def decimate(input_files,output_file,bin_factor):
input_files = glob.glob(input_files)
print "processing %d files"%len(input_files)
img = ndimage_file.read_image(input_files[0])
nsize = img.shape[0]/2
for input_file in input_files:
print 'processing ', input_file
output_file = spider_utility.spider_filename(output_file, input_file)
for i, img in enumerate(ndimage_file.iter_images(input_file)):
img = ndimage_interpolate.downsample(img, bin_factor)
#img = ndimage_interpolate.interpolate_ft(img, (nsize,nsize))
ndimage_file.write_image(output_file, img, i)
'''
import sys
#sys.path.append('/home/robertl/tmp/arachnid-0.0.1/')
from arachnid.core.app import tracing
from arachnid.core.metadata import format
from arachnid.core.image import ndimage_file
from arachnid.core.image import reconstruct
import numpy,logging
if __name__ == "__main__":
image_file = sys.argv[1]
align_file = sys.argv[2]
output = sys.argv[3]
thread_count=16
tracing.configure_logging()
#Note: this code assuming you are reconstructing a dala stack or a translated stack
# Read an alignment file
align,header = format.read_alignment(align_file, ndarray=True)
logging.error("Reconstructing %d particles"%len(align))
assert(header[0]=='id')
index = align[:, 0].astype(numpy.int)
align[:, 1] = numpy.rad2deg(align[:, 1])
iter_single_images = ndimage_file.iter_images(image_file, index)
image_size = ndimage_file.read_image(image_file).shape[0]
vol = reconstruct.reconstruct_bp3f_mp(iter_single_images, image_size, align, thread_count=thread_count)
ndimage_file.write_image(output, vol)
.. literalinclude:: ../../arachnid/snippets/image/shift.py
:language: python
:lines: 17-
:linenos:
'''
import sys
from arachnid.core.metadata import format
from arachnid.core.metadata import spider_utility
from arachnid.core.metadata import relion_utility
from arachnid.core.image import ndimage_file
from arachnid.core.image import ndimage_utility
if __name__ == '__main__':
# Parameters
input_file = sys.argv[1]
output_file = sys.argv[2]
mult=1.0
# Read an alignment file
align = format.read(input_file, numeric=True)
for i in xrange(len(align)):
filename, id = relion_utility.relion_file(align[i].rlnImageName)
img = ndimage_file.read_image(filename, id-1)
img = ndimage_utility.fourier_shift(img, align[i].rlnOriginX, align[i].rlnOriginY)
ndimage_file.write_image(spider_utility.spider_filename(output_file, filename), img, id-1)
Download to edit and run: :download:`reproject_test.py <../../arachnid/snippets/image/reproject_test.py>`
To run:
.. sourcecode:: sh
$ python reproject_test.py vol.spi ref_stack.spi 2
.. literalinclude:: ../../arachnid/snippets/image/reproject_test.py
:language: python
:lines: 22-
:linenos:
'''
import sys
from arachnid.core.image import ndimage_file
from arachnid.core.image import reproject
from arachnid.core.orient import healpix
if __name__ == '__main__':
# Parameters
image_file = sys.argv[1]
output = sys.argv[2]
healpix_order = int(sys.argv[3])
vol = ndimage_file.read_image(image_file)
rad = vol.shape[0] / 2
ang = healpix.angles(healpix_order)
imgs = reproject.reproject_3q(vol, rad, ang)
ndimage_file.write_stack(output, imgs)
if __name__ == "__main__":
tracing.configure_logging()
image_file = sys.argv[1] # phase_flip_dala_stack.spi
align_file = sys.argv[2] # align.spi
param_file = sys.argv[3]
output = sys.argv[4] # raw_vol.spi
bin_factor = float(
sys.argv[5]) if len(sys.argv) > 5 else 1.0 # raw_vol.spi
thread_count = 32
extra = spider_params.read(param_file)
extra.update(spider_params.update_params(bin_factor, **extra))
print "Loaded param file"
extra.update(thread_count=thread_count)
align, header = format.read_alignment(align_file, ndarray=True)
logging.error("Reconstructing %d particles" % len(align))
selection = align[:, 15:17]
align[:, 6:8] /= extra['apix']
iter_single_images = ndimage_file.iter_images(image_file, selection)
image_size = ndimage_file.read_image(image_file).shape[0]
vol = reconstruct.reconstruct_bp3f_mp(iter_single_images,
image_size,
align,
process_image=process_image,
**extra)
if vol is not None:
ndimage_file.write_image(output, vol)
''' Interporate a volume
Download to edit and run: :download:`interpolate_volume.py <../../arachnid/snippets/image/interpolate_volume.py>`
To run:
.. sourcecode:: sh
$ python interpolate_volume.py
.. literalinclude:: ../../arachnid/snippets/image/interpolate_volume.py
:language: python
:lines: 16-
:linenos:
'''
import sys
from arachnid.core.image import ndimage_file
from arachnid.core.image import ndimage_interpolate
if __name__ == '__main__':
# Parameters
input_file = sys.argv[1]
bin_factor = float(sys.argv[2])
output_file = sys.argv[3]
img=ndimage_file.read_image(input_file)
img=ndimage_interpolate.interpolate_bilinear(img, bin_factor)
ndimage_file.write_image(output_file, img)
from arachnid.core.image import ndimage_utility
import glob
if __name__ == '__main__':
# Parameters
input_files = sys.argv[1]
output_file = sys.argv[2]
params_file = sys.argv[3]
bin_factor = int(sys.argv[4])
input_files = glob.glob(input_files)
print "processing %d files"%len(input_files)
radius = spider_params.read(params_file)['pixel_diameter']/2
img = ndimage_file.read_image(input_files[0])
mask = ndimage_utility.model_disk(radius, img.shape)*-1+1
mask = ndimage_interpolate.downsample(mask, bin_factor)
for input_file in input_files:
print 'processing ', input_file
output_file = spider_utility.spider_filename(output_file, input_file)
for i, img in enumerate(ndimage_file.iter_images(input_file)):
img = ndimage_interpolate.downsample(img, bin_factor)
img=ndimage_utility.normalize_standard(img, mask)
ndimage_file.write_image(output_file, img, i)