Converting .STL file into stack of images

imageconverter
stackconverter
3d-viewer
fiji
Tags: #<Tag:0x00007fb87ba37920> #<Tag:0x00007fb87ba37650> #<Tag:0x00007fb87ba37510> #<Tag:0x00007fb87ba373a8>

#41

Hi @kephale,

Sorry, I’ve got no idea wtf is going on with the formatting of this text.

I’ve given it a go. Started with a standard freshly unpacked Fiji distribution (with Java rolled in).
Copied the following jars into \Fiji.app\jars, and stripped off the -201607#### characters :

jinput-platform-2.0.6-natives-windows.jar-20160713083538
cleargl-1.0-SNAPSHOT.jar-20160709090252
cleargl-2.0.0-SNAPSHOT.jar-20160713083538
imagej-ops-0.30.1-SNAPSHOT.jar-20160715145202
jinput-2.0.6.jar-20160709090252
openvr-0.1.jar-20160709090252
jutils-1.0.0.jar-20160709090252
kotlin-stdlib-1.0.2.jar-20160709090252
kotlin-runtime-1.0.2.jar-20160709090252
scenery-1.0-SNAPSHOT.jar-20160715145202

Copied to Fiji.app\plugins and stripped off the -201707##### characters:

ThreeDViewer-0.0.1-SNAPSHOT.jar-20160715145202

Loaded a z-stack, and tried to run ThreeDViewer:

ClearGLWindow: GLProfile[GL4/GL4.hw]
DeferredLightingRenderer: 800 x 600 on GeForce GTX 680/PCIe/SSE2, 4.4.0
Supported OpenGL extensions:
GL_AMD_multi_draw_indirect, GL_AMD_seamless_cubemap_per_texture, GL_ARB_arrays_of_arrays, GL_ARB_base_instance, GL_ARB_bindless_texture, GL_ARB_blend_func_extended, GL_ARB_buffer_storage, GL_ARB_clear_buffer_object, GL_ARB_clear_texture, GL_ARB_color_buffer_float, GL_ARB_compressed_texture_pixel_storage, GL_ARB_conservative_depth, GL_ARB_compute_shader, GL_ARB_compute_variable_group_size, GL_ARB_copy_buffer, GL_ARB_copy_image, GL_ARB_debug_output, GL_ARB_depth_buffer_float, GL_ARB_depth_clamp, GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_draw_buffers_blend, GL_ARB_draw_indirect, GL_ARB_draw_elements_base_vertex, GL_ARB_draw_instanced, GL_ARB_enhanced_layouts, GL_ARB_ES2_compatibility, GL_ARB_ES3_compatibility, GL_ARB_explicit_attrib_location, GL_ARB_explicit_uniform_location, GL_ARB_fragment_coord_conventions, GL_ARB_fragment_layer_viewport, GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, GL_ARB_fragment_shader, GL_ARB_framebuffer_no_attachments, GL_ARB_framebuffer_object, GL_ARB_framebuffer_sRGB, GL_ARB_geometry_shader4, GL_ARB_get_program_binary, GL_ARB_gpu_shader5, GL_ARB_gpu_shader_fp64, GL_ARB_half_float_pixel, GL_ARB_half_float_vertex, GL_ARB_imaging, GL_ARB_indirect_parameters, GL_ARB_instanced_arrays, GL_ARB_internalformat_query, GL_ARB_internalformat_query2, GL_ARB_invalidate_subdata, GL_ARB_map_buffer_alignment, GL_ARB_map_buffer_range, GL_ARB_multi_bind, GL_ARB_multi_draw_indirect, GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query, GL_ARB_occlusion_query2, GL_ARB_pixel_buffer_object, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_program_interface_query, GL_ARB_provoking_vertex, GL_ARB_robust_buffer_access_behavior, GL_ARB_robustness, GL_ARB_sample_shading, GL_ARB_sampler_objects, GL_ARB_seamless_cube_map, GL_ARB_seamless_cubemap_per_texture, GL_ARB_separate_shader_objects, GL_ARB_shader_atomic_counters, GL_ARB_shader_bit_encoding, GL_ARB_shader_draw_parameters, GL_ARB_shader_group_vote, GL_ARB_shader_image_load_store, GL_ARB_shader_image_size, GL_ARB_shader_objects, GL_ARB_shader_precision, GL_ARB_query_buffer_object, GL_ARB_shader_storage_buffer_object, GL_ARB_shader_subroutine, GL_ARB_shader_texture_lod, GL_ARB_shading_language_100, GL_ARB_shading_language_420pack, GL_ARB_shading_language_include, GL_ARB_shading_language_packing, GL_ARB_shadow, GL_ARB_sparse_texture, GL_ARB_stencil_texturing, GL_ARB_sync, GL_ARB_tessellation_shader, GL_ARB_texture_border_clamp, GL_ARB_texture_buffer_object, GL_ARB_texture_buffer_object_rgb32, GL_ARB_texture_buffer_range, GL_ARB_texture_compression, GL_ARB_texture_compression_bptc, GL_ARB_texture_compression_rgtc, GL_ARB_texture_cube_map, GL_ARB_texture_cube_map_array, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3, GL_ARB_texture_float, GL_ARB_texture_gather, GL_ARB_texture_mirror_clamp_to_edge, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_multisample, GL_ARB_texture_non_power_of_two, GL_ARB_texture_query_levels, GL_ARB_texture_query_lod, GL_ARB_texture_rectangle, GL_ARB_texture_rg, GL_ARB_texture_rgb10_a2ui, GL_ARB_texture_stencil8, GL_ARB_texture_storage, GL_ARB_texture_storage_multisample, GL_ARB_texture_swizzle, GL_ARB_texture_view, GL_ARB_timer_query, GL_ARB_transform_feedback2, GL_ARB_transform_feedback3, GL_ARB_transform_feedback_instanced, GL_ARB_transpose_matrix, GL_ARB_uniform_buffer_object, GL_ARB_vertex_array_bgra, GL_ARB_vertex_array_object, GL_ARB_vertex_attrib_64bit, GL_ARB_vertex_attrib_binding, GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, GL_ARB_vertex_shader, GL_ARB_vertex_type_10f_11f_11f_rev, GL_ARB_vertex_type_2_10_10_10_rev, GL_ARB_viewport_array, GL_ARB_window_pos, GL_ATI_draw_buffers, GL_ATI_texture_float, GL_ATI_texture_mirror_once, GL_S3_s3tc, GL_EXT_texture_env_add, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_bindable_uniform, GL_EXT_blend_color, GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_compiled_vertex_array, GL_EXT_Cg_shader, GL_EXT_depth_bounds_test, GL_EXT_direct_state_access, GL_EXT_draw_buffers2, GL_EXT_draw_instanced, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_blit, GL_EXT_framebuffer_multisample, GL_EXTX_framebuffer_mixed_formats, GL_EXT_framebuffer_multisample_blit_scaled, GL_EXT_framebuffer_object, GL_EXT_framebuffer_sRGB, GL_EXT_geometry_shader4, GL_EXT_gpu_program_parameters, GL_EXT_gpu_shader4, GL_EXT_multi_draw_arrays, GL_EXT_packed_depth_stencil, GL_EXT_packed_float, GL_EXT_packed_pixels, GL_EXT_pixel_buffer_object, GL_EXT_point_parameters, GL_EXT_provoking_vertex, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_shader_objects, GL_EXT_separate_specular_color, GL_EXT_shader_image_load_store, GL_EXT_shader_integer_mix, GL_EXT_shadow_funcs, GL_EXT_stencil_two_side, GL_EXT_stencil_wrap, GL_EXT_texture3D, GL_EXT_texture_array, GL_EXT_texture_buffer_object, GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_latc, GL_EXT_texture_compression_rgtc, GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_integer, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, GL_EXT_texture_shared_exponent, GL_EXT_texture_sRGB, GL_EXT_texture_sRGB_decode, GL_EXT_texture_storage, GL_EXT_texture_swizzle, GL_EXT_timer_query, GL_EXT_transform_feedback2, GL_EXT_vertex_array, GL_EXT_vertex_array_bgra, GL_EXT_vertex_attrib_64bit, GL_EXT_import_sync_object, GL_IBM_rasterpos_clip, GL_IBM_texture_mirrored_repeat, GL_KHR_debug, GL_KTX_buffer_region, GL_NV_bindless_multi_draw_indirect, GL_NV_bindless_multi_draw_indirect_count, GL_NV_bindless_texture, GL_NV_blend_equation_advanced, GL_NV_blend_square, GL_NV_compute_program5, GL_NV_conditional_render, GL_NV_copy_depth_to_color, GL_NV_copy_image, GL_NV_depth_buffer_float, GL_NV_depth_clamp, GL_NV_draw_texture, GL_NV_ES1_1_compatibility, GL_NV_ES3_1_compatibility, GL_NV_explicit_multisample, GL_NV_fence, GL_NV_float_buffer, GL_NV_fog_distance, GL_NV_fragment_program, GL_NV_fragment_program_option, GL_NV_fragment_program2, GL_NV_framebuffer_multisample_coverage, GL_NV_geometry_shader4, GL_NV_gpu_program4, GL_NV_gpu_program4_1, GL_NV_gpu_program5, GL_NV_gpu_program5_mem_extended, GL_NV_gpu_program_fp64, GL_NV_gpu_shader5, GL_NV_half_float, GL_NV_light_max_exponent, GL_NV_multisample_coverage, GL_NV_multisample_filter_hint, GL_NV_occlusion_query, GL_NV_packed_depth_stencil, GL_NV_parameter_buffer_object, GL_NV_parameter_buffer_object2, GL_NV_path_rendering, GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_primitive_restart, GL_NV_register_combiners, GL_NV_register_combiners2, GL_NV_shader_atomic_counters, GL_NV_shader_atomic_float, GL_NV_shader_buffer_load, GL_NV_shader_storage_buffer_object, GL_NV_texgen_reflection, GL_NV_texture_barrier, GL_NV_texture_compression_vtc, GL_NV_texture_env_combine4, GL_NV_texture_expand_normal, GL_NV_texture_multisample, GL_NV_texture_rectangle, GL_NV_texture_shader, GL_NV_texture_shader2, GL_NV_texture_shader3, GL_NV_transform_feedback, GL_NV_transform_feedback2, GL_NV_vertex_array_range, GL_NV_vertex_array_range2, GL_NV_vertex_attrib_integer_64bit, GL_NV_vertex_buffer_unified_memory, GL_NV_vertex_program, GL_NV_vertex_program1_1, GL_NV_vertex_program2, GL_NV_vertex_program2_option, GL_NV_vertex_program3, GL_NVX_conditional_render, GL_NVX_gpu_memory_info, GL_NVX_nvenc_interop, GL_NV_shader_thread_group, GL_NV_shader_thread_shuffle, GL_KHR_blend_equation_advanced, GL_SGIS_generate_mipmap, GL_SGIS_texture_lod, GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SUN_slice_accum, GL_WIN_swap_hint, WGL_EXT_swap_control
[ERROR] Module threw exception
java.lang.RuntimeException: com.jogamp.opengl.GLException: Caught NoClassDefFoundError: coremem/types/NativeTypeEnum on thread SciJava-78226c36-Thread-1-Display-.windows_nil-1-EDT-1
	at jogamp.newt.DefaultEDTUtil.invokeImpl(DefaultEDTUtil.java:252)
	at jogamp.newt.DefaultEDTUtil.invoke(DefaultEDTUtil.java:165)
	at jogamp.newt.DisplayImpl.runOnEDTIfAvail(DisplayImpl.java:442)
	at jogamp.newt.WindowImpl.runOnEDTIfAvail(WindowImpl.java:2782)
	at jogamp.newt.WindowImpl.setVisible(WindowImpl.java:1330)
	at jogamp.newt.WindowImpl.setVisible(WindowImpl.java:1335)
	at com.jogamp.newt.opengl.GLWindow.setVisible(GLWindow.java:578)
	at cleargl.ClearGLWindow.setVisible(ClearGLWindow.java:233)
	at scenery.SceneryDefaultApplication.main(SceneryDefaultApplication.kt:137)
	at sc.fiji.ThreeDViewerLauncher.run(ThreeDViewerLauncher.java:30)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: com.jogamp.opengl.GLException: Caught NoClassDefFoundError: coremem/types/NativeTypeEnum on thread SciJava-78226c36-Thread-1-Display-.windows_nil-1-EDT-1
	at com.jogamp.opengl.GLException.newGLException(GLException.java:76)
	at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1327)
	at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
	at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
	at jogamp.opengl.GLAutoDrawableBase.defaultWindowResizedOp(GLAutoDrawableBase.java:260)
	at com.jogamp.newt.opengl.GLWindow.access$200(GLWindow.java:119)
	at com.jogamp.newt.opengl.GLWindow$2.windowResized(GLWindow.java:141)
	at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4383)
	at jogamp.newt.WindowImpl.sendWindowEvent(WindowImpl.java:4317)
	at jogamp.newt.WindowImpl.setVisibleActionImpl(WindowImpl.java:1306)
	at jogamp.newt.WindowImpl$VisibleAction.run(WindowImpl.java:1318)
	at com.jogamp.common.util.RunnableTask.run(RunnableTask.java:145)
	at jogamp.newt.DefaultEDTUtil$NEDT.run(DefaultEDTUtil.java:375)
Caused by: java.lang.NoClassDefFoundError: coremem/types/NativeTypeEnum
	at cleargl.GLFramebuffer.addFloatRGBBuffer(GLFramebuffer.java:66)
	at scenery.rendermodules.opengl.DeferredLightingRenderer.<init>(DeferredLightingRenderer.kt:145)
	at sc.fiji.ThreeDViewer.init(ThreeDViewer.java:45)
	at scenery.SceneryDefaultApplication$main$lClearGLWindowEventListener$1.init(SceneryDefaultApplication.kt:75)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
	at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
	at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
	... 11 more
Caused by: java.lang.ClassNotFoundException: coremem.types.NativeTypeEnum
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 19 more

