def trans_to_tif(file_list, overwrite = False):
if file_list is not None:
for path in file_list:
opts = ImporterOptions()
opts.setId(path)
opts.setVirtual(True)
opts.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
opts.setOpenAllSeries(True)
process = ImportProcess(opts)
try:
process.execute()
except:
pass
else:
process.execute()
try:
imps = ImagePlusReader(process).openImagePlus()
except:
IJ.log(path + "\n" + "This file was not properly processed")
pass
else:
dir_name = os.path.dirname(path)
file_name = os.path.basename(os.path.splitext(path)[0])
save_dir = os.path.join(dir_name, file_name)
if not os.path.exists(save_dir):
os.makedirs(save_dir)
imps = ImagePlusReader(process).openImagePlus()
for i, imp in enumerate(imps):
save_path = os.path.join(save_dir, file_name + "_pos{}.tif".format(i + 1))
if not os.path.exists(save_path):
IJ.saveAsTiff(imp, save_path)
IJ.freeMemory()
else:
if overwrite:
IJ.saveAsTiff(imp, save_path)
IJ.freeMemory()
else:
pass
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()
inner_list = []
for i, imp1 in enumerate(imps):
inner_list.append(imp1)
if len(inner_list) == n:
outer_list.append(inner_list)
inner_list = []
if i + 1 == len(imps) and inner_list != []:
empty_imp = create_empty_imp(imp1)
while n - len(inner_list) > 0:
inner_list.append(empty_imp)
outer_list.append(inner_list)
return outer_list
def integrated_combine(scale, col):
fl = get_file_list()
imps = [IJ.openImage(f) for f in fl]
resized_imps = [resize(imp, scale) for imp in imps]
del imps
imps_list = separate_imps(resized_imps, col)
del resized_imps
combined_imps = [combine_images(imps) for imps in imps_list]
vertival_combined_imp = combine_images(combined_imps, "vertically")
del combined_imps
vertival_combined_imp.show()
integrated_combine(scale = 0.25, col = 3)
IJ.freeMemory()
from ij.plugin import FolderOpener
from ij.plugin.filter import AVI_Writer
from ij.process import ImageConverter
from ij.gui import Arrow
from ij import ImagePlus, IJ
#from loci.plugins.util import BFVirtualStack
#from loci.formats import ChannelSeparator
# Record the starting time to calculate total time cost
startTime = System.currentTimeMillis()
time_stamp = '%06d'%(startTime%1000000)
# Clean up workspace
IJ.run("Close All");
IJ.run("Collect Garbage"); # Release occupied memory
print("Used memory at start: " + IJ.freeMemory())
#-------------------
# Facility functions
#-------------------
# NOTE the difference of two similar functions!
# save_snap_shot_seq_simple saves tif series with *** annotated *** spot
# save_snap_shot_seq saves tif series with *** centered *** spot
def save_snap_shot_seq_simple(imp, xml_filename, input_folder, output_folder,
ZOOM_BY_Z_DEPTH=False, Z1_CLOSE_TO_COVERSLIP=False,
TEST_RUN=False, ANNOTATE_Z=False,
DRAW_DOT=True, DRAW_BOX=True, L_RECT=100,
trackIDs=None, z_number_to_project=1):
def run_it():
# Make an error log file that can be written to
errorFilePath = os.path.join(experimentFolder, "errorFile.txt")
now = datetime.datetime.now()
errorFile = open(errorFilePath, "w")
errorFile.write("\n" + now.strftime("%Y-%m-%d %H:%M") + "\n")
errorFile.write("#### anilyze-data ####" + "\n")
errorFile.close()
#Runs microscope_check and defines the scanList accordingly
microscopeType = microscope_check(experimentFolder)
# Call list_scans and pass it the microscopeType variable. Gets the scanList
if microscopeType == "Olympus":
scanList = list_scans(experimentFolder, microscopeType)
print "The returned scanList is", len(scanList), "item(s) long"
elif microscopeType == "Bruker":
scanList = list_scans(experimentFolder, microscopeType)
print "The returned scanList is", len(scanList), "item(s) long"
# For each scan in the scanList, call the following functions:
for scan in scanList:
try:
basename = os.path.basename(scan) # get the scan name (basename)
#start new line in errorFile
errorFile = open(errorFilePath, "a")
errorFile.write("\n \n -- Processing " + basename + " --" + "\n")
errorFile.close()
make_hyperstack(basename, scan,
microscopeType) # open the hyperstack
imp = IJ.getImage() # select the open image
channels = imp.getNChannels() #gets the number of channels
print "The number of channels is", channels
singleplane = single_plane_check(
) #checks to see if sinegle z-plane
print "The returned value of singleplane is ", singleplane
make_MAX(singleplane
) # make max projection (skips if singleplane == True)
IJ.run("Close All")
#finishes errorFile
errorFile = open(errorFilePath, "a")
errorFile.write("Congrats, it was successful!\n")
errorFile.close()
IJ.freeMemory() # runs garbage collector
except: #if there is an exception to the above code, create or append to an errorFile with the traceback
print "Error with ", basename, "continuing on..."
errorFile = open(errorFilePath, "a")
errorFile.write("\n" + now.strftime("%Y-%m-%d %H:%M") +
"\n") #writes the date and time
errorFile.write("Error with " + basename + "\n" + "\n")
traceback.print_exc(
file=errorFile) # writes the error traceback to the file
errorFile.close()
IJ.run("Close All")
IJ.freeMemory() # runs garbage collector
continue # continue on with the next scan, even if the current one threw an error
#close out errorFile
errorFile = open(errorFilePath, "a")
errorFile.write("\nDone with script.\n")
errorFile.close()
