def prepare_image_stacks(image_dir):
""" For each stack directory in image_dir, load the image sequence as
a stack and spatially calibrate the stack.
Returns:
images (list): The list containing the calibrated image stacks.
Args:
image_dir (str): The directory containing the image stack directories.
"""
images = []
for stack_dir in os.listdir(image_dir):
stack_dir_full_path = str(image_dir) + '/' + stack_dir
imp = FolderOpener.open(stack_dir_full_path)
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = 0.3296485
cal.pixelHeight = 0.3296485
cal.pixelDepth = 0.998834955
imp.setCalibration(cal)
imp.setTitle(
stack_dir) # name the image after its directory, e.g. OP_1
images.append(imp)
return images
def set_xyz_calibration(imp, dx, dy, dz, unit): cal = Calibration(imp) cal.setUnit(unit) cal.pixelWidth = dx cal.pixelHeight = dy cal.pixelDepth = dz imp.setCalibration(cal) return imp
def setSpatialCalibration(img, xwidth, unit="micron"):
""" img is an image object from openImage()
xwidth is the width of the image in units (default micron)
"""
if xwidth <= 0:
# If spatial calibration is not given. Do not try to set it.
return
pixelSize = xwidth / (1.0*img.getWidth())
cal = Calibration(img)
cal.pixelWidth = pixelSize
cal.pixelHeight = pixelSize
cal.setUnit(unit)
img.setCalibration(cal)
return img
n_channels = 1
n_slices = 1 # Z slices
n_frames = 1 # time frames
# Get current image
image = IJ.getImage()
# Check that we have correct dimensions
stack_size = image.getImageStackSize() # raw number of images in the stack
if n_channels * n_slices * n_frames == stack_size:
image.setDimensions(n_channels, n_slices, n_frames)
else:
IJ.log('The product of channels (' + str(n_channels) + '), slices (' +
str(n_slices) + ')')
IJ.log('and frames (' + str(n_frames) + ') must equal the stack size (' +
str(stack_size) + ').')
# Set calibration
pixel_width = 1
pixel_height = 1
pixel_depth = 1
space_unit = 'µm'
frame_interval = 1
time_unit = 's'
calibration = Calibration() # new empty calibration
calibration.pixelWidth = pixel_width
calibration.pixelHeight = pixel_height
calibration.pixelDepth = pixel_depth
calibration.frameInterval = frame_interval
calibration.setUnit(space_unit)
calibration.setTimeUnit(time_unit)
image.setCalibration(calibration)
image.repaintWindow()
# Set dimensions
n_channels = 1
n_slices = 1 # Z slices
n_frames = 1 # time frames
# Get current image
image = IJ.getImage()
# Check that we have correct dimensions
stack_size = image.getImageStackSize() # raw number of images in the stack
if n_channels * n_slices * n_frames == stack_size:
image.setDimensions(n_channels, n_slices, n_frames)
else:
IJ.log('The product of channels ('+str(n_channels)+'), slices ('+str(n_slices)+')')
IJ.log('and frames ('+str(n_frames)+') must equal the stack size ('+str(stack_size)+').')
# Set calibration
pixel_width = 1
pixel_height = 1
pixel_depth = 1
space_unit = 'µm'
frame_interval = 1
time_unit = 's'
calibration = Calibration() # new empty calibration
calibration.pixelWidth = pixel_width
calibration.pixelHeight = pixel_height
calibration.pixelDepth = pixel_depth
calibration.frameInterval = frame_interval
calibration.setUnit(space_unit)
calibration.setTimeUnit(time_unit)
image.setCalibration(calibration)
image.repaintWindow()
log_info += 'track_start: ' + str(track_start) + '\n'
# Get image and calibrate
imps = BF.openImagePlus(input_file)
imp = imps[0]
imp.setDisplayMode(IJ.COLOR)
imp.setC(color)
# imp.setDisplayRange(0.0, 3.0)
# imp.show()
log_info += 'frames: ' + str(imp.getNFrames()) + '\n'
log_info += 'width: ' + str(imp.getWidth()) + '\n'
log_info += 'height: ' + str(imp.getHeight()) + '\n'
cal = Calibration()
cal.setUnit('micron')
cal.pixelHeight = resolution
cal.pixelWidth = resolution
cal.pixelDepth = 0.
