Git log: commit 188d4d2f68a78312ee79b84fa83075cfba80dc13
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Aug 28 21:46:05 2018 -0400
changelog
commit c7291b5c9ecebef137f5740aa8eeb3ad864255da
Merge: 2403df45 0c4a02c2
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Aug 28 21:45:15 2018 -0400
Merge branch 'releases' into debian
* releases: (117 commits)
In CaretHttpManager, change logging level of not important messages from INFO to FINE.
WB-818 Upload Scene File to BALSA - Verify user is owner and study is editable: Disable logic in wb_view that tests for study editable and owned by user as this logic will be moved into the BALSA database. For now, if a '403' is returned by the 'process upload' step, add to error message that this error may be caused by a permissions/ownership problem.
Fix compilation warning and remove debugging print statement.
Updated Guide to Annotations in the Workbench Help (MS Word file saved as HTML).
Resolve WB-818 Upload Scene File to BALSA : Verify that the user is an owner of the study and that the study has an editable status.
Improved format of error message displayed when there is an error reading a file.
Update Workbench Version to 1.3.2
Further work on WB-817: Linux/Mac wb_view is unable to read a scene file that was created on Windows: Change SystemUtilities::relativePath() so that it always uses a forward slash for the separator in file paths (It was using QDir::separator()). The problem with using QDir::separator() is that on Windows, the paths contain backward slashes and do not resolve correctly when attempting to read a file on a Unix operating system.
Resolve WB-817: Linux/Mac wb_view is unable to read a scene file that was created on Windows: Using QDir:cleanPath() did not solve the problem and the problem also exists on Macs. QDir::cleanPath() only converts a backward slash to a forward slash if the native separator is a backward slash (so only on Windows). Added FileInformation::cleanPath() that first converts backward slashes to forward slashes followed by a call to QDir::cleanPath().
WB-817: Linux wb_view is unable to read a scene file that was created on Windows: Adding a call to QDir::cleanPath() in ScenePathName class to hopefully fix this problem on Linux.
The graphics code that converts lines into triangles was outputting some messages at the warning level that are actually minor/trivial items. They remain a warning when compiled debug but now log at the fine level in a release build.
Fixed crash caused by assertion failure when dragging mouse with an annotation in surface space inside a surface montage. An invalid viewport was used causing the assertion failure and has been corrected.
fix error check that used wrong index, fix dumb mistake in qfile write chunking
Fix for missing file in the help files.
Fixed help page HTML for Features ToolBox Annotations tab. It was in a binary format with lots of Microsoft metadata. Excess metadata was removed and file was converted to text html. It now displays properly in Workbench Help.
Add two items to Help Menu->Report a Workbench Bug: (1) wb_command must be run from terminal window; (2) wb_view may crash if used with a remote desktop due to XCB and/or OpenGL problems in the remote desktop.
WB-816 Compare unzip into directory in upload dialog to value in BALSA database:
Disabled code that defaults Upload to Balsa Dialog password with WORKBENCH_BALSA_PD from environment. It is only intended for use in debugging/testing.
On the Upload Scene File To BALSA dialog, add a button that allows the user to display the password (instead of hidden by dots). The password is always hidden by default.
In Upload to BALSA dialog, if the password has not been entered, test for the environment variable WORKBENCH_BALSA_PD. If it is set, use its value for the BALSA password.
...
commit 0c4a02c2921df5703f96697e6daef965578fddd3
Merge: d3a0a342 1c774d37
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Aug 28 21:43:20 2018 -0400
Merge tag 'v1.3.2' into releases
v1.3.2
* tag 'v1.3.2': (117 commits)
In CaretHttpManager, change logging level of not important messages from INFO to FINE.
WB-818 Upload Scene File to BALSA - Verify user is owner and study is editable: Disable logic in wb_view that tests for study editable and owned by user as this logic will be moved into the BALSA database. For now, if a '403' is returned by the 'process upload' step, add to error message that this error may be caused by a permissions/ownership problem.
Fix compilation warning and remove debugging print statement.
Updated Guide to Annotations in the Workbench Help (MS Word file saved as HTML).
Resolve WB-818 Upload Scene File to BALSA : Verify that the user is an owner of the study and that the study has an editable status.
Improved format of error message displayed when there is an error reading a file.
Update Workbench Version to 1.3.2
Further work on WB-817: Linux/Mac wb_view is unable to read a scene file that was created on Windows: Change SystemUtilities::relativePath() so that it always uses a forward slash for the separator in file paths (It was using QDir::separator()). The problem with using QDir::separator() is that on Windows, the paths contain backward slashes and do not resolve correctly when attempting to read a file on a Unix operating system.
Resolve WB-817: Linux/Mac wb_view is unable to read a scene file that was created on Windows: Using QDir:cleanPath() did not solve the problem and the problem also exists on Macs. QDir::cleanPath() only converts a backward slash to a forward slash if the native separator is a backward slash (so only on Windows). Added FileInformation::cleanPath() that first converts backward slashes to forward slashes followed by a call to QDir::cleanPath().
WB-817: Linux wb_view is unable to read a scene file that was created on Windows: Adding a call to QDir::cleanPath() in ScenePathName class to hopefully fix this problem on Linux.
The graphics code that converts lines into triangles was outputting some messages at the warning level that are actually minor/trivial items. They remain a warning when compiled debug but now log at the fine level in a release build.
Fixed crash caused by assertion failure when dragging mouse with an annotation in surface space inside a surface montage. An invalid viewport was used causing the assertion failure and has been corrected.
fix error check that used wrong index, fix dumb mistake in qfile write chunking
Fix for missing file in the help files.
Fixed help page HTML for Features ToolBox Annotations tab. It was in a binary format with lots of Microsoft metadata. Excess metadata was removed and file was converted to text html. It now displays properly in Workbench Help.
Add two items to Help Menu->Report a Workbench Bug: (1) wb_command must be run from terminal window; (2) wb_view may crash if used with a remote desktop due to XCB and/or OpenGL problems in the remote desktop.
WB-816 Compare unzip into directory in upload dialog to value in BALSA database:
Disabled code that defaults Upload to Balsa Dialog password with WORKBENCH_BALSA_PD from environment. It is only intended for use in debugging/testing.
On the Upload Scene File To BALSA dialog, add a button that allows the user to display the password (instead of hidden by dots). The password is always hidden by default.
In Upload to BALSA dialog, if the password has not been entered, test for the environment variable WORKBENCH_BALSA_PD. If it is set, use its value for the BALSA password.
...
commit 2403df4523c6cd12f71d850f7b68fea09bbdd952
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Jun 5 21:46:45 2018 -0400
Dropping also deb_dot_DNDEBUG patch hoping for the best
commit 38f9d05733170fee9a5ef358050299de798e4aaa
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Jun 5 20:09:23 2018 -0400
Dropping all previously CPed patches
commit 98c94fb2f117693793119d7dec7c0cdbb5cc8bd6
Merge: 07622354 d3a0a342
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Jun 5 19:54:32 2018 -0400
Merge branch 'releases' into debian
* releases: (21 commits)
change version to 1.3.1
Update all overlay and map settings editors after update. If there was more than one Overlay and Map Settings Dialog open and set to the same file/map, changing settings in one of the dialogs did not update the other dialog. This has been fixed.
