.encoderConfiguration = encoderConfiguration;
+ this.future1 = future1; //on curves: meanPower. Better use alter table
+ this.future2 = future2; //on curves: meanSpeed
+ this.future3 = future3; //on curves: meanForce
+ //this.exerciseName = exerciseName;
+ }
+
+ public override string ToString()
+ {
+ return string.Format("{0} - {1}", url, filename);
+ }
+}
+
diff --git a/processMultiDatabases/encoderStruct.cs b/processMultiDatabases/encoderStruct.cs
new file mode 100644
index 00000000..4c48580a
--- /dev/null
+++ b/processMultiDatabases/encoderStruct.cs
@@ -0,0 +1,51 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+
+public class EncoderStruct
+{
+ public EncoderStruct() {
+ }
+
+ public string InputData;
+ public string OutputGraph;
+ public string OutputData1;
+ public string EncoderRPath; //to load other R scripts
+ public string EncoderTempPath; //use for Status, Special, GraphParams....
+ public EncoderParams Ep;
+
+ //pass this to R
+ public EncoderStruct(string InputData, string OutputGraph,
+ string OutputData1,
+ string EncoderRPath, string EncoderTempPath,
+ EncoderParams Ep)
+ {
+ this.InputData = InputData;
+ this.OutputGraph = OutputGraph;
+ this.OutputData1 = OutputData1;
+ this.EncoderRPath = EncoderRPath;
+ this.EncoderTempPath = EncoderTempPath;
+ this.Ep = Ep;
+ }
+
+ ~EncoderStruct() {}
+}
+
diff --git a/processMultiDatabases/howto_compile.txt b/processMultiDatabases/howto_compile.txt
new file mode 100644
index 00000000..da55668d
--- /dev/null
+++ b/processMultiDatabases/howto_compile.txt
@@ -0,0 +1 @@
+mcs processMultiDatabases.cs callR.cs constants.cs encoderGraphOptions.cs encoderParams.cs encoderSQL.cs
encoderStruct.cs util.cs utilEncoder.cs -r:Mono.Data.Sqlite -r:System.Data
diff --git a/processMultiDatabases/processMultiDatabases.cs b/processMultiDatabases/processMultiDatabases.cs
new file mode 100644
index 00000000..8d5068e7
--- /dev/null
+++ b/processMultiDatabases/processMultiDatabases.cs
@@ -0,0 +1,239 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+using System.IO; //"File" things. TextWriter. Path
+using System.Collections.Generic; //List<T>
+using Mono.Data.Sqlite;
+
+//TODO: ara falta el CallR
+
+class ProcessMultiDatabases
+{
+ // start of configuration variables ---->
+ //
+ //barcelona
+ private string barcelona1Path =
"/home/xavier/Documents/academic/investigacio/Encoder_SITLESS/carpetes-chronojump-senceres/barcelona/wetransfer-8ba4dd/Encoder_Copies_17_07_2019/database";
+ private int barcelona1ExSitToStand = 7;
+ private int barcelona1BicepsCurl = 8;
+ private int barcelona1ShoppingBag = 9;
+ private int barcelona1ObjectInShelf = 10;
+
+ //hardcoded stuff (search 'hardcoded' on):
+ //callR.cs
+ //utilEncoder.cs
+
+ // <---- end of configuration variables
+
+ private string database = "chronojump.db";
+ private SqliteConnection dbcon;
+ private SqliteCommand dbcmd;
+ private string dbPath = "";
+
+ public static void Main(string[] args)
+ {
+ new ProcessMultiDatabases();
+ }
+
+ public ProcessMultiDatabases()
+ {
+ dbPath = barcelona1Path;
+
+ sqliteCreateConnection();
+ sqliteOpen();
+
+ processDatabase();
+
+ sqliteClose();
+ Console.WriteLine("processMultiDatabases done!");
+ }
+
+ private void processDatabase()
+ {
+ List<EncoderSQL> list = SelectEncoder (barcelona1ExSitToStand);
+
+ TextWriter writer = File.CreateText("/tmp/barcelona1ExSitToStand.csv");
+ writer.WriteLine("city,exercise,person(cjump:
