Merge branch 'master' of https://github.com/palaeoware/SPIERS

.gitignore

@@ -1,2 +1,5 @@
 *.autosave
 *.user
+*.8-pre1
+*.DS_Store
+.DS_Store

README.md

@@ -69,11 +69,37 @@ We recommend you install and use MSYS2 (64-bit) a Windows package manager, based
 
 #### Ubuntu 18.04 64-bit - QT Creator + QT v5.x and VTK v7.1 using GCC (64-bit)
 
-1. The simplest way to install Q5.X on your system is to download and run the installer from Qt: https://www.qt.io/download Further instructions are available here: https://wiki.qt.io/Install_Qt_5_on_Ubuntu
-2. SPIERSview requires VTK: The Linux version of SPIERSview is currently employs VTK7.1, installed from the Ubuntu package (e.g. sudo apt-get install libvtk7-qt-dev)
-3. Using the above package, you should be able to find the required VTK libraries under /usr/include/vtk-7.1/ they can also be included, if needed, in the working directory, and added to the executable at link time using the QMAKE_RPATHDIR variable - e.g. #QMAKE_RPATHDIR += $$PWD/vtk-7.X/
+1. Install GCC and QT5.X on your system. You can do this two ways, by using system packages:
+
+`sudo apt-get install build-essential libgl1-mesa-dev`
+
+`sudo apt install qt5-default`
+
+Or by downloading and running the installer from Qt: https://www.qt.io/download Further instructions are available here: https://wiki.qt.io/Install_Qt_5_on_Ubuntu
+
+2. SPIERSview requires VTK: The Linux version of SPIERSview is currently employs VTK7.1. This can also be installed from the Ubuntu packages:
+
+`sudo apt-get install libvtk7-qt-dev`
+
+3. Using the above package, you should be able to find the required VTK libraries under /usr/include/vtk-7.1/ They can also be included, if needed, in the working directory, and added to the executable at link time using the QMAKE_RPATHDIR variable - e.g. #QMAKE_RPATHDIR += $$PWD/vtk-7.X/
 4. You should then be able to compile SPIERS by opening the .pro file in QT creator and following standard debug/release procedure.
 
+#### macOS Catalina 64-bit - QT Creator + QT v5.x and VTK v8.2 (via Homebrew) using Clang 64-bit/XCode 11 toolchain
+
+1. Install XCode 11 from Apple App Store.
+2. Install QT5.x/QT Creator from https://www.qt.io/download.
+3. Install Homebrew (https://brew.sh/).
+4. Get VTK 8.2 package via Homebrew - you may need to force Homebrew to install a specific VTK version see Homebrew instruction on how to do so: 
+
+`brew install vtk`
+
+5. Check/Update the path to the VTK package in the ./SPIERSview/SPIERSview.pro file, where "8.2.0_10" is your installed version number:
+
+'LIBS += -L$$PWD/../../../../../../usr/local/Cellar/vtk/8.2.0_10/lib/ \'
+
+6. You should then be able to compile SPIERS by opening the .pro file in QT creator and following standard debug/release procedure.
+
+Note: it may be possible to install QT5.x/QT Creator via Homebrew rather than via the Apple App Store.
 _____
 
 ## 4. Minimum Requirements

SPIERS.pro

@@ -3,3 +3,6 @@ SUBDIRS = SPIERSalign \
           SPIERSedit \
           SPIERSview \
           SPIERSutility/SPIERSversion \
+
+CONFIG +=
+    sdk_no_version_check

SPIERSalign/SPIERSalign.pro

@@ -24,6 +24,9 @@ DESTDIR \
     += \
     bin
 
+#Needed to make binaries launchable from file in Ubuntu - GCC default link flag -pie on newer Ubuntu versions this so otherwise recognised as shared library
+QMAKE_LFLAGS += -no-pie
+
 RC_FILE += resources/icon.rc
 
 DISTFILES += \
@@ -37,6 +40,9 @@ OBJECTS_DIR = build
 FORMS += ui/mainwindow.ui \
     ui/about.ui
 
