fix: microviewer installation, pixel value update, scroll direction (#…

…231)

* misc enhancements

* feat: export Vec class for use in other applications

* update displayed pixel value on change of slice

* make mousewheel scrolling direction match w/s keyboard and neuroglancer behavior

* avoid files ending up in site-packages/ext upon installation in python

* refactor: move viewer to microviewer and edit MANIFEST.in

* update_pxvalue for hyperview too. Removed extra lines from merge.

AUTHORS

@@ -4,6 +4,7 @@ Manuel Castro <[email protected]>
 Nicholas Turner <[email protected]>
 Nico Kemnitz <[email protected]>
 Pat Gunn <[email protected]>
+Shang Mu <[email protected]>
 Thomas Macrina <[email protected]>
 William Silversmith <[email protected]>
 William Silversmith <[email protected]>

MANIFEST.in

@@ -1,2 +1 @@
-recursive-include ext
 include LICENSE

cloudvolume/__init__.py

@@ -60,7 +60,7 @@
 from . import secrets
 from . import txrx
 
-from . import viewer
-from .viewer import view, hyperview
+from . import microviewer
+from .microviewer import view, hyperview
 
 __version__ = '0.50.0'

cloudvolume/viewer.py → cloudvolume/microviewer/__init__.py

@@ -12,7 +12,7 @@
 import numpy as np
 from tqdm import tqdm
 
-from .lib import Vec, Bbox, mkdir, save_images, ExtractedPath, yellow
+from cloudvolume.lib import Vec, Bbox, mkdir, save_images, ExtractedPath, yellow
 
 DEFAULT_PORT = 8080
 
@@ -35,7 +35,7 @@ def getoffset(img, offset):
       return Vec(0,0,0)
 
 def to_volumecutout(img, image_type, resolution=None, offset=None, hostname='localhost'):
-  from . import VolumeCutout
+  from cloudvolume.volumecutout import VolumeCutout
   if type(img) == VolumeCutout:
     try:
       img.dataset_name # check if it's an intact VolumeCutout
@@ -85,7 +85,7 @@ def view(
     img, segmentation=False, resolution=None, offset=None,
     hostname="localhost", port=DEFAULT_PORT
   ):
-  from . import VolumeCutout
+  from cloudvolume.volumecutout import VolumeCutout
 
   img = to3d(img)
   resolution = getresolution(img, resolution)
@@ -202,6 +202,6 @@ def serve_file(self):
       path = 'index.html'
 
     dirname = os.path.dirname(__file__)
-    filepath = os.path.join(dirname, '../ext/microviewer/' + path)
+    filepath = os.path.join(dirname, './' + path)
     with open(filepath, 'rb') as f:
       self.wfile.write(f.read())  

ext/microviewer/index.html → cloudvolume/microviewer/index.html

@@ -107,13 +107,6 @@
             SLICE.z = (y * (SIZE.z - 1))|0;
           }
 
-          PXVALUE = [ vol.channel.get(SLICE.x, SLICE.y, SLICE.z) ];
-
-          vol.hover_id = null;
-          if (vol.is_segmentation) {
-            vol.hover_id = PXVALUE[0];
-          }
-
           render(); 
         });
       }
@@ -152,10 +145,6 @@
             SLICE.z = (y * (SIZE.z - 1))|0;
           }
 
-          PXVALUE = [ vol.channel.get(SLICE.x, SLICE.y, SLICE.z) ];
-          vol.hover_id = vol.segmentation.get(SLICE.x, SLICE.y, SLICE.z);
-          PXVALUE.push(vol.hover_id);
-
           render(); 
         });
 
@@ -254,7 +243,7 @@
 
       $(document).on('wheel', function (e) {
         var delta = clamp(e.originalEvent.deltaY, -1, 1);
-        delta = Math.round(delta);
+        delta = -Math.round(delta);
         move_slice(delta);
       });
 
@@ -361,7 +350,22 @@
         elems.shape.text( `<${SIZE.x}, ${SIZE.y}, ${SIZE.z}>` );
       }
 
+      function update_pxvalue () {
+          PXVALUE = [ vol.channel.get(SLICE.x, SLICE.y, SLICE.z) ];
+
+          vol.hover_id = null;
+          if (vol.is_segmentation) {
+            vol.hover_id = PXVALUE[0];
+          }
+
+          if (vol.segmentation) {
+            vol.hover_id = vol.segmentation.get(SLICE.x, SLICE.y, SLICE.z);
+            PXVALUE.push(vol.hover_id);
+          }
+      }
+
       function render () {
+        update_pxvalue();
         _needsrender = true;
       }
 

cloudvolume/volumecutout.py

@@ -8,7 +8,7 @@
 
 from .lib import mkdir, save_images
 
-from . import viewer
+from . import microviewer
 
 class VolumeCutout(np.ndarray):
 
@@ -78,4 +78,4 @@ def save_images(self, directory=None, axis='z', channel=None, global_norm=True,
 
   def viewer(self, port=8080):
     """Start a local web app on the given port that lets you explore this cutout."""
-    viewer.run([ self ], port=port)
+    microviewer.run([ self ], port=port)

setup.py

@@ -9,7 +9,7 @@
   },
   package_data={
     'cloudvolume': [
-      '../ext/microviewer/*',
+      './microviewer/*',
     ],
   },
   long_description_content_type="text/markdown",