342 lines
18 KiB
Perl
342 lines
18 KiB
Perl
#------------------------------------------------------------------------------
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# File: MRC.pm
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#
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# Description: Read MRC (Medical Research Council) image files
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#
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# Revisions: 2021-04-21 - P. Harvey Created
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#
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# References: 1) https://www.ccpem.ac.uk/mrc_format/mrc2014.php
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# 2) http://legacy.ccp4.ac.uk/html/library.html
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# 3) https://github.com/ccpem/mrcfile/blob/master/mrcfile/dtypes.py
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#
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# Notes: The header is basically identical to the older CCP4 file format
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#------------------------------------------------------------------------------
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package Image::ExifTool::MRC;
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use strict;
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use vars qw($VERSION);
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use Image::ExifTool qw(:DataAccess :Utils);
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$VERSION = '1.00';
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my %bool = (
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Format => 'int8u',
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PrintConv => { 0 => 'No', 1 => 'Yes' }
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);
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%Image::ExifTool::MRC::Main = (
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PROCESS_PROC => \&Image::ExifTool::ProcessBinaryData,
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GROUPS => { 0 => 'File', 1 => 'File', 2 => 'Image' },
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VARS => { NO_LOOKUP => 1 }, # omit tags from lookup
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FORMAT => 'int32u',
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NOTES => q{
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Tags extracted from Medical Research Council (MRC) format imaging files.
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See L<https://www.ccpem.ac.uk/mrc_format/mrc2014.php> for the specification.
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},
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0 => 'ImageWidth',
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1 => 'ImageHeight',
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2 => {
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Name => 'ImageDepth',
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Notes => q{
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number of sections. Use ExtractEmbedded option to extract metadata for all
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sections
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},
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RawConv => '$$self{ImageDepth} = $val',
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},
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3 => {
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Name => 'ImageMode',
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PrintConv => {
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0 => '8-bit signed integer',
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1 => '16-bit signed integer',
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2 => '32-bit signed real',
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3 => 'complex 16-bit integer',
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4 => 'complex 32-bit real',
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6 => '16-bit unsigned integer',
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},
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},
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4 => { Name => 'StartPoint', Format => 'int32u[3]' },
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7 => { Name => 'GridSize', Format => 'int32u[3]' },
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10 => { Name => 'CellWidth', Format => 'float', Notes => 'cell size in angstroms' },
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11 => { Name => 'CellHeight',Format => 'float' },
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12 => { Name => 'CellDepth', Format => 'float' },
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13 => { Name => 'CellAlpha', Format => 'float' },
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14 => { Name => 'CellBeta', Format => 'float' },
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15 => { Name => 'CellGamma', Format => 'float' },
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16 => { Name => 'ImageWidthAxis', PrintConv => { 1 => 'X', 2 => 'Y', 3 => 'Z' } },
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17 => { Name => 'ImageHeightAxis', PrintConv => { 1 => 'X', 2 => 'Y', 3 => 'Z' } },
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18 => { Name => 'ImageDepthAxis', PrintConv => { 1 => 'X', 2 => 'Y', 3 => 'Z' } },
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19 => { Name => 'DensityMin', Format => 'float' },
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20 => { Name => 'DensityMax', Format => 'float' },
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21 => { Name => 'DensityMean',Format => 'float' },
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22 => 'SpaceGroupNumber',
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23 => { Name => 'ExtendedHeaderSize', RawConv => '$$self{ExtendedHeaderSize} = $val' },
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26 => { Name => 'ExtendedHeaderType', Format => 'string[4]', RawConv => '$$self{ExtendedHeaderType} = $val' },
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27 => 'MRCVersion',
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49 => { Name => 'Origin', Format => 'float[3]' },
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53 => { Name => 'MachineStamp', Format => 'int8u[4]', PrintConv => 'sprintf("0x%.2x 0x%.2x 0x%.2x 0x%.2x",split " ", $val)' },
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54 => { Name => 'RMSDeviation', Format => 'float' },
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55 => { Name => 'NumberOfLabels', RawConv => '$$self{NLab} = $val' },
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56 => { Name => 'Label0', Format => 'string[80]', Condition => '$$self{NLab} > 0' },
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76 => { Name => 'Label1', Format => 'string[80]', Condition => '$$self{NLab} > 1' },
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96 => { Name => 'Label2', Format => 'string[80]', Condition => '$$self{NLab} > 2' },
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116 => { Name => 'Label3', Format => 'string[80]', Condition => '$$self{NLab} > 3' },
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136 => { Name => 'Label4', Format => 'string[80]', Condition => '$$self{NLab} > 4' },
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156 => { Name => 'Label5', Format => 'string[80]', Condition => '$$self{NLab} > 5' },
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176 => { Name => 'Label6', Format => 'string[80]', Condition => '$$self{NLab} > 6' },
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196 => { Name => 'Label7', Format => 'string[80]', Condition => '$$self{NLab} > 7' },
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216 => { Name => 'Label8', Format => 'string[80]', Condition => '$$self{NLab} > 8' },
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236 => { Name => 'Label9', Format => 'string[80]', Condition => '$$self{NLab} > 9' },
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);
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%Image::ExifTool::MRC::FEI12 = (
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PROCESS_PROC => \&Image::ExifTool::ProcessBinaryData,
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GROUPS => { 0 => 'File', 1 => 'File', 2 => 'Image' },
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VARS => { NO_LOOKUP => 1 }, # omit tags from lookup (way too many!)