Improvements fixing toolbox height too tall in versions of Qt prior to 5.6. Extended QDockWidget and QTabWidget to override the sizeHint() method and added methods to set the size hints. This somewhat replaces the functionality of QMainWindow::resizeDocks() that is only available in Qt 5.6 and newer. BrainBrowserWindowOrientatedToolBox(extends QDockWidget) adjusts its size using the size hint of the its child widget (from QDockWidget documentation) so a size hint width/height is set fort the child widget (WuQTabWidgetWithSizeHint overrides and implements sizeHint() method from QTabWidget).
update wb_shortcuts to resolve "wrong extension" warnings on temporaries, update some copyright years
Fixed crash the occurred when loading a label volume. In voxel color assignment, getMapPaletteColorMapping() without testing to see if the volume file was mapped with a palette. Adding a test for mapping with a palette was added and fixes the crash.
make a copy of the wb_shortcuts part of the bash completions, rather than trying to have installation make a symlink
add -file option to -volume-set-space, to copy space from another file
copy timestep and other header fields in -volume-math, put "Connectome Workbench" and version into volume header description field (not cifti currently)
Fixes so that source will build with Qt-5.5.1
Add 'this' when calling QAction(QObject* parent = nullptr). In Qt 5.7, the parent was made optional so this should fix a compilation error when using earlier versions of Qt. Also, in this instance, the missing parent would result in a small memory leak if the window was closed.
disable testing for SIMD support if not compiling for 64bit
add warnings to roi from extrema commands as an intermediate fix, but make the cifti version error
update copyright years on kloewe directory
attempt fix for avx simd by updating dot library
add pointer values to test output to help pin down simd errors
Resolve WB-800 Replace all scenes shows tab 1 outline highlighted in the regenerated previews: Tab highlighting has been disabled during image capture to prevent a highlighted tab from appearing in any captured image.
Resolve WB-788 Show scene number next to files in 'List Files' Window: For each data file, the scene indices are listed in parenthesis.
add missing period to main help info
remove duplicate information switch from completion
add missing information switches to completion
...
commit d3a0a342ca18df62c1c20e397814ad5970b9c9c3
Merge: abd3e718 dd20e3e0
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Jun 5 19:54:25 2018 -0400
Merge tag 'v1.3.1' into releases
v1.3.1
* tag 'v1.3.1': (21 commits)
change version to 1.3.1
Update all overlay and map settings editors after update. If there was more than one Overlay and Map Settings Dialog open and set to the same file/map, changing settings in one of the dialogs did not update the other dialog. This has been fixed.
Improvements fixing toolbox height too tall in versions of Qt prior to 5.6. Extended QDockWidget and QTabWidget to override the sizeHint() method and added methods to set the size hints. This somewhat replaces the functionality of QMainWindow::resizeDocks() that is only available in Qt 5.6 and newer. BrainBrowserWindowOrientatedToolBox(extends QDockWidget) adjusts its size using the size hint of the its child widget (from QDockWidget documentation) so a size hint width/height is set fort the child widget (WuQTabWidgetWithSizeHint overrides and implements sizeHint() method from QTabWidget).
update wb_shortcuts to resolve "wrong extension" warnings on temporaries, update some copyright years
Fixed crash the occurred when loading a label volume. In voxel color assignment, getMapPaletteColorMapping() without testing to see if the volume file was mapped with a palette. Adding a test for mapping with a palette was added and fixes the crash.
make a copy of the wb_shortcuts part of the bash completions, rather than trying to have installation make a symlink
add -file option to -volume-set-space, to copy space from another file
copy timestep and other header fields in -volume-math, put "Connectome Workbench" and version into volume header description field (not cifti currently)
Fixes so that source will build with Qt-5.5.1
Add 'this' when calling QAction(QObject* parent = nullptr). In Qt 5.7, the parent was made optional so this should fix a compilation error when using earlier versions of Qt. Also, in this instance, the missing parent would result in a small memory leak if the window was closed.
disable testing for SIMD support if not compiling for 64bit
add warnings to roi from extrema commands as an intermediate fix, but make the cifti version error
update copyright years on kloewe directory
attempt fix for avx simd by updating dot library
add pointer values to test output to help pin down simd errors
Resolve WB-800 Replace all scenes shows tab 1 outline highlighted in the regenerated previews: Tab highlighting has been disabled during image capture to prevent a highlighted tab from appearing in any captured image.
Resolve WB-788 Show scene number next to files in 'List Files' Window: For each data file, the scene indices are listed in parenthesis.
add missing period to main help info
remove duplicate information switch from completion
add missing information switches to completion
...
commit dd20e3e04bb65f2e2536fa1a500844f4d107668b
Author: Tim Coalson <tsc5yc@mst.edu>
Date: Mon Jun 4 20:08:38 2018 -0500
change version to 1.3.1
commit 50c9a53779ce090ac8d8e68af981f1b558dcc5f8
Author: John Harwell <john@brainmap.wustl.edu>
Date: Mon Jun 4 12:24:26 2018 -0500
Update all overlay and map settings editors after update. If there was more than one Overlay and Map Settings Dialog open and set to the same file/map, changing settings in one of the dialogs did not update the other dialog. This has been fixed.
commit 3a7ea651a33fbd6be7e1d1808c0ca01df18c8202
Author: John Harwell <john@brainmap.wustl.edu>
Date: Thu May 31 16:25:39 2018 -0500
Improvements fixing toolbox height too tall in versions of Qt prior to 5.6. Extended QDockWidget and QTabWidget to override the sizeHint() method and added methods to set the size hints. This somewhat replaces the functionality of QMainWindow::resizeDocks() that is only available in Qt 5.6 and newer. BrainBrowserWindowOrientatedToolBox(extends QDockWidget) adjusts its size using the size hint of the its child widget (from QDockWidget documentation) so a size hint width/height is set fort the child widget (WuQTabWidgetWithSizeHint overrides and implements sizeHint() method from QTabWidget).
commit 07622354a70451d21bf6f02368b306de04569e39
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun May 27 22:18:08 2018 -0400
Updated copyright for kloewe
commit e36b4dabc662cd12d8036768cd1dd9b70565606c
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun May 27 22:17:02 2018 -0400
added patch changeset_d5e169819bf51adebf786d87532ee6c0199611bb.diff to "cherry-pick" d5e169819bf51adebf786d87532ee6c0199611bb (Fixes so that source will build with Qt-5.5.1)
commit 9468cc2b73aa56a90335589fd9ddbb985d67833f
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun May 27 22:16:29 2018 -0400
commented on patches
commit f85ed2e0888e1beaf5cf3666efd3e5316838527c
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun May 27 22:15:25 2018 -0400
added patch changeset_f8f2092e9756d90ae5cb5ddc68118b2b88fd5e6f.diff to "cherry-pick" f8f2092e9756d90ae5cb5ddc68118b2b88fd5e6f (disable testing for SIMD support if not compiling for 64bit)
commit ab4543f781dc9085e9f6f5d8f455172cab259bd1
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun May 27 22:15:11 2018 -0400
added patch changeset_b10e8fca197dba953203267b7f4d7884d1811669.diff to "cherry-pick" b10e8fca197dba953203267b7f4d7884d1811669 (add pointer values to test output to help pin down simd errors)
commit 772298233d025abd95f0b87d1ff57c79aeb35be5
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun May 27 22:14:25 2018 -0400
fixing up gotcha
commit b3cd01d2598fb56fd8b82eb7589bd158e96e8857
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue May 22 21:54:03 2018 -0400
debian/connectome-workbench.links - symlink bash completions file to wb_shortcuts (provides both completions)
commit 93614c12930d9da43575c7aa5aecca10ff5fe21d
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue May 22 21:38:39 2018 -0400
An additional patch to make it buildable with older Qt
commit b45b778bcf4a4f0126794338aad83b244294ef32
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue May 22 19:41:39 2018 -0400
debian/patches/up_include_cpuinfo to include cpuinfo unconditionally
commit b067b4d9ec917387227ade5427027b44eef497c8
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue May 15 11:23:50 2018 -0400
debian/patches/deb_dot_DNDEBUG to assure having -DNDEBUG for dot
commit 614a5ee9b962c05a20cb57beb8d8e42fe4d9a178
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon May 14 22:22:57 2018 -0400
qt5, patch
commit e747b7471119072526650d77e2a717052a322414
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon May 14 09:08:13 2018 -0400
dropping CPed patch
commit b24f6c84b4c9ffc3a96471bf05f13b95386bddb8
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon May 14 09:06:44 2018 -0400
changelog + explicitly set WORKBENCH_MESA_DIR=/usr as recommended by upstream
commit d1da41805b718977d054536b3107957336a52f14
Merge: 9481cbf9 abd3e718
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue May 8 21:14:01 2018 -0400
Merge branch 'releases' into debian
* releases: (755 commits)
Fixed some help pages that contained myelin file links by changing them to relative paths
Minor fix for help: QFileInfo::basename() chops off at first '.' but some files contain a '.' prior to the filenames's extension. Replace with FileInformation::getFileNameNoExtension()
Updated Help Information
Resolve WB-799 Base directory autodetection does not include scene file itself: Scene file name is now included when aggregating all filenames for finding base directory.
