openchemistry / tomviz Goto Github PK

Currently the widget allows the user to zoom in and out in the data view, but the zoom is always centered on the data center point. It would be useful to be able to zoom in on any part of the data.

In addition to "flashing" comparison mode where the user minimizes the wobble as the display flashes back and forth between images, it would be useful to have a "difference map" comparison, where the user makes the display of (imageA-imageB) flat around the alignment point.

I'm not sure what the best way is to make this fit with the current color map scheme, since it will need to display positive and negative values with magnitude significantly less than the typical data values. Maybe the difference map will need to be scaled to fit in the same range as the original data?

State files are storing absolute file paths for data. If a state file (dir1/state) and data (dir1/data) are packaged in the same directory (dir1), then the entire directory is copied (to dir2) and dir1 is renamed or deleted, opening dir2/state fails and results in an error saying "Initialize: could not open file dir1/data". Relative file paths should be used instead, so that Tomviz tries to open dir2/data.

This is a key issue for scientific reproducibility, as it prevents state files from being shared across computers.

Picking a data file from the "File>Recently Opened" list that has been moved or deleted crashes Tomviz completely, followed by a "Tomviz quit unexpectedly" message on Mac. It would be better to warn the user with an error saying that Tomviz could not find the file.

When importing a .raw file, the "Open File" interface will only display files with *.raw extensions. Often binary files will be stored as a variety of alternative extensions (such as *.bin and *.dat ).

Suggested Solution: when importing raw, either display all files (.) or at least add *.bin and *.dat

The module and data properties as implemented are confusing, it is not clear which module the module properties refer to, and the connection to the data is loose. We always have a selected data item or module - show an integrated properties dialog that shows the properties for the highlighted item.

When saving and loading the tomviz state, the panels and tabs are not restored properly. For example, if one has a tab with three split viz panels and a second tab containing a single viz panel the state will restore with four viz panels in a single tab.

Also, the size / spacing of the panel splits are not saved.

User should be able to pick a static reference image to align to (e.g. align all images to feature in image 15) in addition to using the previous or next images as reference as described in issue 59.

VTK doesn't currently support writing 3D TIFFs, add support and expose this in tomviz.

Tomviz crashes frequently. To alleviate this issue, we should have an auto save state that runs every so often and restores the last known state in the event of a crash. It could prevent a user from losing hours of work.

Merge the datatransform pipeline and the visualization modules pipeline.

The data transforms will appear as objects below the data icon and new transforms will be added below the previous transform. Data transforms will be indented once.

The visualization modules will appear after the data transforms and indented twice.

Improving volume rendering speed on Mac would add value to the project.

Loading a tiff stack with the default settings crashes Tomviz with a segfault. (Observed on Linux.)

Move the view proprties to a dialog as this is confusing, and doesn't seem like a good fit for a panel.

The slice tool displays an arrow perpendicular to its surface and allows the user to change the slices orientation. After a user is done choosing an orientation, they should be able to disable the visibility of the arrow.

Suggested Solution: Add a checkbox in the slice view properties that can disable or enable the orientation arrows visibility.

When adding an animation in the animator, it seems as though only one animation can be added at a time. I'll explain in more detail referencing the following image:

Here, I've added a simple orbit about the z axis as an animation. This animation is represented by the row with a red diagonal cross, a tick box, and the word "camera".
I would like to add a second simple animation, a simple orbit about the x-axis. However, when trying to add another animation (using the blue plus button), nothing happens. The blue plus button is unresponsive.
The only way to add additional animations seems to be to edit the first animation, and build custom paths, which is fun, but time consuming.
Allowing users to put some simple pre-defined orbit animations together to make a movie would be a really nice feature to add. The logical way to do this would seem to be to allow users to add in additional animations with the blue plus button.

Reduce the list of file types for input in order to reduce potential bugs and make the user experience easier.

.jpg, .png, .tiff, .raw, .txt are all useful

I tried loading a tilt series in tiff stack format and running the Auto-Align (xcorr) data transform. It appeared to run successfully (my data looked aligned afterward) but ended up the following to the "Output messages" box (in Windows):

Align Images Complete
ERROR: In C:\DBD\matviz-x64\paraview\src\paraview\VTK\Charts\Core\vtkPlotBar.cxx, line 853 
vtkPlotBar (0000000010BBC7D0): No X column is set (index 0).

The error looks similar on OSX, but obviously with a different file path.

In the manual alignment widget, after applying a significant shift pressing any key (even ones that should do nothing) causes the image to jump to a location not specified by the user-defined shifts. I have only observed this starting with unaligned data.

To replicate clearly (with sample star-particle tilt series):

1. misalign the stack with the cross-correlation auto-align.
2. open stack in manual alignment widget and begin aligning.
3. after aligning 5-10 images so that you need to apply a significant shift to align, hold down space (or any other inactive key) on a well-aligned image pair and you will see the image pair appear misaligned again.

This behavior also happens when doing regular alignment and is confusing, but this is the clearest way to observe it. The spurious shift appears to be in the direction of user-applied shifts, but maybe 1/2 or less in magnitude.

Add context menus to the module views, along with keyboard shortcuts that make it easy to delete things from the data transforms, etc.

• Show tilt angles on the Data Properties panel
• Edit tilt angles on Data Properties panel
• Add option to context menu/toolbar to mark a data set as a tilt series.
• Add checkbox to File | Open to open a file as tilt series.