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NOTES => 'Tags extracted from FEI1 and FEI2 extended headers.',
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0 => { Name => 'MetadataSize', Format => 'int32u', RawConv => '$$self{MetadataSize} = $val' },
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4 => { Name => 'MetadataVersion', Format => 'int32u' },
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8 => {
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Name => 'Bitmask1',
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Format => 'int32u',
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RawConv => '$$self{BitM} = $val',
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PrintConv => 'sprintf("0x%.8x", $val)',
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},
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12 => {
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Name => 'TimeStamp',
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Format => 'double',
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Condition => '$$self{BitM} & 0x01',
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Groups => { 2 => 'Time'},
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# shift from days since Dec 30, 1899 to Unix epoch of Jan 1, 1970
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# (my sample looks like local time, although it should be UTC)
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ValueConv => 'ConvertUnixTime(($val-25569)*24*3600)',
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PrintConv => '$self->ConvertDateTime($val)',
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},
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20 => { Name => 'MicroscopeType', Format => 'string[16]', Condition => '$$self{BitM} & 0x02' },
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36 => { Name => 'MicroscopeID', Format => 'string[16]', Condition => '$$self{BitM} & 0x04' },
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52 => { Name => 'Application', Format => 'string[16]', Condition => '$$self{BitM} & 0x08' },
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68 => { Name => 'AppVersion', Format => 'string[16]', Condition => '$$self{BitM} & 0x10' },
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84 => { Name => 'HighTension', Format => 'double', Condition => '$$self{BitM} & 0x20', Notes => 'volts' },
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92 => { Name => 'Dose', Format => 'double', Condition => '$$self{BitM} & 0x40', Notes => 'electrons/m2' },
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100 => { Name => 'AlphaTilt', Format => 'double', Condition => '$$self{BitM} & 0x80' },
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108 => { Name => 'BetaTilt', Format => 'double', Condition => '$$self{BitM} & 0x100' },
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116 => { Name => 'XStage', Format => 'double', Condition => '$$self{BitM} & 0x200' },
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124 => { Name => 'YStage', Format => 'double', Condition => '$$self{BitM} & 0x400' },
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132 => { Name => 'ZStage', Format => 'double', Condition => '$$self{BitM} & 0x800' },
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140 => { Name => 'TiltAxisAngle', Format => 'double', Condition => '$$self{BitM} & 0x1000' },
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148 => { Name => 'DualAxisRot', Format => 'double', Condition => '$$self{BitM} & 0x2000' },
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156 => { Name => 'PixelSizeX', Format => 'double', Condition => '$$self{BitM} & 0x4000' },
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164 => { Name => 'PixelSizeY', Format => 'double', Condition => '$$self{BitM} & 0x8000' },
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220 => { Name => 'Defocus', Format => 'double', Condition => '$$self{BitM} & 0x400000' },
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228 => { Name => 'STEMDefocus', Format => 'double', Condition => '$$self{BitM} & 0x800000' },
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236 => { Name => 'AppliedDefocus', Format => 'double', Condition => '$$self{BitM} & 0x1000000' },
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244 => { Name => 'InstrumentMode', Format => 'int32u', Condition => '$$self{BitM} & 0x2000000', PrintConv => { 1 => 'TEM', 2 => 'STEM' } },
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248 => { Name => 'ProjectionMode', Format => 'int32u', Condition => '$$self{BitM} & 0x4000000', PrintConv => { 1 => 'Diffraction', 2 => 'Imaging' } },
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252 => { Name => 'ObjectiveLens', Format => 'string[16]', Condition => '$$self{BitM} & 0x8000000' },
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268 => { Name => 'HighMagnificationMode', Format => 'string[16]', Condition => '$$self{BitM} & 0x10000000' },
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284 => { Name => 'ProbeMode', Format => 'int32u', Condition => '$$self{BitM} & 0x20000000', PrintConv => { 1 => 'Nano', 2 => 'Micro' } },
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288 => { Name => 'EFTEMOn', %bool, Condition => '$$self{BitM} & 0x40000000' },
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289 => { Name => 'Magnification', Format => 'double', Condition => '$$self{BitM} & 0x80000000' },
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297 => {
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Name => 'Bitmask2',
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Format => 'int32u',
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RawConv => '$$self{BitM} = $val',
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PrintConv => 'sprintf("0x%.8x", $val)',
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},
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301 => { Name => 'CameraLength', Format => 'double', Condition => '$$self{BitM} & 0x01' },
