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working with HostComputer tiff tag?

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Bill Christens-Barry

working with HostComputer tiff tag?

I'd like to be able to view tiff tags that currently don't appear via the Image>Show Info... menu or
getMetadata() macro command. For example, I have TIFF files in which custom info is crammed into
the HostComputer tag (316).

Other than the TiffDecoder, TiffEncoder, and FileInfo classes, where else will I need to make changes
to implement this - Properties? Is there any tutorial material on this? My naive searches turned up
empty for me.

Thanks.

Bill

ctrueden

Re: working with HostComputer tiff tag?

Hi Bill,

Questions about reading TIFF IFDs have come up a few times on the ImageJ
list lately. Since Bio-Formats has full TIFF parsing capabilities, I thought
I'd write a little utility for reading all the IFDs in a TIFF file. You can
find it here:

https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/utils/TiffDumper.java

It requires loci_tools.jar to compile and run, but has no dependence on
ImageJ. However, you could leverage the code within any ImageJ-based project
you're doing to work with TIFF files more easily.

-Curtis

On Thu, Sep 10, 2009 at 1:29 PM, Bill Christens-Barry <
[hidden email]> wrote:

> I'd like to be able to view tiff tags that currently don't appear via the
> Image>Show Info... menu or
> getMetadata() macro command. For example, I have TIFF files in which custom
> info is crammed into
> the HostComputer tag (316).
>
> Other than the TiffDecoder, TiffEncoder, and FileInfo classes, where else
> will I need to make changes
> to implement this - Properties? Is there any tutorial material on this? My
> naive searches turned up
> empty for me.
>
> Thanks.
>
> Bill
>

Wayne Rasband

Re: working with HostComputer tiff tag?

A plugin version of Curtis' TiffDumper utility is available at

http://rsbweb.nih.gov/ij/plugins/tiff-dumper.html

It uses the Bio-Formats plugin to parse and output all TIFF tags for
the current image.

-wayne

On Sep 10, 2009, at 2:56 PM, Curtis Rueden wrote:

> Hi Bill,
>
> Questions about reading TIFF IFDs have come up a few times on the
> ImageJ list lately. Since Bio-Formats has full TIFF parsing
> capabilities, I thought I'd write a little utility for reading all
> the IFDs in a TIFF file. You can find it here:
>
> https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/utils/TiffDumper.java
>
> It requires loci_tools.jar to compile and run, but has no dependence
> on ImageJ. However, you could leverage the code within any ImageJ-
> based project you're doing to work with TIFF files more easily.
>
> -Curtis
>
> On Thu, Sep 10, 2009 at 1:29 PM, Bill Christens-Barry <[hidden email]
> > wrote:
> I'd like to be able to view tiff tags that currently don't appear
> via the Image>Show Info... menu or
> getMetadata() macro command. For example, I have TIFF files in which
> custom info is crammed into
> the HostComputer tag (316).
>
> Other than the TiffDecoder, TiffEncoder, and FileInfo classes, where
> else will I need to make changes
> to implement this - Properties? Is there any tutorial material on
> this? My naive searches turned up
> empty for me.
>
> Thanks.
>
> Bill
>

Joel Sheffield

Re: working with HostComputer tiff tag?

Hi Wayne,

I just ran into a problem with the plugin. Error message that "can't find
Tiff_Dumper", even though it is listed as a plugin. Loci_tools.jar is also
present.The full error is (java.lang.NoClassDefFound Error:
loci/common/RandomAccessinputStream). I'm using the latest build of IJ.

On Thu, Sep 10, 2009 at 10:39 PM, Wayne Rasband <[hidden email]> wrote:

