i am new to imagej/fiji , i have an stack of images in .tif extension.
1.Load the Stack file ie., .tif file into ImageJ -- File -> Open -> Browse the Stack file(.tif)
2.Convert the Stack file of 16-bit image into 8-bit image-- Image -> Type -> select 8-bit
3.Apply Threshold on the 8-bit image-- Image -> Adjust -> Threshold
4.Now apply Segmentation with the plug-in “Segment blob in 3D Viewer” -- Plugins -> Segmentation -> Segment blob in 3D Viewer
5.Selection of a Seed Point -- plugins -> segmentation -> levelsets
6.Overlapping/Touching Cell Structures -- Process -> Binary -> Watershed
Analyze -> Analyze Particles -> Show -> Outlines -> Display Result
7.Applying the Skeletonize 3D -- Plugins -> Skeleton -> Skeletonize 3D
These tasks are achieved by doing each task individually . i want a single plugin that needs to do all this tasks at once. i don't know how to do this .. please someone help me..
i know we need to use ecllipse to write java code for plugin or macro ..i dont know how to achieve this tasks at once.
For your task, it should be pretty easy to create a macro by recording your work flow instead of hard coding an ImageJ plugin. Start up the command recorder by [Plugins > Macros > Record...] and then follow the steps you described. In the recorder window, a command for each step will be printed.
After executing 7 steps you described, click "Create" button in the top right. There, you will see a text window with commands (ImageJ) or a script editor with commands (Fiji). All you need then is to re-open the image stack and test the macro by [Macros > Run Macro] (ImageJ) or click "Run" button (Fiji script editor).
For more details, see slide 11 - 15 in the PDF linked below.
http://cmci.embl.de/_media/documents/slides/elmi2012.pdf
Or read from page 17 to 22 in the textbook linked in the following page.
http://cmci.embl.de/documents/ijcourses#macro_programming_in_imagej
You might need minor modifications to the automatically recorded commands since your work flow is slightly compicated as you are using the output image of the [Analyze Particle...] command, but please first try without any change.
You could also include your macro as a menu item if you save the macro as a file (.ijm) and save it under
[ImageJ root]/plugins/Scripts/
In this case, the file name should include underscore(_) to let the file name be appearing as a menu item under [Plugins > Scripts >].
Related
In Notepad++, view Settings > Shortcut Mapper > Scintilla commands. The command SCI_LINECOPY, currently assigned to Ctrl + Shift + X, copies the current line to the clipboard for pasting elsewhere. Very nice!
Does Visual Studio 2019 have something similar under Tools > Options > Environment > Keyboard? The Edit.Duplicate command, which copies the current line into the editor though not to the clipboard, is excellent but only superficially similar to SCI_LINECOPY.
For me, without any additional adjustment, this is a normal process as shown in the pictures below.
When the cursor is in the line (1), I can copy it to the clipboard without selecting the text first using Strg+C.
Followed of course by Strg+V (2) or optional by step (3).
The following is my code for building a 3D Earth and showing it:
com.google.ar.sceneform.rendering.Texture.Builder builder= com.google.ar.sceneform.rendering.Texture.builder();
builder.setSource(context,R.drawable.earth);
builder.build().thenAccept(texture ->
MaterialFactory.makeOpaqueWithTexture(context, texture).
thenAccept(material -> {
earthSphereRenderable =
ShapeFactory.makeSphere(0.1f, new Vector3(0.0f, 0.0f, 0.0f), material);
Toast.makeText(context,"All done",Toast.LENGTH_SHORT).show();})
);
The Toast message is coming but I am not able to see any object. Please note that R.drawable.earth is the Earth.jpg file that I put in there, which I want to show in AR.
Here is where I am rendering it
cornerNode = new Node();
cornerNode.setParent(this);
cornerNode.setLocalPosition(localPosition);
cornerNode.setRenderable(earthSphereRenderable);
Moreover, if I replace makeOpaqueWithTexture with makeOpaqueWithColor and but color as Red then the whole thing is working fine (i.e. I can see the sphere)
What must I change here in order to be able to see the sphere with Earth's texture on it?
