drawing and saving chart + cleaning repo

mocos-gui.py

@@ -3,7 +3,7 @@
 import os
 from model.ProjectHandler import ProjectHandler
 from model.ProjectSettings import Cardinalities
-from PyQt5.QtGui import QGuiApplication
+from PyQt5.QtWidgets import QApplication
 from PyQt5.QtQml import QQmlApplicationEngine, qmlRegisterType
 import PyQt5.QtCore
 import logging
@@ -19,15 +19,15 @@ def shutdown():
 
     qmlRegisterType(Cardinalities, "ProjectSettingTypes", 1, 0, "Cardinalities")
 
-    QGuiApplication.setAttribute(PyQt5.QtCore.Qt.AA_EnableHighDpiScaling, True)
-    QGuiApplication.setAttribute(PyQt5.QtCore.Qt.AA_UseHighDpiPixmaps, True)
+    QApplication.setAttribute(PyQt5.QtCore.Qt.AA_EnableHighDpiScaling, True)
+    QApplication.setAttribute(PyQt5.QtCore.Qt.AA_UseHighDpiPixmaps, True)
 
-    app = QGuiApplication([])
+    app = QApplication([])
     engine = QQmlApplicationEngine()
 
     app.aboutToQuit.connect(shutdown)
-    app.setApplicationName("MOCOS")
-    app.setOrganizationDomain("mocos.pl")
+    app.setApplicationName("MOCOS Simulator")
+    app.setOrganizationDomain("https://mocos.pl")
 
     engine.rootContext().setContextProperty("projectHandler", projectHandler)
     engine.rootContext().setContextProperty("initialConditions", projectHandler._settings.initialConditions)

mocos-gui.pyproject

@@ -2,25 +2,27 @@
     "files": [
         "mocos-gui.py",
         "model/ApplicationSettings.py",
+        "model/charts.py",
+        "model/ConfigurationValidator.py",
         "model/ProjectHandler.py",
         "model/ProjectSettings.py",
         "model/SimulationRunner.py",
-        "model/ConfigurationValidator.py",
         "model/Utilities.py",
         "views/ApplicationSettingsWindow.qml",
-        "views/MainWindow.qml",
-        "views/ModulationSettingsView.qml",
-        "views/PhoneTrackingSettingsView.qml",
-        "views/GeneralSettingsView.qml",
-        "views/InitialConditionsView.qml",
-        "views/TransmissionProbabilitiesView.qml",
         "views/ContactTrackingSettingsView.qml",
+        "views/DailyInfectionsChartWindow.qml",
         "views/DoubleNumField.qml",
+        "views/GeneralSettingsView.qml",
+        "views/InitialConditionsView.qml",
         "views/IntNumField.qml",
         "views/KernelEnablingButton.qml",
         "views/LogWindow.qml",
+        "views/MainWindow.qml",
+        "views/ModulationSettingsView.qml",
+        "views/PhoneTrackingSettingsView.qml",
         "views/SpreadingView.qml",
+        "views/TransmissionProbabilitiesView.qml",
         "model/Configuration.schema",
         "model/TanhParameters.schema"
-        ]
+    ]
 }