bad),moment,rep,series,exercise,massBody,massExtra,start,width,height,meanSpeed,maxSpeed,maxSpeedT,meanPower,peakPower,peakPowerT,pp_ppt,meanForce,maxForce,maxForceT,maxForce_maxForceT,workJ,impulse,laterality,inertiaM");
+
+ int count = 0;
+ foreach(EncoderSQL eSQL in list)
+ {
+ Console.WriteLine(string.Format("progress: {0}/{1} - ", count, list.Count) +
eSQL.ToString());
+ double personWeight = SelectPersonWeight(eSQL.personID);
+
+ EncoderParams ep = new EncoderParams(
+ 20,
//preferences.EncoderCaptureMinHeight(encoderConfigurationCurrent.has_inertia),
+ 100, //TODO: change this value depending on exercise
//getExercisePercentBodyWeightFromComboCapture (),
+ Util.ConvertToPoint(personWeight), //
Util.ConvertToPoint(findMass(Constants.MassType.BODY)),
+ Util.ConvertToPoint(eSQL.extraWeight),
//Util.ConvertToPoint(findMass(Constants.MassType.EXTRA)),
+ "c", //findEccon(true),
//force ecS (ecc-conc separated)
+ "curves", //is the same than "curvesAC". was: analysis,
+ "none", //analysisVariables (not needed in
create curves). Cannot be blank
+ "p", //analysisOptions,
+ true, //preferences.encoderCaptureCheckFullyExtended,
+ 4, //preferences.encoderCaptureCheckFullyExtendedValue,
+ "LINEAR", //encoderConfigurationCurrent,
+ "0.7", //Util.ConvertToPoint(preferences.encoderSmoothCon), //R
decimal: '.'
+ 0, //curve is not used here
+ 600, 600, //image_encoder_width, image_encoder_height,
+ "," //preferences.CSVExportDecimalSeparator
+ );
+
+ EncoderStruct es = new EncoderStruct(
+ UtilEncoder.GetEncoderDataTempFileName(),
+ UtilEncoder.GetEncoderGraphTempFileName(),
+ UtilEncoder.GetEncoderCurvesTempFileName(),
+ UtilEncoder.GetEncoderScriptsPathWithoutLastSep(),
+ UtilEncoder.GetEncoderTempPathWithoutLastSep(),
+ ep);
+
+ Console.WriteLine("copying file: " + dbPath + "/../" + eSQL.url + "/" +
eSQL.filename);
+ UtilEncoder.CopyEncoderDataToTemp(dbPath + "/../" + eSQL.url, eSQL.filename);
+ Console.WriteLine("copying file done. Calling R... ");
+
+ new CallR(es);
+ Console.WriteLine("CallR done!");
+
+ //output file is: /tmp/chronojump-last-encoder-curves.txt
+ //1st two lines are:
+
//,series,exercise,massBody,massExtra,start,width,height,meanSpeed,maxSpeed,maxSpeedT,meanPower,peakPower,peakPowerT,pp_ppt,meanForce,maxForce,maxForceT,maxForce_maxForceT,workJ,impulse,laterality,inertiaM
+
//1,1,exerciseName,57.9,0,971,498,755,1.51152519574657,3.20590883396153,307,1694.08480044046,4423.25671303514,243,18202.7025227784,1108.13701938937,1754.09683966977,232,7560.7622399559,1980.64161525193,365.685216398493,,-1e-04
+
+ //
+ //now we have to parse it to fill the big file
+ string filename = "/tmp/chronojump-last-encoder-curves.txt";
+ List<string> lines = Util.ReadFileAsStringList(filename);
+ bool firstLine = true;
+ foreach(string line in lines)
+ {
+ if(firstLine)
+ firstLine = false;
+ else {
+ string line2 = "BARCELONA,SITTOSTAND," + eSQL.personID + ",
(moment)," + line; //TODO: note this personID is not correct because persons sometimes where evaluated on
different chronojump machines
+ writer.WriteLine(line2);
+ writer.Flush();
+ }
+ }
+
+ count ++;
+ /*
+ if(count >= 5)
+ break;
+ */
+
+ System.Threading.Thread.Sleep(200); //rest a bit
+ }
+
+ writer.Close();
+ ((IDisposable)writer).Dispose();
+ Console.WriteLine("processDatabase done!");
+ }
+
+ // ---- sqlite main methods ----
+
+ private void CreateAndOpen()
+ {
+ sqliteCreateConnection();
+ sqliteOpen();
+ }
+
+ private void sqliteCreateConnection()
+ {
