dials.export_bitmaps

Introduction

Export raw diffraction image files as bitmap images, optionally exporting images from intermediate spot-finding steps (local mean and variance maps, or sigma_b, sigma_s or threshold-filtered images). Appearance of the images can be altered via the brightness and colour_scheme parameters, and optionally binning of pixels can be used to reduce image sizes.

Examples:

dials.export_bitmaps image.cbf

dials.export_bitmaps datablock.json

dials.export_bitmaps image.cbf display=variance colour_scheme=inverse_greyscale

Basic parameters

binning = 1
brightness = 100
colour_scheme = *greyscale rainbow heatmap inverse_greyscale
format = jpeg *png tiff
prefix = "image"
padding = 4
output_dir = None
output_file = None
display = *image mean variance dispersion sigma_b sigma_s threshold \
          global_threshold
nsigma_b = 6
nsigma_s = 3
global_threshold = 0
kernel_size = 3,3
min_local = 2
gain = 1
saturation = 0
show_mask = False
png {
  compress_level = 1
}
jpeg {
  quality = 75
}

Full parameter definitions

binning = 1
  .type = int(value_min=1, allow_none=True)
brightness = 100
  .type = float(value_min=0, allow_none=True)
colour_scheme = *greyscale rainbow heatmap inverse_greyscale
  .type = choice
format = jpeg *png tiff
  .type = choice
prefix = "image"
  .type = str
padding = 4
  .type = int(value_min=0, allow_none=True)
output_dir = None
  .type = path
output_file = None
  .help = "Full name of the output file. Overrides 'prefix' and the default "
          "file extension. Only makes sense if a single file is written."
  .type = str
display = *image mean variance dispersion sigma_b sigma_s threshold \
          global_threshold
  .type = choice
nsigma_b = 6
  .type = float(value_min=0, allow_none=True)
nsigma_s = 3
  .type = float(value_min=0, allow_none=True)
global_threshold = 0
  .type = float(value_min=0, allow_none=True)
kernel_size = 3,3
  .type = ints(size=2, value_min=1)
min_local = 2
  .type = int(allow_none=True)
gain = 1
  .type = float(value_min=0, allow_none=True)
saturation = 0
  .type = int(allow_none=True)
show_mask = False
  .type = bool
png {
  compress_level = 1
    .help = "ZLIB compression level, a number between 0 and 9: 1 gives best "
            "speed, 9 gives best compression, 0 gives no compression at all."
    .type = int(value_min=0, value_max=9, allow_none=True)
}
jpeg {
  quality = 75
    .help = "The image quality, on a scale from 1 (worst) to 95 (best)"
    .type = int(value_min=1, value_max=95, allow_none=True)
}