> A plugin version of Curtis' TiffDumper utility is available at
>
> http://rsbweb.nih.gov/ij/plugins/tiff-dumper.html
>
> It uses the Bio-Formats plugin to parse and output all TIFF tags for the
> current image.
>
> -wayne
>
>
>
> On Sep 10, 2009, at 2:56 PM, Curtis Rueden wrote:
>
> Hi Bill,
>>
>> Questions about reading TIFF IFDs have come up a few times on the ImageJ
>> list lately. Since Bio-Formats has full TIFF parsing capabilities, I thought
>> I'd write a little utility for reading all the IFDs in a TIFF file. You can
>> find it here:
>>
>>
>> https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/utils/TiffDumper.java
>>
>> It requires loci_tools.jar to compile and run, but has no dependence on
>> ImageJ. However, you could leverage the code within any ImageJ-based project
>> you're doing to work with TIFF files more easily.
>>
>> -Curtis
>>
>> On Thu, Sep 10, 2009 at 1:29 PM, Bill Christens-Barry <
>> [hidden email]> wrote:
>> I'd like to be able to view tiff tags that currently don't appear via the
>> Image>Show Info... menu or
>> getMetadata() macro command. For example, I have TIFF files in which
>> custom info is crammed into
>> the HostComputer tag (316).
>>
>> Other than the TiffDecoder, TiffEncoder, and FileInfo classes, where else
>> will I need to make changes
>> to implement this - Properties? Is there any tutorial material on this? My
>> naive searches turned up
>> empty for me.
>>
>> Thanks.
>>
>> Bill
>>
>>

--

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs

Aryeh Weiss

Re: working with HostComputer tiff tag?

It is working properly on my system -- latest IJ daily build, MAC OSX,
loci_tools.jar in plugin directory, TiffDumper installed in
plugins/input-output. It is running from the downloaded class file.

Aside -- this list is amazing. Within a few days of posting my problem,
I have in hand the following solutions:

1. Wayne modified getMetadata to read the required tags.

2. Joachim Wesner sent me a plugin that read the raw tiff codes from any
tiff file. Both useful and educational (one sees the raw numbers and
understands better how the tiff tags are built).

3. Curtis sent a stand alone application to read the tags

and before I could start playing with how to use it in ImageJ

4. Wayne sent a plugin version for ImageJ

Thanks to all of you for your kind help.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph: 972-3-5317638
FAX: 972-3-7384050

JOEL B. SHEFFIELD wrote:

> Hi Wayne,
>
> I just ran into a problem with the plugin. Error message that "can't find
> Tiff_Dumper", even though it is listed as a plugin. Loci_tools.jar is also
> present.The full error is (java.lang.NoClassDefFound Error:
> loci/common/RandomAccessinputStream). I'm using the latest build of IJ.
>
> On Thu, Sep 10, 2009 at 10:39 PM, Wayne Rasband <[hidden email]> wrote:
>
>> A plugin version of Curtis' TiffDumper utility is available at
>>
>> http://rsbweb.nih.gov/ij/plugins/tiff-dumper.html
>>
>> It uses the Bio-Formats plugin to parse and output all TIFF tags for the
>> current image.
>>
>> -wayne
>>
>>
>>
>> On Sep 10, 2009, at 2:56 PM, Curtis Rueden wrote:
>>
>> Hi Bill,
>>> Questions about reading TIFF IFDs have come up a few times on the ImageJ
>>> list lately. Since Bio-Formats has full TIFF parsing capabilities, I thought
>>> I'd write a little utility for reading all the IFDs in a TIFF file. You can
>>> find it here:
>>>
>>>
>>> https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/utils/TiffDumper.java
>>>
>>> It requires loci_tools.jar to compile and run, but has no dependence on
>>> ImageJ. However, you could leverage the code within any ImageJ-based project
>>> you're doing to work with TIFF files more easily.
>>>
>>> -Curtis
>>>
>>> On Thu, Sep 10, 2009 at 1:29 PM, Bill Christens-Barry <
>>> [hidden email]> wrote:
>>> I'd like to be able to view tiff tags that currently don't appear via the
>>> Image>Show Info... menu or
>>> getMetadata() macro command. For example, I have TIFF files in which
>>> custom info is crammed into
>>> the HostComputer tag (316).
>>>
>>> Other than the TiffDecoder, TiffEncoder, and FileInfo classes, where else
>>> will I need to make changes
>>> to implement this - Properties? Is there any tutorial material on this? My
>>> naive searches turned up
>>> empty for me.
>>>
>>> Thanks.
>>>
>>> Bill
>>>
>>>
>
>

Gabriel Landini

Re: working with HostComputer tiff tag?

In reply to this post by Joel Sheffield

On Friday 11 September 2009 09:46:55 JOEL B. SHEFFIELD wrote:
> I just ran into a problem with the plugin. Error message that "can't find
> Tiff_Dumper", even though it is listed as a plugin. Loci_tools.jar is also
> present.The full error is (java.lang.NoClassDefFound Error:
> loci/common/RandomAccessinputStream). I'm using the latest build of IJ.