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309 => { Name => 'SpotIndex', Format => 'int32u', Condition => '$$self{BitM} & 0x02' },
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313 => { Name => 'IlluminationArea',Format => 'double', Condition => '$$self{BitM} & 0x04' },
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321 => { Name => 'Intensity', Format => 'double', Condition => '$$self{BitM} & 0x08' },
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329 => { Name => 'ConvergenceAngle',Format => 'double', Condition => '$$self{BitM} & 0x10' },
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337 => { Name => 'IlluminationMode',Format => 'string[16]', Condition => '$$self{BitM} & 0x20' },
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353 => { Name => 'WideConvergenceAngleRange', %bool, Condition => '$$self{BitM} & 0x40' },
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354 => { Name => 'SlitInserted', %bool, Condition => '$$self{BitM} & 0x80' },
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355 => { Name => 'SlitWidth', Format => 'double', Condition => '$$self{BitM} & 0x100' },
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363 => { Name => 'AccelVoltOffset', Format => 'double', Condition => '$$self{BitM} & 0x200' },
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371 => { Name => 'DriftTubeVolt', Format => 'double', Condition => '$$self{BitM} & 0x400' },
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379 => { Name => 'EnergyShift', Format => 'double', Condition => '$$self{BitM} & 0x800' },
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387 => { Name => 'ShiftOffsetX', Format => 'double', Condition => '$$self{BitM} & 0x1000' },
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395 => { Name => 'ShiftOffsetY', Format => 'double', Condition => '$$self{BitM} & 0x2000' },
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403 => { Name => 'ShiftX', Format => 'double', Condition => '$$self{BitM} & 0x4000' },
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411 => { Name => 'ShiftY', Format => 'double', Condition => '$$self{BitM} & 0x8000' },
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419 => { Name => 'IntegrationTime', Format => 'double', Condition => '$$self{BitM} & 0x10000' },
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427 => { Name => 'BinningWidth', Format => 'int32u', Condition => '$$self{BitM} & 0x20000' },
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431 => { Name => 'BinningHeight', Format => 'int32u', Condition => '$$self{BitM} & 0x40000' },
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435 => { Name => 'CameraName', Format => 'string[16]', Condition => '$$self{BitM} & 0x80000' },
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451 => { Name => 'ReadoutAreaLeft', Format => 'int32u', Condition => '$$self{BitM} & 0x100000' },
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455 => { Name => 'ReadoutAreaTop', Format => 'int32u', Condition => '$$self{BitM} & 0x200000' },
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459 => { Name => 'ReadoutAreaRight',Format => 'int32u', Condition => '$$self{BitM} & 0x400000' },
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463 => { Name => 'ReadoutAreaBottom',Format=> 'int32u', Condition => '$$self{BitM} & 0x800000' },
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467 => { Name => 'CetaNoiseReduct', %bool, Condition => '$$self{BitM} & 0x1000000' },
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468 => { Name => 'CetaFramesSummed',Format => 'int32u', Condition => '$$self{BitM} & 0x2000000' },
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472 => { Name => 'DirectDetElectronCounting', %bool, Condition => '$$self{BitM} & 0x4000000' },
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473 => { Name => 'DirectDetAlignFrames', %bool, Condition => '$$self{BitM} & 0x8000000' },
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490 => {
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Name => 'Bitmask3',
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Format => 'int32u',
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RawConv => '$$self{BitM} = $val',
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PrintConv => 'sprintf("0x%.8x", $val)',
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},
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518 => { Name => 'PhasePlate', %bool, Condition => '$$self{BitM} & 0x40' },
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519 => { Name => 'STEMDetectorName',Format => 'string[16]', Condition => '$$self{BitM} & 0x80' },
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535 => { Name => 'Gain', Format => 'double', Condition => '$$self{BitM} & 0x100' },
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543 => { Name => 'Offset', Format => 'double', Condition => '$$self{BitM} & 0x200' },
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571 => { Name => 'DwellTime', Format => 'double', Condition => '$$self{BitM} & 0x8000' },
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579 => { Name => 'FrameTime', Format => 'double', Condition => '$$self{BitM} & 0x10000' },
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587 => { Name => 'ScanSizeLeft', Format => 'int32u', Condition => '$$self{BitM} & 0x20000' },
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591 => { Name => 'ScanSizeTop', Format => 'int32u', Condition => '$$self{BitM} & 0x40000' },
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595 => { Name => 'ScanSizeRight', Format => 'int32u', Condition => '$$self{BitM} & 0x80000' },
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599 => { Name => 'ScanSizeBottom', Format => 'int32u', Condition => '$$self{BitM} & 0x100000' },
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603 => { Name => 'FullScanFOV_X', Format => 'double', Condition => '$$self{BitM} & 0x200000' },
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611 => { Name => 'FullScanFOV_Y', Format => 'double', Condition => '$$self{BitM} & 0x400000' },
