Map segmentation coloring array size mismatch

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005121634 (2020-05-12 16:34:48 UTC)
Description
Cropping volume box style display with mouse while using segmentation colors.

Log:
UCSF ChimeraX version: 1.0rc202005121634 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/layer4/electron-microscopy-volume/data442.cmap
> format cmap

Opened data442.cmap, grid size 1374,2108,1653, pixel 45,45,56, shown at step
1, values uint8  

> volume #1 region 0,0,0,1373,2107,1652 step 8

> volume #1 region 0,0,0,1373,2107,1652 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"

> open /Users/goddard/ucsf/data/layer4/segmentation-volume/seg442.cmap format
> cmap

Opened seg442.cmap, grid size 1374,2108,1653, pixel 45,45,56, shown at step 1,
values uint32  

> segmentation colors #2 red map #1 byAttribute spinehead_id

> ui mousemode right "crop volume"

> volume #1 region 0,0,0,1373,2107,1484

> volume #1 region 0,0,0,1373,2107,1342

> volume #1 level 97,0 level 186,0.8 level 252,1

> volume #1 level 97,0 level 154.9,0.9324 level 252,1

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 233, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1420, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1431, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 756, in draw  
pd = self._update_planes(renderer)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 524, in _update_planes  
pd = self._update_2d_texture_planes(view_dir)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 532, in _update_2d_texture_planes  
pd = self._texture_2d_planes(axis)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 558, in _texture_2d_planes  
pd = self._make_planes(axis)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 686, in _make_planes  
d = Texture2dPlanes(self, axis)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 955, in __init__  
self._update_textures(planes)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1027, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1027, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1034, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1053, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 245, in _color_plane  
self.mask_colors(colors, region)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segment/segment.py", line 88, in seg_color  
segment_ids = seg_matrix.reshape(color_plane.shape[:-1]) # Squeeze out single
plane dimension  
ValueError: cannot reshape array of size 709342 into shape (672,1054)  
  

> volume #1 region 0,0,0,1373,2107,1419




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 3 days 21:57

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tom Goddard]

Fixed.

Image style rendering was sometimes using a region size that did not match the volume region matrix size because it was not aligning to multiples of the step size.