+ dbcon = new SqliteConnection ();
+ string sqlFile = dbPath + Path.DirectorySeparatorChar + database;
+ Console.WriteLine(sqlFile);
+ dbcon.ConnectionString = "version = 3; Data source = " + sqlFile;
+ dbcmd = dbcon.CreateCommand();
+ }
+ private void sqliteOpen()
+ {
+ dbcon.Open();
+ }
+ private void sqliteClose()
+ {
+ dbcon.Close();
+ }
+
+ private double SelectPersonWeight (int personID)
+ {
+ dbcmd.CommandText = "SELECT weight FROM personSession77 WHERE personID = " + personID;
+ SqliteDataReader reader;
+ reader = dbcmd.ExecuteReader();
+
+ double myReturn = 0;
+ if(reader.Read()) {
+ myReturn = Convert.ToDouble(Util.ChangeDecimalSeparator(reader[0].ToString()));
+ }
+ reader.Close();
+
+ return myReturn;
+ }
+
+ //TODO: will need session to process this by sessions or compare with filenames
+ private List<EncoderSQL> SelectEncoder (int exerciseID)
+ {
+ dbcmd.CommandText = "SELECT * FROM encoder WHERE signalOrCurve = 'signal' AND exerciseID = "
+ exerciseID;
+ SqliteDataReader reader;
+ reader = dbcmd.ExecuteReader();
+
+ List<EncoderSQL> list = new List<EncoderSQL>();
+ while(reader.Read())
+ {
+ EncoderSQL eSQL = new EncoderSQL (
+ reader[0].ToString(), //uniqueID
+ Convert.ToInt32(reader[1].ToString()), //personID
+ Convert.ToInt32(reader[2].ToString()), //sessionID
+ Convert.ToInt32(reader[3].ToString()), //exerciseID
+ reader[4].ToString(), //eccon
+ reader[5].ToString(),//laterality
+ Util.ChangeDecimalSeparator(reader[6].ToString()), //extraWeight
+ reader[7].ToString(), //signalOrCurve
+ reader[8].ToString(), //filename
+ fixOSpath(reader[9].ToString()),
//Util.MakeURLabsolute(fixOSpath(reader[9].ToString())), //url
+ Convert.ToInt32(reader[10].ToString()), //time
+ Convert.ToInt32(reader[11].ToString()), //minHeight
+ reader[12].ToString(), //description
+ reader[13].ToString(), //status
+ reader[14].ToString(), //videoURL,
//videoURL
+ reader[15].ToString(), //econf,
//encoderConfiguration
+ Util.ChangeDecimalSeparator(reader[16].ToString()), //future1
(meanPower on curves)
+ reader[17].ToString(), //future2
+ reader[18].ToString()//, //future3
+ //reader[19].ToString() //EncoderExercise.name
+ );
+ list.Add (eSQL);
+ }
+ reader.Close();
+ return list;
+ }
+
+ private static string fixOSpath(string url) {
+ //if(UtilAll.IsWindows())
+ // return url.Replace("/","\\");
+ //else
+ return url.Replace("\\","/");
+ }
+
+
+ // ---- end of sqlite main methods ----
+
+}
+
+
diff --git a/processMultiDatabases/util.cs b/processMultiDatabases/util.cs
new file mode 100644
index 00000000..e7f806bb
--- /dev/null
+++ b/processMultiDatabases/util.cs
@@ -0,0 +1,130 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+using System.Collections.Generic; //List<T>
+using System.IO; //"File" things. TextWriter. Path
+using System.Diagnostics; //for detect OS and for Process
+using System.Text; //StringBuilder
+
+public class Util
+{
+ //all numbers are saved in database with '.' as decimal separator (method for numbers)
+ public static string ConvertToPoint (double myDouble)
+ {
+ StringBuilder myStringBuilder = new StringBuilder(myDouble.ToString());
+ myStringBuilder.Replace(",", ".");
+ return myStringBuilder.ToString();
+ }
+
+ //all numbers are saved in database with '.' as decimal separator
+ //method for the tvString, tcString, and runIntervalTimesString
+ public static string ConvertToPoint (string myString)
+ {
+ StringBuilder myStringBuilder = new StringBuilder(myString);
+ myStringBuilder.Replace(",", ".");
