Fixed non-existent normalization for raw (RGB) volumes, small steps t…

…oward getting dotted lines in webgl view

.gitignore

@@ -3,6 +3,8 @@ scripts
 
 # C extensions
 *.so
+formats.c
+openctm.c
 
 # Packages
 *.egg

cortex/dataset/braindata.py

@@ -201,9 +201,10 @@ def volume(self):
     def save(self, filename, name=None):
         """Save the dataset into an hdf file with the provided name
         """
+        import os
         if isinstance(filename, str):
             fname, ext = os.path.splitext(filename)
-            if ext in (".hdf", ".h5"):
+            if ext in (".hdf", ".h5",".hf5"):
                 h5 = h5py.File(filename, "a")
                 self._write_hdf(h5, name=name)
                 h5.close()

cortex/dataset/views.py

@@ -219,8 +219,14 @@ def raw(self):
                 cm.register_cmap(self.cmap,cmap)
             else:
                 cmap = cm.get_cmap(self.cmap)
-        norm = colors.Normalize(self.vmin, self.vmax) # Does this do anything?
-        return np.rollaxis(cmap(self.data), -1)
+        elif isinstance(self.cmap,colors.Colormap):
+            cmap = self.cmap
+        # Normalize colors according to vmin, vmax
+        norm = colors.Normalize(self.vmin, self.vmax) 
+        cmapper = cm.ScalarMappable(norm=norm, cmap=cmap)
+        color_data = cmapper.to_rgba(self.data.flatten()).reshape(self.data.shape+(4,))
+        # rollaxis puts the last color dimension first, to allow output of separate channels: r,g,b,a = dataset.raw
+        return np.rollaxis(color_data, -1)
 
 class Multiview(Dataview):
     def __init__(self, views, description=""):

cortex/quickflat.py

@@ -175,6 +175,9 @@ def make_figure(braindata, recache=False, pixelwise=True, thick=32, sampler='nea
                 cm.register_cmap(dataview.cmap,cmap)
             else:
                 cmap = dataview.cmap
+        elif isinstance(dataview.cmap,colors.Colormap):
+            # Allow input of matplotlib colormap class
+            cmap = dataview.cmap
         kwargs.update(
             cmap=cmap, 
             vmin=dataview.vmin, 

cortex/webgl/resources/js/svgroi.js

@@ -154,8 +154,20 @@ ROIpack.prototype = {
             lc = "stroke:" + lc;
             lw = "stroke-width:" + lw + "px";
             sw = parseInt(sw);
-
+
+            //WIP!
+            //style_array = [fo, lo, fc, lc, lw]
+            //(Then set style_array per path?) or set style first, then only update strokeDasharray per path?
+            oldstyle = this.layers[layer].attr("style")
+            console.log(oldstyle) // Hrm. This appears to be too late - the style has already been set before this prints out. Why?
+            // ...I thought this next line set the style...?
             this.layers[layer].attr("style", [fo, lo, fc, lc, lw].join(";"));
+            // loop over paths
+            // PROBLEM: Still need to find wth the read-in svg line styles are. Must be where we got paths... but fuck if I know.
+            // for (var pth=0; pth<disp_layers[layer].length; pth++){
+            //     this.layers[layer][pth].strokeDasharray=olddasharray
+            //     this.layers[layer][pth].disp_layers[]
+            // }
         }
 
         var svg_xml = (new XMLSerializer()).serializeToString(this.svgroi);