def bleb_area(membrane_edge, midpoint_anchor):
"""calculate the area of the drawn bleb, accounting for membrane crossing line joining anchors"""
poly = membrane_edge.getFloatPolygon()
xs = [x for x in poly.xpoints]
ys = [y for y in poly.ypoints]
rotangle = membrane_edge.getAngle(int(round(xs[0])), int(round(
ys[0])), int(round(xs[-1])), int(round(ys[-1]))) / 180 * math.pi
rotY = [(x * math.sin(rotangle) + y * math.cos(rotangle))
for x, y in zip(xs, ys)]
rotYmpa = midpoint_anchor[0] * math.sin(
rotangle) + midpoint_anchor[1] * math.cos(rotangle)
meanRotY = sum(rotY) / len(rotY)
seg1 = rotY[:int(round(len(rotY) / 2))]
seg1.reverse()
seg2 = rotY[int(round(len(rotY) / 2)):]
if rotYmpa > rotY[0]:
idx1 = len(seg1) - seg1.index(min(seg1))
idx2 = int(round(len(rotY) / 2)) + seg2.index(min(seg2))
else:
idx1 = len(seg1) - seg1.index(max(seg1))
idx2 = int(round(len(rotY) / 2)) + seg2.index(max(seg2))
area_poly_xs = xs[idx1:idx2 + 1]
area_poly_ys = ys[idx1:idx2 + 1]
len_roi = PolygonRoi(area_poly_xs, area_poly_ys, Roi.POLYLINE)
length = len_roi.getLength()
area_roi = PolygonRoi(area_poly_xs, area_poly_ys, Roi.POLYGON)
area = area_roi.getStatistics().area
#print(area);
return length, area, area_roi
def do_unwrap(tile_imp, unwrap_axis, imp_title=None):
"""given an unwrap axis extending from top to bottom of an image, generate an unwrapped image"""
ip = tile_imp.getProcessor()
ip.setValue(0)
unwrap_poly_xs = [x for x, y in unwrap_axis]
unwrap_poly_ys = [y for x, y in unwrap_axis]
if sum(unwrap_poly_xs) / len(unwrap_poly_xs) > 1.5 * 360:
rhs_poly_xs = unwrap_poly_xs
else:
rhs_poly_xs = [x + 360 for x in unwrap_poly_xs]
for _ in range(2):
rhs_poly_xs.append(0)
unwrap_poly_ys.append(unwrap_poly_ys[-1])
unwrap_poly_ys.append(unwrap_poly_ys[0])
crop_roi = PolygonRoi(rhs_poly_xs, unwrap_poly_ys, Roi.POLYGON)
ip.fillOutside(crop_roi)
ip.setRoi(crop_roi)
ip = ip.crop()
ip.setValue(0)
lhs_poly_xs = [x - 360 for x in rhs_poly_xs[:-2]]
for _ in range(2):
lhs_poly_xs.append(ip.getWidth())
crop_roi = PolygonRoi(lhs_poly_xs, unwrap_poly_ys, Roi.POLYGON)
ip.fillOutside(crop_roi)
ip.setRoi(crop_roi)
ip = ip.crop()
tile_imp.setProcessor(ip)
tile_imp.updateAndRepaintWindow()
if imp_title is not None:
tile_imp.setTitle("{}, twisted and unwrapped".format(imp_title))
else:
tile_imp.setTitle("twisted and unwrapped")
return tile_imp
def trackEnds(imageID, maskID):
index = RoiManager.getInstance2().getSelectedIndex()
inputIMP = WindowManager.getImage(imageID)
maskIMP = WindowManager.getImage(maskID)
points1 = inputIMP.getOverlay().get(0).getContainedPoints()[index]
points2 = inputIMP.getOverlay().get(1).getContainedPoints()[index]
roi = maskIMP.getOverlay().get(index)
outerBounds = roi.getBounds()
impMT, innerBounds = duplicateMaskInRoi(maskIMP, roi, True)
centroid = impMT.getOverlay().get(0).getContourCentroid()
nr, endPoint1, endPoint2 = findEndPointsInSkeleton(impMT)
track1 = trackEnd(impMT, endPoint1, centroid);
track2 = trackEnd(impMT, endPoint2, centroid);
impMT.changes=False
impMT.close()
newTrack1 = []
for point in track1:
newTrack1.append((point.x + outerBounds.x + innerBounds.x - 1,
point.y + outerBounds.y + innerBounds.y - 1))
newTrack2 = []
for point in track2:
newTrack2.append((point.x + outerBounds.x + innerBounds.x - 1,
point.y + outerBounds.y + innerBounds.y - 1))
track1X = [point[0] for point in newTrack1]
track1Y = [point[1] for point in newTrack1]
roiTrack1 = PolygonRoi(track1X, track1Y, Roi.POLYLINE)
inputIMP.getOverlay().add(roiTrack1)
track2X = [point[0] for point in newTrack2]
track2Y = [point[1] for point in newTrack2]
roiTrack2 = PolygonRoi(track2X, track2Y, Roi.POLYLINE)
inputIMP.getOverlay().add(roiTrack2)
inputIMP.repaintWindow()
def get_membrane_edge(roi, fixed_anchors, fixed_midpoint):
"""figure out which edge of the roi is the membrane, since IJ might start the roi from anywhere along the perimeter w.r.t. the user defined anchors"""
