i need to get the current image opened after importing an image sequence to ImageJ.
As i need to save the overlay information to a text file bearing the name of the image
int number = imp.getImageStackSize();
if(number > 1)
{
ImagePlus check = imp.duplicate();
gd.removeAll();
gd.addMessage(check.getTitle());
gd.showDialog();
}
imp.gettitle returns the folder name the images were loaded from.
couldn't find any solution so far :(
Any way to find the text in the status bar would be appreciated..
it was a simple issue..
the name of the current image can be retrieved by the following piece of code..
fileName = imp.getImageStack().getShortSliceLabel(imp.getCurrentSlice());
Thanks everyone..
Related
I am not a coder but trying to turn ThunderSTORM's batch process into an automated one where I have a single input folder and a single output folder.
input_directory = newArray("C:\\Users\\me\\Desktop\\Images");
output_directory = ("C:\\Users\\me\\Desktop\\Results");
for(i = 0; i < input_directory.length; i++) {
open(input_directory[i]);
originalName = getTitle();
originalNameWithoutExt = replace( originalName , ".tif" , "" );
fileName = originalNameWithoutExt;
run("Run analysis", "filter=[Wavelet filter (B-Spline)] scale=2.0 order=3 detector "+
"detector=[Local maximum] connectivity=8-neighbourhood threshold=std(Wave.F1) "+
"estimator=[PSF: Integrated Gaussian] sigma=1.6 method=[Weighted Least squares] fitradius=3 mfaenabled=false "+
"renderer=[Averaged shifted histograms] magnification=5.0 colorizez=true shifts=2 "+
"repaint=50 threed=false");
saveAs(fileName+"_Results", output_directory);
}
This probably looks like a huge mess but the original batch file used arrays and I can't figure out what that is. Taking it out brakes it so I left it in. The main issues I have revolve around the saveAs part not working.
Using run("Export Results") works but I need to manually pick a location and file name. I tried to set this up to take the file name and rename it to the generic image name so it can save a CSV using that name.
Any help pointing out why I'm a moron? I would also love to only open one file at a time (this opens them all) and close it when the analysis is complete. But I will settle for that happening on a different day if I can just manage to save the damn CSV automatically.
For the most part, I broke the code a whole bunch of times but it's in a working condition like this.
I appreciate any and all help. Thank you!
enter image description hereI need help to extract text from scanned pdf. I have tried to extract it using pymupdf and pillow and pytesseract, but I am not getting correct results, there are some text are returned incorrectly.
I tried to increase sharpness and brightness but still did not get a good result.
I have already checked many answers using OpenCV, but I am fairly new to OpenCV. Please help.
def pdf_to_text(pdf_file,text_file_name,rotate_pdf=False,adj_sharpness=False,adj_contract=False,adj_brightness=False):
try:
doc = fitz.open(pdf_file)
zoom_x=2.5
zoom_y=2.5
mat = fitz.Matrix(zoom_x,zoom_y)
files = []
for n in range(doc.page_count):
#print(f'Extracting {n} image')
page = doc.load_page(n)
if rotate_pdf:
page.set_rotation(-90)
#pix = page.get_pixmap(dpi=600)
pix = page.get_pixmap(alpha=False,matrix=mat,dpi=300)
folder=os.path.join(os.getcwd(),"images")
if not os.path.exists(folder):
os.makedirs(folder)
fname = os.path.join(folder,"page-%i.png"%n)
pix.save(fname)
im = Image.open(fname)
im = adjust_sharpness(im,2.5)
im = adjust_brightness(im,1.1)
im = adjust_contrast(im,2.8)
#im = im.filter(ImageFilter.SMOOTH)
im.save(fname)
#remove_lines(fname)
files.append(fname)
#if n>1:
# break
print("Extracting Images Completed")
print("Now Extracting data from image file")
for file in files:
#file = "./images/page-0.png"
text = image_to_string(file, lang_code="eng")
#text = image_to_string(file, lang_code="fra+eng")
make_textfile(text, text_file_name)
print("Extracting and saving text files completed")
except FileNotFoundError:
print(f"File not available {pdf_file}")
return None
pytesseract.image_to_string(image=Image.open(image_name))
The image:
To process tables in Tesseract you are likely to need to remove table lines to help the OCR engine with the segmentation of the image. However, you may try this first to see how Tesseract will perform.
text = image_to_data(file, lang="eng", config="--psm 6")
This will treat your image as a block to avoid missing as much text as possible, but removing the lines and binarizing the image will lead to better results. This link would help you with the removal of lines.