+#Mac icon
+ICON = resources/SPIERSalignIcon.icns
+
 HEADERS += src/mainwindowimpl.h \
     src/globals.h \
     src/scene.h \

SPIERSalign/align.qrc

@@ -1,5 +1,5 @@
 <RCC>
     <qresource prefix="/">
-        <file alias="alignicon.png">resources/alignicon.png</file>
+        <file>resources/SPIERSalignIcon.svg</file>
     </qresource>
 </RCC>

SPIERSalign/docs/conf.py

@@ -22,13 +22,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'SPIERSalign'
-copyright = '2018, Russell Garwood, Mark Sutton, Alan R.T. Spencer'
+copyright = '2018-2019, Russell Garwood, Mark Sutton, Alan R.T. Spencer'
 author = 'Russell Garwood, Mark Sutton, Alan R.T. Spencer'
 
 # The short X.Y version
 version = '3.0.0'
 # The full version, including alpha/beta/rc tags
-release = '3.0.0-rc.1'
+release = '3.0.0'
 
 
 # -- General configuration ---------------------------------------------------

SPIERSalign/resources/icon.rc

@@ -1 +1 @@
-IDI_ICON1               ICON    DISCARDABLE     "icon.ico" 
+IDI_ICON1               ICON    DISCARDABLE     "SPIERSalignIcon.ico" 

SPIERSalign/src/about.cpp

@@ -2,10 +2,10 @@
  * @file
  * About Dialog
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify
@@ -36,7 +36,7 @@ About::About(QWidget *parent) :
 
     ui->header->setVisible(false);
 
-    ui->textLabel_1->setText(theMainWindow->windowTitle());
+    ui->textLabel_1->setText(QString(PRODUCTNAME) + " - Version " + QString(SOFTWARE_VERSION));
     ui->textLabel_1->setObjectName("aboutTextLabel1");
     ui->textLabel_1->setAlignment(Qt::AlignCenter);
 

SPIERSalign/src/about.h

@@ -2,10 +2,10 @@
  * @file
  * Header: About
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify

SPIERSalign/src/globals.cpp

@@ -2,10 +2,10 @@
  * @file
  * Globals
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify

SPIERSalign/src/globals.h

@@ -2,10 +2,10 @@
  * @file
  * Header: Globals
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify
@@ -29,9 +29,10 @@
 #include <QPushButton>
 #include <QString>
 #include <QTransform>
+#include <QSettings>
 
 //Legal Stuff
-#define COPYRIGHT "Copyright © 2018 Mark D. Sutton, Russell J. Garwood, Alan R.T.Spencer"
+#define COPYRIGHT "Copyright © 2018-2020 Mark D. Sutton, Russell J. Garwood, Alan R.T.Spencer"
 #define LICENCE "This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under the conditions of the GPL v3  license"
 
 //Programme Name

SPIERSalign/src/main.cpp

@@ -2,10 +2,10 @@
  * @file
  * Main
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify

SPIERSalign/src/mainwindowimpl.cpp

@@ -2,10 +2,10 @@
  * @file
  * Main Window
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify
@@ -43,6 +43,7 @@
 #include <QUrl>
 #include <QVBoxLayout>
 #include <QFont>
+#include <QStandardPaths>
 
 #include <math.h>
 #include <qbitmap.h>
@@ -72,9 +73,10 @@ MainWindowImpl::MainWindowImpl(QWidget *parent, Qt::WindowFlags f)
 {
     //Set up initial variables
     setupUi(this);
-    setWindowIcon(QIcon (":/alignicon.png"));
 
-    setWindowTitle(QString(PRODUCTNAME) + " v" + QString(SOFTWARE_VERSION) );
+    qDebug() << QImageWriter::supportedImageFormats();
+
+    setWindowTitle(QString(PRODUCTNAME) + " - Version " + QString(SOFTWARE_VERSION));
 
     showMaximized();
 