I can’t get system information either because that throws an exception now that I’ve added the Three D Viewer jars into the mix.

[ERROR] Module threw error
java.lang.IncompatibleClassChangeError: net.imagej.ops.Ops$Geometric and net.imagej.ops.Ops$Geometric$MeshSmoothing disagree on InnerClasses attribute
	at java.lang.Class.getDeclaringClass0(Native Method)
	at java.lang.Class.getDeclaringClass(Class.java:1235)
	at java.lang.Class.getEnclosingClass(Class.java:1277)
	at java.lang.Class.getSimpleBinaryName(Class.java:1443)
	at java.lang.Class.getSimpleName(Class.java:1309)
	at org.scijava.util.StringMaker.makeString(StringMaker.java:95)
	at org.scijava.util.StringMaker.append(StringMaker.java:77)
	at org.scijava.util.StringMaker.append(StringMaker.java:69)
	at org.scijava.plugin.PluginInfo.toString(PluginInfo.java:268)
	at java.lang.String.valueOf(String.java:2994)
	at java.lang.StringBuilder.append(StringBuilder.java:131)
	at org.scijava.plugins.commands.debug.SystemInformation.dumpPlugins(SystemInformation.java:364)
	at org.scijava.plugins.commands.debug.SystemInformation.run(SystemInformation.java:243)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Ok, here’s my system info after a fresh fiji unpack:

ImageJ 2.0.0-rc-49/1.51e; Java 1.8.0_66 [amd64]

