Hi I have 430 files i need to analyse which are in a folder tree
The plugin i am using is this one: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Intensity_Ratio_Nuclei_Cytoplasm_Tool
the files before being analysed need to be converted to 16 bit greyscale image, then a specific threshold applied on some of them (all have the same file start name eg, DAPI.tif, DAPI 2.tif)
Then each DAPI X.tif turned into a mask and analysed using the plugin is analysed with two other files (TRITC X.tif and FITC X.tif) then the results saved.
What is the best way to do this, as it would take me several hours to do this manually?
Btw I am a beginner when it comes to imageJ so detailed instructions would be useful.
Thanks guys
Please take a look at this page of the ImageJ wiki:
https://imagej.net/Batch
I need some command-line tool to create dds (dxt5 format) from two .png files -- one with rgb channels and one with alpha. It's because I have a waste amount of images to process -- I can't do it manually. It's no problem for me to create script for generating batch file to process all images one by one, but I need tool to create dds from two png-s.
Anyone known such command-line tool ?
Thanks.
P.S. nvDXT.exe is very good but it can't combine rgb and alpha from different files.
If you have Photoshop, you could always use Batch Script (see Batch Scripting Tutorial for an example) to merge the channels (with NVidea plug in installed, you could probably even do the DDS conversion too). Just a thought.
I recently discovered that the PDFs exported by the Fast Report's PDF export filter aren't displayed correctly in Mac OSX, iOS and Android devices.
Fast Report informed that their pdf implementation only support Windows and they can't say when the new implementation that they are working on will be available.
I also tried to use the Gnostice export filter, but their demo installer didn't work in Delphi XE and when I contacted them, they took 15 days to send me some attached dcus which also didn't work. So I'm searching for another option.
If you know or use a PDF export filter which works with Fast Report, please let me know.
November 2015: Fast Report now have PDF/A support, with this option enabled the PDFs are fine on all platforms.
October 2014 - Fast Report 5 still seems to generate "Windows-only" PDF. A production-ready solution for this problem would be a benefit for cross-platform developers, given that Fast Report is the report generator bundled with Delphi.
Here is a fresh example generated with the Fast Report 5 demo, displayed with Adobe Reader 11 on Android 4.4:
And on Windows:
Fast Report informed that their pdf implementation only support Windows and they can't say when the new implementation that they are working on will be available.
I'm not sure that should be taken literally, considering PDF is supposed to be a cross platform format. It more likely means they don't actually have the time, equipment or expertise to test with those platforms. The PDF export filter that I'm using is the one built into Fast Report! It surely has some bugs, but I managed to work around them. And I think that might also work for you: Start with a simple document that does export properly, start adding features until it brakes, then you know what brakes it and you'll know how to work around the problem.
From my experience, here's what got me into trouble:
Rounded corners in the PDF document didn't look like the ones in the Fast Report preview. My fix: Found a combination of settings that made the exported PDF look exactly like the preview document. For me rounded corners were just a cosmetic feature, and with cosmetics there's no "One Look"; The alternative worked just fine. This might actually be fixed in the most recent version, but I didn't bother changing the document to test.
Transparency issues and outline issues. When working with the Fast Report editor (and when looking at it's previews) it's easy to overlap objects. You don't see this because of the object opacity. When exporting to PDF overlapped objects somehow managed to "print" outlines, and it obviously looked ugly. My fix: pay closer attention to those objects, make sure they don't overlap or make sure they don't generate outlines if no outlines are supposed to be seen.
Also make sure you test using ADOBE Reader, on any of the given platforms. If it works with the Adobe reader but doesn't work with other readers, there might be a bug in the 3rd party reader!
Edit: Here (link) is a sample PDF document generated by my Fast Reports application. I have no idea what kinds of documents you generate, but in my book that's a mighty complex document. Notice the diagonal line that starts where the table data ends, notice the embedded images (bar code, stamp, signature).
I opened that document on the following mobile devices:
iPad, running iOS: The document renders 90% ok. Images are not rendered at all, but they're not important to my document (and that's very likely a problem with the iOS reader). All the fancy colored lines and rounded corners are properly rendered. Some text is not properly rendered, and I'm pretty sure that didn't render because the "box" that contains it is too small for the contents. That most likely happens because I didn't embed the TTF fonts into the PDF and the Apple font on iOS didn't perfectly match the Microsoft font that was used on Windows.
Samsung Galaxy S2, running Android 2.3: The document renders 100% correctly.
Samsung Something(??), running Windows Mobile 6.5 and the FoxReader: The document is totally gibberish: pictures showed up but the spacing between letters was messed so bad it's impossible to read. I blame the reader, it's not Acrobat and it probably wanted to be "smart". And it broke it's teeth in my text encoding, because my text is not English.