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619 => { Name => 'Element', Format => 'string[16]', Condition => '$$self{BitM} & 0x800000' },
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635 => { Name => 'EnergyIntervalLower', Format => 'double', Condition => '$$self{BitM} & 0x1000000' },
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643 => { Name => 'EnergyIntervalHigher',Format => 'double', Condition => '$$self{BitM} & 0x2000000' },
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651 => { Name => 'Method', Format=> 'int32u', Condition => '$$self{BitM} & 0x4000000' },
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655 => { Name => 'IsDoseFraction', %bool, Condition => '$$self{BitM} & 0x8000000' },
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656 => { Name => 'FractionNumber', Format => 'int32u', Condition => '$$self{BitM} & 0x10000000' },
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660 => { Name => 'StartFrame', Format => 'int32u', Condition => '$$self{BitM} & 0x20000000' },
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664 => { Name => 'EndFrame', Format => 'int32u', Condition => '$$self{BitM} & 0x40000000' },
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668 => { Name =>'InputStackFilename',Format=> 'string[80]', Condition => '$$self{BitM} & 0x80000000' },
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748 => {
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Name => 'Bitmask4',
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Format => 'int32u',
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RawConv => '$$self{BitM} = $val',
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PrintConv => 'sprintf("0x%.8x", $val)',
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},
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752 => { Name => 'AlphaTiltMin', Format => 'double', Condition => '$$self{BitM} & 0x01' },
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760 => { Name => 'AlphaTiltMax', Format => 'double', Condition => '$$self{BitM} & 0x02' },
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#
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# FEI2 header starts here
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#
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768 => { Name => 'ScanRotation', Format => 'double', Condition => '$$self{BitM} & 0x04' },
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776 => { Name => 'DiffractionPatternRotation',Format=>'double', Condition => '$$self{BitM} & 0x08' },
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784 => { Name => 'ImageRotation', Format => 'double', Condition => '$$self{BitM} & 0x10' },
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792 => { Name => 'ScanModeEnumeration',Format => 'int32u', Condition => '$$self{BitM} & 0x20', PrintConv => { 0 => 'Other', 1 => 'Raster', 2 => 'Serpentine' } },
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796 => {
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Name => 'AcquisitionTimeStamp',
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Format => 'int64u',
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Condition => '$$self{BitM} & 0x40',
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Groups => { 2 => 'Time' },
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# microseconds since 1970 UTC
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ValueConv => 'ConvertUnixTime($val / 1e6, 1, 6)',
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PrintConv => '$self->ConvertDateTime($val)',
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},
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804 => { Name => 'DetectorCommercialName', Format => 'string[16]', Condition => '$$self{BitM} & 0x80' },
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820 => { Name => 'StartTiltAngle', Format => 'double', Condition => '$$self{BitM} & 0x100' },
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828 => { Name => 'EndTiltAngle', Format => 'double', Condition => '$$self{BitM} & 0x200' },
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836 => { Name => 'TiltPerImage', Format => 'double', Condition => '$$self{BitM} & 0x400' },
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844 => { Name => 'TitlSpeed', Format => 'double', Condition => '$$self{BitM} & 0x800' },
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852 => { Name => 'BeamCenterX', Format => 'int32u', Condition => '$$self{BitM} & 0x1000' },
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856 => { Name => 'BeamCenterY', Format => 'int32u', Condition => '$$self{BitM} & 0x2000' },
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860 => {
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Name => 'CFEGFlashTimeStamp',
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Format => 'int64u',
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Condition => '$$self{BitM} & 0x4000',
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Groups => { 2 => 'Time' },
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ValueConv => 'ConvertUnixTime($val / 1e6, 1, 6)',
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PrintConv => '$self->ConvertDateTime($val)',
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},
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868 => { Name => 'PhasePlatePosition',Format => 'int32u', Condition => '$$self{BitM} & 0x8000' },
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872 => { Name => 'ObjectiveAperture', Format=>'string[16]',Condition => '$$self{BitM} & 0x10000' },
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);
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#------------------------------------------------------------------------------
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# Extract metadata from a MRC image
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# Inputs: 0) ExifTool object reference, 1) dirInfo reference
