def test_split_single_image_datablock(dials_regression, tmpdir):
tmpdir.chdir()
pytest.importorskip("h5py")
sacla_file = os.path.join(
dials_regression,
"image_examples",
"SACLA_MPCCD_Cheetah",
"run266702-0-subset.h5",
)
db = DataBlockFactory.from_filenames([sacla_file])[0]
assert db.num_images() == 4
imageset = db.extract_imagesets()[0]
subset = imageset[2:3]
subblock = DataBlockFactory.from_imageset(subset)[0]
assert subblock.num_images() == 1
assert get_indices(subblock) == [2]
dumped_filename = "split_datablock.json"
dump = DataBlockDumper(subblock)
dump.as_json(dumped_filename)
db = DataBlockFactory.from_json_file(dumped_filename, check_format=True)[0]
assert db.num_images() == 1
assert get_indices(db) == [2]
db = DataBlockFactory.from_json_file(dumped_filename,
check_format=False)[0]
assert db.num_images() == 1
assert get_indices(db) == [2]
def test_combination_of_multiple_datablocks_and_strong_spots_files(
dials_regression, tmpdir):
tmpdir.chdir()
path = os.path.join(dials_regression,
"centroid_test_data/centroid_####.cbf")
# example combined two different spot-finding settings for the same dataset
# e.d. for comparison with the reciprocal lattice viewer.
cmd = "dials.import template={0}".format(path)
result = easy_run.fully_buffered(cmd).raise_if_errors()
cmd = "dials.find_spots datablock.json output.reflections=strong1.pickle"
result = easy_run.fully_buffered(cmd).raise_if_errors()
cmd = ("dials.find_spots datablock.json sigma_strong=5 "
"output.reflections=strong2.pickle")
result = easy_run.fully_buffered(cmd).raise_if_errors()
cmd = ("dev.dials.combine_datablocks datablock.json datablock.json "
"strong1.pickle strong2.pickle")
result = easy_run.fully_buffered(cmd).raise_if_errors()
# load results
comb_db = DataBlockFactory.from_json_file('combined_datablocks.json')[0]
comb_strong = flex.reflection_table.from_pickle("combined_strong.pickle")
# load reference models and reflections
db = DataBlockFactory.from_json_file('datablock.json')[0]
ref_detector = db.unique_detectors()[0]
ref_beam = db.unique_beams()[0]
ref_scan = db.unique_scans()[0]
ref_goniometer = db.unique_goniometers()[0]
strong1 = flex.reflection_table.from_pickle("strong1.pickle")
strong2 = flex.reflection_table.from_pickle("strong2.pickle")
# check the models have not been modified
for imset in comb_db.extract_imagesets():
assert imset.get_detector() == ref_detector
assert imset.get_beam() == ref_beam
assert imset.get_scan() == ref_scan
assert imset.get_goniometer() == ref_goniometer
# check the reflections are unaffected, except for the change in id
s1 = comb_strong.select(comb_strong['id'] == 0)
s2 = comb_strong.select(comb_strong['id'] == 1)
s2['id'] = flex.size_t(len(s2), 0)
for r1, r2 in zip(s1, strong1):
assert r1 == r2
for r1, r2 in zip(s2, strong2):
assert r1 == r2
def test_find_spots_with_user_defined_mask(dials_regression, tmpdir):
tmpdir.chdir()
# Now with a user defined mask
result = procrunner.run_process([
"dials.find_spots",
"output.reflections=spotfinder.pickle",
"output.shoeboxes=True",
"lookup.mask=" +
os.path.join(dials_regression, "centroid_test_data", "mask.pickle"),
] + glob(
os.path.join(dials_regression, "centroid_test_data", "centroid*.cbf")))
assert result['exitcode'] == 0
assert result['stderr'] == ''
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
from dxtbx.datablock import DataBlockFactory
datablocks = DataBlockFactory.from_json_file(
os.path.join(dials_regression, "centroid_test_data", "datablock.json"))
assert len(datablocks) == 1
imageset = datablocks[0].extract_imagesets()[0]
detector = imageset.get_detector()
beam = imageset.get_beam()
for x, y, z in reflections['xyzobs.px.value']:
d = detector[0].get_resolution_at_pixel(beam.get_s0(), (x, y))
assert d >= 3
def run(self):
from os.path import join, exists
from libtbx import easy_run
import os
input_filename = join(self.path, "datablock.json")
output_filename = "output_datablock.json"
mask_filename = join(self.path, "lookup_mask.pickle")
easy_run.fully_buffered(
['dials.apply_mask',
'input.datablock=%s' % input_filename,
'input.mask=%s' % mask_filename,
'output.datablock=%s' % output_filename]).raise_if_errors()
from dxtbx.datablock import DataBlockFactory
datablocks = DataBlockFactory.from_json_file(output_filename)
assert len(datablocks) == 1
imagesets = datablocks[0].extract_imagesets()
assert len(imagesets) == 1
imageset = imagesets[0]
assert imageset.external_lookup.mask.filename == mask_filename
print 'OK'
def tst_with_bad_external_lookup(self):