attempt to fix "replace" scene action destroying the existing description by default
fix NiftiHeader to properly round-trip qforms
apply new slice changing code to orthogonal mode also, because unusual axis order caused similar problems
fix quaternion handling in nifti headers when voxels are not isotropic
WB-792 Autotext in Scene Description Field: Description field now defaults to empty. If user presses the 'Add Window Info' button the date, commit, and window content are added to the Description field.
Resolve WB-797 Slice Navigation in Oblique View with Oblique form Volume Broken: When a slice index was incremented in both oblique and orthogonal view, the slice coordinate was derived from the new slice index and always zeros for the other slice indices. This works fine for orthogonal and probably only for oblique volumes with an sform that matches an orthogonal view. Now, when changing the slice index for an oblique volume, the new slice index along with the existing slice indices for the other two axes are used to compute the new coordinate and this fixes the problem.
change default of developer flag to use new color bar code and normalization-based inversion method
Resolve WB-784 When more than one decimal is allowed and data is at 0 percentile -0.00/0.00 is shown for zero: When both the negative minimum and positive minimum equate to zero show just a single zero (or zero followed by a percentage symbol for percentile mode).
Resolve WB-792 Autotext in Scene Description: Description of Window/Tab content is no longer added to the Scene Description in the Add/Replace Scene Dialog. This information is still available by clicking the new "Add Window Info" button.
Update for WB-779: Initial implementation caused a warning when user pressed "Show" scene button and the currently loaded scene loaded file's with modified palette color mapping. This warning is no longer produced as an "isModified()" query no longer reports true when a file's palette contains a 'show scene modified status'. When a scene is saved, any files that contain a modified palette (by user or by showing a scene) have palette color mapping saved to the scene. When showing a scene, wb_view avoids reloading files. This reloading test has been updated to reload any file that has a current modified palette (by user or show scene) since the scene may contain different palette color mapping for the file. When showing a scene, the user still receives a warning if a data file contains palette color mapping resulting from user changes to the palette settings.
rewrite the new color bar for normalization-type inversion to clean up edge cases by always adding a virtual zero point if it doesn't exist, only one loop that also handles virtual end bars
implement color bar drawing for inversion during normalize method, by applying inversions to control points, adding a virtual zero point when needed, and chasing down many special cases
For BALSA upload, test for invalid HTTP code prior to parsing JSON returned during 'process upload' step.
Removed the no longer needed palette inversion mode enumerated value.
Placed palette inversion on a developer flag (in Develop Menu) so that one can switch between inversion of Palette or Inversion of Data in Normalization for testing purposes. Drawing of colorbar remains incorrect when data is inverted during normalization.
Resolve WB-795 Base Path Error: On Unixish operating systems, use "/" as the base path when files are on different disks. On Windows Operating System, if files are on different disks, produce an error message since there is no parent directory of the disks.
...
commit abd3e718558c2dd480eec8690075b8597d7d8948
Merge: 5e6fc556 3a9c9751
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue May 8 21:13:53 2018 -0400
Merge tag 'v1.3.0' into releases
v1.3.0
* tag 'v1.3.0': (755 commits)
Fixed some help pages that contained myelin file links by changing them to relative paths
Minor fix for help: QFileInfo::basename() chops off at first '.' but some files contain a '.' prior to the filenames's extension. Replace with FileInformation::getFileNameNoExtension()
Updated Help Information
Resolve WB-799 Base directory autodetection does not include scene file itself: Scene file name is now included when aggregating all filenames for finding base directory.
attempt to fix "replace" scene action destroying the existing description by default
fix NiftiHeader to properly round-trip qforms
apply new slice changing code to orthogonal mode also, because unusual axis order caused similar problems
fix quaternion handling in nifti headers when voxels are not isotropic
WB-792 Autotext in Scene Description Field: Description field now defaults to empty. If user presses the 'Add Window Info' button the date, commit, and window content are added to the Description field.
Resolve WB-797 Slice Navigation in Oblique View with Oblique form Volume Broken: When a slice index was incremented in both oblique and orthogonal view, the slice coordinate was derived from the new slice index and always zeros for the other slice indices. This works fine for orthogonal and probably only for oblique volumes with an sform that matches an orthogonal view. Now, when changing the slice index for an oblique volume, the new slice index along with the existing slice indices for the other two axes are used to compute the new coordinate and this fixes the problem.
change default of developer flag to use new color bar code and normalization-based inversion method
Resolve WB-784 When more than one decimal is allowed and data is at 0 percentile -0.00/0.00 is shown for zero: When both the negative minimum and positive minimum equate to zero show just a single zero (or zero followed by a percentage symbol for percentile mode).
Resolve WB-792 Autotext in Scene Description: Description of Window/Tab content is no longer added to the Scene Description in the Add/Replace Scene Dialog. This information is still available by clicking the new "Add Window Info" button.
Update for WB-779: Initial implementation caused a warning when user pressed "Show" scene button and the currently loaded scene loaded file's with modified palette color mapping. This warning is no longer produced as an "isModified()" query no longer reports true when a file's palette contains a 'show scene modified status'. When a scene is saved, any files that contain a modified palette (by user or by showing a scene) have palette color mapping saved to the scene. When showing a scene, wb_view avoids reloading files. This reloading test has been updated to reload any file that has a current modified palette (by user or show scene) since the scene may contain different palette color mapping for the file. When showing a scene, the user still receives a warning if a data file contains palette color mapping resulting from user changes to the palette settings.
rewrite the new color bar for normalization-type inversion to clean up edge cases by always adding a virtual zero point if it doesn't exist, only one loop that also handles virtual end bars
implement color bar drawing for inversion during normalize method, by applying inversions to control points, adding a virtual zero point when needed, and chasing down many special cases
For BALSA upload, test for invalid HTTP code prior to parsing JSON returned during 'process upload' step.
Removed the no longer needed palette inversion mode enumerated value.
Placed palette inversion on a developer flag (in Develop Menu) so that one can switch between inversion of Palette or Inversion of Data in Normalization for testing purposes. Drawing of colorbar remains incorrect when data is inverted during normalization.
Resolve WB-795 Base Path Error: On Unixish operating systems, use "/" as the base path when files are on different disks. On Windows Operating System, if files are on different disks, produce an error message since there is no parent directory of the disks.