-- Application: ImageJ --
Title = ImageJ
Version = 2.0.0-rc-49/1.51e
groupId = net.imagej
artifactId = imagej
Archiver-Version = Plexus Archiver
Build-Jdk = 1.8.0_72-internal
Built-By = jenkins-maven
Class-Path = imagej-common-0.21.0.jar imglib2-2.9.0.jar imglib2-roi-0.4.2.jar trove4j-3.0.3.jar udunits-4.3.18.jar imagej-ops-0.30.0.jar imglib2-algorithm-0.5.0.jar jama-1.0.3.jar imglib2-algorithm-fft-0.1.2.jar mines-jtk-20151125.jar imglib2-realtransform-2.0.0-beta-31.jar scijava-expression-parser-3.0.1.jar scripting-javascript-0.4.3.jar commons-math3-3.4.1.jar imagej-updater-0.7.9.jar scifio-0.27.2.jar scifio-jai-imageio-1.1.0.jar mapdb-1.0.3.jar scijava-common-2.56.0.jar gentyref-1.1.0.jar eventbus-1.4.jar imagej-legacy-0.20.1.jar ij1-patcher-0.12.3.jar javassist-3.19.0-GA.jar ij-1.50i.jar imglib2-ij-2.0.0-beta-31.jar scijava-ui-awt-0.1.4.jar scijava-ui-swing-0.8.0.jar swing-checkbox-tree-1.0.1.jar jdatepicker-1.3.2.jar imagej-deprecated-0.1.1.jar imagej-plugins-commands-0.6.0.jar object-inspector-0.1.jar base64-2.3.8.jar imagej-plugins-tools-0.3.0.jar imagej-plugins-uploader-ssh-0.3.0.jar jsch-0.1.49.jar imagej-plugins-uploader-webdav-0.2.0.jar imagej-scripting-0.4.0.jar scripting-beanshell-0.3.1.jar bsh-2.0b6.jar scripting-clojure-0.1.4.jar clojure-1.6.0.jar scripting-groovy-0.2.5.jar groovy-2.3.6.jar scripting-java-0.4.0.jar minimaven-2.2.0.jar scripting-jruby-0.2.4.jar jruby-core-1.7.12.jar asm-4.0.jar asm-commons-4.0.jar asm-tree-4.0.jar asm-analysis-4.0.jar asm-util-4.0.jar joni-2.1.1.jar jnr-netdb-1.1.2.jar jnr-enxio-0.4.jar jnr-x86asm-1.0.2.jar jnr-unixsocket-0.3.jar jnr-posix-3.0.1.jar bytelist-1.0.11.jar jnr-constants-0.8.5.jar jcodings-1.0.10.jar jnr-ffi-1.0.7.jar jffi-1.2.7.jar jffi-1.2.7-native.jar snakeyaml-1.13.jar jzlib-1.1.2.jar invokebinder-1.2.jar nailgun-server-0.9.1.jar yecht-1.0.jar joda-time-2.3.jar options-1.1.jar jruby-stdlib-1.7.12.jar scripting-jython-0.3.0.jar jython-shaded-2.5.3.jar scripting-renjin-0.2.0.jar renjin-script-engine-0.8.1906.jar renjin-core-0.8.1906.jar commons-math-2.2.jar gcc-runtime-0.8.1906.jar netlib-java-0.9.3-renjin-patched-2.jar lapack-0.8.jar f2jutil-0.8.jar xerbla-0.8.jar blas-0.8.jar commons-vfs2-2.0.jar commons-logging-1.1.1.jar maven-scm-api-1.4.jar plexus-utils-1.5.6.jar maven-scm-provider-svnexe-1.4.jar maven-scm-provider-svn-commons-1.4.jar regexp-1.3.jar commons-compress-1.4.1.jar xz-1.0.jar jtransforms-2.4.jar jung-api-2.0.1.jar collections-generic-4.01.jar jung-graph-impl-2.0.1.jar guava-18.0.jar codemodel-2.6.jar stats-0.8.1906.jar renjin-appl-0.8.1906.jar renjin-gnur-runtime-0.8.1906.jar methods-0.8.1906.jar datasets-0.8.1906.jar utils-0.8.1906.jar grDevices-0.8.1906.jar graphics-0.8.1906.jar scripting-scala-0.1.0.jar scala-compiler-2.12.0-M4.jar scala-library-2.12.0-M4.jar scala-reflect-2.12.0-M4.jar scala-xml_2.12.0-M4-1.0.5.jar scala-parser-combinators_2.12.0-M4-1.0.4.jar scijava-plugins-commands-0.2.2.jar scijava-plugins-platforms-0.2.0.jar scijava-plugins-text-markdown-0.1.2.jar markdownj-0.3.0-1.0.2b4.jar scijava-plugins-text-plain-0.1.2.jar commons-lang3-3.1.jar imagej-ui-swing-0.19.0.jar rsyntaxtextarea-2.5.8.jar autocomplete-2.5.8.jar languagesupport-2.5.8.jar rhino-1.7.6.jar miglayout-3.7.4-swing.jar jfreechart-1.0.19.jar jcommon-1.0.23.jar jhotdraw-7.6.0.jar imagej-ui-awt-0.3.0.jar
Created-By = Apache Maven 3.0.4
Implementation-Build = e01a259e5d0735e44a8e5b5f353d7c23593d21dc
Implementation-Date = 2016-05-06T16:00:13-0500
Implementation-Title = ImageJ
Implementation-Vendor = ImageJ
Implementation-Vendor-Id = net.imagej
Implementation-Version = 2.0.0-rc-49
Main-Class = net.imagej.Main
Manifest-Version = 1.0
Package = net.imagej
Specification-Title = ImageJ
Specification-Vendor = ImageJ
Specification-Version = 2.0.0-rc-49

