def open_image(username, password, host, server_port, group_id, image_id):
command="location=[OMERO] open=[omero:"
command+="server=%s\n" % server
command+="user=%s\n" % username
command+="port=%s\n" % server_port
command+="pass=%s\n" % password
if group_id > -1:
command+="groupID=%s\n" % group_id
command+="iid=%s] " % image_id
command+="windowless=true "
command+="splitWindows=false "
command+="color_mode=Default view=[%s] stack_order=Default" % ImporterOptions.VIEW_HYPERSTACK
print "Opening image: id", image_id
IJ.runPlugIn("loci.plugins.LociImporter", command)
imp = IJ.getImage()
return imp
def openImagePlus(HOST,USERNAME,PASSWORD,groupId,imageId):
options = ""
options += "location=[OMERO] open=[omero:server="
options += HOST
options += "\nuser="******"\npass="******"\ngroupID="
options += groupId
options += "\niid="
options += imageId
options += "]"
options += " windowless=true "
IJ.runPlugIn("loci.plugins.LociImporter", options);
def open_image_plus(host, username, password, group_id, image_id):
options = ""
options += "location=[OMERO] open=[omero:server="
options += host
options += "\nuser="******"\npass="******"\ngroupID="
options += String.valueOf(group_id)
options += "\niid="
options += String.valueOf(image_id)
options += "]"
options += " windowless=true "
IJ.runPlugIn("loci.plugins.LociImporter", options)
def openImagePlus(HOST,USERNAME,PASSWORD,groupId,imageId):
options = ""
options += "location=[OMERO] open=[omero:server="
options += HOST
options += "\nuser="******"\npass="******"\ngroupID="
options += str(groupId)
options += "\niid="
options += imageId
options += "]"
options += " windowless=true "
IJ.runPlugIn("loci.plugins.LociImporter", options);
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://www.nitrc.org/projects/cmtk/");
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://www.nitrc.org/forum/forum.php?forum_id=857")
from ij.gui import GenericDialog
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
gd = GenericDialog('About CMTK')
gd.addMessage('CMTK Registration suite is open source software released under GPLv3',)
gd.addMessage('Currently installed CMTK version: '+cmtkgui.installed_version())
gd.addMessage('CMTK binary directory: '+cmtkgui.bin_dir())
gd.setCancelLabel("CMTK Web Page")
gd.showDialog()
if gd.wasCanceled():
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://www.nitrc.org/projects/cmtk/")
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://www.nitrc.org/docman/view.php/212/708/UserGuideCMTK.pdf")
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://www.nitrc.org/docman/?group_id=212");
def process_imgdir( directory, close_after ) :
print( 'Processing: ' + directory )
original_image_filename = directory + '/uniform.tif'
probabilities_image_filename = directory + '/probabilities.tif'
cube_rois_filename = directory + '/CubeROIs.csv'
cubes = []
f = open(cube_rois_filename)
lines = f.readlines()
for line in lines[1:]:
#els = [ int(el)-1 for el in line.strip().split(',') ]
els = [ int(el) for el in line.strip().split(',') ]
cubes += [ { 'idx': els[0], 'class': els[1], 'x1':min(els[2],els[5]), 'y1':min(els[3],els[6]), 'z1':min(els[4],els[7]), 'x2':max(els[5],els[2]), 'y2':max(els[6],els[3]), 'z2':max(els[4],els[7]) } ]
f.close()
print( 'Read ' + str(len(cubes)) + ' cubes from file' )
#for cube in cubes:
#for cube_idx in range( len( cubes ) ):
for cube_idx in [0]:
cube = cubes[cube_idx]
print( cube )
all_edt_histograms['name'] += [ directory.split( '/' )[-1] + '_' + str(cube_idx) ]
all_skeleton_edt_histograms['name'] += [ directory.split( '/' )[-1] + '_' + str(cube_idx) ]
cube_basename = directory + '/cube_' + str(cube_idx) + '_'
# Check if we have a parameters file, and evaluate it if so, otherwise make one with defaults
param_filename = cube_basename + 'parameters.py'
# Make a default to start with
no_params_set = False
if not os.path.isfile( param_filename ):
f = open( param_filename, 'w' )
