def run(args):
import os
import libtbx.load_env
from libtbx.utils import Sorry
from dials.util.options import OptionParser
usage = "%s [options] datablock.json | image.cbf" % libtbx.env.dispatcher_name
parser = OptionParser(usage=usage,
phil=phil_scope,
read_datablocks=True,
read_datablocks_from_images=True,
check_format=True,
epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
parser.print_help()
exit(0)
imagesets = datablocks[0].extract_imagesets()
brightness = params.brightness / 100
vendortype = "made up"
# check that binning is a power of 2
binning = params.binning
if not (binning > 0 and ((binning & (binning - 1)) == 0)):
raise Sorry("binning must be a power of 2")
output_dir = params.output_dir
if output_dir is None:
output_dir = "."
elif not os.path.exists(output_dir):
os.makedirs(output_dir)
from rstbx.slip_viewer.tile_generation \
import _get_flex_image, _get_flex_image_multipanel
for imageset in imagesets:
detector = imageset.get_detector()
if len(detector) > 1:
raise Sorry(
'Currently only single panel detectors are supported by %s' %
libtbx.env.dispatcher_name)
panel = detector[0]
scan = imageset.get_scan()
# XXX is this inclusive or exclusive?
saturation = panel.get_trusted_range()[1]
if params.saturation:
saturation = params.saturation
if scan is not None and scan.get_oscillation()[1] > 0:
start, end = scan.get_image_range()
else:
start, end = 0, len(imageset)
for i_image in range(start, end + 1):
image = imageset.get_raw_data(i_image - start)
#if len(detector) == 1:
#image = [image]
trange = [p.get_trusted_range() for p in detector]
mask = imageset.get_mask(i_image - start)
if mask is None:
mask = [
p.get_trusted_range_mask(im)
for im, p in zip(image, detector)
]
if params.show_mask:
for rd, m in zip(image, mask):
rd.set_selected(~m, -2)
image = image_filter(image,
mask,
display=params.display,
gain_value=params.gain,
nsigma_b=params.nsigma_b,
nsigma_s=params.nsigma_s,
global_threshold=params.global_threshold,
min_local=params.min_local,
kernel_size=params.kernel_size)
show_untrusted = params.show_mask
if len(detector) > 1:
# FIXME This doesn't work properly, as flex_image.size2() is incorrect
# also binning doesn't work
assert binning == 1
flex_image = _get_flex_image_multipanel(
brightness=brightness,
panels=detector,
raw_data=image,
beam=imageset.get_beam(),
show_untrusted=show_untrusted)
else:
flex_image = _get_flex_image(brightness=brightness,
data=image[0],
binning=binning,
saturation=saturation,
vendortype=vendortype,
show_untrusted=show_untrusted)
flex_image.setWindow(0, 0, 1)
flex_image.adjust(
color_scheme=colour_schemes.get(params.colour_scheme))
# now export as a bitmap
flex_image.prep_string()
try:
from PIL import Image
except ImportError:
import Image
# XXX is size//binning safe here?
try: # fromstring raises Exception in Pillow >= 3.0.0
pil_img = Image.fromstring('RGB',
(flex_image.size2() // binning,
flex_image.size1() // binning),
flex_image.export_string)
except Exception:
pil_img = Image.frombytes('RGB',
(flex_image.size2() // binning,
flex_image.size1() // binning),
flex_image.export_string)
path = os.path.join(
output_dir,
params.prefix + ("%04d" % i_image) + '.' + params.format)
print "Exporting %s" % path
with open(path, 'wb') as tmp_stream:
pil_img.save(tmp_stream,
format=params.format,
compress_level=params.png.compress_level,
quality=params.jpeg.quality)
def run(args):
import os
import libtbx.load_env
from libtbx.utils import Sorry
from dials.util.options import OptionParser
usage = "%s [options] datablock.json | image.cbf" %libtbx.env.dispatcher_name
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_datablocks=True,
read_datablocks_from_images=True,
check_format=True,
epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
parser.print_help()
exit(0)
imagesets = datablocks[0].extract_imagesets()
brightness = params.brightness / 100
vendortype = "made up"
# check that binning is a power of 2
binning = params.binning
if not (binning > 0 and ((binning & (binning - 1)) == 0)):
raise Sorry("binning must be a power of 2")
output_dir = params.output_dir
if output_dir is None:
output_dir = "."