...
commit 9481cbf93be81e55f3ebc9536f20374ac5b2f030
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Aug 8 00:01:34 2017 -0400
d/p/changeset_cf1faad575229c6519aee2b773f3e50b3d89e17e.diff + changelog to upload to unstable
commit 6815c7cc16f02966b528e843c07f7d378ed80bff
Merge: 4d3e4585 37686f8e
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Aug 7 23:59:46 2017 -0400
Merge branch 'debian-experimental' into debian
* debian-experimental:
debian/patches -- dropped all (all adopted upstream)
changelog for the upload to experimental
Conflicts:
debian/changelog - placed experimental on top
commit 4d3e4585dc92c3a748292c09d3c1d79bcf30ccf7
Merge: ef5f19e2 5e6fc556
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Aug 7 23:58:55 2017 -0400
Merge branch 'releases' into debian
* releases: (40 commits)
test splitting resources to put the largest subfolder into its own separate source file
make simd testing catch NaN values also
add test of simd implementations, small tweak to wb_shortcuts completion
add -simd global option to wb_command, new volume label probability and cifti label to border commands, help info tweaks
some tweaks and helpers for simd to prepare for adding option
further tweak to cifti resample help
add some help for template direction in cifti resample commands
use sddot in cross correlation also
update copyrights, extra stubs for compiling SIMD option code without testing SIMD support defines
Speed up correlation computation using SIMD instructions
make completion behave better for filenames given for string arguments (and for questionably named directories) by adding a trailing slash and no space to directories
wb_shortcuts update
typo in help info
fix error messages for invalid columns in -cifti-merge
small update to wb_shortcuts
update wb_shortcuts, put wb_shortcuts initial switch completion into bash completion
allow use of map names in -cifti-merge
fix wrong help info
update/simplify readme
some help text improvements
...
commit 5e6fc556dd20da58e4d356717547503166eecf0f
Merge: 368646c8 c4c6c905
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Aug 7 23:58:32 2017 -0400
Merge commit 'v1.2.3-41-gc4c6c90' into releases (mtheirs)
* commit 'v1.2.3-41-gc4c6c90': (40 commits)
test splitting resources to put the largest subfolder into its own separate source file
make simd testing catch NaN values also
add test of simd implementations, small tweak to wb_shortcuts completion
add -simd global option to wb_command, new volume label probability and cifti label to border commands, help info tweaks
some tweaks and helpers for simd to prepare for adding option
further tweak to cifti resample help
add some help for template direction in cifti resample commands
use sddot in cross correlation also
update copyrights, extra stubs for compiling SIMD option code without testing SIMD support defines
Speed up correlation computation using SIMD instructions
make completion behave better for filenames given for string arguments (and for questionably named directories) by adding a trailing slash and no space to directories
wb_shortcuts update
typo in help info
fix error messages for invalid columns in -cifti-merge
small update to wb_shortcuts
update wb_shortcuts, put wb_shortcuts initial switch completion into bash completion
allow use of map names in -cifti-merge
fix wrong help info
update/simplify readme
some help text improvements
...
commit ef5f19e20747e17b72bb304cf8b1324a223437e5
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Nov 30 20:05:39 2016 -0500
debian/control - removed libqtwebkit-dev from build-depends (Closes: #784458)
commit befe970bacb1913c38fc8b339c4f739031183c46
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Nov 30 20:03:11 2016 -0500
changelog entry for 1.2.3+git3-g7b83782-1
commit edf784d9f2f40d1d0b158a10333a0546188ef447
Merge: 1d33d98e 368646c8
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Nov 30 20:00:19 2016 -0500
Merge branch 'releases' into debian
* releases:
fix help files updating script for reorganization
further split up resources into general (command and gui), gui, and help (as the largest resource folder, to help compilers on 32bit)
test splitting resources to put the largest subfolder into its own separate source file
commit 368646c88206ebe54a0aabdac5fc1710ab964567
Merge: c170db02 7b83782a
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Nov 30 19:59:10 2016 -0500
Merge (theirs) remote-tracking branch 'origin/v1.2.3_resource_split' into releases
Generated solely for a merge into debian branch to maintain linear
history of "upstream releases"
* origin/v1.2.3_resource_split:
fix help files updating script for reorganization
further split up resources into general (command and gui), gui, and help (as the largest resource folder, to help compilers on 32bit)
test splitting resources to put the largest subfolder into its own separate source file
commit 7b83782a66a82c6f5a7ead3bbdffaae84e4706ec
Author: Tim Coalson <tsc5yc@mst.edu>
Date: Mon Oct 24 16:02:49 2016 -0500
fix help files updating script for reorganization
commit 72839aa68a33abf28b95756f1172e5d586ce8733
Author: Tim Coalson <tsc5yc@mst.edu>
Date: Thu Oct 20 15:06:34 2016 -0500
further split up resources into general (command and gui), gui, and help (as the largest resource folder, to help compilers on 32bit)
commit 09b17f7e5f128225b0218a5929de89eb0997251a
Author: Tim Coalson <tsc5yc@mst.edu>
Date: Wed Oct 19 16:38:15 2016 -0500
test splitting resources to put the largest subfolder into its own separate source file
commit 37686f8ea27b4da49d6853255090d9775cba419c
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Oct 19 20:12:43 2016 -0400
debian/patches -- dropped all (all adopted upstream)
commit 865a2151250cf3bce7a3ba50396b86176caeccf6
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Oct 19 19:35:08 2016 -0400
changelog for the upload to experimental
commit 742eaba8aec929416d74fecbc30ce97aae4cf172
Merge: 1d33d98e c4c6c905
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Oct 19 19:32:50 2016 -0400
Merge commit 'v1.2.3-41-gc4c6c90' into debian-experimental
* commit 'v1.2.3-41-gc4c6c90': (40 commits)
test splitting resources to put the largest subfolder into its own separate source file
make simd testing catch NaN values also
add test of simd implementations, small tweak to wb_shortcuts completion
add -simd global option to wb_command, new volume label probability and cifti label to border commands, help info tweaks
some tweaks and helpers for simd to prepare for adding option
further tweak to cifti resample help
add some help for template direction in cifti resample commands
use sddot in cross correlation also
update copyrights, extra stubs for compiling SIMD option code without testing SIMD support defines
Speed up correlation computation using SIMD instructions
make completion behave better for filenames given for string arguments (and for questionably named directories) by adding a trailing slash and no space to directories
wb_shortcuts update
typo in help info
fix error messages for invalid columns in -cifti-merge
small update to wb_shortcuts
update wb_shortcuts, put wb_shortcuts initial switch completion into bash completion
allow use of map names in -cifti-merge
fix wrong help info
update/simplify readme
some help text improvements
...
commit 1d33d98e5da96f8eb635e4eb4629c7f8a22be0a6
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Oct 14 18:35:46 2016 -0400
Do not provide --parallel on mips architectures to dh in hope to reduce memory impact and avoid FTBFS
commit 041a4c88bd66b4918afea51ffedc4068a45710cf
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Sep 12 16:56:24 2016 -0400
debian/patches/deb_dynamic_GLU - to list .so ahead of .a to provide dynamic linking against GLU and co
commit 62b884f0160ba7b305de910f415e7f6347a854f8
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Sep 12 16:11:09 2016 -0400
cleanup -- removed some up_ patches which were already absorbed or addressed
commit 3ba43030443839ec3c4be3d10d5235a9f8893792
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat Aug 27 17:47:23 2016 -0400
added patch changeset_bf-build.diff to "cherry-pick" bf-build (BF: return NULL (not false) when promised to return VolumeFile*)
commit 72d304717e50e42bfa3d1b4a5cd8358308e1daed
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat Aug 27 12:59:37 2016 -0400
updated for upstream having v prefix in tags
commit 44426f4cbb0edc73903b61e0ce9eb15b9363cfd5
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat Aug 27 12:58:43 2016 -0400
debian/copyright + debian/patches/up_debian_copyright * debian/control - detabified Build-Depends
commit 57c370d137c650c8606057fd61194e711e9523e8
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat Aug 27 12:43:22 2016 -0400
changelog entry for 1.2.3
commit d9ce4df7e3b2a30d35bb72cec64032618d6d3398
Merge: 927a81de c170db02
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat Aug 27 12:42:17 2016 -0400
Merge tag 'v1.2.3' into debian
v1.2.3
* tag 'v1.2.3': (58 commits)
update wb_shortcuts, minor wording change
small hack to make disabling the dynconn layer prevent the computation and show empty string in identification window
set version to 1.2.3
rename dynconn preference
Implement WB-633 : New requirements for updating of connectivity data: (1) A second checkbox that enables dynamic connectivity has been added to Overlay Toolbox --> Connectivity. Dynamic connectivity files are only available in the Overlay --> Layers section if this checkbox is checked; (2) Checkbox labeled "On" has been changed to "Load" on Overlay --> Toolbox; (3) A preference has been added for enabling dynamic connectivity data from data-series file on Preferences Misc tab; (4) Old scenes will default to dynamic connectivity on. Name of dynamic connectivity file in Overlay --> Layers and Overlay --> Connectivity is now prefixed with "dynconn".
make wb_command more unicode-clean, accept some non-ascii dashes in arguments via CommandParser
add an option to output weights for all vertices for ribbon mapping
Forgot to remove a print statement.