Orthoslice and slice icons should be distinguishable. For the orthogonal slice, it does not make sense in tomviz (or paraview) to show a tilted slice icon since this is not possible. However, this is great for the slice tool that allows any angle of slicing.

Suggested solution: "Orthogonal Slice" icon should show an orthogonal green slice. "Slice" icon should show a non-orthogonal slice with different color (maybe pink or blue?).

GUI and icons look pixelated due to lack of retna display support. This may be resolvable with QT5 implementation.

Currently the threshold module renders each voxel as a cube. For some applications this is distracting and aesthetically unappealing, so it would be nice to have the option to render the surfaces smoothly instead.

Currently the user must type the values for single isosurface contours. It would be nice to be able to use a slider for this. The nicest would be if you could have the threshold shown on top of the histogram (I think Chimera's volume viewer works this way) as well.

Using the non-orthogonal slice when the widget first appearsh or when moving the slice plane, I get OpenGL warnings:

Warning: In /home/shawn/dev/tomviz/src/paraview/VTK/Rendering/OpenGL2/vtkOpenGLPolyDataMapper.cxx, line 1418
vtkOpenGLPolyDataMapper (0x6219340): line widths above 1.0 are not supported by OpenGL 3.2

Simple orbit animation only works around z axis. Around x and y axes, the software tries to flip the image over half way through, and spits out an error message:
Warning: In C:\DBD\matviz-x64\paraview\src\paraview\VTK\Rendering\Core\vtkRenderer.cxx, line 1029
vtkOpenGLRenderer (00000000093D9C80): Resetting view-up since view plane normal is parallel.

In addition to setting the tilt-angles associated with a dataset, we need to be able to get them in Python for reconstruction. Right now they are hard-coded into the reconstruction, but in real life every dataset will have a different set of tilt angles.

It would also be good to set the tilt angles from within Python. There may be reasons to change them.

Improving surface rendering speed on Windows would add value to the project.

Pick the subvolume to be opened, only load the subvolume into memory. Provide graphical interface to move the corners etc.

User should be able to change the color of the "Outline" bounding box, like they can change the color of the background. Currently the bounding box is always rendered in white.

In the zoom and view direction controls at the top left of the window, pressing one of the "Set view direction to * " buttons both sets the view direction AND also resets the zoom out to show the full view of the data. Since there is already a "Zoom to data" button, should the "set view direction" buttons just change the direction and let the user keep their zoom?

Need to be able to read .mrc files, a popular format for microscopists doing tomography. Writing is probably not necessary.

When loading state files, if transforms are slow, we currently have no mechanism to cache the previously computed results. That'd be needed to speed up restoring old states.

Hi,

Apparently if I select a stack of images from a folder, it only ends up loading the last one. There should be a way to set the spacing manually or fetching it from either a summary file. I thought that it should be automatically recognized from a DICOM input, but it didn't work on my end...

In order to make the colormap editor more accessible and useable add a colormap to the histogram panel. Tabs will allow users to jump between the histogram and the colormap editor.

Exporting animation as ogg video not working. It currently throws the following error on Mac OSX:

ERROR: In /Users/kitware/Dashboards/MyTests/NightlyBinary/MatVizSuperbuild-Release/paraview/src/paraview/ParaViewCore/Animation/vtkSMAnimationSceneImageWriter.cxx, line 385
pqAnimationSceneImageWriter (0x11c2c4990): Unknown extension .ogv

Right now I can’t edit a custom transform and type in the python interpreter at the same time, which is unfortunate.
--Elliot

Comment: Users will likely test syntax in the Python Shell as they write code in the "Custom Transform" dialogue. If it is not excessively difficult, this would be a good feature to allow.

Reduce the list of file types for input in order to reduce potential bugs and make the user experience easier.

.jpg, .png, .tiff, .raw, .txt are all useful

The crash is recreated simply:

1. Open tomviz and split panel vertical.
2. Move the bottom panel to the top.

Need a datatransform that downsamples the data by factors of 2x, 4x, etc.

Possible solution: Downsampling should not simply read every other datapoint, it should interpolate (most simply, this would be an average of adjacent pixels). This probably means a new dataset will be created in memory - I think this is OK.

Objects need to be rotatable and translatable in the visualization. For example, two datasets, each with their own volume and/or isosurface rendering can be moved and rotated relative to each other. Users can display two datasets side-by-side and rotated them each individually. This probably means that the entire dataset and the visualization modules associated with a single dataset all rotate / translate together.

“Delete data and modules” right now is hidden in the “data transforms” menu. This should be somewhere more obvious. It was one of the first things I looked for in the interface since I loaded my data wrong several times and wanted to clear it without restarting. I expect this will be a common experience.
--Elliot

Proposed solution: Users should be able to delete the data from the pipeline. This would include pressing the delete key and possibly right clicking and selecting 'delete'.

"About" in user menu reads version 0.4, not the current release.

In the current version the user always aligns image n+1 to image n. The user should be able to choose between "align to next" and "align to previous" options.

Need to be able to move the center of rotation in the non-orthogonal slice tool.

Suggested solution, when clicking the central in-plane part of the arrow (the little ball) the arrow can be translated in the plane of the slice. Also / or slider bars in the module properties could be useful for more exact positioning.

Currently the Threshold module does not respond to a change in its color map, instead always rendering grey.