from dxtbx.datablock import DataBlockFactory
from dxtbx.imageset import ImageSweep
from os.path import join
filename = join(self.dials_regression, "centroid_test_data",
"datablock_with_bad_lookup.json")
blocks = DataBlockFactory.from_json_file(filename, check_format=False)
assert (len(blocks) == 1)
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data is None
assert imageset.external_lookup.gain.data is None
assert imageset.external_lookup.pedestal.data is None
blocks = self.encode_json_then_decode(blocks, check_format=False)
assert (len(blocks) == 1)
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data is None
assert imageset.external_lookup.gain.data is None
assert imageset.external_lookup.pedestal.data is None
print 'OK'
def get_arr(json_file_path = None):
if json_file_path != None :
print "json_file_path =", json_file_path
datablocks = DataBlockFactory.from_json_file(json_file_path)
if len(datablocks) > 0:
assert(len(datablocks) == 1)
imagesets = datablocks[0].extract_imagesets()
crystals = None
print "len(datablocks) > 0"
else:
raise RuntimeError("No imageset could be constructed, len(datablocks) <= 0 ")
print "len(imagesets) =", len(imagesets)
print "type(imagesets) =", type(imagesets)
first_data = imagesets[0]
print "type(first_data) =", type(first_data)
my_array = first_data.to_array()
print "type(my_array) =", type(my_array)
my_array_double = my_array.as_double()
print "my_array_double.all() =", my_array_double.all()
else:
print "No DataBlock PATH given"
return my_array_double
def run(args=None):
args = args or sys.argv[1:]
user_phil = []
files = []
for arg in args:
if os.path.isfile(arg):
files.append(arg)
else:
try:
user_phil.append(parse(arg))
except Exception:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
fig = plt.figure()
colormap = plt.cm.gist_ncar
colors = [colormap(i) for i in np.linspace(0, 0.9, len(files))]
for file_name, color in zip(files, colors):
# read the data and get the detector models
try:
datablocks = DataBlockFactory.from_json_file(file_name,
check_format=False)
detectors = sum((db.unique_detectors() for db in datablocks), [])
except Exception:
try:
experiments = ExperimentListFactory.from_json_file(
file_name, check_format=False)
except ValueError:
experiments = ExperimentListFactory.from_filenames([file_name])
detectors = experiments.detectors()
if not params.plot_all_detectors:
detectors = detectors[0:1]
for detector in detectors:
# plot the hierarchy
if params.orthographic:
ax = fig.gca()
else:
ax = fig.gca(projection="3d")
plot_group(
detector.hierarchy(),
color,
ax,
orthographic=params.orthographic,
show_origin_vectors=params.show_origin_vectors,
panel_numbers=params.panel_numbers,
)
plt.xlabel("x")
plt.ylabel("y")
if params.orthographic:
plt.axes().set_aspect("equal", "datalim")
if params.pdf_file:
pp = PdfPages(params.pdf_file)
for i in plt.get_fignums():
pp.savefig(plt.figure(i))
pp.close()
else:
plt.show()
def get_3d_flex_array():
json_file_path = str("../../dummy_unversioned_data/datablock.json")
print "json_file_path =", json_file_path
datablocks = DataBlockFactory.from_json_file(json_file_path)
if len(datablocks) > 0:
assert (len(datablocks) == 1)
imagesets = datablocks[0].extract_imagesets()
crystals = None
print "len(datablocks) > 0"
else:
raise RuntimeError("No imageset could be constructed")
print "len(imagesets) =", len(imagesets)
print "type(imagesets) =", type(imagesets)
first_data = imagesets[0]
print "type(first_data) =", type(first_data)
my_array = first_data.to_array()
print "type(my_array) =", type(my_array)
my_array_double = my_array.as_double()
print "my_array_double.all() =", my_array_double.all()
return my_array_double
def __init__(self):
super(BigWidget, self).__init__()
my_box = QVBoxLayout()
top_box = QHBoxLayout()
left_top_box = QVBoxLayout()
right_top_box = QVBoxLayout()
self.my_painter = ImgPainter()
#json_file_path = "/home/luiso/dui/dui_test/only_9_img/dui_idials_tst_04/dials-1/1_import/datablock.json"
json_file_path = "/home/luiso/dui/dui_test/X4_wide/test_02/dials-1/1_import/datablock.json"
#json_file_path = "/home/lui/dui/dui_test/X4_wide/tst01/datablock.json"
datablocks = DataBlockFactory.from_json_file(json_file_path)
db = datablocks[0]
self.my_sweep = db.extract_sweeps()[0]
print "self.my_sweep.get_array_range() =", self.my_sweep.get_array_range()
print "self.my_sweep.get_image_size() =", self.my_sweep.get_image_size()
n_of_imgs = self.my_sweep.get_array_range()[1]
print "n_of_imgs =", n_of_imgs
self.palette_lst = ["hot ascend", "hot descend", "black2white", "white2black"]