Similar here... but here (suse linux, sun java 1.6) the class not found is:
java.lang.NoClassDefFoundError: /loci/formats/TiffParser

I have both the loci_tools.jar and the bio-formats.jar in the plugins folder.
(I am not sure I need the latter?).

I tried to Update Loci Plugins and I get this error:

java.lang.StackOverflowError
at java.net.PlainSocketImpl.releaseFD(PlainSocketImpl.java:586)
at java.net.SocketInputStream.read(SocketInputStream.java:136)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:256)
at java.io.BufferedInputStream.read(BufferedInputStream.java:317)
at sun.net.www.MeteredStream.read(MeteredStream.java:116)
at java.io.FilterInputStream.read(FilterInputStream.java:116)
at
sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2512)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:258)
at java.io.BufferedInputStream.read(BufferedInputStream.java:317)
at java.io.DataInputStream.read(DataInputStream.java:132)
at loci.common.URLHandle.read(URLHandle.java:114)
at loci.common.URLHandle.read(URLHandle.java:120)
[...]

Regards
G.

Joel Sheffield

Re: working with HostComputer tiff tag?

I had the same problem as Gabriel, although I was able to update the
loci_tools.jar without a problem. However, I get the same Tiff_Parser
missing error. This is on an XP machine.

I also want to echo Aryeh's comment. This list is extraordinary!....and
more thanks that can be expressed for Wayne's constant efforts over many
years.
Joel

On Fri, Sep 11, 2009 at 4:58 AM, Gabriel Landini <[hidden email]>wrote:

> On Friday 11 September 2009 09:46:55 JOEL B. SHEFFIELD wrote:
> > I just ran into a problem with the plugin. Error message that "can't
> find
> > Tiff_Dumper", even though it is listed as a plugin. Loci_tools.jar is
> also
> > present.The full error is (java.lang.NoClassDefFound Error:
> > loci/common/RandomAccessinputStream). I'm using the latest build of IJ.
>
> Similar here... but here (suse linux, sun java 1.6) the class not found is:
> java.lang.NoClassDefFoundError: /loci/formats/TiffParser
>
> I have both the loci_tools.jar and the bio-formats.jar in the plugins
> folder.
> (I am not sure I need the latter?).
>
> I tried to Update Loci Plugins and I get this error:
>
> java.lang.StackOverflowError
> at java.net.PlainSocketImpl.releaseFD(PlainSocketImpl.java:586)
> at java.net.SocketInputStream.read(SocketInputStream.java:136)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:256)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:317)
> at sun.net.www.MeteredStream.read(MeteredStream.java:116)
> at java.io.FilterInputStream.read(FilterInputStream.java:116)
> at
>
> sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2512)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:258)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:317)
> at java.io.DataInputStream.read(DataInputStream.java:132)
> at loci.common.URLHandle.read(URLHandle.java:114)
> at loci.common.URLHandle.read(URLHandle.java:120)
> [...]
>
> Regards
> G.
>

--

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs

ctrueden

Re: working with HostComputer tiff tag?

In reply to this post by Gabriel Landini

Hi Gabriel & Joel,

> The full error is (java.lang.NoClassDefFound Error:
> > loci/common/RandomAccessinputStream). I'm using the latest build of IJ.
>
> Similar here... but here (suse linux, sun java 1.6) the class not found is:
> java.lang.NoClassDefFoundError: /loci/formats/TiffParser
>

Both of these errors indicate out-of-date versions of loci_tools.jar. I
would suggest trying the latest trunk build from the Bio-Formats web site.

I have both the loci_tools.jar and the bio-formats.jar in the plugins
> folder.
> (I am not sure I need the latter?).
>

You only need loci_tools.jar, not bio-formats.jar or any other JAR file.
Best would be to remove any other Bio-Formats-related JAR files.

I tried to Update Loci Plugins and I get this error:
>
> java.lang.StackOverflowError
>

Sorry about that; hopefully you can update the plugin manually for now.

One other thing: Wayne based the TIFF_Dumper plugin on the initial version
of the program, before I updated it to handle IFDs with list entries in a
friendlier way. I have included an updated version of the plugin based on
the latest code.

