Opened 7 months ago

Last modified 7 months ago

#17404 assigned defect

Open TIFF stack: '_TIFF' object has no attribute 'PHOTOMETRIC'

Reported by: gregdp@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.10.dev202503260000 (2025-03-26 00:00:48 UTC)
Description
Opening a file, attached - a segmented layer from nnInteractive.
It opens ok in ChimeraX version 1.9, but not in the latest builds of 1.10 it seems?

Log:
> mousemode shift rightMode zone

> mousemode command wheelMode "contour level"

> mousemode setting "contour level" speed .2

> mousemode middleMode "center or translate"

> mousemode middleMode translate

UCSF ChimeraX version: 1.10.dev202503260000 (2025-03-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43.ccp4"

Opened LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43.ccp4 as #1,
grid size 516,516,516, pixel 0.847, shown at level 5.34, step 4, values
float32  

> volume #1 step 1

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__A.mrc"

Opened
LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__A.mrc
as #2, grid size 77,123,104, pixel 0.847,0.847,0.847, shown at level 4.25,
step 1, values float32  

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__B.mrc"

Opened
LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__B.mrc
as #3, grid size 81,77,75, pixel 0.847,0.847,0.847, shown at level 5.67, step
1, values float32  

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__C.mrc"

Opened
LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__C.mrc
as #4, grid size 113,85,83, pixel 0.847,0.847,0.847, shown at level 4.7, step
1, values float32  

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__D.mrc"

Opened
LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__D.mrc
as #5, grid size 61,64,41, pixel 0.847,0.847,0.847, shown at level 2.84, step
1, values float32  

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__E.mrc"

Opened
LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43__IL_seq_holo_rseqn_48_gly5_is2_w1__E.mrc
as #6, grid size 50,35,35, pixel 0.847,0.847,0.847, shown at level 2.66, step
1, values float32  

> lighting soft

> volume #6 level 1.714

> volume #5 level 1.994

> volume #4 level 2.035

> volume #3 level 2.31

> volume #2 level 2.146

> volume #1 level 3.174

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/IL_seq_holo_rseqn_48_GlyF1_is1.pdb"

Chain information for IL_seq_holo_rseqn_48_GlyF1_is1.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 13239 atom styles  

> hide #7 models

> show #7 models

> open "C:/Users/gregp/OneDrive -
> Stanford/_data/EV/LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43_z2.mrc"

Opened LX249-6_holo_J1531_010_volume_map_zflip_resampled2_autosh43_z2.mrc as
#8, grid size 114,123,115, pixel 0.847,0.847,0.847, shown at level 5.56, step
1, values float32  

> hide #!8 models

> hide #7 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #7 models

> show #!8 models

> show cartoons

> color #8 white models

> color #8 #f0f4ffff models

> color #8 white models

> color #8 #bababaff models

> volume #8 level 1.645

> color #8 #bababa96 models

> color #8 #bababa01 models

> color #8 #bababa64 models

> hide H

> color #7-8 byelement

> select /A

4717 atoms, 4738 bonds, 329 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel olive

> select /B

3764 atoms, 3789 bonds, 270 residues, 1 model selected  

> color sel chartreuse

> select /C

3837 atoms, 3849 bonds, 280 residues, 1 model selected  

> color sel orange

> color sel medium purple

> select /D

477 atoms, 479 bonds, 34 residues, 1 model selected  

> color sel saddle brown

> color sel royal blue

> select /E

444 atoms, 455 bonds, 21 residues, 1 model selected  

> color sel yellow

> color sel byelement

> select clear

> volume #8 level 2.349

> lighting simple

> select /A

4717 atoms, 4738 bonds, 329 residues, 1 model selected  

> color sel cornflower blue

> select /D

477 atoms, 479 bonds, 34 residues, 1 model selected  

> color sel coral

> xr false

> xr true

> mousemode setting zoom speed 0.2

started OpenXR rendering SonySRD System, render size 3840 by 2160  

> hide #!8 models

> hide #7 models

> show #!1 models

> lighting soft

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> ui mousemode right pivot

> select #6

2 models selected  

> color #6.1 yellow

> select #2

2 models selected  

> show #7 models

> color #2.1 cornflower blue

> select #3

2 models selected  

> color #3.1 lime

> hide #!4 models

> show #!4 models

> xr false

> mousemode setting zoom speed 1

> hide #7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> cofr

Center of rotation: 337.83 309.33 209.99 fixed  

> cofr #1

> open "C:/Users/gregp/_data/human_retina/object 1 -
> human_retina_crop2_inv.tiff"

