pwem.emlib.image.image_readers module

class pwem.emlib.image.image_readers.EMANImageReader

Bases: ImageReader

Image reader for eman file formats

static getCompatibleExtensions() → list

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

class pwem.emlib.image.image_readers.ImageReader

Bases: object

classmethod canOpenSlices()

Returns True if the reader can open slices optimally. Without loading the whole file. If so, openSlice method should be implemented

static getCompatibleExtensions() → list

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

classmethod open(path)

Opens the image in the path and returns a numpy array with the whole file (all slices included)

classmethod openSlice(path, slice)

Opens a specific slice

static write(images: ImageStack, fileName: str, isStack: bool) → None

Generate a stack of images or a volume from a list of PIL images. :param images: An ImageStack instance with one or more images :param fileName: Path of the new stack :param isStack: Specifies whether to generate a volume or an image stack

class pwem.emlib.image.image_readers.ImageReadersRegistry

Bases: object

Class to register image readers to provide basic information about an image like dimensions or getting an image

classmethod addReader(imageReader: ImageReader)

classmethod getAvailableExtensions()

Returns all the extensions it can handle

classmethod getReader(filePath) → ImageReader

Returns the reader or None able to deal with filePath based on the extension.

classmethod open(filePath) → ImageStack

Opens an image or image stack from the given file path.

This method serves as a public interface and delegates the actual loading to a cached internal method. It extracts the file last modification time (mtime) to ensure the cache is invalidated if the file changes.

Parameters:

filePath (str): Path to the image file. Can include a slice index in the format

‘1@path/to/image.ext’ to request a specific slice.

Returns:

ImageStack: The loaded image data, either a single slice or a full stack.

classmethod write(imgStack: ImageStack, fileName: str, isStack=False) → None

Generate a stack of images from a list of PIL images.

class pwem.emlib.image.image_readers.ImageStack(images=None, properties=None)

Bases: object

Class to hold image stacks. A single image is considered a stack of one image

Parameters

• images – either None, an image as returned by the readers or a list of them. Images are numpy arrays

• properties – optional: dictionary of key value pairs for header information for those files tha may need it

append(imgStack)

Appends to its local list of images the images inside the imgStack passed as parameter

classmethod asPilImage(npArray, normalize=True)

Returns the npArray a numpy image :param npArray: 2d numpy array (image) :param normalize: by default it has to be normalized. Cancel this is you are sure it hase been normalized before

flip(vertically=True)

Flip all images of an ImageStack horizontally or vertically. Vertically is up-down, horizontally is left-right.

flipH()

Flips this stack horizontally: left to right

classmethod flipSlice(npImage: ndarray, vertically=True)

flipV()

Flips this stack vertically: up to down

getCentralImage(pilImage=False)

Returns the central image

getImage(index=0, pilImage=False)

getImages()

Returns all the images

getProperties()

Returns the properties dictionary

getProperty(property)

Returns the property passed

highlight(stds=2)

Increases de contrast of all slices :param stds: number of STD to apply the contrast

classmethod highlightSlice(npImage: ndarray, stds=2)

Parameters

• npImage – image as 2d numpy array

• stds – number of STD to apply the contrast

invert()

Invert values of all slices

multiply(factor: float)

Multiplies the image stack by a factor :param: factor: to multiply values by it

normalize()

Normalize values of all slices

classmethod normalizeSlice(npImage)

rotate(angle, mode=ROT_MODE.FIXED, bg=None)

rotates all its images the angle (deg) passed and returns a new ImageStack rotated

classmethod rotateSlice(npArray: ndarray, angle: float, mode=ROT_MODE.CONDITIONAL, bg=None) → ndarray

Rotates a numpy array

scale(factors, anti_aliasing=True)

Scales the stack by the factors :param: factors: Scale factors for spatial dimensions.

classmethod scaleSlice(npImage, factors, anti_aliasing=True)

Scales the npImage by the factor/s :param npImage: 2d numpy array :param factors: float or sequence

The zoom factor along the axes. If a float, zoom is the same for each axis. If a sequence, zoom should contain one value for each axis.

Parameters

anti_aliasing –

shift(shifts)

Shifts the whole stack x and y returning a new stack.

