def greyReconstruction(img, mask, greyReconstructionParameter = None, method = None, size = 3, save = None, verbose = False,
subStack = None, out = sys.stdout, **parameter):
"""Calculates the grey reconstruction of the image
Reconstruction is done z-slice by z-slice.
Arguments:
img (array): image data
removeBackGroundParameter (dict):
========= ==================== ===========================================================
Name Type Descritption
========= ==================== ===========================================================
*method* (tuple or None) 'dilation' or 'erosion', if None return original image
*size* (int or tuple) size of structuring element
*save* (str or None) file name to save result of this operation
if None dont save to file
*verbose* (bool or int) print / plot information about this step
========= ==================== ===========================================================
subStack (dict or None): sub-stack information
verbose (bool): print progress info
out (object): object to write progress info to
Returns:
array: grey reconstructed image
"""
method = getParameter(greyReconstructionParameter, "method", method);
size = getParameter(greyReconstructionParameter, "size", size);
save = getParameter(greyReconstructionParameter, "save", save);
verbose= getParameter(greyReconstructionParameter, "verbose", verbose);
if verbose:
writeParameter(out = out, head = 'Grey reconstruction:', method = method, size = size, save = save);
if method is None:
return img;
timer = Timer();
# background subtraction in each slice
se = structureElement('Disk', size).astype('uint8');
for z in range(img.shape[2]):
#img[:,:,z] = img[:,:,z] - grey_opening(img[:,:,z], structure = structureElement('Disk', (30,30)));
#img[:,:,z] = img[:,:,z] - morph.grey_opening(img[:,:,z], structure = self.structureELement('Disk', (150,150)));
img[:,:,z] = img[:,:,z] - reconstruct(img[:,:,z], method = method, selem = se)
if not save is None:
writeSubStack(save, img, subStack = subStack)
if verbose > 1:
plotTiling(img);
if verbose:
out.write(timer.elapsedTime(head = 'Grey reconstruction:') + '\n');
return img
def removeBackground(img, removeBackgroundParameter = None, size = None, save = None, verbose = False,
subStack = None, out = sys.stdout, **parameter):
"""Remove background via subtracting a morphological opening from the original image
Background removal is done z-slice by z-slice.
Arguments:
img (array): image data
removeBackGroundParameter (dict):
========= ==================== ===========================================================
Name Type Descritption
========= ==================== ===========================================================
*size* (tuple or None) size for the structure element of the morphological opening
if None, do not correct for any background
*save* (str or None) file name to save result of this operation
if None dont save to file
*verbose* (bool or int) print / plot information about this step
========= ==================== ===========================================================
subStack (dict or None): sub-stack information
verbose (bool): print progress info
out (object): object to write progress info to
Returns:
array: background corrected image
"""
size = getParameter(removeBackgroundParameter, "size", size);
save = getParameter(removeBackgroundParameter, "save", save);
verbose = getParameter(removeBackgroundParameter, "verbose", verbose);
if verbose:
writeParameter(out = out, head = 'Background Removal:', size = size, save = save);
if size is None:
return img;
img = io.readData(img);
timer = Timer();
# background subtraction in each slice
se = structureElement('Disk', size).astype('uint8');
for z in range(img.shape[2]):
#img[:,:,z] = img[:,:,z] - grey_opening(img[:,:,z], structure = structureElement('Disk', (30,30)));
#img[:,:,z] = img[:,:,z] - morph.grey_opening(img[:,:,z], structure = self.structureELement('Disk', (150,150)));
img[:,:,z] = img[:,:,z] - cv2.morphologyEx(img[:,:,z], cv2.MORPH_OPEN, se)
if not save is None:
writeSubStack(save, img, subStack = subStack)
if verbose > 1:
plotTiling(10*img);
if verbose:
out.write(timer.elapsedTime(head = 'Background') + '\n');
return img
def greyReconstruction(img,
mask,
greyReconstructionParameter=None,
method=None,
size=3,
save=None,
verbose=False,
subStack=None,
out=sys.stdout,
**parameter):
"""Calculates the grey reconstruction of the image
Reconstruction is done z-slice by z-slice.
Arguments:
img (array): image data
removeBackGroundParameter (dict):
========= ==================== ===========================================================
Name Type Descritption
========= ==================== ===========================================================
*method* (tuple or None) 'dilation' or 'erosion', if None return original image
*size* (int or tuple) size of structuring element
*save* (str or None) file name to save result of this operation
if None dont save to file
*verbose* (bool or int) print / plot information about this step
========= ==================== ===========================================================
subStack (dict or None): sub-stack information
verbose (bool): print progress info
out (object): object to write progress info to
Returns:
array: grey reconstructed image
"""
method = getParameter(greyReconstructionParameter, "method", method)
size = getParameter(greyReconstructionParameter, "size", size)
save = getParameter(greyReconstructionParameter, "save", save)
verbose = getParameter(greyReconstructionParameter, "verbose", verbose)
if verbose:
writeParameter(out=out,
head='Grey reconstruction:',
method=method,
size=size,
save=save)
if method is None:
return img
timer = Timer()
# background subtraction in each slice
se = structureElement('Disk', size).astype('uint8')
for z in range(img.shape[2]):
#img[:,:,z] = img[:,:,z] - grey_opening(img[:,:,z], structure = structureElement('Disk', (30,30)));
#img[:,:,z] = img[:,:,z] - morph.grey_opening(img[:,:,z], structure = self.structureELement('Disk', (150,150)));
img[:, :, z] = img[:, :, z] - reconstruct(
img[:, :, z], method=method, selem=se)
if not save is None:
writeSubStack(save, img, subStack=subStack)
if verbose > 1:
plotTiling(img)
if verbose:
out.write(timer.elapsedTime(head='Grey reconstruction:') + '\n')
return img
