I am trying to read the metadata of this file: https://drive.google.com/file/d/10ZTLRazYbgm4pYEc3M7J7bP6590ZjNtY/view?usp=sharing
It is saved in a private tag (34682, see python TiffFileError: invalid tag value offset)
I tried the solution from Read tiff tags in Python:
import tifffile
with tifffile.TiffFile('file.tif') as tif:
tif_tags = {}
for tag in tif.pages[0].tags.values():
name, value = tag.name, tag.value
tif_tags[name] = value
However this will save the whole interesting metadata as one string in the dict key 'FEI_TITAN':
In [150]: tif_tags['FEI_TITAN']
Out[150]: '<?xml version="1.0"?>\r\n<Metadata xmlns:nil="http://schemas.fei.com/Metadata/v1/2013/07" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\r\n <Core>\r\n <Guid>9b7da5e1-be22-4c15-9ea6-3ed4300318c5</Guid>\r\n <UserID>Supervisor</UserID>\r\n <ApplicationSoftware>xT</ApplicationSoftware>\r\n <ApplicationSoftwareVersion>0</ApplicationSoftwareVersion>\r\n </Core>\r\n <Instrument>\r\n <ControlSoftwareVersion>20.1.0.7012</ControlSoftwareVersion>\r\n <Manufacturer>FEI Company</Manufacturer>\r\n <InstrumentClass>Aquilos</InstrumentClass>\r\n <InstrumentID>9925851</InstrumentID>\r\n <ComputerName>AS-MPC</ComputerName>\r\n </Instrument>\r\n <Acquisition>\r\n <AcquisitionDatetime>2021-10-12T12:27:43</AcquisitionDatetime>\r\n <BeamType>Ion</BeamType>\r\n <ColumnType>Sidewinder</ColumnType>\r\n </Acquisition>\r\n <Optics>\r\n <Apertures>\r\n <Aperture>\r\n <Number>1</Number>\r\n <Diameter>2.5E-05</Diameter>\r\n </Aperture>\r\n </Apertures>\r\n <AccelerationVoltage>30000</AccelerationVoltage>\r\n <SpotSize>1.7E-08</SpotSize>\r\n <BeamCurrent>3E-11</BeamCurrent>\r\n <FullScanFieldOfView>\r\n <X>4.8020873382767222E-05</X>\r\n <Y>3.2013915588511481E-05</Y>\r\n </FullScanFieldOfView>\r\n <ScanFieldOfView>\r\n <X>4.8020873382767222E-05</X>\r\n <Y>3.2013915588511481E-05</Y>\r\n </ScanFieldOfView>\r\n <WorkingDistance>0.018943079512039922</WorkingDistance>\r\n <BeamShift>\r\n <X>-7.4036727128018167E-07</X>\r\n <Y>7.8283358087907821E-07</Y>\r\n </BeamShift>\r\n <StigmatorRaw>\r\n <X>0</X>\r\n <Y>0</Y>\r\n </StigmatorRaw>\r\n </Optics>\r\n <StageSettings>\r\n <StagePosition>\r\n <X>-0.0030654519456763526</X>\r\n <Y>0.0027469495002475459</Y>\r\n <Z>0.018902786052566539</Z>\r\n <Rotation>-1.256433216129438</Rotation>\r\n <Tilt>\r\n <Alpha>0.27925259026082394</Alpha>\r\n <Beta>0</Beta>\r\n </Tilt>\r\n </StagePosition>\r\n </StageSettings>\r\n <ScanSettings>\r\n <DwellTime>5E-07</DwellTime>\r\n <ScanSize>\r\n <Width>1536</Width>\r\n <Height>1024</Height>\r\n </ScanSize>\r\n <ScanArea>\r\n <X>0</X>\r\n <Y>0</Y>\r\n <Width>1536</Width>\r\n <Height>1024</Height>\r\n </ScanArea>\r\n <LineTime>0.00078449999999999993</LineTime>\r\n <LineIntegrationCount>1</LineIntegrationCount>\r\n <LineInterlacing>1</LineInterlacing>\r\n <FrameTime>0.80332799999999993</FrameTime>\r\n <ScanRotation>3.1415926535897931</ScanRotation>\r\n </ScanSettings>\r\n <VacuumProperties>\r\n <SamplePressure>0.00011099999999999989</SamplePressure>\r\n <ElectronSourcePressure>4.0754869701231304E-08</ElectronSourcePressure>\r\n <ElectronColumnPressure>1.5793422392106776E-07</ElectronColumnPressure>\r\n </VacuumProperties>\r\n <Detectors>\r\n <ScanningDetector>\r\n <DetectorName>ETD</DetectorName>\r\n <DetectorType>ETD</DetectorType>\r\n <Signal>SE</Signal>\r\n <Gain>8.5319006280647329</Gain>\r\n <Offset>-1.6069335895422618</Offset>\r\n <GridVoltage>600</GridVoltage>\r\n <ContrastNormalized>61.334819889093154</ContrastNormalized>\r\n <BrightnessNormalized>43.305104160356954</BrightnessNormalized>\r\n </ScanningDetector>\r\n <ScanningDetector>\r\n <DetectorName>ICE</DetectorName>\r\n <DetectorType>ICE</DetectorType>\r\n <Signal>SE</Signal>\r\n <Gain>54.199464921714458</Gain>\r\n <Offset>0.47536486052042992</Offset>\r\n <GridVoltage>600</GridVoltage>\r\n <ContrastNormalized>45.384756674519814</ContrastNormalized>\r\n <BrightnessNormalized>54.754484092327296</BrightnessNormalized>\r\n </ScanningDetector>\r\n </Detectors>\r\n <GasInjectionSystems>\r\n <Gis>\r\n <PortName>Port1</PortName>\r\n <NeedleState>Retracted</NeedleState>\r\n <Gases>\r\n <Gas>\r\n <GasType>G1</GasType>\r\n </Gas>\r\n </Gases>\r\n </Gis>\r\n <Gis>\r\n <PortName>Port2</PortName>\r\n <NeedleState>Retracted</NeedleState>\r\n <Gases>\r\n <Gas>\r\n <GasType>G2</GasType>\r\n </Gas>\r\n </Gases>\r\n </Gis>\r\n </GasInjectionSystems>\r\n <BinaryResult>\r\n <AcquisitionUnit>Pixel</AcquisitionUnit>\r\n <CompositionType>Single</CompositionType>\r\n <ImageSize>\r\n <X>1536</X>\r\n <Y>1024</Y>\r\n </ImageSize>\r\n <FilterType>Integrate</FilterType>\r\n <FilterFrameCount>1</FilterFrameCount>\r\n <PixelSize>\r\n <X unit="m" unitPrefixPower="1">3.1263589441905743E-08</X>\r\n <Y unit="m" unitPrefixPower="1">3.1263589441905743E-08</Y>\r\n </PixelSize>\r\n <IntensityScale>1</IntensityScale>\r\n <IntensityOffset>0</IntensityOffset>\r\n <Gamma>1</Gamma>\r\n <AcquisitionArea>\r\n <X>0</X>\r\n <Y>0</Y>\r\n <Width>1</Width>\r\n <Height>1</Height>\r\n </AcquisitionArea>\r\n </BinaryResult>\r\n <CustomSectionGroup>\r\n <CustomSection scope="StageCollection">\r\n <StageCollection>\r\n <Stage>\r\n <Type>BulkStage</Type>\r\n <X>-3.57633333333333 mm</X>\r\n <Y>3.30025 mm</Y>\r\n <Z>36.2439236111111 mm</Z>\r\n <R>288.011679475735 °</R>\r\n <AT>15.9999948400413 °</AT>\r\n <BT />\r\n </Stage>\r\n </StageCollection>\r\n </CustomSection>\r\n <CustomSection scope="ApplicationInfo">\r\n <ApplicationInfo>\r\n <AutomationCoreVersion>1.675.2</AutomationCoreVersion>\r\n <AutomationCoreCommitId>61efd0fd6a1b26289090960a7798059b497eeb42]</AutomationCoreCommitId>\r\n <ApplicationName />\r\n <ApplicationVersion />\r\n <ApplicationCommitId />\r\n </ApplicationInfo>\r\n </CustomSection>\r\n </CustomSectionGroup>\r\n</Metadata>'
Is there a way to retrieve these entries as individual dictionary keys? I already tried Convert a String representation of a Dictionary to a dictionary?, but neither is working for me...
Any ideas?
