Fiji image processing common tools

tools_fiji.py

# tools_fiji.py

from ij import ImagePlus, ImageStack, IJ

print('tools_fiji.py loaded.')


# Image load/save

# Open a list of files.
# Cause error if not all images have the same dimensions.
# return: ImagePlus
def load_images(paths):
    ip = IJ.openImage(paths[0]).getProcessor()
    w = ip.getWidth()
    h = ip.getHeight()
    stk = ImageStack(w, h)
    for path in paths[1:]:
        ip = IJ.openImage(path).getProcessor()
        stk.addSlice(ip)
    return stk


# return: ImagePlus
def load_image_folder(path):
    from ij.plugin import FolderOpener

    return FolderOpener().openFolder(path)


# return: ImagePlus
def load_avi(path, virtual=True):
    from ij.plugin import AVI_Reader

    return AVI_Reader().open(path, virtual)


#
# CSV files load/save.
#


# Loading a commma-separated file (CSV).
# path: Path to a file to save.
# delimiter: Delimiter of csv file.
# auto_skip: Skip n rows (including the first row),
#   where n (>= 1) is the value of the first column in the first row.
def load_csv(path, delimiter=',', auto_skip=True):
    import csv

    f = open(path, 'rU')
    rows = []
    reader = csv.reader(f, delimiter=delimiter)
    skipping = int(reader.next()[0]) if auto_skip else 0
    for _ in range(skipping - 1):
        reader.next()
    for row in reader:
        rows.append(row)
    f.close()
    return rows


def save_csv(path, rows, delimiter=','):
    import csv

    f = open(path, 'wb')
    print('Writing: %s' % path)
    writer = csv.writer(f, delimiter=delimiter)
    for row in rows:
        writer.writerow(row)
    f.close()


#
# Image measurements
#


# ip: ImageProcessor
# Return: [L, A, B] values.
def lab_mean_in_roi(ip, roi):
    ip.setRoi(*roi)
    ip2 = ip.crop()
    imp = ImagePlus("", ip2)
    IJ.run(imp, "RGB to CIELAB", "")
    imp2 = IJ.getImage()
    st = imp2.getStack()
    vs = []
    for i in [1, 2, 3]:
        ip = st.getProcessor(i).convertToFloatProcessor()
        stat = ip.getStatistics()
        vs.append(stat.mean)
    imp2.close()
    return vs


#
# Slice operations
#


# imp: ImagePlus
# n: 1-based index of slice to get
# Return: ImageProcessor
def get_slice(imp, n):
    return imp.getImageStack().getProcessor(n)


# imp: ImagePlus
# slices: a list of slice indices (1-based)
def remove_slices(imp, slices):
    stk = imp.getStack()
    slices = sorted(slices, reverse=True)
    num_slices = stk.getSize()
    for s in slices:
        if s <= num_slices:
            stk.deleteSlice(s)
    return imp


# imp: ImagePlus
# slices: a list of slice indices (1-based)
def take_slices(imp, slices):
    stk = imp.getStack()
    num_slices = stk.getSize()
    slices = diff(range(1, num_slices + 1), slices)
    slices = sorted(slices, reverse=True)
    remove_slices(imp, slices)
    return imp


def map_slices(func, imp, slices=None):
    stk = imp.getStack()
    num_slices = stk.getSize()
    if slices is None:
        slices = range(1, num_slices + 1)
    res = []
    for s in slices:
        imp.setSlice(s)
        res.append(func(imp))
    return res


# This is used in combination with map_slices.
# Return: a function that takes ImagePlus to return a line scan profile).
def linescan(x1, y1, x2, y2):
    from ij.gui import Line, ProfilePlot

    def f(imp):
        line = Line(x1, y1, x2, y2)
        imp.setRoi(line)
        vs = ProfilePlot(imp).getProfile()
        imp.killRoi()
        return vs

    return f


# This is used in combination with map_slices.
# Return: a function that takes ImagePlus to return a polyline scan profile).
def linescan_poly(xs, ys):
    def f(imp):
        from ij.gui import Line, Roi, ProfilePlot, PolygonRoi

        if len(xs) > 1:
            print(xs, ys)
            line = PolygonRoi(xs, ys, len(xs), Roi.POLYLINE)
            imp.setRoi(line)
        else:
            line = Line(xs[0], ys[0], xs[1], ys[1])
            imp.setRoi(line)
        vs = ProfilePlot(imp).getProfile()
        imp.killRoi()
        return vs

    return f


def remove_scale(imp):
    IJ.run(imp, "Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");


def crop(imp, w, h, x, y):
    IJ.run(imp, "Specify...", "width=%d height=%d x=%d y=%d" % (w, h, x, y))
    IJ.run(imp, "Crop", "")
    return imp


#
# List functions
#

def transpose(xss):
    return [list(i) for i in zip(*xss)]


def diff(a, b):
    b = set(b)
    return [aa for aa in a if aa not in b]


#
# Utility
#


def mayint(s):
    try:
        r = int(s)
    except:
        r = None
    return r