Package `scm_electron_microscopes`

Classes

class ZeissSEM (filename)

Class with convenience functions for the Zeiss EVO and Gemini SEMs. By default does not load the image into memory.

Parameters

filename : str: filename of the image to load. The file extension may be but is not required to be included.

Returns

ZeissSEM class instance

Methods

def export_metadata(self, filename=None)

save text file with metadata

Parameters

filename : str, optional: filename to store. The default is the image name with '_metadata.txt' appended.

def export_with_scalebar(self, filename=None, **kwargs)

saves an exported image of the SEM image with a scalebar in one of the four corners, where barsize is the scalebar size in data units (e.g. nm) and scale the overall size of the scalebar and text with respect to the width of the image.

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original SEM file, with '_exported.png' appended.

preprocess : callable, optional

callable to pre-process the image before any other processing is done, useful for e.g. smoothing. Must take and return a numpy.ndarray containing the image data as only arguments, and must not change e.g. the pixel size or the scale bar may be incorrectly sized. The default is None.

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

sets the unit in which the width and height in crop are specified when using the (x,y,w,h) format, with 'pixels' to give the size in pixels or 'data' to specify the size in the physical unit used for the scalebar (after optional unit conversion via the convert parameter). Note that the position of the top left corner is given in pixels. The ((xmin,ymin),(xmax,ymax)) format must be always given in pixels, and crop_unit is ignored if crop is given in this format. The default is 'pixels'.

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to crop and rescale. The default is True.

barsize : float or None, optional

size (in data units matching the original scale bar, e.g. nm) of the scale bar to use. The default None, wich takes the desired length for the current scale and round this to the nearest option from a list of "nice" values.

scale : float, optional

factor to change the size of the scalebar+text with respect to the width of the image. Scale is chosen such, that at scale=1 the font size of the scale bar text is approximately 10 pt when the image is printed at half the width of the text in a typical A4 paper document (e.g. two images side-by-side). The default is 1.

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : one of str, one of ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m']

Unit that will be used for the scale bar, the value will be automatically converted if this unit differs from the pixel size unit. The default is None, which uses the unit of the scalebar on the original image.

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_image(self)

loads the image data

Returns

PIL.Image instance

def get_metadata(self)

extracts embedded metadata from the image file

def get_pixelsize(self)

gets the physical size of a pixel from the metadata

Returns

pixelsize : float: physical size of the pixels in x and y
unit : str: physical unit corresponding to the pixelsize.

def print_metadata(self)

print formatted output of metadata

class helios (filename)

Set of convenience functions for the Helios SEM.

Parameters

filename : string: name of the file to load. Can but is not required to include .tif as extension.

Returns

helios class instance

Methods

def export_metadata(self, filename=None)

save text file with metadata

Parameters

filename : str, optional: filename to store. The default is the image name with '_metadata.txt' appended.

def export_with_scalebar(self, filename=None, **kwargs)

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original SEM file, with '_exported.png' appended.

preprocess : callable, optional

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to strip the original bar and crop. The default is True.

barsize : float or None, optional

scale : float, optional

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : str, one of ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m']

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_image(self)

load the image and split into image and databar

Returns

numpy.array: array of pixel values in the image (not including the data bar)

def get_metadata(self)

Load the metadata footer from Helios SEM files and return xml tree object which can be indexed for extraction of useful parameters. Does not require loading whole file into memory. Attempts first to find xml formatted data, if this is not found it looks for 'human' formatted metadata.

Returns

xml.etree.ElementTree root object: xml root object of the metadata. Can be printed using it as argument to print_metadata, or indexed with xml_root.find('<element name>').

def get_pixelsize(self)

gets the pixel size from the metadata and calculates the unit

Returns

pixelsize : tuple of float: the pixelsize in calibrated (physical) units in (x,y)
unit : string: the physical unit of the pixel size

def print_metadata(self)

print formatted output of metadata

class phenom (filename)

Set of convenience functions for the phenom SEM microscopes.