CodePudding user response：
The string you got here turns out to be encoded as xml. You can have a look here on how to convert an xml-string to dict: How to convert an XML string to a dictionary?
Using one of the answers there, I did the following:
In [6]: from xml.etree import cElementTree as ET
In [7]: ET.XML(tif_tags["FEI_TITAN"])
Out[7]: <Element 'Metadata' at 0x7f9be8207630>
In [8]: from copy import copy
...:
...: def dictify(r,root=True):
...: if root:
...: return {r.tag : dictify(r, False)}
...: d=copy(r.attrib)
...: if r.text:
...: d["_text"]=r.text
...: for x in r.findall("./*"):
...: if x.tag not in d:
...: d[x.tag]=[]
...: d[x.tag].append(dictify(x,False))
...: return d
...:
In [9]: dictify(ET.XML(tif_tags["FEI_TITAN"]))
Out[9]:
{'Metadata': {'_text': '\n ',
'Core': [{'_text': '\n ',
'Guid': [{'_text': '9b7da5e1-be22-4c15-9ea6-3ed4300318c5'}],
'UserID': [{'_text': 'Supervisor'}],
'ApplicationSoftware': [{'_text': 'xT'}],
'ApplicationSoftwareVersion': [{'_text': '0'}]}],
'Instrument': [{'_text': '\n ',
'ControlSoftwareVersion': [{'_text': '20.1.0.7012'}],
'Manufacturer': [{'_text': 'FEI Company'}],
'InstrumentClass': [{'_text': 'Aquilos'}],
'InstrumentID': [{'_text': '9925851'}],
'ComputerName': [{'_text': 'AS-MPC'}]}],
'Acquisition': [{'_text': '\n ',
'AcquisitionDatetime': [{'_text': '2021-10-12T12:27:43'}],
'BeamType': [{'_text': 'Ion'}],
'ColumnType': [{'_text': 'Sidewinder'}]}],
'Optics': [{'_text': '\n ',
'Apertures': [{'_text': '\n ',
'Aperture': [{'_text': '\n ',
'Number': [{'_text': '1'}],
'Diameter': [{'_text': '2.5E-05'}]}]}],
'AccelerationVoltage': [{'_text': '30000'}],
'SpotSize': [{'_text': '1.7E-08'}],
'BeamCurrent': [{'_text': '3E-11'}],
'FullScanFieldOfView': [{'_text': '\n ',
'X': [{'_text': '4.8020873382767222E-05'}],
'Y': [{'_text': '3.2013915588511481E-05'}]}],
'ScanFieldOfView': [{'_text': '\n ',
'X': [{'_text': '4.8020873382767222E-05'}],
'Y': [{'_text': '3.2013915588511481E-05'}]}],
'WorkingDistance': [{'_text': '0.018943079512039922'}],
'BeamShift': [{'_text': '\n ',
'X': [{'_text': '-7.4036727128018167E-07'}],
'Y': [{'_text': '7.8283358087907821E-07'}]}],
'StigmatorRaw': [{'_text': '\n ',
'X': [{'_text': '0'}],
'Y': [{'_text': '0'}]}]}],
'StageSettings': [{'_text': '\n ',
'StagePosition': [{'_text': '\n ',
'X': [{'_text': '-0.0030654519456763526'}],
'Y': [{'_text': '0.0027469495002475459'}],
'Z': [{'_text': '0.018902786052566539'}],
'Rotation': [{'_text': '-1.256433216129438'}],
'Tilt': [{'_text': '\n ',
'Alpha': [{'_text': '0.27925259026082394'}],
'Beta': [{'_text': '0'}]}]}]}],
'ScanSettings': [{'_text': '\n ',
'DwellTime': [{'_text': '5E-07'}],
'ScanSize': [{'_text': '\n ',
'Width': [{'_text': '1536'}],
'Height': [{'_text': '1024'}]}],
'ScanArea': [{'_text': '\n ',
'X': [{'_text': '0'}],
'Y': [{'_text': '0'}],
'Width': [{'_text': '1536'}],
'Height': [{'_text': '1024'}]}],
'LineTime': [{'_text': '0.00078449999999999993'}],
'LineIntegrationCount': [{'_text': '1'}],