poly = roi.getInterpolatedPolygon(0.25, False)
term_index_1 = [(x, y) for x, y in zip(poly.xpoints, poly.ypoints)
].index(fixed_anchors[0])
term_index_2 = [(x, y) for x, y in zip(poly.xpoints, poly.ypoints)
].index(fixed_anchors[1])
start_idx = min(term_index_1, term_index_2)
end_idx = max(term_index_1, term_index_2)
xs = [x for x in poly.xpoints]
ys = [y for y in poly.ypoints]
e1 = FloatPolygon(xs[start_idx:end_idx + 1], ys[start_idx:end_idx + 1])
e2 = FloatPolygon(list(reversed(xs[end_idx:] + xs[:start_idx + 1])),
list(reversed(ys[end_idx:] + ys[:start_idx + 1])))
anchors_midpoint = (int(
round(0.5 * (fixed_anchors[1][0] + fixed_anchors[0][0]))),
int(
round(
0.5 *
(fixed_anchors[1][1] + fixed_anchors[0][1]))))
e1_mean = (sum(e1.xpoints) / e1.npoints, sum(e1.ypoints) / e1.npoints)
e2_mean = (sum(e2.xpoints) / e2.npoints, sum(e2.ypoints) / e2.npoints)
theta_e1 = angle_between_vecs(fixed_anchors[0], fixed_anchors[1],
fixed_anchors[0], e1_mean)
#print("Angle between anchor line and anchor0 to e1mean pos = " + str(theta_e1));
theta_e2 = angle_between_vecs(fixed_anchors[0], fixed_anchors[1],
fixed_anchors[0], e2_mean)
#print("Angle between anchor line and anchor0 to e2mean pos = " + str(theta_e2));
sign = lambda x: (1, -1)[x < 0]
if sign(theta_e1) is not sign(theta_e2):
#print("using angle to decide on edge ID - vectors linking anchor1 and mean edge positions lie on either side of anchor line");
theta_midpoint = angle_between_vecs(fixed_anchors[0], fixed_anchors[1],
fixed_anchors[0], fixed_midpoint)
#print("Angle between anchor line and anchor0 to manual midpoint pos = " + str(theta_midpoint));
(use_edge, other_edge) = (e2, e1) if (sign(theta_midpoint)
== sign(theta_e2)) else (e1, e2)
else:
#print("using distance to decide on edge ID - vectors linking anchor1 and mean edge position lie on same side of anchor line");
#print("position anchor midpoint = " + str(anchors_midpoint));
#print("position e1 mean = " + str(e1_mean));
#print("length anchor midpoint to e1 mean = " + str(vector_length(anchors_midpoint, e1_mean)));
#print("position e2 mean = " + str(e2_mean));
#print("length anchor midpoint to e2 mean = " + str(vector_length(anchors_midpoint, e2_mean)));
#if (vector_length(anchors_midpoint, e1_mean) > vector_length(anchors_midpoint, e2_mean)):
# print("Using e1");
#else:
# print("Using e2");
(use_edge, other_edge) = (e1, e2) if (
vector_length(anchors_midpoint, e1_mean) > vector_length(
anchors_midpoint, e2_mean)) else (e2, e1)
use_roi = PolygonRoi(use_edge, Roi.POLYLINE)
other_roi = PolygonRoi(other_edge, Roi.POLYLINE)
return use_roi, other_roi
def scaleTypeROI(roi): if isinstance(roi,PointRoi): p=roi.getFloatPolygon() x,y=list(p.xpoints),list(p.ypoints) xNew,yNew=map(lambda c:c*scale[0],x),map(lambda c:c*scale[1],y) roiNew=PointRoi(xNew,yNew) elif isinstance(roi,ShapeRoi): roiSels=roi.getRois() roiNews=map(scaleTypeROI,roiSels) roiNew=0 for roi in roiNews: if roiNew==0: roiNew=ShapeRoi(roi) else: roiNew=roiNew.or(ShapeRoi(roi)) else: tp=roi.getType() if tp!=0: p=roi.getPolygon() x,y=list(p.xpoints),list(p.ypoints) posNew=map(lambda pos:(pos[0]*scale[0],pos[1]*scale[1]),zip(x,y)) xNew,yNew=zip(*posNew) roiNew=PolygonRoi(xNew,yNew,tp) else: x,y,w,h=roi.getXBase(),roi.getYBase(),roi.getFloatWidth(),roi.getFloatHeight() xNew,yNew,wNew,hNew=x*scale[0],y*scale[1],w*scale[0],h*scale[1] roiNew=Roi(xNew,yNew,wNew,hNew) return(roiNew)
def parse_roistr_to_roi(self):
"""interpret string saved in parameters JSON as IJ ROI"""
from ij.gui import PolygonRoi, Roi
rect_format_str = "java.awt.Rectangle\[x=(?P<x>\d+)\,y=(?P<y>\d+)\,width=(?P<w>\d+)\,height=(?P<h>\d+)\]"
m1 = re.match(rect_format_str, self.spatial_crop)
if bool(m1):
return Roi(int(m1.groupdict()['x']), int(m1.groupdict()['y']),
int(m1.groupdict()['w']), int(m1.groupdict()['h']))
else:
# if original ROI wasn't a rectangle...
if isinstance(self.spatial_crop, str):
str_list = self.spatial_crop[2:-2].split('), (')
poly_format_str = '(?P<x>\d+)\, (?P<y>\d+)'
xs = []
ys = []
for s in str_list:
m2 = re.match(poly_format_str, s)
if bool(m2):
xs.append(float(m2.groupdict()['x']))
ys.append(float(m2.groupdict()['y']))
else:
xs = [x for (x, y) in self.spatial_crop]
ys = [y for (x, y) in self.spatial_crop]
if len(xs) > 0:
return PolygonRoi(xs, ys, Roi.POLYGON)
else:
return None
def prune_branch(self, i): # i >= 1
if i == 0:
return
temp_min, stemx, stemy, stem_index, branchx, branchy, branch_index = self.get_coord_min_distance(
i)
poly = self.roi_array[i].getFloatPolygon()
poly_npoints = poly.npoints
poly_index = branch_index
if poly_npoints / 2 >= poly_index:
# print 'if', i+1
newx = poly.xpoints[poly_index:]
newy = poly.ypoints[poly_index:]
new_poly = FloatPolygon(newx, newy)
else:
# print 'else', i+1
newx = reversed(poly.xpoints[:poly_index + 1])
newy = reversed(poly.ypoints[:poly_index + 1])
new_poly = FloatPolygon(newx, newy)
new_roi = PolygonRoi(new_poly, Roi.POLYLINE)
new_roi.fitSpline()
self.RoiManager.setRoi(new_roi, i)
def selectionInterpolateAndFitSpline(roi, interval=1.0, smooth=True):
"""implement IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust");IJ.run(imp, "Fit Spline", "");"""
roi = PolygonRoi(roi.getInterpolatedPolygon(-1.0 * interval, smooth),
Roi.FREELINE)
if roi.subPixelResolution():
roi = selectionTrimFloatPolygon(roi, roi.getUncalibratedLength())
else:
roi = selectionTrimPolygon(roi, roi.getUncalibratedLength())
roi.fitSpline()
return roi
def check_edge_order(anchors, edge):
"""Check that edge runs from first anchor to second as expected"""
poly = edge.getPolygon()
start = (poly.xpoints[0], poly.ypoints[0])
if vector_length(start, anchors[0]) > vector_length(start, anchors[1]):
xs = [x for x in poly.xpoints]
ys = [y for y in poly.ypoints]
xs.reverse()
ys.reverse()
edge = PolygonRoi(xs, ys, Roi.POLYLINE)
return edge
def get_convexfull_area(self, i, imp=IJ.getImage()):
convexfull = self.roi_array[i].getFloatConvexHull()
convexfull_roi = PolygonRoi(convexfull, Roi.POLYGON)
imp.setRoi(convexfull_roi)
moptions = Measurements.MEAN | Measurements.INTEGRATED_DENSITY | Measurements.AREA
ip = imp.getProcessor()
cal = Calibration(imp)
stat = ImageStatistics.getStatistics(ip, moptions, cal)
convexfull_are = stat.area
return convexfull_are
def read_vl_file(file_path, cal) :
coord_col_dict = br.csv_to_col_dict(file_path, cast_type=float)
cal_func_dict = {'X' : cal.getRawX, 'Y' : cal.getRawY}
for col_name, cal_func in zip(coord_col_dict.keys(), cal_func_dict.values()) :
for i in range(len(coord_col_dict[col_name])) :
coord_col_dict[col_name][i] = cal_func(coord_col_dict[col_name][i])
vl_roi = PolygonRoi(coord_col_dict['X'], coord_col_dict['Y'],len(coord_col_dict['X']),Roi.POLYGON)
return vl_roi
def load_qcd_edges(input_file_path):
"""load edges from JSON"""
f = open(input_file_path, 'r')
try:
edges = json.loads(f.read())
finally:
f.close()
membrane_edges = []
for edge in edges:
xs = [pt[0] for pt in edge]
ys = [pt[1] for pt in edge]
membrane_edges.append(PolygonRoi(xs, ys, Roi.POLYLINE))
return membrane_edges
def get_distance_from_stem(self, i):
if i == 0:
return 0
min_len, stemx, stemy, stem_index, _1, _2, _3 = self.get_coord_min_distance(
i)
stem_x_array = self.roi_array[0].getFloatPolygon().xpoints[:stem_index]
stem_y_array = self.roi_array[0].getFloatPolygon().ypoints[:stem_index]
new_poly = FloatPolygon(stem_x_array, stem_y_array)
new_roi = PolygonRoi(new_poly, Roi.POLYLINE)
new_roi.fitSpline()
return get_roi_length(new_roi)
def generate_cell_shape_results(rois,
intensity_channel_imp,
cal,
file_name,
no_nuclei_centroids=None,
no_enclosed_nuclei=None):
"""from list of rois, generate results describing the cell enclosed in each roi"""
pixel_width = 1.0 if cal is None else cal.pixelWidth
if no_nuclei_centroids is None:
no_nuclei_centroids = [0 for _ in rois]
if no_enclosed_nuclei is None:
no_enclosed_nuclei = [0 for _ in rois]
cell_shapes = []
for idx, roi in enumerate(rois):
intensity_channel_imp.setRoi(roi)
stats = roi.getStatistics()
I_mean = stats.mean
I_sd = stats.stdDev
area = stats.area * (pixel_width**2)
perimeter = roi.getLength()
aspect_ratio = stats.major / stats.minor
cvh_poly = roi.getConvexHull()
if cvh_poly is not None:
convex_hull_roi = PolygonRoi([x for x in cvh_poly.xpoints],
[y for y in cvh_poly.ypoints],
PolygonRoi.POLYGON)
else:
continue
print("roi length = {}".format(roi.getLength()))
print("convex hull roi length = {}".format(
convex_hull_roi.getLength()))
cell_spikiness_index = roi.getLength() / (pixel_width *
convex_hull_roi.getLength())
cell_shapes.append(
CellShapeResults(
file_name=file_name,
cell_index=idx + 1,
cell_area_um2=area,
cell_perimeter_um=perimeter,
cell_aspect_ratio=aspect_ratio,
cell_spikiness_index=cell_spikiness_index,
