def run(self, in_data):
sub_wedge_merge = []
fast_characterisation = {}
force_zero_rotation_axis_start = False
if "fastCharacterisation" in in_data:
fast_characterisation = in_data["fastCharacterisation"]
force_zero_rotation_axis_start = fast_characterisation.get(
"forceZeroRotationAxisStart", False)
is_fast_characterisation = True
list_subwedge_angles = fast_characterisation["listSubWedgeAngles"]
no_images_in_subwedge = fast_characterisation["noImagesInSubWedge"]
first_image_path = fast_characterisation["firstImagePath"]
image_number = 1
template = first_image_path.replace("0001", "{0:04d}")
list_image_path = []
for subwedge_angle in list_subwedge_angles:
for sub_wedge_image_number in range(no_images_in_subwedge):
image_path = template.format(image_number)
list_image_path.append(image_path)
image_number += 1
elif "imagePath" in in_data:
list_image_path = in_data["imagePath"]
is_fast_characterisation = False
list_subwedge_angles = None
no_images_in_subwedge = None
else:
raise RuntimeError(
"Neither 'imagePath' nor 'fastCharacterisation' in input data."
)
sub_wedge_number = 1
input_read_image_header = {"imagePath": list_image_path}
read_image_header = ReadImageHeader(inData=input_read_image_header)
read_image_header.execute()
if read_image_header.isSuccess():
list_subwedge = read_image_header.outData["subWedge"]
global_axis_start = None
if force_zero_rotation_axis_start:
for subwedge in list_subwedge:
axis_start = subwedge["experimentalCondition"][
"goniostat"]["rotationAxisStart"]
if global_axis_start is None or global_axis_start > axis_start:
global_axis_start = axis_start
for index_subwedge, subwedge in enumerate(list_subwedge):
if is_fast_characterisation:
# Modify the start angle
index_angle = int(index_subwedge / no_images_in_subwedge)
angle_subwedge = list_subwedge_angles[index_angle]
goniostat = subwedge["experimentalCondition"]["goniostat"]
if force_zero_rotation_axis_start:
goniostat["rotationAxisStart"] -= global_axis_start
goniostat["rotationAxisStart"] = (
goniostat["rotationAxisStart"] + angle_subwedge) % 360
goniostat["rotationAxisEnd"] = (
goniostat["rotationAxisEnd"] + angle_subwedge) % 360
else:
subwedge["subWedgeNumber"] = index_subwedge + 1
sub_wedge_merge = UtilsSubWedge.subWedgeMerge(list_subwedge)
out_data = {"subWedge": sub_wedge_merge}
return out_data
def test_execute_ReadImageHeader_eiger4m(self):
referenceDataPath = self.dataPath / 'ReadImageHeader_Eiger4M.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
readImageHeader = ReadImageHeader(inData=inData)
readImageHeader.execute()
self.assertTrue(readImageHeader.isSuccess())
outData = readImageHeader.outData
self.assertIsNotNone(outData)
def run(self, inData):
outData = {}
hdf5File = pathlib.Path(inData['hdf5File'])
# Read the header
inDataReadImageHeader = {
"imagePath": [inData['hdf5File']],
"isFastMesh": False
}
readImageHeader = ReadImageHeader(inData=inDataReadImageHeader)
readImageHeader.execute()
if readImageHeader.isSuccess():
firstSubWedge = readImageHeader.outData["subWedge"][0]
experimentalCondition = firstSubWedge["experimentalCondition"]
detector = experimentalCondition["detector"]
beam = experimentalCondition["beam"]
goniostat = experimentalCondition["goniostat"]
beamX = detector["beamPositionX"] / 2.0 / detector["pixelSizeX"]
beamY = detector["beamPositionY"] / 2.0 / detector["pixelSizeY"]
directory = hdf5File.parent
prefix = UtilsImage.getPrefix(hdf5File)
hdf5ImageNumber = 1
if 'master' in str(hdf5File):
masterFile = hdf5File
else:
if UtilsConfig.isEMBL():
fileName = '{0}_master.h5'.format(prefix)
else:
fileName = '{0}_{1}_master.h5'.format(
prefix, hdf5ImageNumber)
masterFile = directory / fileName
image = fabio.open(str(masterFile))
image.data = image.data.reshape(2181, 2, 2074, 2).sum(3).sum(1)
cbfImage = image.convert("cbf")
pilatus_headers = fabio.cbfimage.PilatusHeader(
"Silicon sensor, thickness 0.000750 m")
pilatus_headers["Start_angle"] = goniostat["rotationAxisStart"]
pilatus_headers["Angle_increment"] = goniostat["oscillationWidth"]
pilatus_headers["Detector"] = "Eiger2 16M binned to 4M"
pilatus_headers["Pixel_size"] = (detector["pixelSizeY"] * 2,
detector["pixelSizeX"] * 2)
pilatus_headers["Exposure_time"] = beam["exposureTime"]
pilatus_headers["Wavelength"] = beam["wavelength"]
pilatus_headers[
"Detector_distance"] = detector["distance"] / 1000.0
pilatus_headers["Beam_xy"] = (beamY, beamX)
pilatus_headers["Count_cutoff"] = 1009869
cbfImage.pilatus_headers = pilatus_headers
directory = inData.get("forcedOutputDirectory",
str(self.getWorkingDirectory()))
cbfImagePath = os.path.join(
directory,
os.path.basename(inData['hdf5File']).replace(".h5", ".cbf"))
cbfImage.save(cbfImagePath)
outData["outputCBFFile"] = cbfImagePath
return outData
def test_executeReadImageHeaderTaskk(self):
referenceDataPath = self.dataPath / 'ControlReadImageHeader.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
readImageHeader = ReadImageHeader(inData=inData)
readImageHeader.execute()
self.assertTrue(readImageHeader.isSuccess())
def test_executeReadImageHeaderTask_id23eh1_1(self):
referenceDataPath = self.dataPath / "id23eh1_1.json"
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
readImageHeader = ReadImageHeader(inData=inData)
readImageHeader.execute()
self.assertTrue(readImageHeader.isSuccess())