python - SimpleITK.Show() generates error in ImageJ on Linux -


edit note: question phrased as

how link simpleitk.show() imagej in linux?

by upgrading simpleitk 1.0.0 1.0.1, able launch imagej simpleitk.show(). however, imagej unable open "sample_mri.hdr". imagej generates following error messages.

file not in supported format, reader

plugin not available, or not found.

root/local/linux/imagej/open("/temp/tempfile-7131-2.nii");

root/local/linux/imagej/rename("/temp/tempfile-7131-2.nii");

i have installed appropriate plugins imagej read hdr/img (analyze format). can open "sample_mri.hdr" imagej directly going file>open

debug messages:

sitk.show(img, 'sample image', debugon=true)

findapplication search path: [ ./fiji.app, /cis/home/vwang/bin/fiji.app, ~/bin/fiji.app, /opt/fiji.app, /usr/local/fiji.app ]

result:

findapplication search path: [ ./fiji.app, /cis/home/vwang/bin/fiji.app, ~/bin/fiji.app, /opt/fiji.app, /usr/local/fiji.app ]

result:

findapplication search path: [ ./imagej, /cis/home/vwang/bin/imagej, ~/bin/imagej, /opt/imagej, /usr/local/imagej ]

result:

findapplication search path: [ ./, /cis/home/vwang/bin/, ~/bin/, /opt/, /usr/local/ ]

result: /usr/local/bin/imagej

show command: '/usr/local/bin/imagej' '-e' 'open("/tmp/sample-4434-0.nii"); rename("sample");'

plugins:

how link simpleitk.show() imagej in linux?

i've downloaded imagej , can view images running imagej directly. similar question asked , answered in past (can not "link"simpleitk::show() fiji), solution windows os. unix equivalent of 

setx sitk_show_command "c:\blah\blah\imagej\imagej.exe

my python code:

import simpleitk sitk  img = sitk.readimage("sample_mri.hdr") sitk.show(img, 'sample image')

error message:

    return _simpleitk.show(*args, **kwargs) runtimeerror: exception thrown in simpleitk show:  /tmp/simpleitk/code/io/src/sitkshow.cxx:500: sitk::error: error in administrating child process: [no such file or directory]

simpleitk unable find imagej. try adding debugon=true parameter show command. show search path it's using try , find imagej.

so show following:

sitk.show(img, 'sample image', debugon=true)

on linux systems, simpleitk searches path following options: fiji.app/imagej-linux64, fiji.app/imagej-linux32, imagej/imagej, imagej, , imagej.

if imagej executable named else, simpleitk won't find it. suggest either soft linking make findable, or using sitk_show_command environment variable.

update: not finding imagej original problem. i'm not sure update, debugon flag set, can see actual command line simpleitk using try , launch imagej.


Comments

Post a Comment

Popular posts from this blog

python Tkinter Capturing keyboard events save as one single string -

is possible store keyboard events 1 string? code below stores 1 char , prints it. card reader or bar code reader, contains collection of character/ string not 1 character @ time. goal save char pressed text variable. from tkinter import * root = tk() def key(event): text= event.char text+= event.char print ("pressed", text) def callback(event): frame.focus_set() print ("clicked at", event.x, event.y) frame = frame(root, width=100, height=100) frame.bind("<key>", key) frame.bind("<button-1>", callback) frame.pack() root.mainloop() currently, creating text variable , everytime key() function gets called, , text stores last character typed. you can define text module level variable , , use module level text inside key function - text = '' def key(event): global text text+= event.char print("pressed", text)
Read more

android - InAppBilling registering BroadcastReceiver in AndroidManifest -

i'm implementing inapp billing in android app. works well, however, i'm trying decouple broadcast receiver activity manifest. suggestion in android's trivialdrive sample: // important: dynamically register broadcast messages updated purchases. // register receiver here instead of <receiver> in manifest // because call getpurchases() @ startup, therefore can ignore // broadcasts sent while app isn't running. // note: registering listener in activity bad idea, done here // because sample. regardless, receiver must registered after // iabhelper setup, before first call getpurchases(). currently there's class extends broadcastreceiver : public class iabbroadcastreceiver extends broadcastreceiver { /** * intent action receiver should filter for. */ public static final string action = "com.android.vending.billing.purchases_updated"; private final iabbroadcastlistener mlistener; public iabbroadcastreceiver(iabbroadcastlistener listener) { m
Read more

javascript - Z-index in d3.js -

i have map , when hover effect on region of map below yellow line , circle, last ones disappear. how can solve problem? http://jsfiddle.net/ot21n9qx/ var arc = g.append("path") .style("fill", "none") .style("stroke", "yellow") .style("stroke-width", 2) .attr("d", "m" + pathorigin[0] + "," + pathorigin[1] + " q" + svgpoint[0] + "," + pathorigin[1] + " " + svgpoint[0] + "," + svgpoint[1]); var circlesize = d3.scale.linear() .domain([0, 0.5, 1]) .range([4, 10, 4]); svg not have z order draws objects in order created. need create path , circle after create highlight regions. here forked fiddle: http://jsfiddle.net/o00fzgaf/1/
Read more