model/ApplicationSettings.py

@@ -1,5 +1,5 @@
 import os
-from model.Utilities import formatPath, getOrEmptyStr, getOr
+from model.Utilities import format_path, get_or_empty_str, get_or
 from PyQt5.QtCore import QObject, pyqtProperty, pyqtSignal, pyqtSlot
 import json
 from enum import Enum
@@ -62,12 +62,12 @@ def __loadCliOptions(self):
             appSettingsFileHandle.close()
             if lines:
                 content = json.loads(lines)
-                self._juliaCommand = getOr(content, ApplicationSettings.PropertyNames.JULIA_COMMAND.value, "julia")
-                self._outputDaily = getOrEmptyStr(content, ApplicationSettings.PropertyNames.OUTPUT_DAILY.value)
-                self._outputSummary = getOrEmptyStr(content, ApplicationSettings.PropertyNames.OUTPUT_SUMMARY.value)
-                self._outputParamsDump = getOrEmptyStr(content, ApplicationSettings.PropertyNames.OUTPUT_PARAMS_DUMP.value)
-                self._outputRunDumpPrefix = getOrEmptyStr(content, ApplicationSettings.PropertyNames.OUTPUT_RUN_DUMP_PREFIX.value)
-                self._numOfThreads = getOr(content, ApplicationSettings.PropertyNames.NUM_OF_THREADS.value, 1)
+                self._juliaCommand = get_or(content, ApplicationSettings.PropertyNames.JULIA_COMMAND.value, "julia")
+                self._outputDaily = get_or_empty_str(content, ApplicationSettings.PropertyNames.OUTPUT_DAILY.value)
+                self._outputSummary = get_or_empty_str(content, ApplicationSettings.PropertyNames.OUTPUT_SUMMARY.value)
+                self._outputParamsDump = get_or_empty_str(content, ApplicationSettings.PropertyNames.OUTPUT_PARAMS_DUMP.value)
+                self._outputRunDumpPrefix = get_or_empty_str(content, ApplicationSettings.PropertyNames.OUTPUT_RUN_DUMP_PREFIX.value)
+                self._numOfThreads = get_or(content, ApplicationSettings.PropertyNames.NUM_OF_THREADS.value, 1)
                 if self._numOfThreads > self.getMaxNumOfThreads():
                     self._numOfThreads = self.getMaxNumOfThreads()
         except OSError:
@@ -142,7 +142,7 @@ def outputRunDumpPrefix(self):
         return self._outputRunDumpPrefix
 
     def __isPathToOutputFileJld2Correct(self, relpath):
-        fullpath = formatPath(self._getworkdir() + "\\" + relpath)
+        fullpath = format_path(self._getworkdir() + "\\" + relpath)
         return (os.path.dirname(fullpath) != fullpath
                 and relpath.endswith(".jld2")
                 and os.access(os.path.dirname(fullpath), os.W_OK))
@@ -169,7 +169,7 @@ def outputParamsDumpAcceptable(self):
 
     @pyqtProperty(bool, notify=outputRunDumpPrefixAcceptabilityCheckReq)
     def outputRunDumpPrefixAcceptable(self):
-        fullpath = formatPath(self._getworkdir() + "\\" + self._outputRunDumpPrefix)
+        fullpath = format_path(self._getworkdir() + "\\" + self._outputRunDumpPrefix)
         return (self._outputRunDumpPrefix == ""
                 or (os.path.dirname(fullpath) != fullpath
                     and os.access(os.path.dirname(fullpath), os.W_OK)))
@@ -185,7 +185,7 @@ def recentFiles(self):
     @juliaCommand.setter
     def juliaCommand(self, cmd):
         if cmd != "julia":
-            cmd = formatPath(cmd)
+            cmd = format_path(cmd)
         if self._juliaCommand != cmd:
             self._juliaCommand = cmd
             self.__saveCliOptions()
@@ -194,7 +194,7 @@ def juliaCommand(self, cmd):
 
     @outputDaily.setter
     def outputDaily(self, path):
-        newpath = formatPath(path, makeRelativeTo=self._getworkdir())
+        newpath = format_path(path, makeRelativeTo=self._getworkdir())
         if self._outputDaily != path:
             self._outputDaily = newpath
             self.__saveCliOptions()
@@ -203,7 +203,7 @@ def outputDaily(self, path):
 
     @outputSummary.setter
     def outputSummary(self, path):
-        newpath = formatPath(path, makeRelativeTo=self._getworkdir())
+        newpath = format_path(path, makeRelativeTo=self._getworkdir())
         if self._outputSummary != path:
             self._outputSummary = newpath
             self.__saveCliOptions()
@@ -212,7 +212,7 @@ def outputSummary(self, path):
 
     @outputParamsDump.setter
     def outputParamsDump(self, path):
-        newpath = formatPath(path, makeRelativeTo=self._getworkdir())
+        newpath = format_path(path, makeRelativeTo=self._getworkdir())
         if self._outputParamsDump != path:
             self._outputParamsDump = newpath
             self.__saveCliOptions()
@@ -221,7 +221,7 @@ def outputParamsDump(self, path):
 
