Minor update

neurolabusc · May 28, 2019 · 0a64681 · 0a64681
1 parent 9b5b6d9
commit 0a64681
Show file tree

Hide file tree

Showing 27 changed files with 1,773 additions and 441 deletions.
diff --git a/README.md b/README.md
@@ -8,6 +8,10 @@ Supported mesh formats include 3DO, 3DS, AC, BYU, CTM, DAE, DXF, FreeSurfer, GII
 
 ![alt tag](https://github.com/neurolabusc/surf-ice/blob/master/Surfice.jpg)
 
+##### Installing
+
+You can get the latest release from [github](https://github.com/neurolabusc/surf-ice/releases) or [NITRC](https://www.nitrc.org/projects/surfice). Releases are provided for Linux, MacOS and Windows. Each release includes two versions of Surf Ice: "Surfice" requires OpenGL 3.3 or later, while "SurficeOld" runs on older computers (requiring OpenGL 2.1). A [wiki](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage) provides a full manual and troubleshooting advice.
+
 ##### Compiling
 
 This project is built using the open source [FreePascal Lazarus](http://www.lazarus-ide.org/) compiler and integrated development environment. You will need to have the LazOpenGLContext and PascalScript packages installed. To do this, launch the Lazarus application and choose Packages/InstallPackages. You will want to select these two packages from the "Available for installation" list. Finally, click the "Save and rebuild" button. Once these are installed, you can load this package and compile it using the Run/Run menu option.
@@ -42,36 +46,9 @@ You can also build this project from the command line (assuming you have FPC Laz
  lazbuild surfice.lpr
 ```
 
-##### Recent Versions
-
-2-February-2018 (v1.0.20180202)
- - [Atlas-based regions of interest](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Atlas-based_Region_of_interest_Analyses).
- - [Python scripting](https://github.com/neurolabusc/surf-ice/blob/master/PYTHON.md).
- - [Outline, ](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Atlas-based_Region_of_interest_Analyses)[Grid and HideCurves shaders added](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Gallery).
-
-20-December-2017 (v1.0.20171220)
- - Support [PALM](https://github.com/andersonwinkler/PALM) format [DPV](https://brainder.org/2011/09/25/braindering-with-ascii-files/).
-
-21-June-2017
- - [Smooth](https://github.com/neurolabusc/OpenGLCoreTutorials) numbers in colorbars.
- - Conversion of images from voxels to mesh now allows the user to specify a minimum cluster size.
- - Pan image by [shift-dragging](https://www.nitrc.org/forum/forum.php?thread_id=7857&forum_id=6713).
- - MacOS retina support (better but slower, use Preferences window to disable).
-
-7-February-2017
- - Ability to individually adjust translucency of overlays (rather than having one value for all).
- - Looks better on Linux high-DPI screens.
- - New command Advanced/ComputeCurvature creates FreeSurfer Format CURV file.
- - Control-clicking overlay name in the overlay panel reverses the overlay colors (and the name is displayed in black instead of blue). Control-click again to switch to normal mode.
- - Support for several variations of the [CIfTI format](https://www.humanconnectome.org/software/get-connectome-workbench.html)(dscalar.nii, dlabel.nii, dtseries.nii).
-
-30-September-2016
- - Add support for the TRK.GZ (DSI studio), DAT (MRI studio) formats.
- - Support for tracks with [scalars](https://github.com/johncolby/along-tract-stats) and [properties](http://trackvis.org/blog/tag/track_merge/).
- - "Faster" track viewing mode looks better (Lucas Nesi's imposter method).
+##### Versions
 
-20-April-2016
- - Add support for the 3DS, MS3D, LWO2, DXF and GTS formats.
+The [releases](https://github.com/neurolabusc/surf-ice/releases) page provides version notes.