Parameters

shift – The shift along the axes. If a float, shift is the same for each axis. If a sequence, shift should contain one value for each axis.

classmethod shiftSlice(image: ndarray, shifts: float, bg=None) → ndarray

Shifts a numpy array :param shifts = float or sequence. If a sequence, first value should be X shift and second Y shift

classmethod thumbnailSlice(npImage, width, height, normalize=True)

Calls PIl thumbnail. It is less precise but faster than scaleSlice

transform(shifts, angle, mode=ROT_MODE.FIXED)

rotates all its images the angle (deg) passed and returns a new ImageStack rotated

classmethod transformSlice(npImage: ndarray, shifts: float, angle: float, mode=ROT_MODE.FIXED, bg=None)

Apply the rotation and the shift to the npImage passed

write(path)

class pwem.emlib.image.image_readers.MRCImageReader

Bases: ImageReader

Image reader for MRC files

classmethod canOpenSlices()

Returns True if the reader can open slices optimally. Without loading the whole file. If so, openSlice method should be implemented

classmethod getArray(filename)

static getCompatibleExtensions() → list

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

classmethod getMrcImage(fileName)

classmethod isMrcStack(mrcImg)

classmethod isMrcVolume(mrcImg)

classmethod open(path: str)

Opens the image in the path and returns a numpy array with the whole file (all slices included)

classmethod openSlice(path, slice)

Reads a given image

:param path (str) –> Image to be read

classmethod write(imageStack: ImageStack, fileName: str, isStack: bool = False, samplingRate: Optional[float] = None) → None

Generate a stack of images or a volume from a list of images.

class pwem.emlib.image.image_readers.PILImageReader

Bases: ImageReader

PIL image reader

static getCompatibleExtensions() → list

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

classmethod open(filePath: str)

Opens the image in the path and returns a numpy array with the whole file (all slices included)

classmethod write(imgStack: ImageStack, fileName: str, isStack=False) → None

Generate a stack of images or a volume from a list of PIL images. :param images: An ImageStack instance with one or more images :param fileName: Path of the new stack :param isStack: Specifies whether to generate a volume or an image stack

class pwem.emlib.image.image_readers.ROT_MODE(value)

Bases: Enum

An enumeration.

CONDITIONAL = 3

FIXED = 1

NATURAL = 2

class pwem.emlib.image.image_readers.STKImageReader(fileName)

Bases: ImageReader

FLOAT32_BYTES = 4

HEADER_OFFSET = 1024

IMG_BYTES = None

TYPE = None

classmethod canOpenSlices()

Returns True if the reader can open slices optimally. Without loading the whole file. If so, openSlice method should be implemented

classmethod getArray(filename)

classmethod getCompatibleExtensions() → list

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

header_info = None

classmethod open(path)

Opens the full stack

classmethod openSlice(path, slice)

Reads a given image

:param filename (str) –> Image to be read

classmethod readAll(filename)

classmethod readBinary(start, end)

Read bytes between start and end

:param start (int) –> Start byte :param end (int) –> End byte :returns the bytes read

classmethod readHeader()

Reads the header of the current file as a dictionary

:returns The current header as a dictionary

classmethod readImage(iid)

Reads a given image in the stack according to its ID

:param iid (int) –> Image id to be read :returns Image as Numpy array

classmethod readNumpy(start, end)

Read bytes between start and end as a Numpy array

:param start (int) –> Start byte :param end (int) –> End byte :returns decoded bytes as Numpy array

classmethod seek(pos)

Move file pointer to a given position

:param pos (int) –> Byte to move the pointer to

stk_handler = None

class pwem.emlib.image.image_readers.TiffImageReader

Bases: ImageReader

Tiff image reader

static getCompatibleExtensions() → list

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

classmethod open(path: str)

Opens the image in the path and returns a numpy array with the whole file (all slices included)

classmethod write(imgStack: ImageStack, fileName: str, isStack=False) → None

Generate a stack of images or a volume from a list of PIL images. :param images: An ImageStack instance with one or more images :param fileName: Path of the new stack :param isStack: Specifies whether to generate a volume or an image stack

class pwem.emlib.image.image_readers.XMIPPImageReader

Bases: ImageReader

static getCompatibleExtensions()

Returns a list of the compatible extensions the reader can handle

static getDimensions(filePath)

Returns the dimensions [X,Y,Z,N] of the file

classmethod open(path)

Opens the image in the path and returns a numpy array with the whole file (all slices included)