-- Application: Fiji --
Title = Fiji
Version = 2.0.0-SNAPSHOT
groupId = sc.fiji
artifactId = fiji
Archiver-Version = Plexus Archiver
Build-Jdk = 1.8.0_77
Built-By = curtis
Class-Path = imagej-2.0.0-rc-49.jar imagej-common-0.21.0.jar imglib2-roi-0.4.2.jar udunits-4.3.18.jar imagej-ops-0.30.0.jar imglib2-algorithm-fft-0.1.2.jar scripting-javascript-0.4.3.jar imagej-updater-0.7.9.jar scifio-0.27.2.jar scifio-jai-imageio-1.1.0.jar mapdb-1.0.3.jar imagej-deprecated-0.1.1.jar imagej-plugins-commands-0.6.0.jar object-inspector-0.1.jar base64-2.3.8.jar imagej-plugins-tools-0.3.0.jar imagej-plugins-uploader-ssh-0.3.0.jar imagej-plugins-uploader-webdav-0.2.0.jar imagej-scripting-0.4.0.jar scripting-beanshell-0.3.1.jar bsh-2.0b6.jar scripting-clojure-0.1.4.jar clojure-1.6.0.jar scripting-groovy-0.2.5.jar groovy-2.3.6.jar scripting-java-0.4.0.jar minimaven-2.2.0.jar scripting-jruby-0.2.4.jar jruby-core-1.7.12.jar asm-4.0.jar asm-commons-4.0.jar asm-tree-4.0.jar asm-analysis-4.0.jar asm-util-4.0.jar joni-2.1.1.jar jnr-netdb-1.1.2.jar jnr-enxio-0.4.jar jnr-x86asm-1.0.2.jar jnr-unixsocket-0.3.jar jnr-posix-3.0.1.jar bytelist-1.0.11.jar jnr-constants-0.8.5.jar jcodings-1.0.10.jar jnr-ffi-1.0.7.jar jffi-1.2.7.jar jffi-1.2.7-native.jar invokebinder-1.2.jar nailgun-server-0.9.1.jar yecht-1.0.jar options-1.1.jar jruby-stdlib-1.7.12.jar scripting-jython-0.3.0.jar scripting-renjin-0.2.0.jar renjin-script-engine-0.8.1906.jar renjin-core-0.8.1906.jar commons-math-2.2.jar gcc-runtime-0.8.1906.jar netlib-java-0.9.3-renjin-patched-2.jar lapack-0.8.jar f2jutil-0.8.jar xerbla-0.8.jar blas-0.8.jar commons-vfs2-2.0.jar maven-scm-api-1.4.jar plexus-utils-1.5.6.jar maven-scm-provider-svnexe-1.4.jar maven-scm-provider-svn-commons-1.4.jar regexp-1.3.jar commons-compress-1.4.1.jar xz-1.0.jar jtransforms-2.4.jar jung-api-2.0.1.jar collections-generic-4.01.jar jung-graph-impl-2.0.1.jar codemodel-2.6.jar stats-0.8.1906.jar renjin-appl-0.8.1906.jar renjin-gnur-runtime-0.8.1906.jar methods-0.8.1906.jar datasets-0.8.1906.jar utils-0.8.1906.jar grDevices-0.8.1906.jar graphics-0.8.1906.jar scripting-scala-0.1.0.jar scala-compiler-2.12.0-M4.jar scala-library-2.12.0-M4.jar scala-reflect-2.12.0-M4.jar scala-xml_2.12.0-M4-1.0.5.jar scala-parser-combinators_2.12.0-M4-1.0.4.jar scijava-plugins-commands-0.2.2.jar scijava-plugins-platforms-0.2.0.jar scijava-plugins-text-markdown-0.1.2.jar markdownj-0.3.0-1.0.2b4.jar scijava-plugins-text-plain-0.1.2.jar commons-lang3-3.1.jar imagej-ui-swing-0.19.0.jar rsyntaxtextarea-2.5.8.jar autocomplete-2.5.8.jar languagesupport-2.5.8.jar rhino-1.7.6.jar miglayout-3.7.4-swing.jar jhotdraw-7.6.0.jar imagej-ui-awt-0.3.0.jar scijava-common-2.56.0.jar scijava-expression-parser-3.0.1.jar gentyref-1.1.0.jar eventbus-1.4.jar imagej-legacy-0.20.1.jar ij1-patcher-0.12.3.jar ij-1.50i.jar imglib2-2.9.0.jar imglib2-ij-2.0.0-beta-31.jar scijava-ui-awt-0.1.4.jar scijava-ui-swing-0.8.0.jar swing-checkbox-tree-1.0.1.jar jdatepicker-1.3.2.jar 3D_Blob_Segmentation-3.0.0.jar vecmath-1.6.0-scijava-2.jar 3D_Objects_Counter-2.0.0.jar 3D_Viewer-4.0.1.jar jama-1.0.3.jar j3dcore-1.6.0-scijava-2.jar j3dutils-1.6.0-scijava-2.jar AnalyzeSkeleton_-3.1.0.jar Analyze_Reader_Writer-2.0.0.jar Anisotropic_Diffusion_2D-2.0.0.jar Archipelago_Plugins-0.5.2.jar Trainable_Segmentation-3.1.0.jar weka-dev-3.7.11.jar java-cup-0.11a.jar pentaho-package-manager-1.0.8.jar Arrow_-2.0.1.jar Auto_Threshold-1.16.2.jar BalloonSegmentation_-2.0.0.jar Bug_Submitter-2.0.2.jar CPU_Meter-2.0.0.jar jna-3.2.7.jar Calculator_Plus-2.0.0.jar Cell_Counter-2.2.0.jar Colocalisation_Analysis-2.2.0.jar imglib2-algorithm-0.5.0.jar itextpdf-5.1.1.jar Color_Histogram-2.0.6.jar Color_Inspector_3D-2.3.1.jar Colour_Deconvolution-3.0.1.jar CorrectBleach_-2.0.1.jar Descriptor_based_registration-2.0.12.jar mpicbg-1.1.1.jar Dichromacy_-2.1.0.jar Differentials_-2.0.0.jar Directionality_-2.0.1.jar jfreechart-1.0.19.jar Extended_Depth_Field-2.0.1.jar FS_Align_TrakEM2-2.0.1.jar Feature_Detection-2.0.1.jar Fiji_Archipelago-2.0.0.jar jsch-0.1.49.jar Fiji_Developer-2.0.4.jar Fiji_Package_Maker-2.1.0.jar Fiji_Plugins-3.0.0.jar Fiji_Updater-2.0.0.jar FlowJ_-1.29.1.jar Graph_Cut-1.0.1.jar Gray_Morphology-2.3.3.jar Helmholtz_Analysis-2.0.1.jar IJ_Robot-2.0.0.jar IO_-2.3.1.jar batik-bridge-1.8.jar batik-anim-1.8.jar batik-awt-util-1.8.jar batik-css-1.8.jar batik-ext-1.8.jar batik-parser-1.8.jar batik-script-1.8.jar batik-svg-dom-1.8.jar batik-util-1.8.jar batik-xml-1.8.jar xml-apis-ext-1.3.04.jar batik-gvt-1.8.jar jpedalSTD-2.80b11.jar jzlib-1.1.2.jar Image_5D-1.2.6.jar Image_Expression_Parser-3.0.0.jar imglib2-algorithm-gpl-0.1.5.jar jep-2.4.2.jar Interactive_3D_Surface_Plot-2.4.1.jar IsoData_Classifier-2.0.0.jar Kuwahara_Filter-2.0.0.jar LSM_Reader-4.1.1.jar LSM_Toolbox-4.1.1.jar Lasso_and_Blow_Tool-2.0.1.jar Linear_Kuwahara-2.0.0.jar LocalThickness_-4.0.0.jar MTrack2_-2.0.0.jar M_I_P-2.0.0.jar Manual_Tracking-2.1.0.jar MosaicJ_-2.0.0.jar Multi_Kymograph-2.0.0.jar PIV_analyser-1.1.1.jar PointPicker_-2.0.0.jar QuickPALM_-1.1.1.jar RATS_-2.0.0.jar Reconstruct_Reader-2.0.2.jar