At this time Google Sceneform 1.8 supports 3D assets in the following formats: .obj, .glTF for which animations not supported) and .fbx with or without animations. Supported textures' formats are: .mtl, .bin, .png and .jpg.
To import a new 3D asset with textures follow these steps:
Verify that your project's app folder contains a sampledata folder. To create the folder, right-click on the app folder in the Project window, then select New > Sample Data Directory.
The sampledata folder is part of your Android Studio project, but its contents will not be included in your APK. Copy your 3D model source asset file (.obj, .fbx, or .gltf), and all of its dependencies in any of the following formats:
.mtl
.bin
.png
.jpg
into the sampledata folder.
Do not copy these source files into your project's assets or res folder, as this will cause them to be included in your APK unnecessarily. Right click the 3D model source asset and select Import Sceneform Asset to begin the import process.
The values are used by the sceneform.asset() entry in the app's build.gradle, and determine where the .sfa and .sfb – ascii and binary asset definition – files (as well as their corresponding texture files .sfm) will be generated in your project. If you're importing a model for the first time, use the default values.
Hope this helps.
Ok, I got the answer to this. It does not accept jpg files but it accepts png files. Weird stuff!
I'm thinking about building a tool to help me visualise the generated LLVM-IR code for each instruction/function on my original source file.
Something like this but for LLVM-IR.
The steps to build such tool so far seem to be:
Start by with LLVM-IR AST builder.
Parse generated IR code.
On caret position get AST element.
Read the element scope, line, column and
file and signal it on the original source file.
Is this the correct way to approach it? Am I trivialising it too much?
I think your approach is quite correct. The UI part will probably be quite long to implement so I'll focus on the llvm part.
Let's say you start from a input file containing your LLVM-IR.
Step 1 process module:
Read file content to a string. Then Build a module from it, and process it to get the debug info:
llvm::MemoryBuffer* buf = llvm::MemoryBuffer::getMemBuffer(llvm::StringRef(fileContent)).release();
llvm::SMDiagnostic diag;
llvm::Module* module = llvm::parseIR(buf->getMemBufferRef(), diag, *context).release();
llvm::DebugInfoFinder* dif = new llvm::DebugInfoFinder();
dif->processModule(*module);
Step 2 iterate on instructions:
Once done with that, you can simply iterate on function and blocks and instructions:
// pseudo code for loops (real code is a bit long)
foreach(llvm::Function f in module.functions)
{
foreach(llvm::BasicBlock b in f.BasicBlockList)
{
foreach(llvm::Instruction inst in b.InstList)
{
llvm::DebugLoc dl = inst.getDebugLoc();
unsigned line = dl->getLine();
// accordingly populate some dictionary between your instructions and source code
}
}
}
Step 3 update your UI
This is another story...
I downloaded the sources of opencv-2.4.5 and I followed the tutorial (on the opencv site for windows) about the installing my own libraries everything. Ok. I created the opencv.sln file with cmake then I opened it with visual studio 2010 professional and I click the build solution but just 9 succeeded. Most of the 200 failed and most of the errors about tbbd.lib not found and opencv_core245d.lib not found with LNK1104 error. I'm trying to solve it for how many days. I've tried to show the ways of files... Anyone can help please? This is about my dissertation. (Build with No Common Language Support)
Collapse
I spent a good 15 hours or so to get the homework finished using OpenCV. 14.5 of those hours were spent just getting it setup properly. I ran through about 7 tutorial videos, several set up guides, and read hundreds of posts containing resolutions to the same erros I was getting.So I understand that simply installing OpenCV is not a trivial task and there are several steps to do this. So here is a straightforward tutorial for setting it up if you want to use openCV.
It is important to understand how things work as far as linking goes. There are three types of files, your headers that you include, the .dlls that contain the functions, and the libraries that contain instructions for how to call the functions in the .dlls. So here, rather than add just the .dlls as dependencies in the input linker, we are going to add the lib files. We will then create a System Environment variable that will tell the machine where to look for the .dll files when their corresponding library files are referenced. We will be creating a Property Sheet so that when we create a new project, we can simply add the settings to our project by clicking "Add Existing Property Sheet" instead of adding a new one. This way, we never have to go through this again.