@@ -507,7 +509,7 @@ void readSuperGlobals()
     //Clear recentfilelist just in case already exists
     recentFileList.clear();
     //New settings to be read from the registry
-    QSettings settings("Mark Sutton", "SPIERSalign 2.0");
+    QSettings settings("Palaeoware", "SPIERSalign");
     int size = settings.beginReadArray("RecentFiles");
     //Read files from registry
     for (int i = 0; i < size; ++i)
@@ -527,7 +529,7 @@ void readSuperGlobals()
 void writeSuperGlobals()
 {
     //New settings to be written
-    QSettings settings("Mark Sutton", "SPIERSalign 2.0");
+    QSettings settings("Palaeoware", "SPIERSalign");
     settings.beginWriteArray("RecentFiles");
     int loop;
     if (recentFileList.size() > 20) loop = 20;
@@ -1927,14 +1929,14 @@ void MainWindowImpl::on_actionOpen_triggered()
 
         notes->clear();
 
-        this->setWindowTitle(QString(PRODUCTNAME) + " v" + QString(SOFTWARE_VERSION));
+        this->setWindowTitle(QString(PRODUCTNAME) + " - Version " + QString(SOFTWARE_VERSION));
     }
     currentImage = 0;
 
     if (fullSettingsFileName.isEmpty())
     {
-        filesDirectoryString = QFileDialog::getExistingDirectory(this, tr("Select folder containing image files"),
-                                                                 "d:/", QFileDialog::ShowDirsOnly);
+        filesDirectoryString = QFileDialog::getExistingDirectory(this, tr("Select folder containing image files; note the files within a folder will not be listed if you are using Windows."),
+                                                                 QString(QStandardPaths::DesktopLocation), QFileDialog::ShowDirsOnly);
         if (filesDirectoryString == "") return; //dialogue cancelled
         filesDirectory = filesDirectoryString; //construct directory object
     }
@@ -1949,7 +1951,7 @@ void MainWindowImpl::on_actionOpen_triggered()
     recentFile(filesDirectoryString);
 
     QStringList FilterList;
-    FilterList << "*.bmp" << "*.jpg" << "*.jpeg" << "*.png";
+    FilterList << "*.bmp" << "*.jpg" << "*.jpeg" << "*.png" << "*.tiff" << "*.tif";
     drectoryFileList = filesDirectory.entryList(FilterList, QDir::Files, QDir::Name);
 
     if (drectoryFileList.count() == 0)
@@ -2101,12 +2103,14 @@ void MainWindowImpl::on_actionOpen_triggered()
     for (i = 0; i < imageList.count(); i++)
     {
         imageList[i]->format = -1;
+        if (imageList[i]->fileName.endsWith(".tif", Qt::CaseInsensitive) || imageList[i]->fileName.endsWith(".tiff", Qt::CaseInsensitive))imageList[i]->format = 3;
         if (imageList[i]->fileName.endsWith(".png", Qt::CaseInsensitive))imageList[i]->format = 2;
         if (imageList[i]->fileName.endsWith(".jpg", Qt::CaseInsensitive) || imageList[i]->fileName.endsWith(".jpeg", Qt::CaseInsensitive))imageList[i]->format = 1;
         if (imageList[i]->fileName.endsWith(".bmp", Qt::CaseInsensitive))imageList[i]->format = 0;
+
         if (imageList[i]->format == -1)
         {
-            QMessageBox::warning(this, "Error", "Please check extensions - should be either .jpg, .jpeg, .bmp or .png", QMessageBox::Ok);
+            QMessageBox::warning(this, "Error", "Please check extensions - should be either .jpg, .jpeg, .bmp, .tif, .tiff or .png", QMessageBox::Ok);
             return;
         }
     }
@@ -2206,10 +2210,10 @@ void  MainWindowImpl::redrawImage()
     LogText("*6\t");
 
     //Title bar
-    QString output = QString(SOFTWARE_VERSION) + imageList[currentImage]->fileName;
+    QString output = " - " + imageList[currentImage]->fileName;
     QString output2;
     output2.sprintf(" - (%d/%d)", currentImage + 1, imageList.count());
-    this->setWindowTitle(QString(PRODUCTNAME) + " v" + output + output2);
+    this->setWindowTitle(QString(PRODUCTNAME) + " - Version " + QString(SOFTWARE_VERSION) + output + output2);
 