'LineInterlacing': [{'_text': '1'}],
'FrameTime': [{'_text': '0.80332799999999993'}],
'ScanRotation': [{'_text': '3.1415926535897931'}]}],
'VacuumProperties': [{'_text': '\n ',
'SamplePressure': [{'_text': '0.00011099999999999989'}],
'ElectronSourcePressure': [{'_text': '4.0754869701231304E-08'}],
'ElectronColumnPressure': [{'_text': '1.5793422392106776E-07'}]}],
'Detectors': [{'_text': '\n ',
'ScanningDetector': [{'_text': '\n ',
'DetectorName': [{'_text': 'ETD'}],
'DetectorType': [{'_text': 'ETD'}],
'Signal': [{'_text': 'SE'}],
'Gain': [{'_text': '8.5319006280647329'}],
'Offset': [{'_text': '-1.6069335895422618'}],
'GridVoltage': [{'_text': '600'}],
'ContrastNormalized': [{'_text': '61.334819889093154'}],
'BrightnessNormalized': [{'_text': '43.305104160356954'}]},
{'_text': '\n ',
'DetectorName': [{'_text': 'ICE'}],
'DetectorType': [{'_text': 'ICE'}],
'Signal': [{'_text': 'SE'}],
'Gain': [{'_text': '54.199464921714458'}],
'Offset': [{'_text': '0.47536486052042992'}],
'GridVoltage': [{'_text': '600'}],
'ContrastNormalized': [{'_text': '45.384756674519814'}],
'BrightnessNormalized': [{'_text': '54.754484092327296'}]}]}],
'GasInjectionSystems': [{'_text': '\n ',
'Gis': [{'_text': '\n ',
'PortName': [{'_text': 'Port1'}],
'NeedleState': [{'_text': 'Retracted'}],
'Gases': [{'_text': '\n ',
'Gas': [{'_text': '\n ', 'GasType': [{'_text': 'G1'}]}]}]},
{'_text': '\n ',
'PortName': [{'_text': 'Port2'}],
'NeedleState': [{'_text': 'Retracted'}],
'Gases': [{'_text': '\n ',
'Gas': [{'_text': '\n ', 'GasType': [{'_text': 'G2'}]}]}]}]}],
'BinaryResult': [{'_text': '\n ',
'AcquisitionUnit': [{'_text': 'Pixel'}],
'CompositionType': [{'_text': 'Single'}],
'ImageSize': [{'_text': '\n ',
'X': [{'_text': '1536'}],
'Y': [{'_text': '1024'}]}],
'FilterType': [{'_text': 'Integrate'}],
'FilterFrameCount': [{'_text': '1'}],
'PixelSize': [{'_text': '\n ',
'X': [{'unit': 'm',
'unitPrefixPower': '1',
'_text': '3.1263589441905743E-08'}],
'Y': [{'unit': 'm',
'unitPrefixPower': '1',
'_text': '3.1263589441905743E-08'}]}],
'IntensityScale': [{'_text': '1'}],
'IntensityOffset': [{'_text': '0'}],
'Gamma': [{'_text': '1'}],
'AcquisitionArea': [{'_text': '\n ',
'X': [{'_text': '0'}],
'Y': [{'_text': '0'}],
'Width': [{'_text': '1'}],
'Height': [{'_text': '1'}]}]}],
'CustomSectionGroup': [{'_text': '\n ',
'CustomSection': [{'scope': 'StageCollection',
'_text': '\n ',
'StageCollection': [{'_text': '\n ',
'Stage': [{'_text': '\n ',
'Type': [{'_text': 'BulkStage'}],
'X': [{'_text': '-3.57633333333333 mm'}],
'Y': [{'_text': '3.30025 mm'}],
'Z': [{'_text': '36.2439236111111 mm'}],
'R': [{'_text': '288.011679475735 °'}],
'AT': [{'_text': '15.9999948400413 °'}],
'BT': [{}]}]}]},
{'scope': 'ApplicationInfo',
'_text': '\n ',
'ApplicationInfo': [{'_text': '\n ',
'AutomationCoreVersion': [{'_text': '1.675.2'}],
'AutomationCoreCommitId': [{'_text': '61efd0fd6a1b26289090960a7798059b497eeb42]'}],
'ApplicationName': [{}],
'ApplicationVersion': [{}],
'ApplicationCommitId': [{}]}]}]}]}}