Initial Debian support

Debian/data-control.txt

@@ -0,0 +1,6 @@
+Package: surfice-data
+Version: <ver>
+Architecture: all
+Maintainer: NeuroDebian Team <[email protected]>
+Description: data files for Surfice
+ Surfice GUI-based visualization for neuroimaging meshes

Debian/make_deb_amd64.sh

@@ -0,0 +1,66 @@
+#!/bin/bash
+# Fail if anything not planed to go wrong, goes wrong
+set -eu
+sw=surfice
+source ../vers.inc
+ver=$kVers
+arch=amd64
+#set widgetset set for default(QT5)
+wigetset=
+sw=${sw}${wigetset}
+
+pkg=${sw}_${ver}_${arch}
+#deb=${pkg}.deb
+exePath=${pkg}/usr/bin/
+appPath=${pkg}/usr/share/applications/
+docPath=${pkg}/usr/share/doc/${sw}/
+iconPath=${pkg}/usr/share/icons/hicolor/scalable/apps/
+manPath=${pkg}/usr/share/man/man1/
+man=${sw}.1.gz
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+cd $SCRIPT_DIR
+
+if [ -z "$wigetset" ]
+then
+      lazbuild --ws=qt5 ../surfice.lpi
+else
+      lazbuild --ws=gtk2 ../surfice.lpi
+fi
+
+#remove previous package files
+rm -rf ${pkg}
+#copy all required files
+#copy control file
+mkdir -p ${pkg}/DEBIAN
+#cp ./${sw}-control.txt ${pkg}/DEBIAN/control
+sed "s/<ver>/$ver/" ./${sw}-control.txt > ${pkg}/DEBIAN/control
+#copy executable
+mkdir -p ${exePath}
+cp ../${sw} ${exePath}${sw}
+#copy desktop file
+mkdir -p ${appPath}
+#cp ${sw}.desktop ${appPath}${sw}.desktop
+sed "s/<ver>/$ver/" ./${sw}.desktop > ${appPath}${sw}.desktop
+
+#copy icon svg
+mkdir -p ${iconPath}
+cp ${sw}.svg ${iconPath}${sw}.svg
+
+#copy documents
+mkdir -p ${docPath}
+cp ../license.txt ${docPath}copyright
+#copy manual
+mkdir -p ${manPath}
+cp ${man} ${manPath}${man}
+
+dpkg-deb --build --root-owner-group ${pkg}
+#remove temporary files
+rm -rf ${pkg}
+
+echo Test the package:
+echo sudo dpkg -I ${pkg}.deb
+echo sudo dpkg -c ${pkg}.deb
+echo sudo dpkg -i ${pkg}.deb
+exit 0
+

Debian/make_deb_data.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+#Create Debian package for all versions of Surfice
+
+# Fail if anything not planed to go wrong, goes wrong
+set -eu
+sw=surfice-data
+source ../vers.inc
+ver=$kVers
+pkg=${sw}_${ver}_all
+#deb=${pkg}.deb
+resourcePath=${pkg}/usr/share/surfice/
+
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+cd $SCRIPT_DIR
+
+#remove previous package files
+rm -rf ${pkg}
+#copy all required files
+mkdir -p ${pkg}/DEBIAN
+#cp ./data-control.txt ${pkg}/DEBIAN/control
+sed "s/<ver>/$ver/" ./data-control.txt > ${pkg}/DEBIAN/control
+
+mkdir -p ${resourcePath}
+cp -a ../Resources/. ${resourcePath}
+#Linux does not need Windows resources python36.dll and python36.zip
+rm -rf ${resourcePath}python*.*
+
+dpkg-deb --build --root-owner-group ${pkg}
+#remove temporary files
+rm -rf ${pkg}
+exit 0
+
+
+
+
+

Debian/surfice-control.txt

@@ -0,0 +1,7 @@
+Package: surfice
+Version: <ver>
+Architecture: amd64
+Maintainer: NeuroDebian Team <[email protected]>
+Depends: libqt5pas1, libc6 (>= 2.14), python3:any (>= 3.6), surfice-data  (= <ver>)
+Description: Surfice
+ Surfice GUI-based visualization for neuroimaging meshes (using QT5)