FOLLOW THESE STEPS EXACTLY AND MAKE SURE VISUAL STUDIO IS CLOSED BEFORE CONTINUING
NOTE: When text is given in quotes with instructions to copy said text, do not include the quotes.
First of all, the easy part - download OpenCV 2.4.5 from their website. http://opencv.org/ and click OpenCV for Windows. It will download OpenCV 2.4.5.exe.
Install OpenCV
When the download finishes, double click OpenCV-2.4.5.exe to run it.
When asked where to extract the files, type ino the text box: "C:\"
C:\opencv should have been created upon completion. Navigate there to make sure.
Setup Environment Variables
WINDOWS 8 USERS:
- Right click the bottom left corner of your screen when the start icon pops up.
- Click "Command Prompt (Admin)"
- Type "SETX -m OPENCV_DIR C:\opencv\build" and press enter to set the opencv build directory as a System Environment Variable. Wait for the console to give you confirmation that it is set.
- Right click the bottom left corner of your screen when the "Start" icon pops up. Click System -> Advanced System Settings -> Environment Variables
- In the "System Variables" list box, under the "Variable" collumn, find "Path".
- Highlight the "Path" row and click edit.
- Click in the "Variable Value" text box and hit the "end" key on your keyboard to scroll to the end of the line and add a semicolon.
- Type the following: "C:\opencv\build\x86\vc10\bin;C:\opencv\build\x86\vc10" and click "OK". This will add the openCV bin directory to the system path.
WINDOWS 7 USERS:
Follow the same steps. The only difference is how you get to the command prompt and the system settings. Google how to set up an environment variable on Windows 7 if needed.
Setup Visial Studio
NOTE: I highly recommend VS2012 Professional because of advanced syntax highlighting that makes life so much easier when programming C++. This version can be downloaded and installed for free from DreamSpark. Just make and account with your student ID. However, the steps for VS2010 and VS2012 are the same.
Open Visual Studio
Click "New Project" and under "C++" select "Win32 Console Application".
When the window opens click "Next", check "Empty Project", and click "Finish". It is very important that you start with an EMPTY PROJECT without a precompiled header.
Locate the "Property Manager." By default, it should be a tab that is sometimes hard to miss. Alternatively it can be accessed by clicking from the toolbar "View" -> "Property Manager".
Right Click "Debug | Win32" and select "Add New Project Property Sheet". Name it "OpenCVProps" and click "Add".
Right Click your new property sheet and select "Properties".
From the left column, go to "C/C++" -> "General" and in the listbox on the right, select "Additional Include Directories" and click "Edit".
Add the following THREE directories:
"$(OPENCV_DIR)\include"
"$(OPENCV_DIR)\include\opencv"
"$(OPENCV_DIR)\include\opencv2"
From the left column, go to "Linker" -> "General" and in the listbox on the right, select "Additional Library Directories" and click "Edit".
Add the following directory:
"$(OPENCV_DIR)\x86\vc10\lib"
From the left column, go to "Linker" -> "Input" and in the listbox on the right, select "Additional Dependenies" and click "Edit".
Add the following .lib files to the depedencies. You may do this by copying and pasting these into that edit box. I have purposely not included a bulletpoint to make it easy for you to copy paste these.
opencv_core245d.lib
opencv_imgproc245d.lib
opencv_highgui245d.lib
opencv_ml245d.lib
opencv_video245d.lib
opencv_features2d245d.lib
opencv_calib3d245d.lib
opencv_objdetect245d.lib
opencv_contrib245d.lib
opencv_legacy245d.lib
opencv_flann245d.lib
NOTE: If building for release, these steps are the same. However, when copying and pasting these files, remove the 'd' from the end of each of them. The 'd' denotes that it is a release library and links to a release .dll.
Congrats! The difficult part is almost done! Click "OK" to close the Window.
