def makeTranslationUI(affines, imp, show=True, print_button_text="Print transforms"):
"""
A GUI to control the translation components of a list of AffineTransform3D instances.
When updated, the ImagePlus is refreshed.
affines: a list (will be read multiple times) of one affine transform per image.
imp: the ImagePlus that hosts the virtual stack with the transformed images.
show: defaults to True, whether to make the GUI visible.
print_button_text: whatever you want the print button to read like, defaults to "Print transforms".
Returns the JFrame, the main JPanel and the lower JButton panel.
"""
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
gc.anchor = GBC.WEST
gc.fill = GBC.NONE
# Column labels
gc.gridy = 0
for i, title in enumerate(["Camera", "translation X", "translation Y", "translation Z"]):
gc.gridx = i
gc.anchor = GBC.CENTER
label = JLabel(title)
gb.setConstraints(label, gc)
panel.add(label)
gc.anchor = GBC.WEST
listeners = []
# One row per affine to control: skip the first
for i, affine in enumerate(affines[1:]):
gc.gridx = 0
gc.gridy += 1
label = JLabel("CM0%i: " % (i + 1))
gb.setConstraints(label, gc)
panel.add(label)
# One JTextField per dimension
for dimension, translation in enumerate(affine.getTranslation()):
tf = JTextField(str(translation), 10)
listener = MatrixTextFieldListener(affine, dimension, tf, imp)
listeners.append(listener)
imp.addImageListener(listener) # to disable the JTextField when closed
tf.addKeyListener(listener)
tf.addMouseWheelListener(listener)
gc.gridx += 1
gb.setConstraints(tf, gc)
panel.add(tf)
# Documentation for the user
help_lines = ["Type a number and push enter,",
"or use the scroll wheel."]
gc.gridx = 0
gc.gridwidth = 4
for line in help_lines:
gc.gridy += 1
help = JLabel(line)
gb.setConstraints(help, gc)
panel.add(help)
# Buttons
printButton = JButton(print_button_text)
def printTransforms(event):
for i, aff in enumerate(affines): # print all, including the first
matrix = zeros(12, 'd')
aff.toArray(matrix)
msg = "# Coarse affine matrix " + str(i) + ": \n" + \
"affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist())
# Print everywhere
print msg
IJ.log(msg)
System.out.println(msg)
printButton.addActionListener(printTransforms)
gc.gridx = 0
gc.gridy += 1
gc.gridwidth = 4
button_panel = JPanel()
button_panel.add(printButton)
gb.setConstraints(button_panel, gc)
panel.add(button_panel)
frame = JFrame("Translation control")
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE)
frame.addWindowListener(CloseControl(destroyables=listeners))
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setVisible(show)
return frame, panel, button_panel
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
def specifyRoiUI(roi=Roi(0, 0, 0, 0)):
# A panel in which to place UI elements
panel = JPanel()
panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10))
gb = GridBagLayout()
panel.setLayout(gb)
gc = GBC()
bounds = roi.getBounds() if roi else Rectangle()
textfields = []
roimakers = []
# Basic properties of most UI elements, will edit when needed
gc.gridx = 0 # can be any natural number
gc.gridy = 0 # idem.
gc.gridwidth = 1 # when e.g. 2, the UI element will occupy two horizontally adjacent grid cells
gc.gridheight = 1 # same but vertically
gc.fill = GBC.NONE # can also be BOTH, VERTICAL and HORIZONTAL
for title in ["x", "y", "width", "height"]:
# label
gc.gridx = 0
gc.anchor = GBC.EAST
label = JLabel(title + ": ")
gb.setConstraints(label, gc) # copies the given constraints 'gc',
# so we can modify and reuse gc later.
panel.add(label)
# text field, below the title
gc.gridx = 1
gc.anchor = GBC.WEST
text = str(getattr(bounds,
title)) # same as e.g. bounds.x, bounds.width, ...
textfield = JTextField(text,
10) # 10 is the size of the field, in digits
gb.setConstraints(textfield, gc)
panel.add(textfield)
textfields.append(
textfield) # collect all 4 created textfields for the listeners
# setup ROI and text field listeners
listener = RoiMaker(textfields,
len(textfields) -
1) # second argument is the index of textfield
# in the list of textfields.
roimakers.append(listener)
textfield.addKeyListener(listener)
textfield.addMouseWheelListener(listener)
# Position next ROI property in a new row by increasing the Y coordinate of the layout grid
gc.gridy += 1
# User documentation (uses HTML to define line breaks)
doc = JLabel(
"<html><body><br />Click on a field to activate it, then:<br />" +
"Type in integer numbers<br />" +
"or use arrow keys to increase by 1<br />" +
"or use the scroll wheel on a field.</body></html>")
gc.gridx = 0 # start at the first column
gc.gridwidth = 2 # Spans both columns
gb.setConstraints(doc, gc)
panel.add(doc)
# Listen to changes in the ROI of imp
roilistener = TextFieldUpdater(textfields)
Roi.addRoiListener(roilistener)
# Show window
frame = JFrame("Specify rectangular ROI")
frame.getContentPane().add(panel)
frame.pack()
frame.setLocationRelativeTo(None) # center in the screen
frame.setDefaultCloseOperation(
JFrame.DO_NOTHING_ON_CLOSE) # prevent closing the window
frame.addWindowListener(
CloseControl(roilistener)) # handles closing the window
frame.setVisible(True)