Debian/surfice.1

@@ -0,0 +1,18 @@
+.TH "SURFICE" "1" "September 2021" "Chris Rorden" "User Commands"
+.SH NAME
+surfice \- neuroimaging mesh viewing tool
+.SH "DESCRIPTION"
+Surfice is a GUI-based visualization and analysis tool for neuroimaging 
+data. It can display triangulated meshes in many formats, including 
+PLY, GIfTI, FreeSurfer, and OBJ. Surfice can also display diffusion tensor
+tractography maps from various formats including TRK and TCK. In addition, 
+it is able to show connectome maps.
+.SH "AUTHOR"
+\fBsurfice\fR was written by Chris Rorden.
+.PP
+This manual page was written by Chris Rorden,
+for the Debian project (but may be used by others).
+.SH "SEE ALSO"
+.BR dcm2niix "(1)"
+.TP
+\fBSurfice Homepage and Wiki:\fR https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage

Debian/surfice.desktop

@@ -0,0 +1,14 @@
+[Desktop Entry]
+Version=<ver>
+Name=Surfice
+GenericName=2D/3D MRI Surface Viewer
+GenericName[de]=2D/3D Betrachter für MRT-Daten
+GenericName[ru]=Просмотр 2D/3D МРТ-данных
+Comment=Edit Exec and Icon paths for your system
+Exec=surfice %F
+TryExec=surfice
+Icon=/usr/share/icons/hicolor/scalable/apps/surfice.svg
+Terminal=false
+Type=Application
+Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;QT5;Viewer;
+

PythonBridge/DynamicImports.inc

@@ -156,7 +156,7 @@ CodePointer(PyFunction_GetCode)        :=Import('PyFunction_GetCode');
 CodePointer(PyFunction_GetGlobals)     :=Import('PyFunction_GetGlobals');
 CodePointer(PyFunction_New)            :=Import('PyFunction_New');
 CodePointer(PyImport_AddModule)        :=Import('PyImport_AddModule');
-CodePointer(PyImport_Cleanup)          :=Import('PyImport_Cleanup');
+//CodePointer(PyImport_Cleanup)          :=Import('PyImport_Cleanup');
 CodePointer(PyImport_GetMagicNumber)   :=Import('PyImport_GetMagicNumber');
 CodePointer(PyImport_ImportFrozenModule):=Import('PyImport_ImportFrozenModule');
 CodePointer(PyImport_ImportModule)     :=Import('PyImport_ImportModule');

PythonBridge/DynamicTypes.inc

@@ -209,7 +209,7 @@ PyFunction_GetCode:function (ob:PPyObject):PPyObject; cdecl;
 PyFunction_GetGlobals:function (ob:PPyObject):PPyObject; cdecl;
 PyFunction_New:function (ob1,ob2:PPyObject):PPyObject; cdecl;
 PyImport_AddModule:function (name:PAnsiChar):PPyObject; cdecl;
-PyImport_Cleanup:procedure; cdecl;
+//PyImport_Cleanup:procedure; cdecl;
 PyImport_GetMagicNumber:function :LONGINT; cdecl;
 PyImport_ImportFrozenModule:function (key:PAnsiChar):integer; cdecl;
 PyImport_ImportModule:function (name:PAnsiChar):PPyObject; cdecl;

PythonBridge/Python3Core.pas

@@ -1,12 +1,11 @@
 {$mode objfpc}
+{$include pyopts.inc} //for  define PYTHON_DYNAMIC
 {$assertions on}
 
 {$ifdef win32}
   {$define cpux86}
 {$endif}
-{$ifdef windows}
-  {$define PYTHON_DYNAMIC}
-{$endif}
+
 
 {$ifdef fpc}
   {$ifdef cpu64}

PythonBridge/PythonBridge.pas

@@ -1,15 +1,13 @@
 {$mode objfpc}
 {$assertions on}
-{$ifdef windows}
-  {$define PYTHON_DYNAMIC}
-{$endif}
+{$include pyopts.inc} //for  define PYTHON_DYNAMIC
 
 
 
 unit PythonBridge;
 interface
 uses
-  {$ifdef windows}windows,{$endif}{$ifdef lcl} dialogs, {$endif} Python3Core, SysUtils;
+  {$ifdef linux}LazFileUtils,{$endif}{$ifdef windows}windows,{$endif}{$ifdef lcl} dialogs, {$endif} Python3Core, SysUtils;
 
 type
   TPythonBridgeMethod = record
@@ -95,6 +93,63 @@ function findDll(resourceDir: string): string; //Detect .DLL version
 Function  SetDllDirectory(lpPathName: LPCTSTR):LongBool; stdcall; external 'kernel32.dll' name 'SetDllDirectoryA'; //uses add windows,sysutils,
 {$endif}
 