I want to merge two sets of fluorescence microscope images into a green & blue image, but I'm having trouble with the macro (haven't used ImageJ before). I have a folder of FITC-images to be coloured green and a folder of DAPI-images to be coloured blue. I have been using this modified version of a macro I found online:
macro "batch_merge_channel"{
count = 1;
setBatchMode(true);
file1= getDirectory("Choose a Directory");
list1= getFileList(file1);
n1=lengthOf(list1);
file2= getDirectory("Choose a Directory");
list2= getFileList(file2);
n2=lengthOf(list2);
open(file1+list1[1]);
open(file2+list2[1]);
small = n1;
if(small<n2)
small = n2;
for(i=0;i<small;i++)
{
run("Merge Channels...", "c2="+list1[1]+ " c3="+list2[1]+ " keep");
name = substring(list1, 0, 13)+")_merge";
saveAs("tiff", "C:\\Merge\\"+name);
first += 2;
close();
setBatchMode(false);
}
This, however returns an error
x.tif is not a valid choice for "C2 (green):"
with x being the name of the first file in the first folder.
If I merge the images manually, two by two, there is no error. So I'm presuming the problem is in the macro code.
I found several cases of this error online, but none of the solutions that seemed to work for those people work for me.
Any help would be appreciated!
In case you didn't solve this already, a great place to get help on ImageJ questions is the forum.
I can suggest a couple of ideas:
Is your image successfully opened by the macro? You could set the batch mode to false to check this.
It looks to me like the for loop does not employ the variable i. It works on the first pair of
images (list1[1], list2[1]), then closes the merged image, but then
tries to process image 1 again. To actually loop through all the
images in the folder, you have to put inside the loop something
like this (you don't need 'keep' -- better to leave it out so the source images will automatically be closed)
open(file1+list1[i]);
open(file2+list2[i]);
run("Merge Channels...", "c2="+list1[i]+ " c3="+list2[i]);
-- Turning off batch mode should be done after the loop, not within the loop.
Here's a version that works for me.
// #File(label = "Green images", style = "directory") file1
// #File(label = "Blue images", style = "directory") file2
// #File(label = "Output directory", style = "directory") output
// Do not delete or move the top 3 lines! They contain essential parameters
setBatchMode(true);
list1= getFileList(file1);
n1=lengthOf(list1);
print("n1 = ",n1);
list2= getFileList(file2);
n2=lengthOf(list2);
small = n1;
if(small<n2)
small = n2;
for(i=0;i<small;i++)
{
image1=list1[i];
image2=list2[i];
open(file1+File.separator+list1[i]);
open(file2+File.separator+list2[i]);
print("processing image",i);
run("Merge Channels...", "c2=&image1 c3=&image2");
name = substring(image1, 0, 13)+"_merge";
saveAs("tiff", output+File.separator+name);
close();
}
setBatchMode(false);
Hope this helps.
i have two volumes (.nrrd) of different qualities. the user can browse through the layers. if a key is pressed
i want to load the slice of the volume with better quality.
my volume is similar to this one: lesson 10 xtk
i've found:
volume.children[2].children[0].children[0].texture.file = "http://path/to/file.ext";
but if i apply some kind of file (.jpg, .dcm) nothing happens.
is this the right approach to change the slice to go inside the children and change the texture?
or shall i load the selected slice seperate as an object and apply it to the "lower-quality-volume" somehow?
edit:
this is what i tried so far (i get errors with dcms but not with jpgs):
if (event.keyCode == 83) { // "s"-button
volume.children[2].children[0].children[0].texture.file = "http://localhost:3000/112.jpg";
volume.children[2].children[0].children[0].modified();
r.render();
}
edit2: this is whats in my r.onShowtime = function() {}
volume.children[2].children[0].texture.file = 'http://localhost:3000/112.jpg';
volume.children[2].children[0].visible = true; // to activate the first layer
volume.children[2].children[0].modified();
console.log(volume.children[2].children[0].visible +" "+ volume.children[2].children[0].texture.file);
it outputs "true hostname/112.jpg"
when i inspect the .jpg in firebug the header is ok but the answer is "null"
when i inspect console.log(volume.children[2].children[0]); with firebug
.texture.file is set to hostname/112.jpg
when i go to "network" the .jpg has been transfered successfully
please notice that 112.jpg and level.jpg are the same. the first one is getting loaded in r.onShowtime and the other one is loaded at a keypressed event.