-Curtis

----------------
//
// TIFF_Dumper.java
//

import ij.*;
import ij.plugin.*;
import ij.io.FileInfo;
import java.awt.Frame;
import java.io.IOException;
import java.lang.reflect.Array;
import java.util.Arrays;
import loci.common.RandomAccessInputStream;
import loci.formats.tiff.*;

/** Parses and outputs all TIFF tags for the current image. */
public class TIFF_Dumper implements PlugIn {

public void run(String arg) {
if (Menus.getCommands().get("Bio-Formats Importer")==null) {
IJ.error("TIFF Dumper", "Bio-Formats plugin required");
return;
}
ImagePlus imp = IJ.getImage();
FileInfo fi = imp.getOriginalFileInfo();
if (fi.directory==null || fi.fileFormat!=FileInfo.TIFF) {
IJ.error("TIFF Dumper", "File path not available or not TIFF file");
return;
}
String path = fi.directory + fi.fileName;
IJ.log("\\Clear");
IJ.log("PATH = "+path);
try {
dumpIFDs(path);
} catch(IOException e) {
IJ.error("Tiff Dumper", ""+e);
}
Frame log = WindowManager.getFrame("Log");
if (log!=null) log.toFront();
}

public static void dumpIFDs(String path) throws IOException {
IJ.showStatus("Parsing IFDs");
RandomAccessInputStream in = new RandomAccessInputStream(path);
TiffParser parser = new TiffParser(in);
IFDList ifdList = parser.getIFDs();
IJ.showStatus("");
for (IFD ifd : ifdList) {
for (Integer key : ifd.keySet()) {
int k = key.intValue();
String name = IFD.getIFDTagName(k);
String value = prettyValue(ifd.getIFDValue(k), 0);
IJ.log(name + " = " + value);
}
}
in.close();
}

private static String prettyValue(Object value, int indent) {
if (!value.getClass().isArray()) return value.toString();

char[] spaceChars = new char[indent];
Arrays.fill(spaceChars, ' ');
String spaces = new String(spaceChars);

StringBuilder sb = new StringBuilder();
sb.append("{\n");
for (int i=0; i<Array.getLength(value); i++) {
sb.append(spaces);
sb.append(" ");
Object component = Array.get(value, i);
sb.append(prettyValue(component, indent + 2));
sb.append("\n");
}
sb.append(spaces);
sb.append("}");
return sb.toString();
}

}

On Fri, Sep 11, 2009 at 3:58 AM, Gabriel Landini <[hidden email]>wrote:

Gabriel Landini

Re: working with HostComputer tiff tag?

Hi Curtis,

On Monday 14 September 2009 08:57:33 Curtis Rueden wrote:

> > The full error is (java.lang.NoClassDefFound Error:
> Both of these errors indicate out-of-date versions of loci_tools.jar. I
> would suggest trying the latest trunk build from the Bio-Formats web site.
>
> I have both the loci_tools.jar and the bio-formats.jar in the plugins
> > folder.
> > (I am not sure I need the latter?).
> >
>
> You only need loci_tools.jar, not bio-formats.jar or any other JAR file.
> Best would be to remove any other Bio-Formats-related JAR files.

Thank you for the tips.
Done that, downloaded the new loci_tools,jar.

The plugin at Wayne's site now works, but I tried to compile the code you
sent last and I get this:

/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:12: package
loci.common does not exist
import loci.common.RandomAccessInputStream;
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:13: package
loci.formats.tiff does not exist
import loci.formats.tiff.*;
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot find
symbol
symbol : class RandomAccessInputStream
location: class TIFF_Dumper
RandomAccessInputStream in = new RandomAccessInputStream(path);
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot find
symbol
symbol : class RandomAccessInputStream
location: class TIFF_Dumper
RandomAccessInputStream in = new RandomAccessInputStream(path);
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot find
symbol
symbol : class TiffParser
location: class TIFF_Dumper
TiffParser parser = new TiffParser(in);
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot find
symbol
symbol : class TiffParser
location: class TIFF_Dumper
TiffParser parser = new TiffParser(in);
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:45: cannot find
symbol
symbol : class IFDList
location: class TIFF_Dumper
IFDList ifdList = parser.getIFDs();
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:47: cannot find
symbol
symbol : class IFD
location: class TIFF_Dumper
for (IFD ifd : ifdList) {
^
/home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:50: cannot find
symbol
symbol : variable IFD
location: class TIFF_Dumper
String name = IFD.getIFDTagName(k);
^
9 errors

Any suggestions

Regards

Gabriel

Joel Sheffield

Re: working with HostComputer tiff tag?

