Blobs LUT?
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It used to be the case that the Blobs sample image had an inverted LUT.
I now see that it is just the normal Grays LUT when I load from the cached Images in IJ1, but it is an inverted LUT when loading in Fiji... Can somebody please confirm this so? Thanks Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gabriel,
"Blobs" still comes with an inverted LUT for me using both ImageJ and Fiji (updated today). I noticed what may be an unrelated issue though, which is that File->Open Samples->Cache Sample Images does not work for me in Fiji as it does in ImageJ, regardless of whether or not I am using SCIFIO for image IO. It spits out a series of errors like this in the log window:- "java.io.FileNotFoundException: http://imagej.nih.gov/ij/images/http://imagej.nih.gov/ij/images/AuPbSn40.jpg http://imagej.nih.gov/ij/images/http://imagej.nih.gov/ij/images/AuPbSn40.jpg " I tried to figure out why, but I didn't get to the bottom of it so I guess I should file a bug report. Regards, Graeme -- --------------------------- Dr. Graeme Ball Light Microscopy Facility College Of Life Sciences University of Dundee Dow Street DD1 5EH Email: [hidden email] Phone: +44-1382-385741 --------------------------- On Wed, Jun 18, 2014 at 3:04 PM, Gabriel Landini <[hidden email]> wrote: > It used to be the case that the Blobs sample image had an inverted LUT. > I now see that it is just the normal Grays LUT when I load from the cached > Images in IJ1, but it is an inverted LUT when loading in Fiji... > > Can somebody please confirm this so? > > Thanks > > Gabriel > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On Wednesday 18 Jun 2014 16:33:19 Graeme Ball wrote:
> "Blobs" still comes with an inverted LUT for me using both ImageJ and Fiji > (updated today). Thanks Graeme. How odd. I cached again the sample images and the blobs.fig does appear without inverted LUT in IJ1. Before I believe it always did I have in Options>Appearance the "Use inverting lookup table" option unticked. If I tick it then all greyscale images have inverting LUTs. So I do not think this is the problem. Now I deleted the ImageJ/samples folder (where the images get cached) and loading the blobs over the net (i.e. not cached) brings the old inverted LUT image, but as soon as I download the cached version, it is not-inverted! I cannot tell where the image is being cached from, but I guess that it is not the same image as IJ calls when there is no cache folder. Does anybody have a clue of what is going on? Many thanks Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gabriel,
Does anybody have a clue of what is going on? > ImageJ 1.x opens sample images differently if they are cached or not. One of these pathways uses SCIFIO (when the image is cached) and one uses ImageJ 1.x (if it's not cached)... I believe because we didn't want to be overly aggressive in inserting SCIFIO into every single ImageJ 1.x operation.. but perhaps this is too confusing in respect to cached images, or at least should be documented in the WELCOME.md. If you disable SCIFIO (Edit > Options > ImageJ2, uncheck the "Use SCIFIO...") both cached and uncached sample images should open the same way. Also, when you have an image open, if you run Image > Show Info you can easily tell if your data was opened with SCIFIO or not. Let me know if you have any other questions. Thanks! - Mark On Wed, Jun 18, 2014 at 10:53 AM, Gabriel Landini <[hidden email]> wrote: > On Wednesday 18 Jun 2014 16:33:19 Graeme Ball wrote: > > > "Blobs" still comes with an inverted LUT for me using both ImageJ and > Fiji > > (updated today). > > Thanks Graeme. How odd. I cached again the sample images and the blobs.fig > does appear without inverted LUT in IJ1. Before I believe it always did > > I have in Options>Appearance the "Use inverting lookup table" option > unticked. > If I tick it then all greyscale images have inverting LUTs. So I do not > think > this is the problem. > > Now I deleted the ImageJ/samples folder (where the images get cached) and > loading the blobs over the net (i.e. not cached) brings the old inverted > LUT > image, but as soon as I download the cached version, it is not-inverted! > > I cannot tell where the image is being cached from, but I guess that it is > not > the same image as IJ calls when there is no cache folder. > > Does anybody have a clue of what is going on? > > Many thanks > > Gabriel > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gabriel, Mark,
using plain ImageJ 1.49b on Mac OS X (no Fiji) and having downloaded the sample images a few minutes ago, blobs.gif opens from disk with inverting LUT, as it does from the Web without cached sample images. The blobs.gif file I downloaded today is identical to the one I downloaded in 2006 into a different directory (tried with 'cmp' on the command line). Edit>Options>Appearance>Use Interting Lookup Table is off. So it really looks like a Fiji/IJ2-related issue; I agree with Mark. Michael ________________________________________________________________ On Jun 18, 2014, at 19:21, Mark Hiner wrote: > Hi Gabriel, > > Does anybody have a clue of what is going on? >> > > ImageJ 1.x opens sample images differently if they are cached or not. One > of these pathways uses SCIFIO (when the image is cached) and one uses > ImageJ 1.x (if it's not cached)... I believe because we didn't want to be > overly aggressive in inserting SCIFIO into every single ImageJ 1.x > operation.. but perhaps this is too confusing in respect to cached images, > or at least should be documented in the WELCOME.md. > > If you disable SCIFIO (Edit > Options > ImageJ2, uncheck the "Use > SCIFIO...") both cached and uncached sample images should open the same way. > > Also, when you have an image open, if you run Image > Show Info you can > easily tell if your data was opened with SCIFIO or not. > > Let me know if you have any other questions. > > Thanks! > - Mark > > > On Wed, Jun 18, 2014 at 10:53 AM, Gabriel Landini <[hidden email]> > wrote: > >> On Wednesday 18 Jun 2014 16:33:19 Graeme Ball wrote: >> >>> "Blobs" still comes with an inverted LUT for me using both ImageJ and >> Fiji >>> (updated today). >> >> Thanks Graeme. How odd. I cached again the sample images and the blobs.fig >> does appear without inverted LUT in IJ1. Before I believe it always did >> >> I have in Options>Appearance the "Use inverting lookup table" option >> unticked. >> If I tick it then all greyscale images have inverting LUTs. So I do not >> think >> this is the problem. >> >> Now I deleted the ImageJ/samples folder (where the images get cached) and >> loading the blobs over the net (i.e. not cached) brings the old inverted >> LUT >> image, but as soon as I download the cached version, it is not-inverted! >> >> I cannot tell where the image is being cached from, but I guess that it is >> not >> the same image as IJ calls when there is no cache folder. >> >> Does anybody have a clue of what is going on? >> >> Many thanks >> >> Gabriel >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On Wednesday 18 Jun 2014 19:48:07 Michael Schmid wrote:
> using plain ImageJ 1.49b on Mac OS X (no Fiji) and having downloaded the > sample images a few minutes ago, blobs.gif opens from disk with inverting > LUT, as it does from the Web without cached sample images. Hi Thanks for the follow up. Here I am talking about the original IJ1 updated to the latest build 1.49c14. I also have installed Fiji in the same computer, but I get the wrong LUT with IJ1 (and not the Fiji install). On Wednesday 18 Jun 2014 12:21:51 Mark Hiner wrote: > If you disable SCIFIO (Edit > Options > ImageJ2, uncheck the "Use > SCIFIO...") both cached and uncached sample images should open the same way. There is no such command in IJ1. I can confirm that the cached blobs.gif loads from the net (when there is no cache) correctly as inverted LUT: Title: blobs.gif Width: 256 pixels Height: 254 pixels Pixel size: 1x1 pixel ID: -16 Coordinate origin: 0,0 Bits per pixel: 8 (inverting grayscale LUT) Display range: 0-255 No Threshold Uncalibrated URL: http://imagej.nih.gov/ij/images/blobs.gif Screen location: 10,148 (1920x1200) No Overlay No Selection but from the cache it shows grays LUT: Title: blobs.gif Width: 256 pixels Height: 254 pixels Pixel size: 1x1 pixel ID: -12 Coordinate origin: 0,0 Bits per pixel: 8 (grayscale LUT) Display range: 0-255 No Threshold Uncalibrated URL: http://imagej.nih.gov/ij/images/blobs.gif Screen location: 10,148 (1920x1200) No Overlay No Selection I cannot imagine this being desirable. Inverted LUTs are confusing enough, to then have the software decide how to load the data. Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On Wed, Jun 18, 2014 at 1:24 PM, Gabriel Landini <[hidden email]>
wrote: > > There is no such command in IJ1. Sorry for any confusion, I saw your comparison of behavior between IJ1 and Fiji and, knowing that there were two different execution paths for opening sample images depending on if they were cached or not, sent my reply without fully reading the history. That command is part of Fiji, for disabling ImageJ2, as I assumed that the problem was with behavior in Fiji. Anyway, the take-away is that I do believe there are separate mechanisms for loading sample images depending on if they are cached or not.. and that is why you're seeing this behavior. I agree that this images loading differently was probably not desired/intentional... it sounds like there is a bug, or at least some extra processing, in the cached loader. - Mark -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Gabriel Landini
On Jun 18, 2014, at 2:24 PM, Gabriel Landini wrote:
> On Wednesday 18 Jun 2014 19:48:07 Michael Schmid wrote: >> using plain ImageJ 1.49b on Mac OS X (no Fiji) and having downloaded the >> sample images a few minutes ago, blobs.gif opens from disk with inverting >> LUT, as it does from the Web without cached sample images. > > Hi Thanks for the follow up. > Here I am talking about the original IJ1 updated to the latest build 1.49c14. > I also have installed Fiji in the same computer, but I get the wrong LUT with > IJ1 (and not the Fiji install). This recent regression is fixed in the latest ImageJ daily build (1.49c15). Cached versions of the blobs.gif sample image again open with an inverting LUT. The new ij.plugin.Gif_Reader plugin, used by File>Open, opens animated GIFs but does not correctly handle inverting LUTs. The daily build works around this problem by using Toolkit.getDefaultToolkit().createImage() to open blobs.gif. -wayne > On Wednesday 18 Jun 2014 12:21:51 Mark Hiner wrote: >> If you disable SCIFIO (Edit > Options > ImageJ2, uncheck the "Use >> SCIFIO...") both cached and uncached sample images should open the same way. > > There is no such command in IJ1. > > I can confirm that the cached blobs.gif loads from the net (when there is no > cache) correctly as inverted LUT: > > Title: blobs.gif > Width: 256 pixels > Height: 254 pixels > Pixel size: 1x1 pixel > ID: -16 > Coordinate origin: 0,0 > Bits per pixel: 8 (inverting grayscale LUT) > Display range: 0-255 > No Threshold > Uncalibrated > URL: http://imagej.nih.gov/ij/images/blobs.gif > Screen location: 10,148 (1920x1200) > No Overlay > No Selection > > but from the cache it shows grays LUT: > > Title: blobs.gif > Width: 256 pixels > Height: 254 pixels > Pixel size: 1x1 pixel > ID: -12 > Coordinate origin: 0,0 > Bits per pixel: 8 (grayscale LUT) > Display range: 0-255 > No Threshold > Uncalibrated > URL: http://imagej.nih.gov/ij/images/blobs.gif > Screen location: 10,148 (1920x1200) > No Overlay > No Selection > > I cannot imagine this being desirable. Inverted LUTs are confusing enough, to > then have the software decide how to load the data. > > Cheers > > Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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