self.palette = self.palette_lst[0]
self.img_num = 0
self.set_img()
img_select = QComboBox()
for num in xrange(n_of_imgs):
labl = "image number:" + str(num)
img_select.addItem(labl)
img_select.setCurrentIndex(0)
img_select.currentIndexChanged.connect(self.img_changed_by_user)
palette_select = QComboBox()
for plt in self.palette_lst:
palette_select.addItem(plt)
palette_select.currentIndexChanged.connect(self.palette_changed_by_user)
left_top_box.addWidget(palette_select)
top_box.addLayout(left_top_box)
right_top_box.addWidget(img_select)
top_box.addLayout(right_top_box)
my_box.addLayout(top_box)
my_scrollable =QScrollArea()
my_scrollable.setWidget(self.my_painter)
my_box.addWidget(my_scrollable)
self.setLayout(my_box)
self.show()
def ini_datablock(self, json_file_path):
if (json_file_path != None):
try:
datablocks = DataBlockFactory.from_json_file(json_file_path)
##TODO check length of datablock for safety
datablock = datablocks[0]
self.my_sweep = datablock.extract_sweeps()[0]
self.img_select.clear()
print "self.my_sweep.get_array_range() =", self.my_sweep.get_array_range(
)
print "self.my_sweep.get_image_size() =", self.my_sweep.get_image_size(
)
n_of_imgs = len(self.my_sweep.indices())
print "n_of_imgs =", n_of_imgs
self.img_select.setMaximum(n_of_imgs)
self.img_select.setMinimum(1)
self.img_step.setMaximum(n_of_imgs / 2)
self.img_step.setMinimum(1)
self.num_of_imgs_to_add.setMaximum(n_of_imgs)
self.num_of_imgs_to_add.setMinimum(1)
except:
print "Failed to load images from datablock.json"
self.btn_first_clicked()
#TODO Find a better way to call this function only onse
self.ini_contrast()
self.set_img()
def load_reference_geometry(self):
if self.params.input.reference_geometry is None: return
try:
ref_datablocks = DataBlockFactory.from_json_file(self.params.input.reference_geometry, check_format=False)
except Exception:
ref_datablocks = None
if ref_datablocks is None:
from dxtbx.model.experiment_list import ExperimentListFactory
try:
ref_experiments = ExperimentListFactory.from_json_file(self.params.input.reference_geometry, check_format=False)
except Exception:
try:
import dxtbx
img = dxtbx.load(self.params.input.reference_geometry)
except Exception:
raise Sorry("Couldn't load geometry file %s"%self.params.input.reference_geometry)
else:
self.reference_detector = img.get_detector()
else:
assert len(ref_experiments.detectors()) == 1
self.reference_detector = ref_experiments.detectors()[0]
else:
assert len(ref_datablocks) == 1 and len(ref_datablocks[0].unique_detectors()) == 1
self.reference_detector = ref_datablocks[0].unique_detectors()[0]
def tst_with_external_lookup(self):
from dxtbx.datablock import DataBlockFactory
from dxtbx.imageset import ImageSweep
from os.path import join
filename = join(self.dials_regression, "centroid_test_data",
"datablock_with_lookup.json")
blocks = DataBlockFactory.from_json_file(filename)
assert(len(blocks) == 1)
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.data is not None
assert imageset.external_lookup.gain.data is not None
assert imageset.external_lookup.pedestal.data is not None
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.all_eq(True)
assert imageset.external_lookup.gain.data.all_eq(1)
assert imageset.external_lookup.pedestal.data.all_eq(0)
blocks = self.encode_json_then_decode(blocks)
assert(len(blocks) == 1)
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.data is not None
assert imageset.external_lookup.gain.data is not None
assert imageset.external_lookup.pedestal.data is not None
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.all_eq(True)
assert imageset.external_lookup.gain.data.all_eq(1)
assert imageset.external_lookup.pedestal.data.all_eq(0)
print 'OK'
def test(dials_regression, tmpdir):
tmpdir.chdir()
input_filename = os.path.join(dials_regression, "centroid_test_data",
"datablock.json")
mask_filename = os.path.join(dials_regression, "centroid_test_data",
"lookup_mask.pickle")
output_filename = "output_datablock.json"
result = procrunner.run_process([
'dials.apply_mask',
'input.datablock=%s' % input_filename,
'input.mask=%s' % mask_filename,
'output.datablock=%s' % output_filename,
])
assert result['exitcode'] == 0
assert result['stderr'] == ''
from dials.array_family import flex # import dependency
from dxtbx.datablock import DataBlockFactory
datablocks = DataBlockFactory.from_json_file(output_filename)
assert len(datablocks) == 1
imagesets = datablocks[0].extract_imagesets()
assert len(imagesets) == 1
imageset = imagesets[0]