EDIT 3: volume.children[2].children[0] is of the type "X.slice", isn't it?
here is my approach: jsFiddle
and this is my actual issue and still not working: jsFiddle
Mhh..
I think a call to object.modified() is missing in the file setter (and in others setters from inject classes). Let's see when Haehn will come if he wants to change something internaly, but for the moment could you try to call it by yourself ?
You can try to add after the modification of texture :
volume.children[2].children[0].children[0].modified();
And if it doesn't work, in addition :
renderer.render();
Edit :
It's strange, I did a similar code and it did something. Can you please try something like that with opening your javascript console (Firefox, Chrome,... has one) and tell me the error you get ?
renderer.onShowtime = {
for (var i=0 ; i< volume.children[2].children.length ; i++) {
volume.children[2].children[i].texture.file="myimage.jpeg";
volume.children[2].children[i].modified();
}
}
It is important you call it in the onShowtime, because before the volume is not loaded, and so slicesX, slicesY... don't exist.
Edit2 :
Hey,
Thanks to the informations you added I think I've got the point ! In the render() method of our renderer3D there is a test on texture._dirty flag, that you cannot change from outside the framework. In addition the 1st rendering with a texture make that flag false, and loading a new texture doesn't seem to set that flag back to true in the current XTK. So, I think, we have to add it in the loader.load(texture, object) method. I'll make an issue on Github and see what Haehn thinks of it !
Can someone post an example of how to use the camera, capture the image, preview the image in an image view, compress the image in jpg and upload the bytes to a remote server? The closest I have been able to find is below. We have the camera, and image capture but we need to know how to preview, compress/resize jpg to 640/480px and around 120kb size then upload bytes to a remote server. Thanks to all of you for your help.
http://android-coding.blogspot.com/2010/12/intent-of-mediastoreactionimagecapture.html
Looking at your code there are some things i notice to be wrong:
-[ for the camera functionality ]-
Don't create a file yourself. This is not necessary. Use the ContentResolver.Insert function to give you back a file URI that will contain the picture, just like done here and also take over the isMounted if you want to check if there is external memory present.
You are checking if there's data and then checking if there is a thumbnail. If there's no thumbnail you'll get the full image. That doesn't make sense unless you want to make a thumb of the full version if the thumb is not given back?? Don't you just want to grab the full version or both but not this OR that?
You are retrieving a string value variable to get the URI to the full image? Just save the uri you get from the code in my first point as a property (let's say "myPhotoURI" in the activity class. In the OnActivityResult function that handles your camera intent result just recall that URI and use it as following (Yes, you're seeing it right; i'm not even using the data intent for this just the remembered uri):
Bitmap imageFromCam = MediaStore.Images.Media.GetBitmap(this.ContentResolver, Android.Net.Uri.Parse(myPhotoURI));
To grab an image from the gallery just use the SelectImageFromStorage() function from this question's answer and retrieve the URI of the chosen image in the OnActivityResult check just use:
Android.Net.Uri selectedImageUri = data.ToURI();
That's what worked like a charm for me.
-[sending the data to a webservice ]-
Assuming you're using a WCF or webservice that'll want to receive the image data as a byte array; the approved answer to this question gives a nice example of how to convert your image to an byte array (which is what a WCF webservice wants, anyway)
I think that these directions will get you going.
here is the closest example to date... this brings back Null data when the extra output is used. Still trying to get access to the full image/photo and not a thumbnail.
private void saveFullImage() {
Intent intent = new Intent(Android.Provider.MediaStore.ActionImageCapture);
string file = System.IO.Path.Combine(Android.OS.Environment.DirectoryDcim.ToString(), "test.jpg");
var outputFileUri = Android.Net.Uri.Parse(file);
intent.PutExtra(Android.Provider.MediaStore.ExtraOutput, outputFileUri);
StartActivityForResult(intent, TAKE_PICTURE);
}
protected override void OnActivityResult(int requestCode, Result resultCode, Intent data)
{
base.OnActivityResult(requestCode, resultCode, data);
if (requestCode == TAKE_PICTURE)
{
Uri imageUri = null;
// Check if the result includes a thumbnail Bitmap
if (data != null)
{
if (data.HasExtra("data"))
{
var thumbnail = data.GetParcelableArrayExtra("data");
// TODO Do something with the thumbnail
}
}
else
{
var outputFileUri = data.GetParcelableArrayExtra("outputFileuri");
// TODO Do something with the full image stored
// in outputFileUri
}
}
}