     @outputRunDumpPrefix.setter
     def outputRunDumpPrefix(self, path):
-        newpath = formatPath(path, makeRelativeTo=self._getworkdir())
+        newpath = format_path(path, makeRelativeTo=self._getworkdir())
         if self._outputRunDumpPrefix != path:
             self._outputRunDumpPrefix = newpath
             self.__saveCliOptions()
@@ -239,3 +239,16 @@ def numOfThreads(self, threadsNum):
     @pyqtSlot(result=int)
     def getMaxNumOfThreads(self):
         return os.cpu_count()
+
+    def abs_path(self, propertyname):
+        if propertyname == ApplicationSettings.PropertyNames.NUM_OF_THREADS:
+            raise ValueError
+        if propertyname == ApplicationSettings.PropertyNames.OUTPUT_DAILY:
+            return "" if not self._outputDaily else format_path(self._getworkdir() + "//" + self._outputDaily)
+        if propertyname == ApplicationSettings.PropertyNames.OUTPUT_PARAMS_DUMP:
+            return "" if not self._outputParamsDump else format_path(self._getworkdir() + "//" + self._outputParamsDump)
+        if propertyname == ApplicationSettings.PropertyNames.OUTPUT_SUMMARY:
+            return "" if not self._outputSummary else format_path(self._getworkdir() + "//" + self._outputSummary)
+        if propertyname == ApplicationSettings.PropertyNames.OUTPUT_RUN_DUMP_PREFIX:
+            return "" if not self._outputRunDumpPrefix else format_path(self._getworkdir() + "//" + self._outputRunDumpPrefix)
+        raise NotImplementedError

model/ProjectHandler.py

@@ -1,14 +1,15 @@
 # This Python file uses the following encoding: utf-8
 from model.ProjectSettings import ModulationFunctions, ProjectSettings, EmptyModulationParams, ValueTypes
 import json
-from PyQt5.QtCore import QAbstractTableModel, pyqtSignal, pyqtSlot, Qt, QByteArray, QObject,  QVariant, pyqtProperty
 import os
+from PyQt5.QtCore import QAbstractTableModel, pyqtSignal, pyqtSlot, Qt, QByteArray, QObject,  QVariant, pyqtProperty
 from model.ConfigurationValidator import ConfigurationValidator
-from model.Utilities import formatPath
+from model.Utilities import format_path
 from model.ApplicationSettings import ApplicationSettings
 from model.SimulationRunner import SimulationRunner
 from jsonschema import ValidationError
 import tempfile
+import model.charts as charts
 
 
 class FunctionParametersModel(QAbstractTableModel):
@@ -116,22 +117,34 @@ def notifyDataChanged(self, topLeft, bottomRight):
 
 
 class ProjectHandler(QObject):
-    _settings = ProjectSettings()
-    _modulationModel = FunctionParametersModel()
-    _applicationSettings = None
-    _simulationRunner = None
     _openedFilePath = None
     _isOpenedConfModified = False
     _isModifyingConfOngoing = True
+    _infectionTrajectories = None
     showErrorMsg = pyqtSignal(str, arguments=['msg'])
     modulationFunctionChanged = pyqtSignal()
     openedNewConf = pyqtSignal()
     openedConfModified = pyqtSignal()
+    infectionTrajectoriesChanged = pyqtSignal()
+    dailyInfectionsDataAvailableChanged = pyqtSignal()
+
+    updateDailyInfectionsChartBegin = pyqtSignal(str, arguments=['filename'])
+    addDailyInfectionSeries = pyqtSignal(str, list, arguments=['name', 'series'])
+    updateDailyInfectionsChartDone = pyqtSignal()
+    logDebug = pyqtSignal(str, arguments=['msg'])
 
