def __init__(self, file_name, graphics_bin=1): #, output_file=None):
from rstbx.slip_viewer.slip_viewer_image_factory import SlipViewerImageFactory as ImageFactory
from iotbx.detectors import ImageException
try:
from PIL import Image
except ImportError:
import Image
try:
img = ImageFactory(file_name)
except ImageException as e:
raise Sorry(str(e))
img.read()
self.img = img
if (img.vendortype in ["Pilatus-6M", "Pilatus-2M", "Pilatus-300K"]):
graphics_bin = 1
flex_img = img.get_flex_image(binning=graphics_bin, brightness=1)
flex_img.setWindow(0.0, 0.0, 1)
flex_img.spot_convention(0)
flex_img.adjust(color_scheme=0)
flex_img.prep_string()
data_string = flex_img.export_string
try: # fromstring raises Exception in Pillow >= 3.0.0
self.imageout = Image.fromstring(
"RGB", (flex_img.ex_size2(), flex_img.ex_size1()), data_string)
except Exception:
self.imageout = Image.frombytes(
"RGB", (flex_img.ex_size2(), flex_img.ex_size1()), data_string)
def test_read_image(test_image, dials_regression):
"""Test that all the regression images can be read"""
if not xfel and test_image.startswith("LCLS"):
pytest.skip("could not import 'xfel'")
if not h5py and test_image.endswith((".h5", ".nxs")):
pytest.skip("could not import 'h5py'")
if dials_regression:
test_image = os.path.join(
dials_regression, "image_examples", *test_image.split("/")
)
format_instance = dxtbx.format.Registry.get_format_class_for_file(test_image)
print("Reading", test_image)
print("Format:", format_instance)
assert format_instance, "no matching format class found"
instance = format_instance(test_image)
# Test metadata reading
instance.get_goniometer()
instance.get_beam()
instance.get_scan()
detector = instance.get_detector()
# From old test_dxtbx; get the image size
if detector is not None:
detector[0].get_image_size()
for panel in detector:
d_mat = scitbx.matrix.sqr(panel.get_d_matrix())
if d_mat.determinant() <= 0:
print(" d matrix with non-positive determinant")
# Test reading of the raw data
# XDS, HKL we expect to fail for this - so skip this part for those
if not test_image.endswith(("XDS", "HKL")):
try:
R_raw_data = instance.get_raw_data()
except TypeError:
R_raw_data = instance.get_raw_data(0)
if not isinstance(R_raw_data, tuple):
R_raw_data = (R_raw_data,)
print("%-40s" % format_instance.__name__, R_raw_data[0].focus())
# Set instance.detectorbase, if available. There used to be a blacklist
# of files not to call this with, but relying on the attribute test
# seems to be just as effective
try:
instance.get_detectorbase()
except NotImplementedError:
pass
print(" Have detectorbase? ", hasattr(instance, "detectorbase"))
# Specific test for cctbx/dxtbx#163. This test will fail if char is unsigned.
if "APS_24IDC" in test_image and "pilatus_1_0001.cbf" in test_image:
d = R_raw_data[0]
assert (
flex.sum(d.as_1d().select(d.as_1d() >= 0)) == 20108255
) # matches total counts from dxtbx.print_header
# test the older detectorbase interface if available
if hasattr(instance, "detectorbase"):
imgfactory = SlipViewerImageFactory(test_image)
imgfactory.read()
print(" Detectorbase:", instance.detectorbase.__class__.__name__)
try:
print(imgfactory.rawdata.focus())
except AttributeError:
# Not all instances have this attribute
print(" multireadout")
I_raw_data = imgfactory.get_raw_data()
if not isinstance(I_raw_data, tuple):
I_raw_data = (I_raw_data,)
