EMD file
EMD file is generated by Velox software. For example this Zenodo entry 
EMD file is actually HDF5 file. The hierarchy looks like:
$ h5ls -r Camera_Nano_Ceta_2044_850_mm.emd
/ Group
/Application Group
/Application/Velox Group
/Application/Velox/DisplayLayout Dataset {1}
/Data Group
/Data/Image Group
/Data/Image/37698bfa8e374ec3897b24d45fe467d8 Group
/Data/Image/37698bfa8e374ec3897b24d45fe467d8/Data Dataset {4096, 4096, 44/Inf}
/Data/Image/37698bfa8e374ec3897b24d45fe467d8/FrameLookupTable Dataset {44/Inf}
/Data/Image/37698bfa8e374ec3897b24d45fe467d8/Metadata Dataset {60000, 44/Inf}
/Data/Text Group
/Data/Text/ccb62378cef544caa7a187f0f16eead4 Dataset {1}
/Experiment Dataset {1}
/Features Group
/Features/CameraFeature Group
/Features/CameraFeature/b88a737bc636458a96d0d18fce5117e6 Dataset {1}
/Features/Features Dataset {1}
/Info Dataset {1}
/Operations Group
/Operations/CameraInputOperation Group
/Operations/CameraInputOperation/39373aca84b243248a6188be46c4d767 Dataset {1}
/Operations/Operations Dataset {1}
/Presentation Group
/Presentation/DisplayIndex Dataset {1}
/Presentation/Displays Group
/Presentation/Displays/HtmlDisplay Group
/Presentation/Displays/HtmlDisplay/a5c3b3993d6a47ed921e84fb09f5999d Dataset {1}
/Presentation/Displays/ImageDisplay Group
/Presentation/Displays/ImageDisplay/dbee57785624425f9585f5e8a9ad0446 Dataset {1}
/Thumbnail.jpg Dataset {326658}
/Version Dataset {1}
Metadata is saved in /Data/Image/*/Metadata. Using python with h5py, it can be read:
def get_metadata(metadata):
mds = []
for i in xrange(metadata.shape[1]):
metadata_array = metadata[:, i].T
mdata_string = metadata_array.tostring().decode("utf-8")
mds.append(json.loads(mdata_string.rstrip('\x00')))
return mds
# get_metadata()
import h5py
h = h5py.File(f, "r")
image_path = h["/Data/Image"]
k = image_path.keys()[0]
metadata = get_metadata(h["/Data/Image/%s/Metadata" % k])Original json data look like:
{
"Core": {
"guid": "00000000000000000000000000000000",
"MetadataSchemaVersion": "v1/2013/07",
"MetadataDefinitionVersion": "7.9"
},
"GasInjectionSystems": "",
"Sample": "",
"Scan": {
"ScanSize": {
"width": "0",
"height": "0"
}
},
"Detectors": {
"Detector-2": {
"ReadOutArea": {
"top": "0",
"right": "4096",
"bottom": "4096",
"left": "0"
},
"ExposureTime": "2",
"ExposureMode": "",
"DetectorName": "EF-CCD",
"Binning": {
"width": "1",
"height": "1"
},
"DetectorType": "ImagingDetector",
"DarkGainCorrectionType": "3",
"Shutters": {
"Shutter-0": {
"Position": "PostSpecimen",
"Type": "Electrostatic"
}
}
},
"Detector-1": {
"ReadOutArea": {
"top": "0",
"right": "4096",
"bottom": "4096",
"left": "0"
},
"ExposureTime": "2",
"ExposureMode": "",
"DetectorName": "BM-Falcon",
"Binning": {
"width": "1",
"height": "1"
},
"DetectorType": "ImagingDetector",
"DarkGainCorrectionType": "3",
"Shutters": {
"Shutter-0": {
"Position": "PostSpecimen",
"Type": "Electrostatic"
}
}
},
"Detector-0": {
"ReadOutArea": {
"top": "0",
"right": "4096",
"bottom": "4096",
"left": "0"
},
"ExposureTime": "2",
"ExposureMode": "",
"DetectorName": "BM-Ceta",
"Binning": {
"width": "1",
"height": "1"
},
"DetectorType": "ImagingDetector",
"DarkGainCorrectionType": "3",
"Shutters": {
"Shutter-0": {
"Position": "PostSpecimen",
"Type": "Electrostatic"
}
}
}
},
"BinaryResult": {
"DetectorIndex": "0",
"PixelUnitX": "m",
"ImageSize": {
"width": "4096",
"height": "4096"
},
"Encoding": "Signed",
"CompositionType": "",
"BitsPerPixel": "32",
"AcquisitionUnit": "CameraImage",
"Offset": {
"y": "-3.2803362865965109e-07",
