ImageIO#

class ImageIO(file=None)#

Reads and writes EM image files in em, mrc and raw formats.

Examples

Reading an image file:

>>> myImage = ImageIO()
>>> myImage.read(file='my_file.em')

Writing an image:

>>> myImage = ImageIO()
>>> myImage.write(file='my_file.em', data=my_array, header=my_header)

Attributes:

fileNamestr: The name of the file being processed.
file_file instance: File instance if it’s already open.

Attributes

`ImageIO.byte_order`
`ImageIO.em`
`ImageIO.emByteOrderTab`
`ImageIO.emByteOrderTabInv`
`ImageIO.emDataTypeTab`
`ImageIO.emDataTypeTabInv`
`ImageIO.emDefaultHeader`
`ImageIO.emDefaultShape`
`ImageIO.emHeaderFields`
`ImageIO.fileFormats`
`ImageIO.machineByteOrder`
`ImageIO.mrc`
`ImageIO.mrcDataTypeTab`
`ImageIO.mrcDataTypeTabInv`
`ImageIO.mrcDefaultHeader`
`ImageIO.mrcDefaultPixel`
`ImageIO.mrcDefaultShape`
`ImageIO.pixelsize`	Pixel size (at specimen level) in nm
`ImageIO.raw`
`ImageIO.tiltAngle`	Tilt angle (in deg)

Methods

`ImageIO.adjustLength`([shape, pixel])	Calculate the length based on shape and pixel size.
`ImageIO.checkFile`(file, mode)	Checks and possibly opens the file.
`ImageIO.fix`([mode, microscope])	Fix wrong values in both header and data.
`ImageIO.fixHeader`([mode, microscope])	Fix wrong values in the microscope image header.
`ImageIO.getFromEMHeader`(name)	Get the value of a variable from the EM header.
`ImageIO.getPixelsize`([diff])	Return pixel size at the specimen level in nanometers.
`ImageIO.getTiltAngle`()	Returns tilt angle in degrees.
`ImageIO.parseMRCHeader`([header])	Parse the MRC header.
`ImageIO.putInEMHeader`(name, value)	Update a value in the EM header.
`ImageIO.read`([file, fileFormat, byteOrder, ...])	Reads image file in em, mrc or raw data formats.
`ImageIO.readData`([shape, memmap])	Reads data from an image file.
`ImageIO.readEM`([file, byteOrder, dataType, ...])	Reads EM file format.
`ImageIO.readEMHeader`([file, byteOrder])	Reads the header of an EM file.
`ImageIO.readHeader`([file, fileFormat, byteOrder])	Reads the header of an image file in em, mrc or raw data formats.
`ImageIO.readMRC`([file, byteOrder, dataType, ...])	Reads MRC file format.
`ImageIO.readMRCHeader`([file, byteOrder])	Reads the header of an MRC file.
`ImageIO.readRaw`([file, dataType, shape, ...])	Read data from a raw file.
`ImageIO.readRawHeader`([file, size])	Read the header from a raw file.
`ImageIO.setData`(data[, shape, pixel])	Reshapes and saves data as an attribute.
`ImageIO.setFileFormat`([fileFormat, file_])	Sets the file format.
`ImageIO.setTiltAngle`(angle)	Set tilt angle for EM format files.
`ImageIO.write`([file, data, fileFormat, ...])	Writes image file with specified header and data.
`ImageIO.writeData`()	Writes data in numpy.ndarray format to an image file.
`ImageIO.writeEM`([file, header, byteOrder, ...])	Writes data to an EM file format.
`ImageIO.writeMRC`([file, header, byteOrder, ...])	Write data to an MRC file.
`ImageIO.writeRaw`([file, header, data, ...])	Writes raw data.