def catchIJErrors(function):
try:
IJ.redirectErrorMessages()
return function()
except:
logWindow = WindowManager.getFrame("Log")
if not logWindow is None:
error_message = logWindow.getTextPanel().getText()
logWindow.close()
return error_message
def catchIJErrors(function):
try:
IJ.redirectErrorMessages()
return function()
except:
logWindow = WindowManager.getFrame("Log")
if not logWindow is None:
error_message = logWindow.getTextPanel().getText()
logWindow.close()
return error_message
def update_menus():
try:
IJ.redirectErrorMessages()
IJ.run('Update Menus')
except:
error_message = 'Error updating menus'
logWindow = WindowManager.getFrame("Log")
if not logWindow is None:
error_message = error_message + ': ' \
+ logWindow.getTextPanel().getText()
logWindow.close()
print error_message
global error
error += 1
if processFilter == 2:
IJ.run(dataImage,"Median...", "radius=2 stack")
theImage.close()
## Now runs the object counter on the processed tile
params = ("volume surface nb_of_obj._voxels " +
"nb_of_surf._voxels integrated_density mean_gray_value " +
"std_dev_gray_value median_gray_value minimum_gray_value " +
"maximum_gray_value centroid mean_distance_to_surface " +
"std_dev_distance_to_surface median_distance_to_surface centre_of_mass " +
"bounding_box dots_size=5 font_size=10 " +
"redirect_to=none")
IJ.run("3D OC Options", params)
params = ("threshold=" + str(intThreshold) +
" slice=1 min.=" + str(sizeThreshold) + " max.=24903680 objects surfaces statistics")
IJ.redirectErrorMessages(True)
IJ.run(dataImage, "3D Objects Counter", params)
dataImage.changes = False
dataImage.close()
## Saves the results table, surfaces image output, and run configuration
surfacesImage = WindowManager.getImage("Surface map of " + dataImage.getTitle())
IJ.run(surfacesImage,"8-bit","")
surfacesImage = make_image_binary(surfacesImage)
IJ.saveAsTiff(surfacesImage,parentLSMFilePath + "_tiles/surfaces/C" + str(analysisChannel) + "-tile_" + str(tile) + ".tif")
surfacesImage.close()
objectsImage = WindowManager.getImage("Objects map of " + dataImage.getTitle())
IJ.run(objectsImage,"8-bit","")
objectsImage = make_image_binary(objectsImage)
IJ.saveAsTiff(objectsImage,parentLSMFilePath + "_tiles/maps/C" + str(analysisChannel) + "-tile_" + str(tile) + ".tif")
objectsImage.close()
def PrepareDatabase(minw, maxw, baseDir, aspectRatio, majorWidth, majorHeight):
outputpath = baseDir + "/" + str(majorWidth) + "_" + str(majorHeight) + "_orig.tif"
#initialize stacks and labels
stackScaled = []
stackOrig = ImageStack(majorWidth, majorHeight)
imageNames = []
for i in range(minw, maxw+1):
stackScaled.append(ImageStack(i, int(round(i/aspectRatio, 0))))
imageNames.append('')
counter = 0
# initialize zip file for originals
zf = zipfile.ZipFile(baseDir + "/originals.zip", mode='w', compression=zipfile.ZIP_DEFLATED, allowZip64=1)
zf.writestr('from_string.txt', 'hello')
zf.close()
zf = zipfile.ZipFile(baseDir + "/originals.zip", mode='a', compression=zipfile.ZIP_DEFLATED, allowZip64=1)
for root, dirs, files in os.walk(str(baseDir)):
for f1 in files:
if f1.endswith(".jpg") or f1.endswith(".jpe") or f1.endswith(".jpeg"):
id = root + "/" + f1
IJ.redirectErrorMessages()
IJ.redirectErrorMessages(1)
imp = IJ.openImage(id)
if imp is None:
print "Couldn\'t open image from file:", id
continue
# skip non RGBimages
if imp.getProcessor().getNChannels() != 3:
print "Skipping non RGB image:", id
continue
#skip images with different aspect ratio
width = imp.getWidth()
height = imp.getHeight()
ratio = round(float(width)/float(height), 2) # this makes the ratio filering approximate, minor variations in image dimensions will be ignored
if ratio != aspectRatio:
IJ.log("Skipping image of size: " + str(width) + "," + str(height))
continue
# now scale the image within a given range
scale = Scale(imp.getProcessor())
IJ.log("Scaling image " + str(counter) + " " + str(id))
for i in range(minw, maxw+1):
stackScaled[i-minw].addSlice(None, ScaleImageToSize(scale, i, int(round(i/aspectRatio, 0))))
imageNames[i-minw] += str(id) + ";"
# save the originals to a temp directory
scaledOrig = ImagePlus(None, ScaleImageToSize(scale, majorWidth, majorHeight))
SaveToZip(zf, scaledOrig, baseDir, counter)
counter += 1
zf.close()
# save the stacks
for i in range(minw, maxw+1):
impScaled = ImagePlus(str(minw) + "_" + str(int(round(i/aspectRatio, 0))), stackScaled[i-minw])
impScaled.show()
#print imageNames
impScaled.setProperty('Info', imageNames[i-minw][:-1])
fs = FileSaver(impScaled)
filepath = baseDir + "/" + str(i) + "_" + str(int(round(i/aspectRatio, 0))) + ".tif"
IJ.log("Saving output stack" + str(filepath))
fs.saveAsTiffStack(filepath)
#IJ.save(impScaled, filepath);
IJ.log("Done")
'Image>Color>Hello, "Cello", Cello')
fake_plugin_jar(temporary_folder + '/test_2.jar',
'Image>Color>Hello, "Bello", Bello' + "\n" +
'Image>Color>Hello, "Allo", Bello' + "\n" +
'Plugins>bla>blub>, "Eldo", Rado' + "\n" +
'Plugins>bla>blub>, "Bubble", Rado' + "\n" +
'Plugins, "Cello", xyz' + "\n" +
'Plugins, "Abracadabra", abc')
# reset the plugins folder to the temporary directory
System.setProperty('plugins.dir', temporary_folder);
# Launch ImageJ
IJ.redirectErrorMessages()
ij = ImageJ()
error = 0
# Must show Duplicate command error
logWindow = WindowManager.getFrame("Log")
if logWindow is None:
print 'No error adding duplicate entries'
error += 1
else:
logText = logWindow.getTextPanel().getText()
if not 'Duplicate command' in logText:
print 'Error adding duplicate entries, but the wrong one'
error += 1
logWindow.close()
gd.addStringField("String to identify your input images", "_deconv")
gd.addRadioButtonGroup("Output", outDirChoices, 3, 1, outDirChoices[0])
gd.addRadioButtonGroup("Threshold Settings", thresholdChoices, 3, 1, thresholdChoices[0])
gd.addRadioButtonGroup("Overwrite", overwriteChoices, 2, 1, overwriteChoices[0])
gd.addCheckboxGroup(2, 1, mipChoices, [False, False], ["Do you want maximum intensity projections of your images?"])