"x": "-3.2803362865965109e-07"
},
"Detector": "BM-Ceta",
"PixelSize": {
"width": "1.6017267024397026e-10",
"height": "1.6017267024397026e-10"
},
"PixelUnitY": "m"
},
"Instrument": {
"InstrumentId": "9950088",
"ComputerName": "TALOS-9950088",
"InstrumentClass": "Talos",
"InstrumentModel": "Talos Arctica",
"ControlSoftwareVersion": "1.14.1",
"Manufacturer": "FEI Company"
},
"Acquisition": {
"AcquisitionStartDatetime": {
"DateTime": "1562657936"
},
"SourceType": "XFEG",
"AcquisitionDatetime": {
"DateTime": "1562657936"
},
"BeamType": ""
},
"CustomProperties": {
"Detectors[BM-Ceta].TimeStamp": {
"type": "int64",
"value": "1562657941799119"
},
"Aperture[SA].Name": {
"type": "string",
"value": "None"
},
"Detectors[BM-Ceta].DigitalGain": {
"type": "double",
"value": "1"
},
"Detectors[BM-Ceta].FrameID": {
"type": "ulong",
"value": "1"
},
"Aperture[OBJ].Name": {
"type": "string",
"value": "None"
},
"Detectors[BM-Ceta].SaturationPoint": {
"type": "long",
"value": "4947"
},
"RecodeFactor": {
"type": "double",
"value": "1"
},
"Detectors[BM-Ceta].MaxPossiblePixelValue": {
"type": "long",
"value": "9805"
},
"StemMagnification": {
"type": "bool",
"value": "0"
},
"Detectors[BM-Ceta].CombinedSubFrames": {
"type": "long",
"value": "1"
},
"Aperture[C2].Name": {
"type": "string",
"value": "50"
},
"Detectors[BM-Ceta].TransferOK": {
"type": "bool",
"value": "1"
}
},
"Vacuum": {
"VacuumMode": "Vented"
},
"Optics": {
"LastMeasuredScreenCurrent": "0",
"Defocus": "-9.519695163107122e-11",
"Projector1LensIntensity": "0.87779033184051514",
"DiffractionLensIntensity": "0.64980185031890869",
"EFTEMOn": "false",
"ExtractorVoltage": "3700",
"OperatingMode": "1",
"SpotIndex": "10",
"GunLensSetting": "4",
"BeamConvergence": "0.0012142857142857142",
"ProbeMode": "2",
"Projector2LensIntensity": "0.96061533689498901",
"HighMagnificationMode": "SA",
"Apertures": {
"Aperture-1": {
"MechanismType": "Motorized",
"Type": "None",
"Name": "OBJ",
"PositionOffset": {
"y": "-0.00028464000000000001",
"x": "7.3759999999999999e-05"
},
"Number": "4"
},
"Aperture-0": {
"Diameter": "5.0000000000000002e-05",
"Name": "C2",
"Enabled": "3",
"Number": "2",
"MechanismType": "Motorized",
"Type": "Circular",
"PositionOffset": {
"y": "0.00080016000000000006",
"x": "0.0095753599999999998"
}
},
"Aperture-2": {
"MechanismType": "Motorized",
"Type": "None",
"Name": "SA",
"PositionOffset": {
"y": "-0.00021968000000000001",
"x": "0.00011024"
},
"Number": "5"
}
},
"IntermediateLensIntensity": "0.59939253330230713",
"IlluminationMode": "None",
"AccelerationVoltage": "200000",
"NominalMagnification": "92246.809999999998",
"ProjectorMode": "2",
"ScreenCurrent": "0",
"TemOperatingSubMode": "BrightField",
"C2LensIntensity": "0.45822128653526306",
"ObjectiveLensMode": "HM",
"ObjectiveLensIntensity": "0.85571491718292236",
"C1LensIntensity": "0.33570191264152527",
"MiniCondenserLensIntensity": "0.91795682907104492"
},
"EnergyFilter": {
"EntranceApertureType": ""
},
"Stage": {
"AlphaTilt": "0.52171428295138011",
"Position": {
"y": "-1.1214399999945335e-07",
"x": "1.7197999999986075e-07",
"z": "-1.7700000000018482e-09"
},
"BetaTilt": "0"
}
}For example metadata["Stage"]["AlphaTilt"] encodes alpha tilt angle in radians, metadata[“CustomProperties”][“Detectors[BM-Ceta].TimeStamp"]["value"] encodes time stamp in microseconds.
Image data is stored in /Data/Image/*/Data as 3D integer array. The n-th image can be obtained with h[data_path][:,:,n].
For data processing with DIALS, please use this format file.