Parameters

filename : str: filename of the image to load

Returns

phenom class instance

Methods

def export_metadata(self, filename=None)

save text file with metadata

Parameters

filename : str, optional: filename to store. The default is the image name with '_metadata.txt' appended.

def export_with_scalebar(self, filename=None, **kwargs)

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original SEM file, with '_exported.png' appended.

preprocess : callable, optional

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to strip the original bar and crop. The default is True.

barsize : float or None, optional

scale : float, optional

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : str, one of ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m']

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_image(self)

load the image and split into image and databar

def get_metadata(self)

Returns

xml.etree.ElementTree object: xml root object of the metadata. Can be printed using it as argument to print_metadata, or indexed with xml_root.find('')

def get_pixelsize(self)

gets the pixel size from the metadata and calculates the unit

Returns

pixelsize : (y,x) tuple of float: physical size of the pixels
unit : str: physical unit corresponding to the pixelsize.

def print_metadata(self)

print formatted output of metadata

class sis (filename)

Set of convenience functions for electron microscopy images of the now defunct tecnai 10 microscope which operated the Olympus Soft Imaging System software (analySIS) which exported to .tif. Initializing the class takes a string containing the filename as only argument, and by default loads in the image.

Parameters

filename : string: name of the file to load. Can but is not required to include .tif as extension.

Methods

def export_with_scalebar(self, filename=None, **kwargs)

saves an exported image of the TEM image with a scalebar in one of the four corners, where barsize is the scalebar size in data units (e.g. nm) and scale the overall size of the scalebar and text with respect to the width of the image.

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original TEM file, with '_exported.png' appended.

preprocess : callable, optional

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

intensity_range : tuple or None or 'automatic'

tuple of (lower,upper) ranges for the (original) pixel values to scale the brightness/contrast in the image to, or 'automatic' to autoscale the intensity to the 0.01th and 99.99th percentile of the input image, or None for the min and max value in the original image. The default is None.

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to strip the original bar and crop. The default is True.

barsize : float or None, optional

scale : float, optional

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : str, one of ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m']

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_metadata(self)

Loads metadata from the file.

NOT IMPLEMENTED

def get_pixelsize(self, convert=None)

Gets the physical size represented by the pixels from the image metadata

Parameters

convert : one of ['m', 'mm', 'um', 'µm', 'nm', 'pm', None], optional: physical unit to use for the pixel size. The default is None, which chooses one of the above automatically based on the value.

Returns

pixelsize : float: the physical size of a pixel in the given unit
unit : str: physical unit of the pixel size

class talos (*args, **kwargs)

Deprecated

The tecnai and Talos classes have been renamed to the tia class to avoid confusion between data aquired using the older TIA and newer Velox software from version 3.0.0 onwards. The old names are available for backwards compatibility and should behave identically, but their use is discouraged.

Class of functions for TEM images from the Talos microscopes operated with the TIA software

Parameters

filename : string: name of the file to load. Can but is not required to include .tif as extension.

Attributes

filename : string: name of the image file
image : np.ndarray: array of pixel values of the image with the optional data/scale bar cropped off
scalebar : numpy.ndarray: if present, the array of pixel values of the original data/scale bar
shape : tuple: shape in (y,x) pixels of the image array
dtype : numpy.dtype: data type of the pixel values, generally unint8 or uint16
PIL_image : PIL.Image: python imaging library Image object of the image file

Returns

tia class instance

Subclasses

scm_electron_microscopes.tem.talos
scm_electron_microscopes.tem.tecnai

Methods

def export_metadata(self, filename=None)

save text file with metadata

Parameters

filename : str, optional: filename to store. The default is the image name with '_metadata.txt' appended.

def export_with_scalebar(self, filename=None, **kwargs)

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original TEM file, with '_exported.png' appended.

preprocess : callable, optional

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

intensity_range : tuple or None or 'automatic', optional

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to strip the original bar and crop. The default is True.

barsize : float or None, optional

scale : float, optional

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : str, one of ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m']

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_metadata(self, asdict=False)

loads xml metadata from .tif file and returns xml tree object or dict

Parameters

asdict : bool, optional: whether to export as a dictionary. When False, an xml.etree.ElementTree is returned. The default is False.

Returns

dictionary or xml root object: dictionary or xml root object of the metadata. Can be indexed with xml_root.find('')

def get_pixelsize(self, convert=None)

Gets the physical size represented by the pixels from the image metadata

Parameters

convert : str, one of [fm,pm,Å,'A',nm,um,µm,mm,cm,dm,m], optional: physical unit to use for the pixel size. The default is None, which chooses one of the above automatically based on the value.

Returns

pixelsize : float: the physical size of a pixel in the given unit
unit : str: physical unit of the pixel size

def get_pixelsize_legacy(self, debug=False, use_legacy_measurement=False)

Deprecated

This function has been deprecated and may give slightly inaccurate result (only accurate to the nearest whole pixel), use tia.get_pixelsize() for more accurate and faster calibration. Included for cases where results using the previous calibration method must be reproduced or compared with.