+{$ifdef linux} {$ifdef PYTHON_DYNAMIC}
+function findLibDebian(base: string): string;
+//https://matthew-brett.github.io/pydagogue/debian_python_paths.html
+// check base of "/usr/local/lib" and "/usr/lib"
+//lib = /usr/lib/python3.9/config-3.9-x86_64-linux-gnu/libpython3.9.so
+//e.g. Ubuntu 18.04
+//lib = /usr/lib/python3.6/config-3.6m-x86_64-linux-gnu/libpython3.6m.so
+var
+  i: integer;
+begin
+  for i := 11 downto 6 do begin
+    result := format('%s/python3.%d/config-3.%d-x86_64-linux-gnu/libpython3.%d.so', [base, i, i, i]);
+    if FileExists(result) then exit;
+    //pymalloc  PEP-3149: ABI version tagged .so files.
+    result := format('%s/python3.%d/config-3.%d-x86_64-linux-gnu/libpython3.%dm.so', [base, i, i, i]);
+    if FileExists(result) then exit;
+  end;
+  writeln('Unable to find a library with a name like '+result);
+  result := '';
+end;
+
+function findFirstRecursive(const SearchPath: String; SearchMask: String): string;
+//example findFirstRecursive('/usr/lib/', 'libpython3*so')
+//uses LazFileUtils
+var
+  ret: string;
+procedure find1(Dir: string);
+var
+   SR: TSearchRec;
+begin
+     if (ret <> '') or (FileIsSymlink(Dir)) then exit;
+     if FindFirst(IncludeTrailingBackslash(Dir) + SearchMask, faAnyFile or faDirectory, SR) = 0 then begin
+         ret := IncludeTrailingBackslash(Dir) +SR.Name;
+         FindClose(SR);
+         exit;
+      end;
+      if FindFirst(IncludeTrailingBackslash(Dir) + '*.*', faAnyFile or faDirectory, SR) = 0 then
+         try
+           repeat
+             if ((SR.Attr and faDirectory) <> 0) and (SR.Name <> '.') and (SR.Name <> '..') then
+               find1(IncludeTrailingBackslash(Dir) + SR.Name);  // recursive call!
+           until FindNext(Sr) <> 0;
+         finally
+           FindClose(SR);
+         end;
+end;
+begin
+ ret := '';
+ find1(SearchPath);
+ result := ret;
+end;
+
+function findLinuxLibPython3(pthroot: string = '/usr/lib/'): string;
+begin
+     result := findFirstRecursive(pthroot, 'libpython3*so');
+end;
+{$endif} {$endif}
 function PythonLoadAndInitialize(resourceDir: ansistring; callback: PythonDataMethodCallback): boolean;
 var
   home: ansistring;
@@ -109,6 +164,31 @@ function PythonLoadAndInitialize(resourceDir: ansistring; callback: PythonDataMe
     Assert(FileExists(home), 'Python home can''t be found at '+home);
     PythonInitialize(home, callback);
   {$else}
+    {$ifdef PYTHON_DYNAMIC}
+    //https://matthew-brett.github.io/pydagogue/debian_python_paths.html
+    home := '';
+    if  (FileExists(resourceDir)) then begin
+        home := ResourceDir;
+        writeln('Assuming this is a valid python library (e.g. "libpython3.9.so")'+home);
+    end;
+    {$ifdef linux}
+    if not (FileExists(home)) then
+       home := findLibDebian('/usr/lib');
+    if not (FileExists(home)) then
+       home := findLibDebian('/usr/local/lib');
+    if not (FileExists(home)) then
+       home := findLinuxLibPython3('/usr/local/lib');
+    {$endif}
+    if not (FileExists(home)) then begin
+      {$ifdef lcl}
+      ShowMessage('Unable to find Python library: '+home);
+      {$else}
+      writeln('Unable to find Python home: '+home);
+      {$endif}
+       exit(false);
+    end;
+    LoadLibrary(home);
+    {$else}
     home := resourceDir + pathdelim + 'python37';
     if not (DirectoryExists(home)) then begin
       {$ifdef lcl}
@@ -118,9 +198,7 @@ function PythonLoadAndInitialize(resourceDir: ansistring; callback: PythonDataMe
       {$endif}
        exit(false);
     end;
-    writeln('Python Home: ' + home);
-    PythonInitialize(home, callback);
-    Assert(DirectoryExists(home), 'Python home can''t be found at '+home);
+    {$endif PYTHON_DYNAMIC}
     PythonInitialize(home, callback);
   {$endif}
   result := true;
@@ -382,8 +460,14 @@ function RedirectIO: boolean;
 function PythonInitialize(pythonHome: ansistring; callback: PythonDataMethodCallback): boolean;
 begin
   DataMethodCallback := callback;
+  {$ifdef unix}
+   {$ifndef PYTHON_DYNAMIC}
+   Py_SetPythonHome(Py_DecodeLocale(PAnsiChar(pythonHome), nil));
+   {$endif}
+  {$else}
   Py_SetPythonHome(Py_DecodeLocale(PAnsiChar(pythonHome), nil));
-  //Py_SetPythonHome(PWideChar(pythonHome));
+
+  {$endif}
   Py_Initialize;
   result := RedirectIO;
 end;