f.write( 'mesh_thresh=200\n' )
f.write( 'interior_coords=[ (1,1,1) ]\n' )
f.close()
no_params_set = True
if os.path.isfile( param_filename ):
f = open( param_filename )
lines = f.readlines()
for line in lines:
if 'mesh_thresh' in line:
mesh_thresh = eval(line.split('=')[1])
if 'interior_coords' in line:
interior_coords = eval(line.split('=')[1])
load_uniform = True
if load_uniform:
#open uniform
uniform = IJ.openImage( original_image_filename )
#crop uniform
uniform.setRoi( cube['x1'], cube['y1'], cube['x2'], cube['y2'] )
IJ.run( uniform, "Crop", "")
IJ.run( uniform, "Make Substack...", "slices=" + str(cube['z1']) + '-' + str(cube['z2']) )
uniform.close()
uniform = IJ.getImage()
IJ.saveAsTiff( uniform, cube_basename + 'raw.tif' )
#save max_projection of uniform
IJ.run(uniform, "Z Project...", "projection=[Max Intensity]")
uniform_mp = IJ.getImage()
IJ.run(uniform_mp, "Enhance Contrast", "saturated=0.35")
IJ.saveAsTiff( uniform_mp, cube_basename + 'raw_maxproj.tif' )
#open probabilites
probabilities = IJ.openImage( probabilities_image_filename )
#crop probabilites
probabilities.setRoi( cube['x1'], cube['y1'], cube['x2'], cube['y2'] )
IJ.run( probabilities, "Crop", "")
IJ.run( probabilities, "Make Substack...", "slices=" + str(cube['z1']) + '-' + str(cube['z2']) )
time.sleep( 5 )
probabilities.close()
probabilities = IJ.getImage()
#IJ.saveAsTiff( probabilities, cube_basename + 'probabilities.tif' )
time.sleep( 5 )
#save max_projection of probabilites
IJ.run(probabilities, "Z Project...", "projection=[Max Intensity]")
probabilities_mp = IJ.getImage()
IJ.run(probabilities_mp, "Enhance Contrast", "saturated=0.35")
IJ.saveAsTiff( probabilities_mp, cube_basename + 'probabilities_maxproj.tif' )
time.sleep( 5 )
# blur probabilities to help smooth the isosurfaces
blur_radius = 2
IJ.run( probabilities, "Gaussian Blur 3D...", 'x=' + str(blur_radius) + ' y=' + str(blur_radius) + ' z=' + str(blur_radius) )
#threshold probabilities
#IJ.run(probabilities, "Enhance Contrast", "saturated=0.35")
IJ.run( probabilities, "8-bit", "")
#IJ.saveAsTiff( probabilities, cube_basename + 'probabilities.tif' )
#for k in range( probabilities.getNSlices() ):
# probabilities.setSlice(k+1)
# probabilities.getProcessor().setThreshold( mesh_thresh - 1, mesh_thresh + 1, 0 )
#IJ.run( probabilities, 'Convert to Mask', 'method=Default background=Dark black')
#time.sleep( 5 )
IJ.saveAsTiff( probabilities, cube_basename + 'probabilities.tif' )
time.sleep( 5 )
#mesh binary_probabilities
#IJ.run( "3D Viewer", "")
threedType = 2
threedName = 'cube_' + str(cube_idx)
IJ.runPlugIn( "ij3d.ImageJ3DViewer", probabilities.getTitle() )
univ = Image3DUniverse.universes.get(0)
univ.addContent( probabilities, Color3f(1,1,1), threedName, mesh_thresh, [True, False, False], 2, threedType )
ImageJ3DViewer.select( threedName )
ImageJ3DViewer.exportContent( 'wavefront', cube_basename + 'mesh.obj' )
#smooth mesh
c = univ.getSelected()
n = c.getContent()
ctm = n.getMesh()
fim = customnode.FullInfoMesh( ctm.getMesh() )
ec = customnode.EdgeContraction( fim, False )
initial_num_verts = ec.getVertexCount()
num_to_remove = int( initial_num_verts * 0.1 )
#v = InteractiveMeshDecimation.simplify( ec, num_to_remove )
enable_smoothing = False
if enable_smoothing:
part = num_to_remove / 10
last = num_to_remove % 10
ret = 0
for i in range(10):
IJ.showProgress(i + 1, 10)
ret = ec.removeNext(part)
if (last != 0):
ret = ec.removeNext(last)
IJ.showProgress(1)
ctm.setMesh( fim.getMesh() )
ImageJ3DViewer.exportContent( 'wavefront', cube_basename + 'smooth_mesh.obj' )
# 3d viewer screenshot
screenshot_3d = univ.takeSnapshot()
IJ.saveAsTiff( screenshot_3d, cube_basename + 'mesh_screenshot.tif' )
#voxelize mesh
voxelizer = InteractiveMeshVoxelization()
voxelizer.voxelize( ctm, probabilities.getWidth(), probabilities.getHeight(), probabilities.getStackSize() )
#voxelization = WindowManager.getImage( ctm.getName() + '_voxelization' )