Resolve WB-643: Loading a scene causes contained files to default to "in spec": The "in spec" status is now preserved when loading a scene. The name of the spec file within the scene must match the name of the current spec file and the data files are matched using their absolute paths.
Resolve WB-644: Timecourse on/off status from charts not saved to scenes: Restoration of the chart selection status has been fixed.
Resolve WB-642 Adjusting the color bar position by typing or arrows does not work. When annotation color bar placement is Automatic, any requests to change color bar's position were ignored. Now, if the user attempts to move the color bar, change the color bar's positioning mode from Automatic to Manual so that the color bar will move.
Resolve WB-641 Overlay and map settings dialog precision issue: In the statistics section of the dialog, the width was fixed for the numeric characters so there was insufficient space when the values were large and clipped at the left side. The space for the values will now shrink and expand as needed so that the numeric values are fully visible.
add note about wb_shortcuts to CommandLine readme
set all of pixdim[] to 1 by default, doesn't change our warnings, better nifti conformance, reduces warnings from other software
restore previous default for capture image method, as it is likely unrelated to OS type
add gedit autosaves to .gitignore
add more comprehensible error messages to -cifti-separate
Resolve WB-639: (Forgot to add ZipSceneFileDialog to repository before committing) Added Zip Scene File Dialog for zipping a a scene file and its data files. Dialog is launched using new "Zip" button on the Scene File Dialog.
Resolve WB-639: Added Zip Scene File Dialog for zipping a a scene file and its data files. Dialog is launched using new "Zip" button on the Scene File Dialog.
default to writing nifti with qfac=1 to help other software
...
commit 927a81dea79b705a5fffe61992d41134233b190b
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Jul 20 22:13:43 2016 -0400
fresh changelog
commit 020803fbbe34f9b14bb92e8f119d3e0a8d3a5281
Merge: a520b607 3fd5e076
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Jul 20 22:06:39 2016 -0400
Merge tag 'v1.2.2' into debian
v1.2.2
* tag 'v1.2.2': (101 commits)
set version to v1.2.2 in case we want to release with recent bugfix without deleting v1.2.1 release tag
fix backwards test of all columns mode in erosion
Changed workbench version to 1.2.1 for release that contains functionality for Nature paper.
Added the border offset to scenes and disallow a negative offset.
continuing last commit, allow negative offset.
Added offset OpenGL polygon offset for borders. BUT, is does not offset borders because borders are drawn as lines and polygon offset does not work on lines. So, the polygon offset is applied when the surface is drawn. This is experimental and controlled in the Features Toolbox->Border->Attributes->Above Offset.
Units listed in border line width spin box was millimeters (mm) and has been corrected to be pixels (px).
Implemented WB-633 New requirements for updating of connectivity data. However, its functionality is disabled due to potential problems with the functionality for users. Can be enabled by changing variable 'allFilesFlag' in CiftiConnectivityMatrixDataFileManager::getDisplayedConnectivityMatrixFiles().
add a newline to -arguments-help for consistency
A flag in Brain.cxx used during spec file reading was set, but not reset, when after reading spec file content from a scene.
WB-626 Dynamic Correlation of Dense Time Series Without Computation of Dense Connectome: The dense dynamic file (encapsulated in a data-series file) is now lazily initialized. This prevents its initialization (and loading of data) when file information is run with an option that inhibits loading of data such as "-no-map-info".
comment out timing info from data series, was breaking scripts
make NiftiIO tolerate attempted multithreaded access (CaretBinaryFile's interface has separate seek and read/write functions, so a mutex there wouldn't achieve much)
quick fix for crashing with -file-information -no-map-info on dtseries (was trying to read cifti rows in parallel from disk, which is not yet reentrant)
Add use of OpenMP to dense dynamic file and timing to load data for a surface node.
Added timing around initialization of dense dynamic file
Resolve WB-631 voxel selection in oblique volume viewing does not go to correct slice: When in an oblique view, allow all of the slice indices to change. This problem was probably caused long ago by a modifictation that prevented the slice index related to the viewed axis from changing in volume slice montage.
Resolve WB-629 Volume crosshairs don't intersect surface contour in oblique view: When drawing crosshairs, unique translations were needed for each slice view plane (axial, coronal, parasagittal).
WB-628 Ability to adjust NIFTI sform dynamically in wb_view: Added ability to adjust the 'depth' of an image displayed in wb_view.
Resolve WB-630 wb_view may crash if tile tabs enabled with fewer cells than tabs: Limit number of tabs drawn to the number of cells.
...
commit a520b6072619045bfed90caca14e19bd2634b9b4
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu May 19 22:55:16 2016 -0400
debian/patches/deb_* to build without git and against system ftgl dropped. Contributions from NeuroFedora team upstream made them unnecessary
commit c5a90432cd99ceaf8a6dc27d9d04fae1a08a46f2
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu May 19 22:47:14 2016 -0400
Fresh upstream release + changelog
* Fresh upstream release
* debian/copyright
- updated to include new bundled fonts
- boosted policy to 3.9.8
commit 251a1800a832384ca66a7d3f4282f7d5c9c55976
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu May 19 22:44:22 2016 -0400
Added missing copyright/licenses for new fonts etc
commit a9b3bc5114a192086d15b9722c5a2a984dee19fa
Merge: b4b3790f 0d43f6b6
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu May 19 22:35:25 2016 -0400
Merge tag 'v1.2.0' into debian
v1.2.0
* tag 'v1.2.0': (684 commits)
Set Workbench version to 1.2.0
"Turn Off Display in Other Tabs" and "Turn On Display in All Tabs" in the Annotation's mode's context-sensitive (pop-up) menu now function with more than one annotation selected.
Corrected disabling of "Turn On Display in All Tabs" to the Annotation's mode's context-sensitive (pop-up) menu.
Add items "Turn Off Display in Other Tabs" and "Turn On Display in All Tabs" to the Annotation's mode's context-sensitive (pop-up) menu. These items are only displayed if the selected annotation is in Stereotaxic or Surface Space.
Another update for mac noodle build script: Target OS X 10.7
Update/fix for Mac noodle build script that is in development. Fix parameter on cmake command.
Update/fix for Mac noodle build script that is in development. Correct path to build scripts.
Update/fix for Mac noodle build script that is in development.
Minor changes to BALSA database dialog.
Added preliminary implementation of scripts for building a Mac version of Workbench on the computer 'noodle' using newer clang compiler.
Starting to create BALSA Database Dialog. For now, it is selected on the Develop menu.
Disable testing for modified files when showing a scene.
Removed change from 19 April 2016 so that palette modified status is set after loading a scene with a modified palette. Otherwise, if the user resaves the scene the palette reverts to its unmodified settings (from the data file).
