def run_stitch(filePath):
basePath,baseName = os.path.split(filePath)
imagePrefix = os.path.splitext(baseName)[0]
resizeName = basePath + "/" + baseName + "_tiles/resized/"
checkName = basePath + "/" + baseName + "_tiles/resized/" + imagePrefix + "_seq/"
activeName = basePath + "/" + baseName + "_tiles"
IJ.log("Stitching " + filePath + "...")
if (not os.path.isdir(checkName)):
thread = Thread.currentThread()
originalThread = thread.getName()
thread.setName("Run$_stitch_process")
options = "choose=" + resizeName + " select=" + activeName + "/tile_info.txt image_prefix=" + imagePrefix
Macro.setOptions(Thread.currentThread(),options)
try:
IJ.run("Stitch wrapper",options)
IJ.log("succeeded")
returnVal = 0
except:
IJ.log("failed")
os.rmdir(checkName)
returnVal = 1
thread.setName(originalThread)
Macro.setOptions(thread,None)
else:
IJ.log("skipped")
returnVal = 2
return returnVal
def findclearcell(inDir, currentDir, fileName):
print "Opening", fileName
file_path= os.path.join(currentDir, fileName)
options = ImporterOptions()
options.setId(file_path)
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
for imp in imps:
imp.show()
if not imps:
return
IJ.selectWindow(fileName + " - C=2")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=1")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=0")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=3")
IJ.run("8-bit")
IJ.run("Options...", "iterations=1 count=1 black edm=8-bit")
IJ.setThreshold(62, 255)
IJ.run("Convert to Mask", "method=Default backgorund=Dark black")
Macro.setOptions("Stack position")
for n in range(4,15):
n+=1
IJ.setSlice(n)
IJ.run(imp, "Analyze Particles...", "size=7.2-9 circularity=0.7-0.95 display")
def run_resize(filePath):
basePath,baseName = os.path.split(filePath)
checkName = basePath + "/" + baseName + "_tiles/resized/"
activeName = basePath + "/" + baseName + "_tiles"
IJ.log("Resizing " + filePath + "...")
if (not os.path.isdir(checkName)):
thread = Thread.currentThread()
originalThread = thread.getName()
thread.setName("Run$_resize_process")
totFileSize = get_directory_size(activeName) / 1048576.0
totFijiMem = Memory().maxMemory() / 1048576.0
IJ.run("Bio-Formats Importer", "open=["+ activeName +"/tile_1.ome.tif] color_mode=Default view=Hyperstack stack_order=XYCZT");
tileImage = WindowManager.getImage("tile_1.ome.tif")
nChannels = tileImage.getNChannels()
tileImage.close()
allowedMem = min(nChannels * totFijiMem/10.0, totFijiMem/3.0)
ratio = allowedMem / totFileSize
if (ratio < 1):
options = "choose=" + activeName + " sizing_ratio=" + str(ratio)
else:
options = "choose=" + activeName + " sizing_ratio=1.00"
Macro.setOptions(Thread.currentThread(),options)
try:
IJ.run("Batch resizer",options)
IJ.log("succeeded with sizing ratio=" + str(ratio))
returnVal = 0
except:
IJ.log("failed")
returnVal = 1
thread.setName(originalThread)
Macro.setOptions(thread,None)
else:
IJ.log("skipped")
returnVal = 2
return returnVal
def run_explode(filePath):
basePath,baseName = os.path.split(filePath)
checkName = basePath + "/" + baseName + "_tiles"
IJ.log("Exploding " + filePath + "...")
if (not os.path.isdir(checkName)):
thread = Thread.currentThread()
originalThread = thread.getName()
thread.setName("Run$_explode_process")
options = "open=" + filePath
Macro.setOptions(Thread.currentThread(),options)
try:
IJ.run("Explode Into Tiles",options)
IJ.log("succeeded")
returnVal = 0
except:
IJ.log("failed")
returnVal = 1
thread.setName(originalThread)
Macro.setOptions(thread,None)
else:
IJ.log("skipped")
returnVal = 2
return returnVal
BinarizeChromosome(impch1)
impch1.show()
ic = ImageCalculator()
#TODO
imp = ic.run("Multiply create stack", impch1, impch2);
imp.show()
IJ.run(imp, "Background Subtractor", "length=10 stack")
#options = "radius=3 cutoff=1 percentile=0.01"
options = "radius=%d cutoff=%d percentile=%f" % (radius, cutoff, percentile)
thread = thr.currentThread()
original_name = thread.getName()
thread.setName("Run$_my_batch_process")
Macro.setOptions(thr.currentThread(), options)
pt = IJ.runPlugIn(imp, "de.embl.cmci.pt3d.Dot_Detector_3D", "")
impdimA = imp.getDimensions()
ims = imp.createEmptyStack()
for i in range(impdimA[3]):
ims.addSlice(None, ByteProcessor(impdimA[0], impdimA[1]))
imp2 = ImagePlus("test", ims)
nSlices = imp2.getNSlices()
rt = ResultsTable.getResultsTable()
xindex = rt.getColumnIndex("x")
yindex = rt.getColumnIndex("y")
zindex = rt.getColumnIndex("z")
xA = rt.getColumn(xindex)
from ij import IJ, Macro
import java.lang.Thread as Thread
# from ij.gui import WaitForUserDialog
import glob, os
__author__ = 'Nichole Wespe'
inputDir = IJ.getDirectory("Choose Source Directory ")
outputDir = IJ.getDirectory("Choose Destination Directory ")
pattern = os.path.join(inputDir, "*Start.jpg")
fileList = glob.glob(pattern)
print "Found " + str(len(fileList)) + " sample files to montage."