About the PDF format: A document is "PDF" if it conforms to the standard, here's some Wikipedia info on that. In theory a PDF document should render exactly the same way any way you look at it, but there are forces at play that might work against this:
Not all readers are "Adobe Acrobat". In theory they're all compatible, in practice they're most like not 100% compatible.
PDFs that don't embed fonts depend on the fonts available on the host system. If they're not the exact same fonts there's trouble ahead, because they might have slightly differing sizes. Since we're talking about PDF's that were generated on Windows and opened on iOS or Android, those are obviously different platforms and they're guaranteed to use different fonts (because fonts are licensed, and I doubt Microsoft will licence it's fonts to Apple. I also doubt Apple would want Microsoft fonts). One possible solution is embedding fonts, but that makes your PDF files significantly larger.
AFAIK you can export your Fast Report pages as metafiles (i.e. vectorial Windows format, which is in fact a raw serialization of GDI commands).
Then you could be able to render those metafiles into PDF using our Open Source SynPDF library. It works from Delphi 5 up to XE, is Unicode ready, can embed true type fonts, and even create PDF/A files.
It is also able to export metafiles included in reports as vectorial pictures (and not bitmaps), and could therefore highly increase the pdf quality and at the same time shrink its size.
See for instance how it can be used for QuickReport. A similar technical should be used with Fast Report.
The Gnostice support answered my e-mail which I reported that their trial installer didn't work and send me some tips about which could be the problem and I was able to install it.
The company I work for already bought me a license and I already replaced the Fast Report Export Filter, which was a task as simple as droping 2 components on the same Form as the frxReport Object and setting 2 or 3 properties.
Also, to export the report programatically was also 2 lines of code and the information was easily found in their FAQ.
In the end, based on the recomendations and after looking for other options just to find abandoned components which doesn't have any updates for years, the Gnostice eDocEngine was the best solution.
Just hope they make their installer a little more "Programmer Friendly" as if it had complained about the lack of Fast Report's units in the search path I would've been able to at least have an idea of what was going on, instead of just getting an error and blaming them for having a trial installer which didn't work.
After replacing the filter and generating the PDF's using the eDocEngine component, the PDFs now work the same in iOS, OSX and Android.
Here is my workaround solution. It's not an universal one, but helped me in my case.
The main idea: use in report font with small file size (I've found Arial-like font with cyrillic charset with size 57kb). So the exported files can be 100-200 kb.
Details is here:
http://dev-doc.blogspot.com/2013/03/fastreport-4-font-reading-and-huge-file.html
I use wPDF from WPcubed components, it's really a great product, good value for money
You can always install one of the PDF printers. These are in fact PDF convertors that install as windows printer. They work from any application including FastReprt components - just print on them.
Is it possible to set Gimp'sPage Setup dialog to units other than inches? I have an image set to millimeter units, I have everything I can see set to millimeters, but when I select File->Page Setup to create a custom page size, the only option I have is inches.
I'm running on Ubuntu with Gimp 2.6.11.
No, it is not possible right now, and that is a bug on the application.
When you find issues like that, you can help further the tool development by filling up a bug report at http://bugs.gnome.org
I know it may seems just "huh?" how can this be unnoticed - the fact is that many open soruce tools, GIMP included are written on developer's spare times and I can tell you most actie GIMP developers don't use it for printing at all - therefore, the printing side of the tool is getting little attention.
I need to do some light image processing on large image, and I try to use ImageMagick for that. Unfortunately, the API documentation has a very low information content, with documentation similar to:
MagickDeleteImageArtifact
MagickDeleteImageArtifact() deletes a wand artifact.
The format of the MagickDeleteImageArtifact method is:
MagickBooleanType MagickDeleteImageArtifact(MagickWand *wand, const char *artifact)
A description of each parameter follows:
image
the image.
artifact
the image artifact.
Could anybody suggest a few information sources for ImageMagick that would have, you know, information?
(and yes, this piece of "documentation" is pasted from ImageMagick web site, with the incorrect parameter)
Edit: Here is the context: I develop an iOS application, so I want to call ImageMagick from the C language (or Objective-C or C++). The need is to split large images that would not fit in the limited amount of RAM of an iOS device into smaller "tiles" (and downsample for lower resolution versions too. But once I have the tiles, I can do that using only iOS facilities).
Edit 2: Using the command line, I can achieve this tiling with the "convert" command with corresponding parameters. So my immediate need would be to translate such a command line command into the relevant set of API calls.