Scripts: flatimage.py

# -----------------------------------------------------------------------------
# Script to make flattened icosahedron virus images for VIPERdb.
#

vdb_dir = '/usr/local/src/staff/goddard/vdbfiles'
image_dir = '/usr/local/src/staff/goddard/vdbimages'

def flattened_icosahedron_images(
  vdb_dir,                         # directory containing *.vdb files.
  image_dir,                       # directory to place images in.
  image_height = 2000,             # screen pixels
  image_format = 'JPEG',           # 'JPEG', 'PNG', 'TIFF'
  image_suffix = '.jpg',
  mesh_color = (.5,.5,.5,1),       # red, green, blue, opacity
  mesh_offset = 0,                 # Can make mesh appear in front of molecules.
  edge_pad = .05,                  # 5% edge padding
  supersample = 3,                 # Smooth jagged edges in images.
  background_color = 'white',
  ):

  from chimera import viewer, runCommand, openModels

  # Find all vdb files in vdb_dir directory.
  import os
  vdb_filenames = [f for f in os.listdir(vdb_dir) if f.endswith('.vdb')]

  # Set window to have correct aspect ratio.
  runCommand('windowsize 400 800')

  # Set background color.
  runCommand('set bg_color %s' % background_color)

  # Set silhouette edges
  runCommand('set silhouette')

  for vdb_filename in vdb_filenames:

    import os.path
    vdb_path = os.path.join(vdb_dir, vdb_filename)

    # Open VIPERdb file
    openModels.open(vdb_path)

    # Flatten multiscale model.
    import FlattenIcosahedron as FI
    mlist = FI.multiscale_models()
    r = FI.model_radius(mlist)
    FI.flatten_icosahedron(mlist, r)

    # Show triangle outlines.
    varray, tarray = FI.flattened_icosahedron_geometry(r)
    varray[:,2] = mesh_offset
    model = mlist[0].surface_model()
    p = model.addPiece(varray, tarray, mesh_color)
    p.displayStyle = p.Mesh

    # Zoom to fit in window.
    runCommand('turn z 90')             # Orient long side vertically.
    viewer.viewAll()                    # Fit in window.
    viewer.scaleFactor *= (1-edge_pad)  # Provide a bit of edge padding.

    # Save image.
    image_filename = os.path.splitext(vdb_filename)[0] + image_suffix
    image_path = os.path.join(image_dir, image_filename)
    image_aspect = 0.5
    image_width = image_aspect * image_height
    from chimera.printer import saveImage
    saveImage(image_path, image_width, image_height,
              format = image_format, supersample = supersample)

    # Close models
    openModels.close(openModels.list())


# Make low-res images.
flattened_icosahedron_images(vdb_dir, image_dir,
                             image_height = 600)

# Make high-res images.
flattened_icosahedron_images(vdb_dir, image_dir,
                             image_height = 2000,
                             image_suffix = '_big.jpg')

# Quit Chimera
#raise SystemExit('Script finished')