Creating and Building a Test Project
Head over to our Solution Explorer. This can be focused from the toolbar via "View" -> "Solution Explorer"
Right click "Source Files" and select "Add" -> "New Item".
Select "C++ File (.cpp)" and name the file "main.cpp". Click "Add".
Copy and paste the following program and press "F7" on your keyboard and watch the bottom left corner of your screen to see if you get a "Build Succeeded" message. If so, only one step left before you compile and run! If not, please retrace your steps, or comment below and maybe I can help.
#include <opencv\cv.h>
#include <opencv\highgui.h>
int main(int argc, char* argv)
{ // openCV .image object
cv::Mat inputImage;
//Create a Window
cv::namedWindow("window",1);
// Initialize our image.
inputImage = cv::imread("Lenna.png");
// Always check to make sure that image has data.
if(inputImage.empty())
{
std::cout << "Image Failed to Load.";
return -1;
}
else
{
// All is well, display me.
cv::imshow("window",inputImage);
// Wait for user to press a key to exit.
cvWaitKey(0);
}
return 0;
}
If the build succeeded, then all that is left is to add the image to your folder. The placement is very important. I have copied the directoy that I have placed mine in. Follow the same directory pattern.
"C:\Users\Josh\Documents\Visual Studio 2012\Projects\ConsoleApplication3\ConsoleApplication3\Lenna.png"
Now hit "Ctrl + F5" To build, compile, and run to observe your image in the window!!
*IF YOU HAVE A WEBCAM*
Copy and paste the following code to check if OpenCV is working without being required to add an image. This is useful because if the above code doesn't work, but this code does, then you know you put the image in the wrong folder.
#include
#include
int main(int argc, char* argv)
{ // openCV .image object
cv::Mat image;
//Create a Window
cv::namedWindow("window",1);
// Create the capture object.
cv::VideoCapture device;
// Open your webcam.
device.open(0);
while (1)
{
// Read data from your device and store it to the image frame.
device >> image;
// Always check to make sure that image has data.
if(image.empty())
{
std::cout<< "Image Failed to Load.";
return -1;
}
else
{
// All is well, display me.
cv::imshow("window",image);
// Wait for user to press a key to exit.
cvWaitKey(33);
}
}
return 0;
}
Happy Coding!! Let me know if something didn't work so I can fix it!
Quick Answer
I have managed to compile OpenCV with TBB support using the tutorial here.
Specs: Visual Studio 2012/ Win 7 (64 bit)/ OpenCV 2.4.5/ CUDA 5
I have downloaded the latest TBB zip and extracted it to C:/src/OpenCV/dep (as suggested in the tutorial linked above).
You have to use the following TBB settings in CMake (adapt depending on your file paths):
TBB_LIB_DIR :: C:/src/OpenCV/dep/tbb41_20130314oss/lib/intel64/vc11
TBB_INCLUDE_DIRS :: C:/src/OpenCV/dep/tbb41_20130314oss/include/
TBB_STDDEF_PATH :: C:/src/OpenCV/dep/tbb41_20130314oss/include/tbb/tbb_stddef.h
WITH_TBB :: checked
BUILD_TBB :: unchecked
More Information
Initially, I also wanted to install OpenCV with CUDA 5 support, but it seems that CUDA 5 is incompatible with VS2012. This is the error I got when compiling
OpenCV:
Building NVCC (Device) object modules/core/CMakeFiles/cuda_compile.dir/src/cuda/Debug/cuda_compile_generated_matrix_operations.cu.obj
nvcc : fatal error : nvcc cannot find a supported cl version. Only MSVC 9.0 and MSVC 10.0 are supported
The good news is that you are using VS2010, which can be used with CUDA, as suggested here.
VS2012 can be set up to create projects with CUDA, but there is currently no way (AFAIK) to compile OpenCV with CUDA support for VS2012 (read this for more info).
In conclusion, people that need CUDA support should compile and use OpenCV with VS2010.