I'll echo that --same errors, new loci_tools.jar from trunk build yesterday,
using pc-xp.

On Tue, Sep 15, 2009 at 4:09 AM, Gabriel Landini <[hidden email]>wrote:

> Hi Curtis,
>
> On Monday 14 September 2009 08:57:33 Curtis Rueden wrote:
> > > The full error is (java.lang.NoClassDefFound Error:
> > Both of these errors indicate out-of-date versions of loci_tools.jar. I
> > would suggest trying the latest trunk build from the Bio-Formats web
> site.
> >
> > I have both the loci_tools.jar and the bio-formats.jar in the plugins
> > > folder.
> > > (I am not sure I need the latter?).
> > >
> >
> > You only need loci_tools.jar, not bio-formats.jar or any other JAR file.
> > Best would be to remove any other Bio-Formats-related JAR files.
>
> Thank you for the tips.
> Done that, downloaded the new loci_tools,jar.
>
> The plugin at Wayne's site now works, but I tried to compile the code you
> sent last and I get this:
>
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:12: package
> loci.common does not exist
> import loci.common.RandomAccessInputStream;
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:13: package
> loci.formats.tiff does not exist
> import loci.formats.tiff.*;
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot find
> symbol
> symbol : class RandomAccessInputStream
> location: class TIFF_Dumper
> RandomAccessInputStream in = new RandomAccessInputStream(path);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot find
> symbol
> symbol : class RandomAccessInputStream
> location: class TIFF_Dumper
> RandomAccessInputStream in = new RandomAccessInputStream(path);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot find
> symbol
> symbol : class TiffParser
> location: class TIFF_Dumper
> TiffParser parser = new TiffParser(in);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot find
> symbol
> symbol : class TiffParser
> location: class TIFF_Dumper
> TiffParser parser = new TiffParser(in);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:45: cannot find
> symbol
> symbol : class IFDList
> location: class TIFF_Dumper
> IFDList ifdList = parser.getIFDs();
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:47: cannot find
> symbol
> symbol : class IFD
> location: class TIFF_Dumper
> for (IFD ifd : ifdList) {
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:50: cannot find
> symbol
> symbol : variable IFD
> location: class TIFF_Dumper
> String name = IFD.getIFDTagName(k);
> ^
> 9 errors
>
> Any suggestions
>
> Regards
>
> Gabriel
>

--

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs

Wayne Rasband

Re: working with HostComputer tiff tag?

In reply to this post by Gabriel Landini

On Sep 15, 2009, at 4:09 AM, Gabriel Landini <[hidden email]>
wrote:

You have to temporarily rename loci_tools.jar so that the name does
not contain an underscore. The Compile and Run command automatically
adds jar files (libraries) in the plugins folder to the javac
compiler's classpath as long as they do not have an underscore in the
name.

-wayne

> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:12: package
> loci.common does not exist
> import loci.common.RandomAccessInputStream;
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:13: package
> loci.formats.tiff does not exist
> import loci.formats.tiff.*;
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot
> find
> symbol
> symbol : class RandomAccessInputStream
> location: class TIFF_Dumper
> RandomAccessInputStream in = new RandomAccessInputStream(path);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot
> find
> symbol
> symbol : class RandomAccessInputStream
> location: class TIFF_Dumper
> RandomAccessInputStream in = new RandomAccessInputStream(path);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot
> find
> symbol
> symbol : class TiffParser
> location: class TIFF_Dumper
> TiffParser parser = new TiffParser(in);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot
> find
> symbol
> symbol : class TiffParser
> location: class TIFF_Dumper
> TiffParser parser = new TiffParser(in);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:45: cannot
> find
> symbol
> symbol : class IFDList
> location: class TIFF_Dumper
> IFDList ifdList = parser.getIFDs();
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:47: cannot
> find
> symbol
> symbol : class IFD
> location: class TIFF_Dumper
> for (IFD ifd : ifdList) {
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:50: cannot
> find
> symbol
> symbol : variable IFD
> location: class TIFF_Dumper
> String name = IFD.getIFDTagName(k);
> ^
> 9 errors
>
> Any suggestions
>
> Regards
>
> Gabriel

Joachim Wesner

Alternative TIFF tag reader - Was: Re: working with HostComputer tiff tag?

