def makeCropUI(imp, images, tgtDir, panel=None, cropContinuationFn=None):
""" imp: the ImagePlus to work on.
images: the list of ImgLib2 images, one per frame, not original but already isotropic.
(These are views that use a nearest neighbor interpolation using the calibration to scale to isotropy.)
tgtDir: the target directory where e.g. CSV files will be stored, for ROI, features, pointmatches.
panel: optional, a JPanel controlled by a GridBagLayout.
cropContinuationFn: optional, a function to execute after cropping,
which is given as arguments the original images,
minC, maxC (both define a ROI), and the cropped images. """
independent = None == panel
if not panel:
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
gc = GBC()
else:
gb = panel.getLayout()
# Constraints of the last component
gc = gb.getConstraints(panel.getComponent(panel.getComponentCount() - 1))
# Horizontal line to separate prior UI components from crop UI
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
gc.anchor = GBC.WEST
gc.fill = GBC.HORIZONTAL
sep = JSeparator()
sep.setMinimumSize(Dimension(200, 10))
gb.setConstraints(sep, gc)
panel.add(sep)
# ROI UI header
title = JLabel("ROI controls:")
gc.gridy +=1
gc.anchor = GBC.WEST
gc.gridwidth = 4
gb.setConstraints(title, gc)
panel.add(title)
# Column labels for the min and max coordinates
gc.gridy += 1
gc.gridwidth = 1
for i, title in enumerate(["", "X", "Y", "Z"]):
gc.gridx = i
gc.anchor = GBC.CENTER
label = JLabel(title)
gb.setConstraints(label, gc)
panel.add(label)
textfields = []
rms = []
# Load stored ROI if any
roi_path = path = os.path.join(tgtDir, "crop-roi.csv")
if os.path.exists(roi_path):
with open(roi_path, 'r') as csvfile:
reader = csv.reader(csvfile, delimiter=',', quotechar="\"")
reader.next() # header
minC = map(int, reader.next()[1:])
maxC = map(int, reader.next()[1:])
# Place the ROI over the ImagePlus
imp.setRoi(Roi(minC[0], minC[1], maxC[0] + 1 - minC[0], maxC[1] + 1 - minC[1]))
else:
# Use whole image dimensions
minC = [0, 0, 0]
maxC = [v -1 for v in Intervals.dimensionsAsLongArray(images[0])]
# Text fields for the min and max coordinates
for rowLabel, coords in izip(["min coords: ", "max coords: "],
[minC, maxC]):
gc.gridx = 0
gc.gridy += 1
label = JLabel(rowLabel)
gb.setConstraints(label, gc)
panel.add(label)
for i in xrange(3):
gc.gridx += 1
tf = JTextField(str(coords[i]), 10)
gb.setConstraints(tf, gc)
panel.add(tf)
textfields.append(tf)
listener = RoiMaker(imp, textfields, len(textfields) -1)
rms.append(listener)
tf.addKeyListener(listener)
tf.addMouseWheelListener(listener)
# Listen to changes in the ROI of imp
rfl = RoiFieldListener(imp, textfields)
Roi.addRoiListener(rfl)
# ... and enable cleanup
ImagePlus.addImageListener(FieldDisabler(rfl, rms))
# Functions for cropping images
cropped = None
cropped_imp = None
def storeRoi(minC, maxC):
if os.path.exists(roi_path):
# Load ROI
with open(path, 'r') as csvfile:
reader = csv.reader(csvfile, delimiter=',', quotechar="\"")
reader.next() # header
same = True
for a, b in izip(minC + maxC, map(int, reader.next()[1:] + reader.next()[1:])):
if a != b:
same = False
# Invalidate any CSV files for features and pointmatches: different cropping
for filename in os.listdir(tgtDir):
if filename.endswith("features.csv") or filename.endswith("pointmatches.csv"):
os.remove(os.path.join(tgtDir, filename))
break
if same:
return
# Store the ROI as crop-roi.csv
with open(roi_path, 'w') as csvfile:
w = csv.writer(csvfile, delimiter=',', quotechar="\"", quoting=csv.QUOTE_NONNUMERIC)
w.writerow(["coords", "x", "y", "z"])
w.writerow(["min"] + map(int, minC))
w.writerow(["max"] + map(int, maxC))
def crop(event):
global cropped, cropped_imp
coords = [int(float(tf.getText())) for tf in textfields]
minC = [max(0, c) for c in coords[0:3]]
maxC = [min(d -1, c) for d, c in izip(Intervals.dimensionsAsLongArray(images[0]), coords[3:6])]
storeRoi(minC, maxC)
print "ROI min and max coordinates"
print minC
print maxC
cropped = [Views.zeroMin(Views.interval(img, minC, maxC)) for img in images]
cropped_imp = showAsStack(cropped, title="cropped")
cropped_imp.setDisplayRange(imp.getDisplayRangeMin(), imp.getDisplayRangeMax())
if cropContinuationFn:
cropContinuationFn(images, minC, maxC, cropped, cropped_imp)
# Buttons to create a ROI and to crop to ROI,
# which when activated enables the fine registration buttons
crop_button = JButton("Crop to ROI")
crop_button.addActionListener(crop)
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
gc.anchor = GBC.WEST
buttons_panel = JPanel()
buttons_panel.add(crop_button)
gb.setConstraints(buttons_panel, gc)
panel.add(buttons_panel)
if independent:
frame = JFrame("Crop by ROI")
frame.getContentPane().add(panel)
frame.pack()
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl(destroyables=rms + [rfl]))
frame.setVisible(True)
else:
# Re-pack the JFrame
parent = panel.getParent()
while not isinstance(parent, JFrame) and parent is not None:
parent = parent.getParent()
if parent:
frame = parent
frame.pack()
found = False
for wl in frame.getWindowListeners():
if isinstance(wl, CloseControl):
wl.addDestroyables(rms + [rfl])
found = True
break
if not found:
frame.addWindowListener(CloseControl(destroyables=rms + [rfl]))
frame.setVisible(True)
return panel