# NOTE dxtbx and image factory arrays are compared here for identical values.
for Ip, Rp in zip(I_raw_data, R_raw_data):
assert (Ip == Rp).all_eq(True)
def test_read_image(test_image_for_reading):
"""Test that all the regression images can be read"""
if "LCLS" in test_image_for_reading and not libtbx.env.has_module('xfel'):
pytest.skip("Ignoring LCLS because xfel missing")
return
format_instance = Registry.find(test_image_for_reading)
instance = format_instance(test_image_for_reading)
print("Reading", test_image_for_reading)
print("Format:", format_instance)
# Test metadata reading
instance.get_goniometer()
instance.get_beam()
instance.get_scan()
detector = instance.get_detector()
# From old test_dxtbx; get the image size
if detector is not None:
detector[0].get_image_size()
for panel in detector:
d_mat = scitbx.matrix.sqr(panel.get_d_matrix())
if d_mat.determinant() == 0:
print(" d matrix with zero determinant")
if d_mat.determinant() < 0:
print(" d matrix with negative determinant")
# Test reading of the raw data
# XDS, HKL we expect to fail for this - so skip this part for those
if not test_image_for_reading[-3:].upper() in {"XDS", "HKL"}:
try:
R_raw_data = instance.get_raw_data()
except TypeError:
R_raw_data = instance.get_raw_data(0)
if not isinstance(R_raw_data, tuple):
R_raw_data = (R_raw_data, )
print("%-40s" % format_instance.__name__, R_raw_data[0].focus())
# Set instance.detectorbase, if available. There used to be a blacklist
# of files not to call this with, but relying on the attribute test
# seems to be just as effective
instance.get_detectorbase()
print(" Have detectorbase? ", hasattr(instance, "detectorbase"))
# test the older detectorbase interface if available
if hasattr(instance, "detectorbase"):
imgfactory = SlipViewerImageFactory(test_image_for_reading)
imgfactory.read()
print(" Detectorbase:", instance.detectorbase.__class__.__name__)
try:
print(imgfactory.rawdata.focus())
except AttributeError:
# Not all instances have this attribute
print(" multireadout")
I_raw_data = imgfactory.get_raw_data()
if not isinstance(I_raw_data, tuple):
I_raw_data = (I_raw_data, )
# NOTE dxtbx and image factory arrays are compared here for identical values.
for Ip, Rp in zip(I_raw_data, R_raw_data):
assert (Ip == Rp).all_eq(True)
convert_image(test_image_for_reading,
graphics_bin=2).output().getvalue()
print
def test_read_image(test_image_for_reading):
"""Test that all the regression images can be read"""
if "LCLS" in test_image_for_reading and not libtbx.env.has_module("xfel"):
pytest.skip("Ignoring LCLS because xfel missing")
return
format_instance = dxtbx.format.Registry.get_format_class_for_file(
test_image_for_reading
)
print("Reading", test_image_for_reading)
print("Format:", format_instance)
assert format_instance, "no matching format class found"
instance = format_instance(test_image_for_reading)
# Test metadata reading
instance.get_goniometer()
instance.get_beam()
instance.get_scan()
detector = instance.get_detector()
# From old test_dxtbx; get the image size
if detector is not None:
detector[0].get_image_size()
for panel in detector:
d_mat = scitbx.matrix.sqr(panel.get_d_matrix())
if d_mat.determinant() == 0:
print(" d matrix with zero determinant")
if d_mat.determinant() < 0:
print(" d matrix with negative determinant")
# Test reading of the raw data
# XDS, HKL we expect to fail for this - so skip this part for those
if not test_image_for_reading[-3:].upper() in {"XDS", "HKL"}:
try:
R_raw_data = instance.get_raw_data()
except TypeError:
R_raw_data = instance.get_raw_data(0)
if not isinstance(R_raw_data, tuple):
R_raw_data = (R_raw_data,)
print("%-40s" % format_instance.__name__, R_raw_data[0].focus())
# Set instance.detectorbase, if available. There used to be a blacklist
# of files not to call this with, but relying on the attribute test
# seems to be just as effective
instance.get_detectorbase()
print(" Have detectorbase? ", hasattr(instance, "detectorbase"))
# Specific test for cctbx/dxtbx#163. This test will fail if char is unsigned.
if (
"APS_24IDC" in test_image_for_reading
and "pilatus_1_0001.cbf" in test_image_for_reading
):
d = R_raw_data[0]
assert (
flex.sum(d.as_1d().select(d.as_1d() >= 0)) == 20108255
) # matches total counts from dxtbx.print_header
# test the older detectorbase interface if available
if hasattr(instance, "detectorbase"):
imgfactory = SlipViewerImageFactory(test_image_for_reading)
imgfactory.read()
print(" Detectorbase:", instance.detectorbase.__class__.__name__)
try:
print(imgfactory.rawdata.focus())
except AttributeError:
# Not all instances have this attribute
print(" multireadout")
I_raw_data = imgfactory.get_raw_data()
if not isinstance(I_raw_data, tuple):
I_raw_data = (I_raw_data,)
# NOTE dxtbx and image factory arrays are compared here for identical values.
for Ip, Rp in zip(I_raw_data, R_raw_data):
assert (Ip == Rp).all_eq(True)