elif not os.path.exists(output_dir):
os.makedirs(output_dir)
from rstbx.slip_viewer.tile_generation \
import _get_flex_image, _get_flex_image_multipanel
for imageset in imagesets:
detector = imageset.get_detector()
panel = detector[0]
# XXX is this inclusive or exclusive?
saturation = panel.get_trusted_range()[1]
if params.saturation:
saturation = params.saturation
for i_image, image in enumerate(imageset):
if len(detector) == 1:
image = [image]
trange = [p.get_trusted_range() for p in detector]
mask = []
mask = imageset.get_mask(i_image)
if mask is None:
mask = [p.get_trusted_range_mask(im) for im, p in zip(image, detector)]
image = image_filter(image, mask, display=params.display, gain_value=params.gain,
nsigma_b=params.nsigma_b,
nsigma_s=params.nsigma_s,
global_threshold=params.global_threshold,
min_local=params.min_local,
kernel_size=params.kernel_size)
if len(detector) > 1:
# FIXME This doesn't work properly, as flex_image.size2() is incorrect
# also binning doesn't work
assert binning == 1
flex_image = _get_flex_image_multipanel(
brightness=brightness,
panels=detector,
raw_data=image)
else:
flex_image = _get_flex_image(
brightness=brightness,
data=image[0],
binning=binning,
saturation=saturation,
vendortype=vendortype)
flex_image.setWindow(0, 0, 1)
flex_image.adjust(color_scheme=colour_schemes.get(params.colour_scheme))
# now export as a bitmap
flex_image.prep_string()
import Image
# XXX is size//binning safe here?
pil_img = Image.fromstring(
'RGB', (flex_image.size2()//binning,
flex_image.size1()//binning),
flex_image.export_string)
path = os.path.join(
output_dir, params.prefix + ("%04d" % i_image) + '.' + params.format)
print "Exporting %s" %path
tmp_stream = open(path, 'wb')
pil_img.save(tmp_stream, format=params.format)
tmp_stream.close()
def run(args):
import os
from libtbx.phil import command_line
from libtbx.utils import Sorry, Usage
if len(args) == 0:
from cStringIO import StringIO
s = StringIO()
master_phil_scope.show(out=s)
raise Usage("""\
dxtbx.export_bitmaps image_files [options]
% s
""" % s.getvalue())
from dxtbx.datablock import DataBlockFactory
unhandled = []
datablocks = DataBlockFactory.from_args(args,
verbose=False,
unhandled=unhandled)
assert len(datablocks) > 0
imagesets = datablocks[0].extract_imagesets()
cmd_line = command_line.argument_interpreter(
master_params=master_phil_scope)
working_phil = cmd_line.process_and_fetch(args=unhandled)
working_phil.show()
params = working_phil.extract()
brightness = params.brightness / 100
vendortype = "made up"
# check that binning is a power of 2
binning = params.binning
if not (binning > 0 and ((binning & (binning - 1)) == 0)):
raise Sorry("binning must be a power of 2")
output_dir = params.output_dir
if output_dir is None:
output_dir = "."
elif not os.path.exists(output_dir):
os.makedirs(output_dir)
from rstbx.slip_viewer.tile_generation \
import _get_flex_image, _get_flex_image_multipanel
for imageset in imagesets:
detector = imageset.get_detector()
panel = detector[0]
# XXX is this inclusive or exclusive?
saturation = panel.get_trusted_range()[1]
for i_image, image in enumerate(imageset):
if len(detector) > 1:
# FIXME This doesn't work properly, as flex_image.size2() is incorrect
# also binning doesn't work
assert binning == 1
flex_image = _get_flex_image_multipanel(
brightness=brightness,
panels=detector,
raw_data=image,
beam=imageset.get_beam())
else:
flex_image = _get_flex_image(brightness=brightness,
data=image,
binning=binning,
saturation=saturation,
vendortype=vendortype)
flex_image.setWindow(0, 0, 1)
flex_image.adjust(
color_scheme=colour_schemes.get(params.colour_scheme))
# now export as a bitmap
flex_image.prep_string()
try:
import PIL.Image as Image
except ImportError:
import Image
# XXX is size//binning safe here?
try:
pil_img = Image.fromstring('RGB',
(flex_image.size2() // binning,
flex_image.size1() // binning),
flex_image.export_string)
except NotImplementedError:
pil_img = Image.frombytes('RGB',
(flex_image.size2() // binning,
flex_image.size1() // binning),
flex_image.export_string)
basename = os.path.basename(
os.path.splitext(imageset.paths()[i_image])[0])
path = os.path.join(output_dir, basename + '.' + params.format)
print "Exporting %s" % path
tmp_stream = open(path, 'wb')
pil_img.save(tmp_stream, format=params.format)
tmp_stream.close()
def imageset_as_bitmaps(imageset, params):
from rstbx.slip_viewer.tile_generation import (
_get_flex_image,
_get_flex_image_multipanel,
)
brightness = params.brightness / 100
vendortype = "made up"
# check that binning is a power of 2
binning = params.binning
if not (binning > 0 and ((binning & (binning - 1)) == 0)):
raise Sorry("binning must be a power of 2")
output_dir = params.output_dir
if output_dir is None:
output_dir = "."
