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 readImageHeaders(listImagePath):
# Read the header(s)
inDataReadImageHeader = {"imagePath": listImagePath}
readImageHeader = ReadImageHeader(
inData=inDataReadImageHeader,
workingDirectorySuffix=UtilsImage.getPrefix(listImagePath[0]),
)
readImageHeader.execute()
listSubWedge = readImageHeader.outData["subWedge"]
return listSubWedge
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_readEiger4mHeader(self):
referenceDataPath = self.dataPath / 'ReadImageHeader_Eiger4M.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
h5MasterFilePath, h5DataFilePath, h5FileNumber = UtilsImage.getH5FilePath(
inData['imagePath'][0])
dictHeader = ReadImageHeader.readHdf5Header(h5MasterFilePath)
self.assertEqual(dictHeader['description'], 'Dectris Eiger 4M')
def test_readEiger16mHeader(self):
referenceDataPath = self.dataPath / "ReadImageHeader_Eiger16M.json"
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
h5MasterFilePath, h5DataFilePath, h5FileNumber = UtilsImage.getH5FilePath(
inData["imagePath"][0]
)
dictHeader = ReadImageHeader.readHdf5Header(h5MasterFilePath)
self.assertEqual(dictHeader["description"], "Dectris EIGER2 CdTe 16M")
def test_readCBFHeader(self):
referenceDataPath = self.dataPath / 'ReadImageHeader_Pilatus2M.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
dictHeader = ReadImageHeader.readCBFHeader(inData['imagePath'][0])
self.assertEqual(dictHeader['Detector:'],
'PILATUS2 3M, S/N 24-0118, ESRF ID23')
def test_executeReadImageHeaderTaskk(self):
referenceDataPath = self.dataPath / 'ControlReadImageHeader.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
readImageHeader = ReadImageHeader(inData=inData)
readImageHeader.execute()
self.assertTrue(readImageHeader.isSuccess())
def run(self, inData):
# Format suffix
format = inData.get("format", "jpeg")
if format == "jpeg":
thumbSuffix = ".jpeg"
elif format == "jpg":
thumbSuffix = ".jpg"
else:
raise RuntimeError("Unsupported format: {0}".format(format))
# Loop through all images
listJPEGTask = []
listThumbTask = []
forcedOutputDirectory = inData.get("forcedOutputDirectory", None)
for imagePath in inData["image"]:
# Check image file extension
imageFileName, suffix = os.path.splitext(
os.path.basename(imagePath))
if not suffix in [".img", ".marccd", ".mccd", ".cbf", ".h5"]:
raise RuntimeError(
"Unknown image file name extension for pyarch thumbnail generator: %s"
% imagePath)
# Wait for image file
if suffix == ".h5":
h5MasterFilePath, h5DataFilePath, h5FileNumber = UtilsImage.getH5FilePath(
imagePath, isFastMesh=True)
waitFilePath = h5DataFilePath
else:
waitFilePath = imagePath
expectedSize = self.getExpectedSize(imagePath)
hasTimedOut, finalSize = UtilsPath.waitForFile(
waitFilePath, expectedSize=expectedSize, timeOut=600)
if hasTimedOut:
raise RuntimeError(
"Waiting for file {0} timed out!".format(imagePath))
outputFileName = imageFileName + thumbSuffix
if forcedOutputDirectory is not None:
outputPath = os.path.join(forcedOutputDirectory,
outputFileName)
else:
outputPath = None
# Create JPEG with resolution rings
inDataReadHeader = {
"imagePath": [imagePath],
"skipNumberOfImages": True,
"isFastMesh": True
}
readHeader = ReadImageHeader(
inData=inDataReadHeader,
workingDirectorySuffix=imageFileName,
)
readHeader.execute()
experimentalCondition = readHeader.outData["subWedge"][0][
"experimentalCondition"]
detector = experimentalCondition["detector"]
beam = experimentalCondition["beam"]
inDataCreateJPEG = {
"image": imagePath,
"height": 1024,
"width": 1024,
"outputFileName": outputFileName,
"outputPath": outputPath,
"doResolutionRings": True,
"pixelSizeX": detector["pixelSizeX"],
"pixelSizeY": detector["pixelSizeY"],
"beamPositionX": detector["beamPositionX"],
"beamPositionY": detector["beamPositionY"],
"distance": detector["distance"],
"wavelength": beam["wavelength"],
}
createJPEG = CreateThumbnail(inData=inDataCreateJPEG,