cell_gfp_I_mean=I_mean,
cell_gfp_I_sd=I_sd,
nuclear_centroids_in_cell=no_nuclei_centroids[idx],
nuclei_enclosed_in_cell=no_enclosed_nuclei[idx],
roi=roi))
return cell_shapes
def generate_r_image(imp, ring_rois, centres, unwrap_axis, threshold_val):
"""for each point in the projection, calculate the distance to the vessel axis and present as an image"""
fp = imp.getProcessor()
fp.setThreshold(threshold_val, fp.maxValue(), FloatProcessor.NO_LUT_UPDATE)
bp = fp.createMask()
bp.dilate()
bp.erode()
mask_imp = ImagePlus("Mask", bp)
tile_mask = make_tiled_imp(mask_imp)
#tile_mask.show();
#WaitForUserDialog("pasue - generated mask").show();
mask_imp = do_unwrap(tile_mask, unwrap_axis, imp_title=mask_imp.getTitle())
#mask_imp.show();
roi = PolygonRoi([x for (x, y) in unwrap_axis],
[y for (x, y) in unwrap_axis], PolygonRoi.POLYLINE)
mask_imp.setRoi(roi)
#WaitForUserDialog("pasue - unwrapped").show();
IJ.run(mask_imp, "Fill Holes", "")
#WaitForUserDialog("pasue - filled holes").show();
IJ.run(mask_imp, "Divide...", "value=255")
#WaitForUserDialog("pasue - scaled to 0-1").show();
#mask_imp.show();
r_list = []
for lidx, (roi, centre) in enumerate(zip(ring_rois, centres)):
r_sublist = [
math.sqrt((x - centre[0])**2 + (y - centre[1])**2)
for x, y in zip(roi.getPolygon().xpoints,
roi.getPolygon().ypoints)
]
r_list.append(r_sublist)
r_imp = ImagePlus("Radii", FloatProcessor([list(x) for x in zip(*r_list)]))
tile_r_imp = make_tiled_imp(r_imp)
r_imp = do_unwrap(tile_r_imp, unwrap_axis, imp_title=r_imp.getTitle())
r_imp = ImageCalculator().run("Multiply create", r_imp, mask_imp)
IJ.run(r_imp, "Cyan Hot", "")
return r_imp, mask_imp
def get_angle(self, i):
_, _, _, stem_index, _, _, _ = self.get_coord_min_distance(i)
stem_x = self.get_xy(0)[0]
stem_y = self.get_xy(0)[1]
branch_x = self.get_xy(i)[0]
branch_y = self.get_xy(i)[1]
between_x = stem_x[stem_index]
between_y = stem_y[stem_index]
start_stem_x = stem_x[stem_index - 10]
start_stem_y = stem_y[stem_index - 10]
end_branch_x = branch_x[10]
end_branch_y = branch_y[10]
xpoints = [start_stem_x, between_x, end_branch_x]
ypoints = [start_stem_y, between_y, end_branch_y]
new_poly_roi = PolygonRoi(xpoints, ypoints, 3, Roi.ANGLE)
return new_poly_roi.getAngle()
def read_vl_file(file_path, cal):
"""open and xy csv file, uncalibrates the values and creates and returns a polygon roi"""
roi_csv_headings = ['X', 'Y']
coord_rows = br.csv_to_rows(file_path, cast_type=float)
if coord_rows[0] == roi_csv_headings:
coord_col_dict = br.csv_to_col_dict(file_path, cast_type=float)
else:
coord_cols = br.rotate(coord_rows)
coord_col_dict = {'X': coord_cols[0], 'Y': coord_cols[1]}
cal_func_dict = {'X': cal.getRawX, 'Y': cal.getRawY}
for col_name, cal_func in zip(coord_col_dict.keys(),
cal_func_dict.values()):
for i in range(len(coord_col_dict[col_name])):
coord_col_dict[col_name][i] = cal_func(coord_col_dict[col_name][i])
vl_roi = PolygonRoi(coord_col_dict['X'], coord_col_dict['Y'],
len(coord_col_dict['X']), Roi.POLYGON)
return vl_roi
def selectionTrimPolygon(roi, length):
x = roi.getXCoordinates()
y = roi.getYCoordinates()
n = roi.getNCoordinates()
x = selectionSmooth(x, n)
y = selectionSmooth(y, n)
curvature = selectionGetCurvature(x, y, n)
r = roi.getBounds()
threshold = selectionRodbard(length)
distance = math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) *
(y[1] - y[0]))
x[0] += r.x
y[0] += r.y
i2 = 1
x2 = 0
y2 = 0
for i in range(1, n - 1):
x1 = x[i]
y1 = y[i]
x2 = x[i + 1]
y2 = y[i + 1]
distance += math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) *
(y2 - y1)) + 1
distance += curvature[i] * 2
if (distance >= threshold):
x[i2] = x2 + r.x
y[i2] = y2 + r.y
i2 += 1
distance = 0.0
typ = Roi.POLYLINE if roi.getType() == Roi.FREELIN else Roi.POLYGON
if (typ == Roi.POLYLINE and distance > 0.0):
x[i2] = x2 + r.x
y[i2] = y2 + r.y
i2 += 1
p = PolygonRoi(x, y, i2, typ)
return p
def selectionTrimFloatPolygon(roi, length):
poly = roi.getFloatPolygon()
x = poly.xpoints
y = poly.ypoints
n = poly.npoints
x = selectionSmooth(x, n)
y = selectionSmooth(y, n)
curvature = selectionGetCurvature(x, y, n)
threshold = selectionRodbard(length)
#IJ.log("trim: "+length+" "+threshold);
distance = math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) *
(y[1] - y[0]))
i2 = 1
x2 = 0
y2 = 0
for i in range(1, n - 1):
x1 = x[i]
y1 = y[i]
x2 = x[i + 1]
y2 = y[i + 1]
distance += math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) *
(y2 - y1)) + 1
distance += curvature[i] * 2
if (distance >= threshold):
x[i2] = float(x2)
y[i2] = float(y2)
i2 += 1
distance = 0.0
typ = Roi.POLYLINE if roi.getType() == Roi.FREELINE else Roi.POLYGON
if (typ == Roi.POLYLINE and distance > 0.0):
x[i2] = float(x2)
y[i2] = float(y2)
i2 += 1
p = PolygonRoi(x, y, i2, typ)
return p
fp = FloatProcessor(width, height, pixels, None)
roi = Roi(400, 200, 400, 300) # Roi(int x, int y, int width, int height)
fp.setRoi(roi)