Reads the scalebar from images of the Tecnai or Talos TEM microscopes using text recognition via pytesseract or with manual input when pytesseract is not installed

Parameters

debug : bool, optional: enable debug mode which prints extra information and figures to troubleshoot any issues with calibration. The default is False.
use_legacy_measurement : bool, optional: if True, use the (incorrect) left-side to left-side distance of the vertical lines of the scale bar (i.e. equal to the centre-to-centre distance of the vertical parts of the line). This was long thought to be the correct way to interpret the scale bar and is available for backwards compatability with older data (analysis). The default is False, which uses the outermost white pixels of the scale bar, i.e. from the leftmost row of white pixels of the left vertical part to the rightmost row of the right vertical part.

Returns

pixelsize : float: the pixelsize in calibrated (physical) units
unit : string: the physical unit of the pixelsize

def print_metadata(self)

prints formatted output of the file's metadata

class util

utility functions

Methods

def image_histogram(image, binsize=1, log=True)

plot histogram of the image grey values

Parameters

image : numpy.array-like: the image to calculate the intensity histogram for.
binsize : float-like, optional: width (in intensity units) of the bins to use. The default is 1.
log : bool, optional: Whether to plot the histogram y axis on a log scale. The default is True.

def print_metadata(xml_root)

print xml attributes/tags of phenom data to inspect elements.

Parameters

xml_root : xml root object: Takes output of get_metadata() and prints formatted metadata to the terminal

class velox (filename=None, quiet=False)

Class for importing the .emd file format used natively by the Velox software used on the Talos microscopes.

Note that one .emd file may contain multiple images / videos, (e.g. when recording with multiple detectors simultaneously), and most functions are available through the velox_image subclass accessible through the get_image function.

Parameters

filename : str or int: The filename to load, extension optional. Alternatively an integer may be given to load the nth file in the current working directory. The default is to load the first file.
quiet : bool: whether to print a list of images contained in the file when the class is initialized. The default is False.

Returns

velox class instance

init class instance, open file container

Methods

def get_dataset(self, dataset)

Returns velox_image class instance containing all data and metadata for a particular image in the file.

Parameters

image : str or int: the image to return the data for, given as the name/tag (when str) or as its integer index in the file, i.e. velox.get_image(0) returns the data container for the first image.

Returns

velox_dataset or velox_image class instance

def print_file_struct(self)

prints a formatted overview of the structure of the .emd file container, useful for accessing additional data manually

class velox_edx (parent, im)

subclass for emd files with edx data

Ancestors

scm_electron_microscopes.tem.velox_dataset

Methods

def get_image(self, energy_ranges=None, frame_range=None, binning=1)

returns edx/eds image where the pixel value is the total number of photon counts within the specified energy range(s) and frame range.

Parameters

energy_ranges : list of tuples, optional: List of (min,max) energy range(s) specifying which photons to count, given in keV. The default is None which takes all photon counts.
frame_range : tuple, optional: Tuple of (min,max) for the frame indices to sum the counts for. The default is None which sums all frames.

Returns

2D numpy.array

def get_spectrum(self)

get overall spectral data for the edx dataset

Returns

energies : numpy.array: energies in keV
counts : numpy.array: number of photon counts per energy

class velox_image (parent, im)

Subclass of the velox_dataset class for individual images (or image series) in an .emd file, such as when simultaneously recording HAADF-STEM and BF-STEM. Not indended to be called directly, rather to be initialized trough the get_image method of the velox class.

Parameters

filename : str: the .emd file to take the image from
im : str or int: name / tag or integer index of the image to initialize

Ancestors

scm_electron_microscopes.tem.velox_dataset

Methods

def export_tiff(self, filename_prefix=None, frame_range=None, **kwargs)

stores the image data to a tiff file with metadata stored in the image description for futher processing or viewing in other software.

Parameters

filename_prefix : str: filename to use for saved file without file extension
frame_range : int or tuple of int: int specifying which frame, or tuple of (start,stop) ints specifying which frames, to save in the tiff file. The default is all frames in the dataset
kwargs : dict: any further keyword arguments will be passed on to tifffile.imsave.