In reply to this post by Joel Sheffield

Hi

You might also try the new updated version of my Tiff tag reader that now
can be directly called from an ImageJ Macro:

http://rsbweb.nih.gov/ij/plugins/tiff-tags.html

It does NOT need any external jar, the reader class is built-in.

Please do not hesitate to report any bugs as the latest version with Macro
capabilty in not yet tested extensively!

Sincerely

Joachim Wesner

"JOEL B.
SHEFFIELD"
<[hidden email]> An
Gesendet von: [hidden email]
ImageJ Interest Kopie
Group
<[hidden email]. Thema
GOV> Re: working with HostComputer tiff
tag?

15.09.2009 14:29

Bitte antworten
an
ImageJ Interest
Group
<[hidden email].
GOV>

I'll echo that --same errors, new loci_tools.jar from trunk build
yesterday,
using pc-xp.

On Tue, Sep 15, 2009 at 4:09 AM, Gabriel Landini
<[hidden email]>wrote:

file.
> > Best would be to remove any other Bio-Formats-related JAR files.
>
> Thank you for the tips.
> Done that, downloaded the new loci_tools,jar.
>
> The plugin at Wayne's site now works, but I tried to compile the code
you

> sent last and I get this:
>
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:12: package
> loci.common does not exist
> import loci.common.RandomAccessInputStream;
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:13: package
> loci.formats.tiff does not exist
> import loci.formats.tiff.*;
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot find
> symbol
> symbol : class RandomAccessInputStream
> location: class TIFF_Dumper
> RandomAccessInputStream in = new RandomAccessInputStream(path);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:43: cannot find
> symbol
> symbol : class RandomAccessInputStream
> location: class TIFF_Dumper
> RandomAccessInputStream in = new RandomAccessInputStream(path);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot find
> symbol
> symbol : class TiffParser
> location: class TIFF_Dumper
> TiffParser parser = new TiffParser(in);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:44: cannot find
> symbol
> symbol : class TiffParser
> location: class TIFF_Dumper
> TiffParser parser = new TiffParser(in);
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:45: cannot find
> symbol
> symbol : class IFDList
> location: class TIFF_Dumper
> IFDList ifdList = parser.getIFDs();
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:47: cannot find
> symbol
> symbol : class IFD
> location: class TIFF_Dumper
> for (IFD ifd : ifdList) {
> ^
> /home/gabriel/ImageJ/plugins/InputOutput/TIFF_Dumper.java:50: cannot find
> symbol
> symbol : variable IFD
> location: class TIFF_Dumper
> String name = IFD.getIFDTagName(k);
> ^
> 9 errors
>
> Any suggestions
>
> Regards
>
> Gabriel
>

--

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs

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Gabriel Landini

Re: Alternative TIFF tag reader - Was: Re: working with HostComputer tiff tag?

On Friday 18 September 2009 10:12:21 Joachim Wesner wrote:
> You might also try the new updated version of my Tiff tag reader that now
> can be directly called from an ImageJ Macro:
>
> http://rsbweb.nih.gov/ij/plugins/tiff-tags.html

Thanks for this Joachim, this complements the other plugin quite nicely (yours
returns the tags numbers and the other tag names).
Both working perfect as far as I could test.
Cheers

Gabriel

Joachim Wesner

Antwort: Re: Alternative TIFF tag reader - Was: Re: working with HostComputer tiff tag?

Hi Gabriel,

thanx too, I am happy if it turns out useful!

Mit freundlichen Grüßen / Best regards

Joachim Wesner

Gabriel Landini
<[hidden email]
C.UK> An
Gesendet von: [hidden email]
ImageJ Interest Kopie
Group
<[hidden email]. Thema
GOV> Re: Alternative TIFF tag reader -
Was: Re: working with HostComputer
tiff tag?
18.09.2009 11:18

Bitte antworten
an
ImageJ Interest
Group
<[hidden email].
GOV>

On Friday 18 September 2009 10:12:21 Joachim Wesner wrote:
> You might also try the new updated version of my Tiff tag reader that now
> can be directly called from an ImageJ Macro:
>
> http://rsbweb.nih.gov/ij/plugins/tiff-tags.html

Thanks for this Joachim, this complements the other plugin quite nicely
(yours
returns the tags numbers and the other tag names).
Both working perfect as far as I could test.
Cheers

Gabriel

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