voxelization = WindowManager.getImage( 'null_voxelization' )
voxelization.setCalibration( probabilities.getCalibration().copy() )
#manually 3D fill vasculature, fill with thresholdable-color
#save selected vasculature
#call('process3d.Flood_Fill.fill', x,y,z)
if not no_params_set:
fill_color = 100
Flood_Fill.fill( voxelization, interior_coords[0][0], interior_coords[0][1], interior_coords[0][2], fill_color )
# Threshold to extract
#IJ.setAutoThreshold( voxelization, 'Default dark' )
#Prefs.blackBackground = true
#IJ.run( voxelization, 'Convert to Mask', 'method=Default background=Dark black')
for k in range( voxelization.getNSlices() ):
voxelization.setSlice(k+1)
voxelization.getProcessor().setThreshold( fill_color - 1, fill_color + 1, 0 )
IJ.run( voxelization, 'Convert to Mask', 'method=Default background=Dark black')
IJ.saveAsTiff( voxelization, cube_basename + 'voxelization.tif' )
# Calculate and record volume HERE
IJ.run(voxelization, "Z Project...", "projection=[Max Intensity]")
voxelization_mp = IJ.getImage()
IJ.run(voxelization_mp, "Enhance Contrast", "saturated=0.35")
IJ.saveAsTiff( voxelization_mp, cube_basename + 'voxelization_maxproj.tif' )
# Calculate EDT
IJ.run( voxelization, "Exact Euclidean Distance Transform (3D)", "" )
edt = WindowManager.getImage( 'EDT' )
IJ.run( edt, 'Fire', '' )
# Get the histogram data in an array
hist_nBins = int( ( hist_max - hist_min ) / hist_step )
#edt_stats = edt.getStatistics( Measurements.MEDIAN, hist_nBins, hist_min, hist_max )
edt_stats = StackStatistics( edt, hist_nBins, hist_min, hist_max )
hist_data = edt_stats.getHistogram()
hist_binLabels = [ ( hist_min + hist_step * el ) for el in range( hist_nBins ) ]
max_radius = 20
IJ.run( edt, 'Histogram', 'bins=' + str(hist_nBins) + ' x_min=' + str(hist_min) + ' x_max=' + str(hist_max) + ' y_max=Auto stack' )
edt_histogram = WindowManager.getImage( 'Histogram of EDT' )
IJ.saveAsTiff( edt_histogram, cube_basename + 'edt_histogram.tif' )
x_unit_scale = uniform.getCalibration().getX(1)
y_unit_scale = uniform.getCalibration().getY(1)
z_unit_scale = uniform.getCalibration().getZ(1)
f = open( cube_basename + 'edt_histogram.csv', 'w' )
for k in range( len( hist_data ) ):
f.write( str(hist_binLabels[k]) + '\t' + str(hist_data[k]*x_unit_scale*y_unit_scale*z_unit_scale) + '\n' )
#f.write( str(hist_binLabels[k]) + '\t' + str(hist_data[k]) + '\n' )
all_edt_histograms[hist_binLabels[k]] += [ hist_data[k] ]
f.close()
# Handling skeletons
IJ.run( voxelization, "Skeletonize (2D/3D)", "")
skeleton = voxelization # For simplicity later, but note that voxelization has been mutated
IJ.run(skeleton, "32-bit", "")
IJ.run(skeleton, "Calculator Plus", 'i1=' + str(skeleton.getTitle()) + ' i2=' + str(skeleton.getTitle()) + ' operation=[Scale: i2 = i1 x k1 + k2] k1=0.003921568627 k2=0' )
IJ.run(skeleton, "Z Project...", "projection=[Max Intensity]")
skeleton_mp = IJ.getImage()
IJ.run(skeleton_mp, "Enhance Contrast", "saturated=0.35")
IJ.saveAsTiff( skeleton_mp, cube_basename + 'skeleton_maxproj.tif' )
ic = ImageCalculator()
skeleton_edt = ic.run("Multiply 32-bit stack", edt, skeleton)
IJ.run( skeleton_edt, 'Fire', '' )
# Get the histogram data in an array
hist_nBins = int( ( hist_max - hist_min ) / hist_step )
#skeleton_edt_stats = edt.getStatistics( Measurements.MEDIAN, hist_nBins, hist_min, hist_max )
skeleton_edt_stats = StackStatistics( edt, hist_nBins, hist_min, hist_max )
hist_data = skeleton_edt_stats.getHistogram()
hist_binLabels = [ ( hist_min + hist_step * el ) for el in range( hist_nBins ) ]
IJ.run( skeleton_edt, 'Histogram', 'bins=' + str(hist_nBins) + ' x_min=' + str(hist_min) + ' x_max=' + str(hist_max) + ' y_max=Auto stack' )
skeleton_edt_histogram = WindowManager.getImage( 'Histogram of EDT' )
IJ.saveAsTiff( skeleton_edt_histogram, cube_basename + 'skeleton_edt_histogram.tif' )
unit_scale = uniform.getCalibration().getX(1)
f = open( cube_basename + 'skeleton_edt_histogram.csv', 'w' )