Returns

None.

def export_with_scalebar(self, frame=0, filename=None, **kwargs)

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original TEM file, with '_exported.png' appended.

frame : int

the frame to export, see get_frame(). The default is 0.

preprocess : callable, optional

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

intensity_range : tuple or None or 'automatic'

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to strip the original bar and crop. The default is True.

barsize : float or None, optional

scale : float, optional

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : str, one of ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m'], optional

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_data(self)

Loads and returns the full image data as numpy array

Returns

numpy.ndarray of pixel value
s

def get_frame(self, i)

returns specific image / video frame from the dataset

Parameters

i : int: the index of the frame to load

Returns

numpy.array of pixel values

def get_frametime(self)

Returns the time in seconds it takes to scan one frame

Returns

float

def get_pixelsize(self, convert=None)

returns the pixel size from the metadata, rescaled to an appropriate unit for convenience

Parameters

convert : one of ['pm', 'nm', 'µm', 'um', 'mm', 'm']: physical data unit to convert the pixel size to, the default is None which chooses a unit based on the magnitude.

Returns

pixelsize : tuple of float: (y,x) pixel sizes
unit : str: physical unit of the pixel size

class xl30sfeg (filename)

Set of convenience functions for the xl30sfeg SEM microscope.

Parameters

filename : str: filename of the image to load

Returns

xl30sfeg class instance

Methods

def export_with_scalebar(self, filename=None, **kwargs)

Parameters

filename : string or None, optional

Filename + extension to use for the export file. The default is the filename sans extension of the original SEM file, with '_exported.png' appended.

preprocess : callable, optional

crop : tuple or None, optional

range describing a area of the original image (before rescaling the resolution) to crop out for the export image. Can have two forms:

((xmin,ymin),(xmax,ymax)), with the integer pixel indices of the top left and bottom right corners respectively.
(xmin,ymin,w,h) with the integer indices of the top left corner and the width and heigth of the cropped image in pixels (prior to optional rescaling using resolution). When this format is used, it is possible to set the width and height in pixels (default) or in data units via the crop_unit parameter.

The default is None which takes the entire image.

crop_unit : 'pixels' or 'data', optional

resolution : int, optional

the resolution along the x-axis (i.e. image width in pixels) to use for the exported image. The default is None, which uses the size of the original image (after optional cropping using crop).

draw_bar : boolean, optional

whether to draw a scalebar on the image, such that this function may be used just to strip the original bar and crop. The default is True.

barsize : float or None, optional

scale : float, optional

loc : int, one of [0,1,2,3], optional

Location of the scalebar on the image, where 0, 1, 2 and 3 refer to the top left, top right, bottom left and bottom right respectively. The default is 2, which is the bottom left corner.

convert : str, ['fm','pm','Å' or A,'nm','µm' or 'um','mm','cm','dm','m']

font : str, optional

filename of an installed TrueType font ('.ttf' file) to use for the text on the scalebar. The default is 'arialbd.ttf'.

fontsize : int, optional

base font size to use for the scale bar text. The default is 16. Note that this size will be re-scaled according to resolution and scale.

fontbaseline : int, optional

vertical offset for the baseline of the scale bar text from the top of the scale bar, in printer points. The default is 10.

fontpad : int, optional

minimum size in printer points of the space/padding between the text and the bar and surrounding box. The default is 10.

barthickness : int, optional

thickness in printer points of the scale bar itself. The default is 16.

barpad : int, optional

size in printer points of the padding between the scale bar and the surrounding box. The default is 10.

box : bool, optional

Whether to put a semitransparent box around the scalebar and text to enhance contrast. The default is True.

boxalpha : float, optional

value between 0 and 1 for the opacity (inverse of transparency) of the box behind the scalebar and text when box=True. The default is 0.8.

invert : bool, optional

If True, a white scalebar and text on a black box are used. The default is False which gives black text on a white background.

boxpad : int, optional

size of the space/padding around the box (with respect to the sides of the image) in printer points. The default is 10.

store_settings : bool, optional

when True, a .txt file is saved along with the image containing all settings passed to this function. The default is False

def get_image(self)

load the image and (if present) scalebar

def get_metadata(self)

Load the metadata footer from XL30SFEG SEM files and return xml tree object which can be indexed for extraction of useful parameters. Does not require loading whole file into memory. Searches for 'human' formatted metadata.

Returns

xml_root : xml.etree.ElementTree object: xml root object of the metadata. Can be printed using it as argument to print_metadata, or indexed with xml_root.find('')

def get_pixelsize(self)

gets the pixel size from the metadata and calculates the unit

Returns

pixelsize : float: physical size of the pixels in x and y
unit : str: physical unit corresponding to the pixelsize.

def print_metadata(self)

print formatted output of metadata

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