PythonBridge/pyopts.inc

@@ -0,0 +1,9 @@
+{$ifdef windows}
+  {$define PYTHON_DYNAMIC}
+{$endif}
+{$ifdef linux}
+  {$define PYTHON_DYNAMIC}
+{$endif}
+{$ifdef darwin}
+  //{$define PYTHON_DYNAMIC}
+{$endif}

README.md

@@ -53,7 +53,7 @@ else
 fi
 ```
 
-You can also build this project from the command line (assuming you have FPC Lazarus and the requried packages installed):
+You can also build this project from the command line (assuming you have FPC Lazarus and the required packages installed):
 
 ```
  lazbuild surfice.lpr

Resources/shaders/Gooch.txt

@@ -65,7 +65,7 @@ void main() {
 // Fluxus Shader Library
 // ---------------------
 // Gooch NPR Shading Model
-// Orginally for technical drawing style
+// Originally for technical drawing style
 // rendering, uses warm and cool colours
 // to depict shading to keep detail in the
 // shadowed areas

Resources/shadersOld/Gooch.txt

@@ -45,7 +45,7 @@ void main() {
 // Fluxus Shader Library
 // ---------------------
 // Gooch NPR Shading Model
-// Orginally for technical drawing style
+// Originally for technical drawing style
 // rendering, uses warm and cool colours
 // to depict shading to keep detail in the
 // shadowed areas

Resources/shadersOld/Wire.txt

@@ -14,7 +14,7 @@ Comment: object shimmers as is rotates. Wires useful for evaluating mesh quality
 // early geometry shaders. Works fine on NVidia GPU on same setup (hybrid laptop) and with
 // Intel drivers that come with OSX.
 
-//#define INTELBUG // <- ENALBE THIS LINE TO WORK WITH BORKED INTEL DRIVERS
+//#define INTELBUG // <- ENABLE THIS LINE TO WORK WITH BORKED INTEL DRIVERS
 #ifdef INTELBUG
 in vec3 vL[3];   //[3] because this makes a triangle
 in vec3 vN[3];

Resources/shadersOld/Wireframe.txt

@@ -15,7 +15,7 @@ Hint: setting FaceAlpha less than one can cause object to shimmer as is rotates.
 // early geometry shaders. Works fine on NVidia GPU on same setup (hybrid laptop) and with
 // Intel drivers that come with OSX.
 
-//#define INTELBUG // <- ENALBE THIS LINE TO WORK WITH BORKED INTEL DRIVERS
+//#define INTELBUG // <- ENABLE THIS LINE TO WORK WITH BORKED INTEL DRIVERS
 #ifdef INTELBUG
 in vec3 vL[3];   //[3] because this makes a triangle
 in vec3 vN[3];

Resources/shadersOld/xExploded.txt

@@ -13,7 +13,7 @@ uniform float Explode;
 // early geometry shaders. Works fine on NVidia GPU on same setup (hybrid laptop) and with
 // Intel drivers that come with OSX.
 
-//#define INTELBUG // <- ENALBE THIS LINE TO WORK WITH BORKED INTEL DRIVERS
+//#define INTELBUG // <- ENABLE THIS LINE TO WORK WITH BORKED INTEL DRIVERS
 #ifdef INTELBUG
 in vec3 vL[3];   //[3] because this makes a triangle
 in vec3 vN[3];