fp.setValue(2.0)
fp.fill()
imp2 = ImagePlus("Rectangle", fp)
imp2.show()
# Polygon ROI를 -3으로 채우기
fp = FloatProcessor(width, height, pixels, None)
xs = [
234, 174, 162, 102, 120, 123, 153, 177, 171, 60, 0, 18, 63, 132, 84, 129,
69, 174, 150, 183, 207, 198, 303, 231, 258, 234, 276, 327, 378, 312, 228,
225, 246, 282, 261, 252
]
ys = [
48, 0, 60, 18, 78, 156, 201, 213, 270, 279, 336, 405, 345, 348, 483, 615,
654, 639, 495, 444, 480, 648, 651, 609, 456, 327, 330, 432, 408, 273, 273,
204, 189, 126, 57, 6
]
proi = PolygonRoi(
xs, ys, len(xs), Roi.POLYGON
) # PolygonRoi(float[] xPoints, float[] yPoints, int nPoints, int type)
fpp = fp
fpp.setRoi(proi)
fpp.setValue(-3)
fpp.fill(proi.getMask())
imp3 = ImagePlus("Polygon", fpp)
imp3.show()
image = IJ.getImage()
# Get current ROI
roi = image.getRoi()
if roi is not None:
# Get ROI points
polygon = roi.getPolygon()
n_points = polygon.npoints
x = polygon.xpoints
y = polygon.ypoints
# Compute center of mass
xc = 0
yc = 0
for i in range(n_points):
xc = xc + x[i]
yc = yc + y[i]
xc = xc / n_points
yc = yc / n_points
# Compute new rotated points
new_x = []
new_y = []
for i in range(n_points):
new_x.append(
int(xc + (x[i] - xc) * math.cos(angle) -
(y[i] - yc) * math.sin(angle)))
new_y.append(
int(yc + (x[i] - xc) * math.sin(angle) +
(y[i] - yc) * math.cos(angle)))
# Create new ROI
new_roi = PolygonRoi(new_x, new_y, n_points, Roi.POLYGON)
image.setRoi(new_roi)
#imp.show()
roi_manager = RoiManager()
for gene in gene_list:
roi_manager.reset()
with open(csv_path) as csvfile:
reader = csv.DictReader(csvfile)
for n, row in enumerate(reader):
# print(row['cell_n'])
poly_name = row['gene_name']
# poly_name = ast.literal_eval(poly_name)
if gene == poly_name:
print(gene, poly_name)
rr = row['row_pixels']
cc = row['col_pixels']
rs = ast.literal_eval(rr)
cs = ast.literal_eval(cc)
proi = PolygonRoi(cs, rs, len(rs), Roi.POLYGON)
roi_manager.addRoi(proi)
roi_manager.runCommand("Deselect")
roi_save_path = os.path.join(dir.getDirectory(), gene + "_RoiSet.zip")
print(roi_save_path)
if not os.path.exists(roi_save_path):
with zipfile.ZipFile(roi_save_path, "w") as file:
pass
file.close()
roi_manager.runCommand("Save", roi_save_path)
def main():
#print (sys.version_info) # debug
#print(sys.path) # debug
data_root = r'C:\Users\dougk\Desktop\test'
# debug
output_root = r'C:\Users\dougk\Desktop\test'
#debug
#default_directory = r'C:\\Users\\Doug\\Desktop\\test';
#data_root, output_root = file_location_chooser(default_directory);
if (data_root is None) or (output_root is None):
raise IOError("File location dialogs cancelled!")
timestamp = datetime.strftime(datetime.now(), "%Y-%m-%d %H.%M.%S")
output_path = os.path.join(output_root, (timestamp + " output"))
for file_path in filterByFileType(os.listdir(data_root), '.tif'):
subfolder_name = os.path.splitext(file_path)[0]
output_subfolder = os.path.join(output_path, subfolder_name)
print(output_subfolder)
os.makedirs(output_subfolder)
imps = bf.openImagePlus(os.path.join(data_root, file_path))
imp = imps[0]
imp.show()
h = imp.height
w = imp.width
slices = imp.getNSlices()
channels = imp.getNChannels()
frames = imp.getNFrames()
# rotation step - since using multiples of 90, TransformJ.Turn is more efficient
IJ.run("Enhance Contrast", "saturated=0.35")
angleZ = 1
while ((angleZ % 90) > 0):
gd = GenericDialog("Rotate?")
gd.addMessage(
"Define rotation angle - increments of 90. Apical at top")
gd.addNumericField("Rotation angle", 0, 0)
gd.showDialog()
angleZ = int(gd.getNextNumber())
if (angleZ > 1):
IJ.run("TransformJ Turn",
"z-angle=" + str(angleZ) + " y-angle=0 x-angle=0")
imp.close()
imp = WindowManager.getCurrentImage()
imp.setTitle(file_path)
# trim time series
IJ.run("Enhance Contrast", "saturated=0.35")
imp.setDisplayMode(IJ.COLOR)
WaitForUserDialog(
"Scroll to the first frame of the period of interest and click OK"
).show()
start_frame = imp.getT()
WaitForUserDialog(
"Scroll to the last frame of the period of interest and click OK"
).show()
end_frame = imp.getT()
trim_imp = Duplicator().run(imp, 1, channels, 1, slices, start_frame,
end_frame)
imp.close()
trim_imp.show()
dup_imp = Duplicator().run(trim_imp)
# create images to process and find bounds for
dup_imps = ChannelSplitter().split(dup_imp)
myo_imp = dup_imps[1]
mem_imp = dup_imps[0]
FileSaver(myo_imp).saveAsTiffStack(
os.path.join(output_subfolder, "myosin_channel.tif"))
FileSaver(mem_imp).saveAsTiffStack(
os.path.join(output_subfolder, "membrane_channel.tif"))
# set basal bounds
myo_imp.show()
ImageConverter(myo_imp).convertToGray8()
frames = myo_imp.getNFrames()
gb = GaussianBlur()
for fridx in range(0, frames):
myo_imp.setSliceWithoutUpdate(fridx + 1)
ip = myo_imp.getProcessor()
gb.blurGaussian(ip, 5.0, 1.0, 0.02)
# assymmetrical Gaussian
IJ.run(myo_imp, "Convert to Mask",
"method=Otsu background=Dark calculate")
IJ.run("Despeckle", "stack")
title = myo_imp.getTitle()
