Bugs with saving loading workspaces in RAW 2.4.1

[Hugh Higinbotham]

Hello,

I have been using the latest version of RAW 2.4.1 installed on Ubuntu 24.04 LTS from source. There seem to be a few bugs with saving and loading workspaces.

• When using the "File > Load Workspace" menu, workspace files are not displayed correctly in the file manager popup. 
  • "Workspace files ..." does not show either .hdf5 or .wsp files
  • "*.wsp" shows only *.hdf5 workspace files
  • All files (*.*) shows all files, but *.wsp files are listed as "Unknown" file type
• There is no option to save a workspace in the previous '.wsp' format, only .hdf5
• When loading a workspace file saved in 2.4.1 (automatically as *.hdf5) after manually changing the colors of some profiles, these profiles fail to load with the following error, indicating a bug saving colors in the correct format:
  • An unexpected error has occurred, please report it to the developers.
    System: Linux-6.14.0-1020-oem-x86_64-with-glibc2.39
    RAW version: 2.4.1
    Prebuilt: False
    ATSAS version: 4.1.3
    
    Error:
    Traceback (most recent call last):
    
      File "/home/hugh/miniconda3/lib/python3.13/site-packages/wx/core.py", line 3425, in <lambda>
        lambda event: event.callable(*event.args, **event.kw) )
                      ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
    
      File "/home/hugh/miniconda3/lib/python3.13/site-packages/bioxtasraw/RAWPlot.py", line 827, in plotSASM
        each.set_color(color)
        ~~~~~~~~~~~~~~^^^^^^^
    
      File "/home/hugh/miniconda3/lib/python3.13/site-packages/matplotlib/lines.py", line 1081, in set_color
        mcolors._check_color_like(color=color)
        ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
    
      File "/home/hugh/miniconda3/lib/python3.13/site-packages/matplotlib/colors.py", line 249, in _check_color_like
        raise ValueError(
        ...<6 lines>...
            f"and pairs combining one of the above with an alpha value")
    
    ValueError: '[0.49803922 0.         1.        ]' is not a valid value for color: supported inputs are (r, g, b) and (r, g, b, a) 0-1 float tuples; '#rrggbb', '#rrggbbaa', '#rgb', '#rgba' strings; named color strings; string reprs of 0-1 floats for grayscale values; 'C0', 'C1', ... strings for colors of the color cycle; and pairs combining one of the above with an alpha value

Please let me know if there is any other info or files from me to investigate. 

Best,

Hugh

[Jesse Hopkins]

Hi Hugh,

Can you send me a screenshot of the first issue? I'm not quite sure what you're describing here.

The second issue is not a bug, the old workspace format is supported as load only going forward.

I'll look into the third issue and get back to you.

All the best.

- Jesse

----

Jesse Hopkins, PhD (he/him)

Director, BioCAT

Sector 18, Advanced Photon Source

Research Associate Professor, Illinois Tech

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[Jesse Hopkins]

Hi Hugh,

The third issue is a bug. I don't know why it happens when you change colors vs. with the default colors, that part doesn't make sense. But in some limited testing I was able to recreate it. I've fixed the issue if you want to grab the latest version from the git, or you can wait for the next release which will contain that fix. Note that this won't affect workspaces saved that currently demonstrate this error. To fix that you would have to go in and manually edit the color in the hdf5 file attribute, which I can tell you how to do if you need to.

All the best.

- Jesse

----

Jesse Hopkins, PhD (he/him)

Director, BioCAT

Sector 18, Advanced Photon Source

Research Associate Professor, Illinois Tech

[Hugh Higinbotham]

Hi Jesse,

Thanks for the quick fix for the third issue! I only had one workspace affected so I don't feel the need to fix it manually.

For the first issue here are the requested screenshots in a test directory with two files, test.wsp and test.hdf5. The issue is whether files are shown correctly given  the dropdown selection in the lower right.

Best,

Hugh

[Jesse Hopkins]

Hi Hugh,

So the 'Unknown' filet ype isn't a bug, but rather just a system thing. The file dialog is a system dialog, and the system doesn't know what a .wsp file is. That shouldn't affect anything. I believe the other issue you mention is due to a malformed wildcard string in the file dialog creation. These strings can't be shown on mac, which is my usual development platform, but I believe I've fixed it and updated the git with this new version. If you wanted to test the version in the git and see if it is fixed and report back that would be appreciated, otherwise I will test it on linux when I have a chance.