assert imageset.external_lookup.mask.filename == mask_filename
def run(self):
from os.path import join
from libtbx import easy_run
input_filename = join(self.path, "datablock.json")
output_filename = "output_datablock.json"
mask_filename = join(self.path, "lookup_mask.pickle")
easy_run.fully_buffered([
'dials.apply_mask',
'input.datablock=%s' % input_filename,
'input.mask=%s' % mask_filename,
'output.datablock=%s' % output_filename
]).raise_if_errors()
from dxtbx.datablock import DataBlockFactory
datablocks = DataBlockFactory.from_json_file(output_filename)
assert len(datablocks) == 1
imagesets = datablocks[0].extract_imagesets()
assert len(imagesets) == 1
imageset = imagesets[0]
assert imageset.external_lookup.mask.filename == mask_filename
print 'OK'
def ini_datablock(self, json_file_path):
if(json_file_path != None):
try:
datablocks = DataBlockFactory.from_json_file(json_file_path)
##TODO check length of datablock for safety
datablock = datablocks[0]
self.my_sweep = datablock.extract_sweeps()[0]
self.img_select.clear()
except:
print "Failed to load images from datablock.json"
try:
print "self.my_sweep.get_array_range() =", self.my_sweep.get_array_range()
n_of_imgs = len(self.my_sweep.indices())
print "n_of_imgs =", n_of_imgs
self.img_select.setMaximum(n_of_imgs)
self.img_select.setMinimum(1)
self.img_step.setMaximum(n_of_imgs / 2)
self.img_step.setMinimum(1)
self.num_of_imgs_to_add.setMaximum(n_of_imgs)
self.num_of_imgs_to_add.setMinimum(1)
except:
print "Failed to set up IMG control dialog"
self.btn_first_clicked()
self.ini_contrast()
self.set_img()
QTimer.singleShot(1000, self.scale2border)
def tst_with_external_lookup(self):
filename = join(self.dials_regression, "centroid_test_data",
"datablock_with_lookup.json")
blocks = DataBlockFactory.from_json_file(filename)
assert(len(blocks) == 1)
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.data is not None
assert imageset.external_lookup.gain.data is not None
assert imageset.external_lookup.pedestal.data is not None
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.all_eq(True)
assert imageset.external_lookup.gain.data.all_eq(1)
assert imageset.external_lookup.pedestal.data.all_eq(0)
blocks = self.encode_json_then_decode(blocks)
assert(len(blocks) == 1)
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.data is not None
assert imageset.external_lookup.gain.data is not None
assert imageset.external_lookup.pedestal.data is not None
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.all_eq(True)
assert imageset.external_lookup.gain.data.all_eq(1)
assert imageset.external_lookup.pedestal.data.all_eq(0)
print 'OK'
def do_import(filename):
logger.info("Loading %s" % os.path.basename(filename))
datablocks = DataBlockFactory.from_filenames([filename])
if len(datablocks) == 0:
try:
datablocks = DataBlockFactory.from_json_file(filename)
except ValueError:
raise Abort("Could not load %s" % filename)
if len(datablocks) == 0:
raise Abort("Could not load %s" % filename)
if len(datablocks) > 1:
raise Abort("Got multiple datablocks from file %s" % filename)
# Ensure the indexer and downstream applications treat this as set of stills
reset_sets = []
from dxtbx.imageset import ImageSetFactory
for imageset in datablocks[0].extract_imagesets():
imageset = ImageSetFactory.imageset_from_anyset(imageset)
imageset.set_scan(None)
imageset.set_goniometer(None)
reset_sets.append(imageset)
return DataBlockFactory.from_imageset(reset_sets)[0]
def test_with_external_lookup(centroid_test_data):
filename = os.path.join(centroid_test_data, "datablock_with_lookup.json")
blocks = DataBlockFactory.from_json_file(filename)
assert len(blocks) == 1
imageset = blocks[0].extract_imagesets()[0]
assert not imageset.external_lookup.mask.data.empty()
assert not imageset.external_lookup.gain.data.empty()
assert not imageset.external_lookup.pedestal.data.empty()
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.tile(0).data().all_eq(True)
assert imageset.external_lookup.gain.data.tile(0).data().all_eq(1)
assert imageset.external_lookup.pedestal.data.tile(0).data().all_eq(0)
blocks = encode_json_then_decode(blocks)
assert len(blocks) == 1
imageset = blocks[0].extract_imagesets()[0]
assert not imageset.external_lookup.mask.data.empty()
assert not imageset.external_lookup.gain.data.empty()
assert not imageset.external_lookup.pedestal.data.empty()
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.tile(0).data().all_eq(True)
assert imageset.external_lookup.gain.data.tile(0).data().all_eq(1)
assert imageset.external_lookup.pedestal.data.tile(0).data().all_eq(0)