# assume that first frame is good quality image...
basal_edges = find_basal_edges(myo_imp)
#myo_imp.hide()
mem_imp.hide()
# draw some edges for checking
roim = RoiManager()
xs = [x for x in range(1,
trim_imp.getWidth() + 1)]
trim_imp.show()
for fridx in range(0, myo_imp.getNFrames()):
trim_imp.setPosition(2, 1, fridx + 1)
IJ.run("Enhance Contrast", "saturated=0.35")
roi = PolygonRoi(xs, basal_edges[fridx], Roi.POLYLINE)
trim_imp.setRoi(roi)
roim.addRoi(roi)
def create_skeleton(image, name, min_branch_length=10, nuclei_rois=None, sample_width=4):
print "Creating skeleton for %s, new name %s" %(image.getTitle(), name)
# analyze skeleton
skel = AnalyzeSkeleton_()
skel.setup("", image)
skelResult = skel.run(AnalyzeSkeleton_.NONE, False, True, None, True, False)
# create copy of input image
pruned_img = image.duplicate()
outStack = pruned_img.getStack()
# get graphs (one per skeleton in the image)
graph = skelResult.getGraph()
# list of end-points
endPoints = skelResult.getListOfEndPoints()
if graph:
for i in range(len(graph)):
listEdges = graph[i].getEdges()
# go through all branches and remove branches < min_branch_length in duplicate image
for e in listEdges:
p = e.getV1().getPoints();
v1End = endPoints.contains( p.get(0) )
p2 = e.getV2().getPoints();
# print "p=",p, "p2=",p2
v2End = endPoints.contains( p2.get(0) )
# if any of the vertices is end-point
if v1End or v2End :
if e.getLength() < min_branch_length:
if v1End:
outStack.setVoxel( p.get(0).x, p.get(0).y, p.get(0).z, 0 )
if v2End:
outStack.setVoxel( p2.get(0).x, p2.get(0).y, p2.get(0).z, 0 )
for p in e.getSlabs():
outStack.setVoxel( p.x, p.y, p.z, 0 )
pruned_img.setTitle(image.getTitle()+"-longestpath")
sppoints = skel.getShortestPathPoints()
if len(sppoints) == 0:
return None, None, None, None, None, None
ais_skeleton = pruned_img.duplicate()
ais_skeleton.setTitle(name);
IJ.run(ais_skeleton, "Select All", "")
IJ.run(ais_skeleton, "Clear", "slice")
points = []
angle = []
b_length = [len(b) for b in sppoints]
longest_branch_idx = b_length.index(max(b_length))
points = [p for p in sppoints[longest_branch_idx]]
closest_nucleus = None
if nuclei_rois is not None:
nroi1,dist1 = find_closest_roi(points[0].x, points[0].y, nuclei_rois)
nroi2,dist2 = find_closest_roi(points[len(points)-1].x, points[len(points)-1].y, nuclei_rois)
if nroi1 != nroi2 and dist2<dist1:
# reverse order
points = points[::-1]
closest_nucleus = nroi2
else:
closest_nucleus = nroi1
closest_nucleus.setName('%s-nucleus-ROI' % (name))
poly = Polygon()
for p in points:
poly.addPoint(int(p.x), int(p.y))
#for branch in sppoints:
# print "Branch %s, len=%d" % (branch, len(branch))
# for p in branch:
# poly.addPoint(int(p.x), int(p.y))
# points.append(p)
angles,orthogonals = local_angles(points, scope=sample_width//2)
ais_roi = PolygonRoi(poly, PolygonRoi.POLYLINE)
ais_roi.setFillColor(Color(0.0,1.0,1.0,0.5));
ais_roi.setStrokeColor(Color(0.0,1.0,1.0,0.5));
ais_roi.setName('%s-AIS-ROI' % (name))
#ais_roi.setStrokeWidth(sample_width)
IJ.run(ais_skeleton, "Analyze Particles...", "size=20-Infinity pixel exclude clear add");
IJ.run(ais_skeleton, "Clear", "slice")
ip = ais_skeleton.getProcessor()
for n in nuclei_rois:
ais_skeleton.setRoi(n)
if n == closest_nucleus:
ip.setValue(128)
else:
ip.setValue(255)
ip.fill(n.getMask())
ais_skeleton.setRoi(ais_roi)
#ip.setValue(200)
#ip.fill()
#rois = RoiManager.getInstance2().getRoisAsArray()
#for roi in rois:
# ais_skeleton.setRoi(roi)
# ip.setValue(255)
# ip.fill(roi.getMask());
for p,a,o in zip(points,angles,orthogonals):
# print "p=%s, a=%s, o=%s" % (p,a,o)
ip.set(int(p.x), int(p.y), int(33+a/2))
ip.set(int(o[0].x), int(o[0].y),255)
ip.set(int(o[1].x), int(o[1].y),255)
IJ.run(ais_skeleton, "Fire", "")
# pruned_img.setRoi(ais_roi)
print "Created ais=%s" % ais_skeleton.getTitle()
print len(skel.getShortestPathPoints()), len(points), len(orthogonals)
return ais_skeleton, skel.getShortestPathPoints(), points, orthogonals, ais_roi, closest_nucleus
from ij.plugin import ImageCalculator as IC
from ij.process import ImageStatistics as IS
from ij.io import FileSaver
from ij import WindowManager
import os
xpoints = [954, 708, 3156, 2760]
ypoints = [1290, 2112, 1920, 1158]
folderds = "F:\\MSc Misis\\4 Semestre\\Tesis 1\\DS Prueba"
folderdsf = "F:\\MSc Misis\\4 Semestre\\Tesis 1\\DS Duplicado"
i = 0
for filename in os.listdir(folderds):
#Establecer Path
Pathfile = ("F:\\MSc Misis\\4 Semestre\\Tesis 1\\DS Prueba\\" + filename)
#Extraer imagen del Path
dsimage = IJ.openImage(Pathfile)
#Creación del área de interés
roi = PolygonRoi(xpoints, ypoints, 4, Roi.POLYGON)
#Creación de la imagen
dsimage.setRoi(roi)
#Duplicación de la imagen
imp2 = dsimage.duplicate()
#conversion a recipiente FileSaver
fs = FileSaver(imp2)
#Nombrar archivo
filename = folderdsf + "\\" + str(i) + ".jpg"
#Guardar archivo como JPEG
fs.saveAsJpeg(filename)
#impresion en consola del proceso
print "Proccessing FinalFile", filename
i = i + 1
def getCells(dicStack):
outStack = ImageStack(W,H)
cells = [None for t in range(T+1)]
for t in range(1,T+1):
mapp = dicStack.getProcessor(t).convertToFloatProcessor()
mapp.subtract( mapp.getStatistics().mean )
mapp.abs()
RankFilters().rank(mapp, 1.0, RankFilters.VARIANCE)
mapp.sqrt()
mapp.blurGaussian(5)
