Opened 6 years ago

Last modified 6 years ago

#2743 assigned defect

Problem opening tif files with brackets in their name

Reported by: vbindoka@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.92 (2020-01-15)
Description
on update to v.92, I can no longer drag/drop tif files or open via file/open. Older projects in gallery do open, so just no new data imports.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.92 (2020-01-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "F:/EASsted/1-10-20/yacu120,70nm-- 1-10-20_ 580-rib, 635-basn
> [only].lif - Series004.tif"

File not found: F:\EASsted\1-10-20\yacu120,70nm-- 1-10-20_ 580-rib, 635-basn
[only].lif - Series004.tif  

> open "F:/EASsted/1-10-20/yacu120,70nm-- 1-10-20_ 580-rib, 635-basn
> [only].lif - Series004.tif"

File not found: F:\EASsted\1-10-20\yacu120,70nm-- 1-10-20_ 580-rib, 635-basn
[only].lif - Series004.tif  

> open "F:/EASsted/1-10-20/yacu120,70nm-- 1-10-20_ 580-rib, 635-basn
> [only].lif - Series004.tif"

File not found: F:\EASsted\1-10-20\yacu120,70nm-- 1-10-20_ 580-rib, 635-basn
[only].lif - Series004.tif  

> open "F:\EASsted\1-8-20\yacu120,70nm-- 1-8-20 var sted tests.lif - Series095
> 532-basn 580-arrstn 635-rib.tif"

Opened multi-channel map yacu120,70nm-- 1-8-20 var sted tests.lif - Series095
532-basn 580-arrstn 635-rib.tif, 4 channels, grid size 1024,1024,47, pixel
18.8,18.8,50, shown at step 2, values float32  

> open "F:/EASsted/1-10-20/yacu120,70nm-- 1-10-20_ Series092 514-glur4
> 520-basn 580-rib, 635-glur2 [dual500s added-up].tif"

File not found: F:\EASsted\1-10-20\yacu120,70nm-- 1-10-20_ Series092 514-glur4
520-basn 580-rib, 635-glur2 [dual500s added-up].tif  

> open "F:/EASsted/1-10-20/MAX_yacu120,70nm-- 1-10-20_ Series092 514-glur4
> 520-basn 580-rib, 635-glur2 [dual500s added-up].tif"

File not found: F:\EASsted\1-10-20\MAX_yacu120,70nm-- 1-10-20_ Series092
514-glur4 520-basn 580-rib, 635-glur2 [dual500s added-up].tif  

> open "F:/EASsted/2-5-19/USM9,5-RL50-mltstkreg-ROFdenoised-2-5-19 514-gfp,
> 580-eaat5,635-gluk1 Zblurry- Series085 raw.tif"

Opened multi-channel map USM9,5-RL50-mltstkreg-ROFdenoised-2-5-19 514-gfp,
580-eaat5,635-gluk1 Zblurry- Series085 raw.tif, 3 channels, grid size
1026,942,141, pixel 1, shown at step 4, values float32  




OpenGL version: 3.3.0 NVIDIA 440.97
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: UnassignedInput/Output
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionProblem opening tif files with brackets in their name

Open PDB files with brackets in their names works.

Reported by Vytas Bindokas

comment:2 by Tom Goddard, 6 years ago

The problem is that these file names have square brackets "and" in them and the ChimeraX tiff reader allows wildcard characters *,?,[,],{,} which it uses to load multiple tiff files, for example open "data_*.tif". The square brackets is a bit more exotic but is a standard glob file name expansion, for example "open data_ch[12]_*.tif would open channels 1 or 2 but not 3 or 4.

Of course if you drag and drop it should not interpret any wildcard characters. I can probably fix that. It may be difficult though since the same file open function is called no matter if the open request comes from the command-line, drag and drop, file history, or an Open File dialog. But it is likely to lead to more problems since the open command won't work on these files since it will allow wildcard characters. One solution is to not handle square bracket wildcards. I think they are sometimes useful as the above channel 1,2 example illustrates. And I think it is rare that people put square brackets in their filenames. Another idea would be to add a wildcard option to the open command to not interpret wildcard characters. It is unlikely anyone would figure that out.

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