def write_roi_numbers(ov, corners, L):
roiID = 1
for [x, y] in corners:
text = TextRoi(x, y, L, L, str(roiID), Font("Arial", Font.PLAIN, 400))
text.setJustification(1)
text.setColor(Color.RED)
ov.add(text)
roiID += 1
return ov
def write_roi_numbers(ov, corners, L):
fontsize = int(L / 1.5)
roiID = 1
for [x, y] in corners:
text = TextRoi(x, y, L, L, str(roiID),
Font("Arial", Font.BOLD, fontsize))
text.setJustification(2)
text.setColor(Color.RED)
ov.add(text)
roiID += 1
return ov
def generate_limit_labels(imp, limits, cb_fraction, params):
"""generate text ROIs in correct positions to label colorbar"""
rois = []
w = imp.getWidth()
h = imp.getHeight()
txt_h_px = float(h) / 15
txt_sz_pt = int(round((18.0 / 24.0) * txt_h_px))
for limit in limits:
roi = TextRoi(1, 1, str(round(limit, 3)),
Font("SansSerif", Font.ITALIC, txt_sz_pt))
roi.setJustification(TextRoi.RIGHT)
roi.setFillColor(Color.BLACK)
roi.setStrokeColor(Color.WHITE)
rois.append(roi)
roim = RoiManager(False)
roim.reset()
imp.show()
mbui.autoset_zoom(imp)
for fridx in range(1, imp.getNSlices() + 1):
imp.setPosition(fridx)
roi_uu = rois[1].clone()
xpos = w - cb_fraction * w - float(w) / 100 - rois[1].getFloatWidth()
roi_uu.setLocation(xpos, 1)
imp.setRoi(roi_uu)
roim.addRoi(roi_uu)
roi_ll = rois[0].clone()
roi_ll.setLocation(xpos, h - rois[0].getFloatHeight())
imp.setRoi(roi_ll)
roim.addRoi(roi_ll)
roim.runCommand("Show All")
FileSaver(imp).saveAsTiff(
os.path.join(params.output_path,
"overlaid curvature nudged labels.tif"))
# nudge positions
roim.reset()
imp.killRoi()
for fridx in range(1, imp.getNSlices() + 1):
imp.setPosition(fridx)
roi_uu = rois[1].clone()
xpos = w - cb_fraction * w - float(w) / 100
roi_uu.setLocation(xpos, 1)
imp.setRoi(roi_uu)
roim.addRoi(roi_uu)
roi_ll = rois[0].clone()
roi_ll.setLocation(xpos, h - rois[0].getFloatHeight())
imp.setRoi(roi_ll)
roim.addRoi(roi_ll)
roim.runCommand("Show All")
FileSaver(imp).saveAsTiff(
os.path.join(params.output_path, "overlaid curvature.tif"))
return imp
def labelMontage(imp, lLabels, cols, rows, w0=12, h0=2, font=24, col=Color.WHITE):
"""labelMontage(imp, lLabels, cols, rows, w0=12, h0=2, font=24, col=Color.WHITE)
Label a montage in the overlay
Inputs:
imp - the ImagePlus of the montage to label
lLabels - a list of labels to write into the overlay
cols - the number of columns in the montage
rows - the number of rows in the montage
w0 - the x offset for the label (defaults to 12 px)
h0 - the y offset for the label (defaults to 2 px)
font - the size of the font (pts, defaults to 24)
col - color of text. Default to Color.WHITE
Returns
an ImagePlus with a labeled, duplicate of the input image
"""
print(cols,rows)
wBase = imp.getWidth()/cols
hBase = imp.getHeight()/rows
print(wBase, hBase)
l = len(lLabels)
xt = 0
y = 0
# make a copy
res = imp.duplicate()
# let's create an array of text rois
ol = Overlay()
for i in range(l):
x = (i % cols+1)-1
if x < xt:
y += 1
xt = x
xL = x * wBase + w0
yL = y * hBase + h0
print(xL,yL)
tr = TextRoi(xL, yL, lLabels[i])
tr.setColor(col)
tr.setFont("SanSerif", font, 1)
tr.setJustification(TextRoi.CENTER)
tr.setAntialiased(True)
ol.add(tr)
res.show()
res.setOverlay(ol)
res.updateAndRepaintWindow()
return res
def measureFeatureLength(imp, lw = 2, csvPath=None, bAppend=True,
offset = -30, digits = 3,
font = 18, linCol = Color.YELLOW,
labCol = Color.WHITE,
bDebug = False):
"""
measureFeatureLength(imp, lw = 2, csvPath=None, bAppend=True,
offset = -30, digits = 3,
font = 18, linCol = Color.YELLOW,
labCol = Color.WHITE,
bDebug = False)
Manually measure the length of a feature in a calibrated ImagePlus
and write the results to the overlay.