subDir = os.path.join(outputDir, "Montages")
if not os.path.exists(subDir):
os.mkdir(subDir)
for f in fileList: # get date, sample from filename before opening
date, sample, time = os.path.basename(f).split(" ")
# find matching End.tif file
f2 = os.path.join(inputDir, str(date) +" "+ str(sample) +" End.jpg")
montage_name = " ".join([date, sample, "Montage.jpg"])
path = os.path.join(subDir, montage_name)
args = "sample=["+montage_name +"] file1=["+ f +"] file2=["+ f2 +"] path=["+ path +"]"
Macro.setOptions(Thread.currentThread(), args)
IJ.run("create horiz montage", args)
def main():
# Get active dataset
#img = IJ.getImage()
display = displayservice.getActiveDisplay()
active_dataset = imagedisplayservice.getActiveDataset(display)
if not active_dataset:
IJ.showMessage('No image opened.')
return
# Get image path
fname = active_dataset.getSource()
dir_path = os.path.dirname(fname)
if not fname:
IJ.showMessage('Source image needs to match a file on the system.')
return
# Open ROIs
rois = RoiManager.getInstance()
if not rois:
roi_path = os.path.join(dir_path, "RoiSet.zip")
if not os.path.isfile(roi_path):
try:
roi_path = glob.glob(os.path.join(dir_path, "*.roi"))[0]
except:
roi_path = None
if not roi_path:
IJ.showMessage('No ROIs. Please use Analyze > Tools > ROI Manager...')
return
rois = RoiManager(True)
rois.reset()
rois.runCommand("Open", roi_path)
IJ.log('Image filename is %s' % fname)
dt = get_dt(active_dataset)
rois_array = rois.getRoisAsArray()
for i, roi in enumerate(rois_array):
crop_id = i + 1
IJ.log("Croping %i / %i" % (crop_id, len(rois_array)))
# Get filename and basename of the current cropped image
crop_basename = "crop%i_%s" % (crop_id, active_dataset.getName())
crop_basename = os.path.splitext(crop_basename)[0] + ".ome.tif"
crop_fname = os.path.join(os.path.dirname(fname), crop_basename)
# Get bounds and crop
bounds = roi.getBounds()
dataset = crop(ij, datasetservice, active_dataset,
bounds.x, bounds.y, bounds.width,
bounds.height, crop_basename)
# Show cropped image
ij.ui().show(dataset.getName(), dataset)
# Save cropped image (ugly hack)
IJ.log("Saving crop to %s" % crop_fname)
imp = IJ.getImage()
bfExporter = LociExporter()
macroOpts = "save=[" + crop_fname + "]"
bfExporter.setup(None, imp)
Macro.setOptions(macroOpts)
bfExporter.run(None)
imp.close()
IJ.log('Done')
# ---------- --- ------ -------------------------------------------------
# 2014-10-15 JRM 0.1.00 Get'er done
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
from ij import IJ
from ij import Macro
from java.lang import Thread
# Prepare options for Bandpass filter
options = "filter_large=40 filter_small=3 suppress=None tolerance=5 autoscale saturate"
# Get the current thread
thread = Thread.currentThread()
original_name = thread.getName()
# Rename current thread
thread.setName("Run$_my_batch_process")
# Set the options for the current thread
Macro.setOptions(Thread.currentThread(), options)
# Get the current image
imp = IJ.getImage();
# Finally, run the bandpass filter without dialogs:
IJ.runPlugIn(imp, "ij.plugin.filter.FFTFilter", "")
# Be nice: undo naming, so other scripts may run with dialogs
thread.setName(original_name);
# Be safe: remove the thread's options from the table
# (which also removes the reference to the thread itself)
Macro.setOptions(thread, None)
def startPlugin(namePlugin): # the argument received is always a folder
IJ.log('Plugin ' + namePlugin + ' started at ' + str(time.strftime('%Y%m%d-%H%M%S')))
externalArguments = Macro.getOptions().replace('"','').replace(' ','')
externalArguments = os.path.normpath(externalArguments)
return externalArguments