 
 ##### License
 

diff --git a/define_types.pas b/define_types.pas
@@ -4,7 +4,7 @@ interface
 uses graphics;
 {$endif}
 const
-  kVers = 'v1.0.20190220';
+  kVers = 'v1.0.20190518';
   NaN : double = 1/0;
   kTab = chr(9);
   kCR = chr (13);

diff --git a/gl_core_3d.pas b/gl_core_3d.pas
@@ -411,7 +411,9 @@ procedure SetTrackUniforms(lineWidth, ScreenPixelX, ScreenPixelY: integer);
 
   glUniform1f(glGetUniformLocation(gShader.programTrackID, pAnsiChar('Ambient')), gShader.TrackAmbient) ;
   glUniform1f(glGetUniformLocation(gShader.programTrackID, pAnsiChar('Diffuse')), gShader.TrackDiffuse) ;
-  glUniform1f(glGetUniformLocation(gShader.programTrackID, pAnsiChar('Specular')), gShader.TrackSpecular) ;
+  //glUniform1f(glGetUniformLocation(gShader.programTrackID, pAnsiChar('Specular')), gShader.TrackSpecular * 0.75) ; //<<<<<<<<<
+  glUniform1f(glGetUniformLocation(gShader.programTrackID, pAnsiChar('Specular')), gShader.TrackSpecular) ; //full glisten
+
   {$ENDIF}
 
 end;

diff --git a/gl_legacy_3d.pas b/gl_legacy_3d.pas
@@ -320,7 +320,7 @@ function BuildDisplayList(var faces: TFaces; vertices: TVertices; vRGBA: TVertex
   fNorm : TPoint3f;
 begin
   //glDeleteLists(mesh.displayList, 1);
-  if  (length(vertices) < 3) or (length(faces) < 1) then exit;
+  if  (length(vertices) < 3) or (length(faces) < 1) then exit(0);
   setlength(vNorm, length(vertices) );
   //compute vertex normals
   fNorm := ptf(0,0,0);

diff --git a/mainunit.lfm b/mainunit.lfm
@@ -1,7 +1,7 @@
 object GLForm1: TGLForm1
-  Left = 137
+  Left = 233
   Height = 684
-  Top = 45
+  Top = 94
   Width = 1047
   AllowDropFiles = True
   Caption = 'Surf Ice'
@@ -422,6 +422,7 @@ object GLForm1: TGLForm1
         BorderSpacing.Top = 2
         DropDownCount = 22
         ItemHeight = 26
+        ItemIndex = 0
         Items.Strings = (
           'a'
           'b'
@@ -435,7 +436,7 @@ object GLForm1: TGLForm1
         ParentFont = False
         Style = csDropDownList
         TabOrder = 3
-        Text = '0'
+        Text = 'a'
       end
       object TrackScalarNameDrop: TComboBox
         AnchorSideLeft.Control = TrackLengthLabel
@@ -516,6 +517,7 @@ object GLForm1: TGLForm1
         BorderSpacing.Right = 2
         DropDownCount = 22
         ItemHeight = 26
+        ItemIndex = 0
         Items.Strings = (
           'a'
           'b'
@@ -529,7 +531,7 @@ object GLForm1: TGLForm1
         ParentFont = False
         Style = csDropDownList
         TabOrder = 0
-        Text = '0'
+        Text = 'a'
       end
       object NodeColorVariesCheck: TCheckBox
         AnchorSideLeft.Control = NodeColorLabel
@@ -723,6 +725,7 @@ object GLForm1: TGLForm1
         BorderSpacing.Top = 2
         DropDownCount = 22
         ItemHeight = 26
+        ItemIndex = 0
         Items.Strings = (
           'a'
           'b'
@@ -736,7 +739,7 @@ object GLForm1: TGLForm1
         ParentFont = False
         Style = csDropDownList
         TabOrder = 0
-        Text = '0'
+        Text = 'a'
       end
       object EdgeColorVariesCheck: TCheckBox