Added date and time to default description for a new scene.
On Scene Dialog, limit the number of lines of text to set the height of each scene on the dialog. Previouly the height of each scene in the dialog was set to the height of the image.
Updated resources to include new documentation for the Edit Menu.
Fixed assertion failure caused by a missing 'break' in a switch statement.
Make default size of help window larger.
Updated resources with revised Workbench 1.2 Help Pages.
Updated resources with revised Workbench 1.2 Help Pages.
...
commit b4b3790f0084aa0ff6d86b9ae4f9a1228dacb87a
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 24 17:54:47 2015 -0400
Fresh upstream release - debian/copyright was updated (upstream, thanks Timothy!) to new locations of 3rd-party modules
commit 74f2e85ad96f233364d1be886418f903e724be8a
Merge: 0e052e38 dde6c19b
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 24 17:53:12 2015 -0400
Merge tag 'v1.1.1' into debian
v1.1.1
* tag 'v1.1.1': (28 commits)
Resolve WB-539 Part 2: When a voxel average was created, the description of the average was not created and so when a dense scalar file was created, its name was not properly initialized.
Resolve WB-539 Part 1: When computing voxel average, the statistics, histogram, and coloring were not updated resulting in improper coloring of data. This has been fixed.
replace placeholder help text in -metric-to-volume-mapping
Clarify that the More button on About wb_view must be pressed to see the selected style (This is listed with wb_view's '-help' option.
Show selected 'Window Style' on the About Workbench dialog. Also list this info on 'wb_view -help' after the -style option.
WB-538: Removed a few minor changes that were made in an attempt to fix strange widget background behavior on some Linux systems.
WB-538: Trying adjustment of spacing in the boolbar widget that contains the user input widgets.
WB-538: Now trying to disabling margins, spacing, and not setting a size policy.
WB-538: Disabling either row of volume toolbar prevents flashing on some linux systems. Now enabling both rows of toolbar and trying a non-zero contents margin.
Disabling part of volume toolbar for testing with WB-538. Now disabling mode part of toolbar.
Disabling part of volume toolbar for testing with WB-538.
Minor cleanup of Desktop/CMakeLists.txt
Changed version to 1.1.1.
Changed version to 1.11.
Resolve WB-533 Default State of Borders in Scenes: If a border file is modified AFTER creation of a scene, any new borders within the the border file WILL NOT be visible when the scene is displayed.
Resolve WB-531 tractography trajectories display for right hem but not left hem in scene files: The problem was that when a file is restored, the file's data from the scene was matched only using the name of the file, excluding any path. In the data that demonstrated the problem, there were two fiber trajectory files that had the same name but different paths and, since the file's scene data was matched only by name, the fiber trajectory files were not properly restored. Now, the full path is saved along with the file's data in the scene file. When restoring, the files are matched using both the file name and by comparing the paths of the files for the most matching characters at the right side of the file's path. The 'most matching right side of path' is used since the path will change when a scene file is moved to another directory or computer.
Added method to count the matching characters starting at the end of two strings. It is used to 'best match' file name paths.
Improved format of error message in DataFileException so that both the path and file are identified to the user.
Fixed file dialog used to choose a new border, foci, or scene file so that it opens in the directory containing the currently loaded spec or scene file. Prior to this change, the default directory for the dialog was the directory from which Workbench was launched.
Finished resolving WB-534 Copy and saving row from Dense file on network fails: Renamed Brain::updateFileNameForReading() to Brain: When a new CIFTI scalar data file is created from a network hosted CIFTI dense file loaded row/column (or Dense Traj from Dense Traj Row), create a new valid, local file name for the new file.
...
commit 0e052e3871d4255a7621283a1d816eba9229acbd
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 10 23:12:32 2015 -0400
updated copyright
commit 66b8171cc13cf270db1b8d92e6cf5d6ccd60f580
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 10 17:41:15 2015 -0400
Fresh upstream release - up* patch dropped (upstreamed)
commit bb7c458e69cc66f9e1997d0738308fce0bddf8e1
Merge: 47e4f1d0 9c9d7bad
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 10 17:38:54 2015 -0400
Merge tag 'v1.1' into debian
v1.1
* tag 'v1.1': (529 commits)
Resolve WB-530 Full palette option does not work for negative values. In FastStatistics, m_leastNeg was initialized to positive float max and has been corrected to being initialized to the negative of float max.
Fixed missing information after an ID operation. When preference for ID symbols was added, the IdentifiedItem(AString) constructor was modified and did not properly set the text and has been corrected.
replace use of map with vector and std::sort, as "number of nodes in ROI" is not a unique value per border
Revise the About Workbench Dialog and content.
Attempt to fix initial size of Border Optimize Dialog.
Changed version to 1.1
Border Optimize Dialog: (1) No horizontal scrollbar; (2) Prevent each 'group' from expanding vertically with extra space; (3) Limit borders to two rows and wrap with additional columns to the right; (4) Remove extra spacing around layouts; and (5) fix some 'stretchiness' issues
One constructor for IdentifiedItem was not initializing all of its members causing improper restoration of scene with some ID symbols on and some off.
Information Properties Dialog: Add text informing user that the display of ID symbols is controlled using Preferences.
Border Optimize Dialog. Put all of dialog content in one scroll area insted of just data files in a scroll area.
Added preferences for enabling/disabling identification symbols for surface and volume. The preference does not change the status of any existing symbols.
On border optimize dialog, list the number of border points inside the ROI next to each border.
Border Optimize Dialog: List borders ordered by number of border points inside the ROI.
fix silly mistake of negative/positive confusion
fix problem with border optimize deleting border when border segment in roi is only 2 points
Border Optimize Dialog Changes: (1) Add option to enable output of the gradient file; (2) Default to one data file; (3) Default Save Results checked; (4) Default Upsampling checked; (5) Limit border pair files for those that match surface structure.
dilate roi by one vertex in border optimize for only the smoothing/gradient operations, to reduce edge effects
fix use of wrong number of nodes in roi splitting of border optimize when upsampling
do roi splitting in border optimize at upsampled resolution
make new border format accept negative weights, treating them as zero, make signed distance barycentric not generate small negatives
...
commit 47e4f1d0e72046589f2e0f03f55abaf4df821908
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat Nov 1 21:09:09 2014 -0400
slight updates to generated copyright + DNDEBUG setting for optimal user performance
commit 90cfbd88989f7ee0cab93f528799638d2613736c
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Oct 21 10:04:45 2014 -0400
adjusted copyrights listing
commit 7957892f463fab618b43675b8553750452f9ea16
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Sep 9 19:37:05 2014 -0400
added a watch file
commit 6a70fd4255a6d355a37d4329973bff956773ee96
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Sep 9 19:32:45 2014 -0400
Changelog entry
commit 9ece9ab84d9cf57de7868b630d504c5106badf37
Merge: da6895ab dfd2086d
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Sep 9 19:27:39 2014 -0400
Merge tag 'v1.0' into debian
v1.0
* tag 'v1.0': (73 commits)
Updated Help Documentation and changed Help Menu->Help to Help Menu->Workbench Help
Changed the 'Help Menu->Help' so that it always displays the help viewer. The action for the help viewer is a toggle action so that the 'Toolbar->Help' button will show/hide the help viewer. But, we never want the menu to hide the help viewer.
Added a shortcut for Help but it does not display on Mac but will display if user does CMD+?. Will check windows and linux after build completes.
Updated help files.
Added tooltip for border editing distances
Added a question mark icon to the toolbar for display of the help dialog.
Resolve WB-459 Report Distance To Border in Edit Borders Popup Dialog: Distance is now listed alongside names of the borders that can change as a result of editing.