SPIM_Opener-2.0.1.jar SPIM_Registration-4.0.0.jar imglib2-realtransform-2.0.0-beta-31.jar formats-api-5.1.8.jar formats-bsd-5.1.8.jar jai_imageio-5.1.8.jar specification-5.1.8.jar turbojpeg-5.1.8.jar native-lib-loader-2.1.3.jar kryo-2.24.0.jar minlog-1.2.jar objenesis-2.1.jar perf4j-0.9.13.jar guava-18.0.jar metadata-extractor-2.6.2.jar xmpcore-5.1.2.jar xercesImpl-2.8.1.jar formats-gpl-5.1.8.jar mdbtools-java-5.1.8.jar metakit-5.1.8.jar ome-poi-5.1.8.jar commons-logging-1.1.1.jar netcdf-4.3.19.jar JWlz-1.4.0.jar ome-xml-5.1.8.jar formats-common-5.1.8.jar jdom2-2.0.6.jar jcommon-1.0.23.jar Samples_-2.0.1.jar Series_Labeler-2.0.0.jar SheppLogan_-2.0.0.jar Simple_Neurite_Tracer-3.0.2.jar commons-math3-3.4.1.jar batik-dom-1.8.jar batik-svggen-1.8.jar Siox_Segmentation-1.0.4.jar Skeletonize3D_-2.0.0.jar Snakuscule_-2.0.0.jar SplineDeformationGenerator_-2.0.0.jar StackReg_-2.0.0.jar Stack_Manipulation-2.0.1.jar Statistical_Region_Merging-2.0.0.jar Stitching_-3.1.0.jar mines-jtk-20151125.jar Sync_Win-1.7-fiji3.jar Thread_Killer-2.0.0.jar Time_Lapse-2.0.1.jar Time_Stamper-2.0.0.jar ToAST_-25.0.1.jar TopoJ_-2.0.0.jar TrackMate_-3.2.1.jar jgrapht-0.8.3.jar jgraphx-1.10.4.1.jar TrakEM2_Archipelago-2.0.1.jar TurboReg_-2.0.0.jar UnwarpJ_-2.0.0.jar VIB-lib-2.1.1.jar VIB_-3.0.0.jar Vaa3d_Reader-2.0.1.jar Vaa3d_Writer-1.0.1.jar Video_Editing-2.0.0.jar View5D_-1.3.1.jar Volume_Calculator-2.0.1.jar Volume_Viewer-2.01.1.jar bUnwarpJ_-2.6.3.jar blockmatching_-2.1.1.jar fiji-compat-2.0.2.jar javassist-3.19.0-GA.jar fiji-lib-2.1.1.jar H5J_Loader_Plugin-1.0.4.jar jhdf5-14.12.5.jar ffmpeg-2.6.1-0.11.jar javacpp-0.11.jar ffmpeg-2.6.1-0.11-macosx-x86_64.jar imageware-2.0.0.jar javac-1.6.0.24-ubuntu-fiji2.jar legacy-imglib1-1.1.5.jar level_sets-1.0.1.jar mij-1.3.6-fiji2.jar pal-optimization-2.0.0.jar panorama_-3.0.1.jar register_virtual_stack_slices-3.0.1.jar registration_3d-2.0.0.jar wavelets-2.0.0.jar Sholl_Analysis-3.6.1.jar jitk-tps-2.1.0.jar ejml-0.24.jar log4j-1.2.17.jar opencsv-2.4.jar mpicbg_-1.1.1.jar bio-formats_plugins-5.1.8.jar jgoodies-forms-1.7.2.jar jgoodies-common-1.7.0.jar slf4j-api-1.7.6.jar logback-core-1.1.1.jar bigwarp_fiji-2.1.2.jar imglib2-ui-2.0.0-beta-30.jar trakem2_tps-1.1.2.jar commons-codec-1.8.jar bigdataviewer-core-2.4.0.jar gson-2.2.4.jar ui-behaviour-1.0.4.jar trove4j-3.0.3.jar snakeyaml-1.13.jar bigdataviewer_fiji-2.1.0.jar spim_data-2.0.1.jar mpicbg-trakem2-1.2.3.jar T2-NIT-1.1.1.jar T2-TreelineGraph-1.1.1.jar TrakEM2_-1.0h.jar postgresql-8.2-507.jdbc3.jar jai-codec-1.1.3.jar jai-core-1.1.3.jar jython-shaded-2.5.3.jar VectorString-2.0.0.jar scifio-bf-compat-2.0.0.jar scifio-hdf5-0.1.1.jar scifio-lifesci-0.7.0.jar scifio-ome-xml-0.13.0.jar scifio-cli-0.3.2.jar args4j-2.0.25.jar scijava-config-2.0.1.jar gluegen-rt-main-2.3.2.jar gluegen-rt-2.3.2.jar gluegen-rt-2.3.2-natives-android-aarch64.jar gluegen-rt-2.3.2-natives-android-armv6.jar gluegen-rt-2.3.2-natives-linux-amd64.jar gluegen-rt-2.3.2-natives-linux-armv6.jar gluegen-rt-2.3.2-natives-linux-armv6hf.jar gluegen-rt-2.3.2-natives-linux-i586.jar gluegen-rt-2.3.2-natives-macosx-universal.jar gluegen-rt-2.3.2-natives-solaris-amd64.jar gluegen-rt-2.3.2-natives-solaris-i586.jar gluegen-rt-2.3.2-natives-windows-amd64.jar gluegen-rt-2.3.2-natives-windows-i586.jar joal-main-2.3.2.jar joal-2.3.2.jar joal-2.3.2-natives-android-aarch64.jar joal-2.3.2-natives-android-armv6.jar joal-2.3.2-natives-linux-amd64.jar joal-2.3.2-natives-linux-armv6.jar joal-2.3.2-natives-linux-armv6hf.jar joal-2.3.2-natives-linux-i586.jar joal-2.3.2-natives-macosx-universal.jar joal-2.3.2-natives-solaris-amd64.jar joal-2.3.2-natives-solaris-i586.jar joal-2.3.2-natives-windows-amd64.jar joal-2.3.2-natives-windows-i586.jar jocl-main-2.3.2.jar jocl-2.3.2.jar jocl-2.3.2-natives-android-aarch64.jar jocl-2.3.2-natives-android-armv6.jar jocl-2.3.2-natives-linux-amd64.jar jocl-2.3.2-natives-linux-armv6.jar jocl-2.3.2-natives-linux-armv6hf.jar jocl-2.3.2-natives-linux-i586.jar jocl-2.3.2-natives-macosx-universal.jar jocl-2.3.2-natives-solaris-amd64.jar jocl-2.3.2-natives-solaris-i586.jar jocl-2.3.2-natives-windows-amd64.jar jocl-2.3.2-natives-windows-i586.jar jogl-all-main-2.3.2.jar jogl-all-2.3.2.jar jogl-all-2.3.2-natives-android-aarch64.jar jogl-all-2.3.2-natives-android-armv6.jar jogl-all-2.3.2-natives-linux-amd64.jar jogl-all-2.3.2-natives-linux-armv6.jar jogl-all-2.3.2-natives-linux-armv6hf.jar jogl-all-2.3.2-natives-linux-i586.jar jogl-all-2.3.2-natives-macosx-universal.jar jogl-all-2.3.2-natives-solaris-amd64.jar jogl-all-2.3.2-natives-solaris-i586.jar jogl-all-2.3.2-natives-windows-amd64.jar jogl-all-2.3.2-natives-windows-i586.jar logback-classic-1.1.1.jar joda-time-2.3.jar
Created-By = Apache Maven 3.3.9
Implementation-Build = f9657ffd399351fca5ef1d2456af5faa74abee01
Implementation-Date = 2016-05-16T17:30:44+0000
Implementation-Title = Fiji
Implementation-Vendor = Fiji
Implementation-Vendor-Id = sc.fiji
Implementation-Version = 2.0.0-SNAPSHOT
Manifest-Version = 1.0
Specification-Title = Fiji
Specification-Vendor = Fiji
Specification-Version = 2.0.0-SNAPSHOT