         AnchorSideLeft.Control = EdgeColorLabel
@@ -1021,7 +1024,7 @@ object GLForm1: TGLForm1
         AnchorSideTop.Side = asrBottom
         AnchorSideRight.Control = MeshBlendTrack
         AnchorSideRight.Side = asrBottom
-        Left = 180
+        Left = 177
         Height = 18
         Hint = 'If checked, edge size varies'
         Top = 34
@@ -1043,8 +1046,8 @@ object GLForm1: TGLForm1
         Left = 2
         Height = 16
         Top = 35
-        Width = 174
-        Caption = 'Shader For Background Only'
+        Width = 171
+        Caption = 'Shader For Background only'
         ParentColor = False
         ParentFont = False
       end
@@ -1617,6 +1620,10 @@ object GLForm1: TGLForm1
       Caption = 'Invert Colors'
       OnClick = LayerInvertColorsMenuClick
     end
+    object LayerAOMapMenu: TMenuItem
+      Caption = 'Darkening layer'
+      OnClick = LayerAOMapMenuClick
+    end
     object LayerShowHeaderMenu: TMenuItem
       Caption = 'Show Header'
       OnClick = LayerShowHeaderMenuClick

diff --git a/mainunit.pas b/mainunit.pas
@@ -31,13 +31,15 @@   TGLForm1 = class(TForm)
 LayerOptionsBtn: TButton;
  LeftSplitter: TSplitter;
  CenterPanel: TPanel;
+ LayerAOMapMenu: TMenuItem;
  NextOverlayMenu: TMenuItem;
  PrevOverlayMenu: TMenuItem;
  OverlaySep: TMenuItem;
  overlayload1: TMenuItem;
  overlayvisible1: TMenuItem;
   PSScript1: TPSScript;
   S3Label: TLabel;
+  BGShader: TLabel;
   SaveScriptDialog: TSaveDialog;
  ScriptingInsertMenu: TMenuItem;
 mesh1: TMenuItem;
@@ -138,7 +140,6 @@   TGLForm1 = class(TForm)
     ColorbarSep: TMenuItem;
     meshAlphaTrack: TTrackBar;
     MeshBlendTrack: TTrackBar;
-    BGShader: TLabel;
     ROImeshMenu: TMenuItem;
     XRayLabel: TLabel;
     TransBlackClrbarMenu: TMenuItem;
@@ -321,6 +322,7 @@ procedure LayerAlphaTrackMouseUp(Sender: TObject; Button: TMouseButton; Shift: T
       var Accept: Boolean);
     procedure LeftSplitterChangeBounds(Sender: TObject);
     procedure LeftSplitterMoved(Sender: TObject);
+    procedure LayerAOMapMenuClick(Sender: TObject);
     procedure PrevOverlayMenuClick(Sender: TObject);
     procedure UpdateLayerBox(NewLayers: boolean);
 
@@ -1838,6 +1840,7 @@ procedure TGLForm1.OpenScript(scriptname: string; isShowScriptPanel: boolean = t
      if not fileexists(scriptname) then exit;
      if (ScriptPanel.Width < 24) and (isShowScriptPanel) then
         ScriptPanel.Width := 240;
+     gPrefs.PrevScript :=  scriptname;
      ScriptMemo.Lines.LoadFromFile(scriptname);
      gPrefs.InitScript:='';
      ScriptingRunMenuClick(nil);
@@ -1923,6 +1926,8 @@ procedure TGLForm1.LayerPopupPopup(Sender: TObject);
   i := LayerList.ItemIndex+ 1;
   if (i < 1) or (i > gMesh.OpenOverlays) then exit;
    LayerInvertColorsMenu.Checked := gMesh.Overlay[i].LUTinvert;
+   LayerAOMapMenu.Checked := gMesh.Overlay[i].aoMap;
+
 end;
 
 procedure TGLForm1.LayerListClickCheck(Sender: TObject);
@@ -2024,6 +2029,16 @@ procedure TGLForm1.LeftSplitterMoved(Sender: TObject);
   //caption := inttostr(random(888));