Scene files contain image files and the image's data is converted to Base64 text so that the image data can be written in the Scene's XML file. Recently, a scene files failed to load due to non-ascii characters being found in an image's base64 encoded data. The logic for converting the image data has been changed to use the bytearray's (used for storing the image's bytes) size() method when converting from base64 characters and adding to the scene.
Fixed compilation failure due to a coding error had 'StructureEnum::StructureEnum::Enum' in a declaration.
Resolve WB-450 Selected Brainordinate -> CIFTI File Row does not show corresponding ID: If volume id mode is enabled for a volume slice and the selected CIFTI row corresponds to a voxel, move the selected volume slices to the voxel's XYZ location.
Resolve WB-461 Data Series Charting selection no functioning for voxel selection: Method for loading series data had its row/column loading inverted (trying to load columns when should have been loading rows and vice versa) and has been fixed.
Removed unused include file from ModelWholeBrain.
When using the Information Window to load a row from a CIFTI file, information about the row is displayed in the Information Window. If the row corresponds to a node, a node identification symbol is displayed on the surface.
Updated Help Viewer so that it properly handles 'mailto:' links
make updating the number of nodes in a border file show the border file as modified, as desired
set border file modified when setStructure or setNumberOfNodes is called
make in-place overwrite work for nifti version convert make CaretBinaryFile's destructor warn rather than throw, to prevent second throw during throw unwinding
This should resolve WB-457 pasting of copied text from WB Help works for some apps, but not others: Copying and pasting text from the Help Viewer to other applications did not work on all Macs. The problem appears to have been caused by using a cascading style sheet to set the font size. Now the HTML 4 Font tag's size attribute is used to set the size of the font.
Added a method to convert a string to an HTML page and set the font size using the HTML Font tag's size attribute.
allow BorderFile to write as old format automatically, with a warning separate GUI operation and writeFile messages for multi-structure errors use new "single structure" function to check for ability to write as version 3
...
commit da6895abf05fb83ceb56f40315b430862d3231fb
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Aug 19 01:28:19 2014 -0400
updated copyright
commit faa8cf5dff1991f7c330c6d2bf888b49cd7b2ba7
Merge: 0cafb510 462f4cf7
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Aug 19 01:27:42 2014 -0400
Merge commit 'v0.85-460-g462f4cf' into debian
* commit 'v0.85-460-g462f4cf': (98 commits)
update help files
remove instruction comment blocks
note command deprecation in short descriptions, uniformity tweaks
some additional tweaks to the CiftiFile functions for on-disk writing with old version
move version convert operations into new -file-convert command change cifti file functions to set version on writing, not when XML is set add version selection writing function to BorderFile
The script to create the resource file gets put into the resource file (there is no way to exclude it). The script was renamed, the old one deleted, and the old one was not found causing compilation errors.
Combined the two scripts for updating resources with new help files 'update_help_files.sh' and creating the resources 'create_resources_qrc_file.h' into a one script named 'update_resources.sh'.
Update WholeBrain model when there is a file changed, made update method public
Update WholeBrain model when there is a file changed.
Resolve WB-451: Change 'File Menu->Close Spec File' to 'File Menu->Close All Files' and on Save/Manage Files Dialog, change 'Remove' column name to 'Close'
Additiona to WB-448: Use file name compactor for Overlay selection.
Added static method for CaretMappableDataFile's to file path name prefix compactor
Added palette color mapping editor for editing a file's color palette and, at this time, is used for editing the palette used for chart matrix visualization.
Renamed EventMapSettingsEditorDialogRequest to EventMapSettingsEditorDialogRequest and renamed MapSettingsEditorDialog to OverlaySettingsEditorDialog as they handle a number of settings related to overlays the map selected in the overlay.
Fixed drawing of background color under colar palette bar so that the background color is under both the color bar and the numeric values just above the color bar.
Part of WB-396 Overlay and Map Settings Palette Histogram Should Be Calculated on the Whole File for Parcellated Datatypes: Added (and implemented) colorbar icon to Overlay ToolBox->Charting->Loading for matrix files.
Disabled context (right-click) menu that enabled capturing an image of the dialog to the clipboard as users sometimes unintentionally cause it to pop up.
Part of WB-436: For Spec File Dialog: (1) Change sprocket menu text for copying filename to 'Copy Path and Filename to Clipboard'; (2) Add 'Copy Path and Filename to Clipboard' to Spec File Entry; and (3) Make 'Copy Path and Filenme to Clipboard' active for files that are not loaded.
Fixed a couple of compilation warnings on unused variables
use multi-part border behavior in -nodes-inside-border, improve edges and speed for all border filling operations some cleanup/preparations to eventually turn the nodes inside border code into a helper
...
commit 0cafb5109928be9c1f8c8892a35c079d004f7c30
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 25 13:58:12 2014 -0400
updated/regenerated debian/copyright and changelog
commit 76869afb5f6a045aee720a2cef652ad050768e11
Merge: f406b57e b605a57b
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri Jul 25 13:57:39 2014 -0400
Merge commit 'v0.85-361-gb605a57' into debian
* commit 'v0.85-361-gb605a57':
improve cifti xml surface structure information in -file-information
make -volume-tfce do subvolumes in parallel
initial update to debian/copyright for FTGL and removing GLF
When configuring with CMake and FreeType is not found, provide information on CMake paramaters that can indicate the location of FreeType include files and library.
Added more help HTML pages for testing HTML formatting.
apply volume optimization of tfce to metric, fix a comment
initial implementation of -cifti-roi suboption to -cifti-correlation -roi-override
remove debug info printing from -volume-tfce
fix some bugs and improve speed of -volume-tfce
new -volume-tfce command
reduce code redundancy in -metric-tfce
Updated two Scene Window help files.
Show HTML for help after it has been placed into and retrieved from a QTextDocument. The result is printed to identify where HTML display is failing.
commit f406b57e7bcf821b9b792d301f20146f66dec5ef
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu Jul 24 15:53:26 2014 -0400
Working on building using system wide ftgl
commit 03315a2989af28e88293af7470cf591e2c318533
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu Jul 24 14:53:47 2014 -0400
copyright for the FTGL
commit ea863f3ec073c0b87848a513294f5e4671b9d254
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Jul 23 17:12:16 2014 -0400
changelog
commit 2d1a760735f20a31473a8132607a7f92efa199fd
Merge: 23210af4 3893c532
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Jul 23 15:02:55 2014 -0400
Merge commit 'v0.85-348-g3893c53' into debian
* commit 'v0.85-348-g3893c53': (261 commits)
Added new scene help HTML files to see what does/does not work.
Starting to add command for generating the Qt resource file used for identifying resources to Qt in the Resource module.
Updated windows 32 build for FreeType
Update windows 64 bit build for newer freetype library.
Define FTGL_LIBRARY_STATIC for windows FTGL/FreeType.
Trying new version of CMake for windows FreeType
fix silly parallel reuse of output array in -metric-tfce
For Windows, specify location of freetype library when running cmake, part 4.
For Windows, specify location of freetype library when running cmake, part 3.
For Windows, specify location of freetype library when running cmake, part 2.
For Windows, specify location of freetype library when running cmake.
Still working on getting windows to configure without freetype
Still working on getting windows to configure without freetype
Change FTGL config to no strndup() function since it is apparently not available on hippocampus.
Attempt at windows freetype issues
Fix for mac compilation and maybe windows.
Add setting of FreeType directory for windows build environment.
More updates for help files
Added search path for FreeType
Add a name for the text renderer and display this name in the OpenGL configuration information available through File (Apple) Menu -> About wb_view -> OpenGL.