Traceback (most recent call last):  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\gui.py", line 740, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2126, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map\\__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map\volume.py", line 3607, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\fileformats.py", line 171, in open_file  
data = open_func(apath, **okw)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\\__init__.py", line 25, in open  
grids.extend(open_stack(path_list, t, c, log=log))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\\__init__.py", line 61, in open_stack  
pgrids = image_stack_grids([p])  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagestack_grid.py", line 21, in
image_stack_grids  
d = imagestack_format.Image_Stack_Data(paths)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagestack_format.py", line 40, in
__init__  
is_rgb = (page0.photometric == TIFF.PHOTOMETRIC.RGB)  
^^^^^^^^^^^^^^^^  
AttributeError: '_TIFF' object has no attribute 'PHOTOMETRIC'  
  
AttributeError: '_TIFF' object has no attribute 'PHOTOMETRIC'  
  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagestack_format.py", line 40, in
__init__  
is_rgb = (page0.photometric == TIFF.PHOTOMETRIC.RGB)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open C:/Users/gregp/_data/human_retina/registered.tiff

Traceback (most recent call last):  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\gui.py", line 740, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2126, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map\\__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map\volume.py", line 3607, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\fileformats.py", line 171, in open_file  
data = open_func(apath, **okw)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\\__init__.py", line 25, in open  
grids.extend(open_stack(path_list, t, c, log=log))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\\__init__.py", line 61, in open_stack  
pgrids = image_stack_grids([p])  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagestack_grid.py", line 21, in
image_stack_grids  
d = imagestack_format.Image_Stack_Data(paths)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagestack_format.py", line 40, in
__init__  
is_rgb = (page0.photometric == TIFF.PHOTOMETRIC.RGB)  
^^^^^^^^^^^^^^^^  
AttributeError: '_TIFF' object has no attribute 'PHOTOMETRIC'  
  
AttributeError: '_TIFF' object has no attribute 'PHOTOMETRIC'  
  
File "C:\Users\gregp\Apps\ChimeraX 1.10.dev202503260000\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagestack_format.py", line 40, in
__init__  
is_rgb = (page0.photometric == TIFF.PHOTOMETRIC.RGB)  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 552.74
OpenGL renderer: NVIDIA RTX 2000 Ada Generation Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 5690
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 33,777,467,392
MaxProcessMemory: 137,438,953,344
CPU: 22 Intel(R) Core(TM) Ultra 9 185H
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.0
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503260000
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.3
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.44
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.1
    coverage: 7.7.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    platformdirs: 4.2.2
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.3.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.13.0
    typing_extensions: 4.12.2
    tzdata: 2025.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.43.0
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2
File attachment: nnInteractive - Label Layer - img.tiff

nnInteractive - Label Layer - img.tiff​

Attachments (1)

nnInteractive - Label Layer - img.tiff​ (478.2 KB ) - added by gregdp@… 7 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by gregdp@…, 7 months ago

Attachment: nnInteractive - Label Layer - img.tiff​ added

Added by email2trac

comment:1 by Eric Pettersen, 7 months ago

Cc: Zach Pearson added
Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Open TIFF stack: '_TIFF' object has no attribute 'PHOTOMETRIC'

Per Greg, 1.10 only -- works in 1.9

comment:2 by Zach Pearson, 7 months ago

Cc: Tom Goddard added; Zach Pearson removed
Owner: changed from Tom Goddard to Zach Pearson

I bumped tiffile on March 17

​https://github.com/RBVI/ChimeraX/commit/5b575a6a449b64f943c36cb5ae51938a176a6635

My breaking change, my bug.

comment:3 by Zach Pearson, 7 months ago

Cc: Zach Pearson added; Tom Goddard removed
Owner: changed from Zach Pearson to Tom Goddard

Should be fixed in tomorrow's daily build. I did notice that when I opened the tiff file you gave me the surface wasn't displayed until I moved the level slider in the volume viewer.

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