def get_3d_flex_array():
json_file_path = str(
"/home/luiso/dui/dui_test/X4_wide/dui_idials_tst_10/dials-1/1_import/datablock.json"
)
print "json_file_path =", json_file_path
datablocks = DataBlockFactory.from_json_file(json_file_path)
if len(datablocks) > 0:
assert (len(datablocks) == 1)
imagesets = datablocks[0].extract_imagesets()
crystals = None
print "len(datablocks) > 0"
else:
raise RuntimeError(
"No imageset could be constructed, len(datablocks) <= 0 ")
print "len(imagesets) =", len(imagesets)
print "type(imagesets) =", type(imagesets)
first_data = imagesets[0]
print "type(first_data) =", type(first_data)
my_array = first_data.to_array()
print "type(my_array) =", type(my_array)
my_array_double = my_array.as_double()
print "my_array_double.all() =", my_array_double.all()
return my_array_double
def loader(x):
try:
obj = DataBlockFactory.from_filenames([x])[0].extract_imagesets()[0]
except IndexError:
import dxtbx.datablock
try:
obj = DataBlockFactory.from_json_file(x)[0].extract_imagesets()[0]
except dxtbx.datablock.InvalidDataBlockError:
obj = ExperimentListFactory.from_json_file(x)[0].imageset
return obj
def run(args):
user_phil = []
files = []
for arg in args:
if os.path.isfile(arg):
files.append(arg)
else:
try:
user_phil.append(parse(arg))
except Exception:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
if not params.orthographic:
from mpl_toolkits.mplot3d import proj3d
fig = plt.figure()
colormap = plt.cm.gist_ncar
colors = [colormap(i) for i in np.linspace(0, 0.9, len(files))]
for file_name, color, in zip(files, colors):
# read the data and get the detector models
try:
datablocks = DataBlockFactory.from_json_file(file_name,
check_format=False)
except Exception:
experiments = ExperimentListFactory.from_json_file(
file_name, check_format=False)
detectors = experiments.detectors()
else:
detectors = []
for datablock in datablocks:
detectors.extend(datablock.unique_detectors())
for detector in detectors:
# plot the hierarchy
if params.orthographic:
ax = fig.gca()
else:
ax = fig.gca(projection='3d')
plot_group(detector.hierarchy(),
color,
ax,
orthographic=params.orthographic,
show_origin_vectors=params.show_origin_vectors,
panel_numbers=params.panel_numbers)
if params.orthographic:
plt.axes().set_aspect('equal', 'datalim')
if params.pdf_file:
pp = PdfPages(params.pdf_file)
for i in plt.get_fignums():
pp.savefig(plt.figure(i))
pp.close()
else:
plt.show()
def do_import(filename):
logger.info("Loading %s" % os.path.basename(filename))
try:
datablocks = DataBlockFactory.from_json_file(filename)
except ValueError:
datablocks = DataBlockFactory.from_filenames([filename])
if len(datablocks) == 0:
raise Abort("Could not load %s" % filename)
if len(datablocks) > 1:
raise Abort("Got multiple datablocks from file %s" % filename)
return datablocks[0]
def from_string(self, s):
from dxtbx.datablock import DataBlockFactory
from os.path import exists
from libtbx.utils import Sorry
if s is None:
return None
if s not in self.cache:
if not exists(s):
raise Sorry('File %s does not exist' % s)
self.cache[s] = FilenameDataWrapper(s,
DataBlockFactory.from_json_file(s,
check_format=self._check_format))
return self.cache[s]
def from_string(self, s):
from dxtbx.datablock import DataBlockFactory
from os.path import exists
from libtbx.utils import Sorry
if s is None:
return None
if s not in self.cache:
if not exists(s):
raise Sorry('File %s does not exist' % s)
self.cache[s] = FilenameDataWrapper(s,
DataBlockFactory.from_json_file(s,
check_format=self._check_format))
return self.cache[s]
def ini_datablock(self, json_file_path):
if json_file_path is not None:
try:
datablocks = DataBlockFactory.from_json_file(json_file_path)
# TODO check length of datablock for safety
datablock = datablocks[0]
self.my_sweep = datablock.extract_sweeps()[0]
self.img_select.clear()
except BaseException as e:
# We don't want to catch bare exceptions but don't know
# what this was supposed to catch. Log it.
logger.error(
"Caught unknown exception type %s: %s", type(e).__name__, e
)
logger.debug("Failed to load images from datablock.json")
try:
logger.debug(
"self.my_sweep.get_array_range() = %s",
self.my_sweep.get_array_range(),
)
n_of_imgs = len(self.my_sweep.indices())
logger.debug("n_of_imgs = %s", n_of_imgs)
self.img_select.setMaximum(n_of_imgs)
self.img_select.setMinimum(1)
self.img_step.setMaximum(n_of_imgs / 2)
self.img_step.setMinimum(1)
self.num_of_imgs_to_add.setMaximum(n_of_imgs)
self.num_of_imgs_to_add.setMinimum(1)
except BaseException as e:
# We don't want to catch bare exceptions but don't know
# what this was supposed to catch. Log it.
logger.error(
"Caught unknown exception type %s: %s", type(e).__name__, e
)
logger.debug("Failed to set up IMG control dialog")
self.btn_first_clicked()
self.ini_contrast()
self.set_img()
QTimer.singleShot(1000, self.scale2border)
def load_reference_geometry(self):
if self.params.input.reference_geometry is None: return
try:
ref_datablocks = DataBlockFactory.from_json_file(self.params.input.reference_geometry, check_format=False)
except Exception:
ref_datablocks = None
if ref_datablocks is None:
from dxtbx.model.experiment.experiment_list import ExperimentListFactory
try:
ref_experiments = ExperimentListFactory.from_json_file(self.params.input.reference_geometry, check_format=False)
except Exception:
raise Sorry("Couldn't load geometry file %s"%self.params.input.reference_geometry)
assert len(ref_experiments.detectors()) == 1
self.reference_detector = ref_experiments.detectors()[0]
else:
assert len(ref_datablocks) == 1 and len(ref_datablocks[0].unique_detectors()) == 1
self.reference_detector = ref_datablocks[0].unique_detectors()[0]
def test_with_bad_external_lookup(centroid_test_data):
filename = os.path.join(centroid_test_data, "datablock_with_bad_lookup.json")
blocks = DataBlockFactory.from_json_file(filename, check_format=False)
assert len(blocks) == 1
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.empty()
assert imageset.external_lookup.gain.data.empty()
assert imageset.external_lookup.pedestal.data.empty()
blocks = encode_json_then_decode(blocks, check_format=False)
assert len(blocks) == 1
imageset = blocks[0].extract_imagesets()[0]
assert imageset.external_lookup.mask.filename is not None
assert imageset.external_lookup.gain.filename is not None
assert imageset.external_lookup.pedestal.filename is not None
assert imageset.external_lookup.mask.data.empty()
assert imageset.external_lookup.gain.data.empty()
assert imageset.external_lookup.pedestal.data.empty()
def do_import(filename):
logger.info("Loading %s"%os.path.basename(filename))
try:
datablocks = DataBlockFactory.from_json_file(filename)
except ValueError:
datablocks = DataBlockFactory.from_filenames([filename])
if len(datablocks) == 0:
raise Abort("Could not load %s"%filename)
if len(datablocks) > 1:
raise Abort("Got multiple datablocks from file %s"%filename)
# Ensure the indexer and downstream applications treat this as set of stills
from dxtbx.imageset import ImageSet
reset_sets = []
for imageset in datablocks[0].extract_imagesets():
imageset = ImageSet(imageset.reader(), imageset.indices())
imageset._models = imageset._models
imageset.set_scan(None)
imageset.set_goniometer(None)
reset_sets.append(imageset)
return DataBlockFactory.from_imageset(reset_sets)[0]
from dxtbx.datablock import DataBlockFactory
#datablocks = DataBlockFactory.from_json_file("/home/luiso/dui/dui_test/only_9_img/idials_tst_04/dials-1/1_import/datablock.json")
datablocks = DataBlockFactory.from_json_file(
"/home/luiso/dui/dui_test/X4_wide/test_02/dials-1/1_import/datablock.json")
print "datablocks[0] =", datablocks[0]
db = datablocks[0]
sw = db.extract_sweeps()[0]
print "sw.get_raw_data(0) =", sw.get_raw_data(0)
print "sw.get_raw_data(1) =", sw.get_raw_data(1)
print "sw.get_raw_data(2) =", sw.get_raw_data(2)
im1 = sw.get_raw_data(0)[0]
print "im1.all() =", im1.all()
# Annotate with panel numbers
ax.text(vcen[0], vcen[1], '%d' % g.index())
else:
ax.plot(z[0], z[1], z[2], color=color)
# Annotate with panel numbers
ax.text(vcen[0], vcen[1], vcen[2], '%d' % g.index())
fig = plt.figure()
colormap = plt.cm.gist_ncar
colors = [colormap(i) for i in np.linspace(0, 0.9, len(files))]
for file_name, color, in zip(files, colors):
# read the data and get the detector models
try:
datablocks = DataBlockFactory.from_json_file(file_name,
check_format=False)
except Exception, e:
experiments = ExperimentListFactory.from_json_file(
file_name, check_format=False)
detectors = experiments.detectors()
else:
detectors = []
for datablock in datablocks:
detectors.extend(datablock.unique_detectors())
for detector in detectors:
# plot the hierarchy
if params.orthographic:
ax = fig.gca()
else:
ax = fig.gca(projection='3d')
plot_group(detector.hierarchy(),
def exercise_spotfinder():
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_spotfinder: dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = glob(os.path.join(data_dir, "centroid*.cbf"))
args = ["dials.find_spots", ' '.join(template), "output.reflections=spotfinder.pickle",