 end;
 
+procedure TGLForm1.LayerAOMapMenuClick(Sender: TObject);
+ var
+    i: integer;
+ begin
+   i := LayerList.ItemIndex+ 1;
+   if (i < 1) or (i > gMesh.OpenOverlays) then exit;
+   gMesh.Overlay[i].aoMap := not gMesh.Overlay[i].aoMap;
+   LayerWidgetChange(sender);
+end;
+
 procedure TGLForm1.PrevOverlayMenuClick(Sender: TObject);
 var
   i: integer;
@@ -2064,7 +2079,7 @@ procedure TGLForm1.UpdateLayerBox(NewLayers: boolean);
                  LayerList.Items.add(format('%d/%d: %s',[gMesh.Overlay[i].CurrentVolume, gMesh.Overlay[i].volumes, s]))
             else
                 LayerList.Items.add(s);
-            LayerList.Checked[i-1] := true;
+            LayerList.Checked[i-1] := gMesh.Overlay[i].LUTvisible <>  kLUTinvisible;//true;
         end;
         LayerList.ItemIndex := gMesh.OpenOverlays - 1;
      end;
@@ -2306,6 +2321,17 @@ procedure TGLForm1.MultiPassRenderingToolsUpdate;
   AOLabel.Visible:= lBetter;
   occlusionTrack.Visible:= lBetter;
   ShaderForBackgroundOnlyCheck.Visible:= lBetter;
+  if lBetter then begin
+   XRayLabel.Caption := 'XRay';
+   BGShader.Caption := 'Shader For Background Only';
+  end else begin
+      XRayLabel.Caption := 'Disabled: ';
+
+      if not gPrefs.SupportBetterRenderQuality then
+         BGShader.Caption := 'Poor Hardware'
+      else
+          BGShader.Caption := 'Poor Quality (see Preferences)';
+  end;
   MeshBlendTrack.Visible:= lBetter;
   meshAlphaTrack.visible :=  lBetter;
 end;
@@ -2348,10 +2374,19 @@ function meshBackgroundOpen: boolean;
 end;
 
 procedure TGLForm1.UpdateToolbar;
+//var
+//  isOverlayNodeTrack : boolean;
 begin
  OverlayBox.Visible := (gMesh.OpenOverlays > 0);
- //OverlayBox.Top := 0;
- BackgroundBox.Visible := (length(gNode.nodes) > 0) or (gTrack.n_count > 0) or ((gMesh.OpenOverlays > 0) and (meshBackgroundOpen));
+ //isOverlays  := (length(gNode.nodes) > 0) or (gTrack.n_count > 0) or ((gMesh.OpenOverlays > 0) and (meshBackgroundOpen));
+ //BGShader.Enabled := isOverlays;
+ //ShaderForBackgroundOnlyCheck.Enabled := isOverlays;
+ //MeshBlendTrack.Enabled := isOverlays;
+ //isOverlayNodeTrack := (length(gNode.nodes) > 0) or (gTrack.n_count > 0) or ((gMesh.OpenOverlays > 0) and (meshBackgroundOpen));
+ //MeshBlendTrack.Visible := isOverlayNodeTrack;
+ //BGShader.Visible := isOverlayNodeTrack;
+ //ShaderForBackgroundOnlyCheck.Visible := isOverlayNodeTrack;
+ //BackgroundBox.Visible := (length(gNode.nodes) > 0) or (gTrack.n_count > 0) or ((gMesh.OpenOverlays > 0) and (meshBackgroundOpen));
  NodeBox.Visible:= (length(gNode.nodes) > 0) ;
  if (length(gNode.edges) > 0) and (EdgeBox.Visible = false) and (BackgroundBox.Visible) then begin
     //this keeps node and edge boxes next to each other
@@ -2607,7 +2642,7 @@ function TGLForm1.OpenMesh(FilenameIN: string): boolean;
      exit;
   end;
   //ext := UpperCase(ExtractFileExt(Filename));
-  if (ext = '.ANNOT') or (ext = '.MGH') or (ext = '.MGZ')  or (ext = '.NII') or (ext = '.HDR')  or (ext = '.NII.GZ') or (ext = '.DPV') or (ext = '.ANNOT') or (ext = '.W') or (ext = '.CURV')  then begin