hist = mapp.getHistogram(256)
stats = mapp.getStatistics()
thresh = AutoThresholder().getThreshold( AutoThresholder.Method.Otsu, hist )
thresh = (thresh/float(255)) * (stats.max-stats.min) + stats.min
mask = ByteProcessor(W,H)
for i in range(W*H):
value = mapp.getf(i)
bite = 255 if value>=thresh else 0
mask.set(i, bite)
fillHoles(mask)
ed = 3
for e in range(ed): mask.erode(1, 0)
for d in range(ed): mask.dilate(1, 0)
watershed(mask)
minA = 5000 #px²
mask.setThreshold(255,255, ImageProcessor.NO_LUT_UPDATE)
composite = ThresholdToSelection().convert(mask)
rois = ShapeRoi(composite).getRois()
keep = []
for roi in rois:
if roi.getStatistics().area >= minA:
if not onEdge(roi):
keep.append(roi)
else:
edgeRoi = ShapeRoi(roi)
edgeRoi.setPosition(0,0,t)
edgeRoi.setStrokeColor(Color.YELLOW)
ol.add(edgeRoi)
print("T"+str(t)+" using "+str(len(keep))+"/"+str(len(rois))+" ROIs")
rois = keep
#rois = [ roi for roi in rois if roi.getStatistics().area >= minA and not onEdge(roi) ] #keep big enough and not on edges
# if there is only one Roi, cut it along the fitted ellipse minor axis
if len(rois)==1:
el = EllipseFitter()
mask.setRoi(rois[0])
el.fit(mask, None)
el.makeRoi(mask)
theta = el.angle * (maths.pi/180.0)
length = el.major/2.0
dy = maths.sin(theta)* length
dx = maths.cos(theta)* length
#major axis
lineX0 = el.xCenter - dx
lineY0 = el.yCenter + dy
lineX1 = el.xCenter + dx
lineY1 = el.yCenter - dy
line = Line(lineX0, lineY0, lineX1, lineY1)
line.setStrokeColor(Color.BLUE)
line.setStrokeWidth(1)
line.setPosition(0,0,t)
ol.add(line)
#minor axis scaled length to make sure cut ends are outside Roi
cutX0 = el.xCenter + dy*100
cutY0 = el.xCenter + dx*100
cutX1 = el.yCenter - dy*100
cutY1 = el.yCenter - dx*100
cut = Line(cutX0,cutY0, cutX1, cutY1)
cut.setStrokeWidth(2)
cut = PolygonRoi( cut.getFloatPolygon(), PolygonRoi.POLYGON )
mask.setColor(0)
mask.fill(cut)
composite = ThresholdToSelection().convert(mask)
rois = ShapeRoi(composite).getRois()
rois = [ roi for roi in rois if roi.getStatistics().area >= minA ]
print(str(t) + ":" + str(len(rois)))
rois = [ PolygonRoi(roi.getInterpolatedPolygon(20, True), PolygonRoi.POLYGON) for roi in rois ]
rois = [ PolygonRoi(roi.getConvexHull(), PolygonRoi.POLYGON) for roi in rois ]
rois = sorted(list(rois), key=lambda roi:roi.getLength() ) #size order
rois = rois[-2:] #keep 2 biggest
rois = sorted(list(rois), key=lambda roi:roi.getStatistics().xCentroid+roi.getStatistics().yCentroid ) #top left to bottom right order
if len(rois)>0:
rois[0].setStrokeColor(Color.RED)
rois[0].setPosition(0, 0, t)
ol.add(rois[0])
if len(rois)>1:
rois[1].setStrokeColor(Color.GREEN)
rois[1].setPosition(0, 0, t)
ol.add(rois[1])
cells[t] = (rois[0], rois[1])
return cells
def do_angular_projection(imp,
max_r_pix=60,
min_r_pix=10,
generate_roi_stack=True):
"""perform ray-based projection of vessel wall, c.f. ICY TubeSkinner (Lancino 2018)"""
Prefs.blackBackground = True
print("do angular projection input imp = " + str(imp))
split_chs = ChannelSplitter().split(imp)
mch_imp = split_chs[0]
IJ.setAutoThreshold(mch_imp, "IsoData dark stack")
egfp_imp = split_chs[1]
proj_imp = Duplicator().run(egfp_imp)
cl_imp = split_chs[2]
if generate_roi_stack:
egfp_imp_disp = Duplicator().run(egfp_imp)
roi_stack = IJ.createImage("rois", egfp_imp.getWidth(),
egfp_imp.getHeight(), egfp_imp.getNSlices(),
16)
centres = []
projected_im_pix = []
ring_rois = []
for zidx in range(cl_imp.getNSlices()):
if ((zidx + 1) % 100) == 0:
print("Progress = " +
str(round(100 * (float(zidx + 1) / cl_imp.getNSlices()))))
projected_im_row = []
proj_imp.setZ(zidx + 1)
mch_imp.setZ(zidx + 1)
bp = mch_imp.createThresholdMask()
bp.dilate()
bp.erode()
bp.erode()
bp.erode()
mask_imp = ImagePlus("mask", bp)
IJ.run(mask_imp, "Create Selection", "")
roi = mask_imp.getRoi()
proj_imp.setRoi(roi)
IJ.run(proj_imp, "Set...", "value=0 slice")
IJ.run(proj_imp, "Make Inverse", "")
roi = proj_imp.getRoi()
centre = (roi.getStatistics().xCentroid, roi.getStatistics().yCentroid)
centres.append(centre)
ring_roi_xs = []
ring_roi_ys = []
for theta in range(360):
pt1 = (centre[0] + min_r_pix * math.cos(math.radians(theta)),
centre[1] + min_r_pix * math.sin(math.radians(theta)))
pt2 = (centre[0] + max_r_pix * math.cos(math.radians(theta)),
centre[1] + max_r_pix * math.sin(math.radians(theta)))
roi = Line(pt1[0], pt1[1], pt2[0], pt2[1])
proj_imp.setRoi(roi)
profile = roi.getPixels()
projected_im_row.append(max(profile))
try:
ring_roi_xs.append(roi.getContainedPoints()[profile.index(
max(profile))].x)
except IndexError:
ring_roi_xs.append(pt2[0])
try:
ring_roi_ys.append(roi.getContainedPoints()[profile.index(
max(profile))].y)
except IndexError:
ring_roi_ys.append(pt2[1])
proj_imp.killRoi()
ring_roi = PolygonRoi(ring_roi_xs, ring_roi_ys, Roi.FREELINE)
ring_rois.append(ring_roi)
if generate_roi_stack:
roi_stack.setZ(zidx + 1)
roi_stack.setRoi(ring_roi)
IJ.run(roi_stack, "Line to Area", "")
IJ.run(
roi_stack, "Set...",
"value=" + str(roi_stack.getProcessor().maxValue()) + " slice")
#egfp_imp.setRoi(ring_roi);
projected_im_pix.append(projected_im_row)
# for ch in split_chs:
# ch.close();
out_imp = ImagePlus(
"projected", FloatProcessor([list(x) for x in zip(*projected_im_pix)]))
if generate_roi_stack:
roi_stack.show()
egfp_imp_disp.show()