"output.shoeboxes=True"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 653, len(reflections)
refl = reflections[0]
assert approx_equal(refl['intensity.sum.value'], 42)
assert approx_equal(refl['bbox'], (1398, 1400, 513, 515, 0, 1))
assert approx_equal(refl['xyzobs.px.value'],
(1399.1190476190477, 514.2142857142857, 0.5))
assert "shoebox" in reflections
print 'OK'
# now with a resolution filter
args = ["dials.find_spots", "filter.d_min=2", "filter.d_max=15",
' '.join(template), "output.reflections=spotfinder.pickle", "output.shoeboxes=False"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 467, len(reflections)
assert "shoebox" not in reflections
print 'OK'
# now with more generous parameters
args = ["dials.find_spots", "min_spot_size=3",
"max_separation=3",
' '.join(template), "output.reflections=spotfinder.pickle"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 678, len(reflections)
print 'OK'
# Now with a user defined mask
template = glob(os.path.join(data_dir, "centroid*.cbf"))
args = ["dials.find_spots", ' '.join(template), "output.reflections=spotfinder.pickle",
"output.shoeboxes=True",
"lookup.mask=%s" % os.path.join(data_dir, "mask.pickle")]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
from dxtbx.datablock import DataBlockFactory
datablocks = DataBlockFactory.from_json_file(os.path.join(data_dir,
"datablock.json"))
assert(len(datablocks) == 1)
imageset = datablocks[0].extract_imagesets()[0]
detector = imageset.get_detector()
beam = imageset.get_beam()
for x, y, z in reflections['xyzobs.px.value']:
d = detector[0].get_resolution_at_pixel(beam.get_s0(), (x, y))
assert(d >= 3)
# Now with a user defined mask
template = glob(os.path.join(data_dir, "centroid*.cbf"))
args = ["dials.find_spots", ' '.join(template), "output.reflections=spotfinder.pickle",
"output.shoeboxes=True",
"region_of_interest=800,1200,800,1200"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
x, y, z = reflections['xyzobs.px.value'].parts()
assert x.all_ge(800)
assert y.all_ge(800)
assert x.all_lt(1200)
assert y.all_lt(1200)
print 'OK'
# now with XFEL stills
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/spotfinding_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "idx-s00-20131106040302615.cbf")
args = ["dials.find_spots", template, "output.reflections=spotfinder.pickle"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 2643, len(reflections)
print 'OK'
def exercise_spotfinder():
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_spotfinder: dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(relative_path="dials_regression/centroid_test_data", test=os.path.isdir)
template = glob(os.path.join(data_dir, "centroid*.cbf"))
args = ["dials.find_spots", " ".join(template), "output.reflections=spotfinder.pickle", "output.shoeboxes=True"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 653, len(reflections)
refl = reflections[0]
assert approx_equal(refl["intensity.sum.value"], 42)
assert approx_equal(refl["bbox"], (1398, 1400, 513, 515, 0, 1))
assert approx_equal(refl["xyzobs.px.value"], (1399.1190476190477, 514.2142857142857, 0.5))
assert "shoebox" in reflections
print "OK"
# now with a resolution filter
args = [
"dials.find_spots",
"filter.d_min=2",
"filter.d_max=15",
" ".join(template),
"output.reflections=spotfinder.pickle",
"output.shoeboxes=False",
]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 467, len(reflections)
assert "shoebox" not in reflections
print "OK"
# now with more generous parameters
args = [
"dials.find_spots",
"min_spot_size=3",
"max_separation=3",
" ".join(template),
"output.reflections=spotfinder.pickle",
]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 678, len(reflections)
print "OK"
# Now with a user defined mask
template = glob(os.path.join(data_dir, "centroid*.cbf"))
args = [
"dials.find_spots",
" ".join(template),
"output.reflections=spotfinder.pickle",
"output.shoeboxes=True",
"lookup.mask=%s" % os.path.join(data_dir, "mask.pickle"),
]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
from dxtbx.datablock import DataBlockFactory
datablocks = DataBlockFactory.from_json_file(os.path.join(data_dir, "datablock.json"))
assert len(datablocks) == 1
imageset = datablocks[0].extract_imagesets()[0]
detector = imageset.get_detector()
beam = imageset.get_beam()
for x, y, z in reflections["xyzobs.px.value"]:
d = detector[0].get_resolution_at_pixel(beam.get_s0(), (x, y))
assert d >= 3
# Now with a user defined mask
template = glob(os.path.join(data_dir, "centroid*.cbf"))
args = [