Also, when compiling OpenCV, I got the following errors:
error C3859: virtual memory range for PCH exceeded; please recompile with a command line option of '-Zm118' or greater
fatal error C1076: compiler limit : internal heap limit reached; use /Zm to specify a higher limit
I used the instructions here to finally compile OpenCV. I created a Property Sheet which had /Zm130 as an additional option in Common Properties > C/C++ > Command Line and added it
to all of the generated OpenCV projects.
For your reference, I also attach the CMake configuration and CMakeCache.txt file that I've used (CUDA is disabled as I am using VS2012):
CMake configuration: http://pastebin.com/8rJZGZ3T
CMakeCache.txt: http://pastebin.com/A0q8YgJg
Hope this helps and please comment if you need me to elaborate on any step.
I installed again opencv-master, opencv-2.4.5 and opencv-2.4.7 both to my new laptop. OpenCV-2.4.7's imread function returned always null but C-cvImageLoad worked well and opencv-master's cvLoadImage didn't work cvImageLoad or I missed something. But TBB's dir must be .../bin/ia32 not intel64 my OS is 64-bit but VS201x 32-bit this was my error. And I've get stitching and gpu errors and visual studio is telling about the error and this is usually memory allocation limit error and I did same things like your said #dilgenter and now it's working well but just 2.4.5 well and the python_d.lib error can be occur this is not a problem at debug mode I've read about this from a lot of forum sites. I'll try to find why 2.4.7's imread returning null Mat element. But now I'm too busy and this is
I am printing an EPS File generated with following credentials.
%-12345X#PJL JOB
#PJL ENTER LANGUAGE = POSTSCRIPT
%!PS-Adobe-3.0
%%Title: InvoiceDetail_combine
%%Creator: PScript5.dll Version 5.2.2
%%CreationDate: 10/7/2011 4:46:59
%%For: Administrator
%%BoundingBox: (atend)
%%Pages: (atend)
%%Orientation: Portrait
%%PageOrder: Special
%%DocumentNeededResources: (atend)
%%DocumentSuppliedResources: (atend)
%%DocumentData: Clean7Bit
%%TargetDevice: (HP Color LaserJet 4500) (2014.200) 0
%%LanguageLevel: 2
%%EndComments
While doing Selection Printing on Ricoh Afficio 2090 or any other drivers/printers get the following error printed on the sheets
ERROR: undefined
OFFENDING COMMAND: F4S47
Stack:
.
Kindly Review and suggest a turn around for the same as i am already stuck in this hell. I have tried to convert/extract in PS but all in vain. I am using gsview to Print and view these files.
This is the problem:
%%PageOrder: Special
A ps document with "Special" page order can NOT be re-ordered. You cannot do a selection or range with this file because it is broken for this use. You must reprocess the file using Distiller or ghostscript (ps2ps or ps2pdf) in order to print selected or re-ordered pages from the document.
You can avoid this by generating your postscript files with a real Postscript™ driver (one not created by Microsoft).
The GSView Documentation has more about this.
Previously:
This line ...
%%TargetDevice: (HP Color LaserJet 4500) (2014.200) 0
... tells us that the file was generated with HP printers as a target. So this really is not an EPS file. Because it's not Encapsulatable. To generate output on a printer the file has to execute the showpage operator, which is a no-no for EPS files.
So uncheck the EPS box (it's a big fat lie, anyway), and select (install) a Generic Postscript driver. If you need to send it to multiple makes of printer, the file needs to make as few assumptions about the printer as possible.
The first thing is that this is not a valid EPS file, as it has PJL attached at the front. Many PostScript printers will strip this off, but by no means all.
This probably is not the source of the problem.
There is no way to 'review' the problem as you have not supplied the complete PostScript program. Without that there is no way to tell what is actually wrong, the error message tells you that the interpreter encountered 'F4547' while trying to parse a token, and that this has not been defined as a routine.
Most likely the file is corrupt, either damaged in some way, or possibly it is a biinary file and has been transmitted by some process which does has done some kind of conversion (CR/LF is common). The offending command looks like its ASCIIHex encoded, so that may be a red herring.
If you want additional help, you are going to have to make the whole program available somewhere.