Version of 2016-08-04
Parameters
----------
imp: ImagePlus
The image to process
lw: int (2)
The linewidth for the line
csvPath: string (None)
The path to a csv file to write measurements
bAppend: Boolean (True)
A flag. If True new results are appended to the file
offset: int (-30)
The Y offset for the label. If negative, the label will
be written above the measurement, if positive below.
digits: int (3)
Round the output (in calibrated units) to this number of decimal
points.
font: int (18)
The font size for the measurement.
linCol: A color constant (Color.YELLOW)
The color for the line in the overlay.
labCol: A color constant (Color.WHITE)
The color for the label
bDebug: A Boolean (False)
A flag to print diagnostic incormation
Returns
-------
None - it does draw in the overlay of the image and write an
optional .csv file.
Known Issues
------------
With large line widths the length of the drawn line appears lw
pixels too long.
"""
# First define some convenience functions
def resetLastMeasureCount():
Prefs.set("JRM.meas.counter", 0)
def GetLastMeasureCount():
myCount = Prefs.get("JRM.meas.counter", int(-1))
if myCount < 0:
# it was not set, so set it to zero
resetLastMeasureCount()
return 0
else:
myCount = int(myCount)
return myCount
def setLastMeasureCount(count):
count = int(count)
Prefs.set("JRM.meas.counter", count)
imp = IJ.getImage()
if imp == None:
print("You need an image...")
return
else:
roi = imp.getRoi()
if roi != None:
if roi.getType() == Roi.LINE:
# print(roi)
cal = imp.getCalibration()
# print(cal)
unit = cal.getUnits()
width = cal.pixelWidth
height = cal.pixelHeight
x1 = roi.x1 * width
y1 = roi.y1 * height
x2 = roi.x2 * width
y2 = roi.y2 * height
length = sqrt((x2-x1)*(x2-x1)+(y2-y1)*(y2-y1));
if bDebug:
sOut = "X1: %d Y1 %d X2 %d Y2 %d" % (roi.x1, roi.y1,
roi.x2, roi.y2)
print(sOut)
print(length, unit)
ip = imp.getProcessor()
ip.setColor(linCol)
oldLW = ip.getLineWidth()
ip.setLineWidth(lw)
ip.drawLine(roi.x1, roi.y1, roi.x2, roi.y2)
ip.setLineWidth(oldLW)
imp.updateAndDraw()
ol = imp.getOverlay()
if ol == None:
ol = Overlay()
res = imp.duplicate()
# first a dummy text ROI to set the font
tr = TextRoi(10, 10, "Foo")
tr.setColor(labCol)
tr.setFont("SanSerif", font, 1)
tr.setJustification(TextRoi.CENTER)
tr.setAntialiased(True)
# explicitly save preferences
Prefs.savePreferences()
xL = roi.x1 + roi.x2
xL /= 2
if offset < 0:
yL = min(roi.y1, roi.y2)
yL += offset
else:
yL = max(roi.y1, roi.y2)
yL += offset
length = round(length, 3)
label = "%g %s" % (length, unit)
tr = TextRoi(xL, yL, label)
tr.setColor(labCol)
tr.setFont("SanSerif", font, 1)
tr.setJustification(TextRoi.CENTER)
tr.setAntialiased(True)
ol.add(tr)
imp.setOverlay(ol)
imp.show()
if csvPath != None:
if bAppend:
if os.path.isfile(csvPath):
theCount = GetLastMeasureCount() + 1
f=open(csvPath, 'a')
else:
f=open(csvPath, 'w')
resetLastMeasureCount()
theCount = 1
strLine = 'img, num, length (%s)\n' % unit
f.write(strLine)
else:
f=open(csvPath, 'w')
resetLastMeasureCount()
theCount = 1
strLine = 'img, num, length (%s)\n' % unit
f.write(strLine)
strLine = "%s, %d, %.6f\n" % (imp.getShortTitle(), theCount, length)
f.write(strLine)
f.close()
setLastMeasureCount(theCount)
strMsg = "measured %s count = %d" % (imp.getShortTitle(), theCount)
print(strMsg)
else:
print("You need a line ROI")
# finally deselect
IJ.run("Select None")