ims usage

Example of imageseries usage

Here is an example of how the imageseries is used. One thing we commonly do is to process the raw image files by adding flips and subtract off the background. Then we save it as a new imageseries. This example saves it into a HDF5 file, but it is more common to use the frame-cache (sparse matrices), which is way smaller.

import numpy as np

from hexrd import imageseries
from hexrd.imageseries.omega import OmegaWedges

# Inputs
DarkFile = 'dark-50pct-100f'
H5File = 'example.h5'
fname = 'example-images.yml'
mypath = '/example'

# Raw image series: directly from imagefiles
imgs = imageseries.open(fname, 'image-files')
print "number of frames: ", len(imgs),
      "\ndtype: ", imgs.dtype,
      "\nshape: ", imgs.shape

# Make dark image from first 100 frames
pct = 50
nf_to_use = 100
dark = imageseries.stats.percentile(imgs, pct, nf_to_use)
np.save(DarkFile, dark)


# Now, apply the processing options
ProcessedIS = imageseries.process.ProcessedImageSeries
ops = [('dark', dark), ('flip', 'h')]
pimgs = ProcessedIS(imgs, ops)


# Save the processed imageseries in HDF5 format
print "writing HDF5 file (may take a while): %s" % H5File
imageseries.write(pimgs, H5File, 'hdf5', path=mypath)

Here is the YAML file for the raw image-series.

image-files:
  directory: GE
  files: "ti7_*.ge2"
options:
  empty-frames: 0
  max-frames: 2
meta:
  omega: "! load-numpy-array example-omegas.npy"