-- Application: SciJava --
Title = SciJava
Version = 2.56.0
groupId = org.scijava
artifactId = scijava-common
Archiver-Version = Plexus Archiver
Build-Jdk = 1.8.0_72-internal
Built-By = jenkins-maven
Class-Path = scijava-expression-parser-3.0.0.jar gentyref-1.1.0.jar eventbus-1.4.jar
Created-By = Apache Maven 3.0.4
Implementation-Build = 86a47fbef4342e9359765763406106aafcb535be
Implementation-Date = 2016-04-20T20:22:14-0500
Implementation-Title = SciJava Common
Implementation-Vendor = SciJava
Implementation-Vendor-Id = org.scijava
Implementation-Version = 2.56.0
Manifest-Version = 1.0
Package = org.scijava
Specification-Title = SciJava Common
Specification-Vendor = SciJava
Specification-Version = 2.56.0

-- Application: SCIFIO --
Title = SCIFIO
Version = 0.27.2
groupId = io.scif
artifactId = scifio
Archiver-Version = Plexus Archiver
Build-Jdk = 1.8.0_72-internal
Built-By = jenkins-maven
Class-Path = scifio-jai-imageio-1.1.0.jar imagej-common-0.18.1.jar imglib2-roi-0.4.2.jar trove4j-3.0.3.jar udunits-4.3.18.jar imglib2-2.4.1.jar scijava-common-2.49.1.jar gentyref-1.1.0.jar eventbus-1.4.jar mapdb-1.0.3.jar
Manifest-Version = 1.0
Specification-Title = SCIFIO Core
Specification-Vendor = SCIFIO
Specification-Version = 0.27.2

-- Application: ImageJ1 --
Title = ImageJ1
Version = 1.51e
groupId = net.imagej
artifactId = ij
Archiver-Version = Plexus Archiver
Build-Jdk = 1.8.0_72-internal
Built-By = jenkins-maven
Class-Path = scifio-0.27.2.jar scifio-jai-imageio-1.1.0.jar mapdb-1.0.3.jar ij1-patcher-0.12.3.jar javassist-3.19.0-GA.jar ij-1.50i.jar imagej-common-0.20.1.jar imglib2-roi-0.4.2.jar trove4j-3.0.3.jar udunits-4.3.18.jar imagej-ui-swing-0.18.0.jar imagej-deprecated-0.1.1.jar imagej-ops-0.27.0.jar imglib2-algorithm-0.4.0.jar jama-1.0.3.jar imglib2-algorithm-fft-0.1.2.jar mines-jtk-20151125.jar imglib2-realtransform-2.0.0-beta-31.jar scripting-javascript-0.4.3.jar commons-math3-3.5.jar imagej-updater-0.7.9.jar scripting-java-0.4.0.jar minimaven-2.2.0.jar rsyntaxtextarea-2.5.8.jar autocomplete-2.5.8.jar languagesupport-2.5.8.jar rhino-1.7.6.jar miglayout-3.7.4-swing.jar jfreechart-1.0.19.jar jcommon-1.0.23.jar jhotdraw-7.6.0.jar imagej-ui-awt-0.3.0.jar imglib2-2.7.0.jar imglib2-ij-2.0.0-beta-31.jar scijava-common-2.55.1.jar scijava-expression-parser-3.0.1.jar gentyref-1.1.0.jar eventbus-1.4.jar scijava-ui-awt-0.1.4.jar scijava-ui-swing-0.8.0.jar swing-checkbox-tree-1.0.1.jar object-inspector-0.1.jar jdatepicker-1.3.2.jar scijava-plugins-commands-0.2.2.jar scripting-beanshell-0.3.1.jar bsh-2.0b6.jar scijava-plugins-text-plain-0.1.2.jar commons-lang3-3.1.jar scijava-plugins-text-markdown-0.1.2.jar markdownj-0.3.0-1.0.2b4.jar
..
os.arch = amd64
os.name = Windows 7
os.version = 6.1
path.separator = ;
plugins.dir = C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app
sun.arch.data.model = 64
sun.boot.class.path = {
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\resources.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\rt.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\sunrsasign.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\jsse.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\jce.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\charsets.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\lib\jfr.jar
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\classes
}
sun.boot.library.path = {
	C:\Users\####\DOWNLO~1\FIJI-W~2\Fiji.app\java\win64\jdk1.8.0_66\jre\bin
}

I’m happy to help more, if you can get me out of this pickle!