"dials.find_spots",
" ".join(template),
"output.reflections=spotfinder.pickle",
"output.shoeboxes=True",
"region_of_interest=800,1200,800,1200",
]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
x, y, z = reflections["xyzobs.px.value"].parts()
assert x.all_ge(800)
assert y.all_ge(800)
assert x.all_lt(1200)
assert y.all_lt(1200)
print "OK"
# now with XFEL stills
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/spotfinding_test_data", test=os.path.isdir
)
template = os.path.join(data_dir, "idx-s00-20131106040302615.cbf")
args = ["dials.find_spots", template, "output.reflections=spotfinder.pickle"]
result = easy_run.fully_buffered(command=" ".join(args)).raise_if_errors()
assert os.path.exists("spotfinder.pickle")
with open("spotfinder.pickle", "rb") as f:
reflections = pickle.load(f)
assert len(reflections) == 2643, len(reflections)
print "OK"
def run(args):
user_phil = []
files = []
for arg in args:
if os.path.isfile(arg):
files.append(arg)
else:
try:
user_phil.append(parse(arg))
except Exception:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
if not params.orthographic:
from mpl_toolkits.mplot3d import proj3d
def plot_group(g, color, orthographic=False):
# recursively plot a detector group
p = g.parent()
if params.show_origin_vectors:
if p is None:
#parent origin
pori = (0, 0, 0)
else:
#parent origin
pori = p.get_origin()
ori = g.get_origin()
if not orthographic:
a = Arrow3D([pori[0], ori[0]], [pori[1], ori[1]],
[pori[2], ori[2]],
mutation_scale=20,
lw=1,
arrowstyle="-|>",
color='gray')
ax.add_artist(a)
if g.is_group():
for c in g:
# plot all the children
plot_group(c, color, orthographic)
else:
# plot the panel boundaries
size = g.get_image_size()
p0 = col(g.get_pixel_lab_coord((0, 0)))
p1 = col(g.get_pixel_lab_coord((size[0] - 1, 0)))
p2 = col(g.get_pixel_lab_coord((size[0] - 1, size[1] - 1)))
p3 = col(g.get_pixel_lab_coord((0, size[1] - 1)))
v1 = p1 - p0
v2 = p3 - p0
vcen = ((v2 / 2) + (v1 / 2)) + p0
z = zip(p0, p1, p2, p3, p0)
if orthographic:
ax.plot(z[0], z[1], color=color)
if params.panel_numbers:
# Annotate with panel numbers
ax.text(vcen[0], vcen[1], '%d' % g.index())
else:
ax.plot(z[0], z[1], z[2], color=color)
if params.panel_numbers:
# Annotate with panel numbers
ax.text(vcen[0], vcen[1], vcen[2], '%d' % g.index())
fig = plt.figure()
colormap = plt.cm.gist_ncar
colors = [colormap(i) for i in np.linspace(0, 0.9, len(files))]
for file_name, color, in zip(files, colors):
# read the data and get the detector models
try:
datablocks = DataBlockFactory.from_json_file(file_name,
check_format=False)
except Exception:
experiments = ExperimentListFactory.from_json_file(
file_name, check_format=False)
detectors = experiments.detectors()
else:
detectors = []
for datablock in datablocks:
detectors.extend(datablock.unique_detectors())
for detector in detectors:
# plot the hierarchy
if params.orthographic:
ax = fig.gca()
else:
ax = fig.gca(projection='3d')
plot_group(detector.hierarchy(),
color,
orthographic=params.orthographic)
if params.orthographic:
plt.axes().set_aspect('equal', 'datalim')
if params.pdf_file:
pp = PdfPages(params.pdf_file)
for i in plt.get_fignums():
pp.savefig(plt.figure(i))
pp.close()
else:
plt.show()
creator = flex.PixelListShoeboxCreator(
pixel_labeller,
0, # panel
0, # zrange
True, # twod
min_spot_size, # min_pixels
max_spot_size, # max_pixels
False,
)
shoeboxes = creator.result()
centroid = shoeboxes.centroid_valid()
intensity = shoeboxes.summed_intensity()
observed = flex.observation(shoeboxes.panels(), centroid, intensity)
return flex.reflection_table(observed, shoeboxes)
if __name__ == "__main__":
import sys
from dxtbx.datablock import DataBlockFactory
db = DataBlockFactory.from_json_file(sys.argv[1])
iset = db[0].extract_imagesets()[0]
image = iset.get_raw_data(0)[0]
mask = iset.get_mask(0)[0]
reflections = find_spots(image, mask)
print(len(reflections))
from __future__ import absolute_import, division, print_function
from dxtbx.datablock import DataBlockFactory, DataBlockDumper
import sys
from six.moves import range
fin = sys.argv[1]
px_size = 0.05 # in mm
dpx = [0, 0, 1, 1, 0, 1, 1, 0] # in px
dpy = [0, 0, 1, 1, 0, 1, 1, 0] # in px
db = DataBlockFactory.from_json_file(fin)
db0 = db[0]
dd = db0.to_dict()
for i in range(8):
x = dd['detector'][0]['panels'][i]['origin'][0] + dpx[i] * px_size
y = dd['detector'][0]['panels'][i]['origin'][1] + dpy[i] * px_size
dd['detector'][0]['panels'][i]['origin'] = (x, y, 0)
xx = DataBlockFactory.from_dict(dd)
yy = DataBlockDumper(xx)
yy.as_file('new_detector_geom.json')