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# Returns: 1 on success, 0 if this wasn't a valid MRC file
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sub ProcessMRC($$)
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{
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my ($et, $dirInfo) = @_;
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my $raf = $$dirInfo{RAF};
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my ($buff, $tagTablePtr, $i);
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# verify this is a valid MRC file
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return 0 unless $raf->Read($buff, 1024) == 1024;
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# validate axes, "MAP" file type and machine stamp
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return 0 unless $buff =~ /^.{64}[\x01\x02\x03]\0\0\0[\x01\x02\x03]\0\0\0[\x01\x02\x03]\0\0\0.{132}MAP[\0 ](\x44\x44|\x44\x41|\x11\x11)\0\0/s;
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$et->SetFileType();
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SetByteOrder('II');
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my %dirInfo = (
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DataPt => \$buff,
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DirStart => 0,
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DirLen => length($buff),
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);
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$tagTablePtr = GetTagTable('Image::ExifTool::MRC::Main');
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$et->ProcessDirectory(\%dirInfo, $tagTablePtr);
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# (I don't have any samples with extended headers for testing, so these are not yet decoded)
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if ($$et{ExtendedHeaderSize} and $$et{ExtendedHeaderType} =~ /^FEI[12]/) {
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unless ($raf->Read($buff,4)==4 and $raf->Seek(-4,1)) { # read metadata size
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$et->Warn('Error reading extended header');
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return 1;
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}
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my $size = Get32u(\$buff, 0);
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if ($size * $$et{ImageDepth} > $$et{ExtendedHeaderSize}) {
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$et->Warn('Corrupted extended header');
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return 1;
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}
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$dirInfo{DirLen} = $size;
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$tagTablePtr = GetTagTable('Image::ExifTool::MRC::FEI12');
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for ($i=0; ;) {
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$dirInfo{DataPos} = $raf->Tell();
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$raf->Read($buff, $size) == $size or $et->Warn("Error reading extended header $i"), last;
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$et->ProcessDirectory(\%dirInfo, $tagTablePtr);
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last if ++$i >= $$et{ImageDepth};
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unless ($$et{OPTIONS}{ExtractEmbedded}) {
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$et->Warn('Use the ExtractEmbedded option to read metadata for all frames',3);
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last;
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}
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$$et{DOC_NUM} = ++$$et{DOC_COUNT};
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}
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delete $$et{DOC_NUM};
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}
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return 1;
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}
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1; # end
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__END__
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=head1 NAME
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Image::ExifTool::MRC - Read MRC meta information
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=head1 SYNOPSIS
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This module is used by Image::ExifTool
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=head1 DESCRIPTION
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This module contains definitions required by Image::ExifTool to read
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metadata from Medical Research Council (MRC) images.
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=head1 AUTHOR
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Copyright 2003-2025, Phil Harvey (philharvey66 at gmail.com)
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This library is free software; you can redistribute it and/or modify it
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under the same terms as Perl itself.
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=head1 REFERENCES
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=over 4
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=item L<https://www.ccpem.ac.uk/mrc_format/mrc2014.php>
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=item L<http://legacy.ccp4.ac.uk/html/library.html>
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=item L<https://github.com/ccpem/mrcfile/blob/master/mrcfile/dtypes.py>
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=back
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=head1 SEE ALSO
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L<Image::ExifTool::TagNames/MRC Tags>,
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L<Image::ExifTool(3pm)|Image::ExifTool>
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=cut
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|