+ return myStringBuilder.ToString();
+ }
+
+ public static string ChangeDecimalSeparator(string myString) {
+ if(myString == "") {
+ return "0";
+ }
+ System.Globalization.NumberFormatInfo localeInfo = new
System.Globalization.NumberFormatInfo();
+ localeInfo = System.Globalization.NumberFormatInfo.CurrentInfo;
+
+ StringBuilder myStringBuilder = new StringBuilder(myString);
+ if(localeInfo.NumberDecimalSeparator != ".") {
+ myStringBuilder.Replace(".", localeInfo.NumberDecimalSeparator);
+ }
+ return myStringBuilder.ToString();
+ }
+
+ /*
+ public static string MakeURLabsolute(string url) {
+ string parentDir = Util.GetParentDir(true); //add final '/' or '\'
+ if( ! url.StartsWith(parentDir) )
+ url = parentDir + url;
+
+ return url;
+ }
+ */
+
+ public static void DeleteFile(string filename)
+ {
+ Console.WriteLine("Deleting... " + filename);
+ if (File.Exists(filename))
+ File.Delete(filename);
+ Console.WriteLine("Deleted " + filename);
+ }
+
+ public static bool FileReadable(string filename)
+ {
+ //http://stackoverflow.com/a/17318735
+ try {
+ File.Open(filename, FileMode.Open, FileAccess.Read).Dispose();
+ //LogB.Information("success at Util.FileReadable: " + filename);
+ return true;
+ }
+ catch (IOException) {
+ System.Threading.Thread.Sleep(10);
+ return false;
+ }
+ }
+
+ public static string GetPrefixDir(){
+ string baseDirectory = System.IO.Path.Combine(System.AppDomain.CurrentDomain.BaseDirectory,
"..");
+ if (! Directory.Exists(Path.Combine(baseDirectory, "lib" + Path.DirectorySeparatorChar +
"chronojump"))) {
+ baseDirectory = System.IO.Path.Combine(baseDirectory, "..");
+ }
+ return baseDirectory;
+ }
+
+ public static string GetDataDir(){
+ return System.IO.Path.Combine(GetPrefixDir(),
+ "share" + Path.DirectorySeparatorChar + "chronojump");
+ }
+
+ public static string BoolToRBool (bool myBool) {
+ if(myBool)
+ return "TRUE";
+ else
+ return "FALSE";
+ }
+
+ public static List<string> ReadFileAsStringList(string fileName)
+ {
+ try {
+ List<string> lines = new List<string>();
+ using (var sr = new StreamReader(fileName))
+ {
+ while (sr.Peek() >= 0)
+ {
+ lines.Add(sr.ReadLine());
+ }
+ }
+ return(lines);
+ } catch {
+ return null;
+ }
+ }
+
+}
+
diff --git a/processMultiDatabases/utilEncoder.cs b/processMultiDatabases/utilEncoder.cs
new file mode 100644
index 00000000..266b9a58
--- /dev/null
+++ b/processMultiDatabases/utilEncoder.cs
@@ -0,0 +1,154 @@
+/*
+ * This file is part of ChronoJump
+ *
+ * ChronoJump is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * ChronoJump is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ * Copyright (C) 2019 Xavier de Blas <xaviblas gmail com>
+ */
+
+using System;
+using System.IO; //for detect OS
+
+public class UtilEncoder
+{
+ public static EncoderGraphROptions PrepareEncoderGraphOptions(
+ string title, EncoderStruct es, bool neuromuscularProfileDo, bool translate, bool
debug, bool crossValidate,
+ bool cutByTriggers, string triggerStr, bool separateSessionInDays,
EncoderGraphROptions.AnalysisModes analysisMode)
+ {
+ string operatingSystem = OperatingSystemForRGraphs();
+
+ /*
+ title = Util.RemoveBackSlash(title);
+ title = Util.RemoveChar(title, '\'');
+ */
+ title = "hola";
+
+ /*
+ if (UtilAll.IsWindows()) {
+ //convert accents to Unicode in order to be plotted correctly on R windows
+ title = Util.ConvertToUnicode(title);
+
+ //On win32 R understands backlash as an escape character and