# merge?
else:
roi_stack = None
return out_imp, roi_stack, ring_rois, centres
egfp_imp.setRoi(roi)
profile = roi.getPixels()
projected_im_row.append(max(profile))
try:
ring_roi_xs.append(roi.getContainedPoints()[profile.index(
max(profile))].x)
except IndexError:
ring_roi_xs.append(pt2[0])
try:
ring_roi_ys.append(roi.getContainedPoints()[profile.index(
max(profile))].y)
except IndexError:
ring_roi_ys.append(pt2[1])
#print("Max val = " + str(max(profile)));
egfp_imp.killRoi()
ring_roi = PolygonRoi(ring_roi_xs, ring_roi_ys, Roi.FREELINE)
ring_rois.append(ring_roi)
roi_stack.setZ(zidx + 1)
roi_stack.setRoi(ring_roi)
IJ.run(roi_stack, "Line to Area", "")
IJ.run(roi_stack, "Set...",
"value=" + str(roi_stack.getProcessor().maxValue()) + " slice")
min_idx = projected_im_row.index(min(projected_im_row))
# print("min idx = " + str(min_idx));
unzip_axis.append(min_idx)
egfp_imp.setRoi(ring_roi)
projected_im_pix.append(projected_im_row)
# WaitForUserDialog("pause").show();
#print(centres);
for ch in split_chs:
def straighten_vessel(imp, smooth_centres, it=1, save_output=False):
"""use IJ straigtening tool to deal with convoluted vessels"""
print("straighten vessel input image dims = " + str(imp.getWidth()) + "x" +
str(imp.getHeight()))
rot_imp = utils.rot3d(imp, axis='x')
if it == 1:
roi = PolygonRoi([x for x, y, z in smooth_centres],
[z for x, y, z in smooth_centres], Roi.FREELINE)
print("len interp polygon = " +
str(roi.getInterpolatedPolygon().npoints))
elif it == 2:
new_zs = [z for z in range(rot_imp.getWidth())]
new_ys = lin_interp_1d([z for x, y, z in smooth_centres],
[y for x, y, z in smooth_centres], new_zs)
roi = PolygonRoi(new_zs, new_ys, Roi.FREELINE)
split_ch = ChannelSplitter().split(rot_imp)
mch_imp = split_ch[0]
egfp_imp = split_ch[1]
roi_imp = split_ch[2]
roi_imp.setRoi(roi)
for zidx in range(egfp_imp.getNSlices()):
for chidx in range(3):
split_ch[chidx].setZ(zidx + 1)
split_ch[chidx].setRoi(roi)
ip = Straightener().straightenLine(split_ch[chidx], 150)
if chidx == 1:
if zidx == 0:
egfp_straight_stack = ImageStack(ip.getWidth(),
ip.getHeight())
egfp_straight_stack.addSlice(ip)
elif chidx == 0:
if zidx == 0:
mch_straight_stack = ImageStack(ip.getWidth(),
ip.getHeight())
mch_straight_stack.addSlice(ip)
else:
if zidx == 0:
roi_straight_stack = ImageStack(ip.getWidth(),
ip.getHeight())
roi_straight_stack.addSlice(ip)
egfp_out_imp = ImagePlus("Straightened EGFP", egfp_straight_stack)
mch_out_imp = ImagePlus("Straightened mCh", mch_straight_stack)
roi_out_imp = ImagePlus("Straightened ROI", roi_straight_stack)
if it == 2:
egfp_out_imp = utils.rot3d(egfp_out_imp, axis='y')
mch_out_imp = utils.rot3d(mch_out_imp, axis='y')
roi_out_imp = utils.rot3d(roi_out_imp, axis='y')
egfp_out_imp.show()
mch_out_imp.show()
roi_out_imp.show()
IJ.run(
"Merge Channels...",
"c1=[" + mch_out_imp.getTitle() + "] c2=[" + egfp_out_imp.getTitle() +
"] c7=[" + roi_out_imp.getTitle() + "] create keep")
# WaitForUserDialog("pause").show();
# if it==1:
egfp_out_imp.close()
mch_out_imp.close()
roi_out_imp.close()
new_composite = IJ.getImage()
if save_output:
FileSaver(new_composite).saveAsTiffStack(
os.path.join(output_path, "after rotation " + str(it) + ".tif"))
return new_composite
def makePolygon(xs, ys):
imp = IJ.getImage()
imp.setRoi(PolygonRoi(xs, ys, len(xs), Roi.POLYGON))