...
commit 23210af4ecc41be40c6728b79b8ae53a8be13a01
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 23 12:33:03 2014 -0400
BF: adjust for rename of workbench to wb_view to match other wb_ commands
commit 998c1cd19ad716be17b799b7143ca3defe19fa37
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 23 10:01:51 2014 -0400
generate/update debian/copyright + new changelog entry
commit 767c24c8b509a8c1a5b54ce0e8c89669c9907281
Merge: 4d0f502f ce714a3e
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 23 09:56:39 2014 -0400
Merge commit '0.85-87-gce714a3' into debian
* commit '0.85-87-gce714a3': (60 commits)
more informative errors for people who try to use -cifti-convert -from-gifti-ext on metric files
ENH: src/debian/copyright -- prune redundant 'Copyright's and update FSF address for GPL license stub
Seem to have fixed problem with Mac failing to launch when started from Finder. For some reason, a parameter that begins with '-psn_' followed by a number is passed to the wb_view which does not recognized it and then exits. Because wb_view is started from the Finder, the error messge is never seen by the user. http://stackoverflow.com/questions/10242115/os-x-strange-psn-command-line-parameter-when-launched-from-finder
reduce redundancy of VolumeSpace::matchesVolumeSpace()
switch all uses of NiftiFile to NiftiIO or VolumeFile, remove NiftiFile, NiftiMatrix, Layout
fix case issue in #include
Updated with new help files from Jenn.
Resolve WB-373: Add access to loaded file's path through Save/Manager Files Dialog by adding 'More' menu item that copies a file's path to the clipboard.
Fix to remove duplicate entries from resources.qrc
Reorganized files in Resources
Update for some new help files from Jenn
Fixed yoking status for the Clipping Planes Dialog's Reset button.
Remove some logging message to avoid excessive message when logging is FINE or ALL
update README with new executable names
Moved the OSMesaDummy functions from GuiQt into their own, new module OSMesaDummy. Having the dummy OSMesa functions in GuiQt did not work for linking on all systems. As mentioned in a previous commit, the dummy OSMesa functions are needed to prevent OpenGL 'clashes' now the the 'wb_command -show-scene' command is used in Workbench as part of the Help System.
Fix compilation with ZLIB on John's Mac.
Additonal changes for Help Dialog: Add help for each 'wb_command' operation. Use a Tree Widget (hierarchy) for the help topics. Added deletion of CommandOperationManager to wb_view. Had to create some 'dummy OSMesa' functions for linking to the GUI. If the real OSMesa library was linked by the GUI, it totally screwed up the GUIs OpenGL.
fix uninitialized memory in ZFileImpl
change -nifti-convert to an operation, add argument for output version to make it more general
add some additional explanation to the interfaces in AbstractOperation.h
...
commit 4d0f502f0132af46e911fb467a1cd93ca1dc7a44
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Apr 22 13:37:12 2014 -0400
tune ups to copyright from upstream 0.85-84-gd2525fe
commit 3d136b13b4c09801b1f517f6a959ef5379431bb4
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 17:54:34 2014 -0400
updated changelog
commit 0c8a77641ac6bbabaf1e35ad2f9672ab3fdc2c53
Merge: bb96e75e 72866b8c
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 17:53:33 2014 -0400
Merge commit '0.85-26-g72866b8' into debian
* commit '0.85-26-g72866b8':
resolve #6, workbench -help requiring DISPLAY
Fixed WB-383, Workbench crashes with right-click (context sensitive menu pop-up) on volume slices.
commit bb96e75e289defcb0db3fc24e64b88b499fd3532
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 15:21:13 2014 -0400
Patch to not fail to build outside of git + add indication of NeuroDebian build
commit d1140a2e38ab57794018433c828b9b8750fa3239
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 14:45:08 2014 -0400
typos, build-depends, fixed FSF address
commit 2cc2d65da8f170f3fd5719058f434d2cda995bbf
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 01:10:18 2014 -0400
core build-depeds -- rest to figure out
commit a2baafe344605c2e6be77e69f458505e051999a9
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 01:05:53 2014 -0400
dropping obsolete now patch and adjusting revision
commit 97abd4522b7367eaaa0b18e39756f4fa62694100
Merge: 970d37a1 ff1307fb
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 01:04:33 2014 -0400
Merge commit '0.85-24-gff1307f' into debian
* commit '0.85-24-gff1307f': (22 commits)
disallow use of both -only options in -file-information
add -only-number-of-maps to -file-information
prevent string matching of partial command switch if more arguments are present
add tips to -cifti-reorder about direction to use for particular cifti types
document the ability to use "make install", and using OSMesa, fix version info of Quazip
WB-382: Draw Borders as Unstretched Lines: Instead of implementing the unstretched lines functionality, lines are not drawn when one of the endpoints does not project to the flat surface, typically due to a cut or medial wall removal.
Fixed OpenGL Invalid Operation. Border line drawing mistakenly contained a glBegin/glEnd pair inside another glBegin/glEnd pair.
ENH: install target binaries
add casts to make sure int-to-float error checking does what is intended
make reading functions for GiftiLabelTable consistent, fix bug preventing warning of multiple labels that should be interpreted as unlabeled
update Quazip to 0.6 (last LGPLv2 version) as an attempt at issue #1
fix bug where -zip-scene-file doesn't include the scene file
Fix compilation error on 32-bit systems
Changed operation NiftiInformation so that when the '-print-header' operation is used, it reads only the NiftiHeader and not the entire NiftiFile. There is no need to read the entire file for this operation and for very large files, this operation either took a very long time or crashed.
Fixed compilation warning in metric file.
make -label-merge preserve column names
Moved helper method for creating cartesian chart data from CiftiMappableDataFile to CaretMappableDataFile so that it can be used by Metric and Volume Files. Added loading of charts from a multi-map volume file. Added Charting library for include files in CommandLine and Test caused by addtions to VolumeFile.h
ChartableInterface::getCaretMappableDataFile() was pure virtual but implemented identically in all implementing classes. Since it does not require any 'member data' it is now implemented in the interface and implementation has been removed from all of the implementing classes.
I thought I had committed these changes to metric file charting prior to pulling from repository but I guess not.
Adding Charting include files to MetricFile.h required adding the Charting Module to both Commands and OperationsBase CMakeLists.txt files to enable compilation.
...
commit 970d37a1d4a49817c4bc2bdfad4c87be4b406de2
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 00:59:21 2014 -0400
basic manpages using help2man
commit 9a997252c0a639e8dad7d25a13d5a639791ba7a7
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed Apr 9 00:46:08 2014 -0400
Install icon/desktop file(s)
commit cc3e2d567da0ef3c98e9fda2cdd107efb847322a
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Apr 8 19:29:16 2014 -0400
Suggest ffmpeg (not in Debian proper) and provide -dbg pkg
commit 4d819b1f34c7fec3d1c921c563f90a449c22a194
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Apr 8 19:13:45 2014 -0400
First attempt to build with dynamic linking against generated libraries
That could help reduce size of perspective -dbg package since
API would not be replicated in two executables.
Difficulty -- required placing code using osmesa for offscreen rendering
into a separate library and then still listing all needed libraries for
linking for each internal library... no time ;-)
commit c58042bea4a496881abae2eb6b84e060d967bcd3
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Apr 8 10:10:06 2014 -0400
trying to build with shared libs and osmesa
commit 909f4d55aba14a27015dce4b67868732171a7ea0
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue Apr 8 10:09:54 2014 -0400
install targets
commit 454ee77d37ec3135b1684fe7c5c6b881db233131
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Apr 7 16:58:44 2014 -0400
fixing a typo for Vcs field
commit 14823affe51ee03a2c4b48f5339794868cd47387
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Apr 7 16:11:39 2014 -0400
debian/copyright: tuning up to meet DEP5
commit 874ccab847068bf805ef0fc98e10dad62689af57
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon Apr 7 16:09:44 2014 -0400
initial skeleton for packaging with stock copyright (thanks for following DEP)