All the best.

- Jesse

----

Jesse Hopkins, PhD (he/him)

Director, BioCAT

Sector 18, Advanced Photon Source

Research Associate Professor, Illinois Tech

To view this discussion visit https://groups.google.com/d/msgid/bioxtas_raw/01489617-92ea-431f-a62f-b348d238498cn%40googlegroups.com.

[Hugh Higinbotham]

Hi Jesse,

Forgot to reply but yes, I cloned the latest from git and everything is fixed! Thanks so much for the quick work.

Best,

Hugh

[Jesse Hopkins]

Hi Hugh,

Thanks for confirming the fix. Glad it's working for you.

- Jesse

----

Jesse Hopkins, PhD (he/him)

Director, BioCAT

Sector 18, Advanced Photon Source

Research Associate Professor, Illinois Tech

To view this discussion visit https://groups.google.com/d/msgid/bioxtas_raw/6dfb8b07-55c9-4410-91bd-7717d8592551n%40googlegroups.com.

[Shanel Wijeratne]

Hi Jesse

We've run into an issue which I believe could be the same bug you're talking about here? We're using the latest release (from January), but I see this bug was patched in March. Are you able to please tell us how we can manually fix the broken HDF5 file? Copy of the error below. Thanks!

An unexpected error has occurred, please report it to the developers.

System: Windows-10-10.0.26200-SP0
RAW version: 2.4.1
Prebuilt: True
ATSAS version: 3.2.1

Error:
Traceback (most recent call last)

File "wx\core.py", line 3425, in <lambda>
File "bioxtasraw\RAWPlot.py", line 827, in plotSASM
File "matplotlib\lines.py", line 1081, in set_color
File "matplotlib\colors.py", line 249, in _check_color_like
ValueError: '[1. 0.49803922 0.05490196]' is not a valid value for color: supported inputs are (r, g, b) and (r, g, b, a) 0-1 float tuples; '#rrggbb', '#rrggbbaa', '#rgb', '#rgba' strings; named color strings; string reprs of 0-1 floats for grayscale values; 'C0', 'C1', ... strings for colors of the color cycle; and pairs combining one of the above with an alpha value

Thanks,
Shanel.

[Jesse Hopkins]

Hi Shanel,

Sure, here's how you would fix it manually. You'll need a program that can read and edit HDF5 files. I use HDFView (https://www.hdfgroup.org/download-hdfview/) but I'm sure there's other appropriate software out there. You could also write a python script to do this pretty easily in an automated fashion if you wanted. Here's how I would do it in HDF5View, the general process should be the same for other programs. Note that you only have to do this process for the values that are causing problems, not for all values in the file.

1. Open the hdf5 workspace file.

2. In HDFView right lick on the top level node (filename) and select Reload File As -> Read/Write

3. Expand one of the data notes (e.g. ifts) to show the data of that type in the workspace. Click on the filename to show the associated attributes.

4. For any attribute that is a line or marker color (e.g. qf_line_color, qf_line_marker_edge_color, etc.) right click and select View/Edit Attribute Value

5. In the window that opens you will see three numbers in brackets, in your case the errors shows an issue with: [1. 0.49803922 0.05490196]. This is an RGB code. Convert it to a Hex color code (e.g. with https://htmlcolorcodes.com/rgb-to-hex/). Double click in the cell and enter the corresponding hex code.

6. Close the window and save the changes when it asks (note that in my version of HDFView the window that pops up asking to confirm save changes doesn't have any buttons, but just closing it with the x at the top left seems to save the changes).

7. Click away from the data node and back to reload the attributes and verify the change took.

8. Repeat as necessary for all values causing errors on load.

9. Close the HDF5 file.

Let me know if you have any issues.

----

Jesse Hopkins, PhD (he/him)

Director, BioCAT

Sector 18, Advanced Photon Source

Research Associate Professor, Illinois Tech

To view this discussion visit https://groups.google.com/d/msgid/bioxtas_raw/b012411a-5953-487f-ba16-a5a30c784285n%40googlegroups.com.