Merge pull request #110 from gallantlab/animation_edits

Animation edits

cortex/brainctm.py

@@ -89,7 +89,18 @@ def addCurvature(self, **kwargs):
             self.left.aux[:,1] = npz.left
             self.right.aux[:,1] = npz.right
 
-    def save(self, path, method='mg2', disp_layers=['rois'], **kwargs):
+    def save(self, path, method='mg2', disp_layers=['rois'], extra_disp=None, **kwargs):
+        """Save CTM file for static html display. 
+
+        Parameters
+        ----------
+        path : string filepath
+        method : idkwtf
+        disp_layers : tuple|list
+            list of strings; names of layers from rois.svg to show
+        extra_disp : tuple
+            (svgfile,[layers]) - tuple of (external display .svg filename, [list_of,layers_in_file,to_display])
+        """
         ctmname = path+".ctm"
         svgname = path+".svg"
         jsname = path+".json"
@@ -104,7 +115,7 @@ def save(self, path, method='mg2', disp_layers=['rois'], **kwargs):
             offsets.append(fp.tell())
             fp.write(rbin)
 
-        # Save the JSON descriptor
+        # Save the JSON descriptor | Need to add to this for extra_disp?
         jsdict = dict(rois=os.path.split(svgname)[1],
                       data=os.path.split(ctmname)[1],
                       names=self.types, 
@@ -130,8 +141,13 @@ def save(self, path, method='mg2', disp_layers=['rois'], **kwargs):
             # add sulci & display layers
             flatpts = np.vstack([self.left.flat, self.right.flat])
             roipack = db.get_overlay(self.subject, pts=flatpts, otype=disp_layers)
+            # optionally add extra display layers
+            if not extra_disp is None:
+                esvgfile,elayerlist = extra_disp
+                eroipack = db.get_overlay(self.subject,pts=flatpts, otype='external',
+                    svgfile=esvgfile,layer=elayerlist)
+                roipack = roipack + eroipack
             layers = roipack.setup_labels()
-
             if not isinstance(layers, (tuple, list)):
                 layers = (layers,)
 
@@ -223,7 +239,7 @@ def addSurf(self, pts, **kwargs):
         super(DecimatedHemi, self).addSurf(pts[self.mask], **kwargs)
 
 def make_pack(outfile, subj, types=("inflated",), method='raw', level=0,
-              decimate=False, disp_layers=['rois']):
+              decimate=False, disp_layers=['rois'],extra_disp=None):
     """Generates a cached CTM file"""
 
     ctm = BrainCTM(subj, decimate=decimate)
@@ -237,7 +253,8 @@ def make_pack(outfile, subj, types=("inflated",), method='raw', level=0,
     return ctm.save(os.path.splitext(outfile)[0],
                     method=method,
                     level=level,
-                    disp_layers=disp_layers)
+                    disp_layers=disp_layers,
+                    extra_disp=extra_disp)
 
 def read_pack(ctmfile):
     fname = os.path.splitext(ctmfile)[0]

cortex/dataset/views.py

@@ -89,7 +89,18 @@ def _from_hdf_view(h5, data, xfmname=None, vmin=None, vmax=None,  **kwargs):
         raise ValueError("Invalid Dataview specification")
 
 class Dataview(object):
-    def __init__(self, cmap=None, vmin=None, vmax=None, description="", state=None, **kwargs):
+    def __init__(self, cmap=None, vmin=None, vmax=None, description="", state=None, 
+        cvmin=None,cvmax=None,cvthr=False,**kwargs):
+        """
+        MOAR HELP PLEASE. or maybe not. Is this even visible in inherited classes?
+
+        cvmin : float,optional
+            Minimum value for curvature colormap. Defaults to config file value.
+        cvmax : float, optional
+            Maximum value for background curvature colormap. Defaults to config file value.
+        cvthr : bool,optional
+            Apply threshold to background curvature
+        """
         if self.__class__ == Dataview:
             raise TypeError('Cannot directly instantiate Dataview objects')
 