#42

Ok, the answers are:

  1. Life will generally be easier when using the update sites through either the FIJI GUI or command-line interfaces, instead of manually obtaining the jars like this. In fact, this is actually part of the problem. The cleargl-1.0 should not be installed. The update site stores old versions of files as well, which is why there is an additional file in the root directory that stores information about which files should actually get installed.

  2. The error from running ThreeDViewer came from a missing dependency (coremem); however, the CoreMem dependency has been eliminated. Removing cleargl-1.0 should fix this (might as well update your cleargl-2.0.0 as well).

  3. The imagej-ops error came up because there are some deeper changes that need to be made to get all of the functionality we really want out of ThreeDViewer, and I was getting a bit too ahead of myself with changes in imagej-ops. Anyway, updating the jars to use imagej-ops-0.31.1-SNAPSHOT should fix this.

Note that I updated the ThreeDViewer and scenery jars as well.


#43

For greater permanency, I’ve started an ImageJ wiki entry for this procedure, see http://imagej.net/Voxelization


#44

Hey kephale, I am the one who started this question. I haven’t touched the 3DViewer for quite some time so I am a little behind the times in terms of updates, but from what I’ve read in this thread there have been some changes made. So the “Voxelisation” tool has now been migrated to a plugin called ThreeDViewer, and can be accessed through the update sites, however I do not have ThreeDViewer within my list of available update sites.


#45

You can add the site manually using the Add update site button in the updater and entering the URL http://sites.imagej.net/ThreeDViewer/.


#46

When I attempt to import an .STL file I get this error in the console for the ThreeDViewer plugin:

[ERROR] Cannot create module: sc.fiji.threedviewer.io.ImportSTL
org.scijava.module.ModuleException: org.scijava.InstantiableException: Class not found: sc.fiji.threedviewer.io.ImportSTL
	at org.scijava.command.CommandInfo.createModule(CommandInfo.java:320)
	at org.scijava.module.DefaultModuleService.createModule(DefaultModuleService.java:156)
	at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:195)
	at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:186)
	at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:171)
	at org.scijava.command.DefaultCommandService.run(DefaultCommandService.java:185)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:270)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:161)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:662)
Caused by: org.scijava.InstantiableException: Class not found: sc.fiji.threedviewer.io.ImportSTL
	at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:285)
	at org.scijava.command.CommandInfo.loadClass(CommandInfo.java:245)
	at org.scijava.command.CommandInfo.createModule(CommandInfo.java:314)
	... 11 more

#47

Did you “Launch” ThreeDViewer first (this should be made automatic eventually)? Is “ThreeDViewer-0.0.1-SNAPSHOT.jar” in your plugins directory?

I just downloaded a fresh version of Fiji, installed ThreeDViewer, and import STL works for me (on OS X).


#48

Yes, I launched the ThreeDViewer first, however, I don’t know where the SNAPSHOT.jar is in the plugin directory. I only updated the site “ThreeDViewer” to my list of update sites. Do I simply copy and paste the .jar file into my plugin folder for ImageJ?


#49

You shouldn’t need to modify or move any files when installing via an update site.

Here is a more effective test:

If you still have Funimage installed, then use the menu Funimage>REPL
Otherwise, use the menu Plugins>Scripting>Clojure Interpreter

Run the command:
(println (filter identity (map #(re-find #"ThreeD" (str %)) (seq (.getURLs (java.lang.ClassLoader/getSystemClassLoader))))))

If the result is:
(ThreeD)
Then, ThreeDViewer is on your classpath, and some serious digging is required.
Otherwise the result will be:
()
Which means something went wrong with the installation from the update site (which is also odd).

Another thing to check is through the command finder (Plugins>Utilities>Find Commands), and search for ThreeD. There should be an entry for “STL”


#50

Hi kephale, so the result of the command was: ThreeD (nil), which is odd as you say as I was able to select Lauch and attempt to import and .STL, regardless, I will attempt to load a fresh copy of Fiji with ThreeDViewer and attempt this again. I will keep you updated on any results.


#51

Right, in a fresh edition of Fiji, I was able to import an STL:

Reading from binary STL file \\icnas1.cc.ic.ac.uk\azi15\test4_smoothed_simple_smoothed_50 (repaired).stl
Read 450000 vertices/450000 normals of model  in 496.765743 ms
Number of nodes in scene: 1

Am I meant to see the STL in “scenery: ThreeDViewer” window?


#52

Yes, ideally you would see your STL in that window. At the moment the view does not get automatically updated with respect to the object’s center and bounding box.

If you use the menu ThreeDViewer>Controls>Arc Ball, then the viewer should focus on your object’s center, mouse controls should rotate your object, and mouse scroll/wheel should zoom in/out.

I’m guessing your question arises because your object isn’t immediately visible after being imported?


#53

Yes, I’ve followed your instruction on the controls>Arc Ball, all I get is the “Exception” window pop-up if that’s of any consequence? Could there be a lighting issue?


#54

Are there any developments on this? Am I the only person who has had this problem?


#55

Today is the first chance I’ve ended up with to look into this, more by midweek.


#56

No worries, I’ll keep trying uninstalling and installing ImageJ and try different .STL’s


#57

I can not open the ThreeDViewer. I just added it to my update sites. However, once I try clicking on launch, I get this NullPointer:

[ERROR] Module threw exception
java.lang.NullPointerException
	at sc.fiji.threed.ThreeDViewerLauncher.run(ThreeDViewerLauncher.java:23)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

#58

Sorry I am slightly bogged down at the moment, but I’ll check/fix this in the next few days. If 1 week passes without a response, feel free to vigorously poke me.


#59

Hi @kephale,

Today I added update site ThreeDViewer (and installed fresh Fiji), and after following the instructions (click Launch), I got this error message. I also ran the command using Funimage>REPL as you described and I got .

[ERROR] Module threw error
java.lang.NoClassDefFoundError: graphics/scenery/SceneryDefaultApplication
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:760)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at sc.fiji.threed.ThreeDViewerLauncher.run(ThreeDViewerLauncher.java:31)
	at org.scijava.command.CommandModule.run(CommandModule.java:198)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: graphics.scenery.SceneryDefaultApplication
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 22 more

#60

Same happens for me now.