workingDirectorySuffix=imageFileName +
"_JPEG")
createJPEG.start()
listJPEGTask.append(createJPEG)
# Create thumbnail
outputFileName = imageFileName + ".thumb" + thumbSuffix
if forcedOutputDirectory is not None:
outputPath = os.path.join(forcedOutputDirectory,
outputFileName)
else:
outputPath = None
inDataCreateThumb = {
"image": imagePath,
"height": 256,
"width": 256,
"outputFileName": outputFileName,
"outputPath": outputPath,
"doResolutionRings": True,
"pixelSizeX": detector["pixelSizeX"],
"pixelSizeY": detector["pixelSizeY"],
"beamPositionX": detector["beamPositionX"],
"beamPositionY": detector["beamPositionY"],
"distance": detector["distance"],
"wavelength": beam["wavelength"],
}
createThumb = CreateThumbnail(
inData=inDataCreateThumb,
workingDirectorySuffix=imageFileName + "_thumbnail")
createThumb.start()
listThumbTask.append(createThumb)
outData = {"pathToJPEGImage": [], "pathToThumbImage": []}
for task in listJPEGTask:
task.join()
if forcedOutputDirectory:
outData["pathToJPEGImage"].append(task.outData["thumbNail"])
else:
pyarchPath = self.copyThumbnailToPyarch(task)
outData["pathToJPEGImage"].append(pyarchPath)
for task in listThumbTask:
task.join()
if forcedOutputDirectory:
outData["pathToThumbImage"].append(task.outData["thumbNail"])
else:
pyarchPath = self.copyThumbnailToPyarch(task)
outData["pathToThumbImage"].append(pyarchPath)
return outData
def test_readCBFHeader(self):
referenceDataPath = self.dataPath / "ReadImageHeader_Pilatus2M.json"
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
dictHeader = ReadImageHeader.readCBFHeader(inData["imagePath"][0])
self.assertEqual(dictHeader["Detector:"], "PILATUS2 3M, S/N 24-0118, ESRF ID23")
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())
def generateMOSFLMInData(cls, inData):
if "imagePath" in inData:
inDataReadImageHeader = {"imagePath": inData["imagePath"]}
readImageHeader = ReadImageHeader(inData=inDataReadImageHeader)
readImageHeader.execute()
listSubWedges = readImageHeader.outData["subWedge"]
elif "subWedge" in inData:
listSubWedges = inData["subWedge"]
else:
# Here we assume that we have inData in MOSFLM format...
return inData
firstSubWedge = listSubWedges[0]
experimentalCondition = firstSubWedge["experimentalCondition"]
detector = experimentalCondition["detector"]
beam = experimentalCondition["beam"]
goniostat = experimentalCondition["goniostat"]
detectorType = detector["type"]
if detectorType.startswith("pilatus"):
mosflmDetector = "PILATUS"
elif detectorType.startswith("eiger"):
mosflmDetector = "EIGER"
else:
raise RuntimeError("Unknown detecor type for MOSFLM: " +
detectorType)
listImage = firstSubWedge["image"]
firstImage = listImage[0]
firstPath = firstImage["path"]
mosflmInData = {
# The MOSFLM beam position convention is opposite to the XDS / CBF/ Dozor convention
"beam": {
"x": detector["beamPositionY"],
"y": detector["beamPositionX"]
},
"detector": {
"numberPixelX": detector["numberPixelX"],
"numberPixelY": detector["numberPixelY"],
"pixelSizeX": detector["pixelSizeX"],
"pixelSizeY": detector["pixelSizeY"],
"type": mosflmDetector
},
"directory": os.path.dirname(firstPath),
"distance": detector["distance"],
"template": UtilsImage.getTemplate(firstPath),
"wavelength": beam["wavelength"]
}
listMosflmImage = []
for subWedge in listSubWedges:
goniostat = subWedge["experimentalCondition"]["goniostat"]
rotationAxisStart = goniostat['rotationAxisStart']
oscillationWidth = goniostat['oscillationWidth']
imageIndex = 0
for image in subWedge["image"]:
number = UtilsImage.getImageNumber(image["path"])
rotationAxisStart = rotationAxisStart + oscillationWidth * imageIndex
rotationAxisEnd = rotationAxisStart + oscillationWidth
mosflmImage = {
"number": number,
"rotationAxisStart": rotationAxisStart,
"rotationAxisEnd": rotationAxisEnd
}
listMosflmImage.append(mosflmImage)
mosflmInData["image"] = listMosflmImage
return mosflmInData