@@ -207,7 +218,7 @@ def raw(self):
                 # Register colormap while we're at it
                 cm.register_cmap(self.cmap,cmap)
             else:
-                cmap = self.cmap
+                cmap = cm.get_cmap(self.cmap)
         norm = colors.Normalize(self.vmin, self.vmax) # Does this do anything?
         return np.rollaxis(cmap(self.data), -1)
 

cortex/quickflat.py

@@ -244,14 +244,18 @@ def make_figure(braindata, recache=False, pixelwise=True, thick=32, sampler='nea
         overlays.append(sulc)
     if not extra_disp is None:
         svgfile,layer = extra_disp
-        disp = db.get_overlay(dataview.subject,
+        if not isinstance(layer,(list,tuple)):
+            layer = [layer]
+        for extralayer in layer:
+            # Allow multiple extra layer overlays
+            disp = db.get_overlay(dataview.subject,
                               otype='external',
                               shadow=shadow,
                               labelsize=labelsize,
                               labelcolor=labelcolor,
-                              layer=layer,
+                              layer=extralayer,
                               svgfile=svgfile)
-        overlays.append(disp)
+            overlays.append(disp)
     for oo in overlays:
         roitex = oo.get_texture(height, labels=with_labels)
         roitex.seek(0)

cortex/svgroi.py

@@ -36,7 +36,7 @@ def __init__(self, tcoords, svgfile, callback=None, linewidth=None,
         can contain multiple paths. 
         If those paths are closed (i.e., if these are all ROIs), then 
         you can use the method ROIpack.get_roi() to get an index of the
-        vertices associated with 
+        vertices associated with each roi.
 
         Parameters
         ----------
@@ -95,7 +95,7 @@ def __init__(self, tcoords, svgfile, callback=None, linewidth=None,
             else:
                 # Unknown display layer; default to values for ROIs
                 import warnings
-                warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file')
+                warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file'%layer)
                 dlayer = 'rois'                
             self.linewidth = float(config.get(dlayer, "line_width")) if linewidth is None else linewidth
             self.linecolor = tuple(map(float, config.get(dlayer, "line_color").split(','))) if linecolor is None else linecolor
@@ -106,7 +106,6 @@ def __init__(self, tcoords, svgfile, callback=None, linewidth=None,
             self.dashtype = dashtype
             self.dashoffset = dashoffset
 
-
             self.reload(size=labelsize, color=labelcolor)
 
     def reload(self, **kwargs):
@@ -610,6 +609,39 @@ def names(self):
     def __getitem__(self, name):
         return self.rois[name]
 
+    def __add__(self,other_roipack):
+        """Combine layers from two roipacks. Layers / svg file from first is maintained."""
+        comb = copy.deepcopy(self)
+        if hasattr(comb,'layers'):
+            lay1 = self.layer_names
+        else:    
+            # Convert single-layer to multi-layer ROI
+            comb.layers = {self.layer:self}
+            comb.layer = 'multi_layer'
+            lay1 = [self.layer]
+        svg_fin = copy.copy(comb.svg)
+        if hasattr(other_roipack,'layers'):
+            lay2 = other_roipack.layer_names
+            for k,L in other_roipack.layers.items():
+                comb.layers[k] = L
+                comb.rois.update(L.rois)
+                to_add = _find_layer(L.svg, k)
+                svg_fin.getroot().insert(0, to_add)
+        else:
+            comb.layers[other_roipack.layer] = other_roipack
+            to_add = _find_layer(other_roipack.svg, other_roipack.layer)
+            svg_fin.getroot().insert(0, to_add)
+            lay2 = [other_roipack.layer]
+        # Maintain order of layers according to order of addition
+        comb.layer_names = lay1+lay2 
+        comb.svg = svg_fin
+        comb.kdt = cKDTree(self.kdt.data) # necessary?
+        for L in comb.layer_names:
+            comb.layers[L].kdt = comb.kdt # Why the hell do I have to do this?
+        #for r in comb.rois:
+        #    r.parent = comb # necessary?
+        return comb
+
     def setup_labels(self, size=None, color=None, shadow=None):
         """Sets up coordinates for labels wrt SVG file (2D flatmap)"""
         # Recursive call for multiple layers
@@ -619,10 +651,17 @@ def setup_labels(self, size=None, color=None, shadow=None):
                 label_layers.append(self.layers[L].setup_labels())
                 self.svg.getroot().insert(0, label_layers[-1])
             return label_layers
+        if self.layer in config.sections():
+            dlayer = self.layer
+        else:
+            # Unknown display layer; default to values for ROIs
+            import warnings
+            warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file'%self.layer)
+            dlayer = 'rois'                
         if size is None:
-            size = config.get(self.layer, "labelsize")
+            size = config.get(dlayer, "labelsize")
         if color is None:
-            color = tuple(map(float, config.get(self.layer, "labelcolor").split(",")))
+            color = tuple(map(float, config.get(dlayer, "labelcolor").split(",")))
         if shadow is None:
             shadow = self.shadow
 