for k in range( len( hist_data ) ):
f.write( str(hist_binLabels[k]) + '\t' + str(hist_data[k] * unit_scale) + '\n' )
all_skeleton_edt_histograms[hist_binLabels[k]] += [ hist_data[k] * unit_scale ]
f.close()
else:
IJ.saveAsTiff( voxelization, cube_basename + 'voxelization.tif' )
# Free up resources
if close_after:
ImageJ3DViewer.close()
IJ.run( 'Close All', '' )
IJ.freeMemory()
# ---------- --- ------ -------------------------------------------------
# 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)
from ij.gui import GenericDialog
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
gd = GenericDialog('About CMTK GUI')
gd.addMessage('CMTK GUI is open source software released under GPLv3')
gd.addMessage('CMTK GUI is independently developed by Greg Jefferis and is NOT supported by CMTK team')
gd.setCancelLabel("CMTK GUI Web Page")
gd.showDialog()
if gd.wasCanceled():
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "https://github.com/jefferis/fiji-cmtk-gui")
# @ String (label="Omero User") user
# @ String (label="Omero Password", style="password") pwd
# @ String (label="Omero Server", value="omero.hpc.virginia.edu") server
# @ Integer (label="Omero Port", value=4064) port
# @ Integer (label="Omero Group ID", min=-1, value=53) omero_group_id
# @ Integer (label="Image ID", value=2014) image_id
from ij import IJ
from loci.plugins.in import ImporterOptions
# Main code
command="location=[OMERO] open=[omero:"
command+="server=%s\n" % server
command+="user=%s\n" % user
command+="port=%s\n" % port
command+="pass=%s\n" % pwd
if omero_group_id > -1:
command+="groupID=%s\n" % omero_group_id
command+="iid=%s] " % image_id
command+="windowless=true view=\'%s\' " % ImporterOptions.VIEW_HYPERSTACK
IJ.runPlugIn("loci.plugins.LociImporter", command)
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher",
"http://www.nitrc.org/forum/forum.php?forum_id=857")
def natural_keys(text):
return [ atoi(c) for c in re.split('(\d+)', text) ]
os.chdir(mypath)
alist = os.listdir(mypath)
alist.sort(key=natural_keys)
imp = IJ.openImage(mypath + alist[0])
signedpix = imp.getProcessor().toFloat(1, None)
width=signedpix.getWidth()
height=signedpix.getHeight()
stack = ImageStack(width, height)
i=0
for file in alist[:10]:
print("Current File Being Processed is: " + file)
imp = IJ.openImage(mypath + file)
signedpix = imp.getProcessor().toFloat(1, None)
stack.addSlice(str(i), signedpix)
i = i + 1
imp = ImagePlus("", stack)
ImageConverter(imp).convertToGray8()
imp.show()
IJ.runPlugIn("ij3d.ImageJ3DViewer", "")
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher",
"http://www.nitrc.org/docman/?group_id=212")
from ij import IJ
import jmFijiGen as jmg
import InvertGray8
# gitDir = os.environ['GIT_HOME']
# relImg = "/OSImageAnalysis/images"
# strImg = gitDir + relImg + "/bridge.gif"
# strImg = gitDir + relImg + "/latex.tif"
imgDir = os.environ['IMG_ROOT']
strImg = imgDir + "/key-test/KMAG/KMag1500Sei.tif"
print(strImg)
# 1. Open an image
imp = IJ.openImage(strImg)
imp.show()
# IJ.runPlugIn(imp, "ij.plugin.PNG_Writer", "/Users/jrminter/Desktop/Kmag1500Sei.png"
ip = imp.getProcessor()
IJ.runPlugIn("fiji.InvertGray8", imp);
IJ.runPlugIn("ij.plugin.PNG_Writer", "/Users/jrminter/Desktop/Kmag1500Sei.png")
# IJ.runPlugIn("fiji.InvertGray8", ip);
# print("dir out")
# print(out)
# res = InvertGray8()
# imp.show()
# IJ.runPlugIn(imp, "ij.plugin.PNG_Writer", "/Users/jrminter/Desktop/Kmag1500SeiInv.png")
from ij.gui import GenericDialog
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
gd = GenericDialog('About CMTK GUI')
gd.addMessage('CMTK GUI is open source software released under GPLv3')
gd.addMessage(
'CMTK GUI is independently developed by Greg Jefferis and is NOT supported by CMTK team'
)
gd.setCancelLabel("CMTK GUI Web Page")
gd.showDialog()
if gd.wasCanceled():
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher",
"https://github.com/jefferis/fiji-cmtk-gui")