+ //a file path uses Unix-like path separator '/'
+ es.InputData = es.InputData.Replace("\\","/");
+ es.OutputGraph = es.OutputGraph.Replace("\\","/");
+ es.OutputData1 = es.OutputData1.Replace("\\","/");
+ //es.OutputData2 = es.OutputData2.Replace("\\","/");
+ //es.SpecialData = es.SpecialData.Replace("\\","/");
+ es.EncoderTempPath = es.EncoderTempPath.Replace("\\","/");
+ }
+ */
+
+ //if translators add ";", it will be converted to ','
+ //if translators add a "\n", it will be converted to " "
+ /*
+ int count = 0;
+ string temp = "";
+ string [] encoderTranslatedWordsOK = new String [Constants.EncoderTranslatedWords.Length];
+
+ //if ! translate, then just print the english words
+ if(translate) {
+ foreach(string etw in Constants.EncoderTranslatedWords) {
+ temp = Util.ChangeChars(Catalog.GetString(etw), ";", ",");
+ temp = Util.RemoveChar(temp, '\'');
+ temp = Util.RemoveNewLine(temp, true);
+ temp = Util.RemoveChar(temp, '#'); //needed to distinguish comments '#' than
normal lines like the EncoderTranslatedWords
+
+ if (UtilAll.IsWindows()) {
+ LogB.Debug(" (1) Unicoding:", temp);
+ temp = Util.ConvertToUnicode(temp);
+ LogB.Debug(" (2) Unicoded:", temp);
+ }
+
+ encoderTranslatedWordsOK[count++] = temp;
+
+ }
+ } else
+ encoderTranslatedWordsOK = Constants.EncoderEnglishWords;
+ */
+
+ return new EncoderGraphROptions(
+ es.InputData, es.OutputGraph, es.OutputData1,
+ //es.OutputData2, es.SpecialData,
+ es.EncoderRPath, es.EncoderTempPath,
+ es.Ep,
+ title, operatingSystem,
+ "hola2", // Util.StringArrayToString(Constants.EncoderEnglishWords,";"),
+ "hola3", // Util.StringArrayToString(encoderTranslatedWordsOK,";"),
+ debug, crossValidate, cutByTriggers, triggerStr, separateSessionInDays,
analysisMode
+ );
+ }
+
+ public static string OperatingSystemForRGraphs()
+ {
+ string operatingSystem = "Linux";
+ //if (UtilAll.IsWindows())
+ // operatingSystem = "Windows";
+
+ return operatingSystem;
+ }
+
+ public static string GetEncoderDataTempFileName() {
+ return Path.Combine(Path.GetTempPath(), Constants.EncoderDataTemp);
+ }
+ public static string GetEncoderCurvesTempFileName() {
+ return Path.Combine(Path.GetTempPath(), Constants.EncoderCurvesTemp);
+ }
+ public static string GetEncoderGraphTempFileName() {
+ return Path.Combine(Path.GetTempPath(), Constants.EncoderGraphTemp);
+ }
+ public static string GetEncoderScriptsPathWithoutLastSep()
+ {
+ /*
+ string s = System.IO.Path.Combine(Util.GetDataDir(), "encoder");
+
+ //but send it without the final '\' or '/' (if found)
+ if(s.EndsWith("/") || s.EndsWith("\\"))
+ s = s.Substring(0, s.Length -1);
+
+ return s;
+ */
+ //harcoded:
+ return "/usr/local/lib/chronojump/../../share/chronojump/encoder";
+ }
+ public static string GetEncoderTempPathWithoutLastSep() {
+ string s = Path.GetTempPath(); //is just temp path
+
+ //but send it without the final '\' or '/' (if found)
+ if(s.EndsWith("/") || s.EndsWith("\\"))
+ s = s.Substring(0, s.Length -1);
+
+ return s;
+ }
+
+ public static bool CopyEncoderDataToTemp(string url, string fileName)
+ {
+ string origin = url + Path.DirectorySeparatorChar + fileName;
+ string dest = GetEncoderDataTempFileName();
+ if(File.Exists(origin)) {
+ try {
+ File.Copy(origin, dest, true);
+ } catch {
+ Console.WriteLine(Constants.FileCopyProblemStr());
+ return false;
+ }
+ return true;
+ }
+
+ Console.WriteLine(Constants.FileNotFoundStr());
+ return false;
+ }
+
+}
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