@@ -785,8 +824,9 @@ def get_labelpos(self, pts=None, norms=None, fancy=False):
         if not hasattr(self, "coords"):
             allpaths = itertools.chain(*[_split_multipath(path.get("d")) for path in self.paths])
             cpts = [self._parse_svg_pts(p) for p in allpaths]
+            # Bug here. I have no idea why the combined roipack fails here but the non-combined one doesn't
             self.coords = [ self.parent.kdt.query(p)[1] for p in cpts ]
-        
+
         if pts is None:
             pts = self.parent.tcoords
 

cortex/utils.py

@@ -30,7 +30,7 @@ def get_roipack(*args, **kwargs):
 get_mapper = DocLoader("get_mapper", ".mapper", "cortex")
 
 def get_ctmpack(subject, types=("inflated",), method="raw", level=0, recache=False,
-                decimate=False, disp_layers=['rois']):
+                decimate=False, disp_layers=['rois'],extra_disp=None):
     """Creates ctm file for the specified input arguments.
 
     This is a cached file that specifies (1) the surfaces between which
@@ -39,14 +39,17 @@ def get_ctmpack(subject, types=("inflated",), method="raw", level=0, recache=Fal
     """   
     lvlstr = ("%dd" if decimate else "%d")%level
     # Generates different cache files for each combination of disp_layers
-    ctmcache = "%s_[{types}]_{method}_{level}_{layers}.json"%subject
+    ctmcache = "%s_[{types}]_{method}_{level}_{layers}{extra}.json"%subject
+    # Mark any ctm file containing extra_disp as unique (will be over-written every time)
     ctmcache = ctmcache.format(types=','.join(types),
                                method=method,
                                level=lvlstr,
-                               layers=repr(sorted(disp_layers)))
+                               layers=repr(sorted(disp_layers)),
+                               extra='' if extra_disp is None else '_xx')
     ctmfile = os.path.join(db.get_cache(subject), ctmcache)
 
-    if os.path.exists(ctmfile) and not recache:
+    if os.path.exists(ctmfile) and not recache: # and extra_disp is None:
+        # (never load cache with extra_disp, which is based on files outside pycortex)
         return ctmfile
 
     print("Generating new ctm file...")
@@ -57,7 +60,8 @@ def get_ctmpack(subject, types=("inflated",), method="raw", level=0, recache=Fal
                                method=method, 
                                level=level,
                                decimate=decimate,
-                               disp_layers=disp_layers)
+                               disp_layers=disp_layers,
+                               extra_disp=extra_disp)
     return ctmfile
 
 def get_ctmmap(subject, **kwargs):
@@ -181,7 +185,6 @@ def add_roi(data, name="new_roi", open_inkscape=True, add_path=True, **kwargs):
     if isinstance(dv, dataset.Dataset):
         raise TypeError("Please specify a data view")
 
-    #rois = db.get_overlay(dv.data.subject)
     rois = db.get_overlay(dv.subject)
     try:
         import cStringIO

cortex/webgl/FallbackLoader.py

@@ -2,8 +2,8 @@
 from tornado import template
 
 class FallbackLoader(template.BaseLoader):
-    """Loads templates from a multiple directories, falling back to next
-    if the template is not found in the first directory.
+    """Loads templates from one of multiple potential directories, falling back 
+    to next if the template is not found in the first directory.
     """
     def __init__(self, root_directories, **kwargs):
         super(FallbackLoader, self).__init__(**kwargs)

cortex/webgl/resources/js/LandscapeControls.js

@@ -252,6 +252,7 @@ THREE.LandscapeControls.prototype = {
     resize: function(w, h) {
         this.domElement.style.width = w+"px";
         this.domElement.style.height = h+"px";
+        this._zoom(1.0) // To set orthographic zoom correctly
     },
 
     getMouse: function ( event ) {
@@ -275,7 +276,7 @@ THREE.LandscapeControls.prototype = {
         }
 
         this._limitview();
-
+        this._zoom(1.0) // Establish zoom (?)
         var altrad = this.altitude*Math.PI / 180;
         var azirad = (this.azimuth+90)*Math.PI / 180;
 