     def __init__(self):
         super().__init__()
+        self._settings = ProjectSettings()
+        self._modulationModel = FunctionParametersModel()
         self._applicationSettings = ApplicationSettings(lambda: self.workdir())
         self._simulationRunner = SimulationRunner(lambda: self.workdir())
+        self._chart_preparer = charts.DailyInfectionsSeriesPreparer(
+            lambda: self._applicationSettings.abs_path(
+                ApplicationSettings.PropertyNames.OUTPUT_DAILY))
+        self.connect_signals()
+
+    def connect_signals(self):
         def setModifiedToTrue(): return self.setOpenedConfModifiedIfModificationOngoing()
         self._settings.generalSettings.numTrajectoriesChanged.connect(setModifiedToTrue)
         self._settings.generalSettings.populationPathChanged.connect(setModifiedToTrue)
@@ -157,16 +170,29 @@ def setModifiedToTrue(): return self.setOpenedConfModifiedIfModificationOngoing(
         self._settings.spreading.x0Changed.connect(setModifiedToTrue)
         self._settings.spreading.truncationChanged.connect(setModifiedToTrue)
         self._modulationModel.dataChanged.connect(lambda tr, bl, role: setModifiedToTrue())
-        self.openedNewConf.connect(self._applicationSettings.recheckPaths)
+        self.openedNewConf.connect(self._applicationSettings.recheckPaths, type=Qt.QueuedConnection)
+        self.openedNewConf.connect(self.dailyInfectionsDataAvailableChanged, type=Qt.QueuedConnection)
+        self._applicationSettings.outputDailyChanged.connect(
+            self.dailyInfectionsDataAvailableChanged, type=Qt.QueuedConnection)
+        self.dailyInfectionsDataAvailableChanged.connect(
+            self.prepareDailyInfectionsData, type=Qt.QueuedConnection)
+        self._simulationRunner.isRunningChanged.connect(
+            self.dailyInfectionsDataAvailableChanged, type=Qt.QueuedConnection)
+        self._chart_preparer.series_prepared.connect(self.addDailyInfectionSeries)
+        self._chart_preparer.preparing_begin.connect(
+            self.updateDailyInfectionsChartBegin, type=Qt.QueuedConnection)
+        self._chart_preparer.preparing_done.connect(
+           self.updateDailyInfectionsChartDone, type=Qt.QueuedConnection)
+        self._chart_preparer.log_debug.connect(self.logDebug)
 
     def setOpenedConfModifiedIfModificationOngoing(self):
         if self._isModifyingConfOngoing:
             self.setOpenedConfModified(True)
 
-    def __saveConfToTempFile(self):
+    def _saveConfToTempFile(self):
         fh = tempfile.NamedTemporaryFile(mode='w', encoding='utf-8', delete=False)
         json.dump(self._settings.serialize(), fh, indent=4, ensure_ascii=False)
-        path = formatPath(fh.name)
+        path = format_path(fh.name)
         fh.close()
         return path
 
@@ -177,7 +203,7 @@ def workdir(self):
 
     @pyqtSlot(str)
     def saveAs(self, path):
-        path = formatPath(path)
+        path = format_path(path)
         fh = open(path, "w", encoding='utf-8')
         json.dump(self._settings.serialize(), fh, indent=4, ensure_ascii=False)
         fh.close()
@@ -193,7 +219,8 @@ def quickSave(self):
     @pyqtSlot(str)
     def open(self, path):
         try:
-            path = formatPath(path)
+            self._chart_preparer.stop()
+            path = format_path(path)
             inputFileHandle = open(path, 'r', encoding='utf-8')
             data = json.loads(inputFileHandle.read())
             ConfigurationValidator.validateAgainstSchema(data)
@@ -210,6 +237,8 @@ def open(self, path):
             self.showErrorMsg.emit("File: json schema is corrupted: {0}".format(str(error)))
         except ValidationError as error:
             self.showErrorMsg.emit("Unable to open file at: {0} due to wrong input data: {1}".format(path, str(error)))
+        finally:
+            inputFileHandle.close()
 
     @pyqtSlot(result=str)
     def getOpenedConfName(self):
@@ -254,10 +283,6 @@ def loadParamsForFunction(self, funcType, isModifyingConf):
         else:
             self._isModifyingConfOngoing = True
 
