def run():
# Ask for a folder containing all the time points, one per folder
#dc = DirectoryChooser("Choose folder")
#folder = dc.getDirectory()
#folder = '/run/user/52828/gvfs/smb-share:server=keller-s7,share=microscopy1/SV3/RC_17-10-31/GCaMP6s_2_20171031_145624.corrected/SPM00'
#folder = "/home/albert/shares/zlaticlab/Nadine/Raghav/2017-05-10/GCaMP6s_1_20170510_115003.corrected/dff_on_fused/from_Raghav/MVD_Results/"
folder = "/home/albert/shares/zlaticlab/Nadine/Raghav/2017-05-10/GCaMP6s_1_20170510_115003.corrected/tests/dff_on_4view_fused/from_Raghav/MVD_Results/"
print folder
if not folder:
return
# Find the list of directories in that folder, and pick
# one single file inside each, ending in:
ending = "CM00_CHN00.klb"
#DEBUGGING
num_timepoints = 100
java = Weaver.method(
"""
static public final void maxer(final KLB klb, final ImgPlus target, final String path) throws java.io.IOException {
Cursor c1 = target.cursor();
Cursor c2 = klb.readFull(path).cursor();
while (c1.hasNext()) {
c1.next();
c2.next();
UnsignedShortType s1 = (UnsignedShortType) c1.get();
UnsignedShortType s2 = (UnsignedShortType) c2.get();
s1.set( (short) Math.max( s1.get(), s2.get() ) );
}
}
""", [KLB, ImgPlus, Cursor, UnsignedShortType])
max_img = None
klb = KLB.newInstance()
counter = 0
for root, dirs, files in os.walk(folder):
for filename in files:
if filename.endswith(ending):
counter += 1
path = os.path.join(root, filename)
print counter, path
# Use the first opened stack as the image stack into which to accumulate max values
if max_img is None:
max_img = klb.readFull(path)
else:
java.maxer(klb, max_img, path)
num_timepoints -= 1
if num_timepoints < 0:
break
# DONE
IJF.show(max_img)
class CellLoader(CacheLoader):
klb = KLB.newInstance()
def get(self, index):
img = CellLoader.klb.readFull(timepoint_paths[index]).getImg()
# Each cell has "1" as its dimension in the last axis (time)
# and index as its min coordinate in the last axis (time)
return Cell(
Intervals.dimensionsAsIntArray(img) + array([1], 'i'),
Intervals.minAsLongArray(img) + array([index], 'l'),
extractArrayAccess(img))
def openImage():
print rel_path
if rel_path.endswith(".klb"):
try:
klb = KLB.newInstance()
img = klb.readFull(os.path.join(base_path, rel_path))
IL.wrap(img, rel_path).show()
except:
print sys.exc_info()
else:
print "via IJ.open"
IJ.open(os.path.join(base_path, rel_path))
def openImage():
print rel_path
if rel_path.endswith(".klb"):
if (KLB == None):
print "Cannot open KLB due to missing module"
try:
klb = KLB.newInstance()
img = klb.readFull(os.path.join(base_path, rel_path))
IL.wrap(img, rel_path).show()
except:
print sys.exc_info()
else:
print "via IJ.open"
IJ.open(os.path.join(base_path, rel_path))
"maxTrust": 4, # for rejecting candidates
}
# Parameters for all to all registration
paramsTileConfiguration = {
"all_to_all": True,
"fixed_tile_index": [0], # tiles that won't move
"maxAllowedError": 0, # zero, as recommended by Saalfeld
"maxPlateauwidth": 200, # like in TrakEM2
"maxIterations": 1000, # like in TrakEM2
"damp": 1.0, # default
}
# STOP EDITING HERE
klb = KLB.newInstance()
# paths for same timepoint, 4 different cameras
paths = []
timepointDir = srcDir + "TM000000/"
for camera_index, channel_index in zip(xrange(4), [1, 1, 0, 0]):
paths.append(timepointDir + "SPM00_TM000000_CM0" + str(camera_index) +
"_CHN0" + str(channel_index) + ".klb")
for path in paths:
print basename(path)
img0 = klb.readFull(paths[0])
img1 = klb.readFull(paths[1])
img2 = klb.readFull(paths[2])
img3 = klb.readFull(paths[3])
def __init__(self, dimensions, filenames):
super(Thread, self).__init__()
self.filenames = filenames
self.aimg = ArrayImgs.floats(dimensions)
self.klb = KLB.newInstance()
def __init__(self):
self.klb = KLB.newInstance()
""" Read a file as an ArrayImg of UnsignedShortType """
ra = RandomAccessFile(path, 'r')
try:
if header < 0:
# Interpret from the end: useful for files with variable header lengths
# such as some types of uncompressed TIFF formats
header = ra.length() + header
ra.skipBytes(header)
bytes = zeros(reduce(operator.mul, dimensions), 'b')
ra.read(bytes)
return ArrayImgs.unsignedBytes(bytes, dimensions)
finally:
ra.close()
__klb__ = KLB.newInstance()
def readKLB(path):
return __klb__.readFull(path)
def writeZip(img, path, title=""):
if isinstance(img, RandomAccessibleInterval):
imp = IL.wrap(img, title)
elif isinstance(img, ImagePlus):
imp = img
if title:
imp.setTitle(title)
else:
syncPrint("Cannot writeZip to %s:\n Unsupported image type %s" %
def __init__(self, transforms, calibration):
self.transforms = transforms
self.klb = KLB.newInstance()