@@ -344,8 +345,9 @@ THREE.LandscapeControls.prototype = {
     },
 
     _zoom: function( factor ) {
+        this.radius *= factor;
         if (this.camera.inPerspectiveMode) {
-            this.radius *= factor;
+            // Perspective mode, zoom by changing radius from camera to object
             if (this.radius > this.maxRadius) { 
                 this.radius = this.maxRadius; 
             }
@@ -354,10 +356,13 @@ THREE.LandscapeControls.prototype = {
             }
         } else {
             // Orthographic mode, zoom by changing frustrum limits
-            this.camera.cameraO.top *= factor;
-            this.camera.cameraO.bottom *= factor;
-            this.camera.cameraO.right *= factor;
-            this.camera.cameraO.left *= factor;
+            var aspect = this.camera.cameraP.aspect
+            var height = 2.0*this.radius*Math.tan(this.camera.cameraP.fov/2.0)
+            var width = aspect*height
+            this.camera.cameraO.top = height/2.0
+            this.camera.cameraO.bottom = -height/2.0
+            this.camera.cameraO.right = width/2.0
+            this.camera.cameraO.left = -width/2.0
             this.camera.cameraO.updateProjectionMatrix();
         }
     },

cortex/webgl/resources/js/mriview.js

@@ -95,7 +95,7 @@ var mriview = (function(module) {
                 vmax:       { type:'fv1',value:[1,1]},
 
                 curvAlpha:  { type:'f', value:1.},
-                curvScale:  { type:'f', value:.5},
+                curvScale:  { type:'f', value:2.0},//0.5 TEMP FIX!!
                 curvLim:    { type:'f', value:.2},
                 dataAlpha:  { type:'f', value:1.0},
                 hatchAlpha: { type:'f', value:1.},
@@ -339,7 +339,7 @@ var mriview = (function(module) {
                 return $(this.object).find("#mix").slider("value");
             case 'pivot':
                 //return $("#pivot").slider("value");
-            return this._pivot;
+                return this._pivot;
             case 'frame':
                 return this.frame;
             case 'azimuth':
@@ -370,6 +370,8 @@ var mriview = (function(module) {
                     return 'orthographic'}
                 else if (this.camera.inPerspectiveMode) {
                     return 'perspective'}
+            case 'slices':
+                return [this.planes[0].slice, this.planes[1].slice, this.planes[2].slice]
         };
     };
     module.Viewer.prototype.setState = function(state, value) {
@@ -398,6 +400,10 @@ var mriview = (function(module) {
             case 'visR':
                 if (this.roipack) this.roipack._updatemove = true;
                 return this.meshes.right.visible = value;
+            //case 'volume_vis':
+            //    this.planes[0].mesh.visible = value[0]
+            //    this.planes[1].mesh.visible = value[1]
+            //    this.planes[2].mesh.visible = value[2]
             case 'rotationL':
                 if (this.roipack) this.roipack._updatemove = true;
                 return this.meshes.left.rotation.set(value[0], value[1], value[2]);
@@ -406,15 +412,21 @@ var mriview = (function(module) {
                 return this.meshes.right.rotation.set(value[0], value[1], value[2]);
             case 'alpha':
                 return this.renderer.setClearColor(0,value);
+            case 'specularity':
+                return this.specularity = value
             case 'data':
                 return this.setData(value)
             case 'labels':
                 return this.labelshow = value;
+            case 'pivot':
+                return 'SORRY NOT YET'
             case 'projection':
                 if (value=='perspective'){
                     return this.controls.camera.toPerspective()}
                 else if (value=='orthographic'){
                     return this.controls.camera.toOrthographic()}
+            case 'slices':
+                return [this.planes[0].update(value[0]), this.planes[1].update(value[1]), this.planes[2].update(value[2])];
         };
     };
     module.Viewer.prototype.animate = function(animation) {
@@ -922,7 +934,6 @@ var mriview = (function(module) {
         }
         this.figure.notify("playtoggle", this);
     };
-
     module.Viewer.prototype.getImage = function(width, height, post) {
         if (width === undefined)
             width = this.canvas.width();
@@ -943,6 +954,7 @@ var mriview = (function(module) {
         var oldw = this.canvas.width(), oldh = this.canvas.height();
         this.camera.setSize(width, height);
         this.camera.updateProjectionMatrix();
+        this.controls._zoom(1.0) // To assure orthographic zoom is set correctly
         //this.renderer.setSize(width, height);
         this.renderer.setClearColorHex(0x0, 0);
         this.renderer.render(this.scene, this.camera, renderbuf);