-    @pyqtSlot(str)
-    def setPopulationFilePath(self, path):
-        self._settings.generalSettings.populationPath = formatPath(path)
-
     @pyqtSlot()
     def runSimulation(self):
         if not self._settings.generalSettings._populationPath:
@@ -273,9 +298,10 @@ def runSimulation(self):
                 or not self._applicationSettings.outputRunDumpPrefixAcceptable):
             self.showErrorMsg.emit("Simulation can't be run: simulation settings are incorrect.")
             return
+        self._chart_preparer.stop()
         self._simulationRunner.openedFilePath = self._openedFilePath
         if not self._simulationRunner.openedFilePath:
-            self._simulationRunner.openedFilePath = self.__saveConfToTempFile()
+            self._simulationRunner.openedFilePath = self._saveConfToTempFile()
         self._simulationRunner.juliaCommand = self._applicationSettings.juliaCommand
         self._simulationRunner.outputDaily = self._applicationSettings.outputDaily
         self._simulationRunner.outputSummary = self._applicationSettings.outputSummary
@@ -287,3 +313,21 @@ def runSimulation(self):
     @pyqtSlot()
     def stopSimulation(self):
         self._simulationRunner.stop()
+
+    @pyqtSlot()
+    def prepareDailyInfectionsData(self):
+        self._chart_preparer.start_preparing_data()
+
+    @pyqtProperty(bool, notify=dailyInfectionsDataAvailableChanged)
+    def isDailyInfectionsDataAvailable(self):
+        dailypath = self._applicationSettings.abs_path(ApplicationSettings.PropertyNames.OUTPUT_DAILY)
+        return charts.is_daily_infections_data_available(dailypath)
+
+    @pyqtSlot()
+    def addNextDailyInfectionSeries(self):
+        self._chart_preparer.on_series_added()
+
+    @pyqtSlot()
+    def beforeClosingMainWindow(self):
+        self.stopSimulation()
+        self._chart_preparer.stop()

model/ProjectSettings.py

@@ -1,7 +1,7 @@
 # This Python file uses the following encoding: utf-8
 from enum import Enum
 from PyQt5.QtCore import QObject, pyqtProperty, pyqtSignal, QVariant
-from model.Utilities import formatPath
+from model.Utilities import format_path
 
 
 class GeneralSettings(QObject):
@@ -45,7 +45,7 @@ def numTrajectories(self, val):
 
     @populationPath.setter
     def populationPath(self, path):
-        path = formatPath(path)
+        path = format_path(path)
         if self._populationPath != path:
             self._populationPath = path
             self.populationPathChanged.emit()

model/SimulationRunner.py

@@ -8,7 +8,7 @@
 import queue
 import tempfile
 from shutil import which
-from model.Utilities import formatPath, ABS_PATH_TO_ADVANCED_CLI
+from model.Utilities import format_path, ABS_PATH_TO_ADVANCED_CLI
 
 
 def enqueueOutStream(output, q):
@@ -94,16 +94,16 @@ def _createCommand(self):
         cmd.append(cliname)
         if self.outputParamsDump:
             cmd.append("--output-params-dump")
-            cmd.append(formatPath(self._getworkdir() + "\\" + self.outputParamsDump))
+            cmd.append(format_path(self._getworkdir() + "\\" + self.outputParamsDump))
         if self.outputDaily:
             cmd.append("--output-daily")
-            cmd.append(formatPath(self._getworkdir() + "\\" + self.outputDaily))
+            cmd.append(format_path(self._getworkdir() + "\\" + self.outputDaily))
         if self.outputSummary:
             cmd.append("--output-summary")
-            cmd.append(formatPath(self._getworkdir() + "\\" + self.outputSummary))
+            cmd.append(format_path(self._getworkdir() + "\\" + self.outputSummary))
         if self.outputRunDumpPrefix:
             cmd.append("--output-run-dump-prefix")
-            cmd.append(formatPath(self._getworkdir() + "\\" + self.outputRunDumpPrefix))
+            cmd.append(format_path(self._getworkdir() + "\\" + self.outputRunDumpPrefix))
         cmd.append(self.openedFilePath)
         return cmd
 
@@ -218,5 +218,5 @@ def stop(self):
             self._process = None
 
     def clean(self):
-        if self.openedFilePath.find(formatPath(tempfile.gettempdir())) != -1:
+        if self.openedFilePath.find(format_path(tempfile.gettempdir())) != -1:
             os.remove(self.openedFilePath)