+  if (ext = '.COL') or (ext = '.ANNOT') or (ext = '.MGH') or (ext = '.MGZ')  or (ext = '.NII') or (ext = '.HDR')  or (ext = '.NII.GZ') or (ext = '.DPV') or (ext = '.ANNOT') or (ext = '.W') or (ext = '.CURV')  then begin
     OpenOverlay(Filename);
     exit;
   end else if (ext = '.VTK') and (not isVtkMesh (Filename)) then begin
@@ -4299,7 +4334,7 @@ function TGLForm1.UpdateClrBar: integer;
  if (gMesh.OpenOverlays > 0) then
     for lI := 1 to gMesh.OpenOverlays do
         //https://www.nitrc.org/forum/forum.php?thread_id=10001&forum_id=6713
-        if (length(gMesh.overlay[lI].intensity) > 0) and (gMesh.overlay[lI].LUTvisible <> kLUTinvisible) and (not isFreeSurferLUT(gMesh.overlay[lI].LUTindex)) then begin
+        if (length(gMesh.overlay[lI].intensity) > 0) and (not gMesh.overlay[lI].aoMap) and (gMesh.overlay[lI].LUTvisible <> kLUTinvisible) and (not isFreeSurferLUT(gMesh.overlay[lI].LUTindex)) then begin
          isDuplicate := false;
          lJ := 1;
          while (lJ < lI) do begin
@@ -5643,10 +5678,13 @@ procedure TGLForm1.SaveMesh(var mesh: TMesh; isSaveOverlays: boolean);
 {$ELSE}
 procedure TGLForm1.SaveMesh(var mesh: TMesh; isSaveOverlays: boolean);
 const
-      kMeshFilter = 'OBJ (Widely supported)|*.obj|GIfTI (Neuroimaging)|*.gii|MZ3 (Small and fast)|*.mz3|PLY (Widely supported)|*.ply|VRML (Shapeways color printing)|*.wrl';
+     //kMeshFilter = 'OBJ (Widely supported)|*.obj|GIfTI (Neuroimaging)|*.gii|MZ3 (Small and fast)|*.mz3|PLY (Widely supported)|*.ply|VRML (Shapeways color printing)|*.wrl|WebGL PRWM|*.prwm';
+     //prwm expects normals
+     kMeshFilter = 'OBJ (Widely supported)|*.obj|GIfTI (Neuroimaging)|*.gii|MZ3 (Small and fast)|*.mz3|PLY (Widely supported)|*.ply|VRML (Shapeways color printing)|*.wrl|STL (Large and slow)|*.stl';
 var
    nam, ext, x: string;
 begin
+  //mesh.SaveMesh('/Users/rorden/nrrdify/tst.prwm'); exit;
   if length(mesh.Faces) < 1 then begin
      showmessage('Unable to save: no mesh is loaded (use File/Open).');
      exit;
@@ -5660,7 +5698,7 @@ procedure TGLForm1.SaveMesh(var mesh: TMesh; isSaveOverlays: boolean);
   else if gPrefs.SaveAsFormat = 1 then
     ext := '.gii'
   else
-    ext := '.mz3';
+    ext := '.mz3'; //2
   SaveMeshDialog.DefaultExt := ext;
   if (fileexists(gPrefs.PrevFilename[1])) or (not isSaveOverlays) then begin
      if isSaveOverlays then
@@ -5677,7 +5715,7 @@ procedure TGLForm1.SaveMesh(var mesh: TMesh; isSaveOverlays: boolean);
   if length(SaveMeshDialog.Filename) < 1 then exit;
   //caption := inttostr(SaveMeshDialog.FilterIndex)+' '+SaveMeshDialog.Filename; exit; //666
   x := UpperCase(ExtractFileExt(SaveMeshDialog.Filename));
-  if (x <> '.MZ3') and (x <> '.PLY') and (x <> '.OBJ')  and (x <> '.GII') and (x <> '.WRL') then begin
+  if (x <> '.STL') and (x <> '.MZ3') and (x <> '.PLY') and (x <> '.OBJ')  and (x <> '.GII') and (x <> '.WRL') and (x <> '.PRWM')then begin
      x := ext;
      SaveMeshDialog.Filename := SaveMeshDialog.Filename + x;
   end;