cal.fps = 1
cal.frameInterval = 1
imp.setCalibration(cal)
#-------------------------
# Instantiate model object
#-------------------------
model = Model()
model.setPhysicalUnits('micron', 'frames')
# Set logger
def set_calibration_obj(metadata_dict):
cal = Calibration()
cal.setUnit(metadata_dict["unit"])
cal.pixelWidth = 1 / metadata_dict["xpix"]
cal.pixelHeight = 1 / metadata_dict["ypix"]
return cal
def setScale(self, distCm, distPixel):
cal = Calibration()
cal.setUnit("cm")
cal.pixelWidth = distCm / distPixel
cal.pixelHeight = distCm / distPixel
ImagePlus().setGlobalCalibration(cal)
# call template=make_template(well, data_dir) here.
use_template = True
template = None #or make_template('B1', '10X_c2-SBS-2_2')
data_dirs = ['test']
# usually xyzct, except on bad days when it's xyczt(default)
# order = 'xyzct'
order = 'xyczt(default)'
rows = 'ABH'
columns = [str(x) for x in range(1, 13)]
wells = [row + column for row in rows for column in columns]
wells = ['A1']
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = pixel_width
cal.pixelHeight = pixel_width
def savename(well, data_dir):
# TODO better naming convention, use Site_0?
return home_dir + data_dir + '_MMStack_' + well + '.stitched.tif'
def tile_config_name(well, data_dir):
return
def macro_dir(s):
"""Wrap directory string so ImageJ macro accepts it as parameter.
def make_calibration(magnification):
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = args.magnification
cal.pixelHeight = cal.pixelWidth
return cal
if True:
# osx, unix
filesep = '/'
home_dir = '/broad/blainey_lab/David/lasagna/20150817 6 round/data/'
home_dir = '/Users/feldman/Downloads/20151209/'
else:
# windows
home_dir = 'D:\\User Folders\\David\\lasagna\\20151122_96W-G020\\'
# home_dir = '\\\\neon-cifs\\blainey_lab\\David\\lasagna\\20150817 6 round\\analysis\\calibrated\\raw\\'
filesep = '\\'
data_dirs = ['stack']
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = pixel_width
cal.pixelHeight = pixel_width
def savename(well, data_dir):
# TODO better naming convention, use Site_0?
return home_dir + data_dir + '_MMStack_' + well + '.stitched.tif'
def stitch_cmd_file(directory, layout_file):
s = """type=[Positions from file] order=[Defined by TileConfiguration] directory=%s layout_file=%s fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 computation_parameters=[Save computation time (but use more RAM)] image_output=[Fuse and display]"""
return s % (directory, layout_file)
for data_dir in data_dirs:
print home_dir + data_dir + filesep + '*.registered.tif'
files = glob(home_dir + data_dir + filesep + '*.registered.txt')
filters.setup("median", frame)
filters.rank(processor, filter_window, filters.MEDIAN)
# Perform gamma correction
processor.gamma(gamma)
frame = ImagePlus("Frame " + str(frame_i), processor)
# Rolling ball background subtraction
processor = frame.getProcessor()
bg_subtractor = BackgroundSubtracter()
bg_subtractor.setup("", frame)
bg_subtractor.rollingBallBackground(processor, rolling_ball_size/pixel_size, False, False, False, False, True)
frame = ImagePlus("Frame " + str(frame_i), processor)
# Calibrate pixels
calibration = Calibration()
calibration.setUnit("pixel")
calibration.pixelWidth = pixel_size
calibration.pixelHeight = pixel_size
calibration.pixelDepth = 1.0
frame.setCalibration(calibration)
# Save to output dir
file_name = output_dir + "/" + str(frame_i).zfill(4) + ".tif"
FileSaver(frame).saveAsTiff(file_name)
frame_i = frame_i + 1
