roi

roi#

class pyleem.roi.ROIMeasurement(mean, total, minimum, maximum, n_pixels, profile=None)[source]#

Bases: object

ROI measurement result.

Parameters:

  • mean (float)

  • total (float)

  • minimum (float)

  • maximum (float)

  • n_pixels (int)

  • profile (ndarray | None)

pyleem.roi.measure_values(values, profile=None)[source]#

Measure intensity statistics from selected values.

class pyleem.roi.ROI(roi_file=None)[source]#

Bases: ABC

Abstract base class for ImageJ-compatible regions of interest.

Parameters:

roi_file (str | None)

validate()[source]#

Validate ROI parameters.

validate_roi_type(roi, expected_type)[source]#

When loading from roi file, validate the ROI type.

abstractmethod measure(image, **kwargs)[source]#

Measure image properties.

abstractmethod profile(image, **kwargs)[source]#

Extract profile data from image.

abstractmethod fromfile(roi)[source]#

Load ROI from ImageJ file.

abstractmethod tofile(filename)[source]#

Save ROI to roifile.ImagejRoi file.

Use roi.tofile(filename) to save the ROI to a file.

class pyleem.roi.NoROI(roi_file=None)[source]#

Bases: ROI

NoROI placeholder for analyzer.

Parameters:

roi_file (str | None)

measure(image, **kwargs)[source]#

Measure image intensity.

profile(image, **kwargs)[source]#

Extract line profile from image.

fromfile(roi)[source]#

Load ROI from roifile.ImagejRoi object.

tofile(filename)[source]#

Save ROI to roifile.ImagejRoi file.

class pyleem.roi.LineROI(roi_file=None, src=None, dst=None, linewidth=None)[source]#

Bases: ROI

Line ROI for use with skimage.measure.profile_line.

Variables:

  • src (tuple) – Starting point (y, x) in image coordinates.

  • dst (tuple) – Ending point (y, x) in image coordinates.

  • linewidth (int) – Width of line profile in pixels.

  • order (int) – Interpolation order (1 for linear).

  • mode (str) – How to handle values outside image.

  • cval (float) – Fill value for ‘constant’ mode.

  • reduce_func (callable) – Function to aggregate values across line width.

Parameters:

  • roi_file (str | None)

  • src (tuple)

  • dst (tuple)

  • linewidth (int)

validate()[source]#

Validate line ROI parameters.

profile(image, **kwargs)[source]#

Extract line profile from image.

measure(image, **kwargs)[source]#

Measure image intensity along the ROI.

fromfile(roi)[source]#

Load ROI from roifile.ImagejRoi object.

tofile(filename)[source]#

Save to roifile.ImagejRoi object.

class pyleem.roi.AreaROI(roi_file=None)[source]#

Bases: ROI

Base class for area regions of interest.

Parameters:

roi_file (str | None)

abstractmethod mask(shape)[source]#

Return the selected pixels as a boolean mask.

profile(image, **kwargs)[source]#

Return a profile for the area ROI, if available.

measure(image, **kwargs)[source]#

Measure image intensity inside the ROI.

class pyleem.roi.RectROI(roi_file=None, top=None, left=None, bottom=None, right=None)[source]#

Bases: AreaROI

Rectangular area ROI.

Parameters:

  • roi_file (str | None)

  • top (int)

  • left (int)

  • bottom (int)

  • right (int)

property height#

Return the height of the ROI.

property width#

Return the width of the ROI.

fromfile(roi)[source]#

Load ROI from roifile.ImagejRoi object.

validate()[source]#

Validate rectangular ROI parameters.

mask(shape)[source]#

Return the selected pixels as a boolean mask.

tofile(filename)[source]#

Save to roifile.ImagejRoi object.

class pyleem.roi.OvalROI(roi_file=None, top=None, left=None, bottom=None, right=None)[source]#

Bases: AreaROI

Oval area ROI.

Parameters:

  • roi_file (str | None)

  • top (int)

  • left (int)

  • bottom (int)

  • right (int)

property height#

Return the height of the ROI.

property width#

Return the width of the ROI.

fromfile(roi)[source]#

Load ROI from roifile.ImagejRoi object.

validate()[source]#

Validate oval ROI parameters.

mask(shape)[source]#

Return the selected pixels as a boolean mask.

tofile(filename)[source]#

Save to roifile.ImagejRoi object.

class pyleem.roi.PolygonROI(roi_file=None, rows=None, cols=None)[source]#

Bases: AreaROI

Polygon area ROI.

Parameters:

  • roi_file (str | None)

  • rows (tuple)

  • cols (tuple)

validate()[source]#

Validate polygon ROI parameters.

mask(shape)[source]#

Return the selected pixels as a boolean mask.

fromfile(roi)[source]#

Load ROI from roifile.ImagejRoi object.

tofile(filename)[source]#

Save to roifile.ImagejRoi object.