gd.showDialog()
if gd.wasCanceled():
exit()
fileID = gd.getNextString()
outDirPref = gd.getNextRadioButton()
thresholdPref = gd.getNextRadioButton()
overwritePref = gd.getNextRadioButton()
mipPrefTIFF = gd.getNextBoolean()
mipPrefJPG = gd.getNextBoolean()
IJ.redirectErrorMessages(True)
inDir = IJ.getDirectory("Choose Directory Containing Input Files")
if inDir is None:
exit('No input directory selected!')
if outDirPref == outDirChoices[2]:
outDir = inDir
else:
outDir = IJ.getDirectory("Choose Directory For Output")
if outDir is None:
exit('No output directory selected!')
if outDirPref == outDirChoices[1]:
for dirpath, dirnames, filenames in os.walk(inDir):
if any([fileExt in f for f in filenames]):
structure = os.path.join(outDir, dirpath[len(inDir):])
def PrepareDatabase(minw, maxw, baseDir, aspectRatio, majorWidth, majorHeight):
outputpath = baseDir + "/" + str(majorWidth) + "_" + str(
majorHeight) + "_orig.tif"
#initialize stacks and labels
stackScaled = []
stackOrig = ImageStack(majorWidth, majorHeight)
imageNames = []
for i in range(minw, maxw + 1):
stackScaled.append(ImageStack(i, int(round(i / aspectRatio, 0))))
imageNames.append('')
counter = 0
# initialize zip file for originals
zf = zipfile.ZipFile(baseDir + "/originals.zip",
mode='w',
compression=zipfile.ZIP_DEFLATED,
allowZip64=1)
zf.writestr('from_string.txt', 'hello')
zf.close()
zf = zipfile.ZipFile(baseDir + "/originals.zip",
mode='a',
compression=zipfile.ZIP_DEFLATED,
allowZip64=1)
for root, dirs, files in os.walk(str(baseDir)):
for f1 in files:
if f1.endswith(".jpg") or f1.endswith(".jpe") or f1.endswith(
".jpeg"):
id = root + "/" + f1
IJ.redirectErrorMessages()
IJ.redirectErrorMessages(1)
imp = IJ.openImage(id)
if imp is None:
print "Couldn\'t open image from file:", id
continue
# skip non RGBimages
if imp.getProcessor().getNChannels() != 3:
print "Converting non RGB image:", id
if imp.getStackSize() > 1:
StackConverter(imp).convertToRGB()
else:
ImageConverter(imp).convertToRGB()
#skip images with different aspect ratio
width = imp.getWidth()
height = imp.getHeight()
ratio = round(
float(width) / float(height), 2
) # this makes the ratio filering approximate, minor variations in image dimensions will be ignored
if ratio != aspectRatio:
IJ.log("Skipping image of size: " + str(width) + "," +
str(height))
continue
# now scale the image within a given range
scale = Scale(imp.getProcessor())
IJ.log("Scaling image " + str(counter) + " " + str(id))
for i in range(minw, maxw + 1):
stackScaled[i - minw].addSlice(
None,
ScaleImageToSize(scale, i,
int(round(i / aspectRatio, 0))))
imageNames[i - minw] += str(id) + ";"
# save the originals to a temp directory
scaledOrig = ImagePlus(
None, ScaleImageToSize(scale, majorWidth, majorHeight))
SaveToZip(zf, scaledOrig, baseDir, counter)
counter += 1
zf.close()
# save the stacks
for i in range(minw, maxw + 1):
impScaled = ImagePlus(
str(minw) + "_" + str(int(round(i / aspectRatio, 0))),
stackScaled[i - minw])
impScaled.show()
#print imageNames
impScaled.setProperty('Info', imageNames[i - minw][:-1])
fs = FileSaver(impScaled)
filepath = baseDir + "/" + str(i) + "_" + str(
int(round(i / aspectRatio, 0))) + ".tif"
IJ.log("Saving output stack" + str(filepath))
fs.saveAsTiffStack(filepath)
#IJ.save(impScaled, filepath);
IJ.log("Done")