     LogText("*7\t");
     //Rescale view
@@ -3442,6 +3446,7 @@ void MainWindowImpl::on_actionApply_Propogation_triggered()
             if (imageList[i]->format == 0)imageToDraw.save(savename, "BMP", 100);
             if (imageList[i]->format == 1)imageToDraw.save(savename, "JPG", 100);
             if (imageList[i]->format == 2)imageToDraw.save(savename, "PNG", 50);
+            if (imageList[i]->format == 3)imageToDraw.save(savename, "TIFF");
         }
     }
     else if (actionLock_Back->isChecked())
@@ -3552,6 +3557,7 @@ void MainWindowImpl::on_actionApply_Propogation_triggered()
             if (imageList[i]->format == 0)imageToDraw.save(savename, "BMP", 100);
             if (imageList[i]->format == 1)imageToDraw.save(savename, "JPG", 100);
             if (imageList[i]->format == 2)imageToDraw.save(savename, "PNG", 50);
+            if (imageList[i]->format == 3)imageToDraw.save(savename, "TIFF");
         }
     }
     else QMessageBox::warning(this, "Error", "You should never see this - propagation failed, email me.", QMessageBox::Ok);
@@ -4267,8 +4273,8 @@ void MainWindowImpl::on_actionLoad_Settings_File_triggered()
 
     int i, j = 0;
     if ((QMessageBox::question(nullptr, "Confirm", "Are you sure you want to load a settings file? This will overwrite the current settings and apply the new ones to the currently open dataset.",
-                               QMessageBox::Ok, QMessageBox::Cancel)) == QMessageBox::Cancel)return;
-    QString settingsFile = QFileDialog::getOpenFileName(this, tr("Select settings file"), "d:/");
+                               QMessageBox::Ok, QMessageBox::Cancel)) == QMessageBox::Cancel) return;
+    QString settingsFile = QFileDialog::getOpenFileName(this, tr("Select settings file"), QString(QStandardPaths::DesktopLocation));
     if (settingsFile == "") return;
 
     QFile settings(settingsFile);
@@ -4356,6 +4362,7 @@ void MainWindowImpl::on_actionLoad_Settings_File_triggered()
     for (i = 0; i < imageList.count(); i++)
     {
         imageList[i]->format = -1;
+        if (imageList[i]->fileName.endsWith(".tif", Qt::CaseInsensitive) || imageList[i]->fileName.endsWith(".tiff", Qt::CaseInsensitive))imageList[i]->format = 3;
         if (imageList[i]->fileName.endsWith(".png", Qt::CaseInsensitive))imageList[i]->format = 2;
         if (imageList[i]->fileName.endsWith(".jpg", Qt::CaseInsensitive) || imageList[i]->fileName.endsWith(".jpeg", Qt::CaseInsensitive))imageList[i]->format = 1;
         if (imageList[i]->fileName.endsWith(".bmp", Qt::CaseInsensitive))imageList[i]->format = 0;
@@ -4430,6 +4437,7 @@ void MainWindowImpl::on_actionLoad_Settings_File_triggered()
             if (imageList[i]->format == 0)imageToDraw.save(savename, "BMP", 100);
             if (imageList[i]->format == 1)imageToDraw.save(savename, "JPG", 100);
             if (imageList[i]->format == 2)imageToDraw.save(savename, "PNG", 50);
+            if (imageList[i]->format == 3)imageToDraw.save(savename, "TIFF");
 
             redrawImage();
         }

SPIERSalign/src/mainwindowimpl.h

@@ -2,10 +2,10 @@
  * @file
  * Header: Main Window
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify

SPIERSalign/src/scene.cpp

@@ -2,10 +2,10 @@
  * @file
  * Scene
  *
- * All SPIERSview code is released under the GNU General Public License.
+ * All SPIERSalign code is released under the GNU General Public License.
  * See LICENSE.md files in the programme directory.
  *
- * All SPIERSview code is Copyright 2008-2018 by Russell J. Garwood, Mark D. Sutton,
+ * All SPIERSalign code is Copyright 2008-2019 by Russell J. Garwood, Mark D. Sutton,
  * and Alan R.T. Spencer.
  *
  * This program is free software; you can redistribute it and/or modify