elif not os.path.exists(output_dir):
os.makedirs(output_dir)
output_files = []
detector = imageset.get_detector()
panel = detector[0]
scan = imageset.get_scan()
# XXX is this inclusive or exclusive?
saturation = panel.get_trusted_range()[1]
if params.saturation:
saturation = params.saturation
if scan is not None and scan.get_oscillation(
)[1] > 0 and not params.imageset_index:
start, end = scan.get_image_range()
else:
start, end = 1, len(imageset)
# If the user specified an image range index, only export those
image_range = [
i for i in range(start, end + 1)
if not params.imageset_index or i in params.imageset_index
]
if params.output_file and len(image_range) != 1:
sys.exit(
"output_file can only be specified if a single image is exported")
for i_image in image_range:
image = imageset.get_raw_data(i_image - start)
mask = imageset.get_mask(i_image - start)
if mask is None:
mask = [
p.get_trusted_range_mask(im) for im, p in zip(image, detector)
]
if params.show_mask:
for rd, m in zip(image, mask):
rd.set_selected(~m, -2)
image = image_filter(
image,
mask,
display=params.display,
gain_value=params.gain,
nsigma_b=params.nsigma_b,
nsigma_s=params.nsigma_s,
global_threshold=params.global_threshold,
min_local=params.min_local,
kernel_size=params.kernel_size,
)
show_untrusted = params.show_mask
if len(detector) > 1:
# FIXME This doesn't work properly, as flex_image.size2() is incorrect
# also binning doesn't work
flex_image = _get_flex_image_multipanel(
brightness=brightness,
panels=detector,
raw_data=image,
binning=binning,
beam=imageset.get_beam(),
show_untrusted=show_untrusted,
)
else:
flex_image = _get_flex_image(
brightness=brightness,
data=image[0],
binning=binning,
saturation=saturation,
vendortype=vendortype,
show_untrusted=show_untrusted,
)
flex_image.setWindow(0, 0, 1)
flex_image.adjust(
color_scheme=colour_schemes.get(params.colour_scheme))
# now export as a bitmap
flex_image.prep_string()
from PIL import Image
# XXX is size//binning safe here?
pil_img = Image.frombytes(
"RGB", (flex_image.ex_size2(), flex_image.ex_size1()),
flex_image.as_bytes())
if params.output_file:
path = os.path.join(output_dir, params.output_file)
else:
path = os.path.join(
output_dir,
"{p.prefix}{image:0{p.padding}}.{p.format}".format(
p=params, image=i_image),
)
print("Exporting %s" % path)
output_files.append(path)
with open(path, "wb") as tmp_stream:
pil_img.save(
tmp_stream,
format=params.format,
compress_level=params.png.compress_level,
quality=params.jpeg.quality,
)
return output_files
def run(args):
import os
from libtbx.phil import command_line
from libtbx.utils import Sorry, Usage
if len(args) == 0:
from cStringIO import StringIO
s = StringIO()
master_phil_scope.show(out=s)
raise Usage("""\
dxtbx.export_bitmaps image_files [options]
% s
""" %s.getvalue())
from dxtbx.datablock import DataBlockFactory
unhandled = []
datablocks = DataBlockFactory.from_args(
args, verbose=False, unhandled=unhandled)
assert len(datablocks) > 0
imagesets = datablocks[0].extract_imagesets()
cmd_line = command_line.argument_interpreter(master_params=master_phil_scope)
working_phil = cmd_line.process_and_fetch(args=unhandled)
working_phil.show()
params = working_phil.extract()
brightness = params.brightness / 100
vendortype = "made up"
# check that binning is a power of 2
binning = params.binning
if not (binning > 0 and ((binning & (binning - 1)) == 0)):
raise Sorry("binning must be a power of 2")
output_dir = params.output_dir
if output_dir is None:
output_dir = "."
elif not os.path.exists(output_dir):
os.makedirs(output_dir)
from rstbx.slip_viewer.tile_generation \
import _get_flex_image, _get_flex_image_multipanel
for imageset in imagesets:
detector = imageset.get_detector()
panel = detector[0]
# XXX is this inclusive or exclusive?
saturation = panel.get_trusted_range()[1]
for i_image, image in enumerate(imageset):
if len(detector) > 1:
# FIXME This doesn't work properly, as flex_image.size2() is incorrect
# also binning doesn't work
assert binning == 1
flex_image = _get_flex_image_multipanel(
brightness=brightness,
panels=detector,
raw_data=image)
else:
flex_image = _get_flex_image(
brightness=brightness,
data=image,
binning=binning,
saturation=saturation,
vendortype=vendortype)
flex_image.setWindow(0, 0, 1)
flex_image.adjust(color_scheme=colour_schemes.get(params.colour_scheme))
# now export as a bitmap
flex_image.prep_string()
import Image
# XXX is size//binning safe here?
pil_img = Image.fromstring(
'RGB', (flex_image.size2()//binning,
flex_image.size1()//binning),
flex_image.export_string)
basename = os.path.basename(os.path.splitext(imageset.paths()[i_image])[0])
path = os.path.join(
output_dir, basename + '.' + params.format)
print "Exporting %s" %path
tmp_stream = open(path, 'wb')
pil_img.save(tmp_stream, format=params.format)
tmp_stream.close()